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Luo C, Li S, Ren P, Yan F, Wang L, Guo B, Zhao Y, Yang Y, Sun J, Gao P, Ji P. Enhancing the carbon content of coal gangue for composting through sludge amendment: A feasibility study. Environ Pollut 2024; 348:123439. [PMID: 38325505 DOI: 10.1016/j.envpol.2024.123439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/03/2024] [Accepted: 01/22/2024] [Indexed: 02/09/2024]
Abstract
Cocomposting coal gangue and sludge eliminates the challenge of utilizing coal gangue. However, there is limited understanding about the feasibility of cocomposting sludge and coal gangue, as well as the composting indicators, functional microorganisms, and safety risks involved. Therefore, this study evaluated the feasibility of enhancing carbon composting in coal gangue by incorporating sludge along with sawdust as a conditioner. Three laboratory-scale reactors were designed and labeled as T1 (20 % coal gangue, 60 % sludge, and 20 % sawdust), T2 (40 % coal gangue, 40 % sludge, and 20 % sawdust), and T3 (60 % coal gangue, 20 % sludge, and 20 % sawdust). Seed germination and plant growth assessments were conducted to ensure compost stability and assess phytotoxicity to cabbage (Brassica rapa chinensis L.) in terms of growth and biomass. The results indicated that the temperature, pH, EC and ammonia nitrogen of all three reactor conditions met the requirements for product decomposition. Composting was successfully achieved when the sludge proportion was 20 % (T3). However, when the sludge proportion was markedly high (T1), the harmlessness of the compost was reduced. The germination indices of T1, T2, and T3 reached 95 %, 122 %, and 119 % at maturity, respectively. This confirmed that the harmless cycle, which involved promoting condensation and aromatization, enhancing decay, and reducing composting time, was shorter in T2 and T3 than in T1. Coal gangue can also serve as a beneficial habitat for microorganisms, promoting an increase in their population and activity. Potting experiments in sandy soil revealed that the mechanism of action of compost products in soil included not only the enhancement of soil nutrients but also the improvement of soil texture. The results of this study suggest that using coal gangue as a raw material for composting is an efficient and environmentally friendly approach for producing organic fertilizers.
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Affiliation(s)
- Chi Luo
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Shaohua Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Pengyu Ren
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Fan Yan
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Lu Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Bin Guo
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yimo Zhao
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yue Yang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jian Sun
- Institute of Agricultural Quality Standard and Testing Technology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Pengcheng Gao
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Puhui Ji
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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2
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Wang H, Wen L, Jiang F, Ren P, Yang Y, Song S, Yang Z, Wang Y. A comprehensive review of advances in hepatocyte microencapsulation: selecting materials and preserving cell viability. Front Immunol 2024; 15:1385022. [PMID: 38694507 PMCID: PMC11061843 DOI: 10.3389/fimmu.2024.1385022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 03/28/2024] [Indexed: 05/04/2024] Open
Abstract
Liver failure represents a critical medical condition with a traditionally grim prognosis, where treatment options have been notably limited. Historically, liver transplantation has stood as the sole definitive cure, yet the stark disparity between the limited availability of liver donations and the high demand for such organs has significantly hampered its feasibility. This discrepancy has necessitated the exploration of hepatocyte transplantation as a temporary, supportive intervention. In light of this, our review delves into the burgeoning field of hepatocyte transplantation, with a focus on the latest advancements in maintaining hepatocyte function, co-microencapsulation techniques, xenogeneic hepatocyte transplantation, and the selection of materials for microencapsulation. Our examination of hepatocyte microencapsulation research highlights that, to date, most studies have been conducted in vitro or using liver failure mouse models, with a notable paucity of experiments on larger mammals. The functionality of microencapsulated hepatocytes is primarily inferred through indirect measures such as urea and albumin production and the rate of ammonia clearance. Furthermore, research on the mechanisms underlying hepatocyte co-microencapsulation remains limited, and the practicality of xenogeneic hepatocyte transplantation requires further validation. The potential of hepatocyte microencapsulation extends beyond the current scope of application, suggesting a promising horizon for liver failure treatment modalities. Innovations in encapsulation materials and techniques aim to enhance cell viability and function, indicating a need for comprehensive studies that bridge the gap between small-scale laboratory success and clinical applicability. Moreover, the integration of bioengineering and regenerative medicine offers novel pathways to refine hepatocyte transplantation, potentially overcoming the challenges of immune rejection and ensuring the long-term functionality of transplanted cells. In conclusion, while hepatocyte microencapsulation and transplantation herald a new era in liver failure therapy, significant strides must be made to translate these experimental approaches into viable clinical solutions. Future research should aim to expand the experimental models to include larger mammals, thereby providing a clearer understanding of the clinical potential of these therapies. Additionally, a deeper exploration into the mechanisms of cell survival and function within microcapsules, alongside the development of innovative encapsulation materials, will be critical in advancing the field and offering new hope to patients with liver failure.
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Affiliation(s)
- Hailian Wang
- Clinical Immunology Translational Medicine Key Laboratory of Sichuan Province, Center of Organ Transplantation, Sichuan Academy of Medical Science and Sichuan Provincial People’s Hospital, Chengdu, China
| | - Lebin Wen
- Department of Thyroid, Sichuan Second Hospital of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Fengdi Jiang
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Pengyu Ren
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yixin Yang
- Department of Clinical Medicine, The First Clinical Medical College of Norman Bethune University of Medical Sciences, Jilin, China
| | - Siyuan Song
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
| | - Zhengteng Yang
- Department of Pharmacy, Guangxi University of Chinese Medicine, Nanning, China
| | - Yi Wang
- Clinical Immunology Translational Medicine Key Laboratory of Sichuan Province, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
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3
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Thiel A, Speranza MJ, Jadhav S, Stevens LL, Unruh DK, Ren P, Ponder JW, Shen J, Schnieders MJ. Constant-pH Simulations with the Polarizable Atomic Multipole AMOEBA Force Field. J Chem Theory Comput 2024; 20:2921-2933. [PMID: 38507252 PMCID: PMC11008096 DOI: 10.1021/acs.jctc.3c01180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 03/05/2024] [Accepted: 03/05/2024] [Indexed: 03/22/2024]
Abstract
Accurately predicting protein behavior across diverse pH environments remains a significant challenge in biomolecular simulations. Existing constant-pH molecular dynamics (CpHMD) algorithms are limited to fixed-charge force fields, hindering their application to biomolecular systems described by permanent atomic multipoles or induced dipoles. This work overcomes these limitations by introducing the first polarizable CpHMD algorithm in the context of the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field. Additionally, our implementation in the open-source Force Field X (FFX) software has the unique ability to handle titration state changes for crystalline systems including flexible support for all 230 space groups. The evaluation of constant-pH molecular dynamics (CpHMD) with the AMOEBA force field was performed on 11 crystalline peptide systems that span the titrating amino acids (Asp, Glu, His, Lys, and Cys). Titration states were correctly predicted for 15 out of the 16 amino acids present in the 11 systems, including for the coordination of Zn2+ by cysteines. The lone exception was for a HIS-ALA peptide where CpHMD predicted both neutral histidine tautomers to be equally populated, whereas the experimental model did not consider multiple conformers and diffraction data are unavailable for rerefinement. This work demonstrates the promise polarizable CpHMD simulations for pKa predictions, the study of biochemical mechanisms such as the catalytic triad of proteases, and for improved protein-ligand binding affinity accuracy in the context of pharmaceutical lead optimization.
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Affiliation(s)
- Andrew
C. Thiel
- Department
of Biomedical Engineering, University of
Iowa, Iowa City, Iowa 52242, United States
| | - Matthew J. Speranza
- Department
of Biomedical Engineering, University of
Iowa, Iowa City, Iowa 52242, United States
| | - Sanika Jadhav
- Department
of Pharmaceutical Sciences and Experimental Therapeutics, University of Iowa, Iowa City, Iowa 52242, United States
| | - Lewis L. Stevens
- Department
of Pharmaceutical Sciences and Experimental Therapeutics, University of Iowa, Iowa City, Iowa 52242, United States
| | - Daniel K. Unruh
- Office
of the Vice President for Research, University
of Iowa, Iowa City, Iowa 52242, United
States
| | - Pengyu Ren
- Department
of Biomedical Engineering, University of
Texas, Austin, Texas 78712, United States
| | - Jay W. Ponder
- Department
of Chemistry, Washington University in St.
Louis, St. Louis, Missouri 63130, United
States
| | - Jana Shen
- Department
of Pharmaceutical Sciences, University of
Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Michael J. Schnieders
- Department
of Biomedical Engineering, University of
Iowa, Iowa City, Iowa 52242, United States
- Department
of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United States
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4
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Shin D, Ievlev AV, Beckmann K, Li J, Ren P, Cady N, Li Y. Oxygen tracer diffusion in amorphous hafnia films for resistive memory. Mater Horiz 2024. [PMID: 38506727 DOI: 10.1039/d3mh02113k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
The oxygen diffusion rate in hafnia (HfO2)-based resistive memory plays a pivotal role in enabling nonvolatile data retention. However, the information retention times obtained in HfO2 resistive memory devices are many times higher than the expected values obtained from oxygen diffusion measurements in HfO2 materials. In this study, we resolve this discrepancy by conducting oxygen isotope tracer diffusion measurements in amorphous hafnia (a-HfO2) thin films. Our results show that the oxygen tracer diffusion in amorphous HfO2 films is orders of magnitude lower than that of previous measurements on monoclinic hafnia (m-HfO2) pellets. Moreover, oxygen tracer diffusion is much lower in denser a-HfO2 films deposited by atomic layer deposition (ALD) than in less dense a-HfO2 films deposited by sputtering. The ALD films yield similar oxygen diffusion times as experimentally measured device retention times, reconciling this discrepancy between oxygen diffusion and retention time measurements. More broadly, our work shows how processing conditions can be used to control oxygen transport characteristics in amorphous materials without long-range crystal order.
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Affiliation(s)
- Dongjae Shin
- Materials Science and Engineering, University of Michigan, Ann Arbor, MI, USA.
| | - Anton V Ievlev
- Center for Nanophase Materials Science, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Karsten Beckmann
- College of Nanotechnology, Science and Engineering, University at Albany, Albany, NY, USA
- NY CREATES, Albany, NY, USA
| | - Jingxian Li
- Materials Science and Engineering, University of Michigan, Ann Arbor, MI, USA.
| | - Pengyu Ren
- Materials Science and Engineering, University of Michigan, Ann Arbor, MI, USA.
| | - Nathaniel Cady
- College of Nanotechnology, Science and Engineering, University at Albany, Albany, NY, USA
| | - Yiyang Li
- Materials Science and Engineering, University of Michigan, Ann Arbor, MI, USA.
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5
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Wang Y, Inizan TJ, Liu C, Piquemal JP, Ren P. Incorporating Neural Networks into the AMOEBA Polarizable Force Field. J Phys Chem B 2024; 128:2381-2388. [PMID: 38445577 PMCID: PMC10985787 DOI: 10.1021/acs.jpcb.3c08166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Neural network potentials (NNPs) offer significant promise to bridge the gap between the accuracy of quantum mechanics and the efficiency of molecular mechanics in molecular simulation. Most NNPs rely on the locality assumption that ensures the model's transferability and scalability and thus lack the treatment of long-range interactions, which are essential for molecular systems in the condensed phase. Here we present an integrated hybrid model, AMOEBA+NN, which combines the AMOEBA potential for the short- and long-range noncovalent atomic interactions and an NNP to capture the remaining local covalent contributions. The AMOEBA+NN model was trained on the conformational energy of the ANI-1x data set and tested on several external data sets ranging from small molecules to tetrapeptides. The hybrid model demonstrated substantial improvements over the baseline models in term of accuracy as the molecule size increased, suggesting its potential as a next-generation approach for chemically accurate molecular simulations.
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Affiliation(s)
- Yanxing Wang
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Théo Jaffrelot Inizan
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS, Paris 75005, France
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jean-Philip Piquemal
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS, Paris 75005, France
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
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6
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Ren P, Niu D, Chang S, Yu L, Ren J, Ma Y, Lan K. RUNX3 inhibits KSHV lytic replication by binding to the viral genome and repressing transcription. J Virol 2024; 98:e0156723. [PMID: 38197631 PMCID: PMC10878072 DOI: 10.1128/jvi.01567-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 12/11/2023] [Indexed: 01/11/2024] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) belongs to the gamma herpesvirus family, which can cause human malignancies including Kaposi sarcoma, primary effusion lymphoma, and multicentric Castleman's diseases. KSHV typically maintains a persistent latent infection within the host. However, after exposure to intracellular or extracellular stimuli, KSHV lytic replication can be reactivated. The reactivation process of KSHV triggers the innate immune response to limit viral replication. Here, we found that the transcriptional regulator RUNX3 is transcriptionally upregulated by the NF-κB signaling pathway in KSHV-infected SLK cells and B cells during KSHV reactivation. Notably, knockdown of RUNX3 significantly promotes viral lytic replication as well as the gene transcription of KSHV. Consistent with this finding, overexpression of RUNX3 impairs viral lytic replication. Mechanistically, RUNX3 binds to the KSHV genome and limits viral replication through transcriptional repression, which is related to its DNA- and ATP-binding ability. However, KSHV has also evolved corresponding strategies to antagonize this inhibition by using the viral protein RTA to target RUNX3 for ubiquitination and proteasomal degradation. Altogether, our study suggests that RUNX3, a novel host-restriction factor of KSHV that represses the transcription of viral genes, may serve as a potential target to restrict KSHV transmission and disease development.IMPORTANCEThe reactivation of Kaposi's sarcoma-associated herpesvirus (KSHV) from latent infection to lytic replication is important for persistent viral infection and tumorigenicity. However, reactivation is a complex event, and the regulatory mechanisms of this process are not fully elucidated. Our study revealed that the host RUNX3 is upregulated by the NF-κB signaling pathway during KSHV reactivation, which can repress the transcription of KSHV genes. At the late stage of lytic replication, KSHV utilizes a mechanism involving RTA to degrade RUNX3, thus evading host inhibition. This finding helps elucidate the regulatory mechanism of the KSHV life cycle and may provide new clues for the development of therapeutic strategies for KSHV-associated diseases.
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Affiliation(s)
- Pengyu Ren
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Danping Niu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Sijia Chang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Lei Yu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Junrui Ren
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yuanming Ma
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Ke Lan
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
- Department of Infectious Diseases, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
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7
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Ren P, Chen M, Liu Q, Wu J, Li R, Lin Z, Li J. Gga-let-7a-3p inhibits the proliferation and differentiation of chicken intramuscular preadipocytes. Br Poult Sci 2024; 65:34-43. [PMID: 37807894 DOI: 10.1080/00071668.2023.2264807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 09/11/2023] [Indexed: 10/10/2023]
Abstract
1. Intramuscular fat (IMF) is a key parameter for chicken meat quality. IMF deposition is driven by genetic, nutritional and management factors, with genetics being the determining factor. Previous whole transcriptome sequencing revealed that microRNA gga-let-7a-3p was related to lipid metabolism in breast muscle. This study further investigated the potential role of gga-let-7a-3p in IMF deposition.2. The mimic and inhibitor of gga-let-7a-3p were individually transfected into chicken intramuscular preadipocytes. Subsequently, the proliferation and differentiation states of the cells were detected. Transcriptome sequencing was performed on cells transfected with gga-let-7a-3p mimic.3. The results indicated that gga-let-7a-3p suppressed the mRNA levels of proliferation and differentiation-related genes, as well as the protein levels. EdU and Oil Red O assays revealed that gga-let-7a-3p restrained preadipocyte proliferation and differentiation. In addition, a total of 333 up-regulated genes and 807 down-regulated genes were identified in cells transfected with gga-let-7a-3p mimic. Using Kyoto Encyclopaedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analysis, differential genes were found to be enriched in processes such as the peroxisome proliferator activated receptor (PPAR) signalling pathway and oxidative phosphorylation.4. The study demonstrated that gga-let-7a-3p inhibits the proliferation and differentiation of chicken intramuscular preadipocytes, which provides new understanding to further unravel the function of gga-let-7a-3p.
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Affiliation(s)
- P Ren
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - M Chen
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Q Liu
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - J Wu
- Institute of Animal Science and Technology of Aba Tibetan and Qiang Autonomous Prefecture, Aba, Sichuan, China
| | - R Li
- Institute of Animal Science and Technology of Aba Tibetan and Qiang Autonomous Prefecture, Aba, Sichuan, China
| | - Z Lin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - J Li
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
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8
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Lee J, Guo HF, Wang S, Maghsoud Y, Vázquez-Montelongo EA, Jing Z, Sammons RM, Cho EJ, Ren P, Cisneros GA, Kurie JM, Dalby KN. Unleashing the Potential of 1,3-Diketone Analogues as Selective LH2 Inhibitors. ACS Med Chem Lett 2023; 14:1396-1403. [PMID: 37849534 PMCID: PMC10577891 DOI: 10.1021/acsmedchemlett.3c00305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 09/13/2023] [Indexed: 10/19/2023] Open
Abstract
Lysyl hydroxylase 2 (LH2) catalyzes the formation of highly stable hydroxylysine aldehyde-derived collagen cross-links (HLCCs), thus promoting lung cancer metastasis through its capacity to modulate specific types of collagen cross-links within the tumor stroma. Using 1 and 2 from our previous high-throughput screening (HTS) as lead probes, we prepared a series of 1,3-diketone analogues, 1-18, and identified 12 and 13 that inhibit LH2 with IC50's of approximately 300 and 500 nM, respectively. Compounds 12 and 13 demonstrate selectivity for LH2 over LH1 and LH3. Quantum mechanics/molecular mechanics (QM/MM) modeling indicates that the selectivity of 12 and 13 may stem from noncovalent interactions like hydrogen bonding between the morpholine/piperazine rings with the LH2-specific Arg661. Treatment of 344SQ WT cells with 13 resulted in a dose-dependent reduction in their migration potential, whereas the compound did not impede the migration of the same cell line with an LH2 knockout (LH2KO).
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Affiliation(s)
- Juhoon Lee
- Division
of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
- Targeted Therapeutic Drug Discovery and Development Program, College
of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Hou-fu Guo
- Department
of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, Kentucky 40536, United States
| | - Shike Wang
- Department
of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Yazdan Maghsoud
- Department
of Chemistry and Biochemistry, The University
of Texas at Dallas, Richardson, Texas 75080, United States
| | - Erik Antonio Vázquez-Montelongo
- Department
of Physical Medicine and Rehabilitation, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Zhifeng Jing
- Department
of Biomedical Engineering, The University
of Texas at Austin, Austin, Texas 78712, United States
| | - Rae M. Sammons
- Division
of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
- Targeted Therapeutic Drug Discovery and Development Program, College
of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Eun Jeong Cho
- Division
of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
- Targeted Therapeutic Drug Discovery and Development Program, College
of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Pengyu Ren
- Department
of Biomedical Engineering, The University
of Texas at Austin, Austin, Texas 78712, United States
| | - G. Andrés Cisneros
- Department
of Chemistry and Biochemistry, The University
of Texas at Dallas, Richardson, Texas 75080, United States
- Department
of Physics, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Jonathan M. Kurie
- Department
of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Kevin N. Dalby
- Division
of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
- Targeted Therapeutic Drug Discovery and Development Program, College
of Pharmacy, University of Texas, Austin, Texas 78712, United States
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9
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Fu L, Yu B, Lv B, Tian Y, Zhang Y, Chen H, Yang S, Hu Y, Ren P, Li J, Gong S. Negative regulation of angiogenesis and the MAPK pathway may be a shared biological pathway between IS and epilepsy. PLoS One 2023; 18:e0286426. [PMID: 37792772 PMCID: PMC10550183 DOI: 10.1371/journal.pone.0286426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 05/16/2023] [Indexed: 10/06/2023] Open
Abstract
Ischemia stroke and epilepsy are two neurological diseases that have significant patient and societal burden, with similar symptoms of neurological deficits. However, the underlying mechanism of their co-morbidity are still unclear. In this study, we performed a combined analysis of six gene expression profiles (GSE58294, GSE22255, GSE143272, GSE88723, GSE163654, and GSE174574) to reveal the common mechanisms of IS and epilepsy. In the mouse datasets, 74 genes were co-upregulated and 7 genes were co-downregulated in the stroke and epilepsy groups. Further analysis revealed that the co-expressed differentially expressed genes (DEGs) were involved in negative regulation of angiogenesis and the MAPK signaling pathway, and this was verified by Gene Set Enrichment Analysis of human datasets and single cell RNA sequence of middle cerebral artery occlusion mice. In addition, combining DEGs of human and mouse, PTGS2, TMCC3, KCNJ2, and GADD45B were identified as cross species conserved hub genes. Meanwhile, molecular docking results revealed that trichostatin A and valproic acid may be potential therapeutic drugs. In conclusion, to our best knowledge, this study conducted the first comorbidity analysis of epilepsy and ischemic stroke to identify the potential common pathogenic mechanisms and drugs. The findings may provide an important reference for the further studies on post-stroke epilepsy.
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Affiliation(s)
- Longhui Fu
- Department of Neurourgery, Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
| | - Beibei Yu
- Department of Neurourgery, Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
| | - Boqiang Lv
- Department of Neurourgery, Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
| | - Yunze Tian
- Department of Neurourgery, Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
| | - Yongfeng Zhang
- Department of Neurourgery, Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
| | - Huangtao Chen
- Department of Neurourgery, Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
| | - Shijie Yang
- Department of Neurourgery, Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
| | - Yutian Hu
- Department of Neurourgery, Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
| | - Pengyu Ren
- Department of Neurourgery, Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
| | - Jianzhong Li
- Department of Thoracic Surgery, Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
| | - Shouping Gong
- Department of Neurourgery, Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
- Xi’an Medical University, Xi’an, China
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Wu R, Luo Y, Ren P, Ran F, Yang X, Gu M, Tuo A, Yan Z. Impact of Learning Burnout on Mobile Phone Dependence Among Adolescents in Western China Under the "Double Reduction" Policy: The Mediating Role of Social Support. Psychol Res Behav Manag 2023; 16:3171-3183. [PMID: 37584040 PMCID: PMC10424684 DOI: 10.2147/prbm.s420711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/30/2023] [Indexed: 08/17/2023] Open
Abstract
Purpose This paper investigated the prevalence of mobile phone dependence (MPD) and its associated with learning burnout under the "double reduction" policy among adolescents in Guizhou Province in western China. In addition, the influence of the mediating mechanism of social support on this relationship was investigated. Methods The sample was collected from 16,216 adolescents in West China's Guizhou province, from December 2021 to January 2022 via multistage stratified random sampling. The Self-rating Questionnaire for Adolescent Problematic Mobile Phone Use (SQAPMPU) was used to assess the MPD, the Adolescent Student Burnout Scale (ASBI) was used to assess the learning burnout, and the Social Support Scale (SSS) was used to assess the social support. A hierarchical linear regression model was used to analyze the relationship between MPD, learning burnout, and social support. The mediating effect of social support between MPD and learning burnout was analyzed by structural equation model. Results Prevalence of MPD was 26.4% among adolescents in Guizhou province in western China. After adjusting for confounding variables like demographics, multiple linear regression model has revealed that learning burnout positively predicted MPD and social support negatively predicted MPD. The structural equation model showed that 10.9% of the effect was explained by the mediating effect of social support. Conclusion These findings could inform service delivery and policy formulation to reduce learning and avoid MPD in adolescents.
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Affiliation(s)
- Rong Wu
- Department of Epidemiology and Health Statistics, School of Public Health, Guizhou Medical University, Guiyang, Guizhou, People’s Republic of China
| | - Yuan Luo
- Department of Epidemiology and Health Statistics, School of Public Health, Guizhou Medical University, Guiyang, Guizhou, People’s Republic of China
| | - Pengyu Ren
- Guizhou Drug Evaluation Center, Guiyang, Guizhou, People’s Republic of China
| | - Fengjiao Ran
- Department of Epidemiology and Health Statistics, School of Public Health, Guizhou Medical University, Guiyang, Guizhou, People’s Republic of China
| | - Xiantao Yang
- School of Public Health, Guizhou Medical University, Guiyang, Guizhou, People’s Republic of China
| | - Manting Gu
- School of Public Health, Guizhou Medical University, Guiyang, Guizhou, People’s Republic of China
| | - Anxie Tuo
- School of Medical Humanities, Guizhou Medical University, Guiyang, Guizhou, People’s Republic of China
| | - Zheng Yan
- Department of Epidemiology and Health Statistics, School of Public Health, Guizhou Medical University, Guiyang, Guizhou, People’s Republic of China
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Corrigan RA, Thiel AC, Lynn JR, Casavant TL, Ren P, Ponder JW, Schnieders MJ. A generalized Kirkwood implicit solvent for the polarizable AMOEBA protein model. J Chem Phys 2023; 159:054102. [PMID: 37526158 PMCID: PMC10396400 DOI: 10.1063/5.0158914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 07/17/2023] [Indexed: 08/02/2023] Open
Abstract
Computational simulation of biomolecules can provide important insights into protein design, protein-ligand binding interactions, and ab initio biomolecular folding, among other applications. Accurate treatment of the solvent environment is essential in such applications, but the use of explicit solvents can add considerable cost. Implicit treatment of solvent effects using a dielectric continuum model is an attractive alternative to explicit solvation since it is able to describe solvation effects without the inclusion of solvent degrees of freedom. Previously, we described the development and parameterization of implicit solvent models for small molecules. Here, we extend the parameterization of the generalized Kirkwood (GK) implicit solvent model for use with biomolecules described by the AMOEBA force field via the addition of corrections to the calculation of effective radii that account for interstitial spaces that arise within biomolecules. These include element-specific pairwise descreening scale factors, a short-range neck contribution to describe the solvent-excluded space between pairs of nearby atoms, and finally tanh-based rescaling of the overall descreening integral. We then apply the AMOEBA/GK implicit solvent to a set of ten proteins and achieve an average coordinate root mean square deviation for the experimental structures of 2.0 Å across 500 ns simulations. Overall, the continued development of implicit solvent models will help facilitate the simulation of biomolecules on mechanistically relevant timescales.
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Affiliation(s)
- Rae A Corrigan
- Roy J. Carver Department of Biomedical Engineering, The University of Iowa, Iowa City, Iowa 52242, USA
| | - Andrew C Thiel
- Roy J. Carver Department of Biomedical Engineering, The University of Iowa, Iowa City, Iowa 52242, USA
| | - Jack R Lynn
- Roy J. Carver Department of Biomedical Engineering, The University of Iowa, Iowa City, Iowa 52242, USA
| | - Thomas L Casavant
- Department of Electrical and Computer Engineering, The University of Iowa, Iowa City, Iowa 52242, USA
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas in Austin, Austin, Texas 78712, USA
| | - Jay W Ponder
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - Michael J Schnieders
- Roy J. Carver Department of Biomedical Engineering, The University of Iowa, Iowa City, Iowa 52242, USA
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, Iowa 52242, USA
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Foley CD, Allen CD, Au K, Lee C, Rempe SB, Ren P, Sibert EL, Zwier TS. Molecular Cage Reports on Its Contents: Spectroscopic Signatures of Cryo-Cooled K +- and Ba 2+-Benzocryptand Complexes. J Phys Chem A 2023. [PMID: 37478410 DOI: 10.1021/acs.jpca.3c03457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
UV photofragment spectroscopy and IR-UV double resonance methods are used to determine the structure and spectroscopic responses of a three-dimensional [2.2.2]-benzocryptand cage to the incorporation of a single K+ or Ba2+ imbedded inside it (labeled as K+-BzCrypt, Ba2+-BzCrypt). We studied the isolated ion-cryptand complex under cryo-cooled conditions, brought into the gas phase by nano-electrospray ionization. Incorporation of a phenyl ring in place of the central ethyl group in one of the three N-CH2-CH2-O-CH2-CH2-O-CH2-CH2-N chains provides a UV chromophore whose S0-S1 transition we probe. K+-BzCrypt and Ba2+-BzCrypt have their S0-S1 origin transitions at 35,925 and 36,446 cm-1, respectively, blue-shifted by 174 and 695 cm-1 from that of 1,2-dimethoxybenzene. These origins are used to excite a single conformation of each complex selectively and record their IR spectra using IR-UV dip spectroscopy. The alkyl CH stretch region (2800-3000 cm-1) is surprisingly sensitive to the presence and nature of the encapsulated ion. We carried out an exhaustive conformational search of cage conformations for K+-BzCrypt and Ba2+-BzCrypt, identifying two conformations (A and B) that lie below all others in energy. We extend our local mode anharmonic model of the CH stretch region to these strongly bound ion-cage complexes to predict conformation-specific alkyl CH stretch spectra, obtaining quantitative agreement with experiment for conformer A, the gas-phase global minimum. The large electrostatic effect of the charge on the O- and N-lone pairs affects the local mode frequencies of the CH2 groups adjacent to these atoms. The localized CH2 scissors modes are pushed up in frequency by the adjacent O/N-atoms so that their overtones have little effect on the alkyl CH stretch region. However, the localized CH2 wags are nearly degenerate and strongly coupled to one another, producing an array of delocalized wag normal modes, whose highest frequency members reach up above 1400 cm-1. As such, their overtones mix significantly with the CH stretch modes, most notably involving the CH2 symmetric stretch fundamentals of the central ethyl groups in the all-alkyl chains and the CH stretches adjacent to the N-atoms and antiperiplanar to the nitrogen lone pair.
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Affiliation(s)
- Casey D Foley
- Gas Phase Chemical Physics, Sandia National Laboratories, Livermore, California 94550, United States
| | - Cole D Allen
- Department of Biomedical Engineering, University of Texas-Austin, Austin, Texas 78712, United States
| | - Kendrew Au
- Gas Phase Chemical Physics, Sandia National Laboratories, Livermore, California 94550, United States
| | - Chin Lee
- Gas Phase Chemical Physics, Sandia National Laboratories, Livermore, California 94550, United States
| | - Susan B Rempe
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Pengyu Ren
- Department of Biomedical Engineering, University of Texas-Austin, Austin, Texas 78712, United States
| | - Edwin L Sibert
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Timothy S Zwier
- Gas Phase Chemical Physics, Sandia National Laboratories, Livermore, California 94550, United States
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13
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Lin YC, Ren P, Webb LJ. AMOEBA Force Field Predicts Accurate Hydrogen Bond Counts of Nitriles in SNase by Revealing Water-Protein Interaction in Vibrational Absorption Frequencies. J Phys Chem B 2023; 127:5609-5619. [PMID: 37339399 PMCID: PMC10851345 DOI: 10.1021/acs.jpcb.3c02060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
Abstract
Precisely quantifying the magnitude and direction of electric fields in proteins has long been an outstanding challenge in understanding biological functions. Nitrile vibrational Stark effect probes have been shown to be minimally disruptive to the protein structure and can be better direct reporters of local electrostatic field in the native state of a protein than other measures such as pKa shifts of titratable residues. However, interpretations of the connection between measured vibrational energy and electric field rely on the accurate molecular understanding of interactions of the nitrile group and its environment, particularly from hydrogen bonding. In this work, we compared the extent of hydrogen bonding calculated in two common force fields, the fixed charge force field Amber03 and polarizable force field AMOEBA, at 10 locations of cyanocysteine (CNC) in staphylococcal nuclease (SNase) against the experimental nitrile absorption frequency in terms of full width at half-maximum (FWHM) and frequency temperature line slope (FTLS). We observed that the number of hydrogen bonds correlated well in AMOEBA trajectories with respect to both the FWHM (r = 0.88) and the FTLS (r = -0.85), whereas the correlation of Amber03 trajectories was less reliable because the Amber03 force field predicted more hydrogen bonds in some mutants. Moreover, we demonstrated that contributions from the interactions between CNC and nearby water molecules were significant in AMOEBA trajectories but were not predicted by Amber03. We conclude that although the nitrile absorption peak shape could be qualitatively predicted by the fixed charge Amber03 force field, the detailed electrostatic environment measured by the nitrile probe in terms of the extent of hydrogen bonding could only be accurately observed in the AMOEBA trajectories, where the permanent dipole, quadrupole, and dipole-induced-dipole polarizable interactions were all taken into account. The significance of this finding to the goal of accurately predicting electric fields in complex biomolecular environments is discussed.
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Affiliation(s)
- Yu-Chun Lin
- Department of Chemistry, Texas Materials Institute, and Interdisciplinary Life Sciences Program, The University of Texas at Austin, 105 E 24th St. STOP A5300, Austin, TX, 78712, USA
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Lauren J. Webb
- Department of Chemistry, Texas Materials Institute, and Interdisciplinary Life Sciences Program, The University of Texas at Austin, 105 E 24th St. STOP A5300, Austin, TX, 78712, USA
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Fu L, Yu B, Zhang Y, Cao S, Lv B, Tian Y, Chen H, Yang S, Hu Y, Hua J, Ren P, Li J, Gong S. Integrative analysis of single-cell and bulk RNA sequencing unveils the senescence landscape in ischemic stroke. Aging (Albany NY) 2023; 15:5497-5513. [PMID: 37382646 PMCID: PMC10333064 DOI: 10.18632/aging.204804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 05/27/2023] [Indexed: 06/30/2023]
Abstract
Ischemic stroke (IS) is a fatal neurological disease that occurs when the blood flow to the brain is disrupted, leading to brain tissue damage and functional impairment. Cellular senescence, a vital characteristic of aging, is associated with a poor prognosis for IS. This study explores the potential role of cellular senescence in the pathological process following IS by analyzing transcriptome data from multiple datasets (GSE163654, GSE16561, GSE119121, and GSE174574). By using bioinformatics methods, we identified hub-senescence-related genes such as ANGPTL4, CCL3, CCL7, CXCL16, and TNF and verified them using quantitative reverse transcription polymerase chain reaction. Further analysis of single-cell RNA sequencing data suggests that MG4 microglial is highly correlated with cellular senescence in MCAO, and might play a crucial role in the pathological process after IS. Additionally, we identified retinoic acid as a potential drug for improving the prognosis of IS. This comprehensive investigation of cellular senescence in various brain tissues and peripheral blood cell types provides valuable insights into the underlying mechanisms of the pathology of IS and identifies potential therapeutic targets for improving patient outcomes.
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Affiliation(s)
- Longhui Fu
- Xi’an Jiaotong University, Xi’an, China
- Department of Neurosurgery, Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
| | - Beibei Yu
- Xi’an Jiaotong University, Xi’an, China
- Department of Neurosurgery, Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
| | - Yongfeng Zhang
- Xi’an Jiaotong University, Xi’an, China
- Department of Neurosurgery, Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
| | - Shuai Cao
- Department of Orthopedics, Civil Aviation General Hospital, Chaoyang, Beijing, China
| | - Boqiang Lv
- Xi’an Jiaotong University, Xi’an, China
- Department of Neurosurgery, Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
| | - Yunze Tian
- Xi’an Jiaotong University, Xi’an, China
- Department of Neurosurgery, Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
- Department of Thoracic Surgery, Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
| | - Huangtao Chen
- Xi’an Jiaotong University, Xi’an, China
- Department of Neurosurgery, Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
| | - Shijie Yang
- Xi’an Jiaotong University, Xi’an, China
- Department of Neurosurgery, Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
| | - Yutian Hu
- Xi’an Jiaotong University, Xi’an, China
- Department of Neurosurgery, Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
| | - Jinghua Hua
- Xi’an Jiaotong University, Xi’an, China
- Department of Neurosurgery, Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
| | - Pengyu Ren
- Xi’an Jiaotong University, Xi’an, China
- Department of Neurosurgery, Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
| | - Jianzhong Li
- Xi’an Jiaotong University, Xi’an, China
- Department of Thoracic Surgery, Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
| | - Shouping Gong
- Xi’an Jiaotong University, Xi’an, China
- Department of Neurosurgery, Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
- Xi’an Medical University, Xi’an, China
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15
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Jaffrelot Inizan T, Plé T, Adjoua O, Ren P, Gökcan H, Isayev O, Lagardère L, Piquemal JP. Scalable hybrid deep neural networks/polarizable potentials biomolecular simulations including long-range effects. Chem Sci 2023; 14:5438-5452. [PMID: 37234902 PMCID: PMC10208042 DOI: 10.1039/d2sc04815a] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 04/03/2023] [Indexed: 07/28/2023] Open
Abstract
Deep-HP is a scalable extension of the Tinker-HP multi-GPU molecular dynamics (MD) package enabling the use of Pytorch/TensorFlow Deep Neural Network (DNN) models. Deep-HP increases DNNs' MD capabilities by orders of magnitude offering access to ns simulations for 100k-atom biosystems while offering the possibility of coupling DNNs to any classical (FFs) and many-body polarizable (PFFs) force fields. It allows therefore the introduction of the ANI-2X/AMOEBA hybrid polarizable potential designed for ligand binding studies where solvent-solvent and solvent-solute interactions are computed with the AMOEBA PFF while solute-solute ones are computed by the ANI-2X DNN. ANI-2X/AMOEBA explicitly includes AMOEBA's physical long-range interactions via an efficient Particle Mesh Ewald implementation while preserving ANI-2X's solute short-range quantum mechanical accuracy. The DNN/PFF partition can be user-defined allowing for hybrid simulations to include key ingredients of biosimulation such as polarizable solvents, polarizable counter ions, etc.… ANI-2X/AMOEBA is accelerated using a multiple-timestep strategy focusing on the model's contributions to low-frequency modes of nuclear forces. It primarily evaluates AMOEBA forces while including ANI-2X ones only via correction-steps resulting in an order of magnitude acceleration over standard Velocity Verlet integration. Simulating more than 10 μs, we compute charged/uncharged ligand solvation free energies in 4 solvents, and absolute binding free energies of host-guest complexes from SAMPL challenges. ANI-2X/AMOEBA average errors are discussed in terms of statistical uncertainty and appear in the range of chemical accuracy compared to experiment. The availability of the Deep-HP computational platform opens the path towards large-scale hybrid DNN simulations, at force-field cost, in biophysics and drug discovery.
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Affiliation(s)
- Théo Jaffrelot Inizan
- Sorbonne Université, Laboratoire de Chimie Théorique UMR 7616 CNRS Paris 75005 France
| | - Thomas Plé
- Sorbonne Université, Laboratoire de Chimie Théorique UMR 7616 CNRS Paris 75005 France
| | - Olivier Adjoua
- Sorbonne Université, Laboratoire de Chimie Théorique UMR 7616 CNRS Paris 75005 France
| | - Pengyu Ren
- Department of Biomedical Engineering, University of Texas at Austin Austin Texas USA
| | - Hatice Gökcan
- Department of Chemistry, Carnegie Mellon University Pittsburgh Pennsylvania USA
| | - Olexandr Isayev
- Department of Chemistry, Carnegie Mellon University Pittsburgh Pennsylvania USA
| | - Louis Lagardère
- Sorbonne Université, Laboratoire de Chimie Théorique UMR 7616 CNRS Paris 75005 France
- Sorbonne Université, Institut Parisien de Chimie Physique et Théorique FR 2622 CNRS Paris France
| | - Jean-Philip Piquemal
- Sorbonne Université, Laboratoire de Chimie Théorique UMR 7616 CNRS Paris 75005 France
- Department of Biomedical Engineering, University of Texas at Austin Austin Texas USA
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Li D, Cao F, Han J, Wang M, Lai C, Zhang J, Xu T, Bouakaz A, Wan M, Ren P, Zhang S. The sustainable antihypertensive and target organ damage protective effect of transcranial focused ultrasound stimulation in spontaneously hypertensive rats. J Hypertens 2023; 41:852-866. [PMID: 36883470 DOI: 10.1097/hjh.0000000000003407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
OBJECTIVE In this study, we aimed to investigate the sustainable antihypertensive effects and protection against target organ damage caused by low-intensity focused ultrasound (LIFU) stimulation and the underlying mechanism in spontaneously hypertensive rats (SHRs) model. METHODS AND RESULTS SHRs were treated with ultrasound stimulation of the ventrolateral periaqueductal gray (VlPAG) for 20 min every day for 2 months. Systolic blood pressure (SBP) was compared among normotensive Wistar-Kyoto rats, SHR control group, SHR Sham group, and SHR LIFU stimulation group. Cardiac ultrasound imaging and hematoxylin-eosin and Masson staining of the heart and kidney were performed to assess target organ damage. The c-fos immunofluorescence analysis and plasma levels of angiotensin II, aldosterone, hydrocortisone, and endothelin-1 were measured to investigate the neurohumoral and organ systems involved. We found that SBP was reduced from 172 ± 4.2 mmHg to 141 ± 2.1 mmHg after 1 month of LIFU stimulation, P < 0.01. The next month of treatment can maintain the rat's blood pressure at 146 ± 4.2 mmHg at the end of the experiment. LIFU stimulation reverses left ventricular hypertrophy and improves heart and kidney function. Furthermore, LIFU stimulation enhanced the neural activity from the VLPAG to the caudal ventrolateral medulla and reduced the plasma levels of ANGII and Aldo. CONCLUSION We concluded that LIFU stimulation has a sustainable antihypertensive effect and protects against target organ damage by activating antihypertensive neural pathways from VLPAG to the caudal ventrolateral medulla and further inhibiting the renin-angiotensin system (RAS) activity, thereby supporting a novel and noninvasive alternative therapy to treat hypertension.
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Affiliation(s)
- Dapeng Li
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Department of Biomedical Engineering, School of Life Science and Technology, Xi'an Jiaotong University
| | - Fangyuan Cao
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Department of Biomedical Engineering, School of Life Science and Technology, Xi'an Jiaotong University
| | - Jie Han
- Department of Cardiology, The Second Affiliated Hospital of Xi'an Jiaotong University, China
| | - Mengke Wang
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Department of Biomedical Engineering, School of Life Science and Technology, Xi'an Jiaotong University
| | - Chunhao Lai
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Department of Biomedical Engineering, School of Life Science and Technology, Xi'an Jiaotong University
| | - Jingjing Zhang
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Department of Biomedical Engineering, School of Life Science and Technology, Xi'an Jiaotong University
| | - Tianqi Xu
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Department of Biomedical Engineering, School of Life Science and Technology, Xi'an Jiaotong University
| | | | - Mingxi Wan
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Department of Biomedical Engineering, School of Life Science and Technology, Xi'an Jiaotong University
| | - Pengyu Ren
- Institute of Medical Artificial Intelligence
- Department of Neurosurgery, The Second Affiliated Hospital of Xi'an Jiaotong University
| | - Siyuan Zhang
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Department of Biomedical Engineering, School of Life Science and Technology, Xi'an Jiaotong University
- Sichuan Digital Economy Industry Development Research Institute, China
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Lu Q, Chai Y, Ren L, Ren P, Zhou J, Lin C. Research on quality evaluation of innovation and entrepreneurship education for college students based on random forest algorithm and logistic regression model. PeerJ Comput Sci 2023; 9:e1329. [PMID: 37346726 PMCID: PMC10280670 DOI: 10.7717/peerj-cs.1329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/15/2023] [Indexed: 06/23/2023]
Abstract
The quality evaluation of innovation and entrepreneurship (I&E) in the education sector is achieving worldwide attention as empowering nations with high quality talents is quintessential for economic progress. China, a pioneer in the world market in almost all sectors have transformed its educational policies and incorporated entrepreneurial skills as a part of their education models to further catalyst the country's economic progress. This research focuses on building a novel hybrid Machine Learning (ML) model by integrating two powerful algorithms namely Random Forest (RF) and Logistic Regression (LR) to assess the intensity of the I&E in education from the data acquired from 25 leading Higher Educational Institution's (HEI) in different provinces. The major contributions to the work are, (1) construction of quality index for each topic of interest using individual RF, (2) ranking the indicators based on the quality index to assess the strength and weaknesses, (3) and finally use the LR algorithm study the quality of each indicator. The efficacy of the proposed hybrid model is validated using the benchmark classification metrics to assess its learning and prediction performance in evaluating the quality of I&E education. The result of the research portrays that the universities have now started to integrate entrepreneurship skills as a part of the curriculum, which is evident from the better ranking of the topic curriculum development which is followed by the enrichment of skills. This comprehensive research will help the institutions to identify the potential areas of growth to boost the economic development and improve the skill set necessary for I&E education among college students.
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Affiliation(s)
- Qianqian Lu
- Administrative Office, Zhejiang Guangsha Vocational and Technical University of Construction, Dongyang, China
| | - Yongxiang Chai
- School of Information, Zhejiang Guangsha Vocational and Technical University of Construction, Dongyang, China
| | - Lihui Ren
- Department of Public Physical Education, Zhejiang Guangsha Vocational and Technical University of Construction, Dongyang, China
| | - Pengyu Ren
- Department of Public Physical Education, Zhejiang Guangsha Vocational and Technical University of Construction, Dongyang, China
| | - Junhui Zhou
- Department of Public Physical Education, Zhejiang Guangsha Vocational and Technical University of Construction, Dongyang, China
| | - Chunlei Lin
- Department of Education and Engineering, Zhejiang Guangsha Vocational and Technical University of Construction, Dongyang, China
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18
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Liu X, Xu Z, Liang J, Yu L, Ren P, Zhou HB, Wu S, Lan K. Identification of a novel acylthiourea-based potent broad-spectrum inhibitor for enterovirus 3D polymerase in vitro and in vivo. Antiviral Res 2023; 213:105583. [PMID: 36965527 DOI: 10.1016/j.antiviral.2023.105583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 03/16/2023] [Accepted: 03/20/2023] [Indexed: 03/27/2023]
Abstract
Enterovirus infections have become a serious public health threat to young children, leading to hand-foot-and-mouth disease and more severe nervous system diseases. Due to the lack of licensed anti enterovirus drugs, we reported herein that a Tenovin-1 analog, acylthiourea-based 4-(tert-butyl)-N-((4-(4-(tert-butyl)benzamido)phenyl)carbamothioyl) benzamide (AcTU), displayed low nanomolar anti-EV-A71 activity with an EC50 of 1.0 nM in RD cells. Moreover, AcTU exhibited nanomolar to picomolar inhibitory activity against a series of enteroviruses including EV-D68, CV-A21, CV-A16 and CV-B1 (EC50 = 0.75-17.15 nM). Mechanistic studies indicated that AcTU inhibited enterovirus proliferation by targeting 3D polymerase. In addition, AcTU displayed moderate pharmacokinetic properties in rats (F = 7.4%, T1/2 = 3.26 h), and in vivo protection studies demonstrated that AcTU orally administered at 0.6 mg/kg/d was highly protective against lethal EV-A71 challenge in mice, potentially reducing mortality from 100% to 20% as well as alleviating symptoms. These results suggested that AcTU could be a potent clinical candidate for the treatment of enterovirus infections.
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Affiliation(s)
- Xinjin Liu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhichao Xu
- Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals, Frontier Science Center for Immunology and Metabolism, Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China
| | - Jinsen Liang
- Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals, Frontier Science Center for Immunology and Metabolism, Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China
| | - Lei Yu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Pengyu Ren
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Hai-Bing Zhou
- Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals, Frontier Science Center for Immunology and Metabolism, Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China.
| | - Shuwen Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
| | - Ke Lan
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, Hubei, China.
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19
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Wait EE, Gourary J, Liu C, Spoerke ED, Rempe SB, Ren P. Development of AMOEBA Polarizable Force Field for Rare-Earth La 3+ Interaction with Bioinspired Ligands. J Phys Chem B 2023; 127:1367-1375. [PMID: 36735638 PMCID: PMC9957963 DOI: 10.1021/acs.jpcb.2c07237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Rare-earth metals (REMs) are crucial for many important industries, such as power generation and storage, in addition to cancer treatment and medical imaging. One promising new REM refinement approach involves mimicking the highly selective and efficient binding of REMs observed in relatively recently discovered proteins. However, realizing any such bioinspired approach requires an understanding of the biological recognition mechanisms. Here, we developed a new classical polarizable force field based on the AMOEBA framework for modeling a lanthanum ion (La3+) interacting with water, acetate, and acetamide, which have been found to coordinate the ion in proteins. The parameters were derived by comparing to high-level ab initio quantum mechanical (QM) calculations that include relativistic effects. The AMOEBA model, with advanced atomic multipoles and electronic polarization, is successful in capturing both the QM distance-dependent La3+-ligand interaction energies and experimental hydration free energy. A new scheme for pairwise polarization damping (POLPAIR) was developed to describe the polarization energy in La3+ interactions with both charged and neutral ligands. Simulations of La3+ in water showed water coordination numbers and ion-water distances consistent with previous experimental and theoretical findings. Water residence time analysis revealed both fast and slow kinetics in water exchange around the ion. This new model will allow investigation of fully solvated lanthanum ion-protein systems using GPU-accelerated dynamics simulations to gain insights on binding selectivity, which may be applied to the design of synthetic analogues.
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Affiliation(s)
- Elizabeth E. Wait
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Justin Gourary
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Erik D. Spoerke
- Electronic, Optical, and Nano Materials Department, Sandia National Laboratories, Albuquerque, NM 87185, USA
| | - Susan B. Rempe
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM 87185, USA
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
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20
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Maghsoud Y, Vázquez-Montelongo EA, Yang X, Liu C, Jing Z, Lee J, Harger M, Smith AK, Espinoza M, Guo HF, Kurie JM, Dalby KN, Ren P, Cisneros GA. Computational Investigation of a Series of Small Molecules as Potential Compounds for Lysyl Hydroxylase-2 (LH2) Inhibition. J Chem Inf Model 2023; 63:986-1001. [PMID: 36779232 PMCID: PMC10233724 DOI: 10.1021/acs.jcim.2c01448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The catalytic function of lysyl hydroxylase-2 (LH2), a member of the Fe(II)/αKG-dependent oxygenase superfamily, is to catalyze the hydroxylation of lysine to hydroxylysine in collagen, resulting in stable hydroxylysine aldehyde-derived collagen cross-links (HLCCs). Reports show that high amounts of LH2 lead to the accumulation of HLCCs, causing fibrosis and specific types of cancer metastasis. Some members of the Fe(II)/αKG-dependent family have also been reported to have intramolecular O2 tunnels, which aid in transporting one of the required cosubstrates into the active site. While LH2 can be a promising target to combat these diseases, efficacious inhibitors are still lacking. We have used computational simulations to investigate a series of 44 small molecules as lead compounds for LH2 inhibition. Tunneling analyses indicate the existence of several intramolecular tunnels. The lengths of the calculated O2-transporting tunnels in holoenzymes are relatively longer than those in the apoenzyme, suggesting that the ligands may affect the enzyme's structure and possibly block (at least partially) the tunnels. The sequence alignment analysis between LH enzymes from different organisms shows that all of the amino acid residues with the highest occurrence rate in the oxygen tunnels are conserved. Our results suggest that the enolate form of diketone compounds establishes stronger interactions with the Fe(II) in the active site. Branching the enolate compounds with functional groups such as phenyl and pyridinyl enhances the interaction with various residues around the active site. Our results provide information about possible leads for further LH2 inhibition design and development.
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Affiliation(s)
- Yazdan Maghsoud
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Erik Antonio Vázquez-Montelongo
- Department of Physical Medicine and Rehabilitation, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Xudong Yang
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Zhifeng Jing
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Juhoon Lee
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Matthew Harger
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Ally K Smith
- Department of Chemistry, University of North Texas, Denton, Texas 76201, United States
| | - Miguel Espinoza
- Department of Chemistry, University of North Texas, Denton, Texas 76201, United States
| | - Hou-Fu Guo
- Department of Molecular and Cellular Biochemistry, College of Medicine, The University of Kentucky, Lexington, Kentucky 40536, United States
| | - Jonathan M Kurie
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77005, United States
| | - Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - G Andrés Cisneros
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
- Department of Physics, The University of Texas at Dallas, Richardson, Texas 75080, United States
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21
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Arabzadeh H, Walker B, Sperling JM, Acevedo O, Ren P, Yang W, Albrecht-Schönzart TE. Molecular Dynamics and Free Energy Calculations of Dicyclohexano-18-crown-6 Diastereoisomers with Sm 2+, Eu 2+, Dy 2+, Yb 2+, Cf 2+, and Three Halide Salts in Tetrahydrofuran and Acetonitrile Using the AMOEBA Force Field. J Phys Chem B 2022; 126:10721-10731. [PMID: 36508277 PMCID: PMC9999210 DOI: 10.1021/acs.jpcb.2c04613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
With the continual development of lanthanides (Ln) in current technological devices, an efficient separation process is needed that can recover greater amounts of these rare elements. Dicyclohexano-18-crown-6 (DCH18C6) is a crown ether that may be a promising candidate for Ln separation, but additional research is required. As such, molecular dynamics (MD) simulations have been performed on four divalent lanthanide halide salts (Sm2+, Eu2+, Dy2+, and Yb2+) and one divalent actinide halide salt (Cf2+) bound to three diastereoisomers of DCH18C6. Dy2+, Yb2+, Cf2+, DCH18C6, and tetrahydrofuran (THF) solvent were parameterized for the AMOEBA polarizable force field for the first time, whereas existing parameters for Sm2+ and Eu2+ were utilized from our previous efforts. A coordination number (CN) of six for Ln2+/An2+-O solvated in THF indicated that the cations interacted almost entirely with the oxygens of the polyether ring. A CN of one for Ln2+/An2+-N solvated in acetonitrile for systems containing iodide suggested that the N atom of acetonitrile was competitive with I- for cation interactions. Fluctuation between five and six CNs for Dy2+ and Yb2+ suggested that although the cations remained in the polyether ring, the size of the ring may not be an ideal fit as these cations possess comparatively smaller ionic radii. Gibbs binding free energies of Sm2+ in all DCH18C6 diastereoisomers solvated in THF were calculated. The binding free energy of the cis-syn-cis diastereoisomer was the most favorable, followed by cis-anti-cis, and then trans-anti-trans. Finally, two major types of conformation were observed for each diastereoisomer that were related to the electrostatic interactions and charge density of the cations.
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Affiliation(s)
- Hesam Arabzadeh
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Brandon Walker
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Joseph M. Sperling
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Orlando Acevedo
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA
| | - Pengyu Ren
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Wei Yang
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
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22
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Wang Y, Walker BD, Liu C, Ren P. An Efficient Approach to Large-Scale Ab Initio Conformational Energy Profiles of Small Molecules. Molecules 2022; 27:8567. [PMID: 36500658 PMCID: PMC9738817 DOI: 10.3390/molecules27238567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/19/2022] [Accepted: 11/27/2022] [Indexed: 12/12/2022] Open
Abstract
Accurate conformational energetics of molecules are of great significance to understand maby chemical properties. They are also fundamental for high-quality parameterization of force fields. Traditionally, accurate conformational profiles are obtained with density functional theory (DFT) methods. However, obtaining a reliable energy profile can be time-consuming when the molecular sizes are relatively large or when there are many molecules of interest. Furthermore, incorporation of data-driven deep learning methods into force field development has great requirements for high-quality geometry and energy data. To this end, we compared several possible alternatives to the traditional DFT methods for conformational scans, including the semi-empirical method GFN2-xTB and the neural network potential ANI-2x. It was found that a sequential protocol of geometry optimization with the semi-empirical method and single-point energy calculation with high-level DFT methods can provide satisfactory conformational energy profiles hundreds of times faster in terms of optimization.
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Affiliation(s)
| | | | | | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
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23
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Ren P, Liu X, Li F, Zang D. Clean Household Energy Consumption and Residents' Well-Being: Empirical Analysis and Mechanism Test. Int J Environ Res Public Health 2022; 19:14057. [PMID: 36360933 PMCID: PMC9657123 DOI: 10.3390/ijerph192114057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/24/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
Improving well-being is a critical problem for worldwide social progress. Research on well-being effects of clean household energy consumption is of great significance for the realization of United Nation's Sustainable Development Goals (SDGs). Due to the multifaceted role of clean household energy in enhancing well-being as a sustainable development goal, it has attracted extensive academic attention and research but still needs to be further refined through new perspectives. This paper uses data from the 2018 China Health and Retirement Longitudinal Study to conduct an empirical analysis of clean household energy consumption and residents' well-being using an ordered probit model, the instrumental variables method, a conditional mixed process (CMP) method, and a mechanism analysis model. The results show that (1) household clean energy consumption contributes to residents' well-being, and the results remained significant after selecting "Do you have an electric Bicycle?" as an instrumental variable to address the endogeneity question. (2) According to heterogeneity research, women's wellbeing is impacted by clean energy consumption in the household more than men's. Only in rural locations can clean household energy consumption significantly boost well-being; urban and suburban areas are unaffected. (3) In the mechanism analysis, health condition and depression played a mediating role on the impact of clean household energy consumption on well-being, and social contact played a moderating role on the impact of clean household energy consumption on well-being. The findings and policy recommendations in this paper are suggestive of how we can improve the well-being of residents in low- and middle-income countries and provide reference values for research in related fields around the world.
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24
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Lin YC, Ren P, Webb LJ. AMOEBA Force Field Trajectories Improve Predictions of Accurate p Ka Values of the GFP Fluorophore: The Importance of Polarizability and Water Interactions. J Phys Chem B 2022; 126:7806-7817. [PMID: 36194474 PMCID: PMC10851343 DOI: 10.1021/acs.jpcb.2c03642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Precisely quantifying the magnitude, direction, and biological functions of electric fields in proteins has long been an outstanding challenge in the field. The most widely implemented experimental method to measure such electric fields at a particular residue in a protein has been through changes in pKa of titratable residues. While many computational strategies exist to predict these values, it has been difficult to do this accurately or connect predicted results to key structural or mechanistic features of the molecule. Here, we used experimentally determined pKa values of the fluorophore in superfolder green fluorescent protein (GFP) with amino acid mutations made at position Thr 203 to evaluate the pKa prediction ability of molecular dynamics (MD) simulations using a polarizable force field, AMOEBA. Structure ensembles from AMOEBA were used to calculate pKa values of the GFP fluorophore. The calculated pKa values were then compared to trajectories using a conventional fixed charge force field (Amber03 ff). We found that the position of water molecules included in the pKa calculation had opposite effects on the pKa values between the trajectories from AMOEBA and Amber03 force fields. In AMOEBA trajectories, the inclusion of water molecules within 35 Å of the fluorophore decreased the difference between the predicted and experimental values, resulting in calculated pKa values that were within an average of 0.8 pKa unit from the experimental results. On the other hand, in Amber03 trajectories, including water molecules that were more than 5 Å from the fluorophore increased the differences between the calculated and experimental pKa values. The inaccuracy of pKa predictions determined from Amber03 trajectories was caused by a significant stabilization of the deprotonated chromophore's free energy compared to the result in AMOEBA. We rationalize the cutoffs for explicit water molecules when calculating pKa to better predict the electrostatic environment surrounding the fluorophore buried in GFP. We discuss how the results from this work will assist the prospective prediction of pKa values or other electrostatic effects in a wide variety of folded proteins.
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Affiliation(s)
- Yu-Chun Lin
- Department of Chemistry, Texas Materials Institute, and Interdisciplinary Life Sciences Program, The University of Texas at Austin, 105 E 24th St. STOP A5300, Austin, TX 78712-1224
| | - Pengyu Ren
- Department of Chemistry, Texas Materials Institute, and Interdisciplinary Life Sciences Program, The University of Texas at Austin, 105 E 24th St. STOP A5300, Austin, TX 78712-1224
| | - Lauren J. Webb
- Department of Chemistry, Texas Materials Institute, and Interdisciplinary Life Sciences Program, The University of Texas at Austin, 105 E 24th St. STOP A5300, Austin, TX 78712-1224
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25
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Jing Z, Ren P. Molecular Dynamics Simulations of Protein RNA Complexes by Using an Advanced Electrostatic Model. J Phys Chem B 2022; 126:7343-7353. [PMID: 36107618 PMCID: PMC9530969 DOI: 10.1021/acs.jpcb.2c05278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein-RNA interactions are integral to the biological functions of RNA. It is well recognized that molecular dynamics (MD) simulations of protein-RNA complexes are more challenging than those of each component. The difficulty arises from the strong electrostatic interactions and the delicate balance between various types of physical forces at the interface. Previously, MD simulations of protein-RNA complexes have predominantly employed fixed-charge force fields. Although force field modifications have been developed to address problems identified in the simulations, some protein-RNA structures are still hard to reproduce by simulations. Here, we present MD simulations of two representative protein-RNA complexes using the AMOEBA polarizable force field. The van der Waals parameters were refined to reproduce accurate quantum-mechanical data of base-base and base-amino acid interactions. It was found that the refined parameters produced a more stable hydrogen-bond network in the interface. One of the complexes remained stable during the short simulations, whereas it could quickly break down in previous simulations using fixed-charge force fields. There was reversible breaking and formation of hydrogen bonds that are observed in the crystal structure, which may indicate the difference in solution and crystal structures. While further improvement and validation of the force fields are still needed, this work demonstrates that polarizable force fields are promising for the study of protein-RNA complexes.
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Affiliation(s)
- Zhifeng Jing
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712
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26
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Zhang Y, Yu B, Tian Y, Ren P, Lyu B, Fu L, Chen H, Li J, Gong S. A novel risk score model based on fourteen chromatin regulators-based genes for predicting overall survival of patients with lower-grade gliomas. Front Genet 2022; 13:957059. [PMID: 36246611 PMCID: PMC9554745 DOI: 10.3389/fgene.2022.957059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 08/31/2022] [Indexed: 12/02/2022] Open
Abstract
Background: Low grade gliomas(LGGs) present vexatious management issues for neurosurgeons. Chromatin regulators (CRs) are emerging as a focus of tumor research due to their pivotal role in tumorigenesis and progression. Hence, the goal of the current work was to unveil the function and value of CRs in patients with LGGs. Methods: RNA-Sequencing and corresponding clinical data were extracted from The Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA) database. A single-cell RNA-seq dataset was sourced from the Gene Expression Omnibus (GEO) database. Altogether 870 CRs were retrieved from the published articles in top academic journals. The least absolute shrinkage and selection operator (LASSO) algorithm and Cox regression analysis were applied to construct the prognostic risk model. Patients were then assigned into high- and low-risk groups based on the median risk score. The Kaplan–Meier (K-M) survival curve and receiver operating characteristic curve (ROC) were performed to assess the prognostic value. Sequentially, functional enrichment, tumor immune microenvironment, tumor mutation burden, drug prediction, single cell analysis and so on were analyzed to further explore the value of CR-based signature. Finally, the expression of signature genes were validated by immunohistochemistry (IHC) and quantitative real-time PCR (qRT-PCR). Results: We successfully constructed and validated a 14 CRs-based model for predicting the prognosis of patients with LGGs. Moreover, we also found 14 CRs-based model was an independent prognostic factor. Functional analysis revealed that the differentially expressed genes were mainly enriched in tumor and immune related pathways. Subsequently, our research uncovered that LGGs patients with higher risk scores exhibited a higher TMB and were less likely to be responsive to immunotherapy. Meanwhile, the results of drug analysis offered several potential drug candidates. Furthermore, tSNE plots highlighting the magnitude of expression of the genes of interest in the cells from the scRNA-seq assay. Ultimately, transcription expression of six representative signature genes at the mRNA level was consistent with their protein expression changes. Conclusion: Our findings provided a reliable biomarker for predicting the prognosis, which is expected to offer new insight into LGGs management and would hopefully become a promising target for future research.
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Affiliation(s)
- Yongfeng Zhang
- Department of Neurourgery, The Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
| | - Beibei Yu
- Department of Neurourgery, The Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
| | - Yunze Tian
- Department of Neurourgery, The Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
| | - Pengyu Ren
- Department of Neurourgery, The Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
| | - Boqiang Lyu
- Department of Neurourgery, The Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
| | - Longhui Fu
- Department of Neurourgery, The Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
| | - Huangtao Chen
- Department of Neurourgery, The Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
| | - Jianzhong Li
- Department of Thoracic Surgery, The Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
- *Correspondence: Jianzhong Li, ; Shouping Gong,
| | - Shouping Gong
- Department of Neurourgery, The Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
- *Correspondence: Jianzhong Li, ; Shouping Gong,
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27
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Walker B, Liu C, Wait E, Ren P. Automation of AMOEBA polarizable force field for small molecules: Poltype 2. J Comput Chem 2022; 43:1530-1542. [PMID: 35778723 PMCID: PMC9329217 DOI: 10.1002/jcc.26954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 05/02/2022] [Accepted: 06/09/2022] [Indexed: 11/10/2022]
Abstract
A next-generation protocol (Poltype 2) has been developed which automatically generates AMOEBA polarizable force field parameters for small molecules. Both features and computational efficiency have been drastically improved. Notable advances include improved database transferability using SMILES, robust torsion fitting, non-aromatic ring torsion parameterization, coupled torsion-torsion parameterization, Van der Waals parameter refinement using ab initio dimer data and an intelligent fragmentation scheme that produces parameters with dramatically reduced ab initio computational cost. Additional improvements include better local frame assignment for atomic multipoles, automated formal charge assignment, Zwitterion detection, smart memory resource defaults, parallelized fragment job submission, incorporation of Psi4 quantum package, ab initio error handling, ionization state enumeration, hydration free energy prediction and binding free energy prediction. For validation, we have applied Poltype 2 to ~1000 FDA approved drug molecules from DrugBank. The ab initio molecular dipole moments and electrostatic potential values were compared with Poltype 2 derived AMOEBA counterparts. Parameters were further substantiated by calculating hydration free energy (HFE) on 40 small organic molecules and were compared with experimental data, resulting in an RMSE error of 0.59 kcal/mol. The torsion database has expanded to include 3543 fragments derived from FDA approved drugs. Poltype 2 provides a convenient utility for applications including binding free energy prediction for computational drug discovery. Further improvement will focus on automated parameter refinement by experimental liquid properties, expansion of the Van der Waals parameter database and automated parametrization of modified bio-fragments such as amino and nucleic acids.
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Affiliation(s)
- Brandon Walker
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Elizabeth Wait
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
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28
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Yang X, Liu C, Kuo YA, Yeh HC, Ren P. Computational study on the binding of Mango-II RNA aptamer and fluorogen using the polarizable force field AMOEBA. Front Mol Biosci 2022; 9:946708. [PMID: 36120549 PMCID: PMC9478177 DOI: 10.3389/fmolb.2022.946708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
Fluorescent light-up aptamers (FLAPs) are well-performed biosensors for cellular imaging and the detection of different targets of interest, including RNA, non-nucleic acid molecules, metal ions, and so on. They could be easily designed and emit a strong fluorescence signal once bound to specified fluorogens. Recently, one unique aptamer called Mango-II has been discovered to possess a strong affinity and excellent fluorescent properties with fluorogens TO1-Biotin and TO3-Biotin. To explore the binding mechanisms, computational simulations have been performed to obtain structural and thermodynamic information about FLAPs at atomic resolution. AMOEBA polarizable force field, with the capability of handling the highly charged and flexible RNA system, was utilized for the simulation of Mango-II with TO1-Biotin and TO3-Biotin in this work. The calculated binding free energy using published crystal structures is in excellent agreement with the experimental values. Given the challenges in modeling complex RNA dynamics, our work demonstrates that MD simulation with a polarizable force field is valuable for understanding aptamer-fluorogen binding and potentially designing new aptamers or fluorogens with better performance.
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Affiliation(s)
- Xudong Yang
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Yu-An Kuo
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Hsin-Chih Yeh
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, United States
- Texas Materials Institute, University of Texas at Austin, Austin, TX, United States
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, United States
- Oden Institute for Computational Engineering and Science, Austin, TX, United States
- Interdisciplinary Life Science Graduate Programs, Austin, TX, United States
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29
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Ren P, Zhang Q, Han P, Xu S, Xu C, Li Z, Yang J. [The working principle and prototype construction of the Chinese vestibular prosthesis]. Lin Chuang Er Bi Yan Hou Tou Jing Wai Ke Za Zhi 2022; 36:690-697. [PMID: 36036070 PMCID: PMC10127630 DOI: 10.13201/j.issn.2096-7993.2022.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Indexed: 04/30/2023]
Abstract
Objective:To complete the working principle design and prototype construction of the Chinese multichannel vestibular prosthesis (CMVP) with independent intellectual property rights, and verify its working performance, so as to lay the foundation for the clinical promotion and application of CMVP. Methods:On the basis of previous research, the working principle of CMVP was constructed based on the information encoding principle of vestibular nervous system, and the circuit was designed according to the principle. Then, appropriate electronic components and software systems were selected to construct a CMVP prototype according to the design. Finally, the input and output characteristics of the CMVP prototype were verified through the performance test. Results:In the present study, a block diagram of the working principle of the CMVP was successfully designed and drawn, and the working principle was explained in detail according to the block diagram. Further, the circuit diagram of the CMVP was designed and drawn based on the working principle, then the selected electronic components and software systems were combined one by one to complete the construction of a prototype. Finally, the performance test for the prototype was completed, which showed that all stimulus electrodes of the prototype could output biphasic pulse current, and the frequency of biphasic pulse current was modulated by the spatial rotation data input sensed by a motion sensor. Conclusion:The working principle and circuit design of the CMVP are reasonable; the CMVP prototype in China has been successfully constructed; the spatial rotation motion sensing input and the modulated pulse current output are stable and reliable.
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Affiliation(s)
- Pengyu Ren
- Institute of Medical Artificial Intelligence,the Second Affiliated Hospital of Xi'an Jiaotong University,Xi'an,710061,China
- Department of Neurosurgery,the Second Affiliated Hospital of Xi'an Jiaotong University
| | - Qing Zhang
- Department of Otorhinolaryngology-Head & Neck Surgery,Xinhua Hospital,Shanghai Jiaotong University School of Medicine
| | - Peng Han
- Department of Otolaryngology-Head & Neck Surgery,the First Affiliated Hospital of Xi'an Jiaotong University
| | - Songhua Xu
- Institute of Medical Artificial Intelligence,the Second Affiliated Hospital of Xi'an Jiaotong University,Xi'an,710061,China
| | - Chuangxin Xu
- Institute of Medical Artificial Intelligence,the Second Affiliated Hospital of Xi'an Jiaotong University,Xi'an,710061,China
| | - Zongfang Li
- Institute of Medical Artificial Intelligence,the Second Affiliated Hospital of Xi'an Jiaotong University,Xi'an,710061,China
| | - Jun Yang
- Department of Otorhinolaryngology-Head & Neck Surgery,Xinhua Hospital,Shanghai Jiaotong University School of Medicine
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Niu X, Han P, Duan M, Chen Z, Hu J, Chen Y, Xu M, Ren P, Zhang Q. Bilateral Dysfunction of Otolith Pathway in Patients With Unilateral Idiopathic BPPV Detected by ACS-VEMPs. Front Neurol 2022; 13:921133. [PMID: 36090849 PMCID: PMC9462380 DOI: 10.3389/fneur.2022.921133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Abstract
ObjectiveTo observe the functional status of the otolith pathway in patients with unilateral idiopathic benign paroxysmal positional vertigo (BPPV) by combining air-conducted sound elicited cervical vestibular-evoked myogenic potential (ACS-cVEMP) and ocular vestibular-evoked myogenic potential (ACS-oVEMP).MethodsOne hundred and eighty patients with BPPV were recruited for conventional cVEMP and oVEMP tests. The abnormal rates of VEMPs were compared between BPPV patients and control participants.ResultsThe abnormal rates of cVEMP and oVEMP in BPPV patients were 46.7% (84/180) and 57.2% (103/180) in affected ears, respectively, and 45.0% (81/180) and 56.7% (102/180) in unaffected ears, respectively; both were significantly higher than the abnormal rates of cVEMP and oVEMP in normal control ears. Compared with normal subjects, the cVEMP response rate was lower in affected and unaffected ears in BPPV patients. The abnormal rates of cVEMP and oVEMP were 48.1% (76/158) and 57.6% (91/158) in patients with posterior semicircular canal BPPV, and 36.4% (8/22) and 54.5% (12/22) in lateral semicircular canal BPPV. There was no significant difference in VEMP abnormalities between posterior semicircular canal BPPV and lateral semicircular canal BPPV.ConclusionThe prevalence of abnormal cVEMPs and oVEMPs in both affected and unaffected ears of patients with BPPV was significantly higher than that observed in the control group. The pathological mechanism of unilateral idiopathic BPPV may be associated with bilateral degeneration of otolith pathways.
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Affiliation(s)
- Xiaorong Niu
- Department of Otorhinolaryngology Head and Neck Surgery, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Peng Han
- Department of Otorhinolaryngology Head and Neck Surgery, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Maoli Duan
- Department of Otolaryngology Head and Neck Surgery, Department of Clinical Science, Intervention and Technology, Karolinska University Hospital, Karolinska Institute, Stockholm, Sweden
| | - Zichen Chen
- Department of Otorhinolaryngology Head and Neck Surgery, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Juan Hu
- Department of Otorhinolaryngology Head and Neck Surgery, Ear Institute, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yanfei Chen
- Department of Otorhinolaryngology Head and Neck Surgery, Ear Institute, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Min Xu
- Department of Otorhinolaryngology Head and Neck Surgery, Ear Institute, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Pengyu Ren
- Department of Otorhinolaryngology Head and Neck Surgery, Ear Institute, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
- Pengyu Ren
| | - Qing Zhang
- Department of Otorhinolaryngology Head and Neck Surgery, Ear Institute, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
- Department of Otorhinolaryngology Head and Neck Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai Jiaotong University School of Medicine Ear Institute, Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
- *Correspondence: Qing Zhang
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Arabzadeh H, Liu C, Acevedo O, Ren P, Yang W, Albrecht-Schönzart T. Hydration of divalent lanthanides, Sm 2+ and Eu 2+ : A molecular dynamics study with polarizable AMOEBA force field. J Comput Chem 2022; 43:1286-1297. [PMID: 35648124 PMCID: PMC10052752 DOI: 10.1002/jcc.26933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/31/2022] [Accepted: 05/08/2022] [Indexed: 11/06/2022]
Abstract
The chemistry of divalent lanthanides, Ln2+ , is a growing sub-field of heavy element chemistry owing to new synthetic approaches. However, some theoretical aspects of these unusual cations are currently underdeveloped, especially as they relate to their dynamic properties in solution. In this work, we address the hydration of two of the classical Ln2+ cations, Sm2+ and Eu2+ , using atomic multipole optimized energetic for biomolecular applications (AMOEBA) force fields. These cations have not been parameterized to date with AMOEBA, and few studies are available because of their instability with respect to oxidation in aqueous media. Coordination numbers (CN's) of 8.2 and 8.1 respectively for Sm2+ and Eu2+ , and 8.8 for both Sm3+ and Eu3+ have been obtained and are in good agreement with the few available AIMD and X-ray absorption fine structures studies. The decreased CN of Ln2+ compared with Ln3+ arises from progressive water exchange events that indicates the gradual stabilization of 8-coordinate structures with respect to 9-coordinate geometries. Moreover, the effects of the chloride counter anions on the coordination of Ln2+ cations have been studied at different chloride concentrations in this work. Lastly, water exchange times of Ln2+ cations have been calculated to provide a comprehensive understanding of the behavior of Eu2+ and Sm2+ in aqueous chloride media.
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Affiliation(s)
- Hesam Arabzadeh
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Chengwen Liu
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA
| | - Orlando Acevedo
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Pengyu Ren
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA
| | - Wei Yang
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA
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Ma Y, Ren P, Tong X, Hu Z, Yang W, Jin J, Zhang Y, Zhang S. O-235 ACLY entry into the nucleus to bind with EP300 and regulate the genomic DNA and ribosomal DNA transcription during early embryonic development. Hum Reprod 2022. [DOI: 10.1093/humrep/deac106.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Study question
ATP citrate lyase (ACLY) is one of the key enzymes to produce acetyl coenzyme A. What is its role in early embryonic development?
Summary answer
ACLY affected by activation of T447, S451 and S455 sites into nucleus and band with EP300 to affect genomic DNA and ribosomal DNA transcription.
What is known already
ACLY is one of the key enzymes to produce acetyl coenzyme A, which participates in fatty acid metabolism and regulates acetylation. Studies have found that ACLY knockout cells can survive, while the cell proliferation capacity will be weakened. ACLY is highly expressed in the cytoplasm of Hela cells colon cancer cells and other somatic cells. When AKT phosphorylates S455 site, ACLY enters the nucleus and participates in DNA damage repair. Its localization and role in embryos have not been studied. The only thing we know is homozygous mice could not be detected at E8.5 days after implantation.
Study design, size, duration
Twenty-four human day 6 developmentally arrested embryos were used to detect ACLY localization. Dozens of ACLY heterozygous female mice were used to test the time points of ACLY homozygous lethality after mating with heterozygous male mice. After zygotes were taken from wild-type C57BL6 mice, microinjection technology was used to explore the effects of knocking down ACLY, changing ACLY location or mutating ACLY. HeLa cells were used to explore at the molecular level.
Participants/materials, setting, methods
In this experiment, we used human abandoned or donated embryos, gene knockout mice, wild-type C57BL6 mice and Hela cell.
The experimental techniques used include in vitro embryo culture, EU staining, plasmid transfection, immunoprecipitation, western blot analysis, in vitro transcription, microinjection, immunofluorescence, RT-PCR and RNA-seq.
Main results and the role of chance
Firstly, our study found its special nuclear localization in early embryos for the first time and proved that its localization was related to embryonic development potential.
Secondly, the specific period of ACLY homozygous death was identified by ACLY heterozygous mice. And by knocking down ACLY or adding inhibitor SB204990, It was found that ACLY played an important role in cell proliferation, blastocyst formation and lineage differentiation of early embryo development.
Thirdly, we proved that ACLY nucleation played an important role in the development of early embryos. and the activated form of T447, S451 and S455 three sites led to ACLY nucleation.
Finally, we found that ACLY affected the level of histone acetylation and UBF acetylation. And then genomic DNA and ribosomal DNA transcription level were decreased. We further explored how the acetyl group produced by ACLY regulated transcription. The interaction between ACLY and EP300 was confirmed by immunofluorescence and COIP experiments. After knocking down EP300 in embryos or inhibiting its function with inhibitor c646, the results are consistent with knocking down ACLY. The above experimental data prove that ACLY affects histone acetylation level and regulates gene opening through the interaction with EP300.
Limitations, reasons for caution
We need to further explore the factors that promote ACLY into the nucleus, so as to add it to in vitro culture to enhance the embryonic development potential.
Wider implications of the findings
The study provides a new mechanism for insulin or lysophosphatidic acid to promote embryo development, and helps to improve the quality of embryo development in the process of embryo culture in vitro.
Trial registration number
not applicable
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Affiliation(s)
- Y Ma
- Assisted Reproduction Unit- Department of Obstetrics and Gynecology- Sir Run Run Shaw Hospital, School of Medicine- Zhejiang University , Hangzhou, China
| | - P Ren
- Assisted Reproduction Unit- Department of Obstetrics and Gynecology- Sir Run Run Shaw Hospital, School of Medicine- Zhejiang University , Hangzhou, China
| | - X Tong
- Assisted Reproduction Unit- Department of Obstetrics and Gynecology- Sir Run Run Shaw Hospital, School of Medicine- Zhejiang University , Hangzhou, China
| | - Z Hu
- Assisted Reproduction Unit- Department of Obstetrics and Gynecology- Sir Run Run Shaw Hospital, School of Medicine- Zhejiang University , Hangzhou, China
| | - W Yang
- Assisted Reproduction Unit- Department of Obstetrics and Gynecology- Sir Run Run Shaw Hospital, School of Medicine- Zhejiang University , Hangzhou, China
| | - J Jin
- Assisted Reproduction Unit- Department of Obstetrics and Gynecology- Sir Run Run Shaw Hospital, School of Medicine- Zhejiang University , Hangzhou, China
| | - Y Zhang
- Assisted Reproduction Unit- Department of Obstetrics and Gynecology- Sir Run Run Shaw Hospital, School of Medicine- Zhejiang University , Hangzhou, China
| | - S Zhang
- Assisted Reproduction Unit- Department of Obstetrics and Gynecology- Sir Run Run Shaw Hospital, School of Medicine- Zhejiang University , Hangzhou, China
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Naseem-Khan S, Lagardère L, Narth C, Cisneros GA, Ren P, Gresh N, Piquemal JP. Development of the Quantum-Inspired SIBFA Many-Body Polarizable Force Field: Enabling Condensed-Phase Molecular Dynamics Simulations. J Chem Theory Comput 2022; 18:3607-3621. [PMID: 35575306 PMCID: PMC10851344 DOI: 10.1021/acs.jctc.2c00029] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We present the extension of the Sum of Interactions Between Fragments Ab initio Computed (SIBFA) many-body polarizable force field to condensed-phase molecular dynamics (MD) simulations. The quantum-inspired SIBFA procedure is grounded on simplified integrals obtained from localized molecular orbital theory and achieves full separability of its intermolecular potential. It embodies long-range multipolar electrostatics (up to quadrupole) coupled to a short-range penetration correction (up to charge-quadrupole), exchange repulsion, many-body polarization, many-body charge transfer/delocalization, exchange dispersion, and dispersion (up to C10). This enables the reproduction of all energy contributions of ab initio symmetry-adapted perturbation theory (SAPT(DFT)) gas-phase reference computations. The SIBFA approach has been integrated within the Tinker-HP massively parallel MD package. To do so, all SIBFA energy gradients have been derived and the approach has been extended to enable periodic boundary conditions simulations using smooth particle mesh Ewald. This novel implementation also notably includes a computationally tractable simplification of the many-body charge transfer/delocalization contribution. As a proof of concept, we perform a first computational experiment defining a water model fitted on a limited set of SAPT(DFT) data. SIBFA is shown to enable a satisfactory reproduction of both gas-phase energetic contributions and condensed-phase properties highlighting the importance of its physically motivated functional form.
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Affiliation(s)
- Sehr Naseem-Khan
- LCT, UMR 7616 CNRS, Sorbonne Université, 75005 Paris, France
- Department of Chemistry, University of North Texas, Denton, Texas 76201, United States
| | - Louis Lagardère
- LCT, UMR 7616 CNRS, Sorbonne Université, 75005 Paris, France
- IP2CT, FR 2622, CNRS, Sorbonne Université, 75005 Paris, France
| | | | - G Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, Texas 76201, United States
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Nohad Gresh
- LCT, UMR 7616 CNRS, Sorbonne Université, 75005 Paris, France
| | - Jean-Philip Piquemal
- LCT, UMR 7616 CNRS, Sorbonne Université, 75005 Paris, France
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
- Institut Universitaire de France, 75005 Paris, France
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Yang X, Liu C, Ren P. High Order Ab Initio Valence Force Field with Chemical Pattern Based Parameter Assignment. J Comput Biophys Chem 2022; 21:431-447. [PMID: 35784097 PMCID: PMC9248749 DOI: 10.1142/s2737416521420047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Bonded (or valence) interactions, which directly determine the local structures of the molecules, are fundamental parts of molecular mechanics force fields (FFs). Most popular classical FFs adopt the simple harmonic models for bond stretching and angle bending and ignore cross-coupling effects among the valence terms. This may lead to less accurate vibrational properties and configurations in molecular dynamics (MD) simulations. AMOEBA models utilize an MM3(MM4)-style bonded interaction model, in which the vibrational anharmonicity, the coupling effects among different energy terms, and the out-of-plane bending for sp2-hybridized atoms are considered. In this work, we report the development of bonded interaction parameters for a wide range of chemistry based on quantum mechanics (QM). About 270 atomic types defined by SMARTS strings were used to model the valence interactions. Our results indicate that the resulting valence parameters produce accurate vibrational frequencies (RMSD from QM is less than ~36.6 cm-1) over a large set of molecules with diverse functional groups (445 molecules). By contrast, the harmonic models usually give an RMS error greater than 60 cm-1. Meanwhile, this model accurately reflects the potential energy surface of the out-of-plane bending. Our model can generally be applied to the AMOEBA family and any MM3(MM4)-based molecular mechanics FFs.
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Wang J, Quan Y, Lv J, Gong S, Ren P. Inhibition of FAM83D displays antitumor effects in glioblastoma via down-regulation of the AKT/Wnt/β-catenin pathway. Environ Toxicol 2022; 37:1343-1356. [PMID: 35150198 DOI: 10.1002/tox.23488] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 12/01/2021] [Accepted: 01/29/2022] [Indexed: 06/14/2023]
Abstract
Up-regulation of family with sequence similarity 83 member D (FAM83D) has been acknowledged as a vital contributor for the carcinogenesis of numerous cancers. The relevance of FAM83D in glioblastoma (GBM), however, is not well understood. This current work aimed to determine the possible roles and mechanisms of FAM83D in GBM. By analyzing The Cancer Genome Atlas (TCGA) data, we found dramatic increases in FAM83D expression in GBM tissue. We also observed elevated levels of FAM83D in the clinical specimens of GBM. In vitro data showed that silencing FAM83D resulted in remarkable antitumor effects via inhibiting the proliferation, invasion and epithelial-mesenchymal transition of GBM cells. Moreover, the knockdown of FAM83D improved sensitivity to the chemotherapy drug temozolomide. In-depth mechanism research revealed that the silencing of FAM83D strikingly decreased the phosphorylation levels of AKT and glycogen synthase kinase-3β, and prohibited activation of the Wnt/β-catenin pathway. The suppression of AKT abolished FAM83D-mediated activation of the Wnt/β-catenin pathway. The re-expression of β-catenin reversed FAM83D-silencing-induced antitumor effects in GBM cells. In addition, GBM cells with FAM83D silencing exhibited reduced tumorigenic potential in vivo. Overall, the data from this work show that the inhibition of FAM83D displays antitumor effects in GBM via down-regulation of the AKT/Wnt/β-catenin pathway and propose FAM83D as a new therapeutic target for GBM.
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Affiliation(s)
- Jubo Wang
- Department of Neurosurgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yu Quan
- Department of Neurosurgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jian Lv
- Department of Neurosurgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Shouping Gong
- Department of Neurosurgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Pengyu Ren
- Department of Neurosurgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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Zhang Y, Chen Z, Zhao H, Shen J, Zhong B, Wu Q, Yang J, Jin Y, Zhang Q, Ren P. B81 Bone Vibrator-Induced Vestibular-Evoked Myogenic Potentials: Normal Values and the Effect of Age. Front Neurol 2022; 13:881682. [PMID: 35645948 PMCID: PMC9131004 DOI: 10.3389/fneur.2022.881682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
ObjectiveTo define the normal values and examine the influence of aging on B81 bone vibrator-induced cervical vestibular-evoked myogenic potentials (B81-cVEMPs) and ocular vestibular-evoked myogenic potentials (B81-oVEMPs).MethodsSeventy healthy subjects, divided into seven groups according to their ages, were enrolled in this study. The 4–9-, 10–19-, 20–29-, 30–39-, 40–49-, 50–59-, and 60–70-year-old participants were divided into groups I–VII, respectively. B81-cVEMP and B81-oVEMP were recorded in each group.ResultsThe B81-cVEMP response rates for groups I–VII were 100, 100, 100, 100, 95, 95, and 75%, respectively, with significant differences only between groups I–VI and group VII (p = 0.047, p < 0.05). The B81-oVEMP response rates for groups I–VII were 100, 100, 100, 100, 70, 65, and 40%, respectively, with significant differences only between groups I–IV and groups V–VII (p = 0.020, p = 0.008, p = 0.000; p < 0.05). The threshold, P13, and N23 latencies of B81-cVEMP positively correlated with age (r = 0.756, p = 0.000; r = 0.357, p = 0.003; r = 0.316, p = 0.009; p < 0.05). The raw amplitudes and corrected amplitudes negatively correlated with age (r = −0.641, p = 0.000; r = −0.609, p = 0.000, p < 0.05). For B81-oVEMP, the corrected amplitudes negatively correlated with age (r = −0.638, p = 0.000, p<0.05), but the threshold and N10 latency positively correlated with age (r = 0.768, p = 0.000; r = 0.334, p = 0.009, p < 0.05). Moreover, the interaural asymmetry ratio did not significantly correlate with age for B81-cVEMP and B81-oVEMP.ConclusionAs age increased, the B81-cVEMP response rate decreased, the thresholds increased, P13 and N23 latencies were prolonged, and the raw amplitude and corrected amplitude decreased. The B81-oVEMP response rate and corrected amplitude decreased, the thresholds increased, and N10 latency was prolonged with age. These changes are probably due to the occurrence of morphological and functional changes in the vestibular system with aging. Therefore, we suggest establishing different reference values according to different age groups when evaluating the VEMP results in patients with vestibular diseases.
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Affiliation(s)
- Yuzhong Zhang
- Department of Otorhinolaryngology, Head and Neck Surgery, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Zichen Chen
- Department of Otorhinolaryngology, Head and Neck Surgery, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Huandi Zhao
- Department of Otorhinolaryngology, Head and Neck Surgery, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jiali Shen
- Department of Otorhinolaryngology, Head and Neck Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Ear Science, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Otolaryngology and Translational Medicine, Shanghai, China
| | - Bo Zhong
- Division of Mechanics and Acoustics, National Institute of Metrology, Beijing, China
| | - Qiong Wu
- Department of Otorhinolaryngology, Head and Neck Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Ear Science, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Otolaryngology and Translational Medicine, Shanghai, China
| | - Jun Yang
- Department of Otorhinolaryngology, Head and Neck Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Ear Science, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Otolaryngology and Translational Medicine, Shanghai, China
| | - Yulian Jin
- Department of Otorhinolaryngology, Head and Neck Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Ear Science, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Otolaryngology and Translational Medicine, Shanghai, China
- Yulian Jin
| | - Qing Zhang
- Department of Otorhinolaryngology, Head and Neck Surgery, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
- Department of Otorhinolaryngology, Head and Neck Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Ear Science, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Otolaryngology and Translational Medicine, Shanghai, China
- Qing Zhang
| | - Pengyu Ren
- Department of Otorhinolaryngology, Head and Neck Surgery, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
- *Correspondence: Pengyu Ren
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Allen CD, Rempe SLB, Zwier TS, Ren P. Trapping Ca + inside a molecular cavity: computational study of the potential energy surfaces for Ca +-[ n]cycloparaphenylene, n = 5-12. Phys Chem Chem Phys 2022; 24:10085-10094. [PMID: 35416200 DOI: 10.1039/d2cp00717g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ion trap quantum computing utilizes electronic states of atomic ions such as Ca+ to encode information on to a qubit. To explore the fundamental properties of Ca+ inside molecular cavities, we describe here a computational study of Ca+ bound inside neutral [n]-cycloparaphenylenes (n = 5-12), often referred to as "nanohoops". This ab initio study characterizes optimized structures, harmonic vibrational frequencies, potential energy surfaces, and ion molecular orbital distortion as functions of increasing nanohoop size. The results of this work provide a first step in guiding experimental studies of the spectroscopy of these ion-molecular cavity complexes.
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Affiliation(s)
- Cole D Allen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, USA.
| | - Susan L B Rempe
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - Timothy S Zwier
- Sandia National Laboratories, Gas Phase Chemical Physics, Livermore, CA 94550, USA
| | - Pengyu Ren
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, USA.
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Ma FX, Ren P, Cao J, Bian YQ, Zhou JH, Zhao CY. [Clinical application of three-dimensional printed preformed titanium mesh combined with free latissimus dorsi muscle flap in the treatment of squamous cell carcinoma with skull defect in the vertex]. Zhonghua Shao Shang Yu Chuang Mian Xiu Fu Za Zhi 2022; 38:341-346. [PMID: 35462512 DOI: 10.3760/cma.j.cn501120-20201221-00538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Objective: To explore the clinical effects of three-dimensional printed preformed titanium mesh combined with latissimus dorsi muscle flap free transplantation in the treatment of wounds with skull defect after radical surgery of squamous cell carcinoma in the vertex. Methods: A retrospective observational study was conducted. From January 2010 to December 2019, 5 patients with squamous cell carcinoma in the vertex accompanied with skull invasion who met the inclusion criteria were admitted to the Department of Burns and Plastic Surgery of the Second Affiliated Hospital of Air Force Medical University, including four males and one female, aged 50 to 65 years. The original lesion areas ranged from 5 cm×4 cm to 15 cm×8 cm. The titanium mesh was prefabricated via three-dimensional technic based on the result the scope of skull resection predicted with computerized tomography three-dimensional reconstruction before surgery. During the first stage, the soft tissue defect area of scalp (8 cm×7 cm to 18 cm×11 cm) after tumor enlargement resection was repaired with the preformed titanium mesh, and the titanium mesh was covered with latissimus dorsi muscle flap, with area of 10 cm×9 cm to 20 cm×13 cm. The thoracodorsal artery/vein was anastomosed with the superficial temporal artery/vein on one side. The muscle ends in the donor site were sutured together or performed with transfixion, and then the skin on the back were covered back to the donor site. On the 10th day after the first-stage surgery, the second-stage surgery was performed. The thin intermediate thickness skin graft was taken from the anterolateral thigh to cover the latissimus dorsi muscle flap. The duration and intraoperative blood loss of first-stage surgery were recorded. The postoperative muscle flap survival after the first-stage surgery and skin graft survival after the second-stage surgery was observed. The occurrence of complications, head appearance, and recurrence of tumor were followed up. Results: The average first-stage surgery duration of patients was 12.1 h, and the intraoperative blood loss was not more than 1 200 mL. The muscle flaps in the first-stage surgery and the skin grafts in the second-stage surgery all survived well. During the follow-up of 6-18 months, no complications such as exposure of titanium mesh or infection occurred, with good shape in the recipient sites in the vertex, and no recurrence of tumor. Conclusions: Three-dimensional printed preformed titanium mesh combined with latissimus dorsi muscle flap free transplantation and intermediate thickness skin graft cover is an effective and reliable method for repairing the wound with skull defect after extended resection of squamous cell carcinoma in the vertex. This method can cover the wound effectively as well as promote both recipient and donor sites to obtain good function and appearance.
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Affiliation(s)
- F X Ma
- Department of Burns and Plastic Surgery, the Second Affiliated Hospital of Air Force Medical University, Xi'an 710038, China
| | - P Ren
- Department of Burns and Plastic Surgery, the Second Affiliated Hospital of Air Force Medical University, Xi'an 710038, China
| | - J Cao
- Department of Burns and Plastic Surgery, the Second Affiliated Hospital of Air Force Medical University, Xi'an 710038, China
| | - Y Q Bian
- Department of Burns and Plastic Surgery, the Second Affiliated Hospital of Air Force Medical University, Xi'an 710038, China
| | - J H Zhou
- Department of Neurosurgery, the Second Affiliated Hospital of Air Force Medical University, Xi'an 710038, China
| | - C Y Zhao
- Department of Burns and Plastic Surgery, the Second Affiliated Hospital of Air Force Medical University, Xi'an 710038, China
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Yu Z, Ren P, Zhang H, Chen H, Ma FX. [Research advances on application of botulinum toxin type A in scar prevention and treatment]. Zhonghua Shao Shang Yu Chuang Mian Xiu Fu Za Zhi 2022; 38:385-388. [PMID: 35462519 DOI: 10.3760/cma.j.cn501120-20210208-00054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The wound healing time, tension of wound edge, proliferation of fibroblast, and extracellular matrix deposition are the important factors of scar formation, and botulinum toxin type A can regulate the above. Prevention and treatment of scar with botulinum toxin type A is one of the hot topics of clinical research in recent years. This paper briefly reviews researches by scholars at home and abroad on the mechanism, clinical application, complications, and adverse effects of botulinum toxin type A in scar prevention and treatment.
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Affiliation(s)
- Z Yu
- The Plastic and Reconstructive Surgery Department of Xi'an People's Hospital (Xi'an Fourth Hospital), Xi'an 710004, China
| | - P Ren
- Department of Burns and Plastic Surgery, the Second Affiliated Hospital of Air Force Medical University, Xi'an 710038, China
| | - H Zhang
- The Plastic and Reconstructive Surgery Department of Xi'an People's Hospital (Xi'an Fourth Hospital), Xi'an 710004, China
| | - H Chen
- The Plastic and Reconstructive Surgery Department of Xi'an People's Hospital (Xi'an Fourth Hospital), Xi'an 710004, China
| | - F X Ma
- Department of Burns and Plastic Surgery, the Second Affiliated Hospital of Air Force Medical University, Xi'an 710038, China
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Ren P, Niu X, Zhao R, Liu J, Ren W, Dai H, Chen J, Yan J, Li B, Shao Y, Bai Y, Han P. Long non-coding RNA AGAP2-AS1 promotes cell proliferation and invasion through regulating miR-193a-3p/LOXL4 axis in laryngeal squamous cell carcinoma. Cell Cycle 2022; 21:697-707. [PMID: 35113007 PMCID: PMC8973330 DOI: 10.1080/15384101.2021.2016197] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Laryngeal squamous cell carcinoma (LSCC) is an aggressive malignancy with highly mortality rate. Long non-coding RNA (lncRNA) AGAP2-AS1 is an identified oncogene in several types of cancers. However, the role of AGAP2-AS1 in LSCC remains unclear. The expression levels of AGAP2-AS1 in LSCC tissues and cell lines were measured using qRT-PCR. AGAP2-AS1 was knocked down in LSCC cells through transfection with siRNA-AGAP2-AS1. Cell proliferation and invasion were detected using MTT and transwell assays. Dual-luciferase reporter gene assay was performed to confirm the interaction with AGAP2-AS1 and downstream genes. Our results showed that AGAP2-AS1 expression was remarkably increased in human LSCC tissues and cell lines. Knockdown of AGAP2-AS1 significantly inhibited the proliferation and invasion of LSCC cells. In addition, AGAP2-AS1 sponged miR-193a-3p and regulated its expression in LSCC cells. Inhibition of miR-193a-3p reversed the effects of AGAP2-AS1 knockdown on LSCC cells. Furthermore, Lysyl oxidase-like 4 (LOXL4) was a target gene of miR-193a-3p and the role of miR-193a-3p was mediated by LOXL4. In conclusion, these findings suggest that knockdown of AGAP2-AS1 inhibited the proliferation and invasion of LSCC cells through regulating the miR-193a-3p/LOXL4 axis.
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Affiliation(s)
- Pengyu Ren
- Department of Otorhinolaryngology-Head and Neck Surgery, First Affiliated Hospital, Xi’an Jiaotong University College of Medicine, Xi’an, Shaanxi, China,Department of Neurosurgery, Second Affiliated Hospital of Xi’an Jiaotong University College of Medicine, Xi’an, Shaanxi, China
| | - Xiaorong Niu
- Department of Otorhinolaryngology-Head and Neck Surgery, First Affiliated Hospital, Xi’an Jiaotong University College of Medicine, Xi’an, Shaanxi, China
| | - Ruimin Zhao
- Department of Otorhinolaryngology-Head and Neck Surgery, First Affiliated Hospital, Xi’an Jiaotong University College of Medicine, Xi’an, Shaanxi, China
| | - Junsong Liu
- Department of Otorhinolaryngology-Head and Neck Surgery, First Affiliated Hospital, Xi’an Jiaotong University College of Medicine, Xi’an, Shaanxi, China
| | - Wanli Ren
- Department of Otorhinolaryngology-Head and Neck Surgery, First Affiliated Hospital, Xi’an Jiaotong University College of Medicine, Xi’an, Shaanxi, China
| | - Hao Dai
- Department of Otorhinolaryngology-Head and Neck Surgery, First Affiliated Hospital, Xi’an Jiaotong University College of Medicine, Xi’an, Shaanxi, China
| | - Jiayu Chen
- Department of Otorhinolaryngology-Head and Neck Surgery, First Affiliated Hospital, Xi’an Jiaotong University College of Medicine, Xi’an, Shaanxi, China
| | - Jinfeng Yan
- Department of Otorhinolaryngology-Head and Neck Surgery, First Affiliated Hospital, Xi’an Jiaotong University College of Medicine, Xi’an, Shaanxi, China
| | - Baiya Li
- Department of Otorhinolaryngology-Head and Neck Surgery, First Affiliated Hospital, Xi’an Jiaotong University College of Medicine, Xi’an, Shaanxi, China
| | - Yuan Shao
- Department of Otorhinolaryngology-Head and Neck Surgery, First Affiliated Hospital, Xi’an Jiaotong University College of Medicine, Xi’an, Shaanxi, China
| | - Yanxia Bai
- Department of Otorhinolaryngology-Head and Neck Surgery, First Affiliated Hospital, Xi’an Jiaotong University College of Medicine, Xi’an, Shaanxi, China,CONTACT Yanxia Bai
| | - Peng Han
- Department of Otorhinolaryngology-Head and Neck Surgery, First Affiliated Hospital, Xi’an Jiaotong University College of Medicine, Xi’an, Shaanxi, China,Peng Han Department of Otorhinolaryngology-Head and Neck Surgery, First Affiliated Hospital, Xi’an Jiaotong University College of Medicine, Xi’an, Shaanxi710061, China
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El Khoury L, Jing Z, Cuzzolin A, Deplano A, Loco D, Sattarov B, Hédin F, Wendeborn S, Ho C, El Ahdab D, Jaffrelot Inizan T, Sturlese M, Sosic A, Volpiana M, Lugato A, Barone M, Gatto B, Macchia ML, Bellanda M, Battistutta R, Salata C, Kondratov I, Iminov R, Khairulin A, Mykhalonok Y, Pochepko A, Chashka-Ratushnyi V, Kos I, Moro S, Montes M, Ren P, Ponder JW, Lagardère L, Piquemal JP, Sabbadin D. Computationally driven discovery of SARS-CoV-2 M pro inhibitors: from design to experimental validation. Chem Sci 2022; 13:3674-3687. [PMID: 35432906 PMCID: PMC8966641 DOI: 10.1039/d1sc05892d] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 02/03/2022] [Indexed: 11/21/2022] Open
Abstract
We report a fast-track computationally driven discovery of new SARS-CoV-2 main protease (Mpro) inhibitors whose potency ranges from mM for the initial non-covalent ligands to sub-μM for the final covalent compound (IC50 = 830 ± 50 nM). The project extensively relied on high-resolution all-atom molecular dynamics simulations and absolute binding free energy calculations performed using the polarizable AMOEBA force field. The study is complemented by extensive adaptive sampling simulations that are used to rationalize the different ligand binding poses through the explicit reconstruction of the ligand–protein conformation space. Machine learning predictions are also performed to predict selected compound properties. While simulations extensively use high performance computing to strongly reduce the time-to-solution, they were systematically coupled to nuclear magnetic resonance experiments to drive synthesis and for in vitro characterization of compounds. Such a study highlights the power of in silico strategies that rely on structure-based approaches for drug design and allows the protein conformational multiplicity problem to be addressed. The proposed fluorinated tetrahydroquinolines open routes for further optimization of Mpro inhibitors towards low nM affinities. The dominant binding mode of the QUB-00006-Int-07 main protease inhibitor during absolute binding free energy simulations.![]()
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Affiliation(s)
- Léa El Khoury
- Qubit Pharmaceuticals, Incubateur Paris Biotech Santé 24 Rue du Faubourg Saint Jacques 75014 Paris France
| | - Zhifeng Jing
- Qubit Pharmaceuticals, Incubateur Paris Biotech Santé 24 Rue du Faubourg Saint Jacques 75014 Paris France
| | - Alberto Cuzzolin
- Chiesi Farmaceutici S.p.A, Nuovo Centro Ricerche Largo Belloli 11a 43122 Parma Italy
| | - Alessandro Deplano
- Pharmacelera, Torre R, 4a planta Despatx A05, Parc Cientific de Barcelona, Baldiri Reixac 8 08028 Barcelona Spain
| | - Daniele Loco
- Qubit Pharmaceuticals, Incubateur Paris Biotech Santé 24 Rue du Faubourg Saint Jacques 75014 Paris France
| | - Boris Sattarov
- Qubit Pharmaceuticals, Incubateur Paris Biotech Santé 24 Rue du Faubourg Saint Jacques 75014 Paris France
| | - Florent Hédin
- Qubit Pharmaceuticals, Incubateur Paris Biotech Santé 24 Rue du Faubourg Saint Jacques 75014 Paris France
| | - Sebastian Wendeborn
- University of Applied Sciences and Arts Northwestern Switzerland, School of LifeSciences Hofackerstrasse 30 CH-4132 Muttenz Switzerland
| | - Chris Ho
- Qubit Pharmaceuticals, Incubateur Paris Biotech Santé 24 Rue du Faubourg Saint Jacques 75014 Paris France
| | - Dina El Ahdab
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS 75005 Paris France
| | - Theo Jaffrelot Inizan
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS 75005 Paris France
| | - Mattia Sturlese
- Molecular Modeling Section, Department of Pharmaceutical and Pharmacological Sciences, University of Padua via F. Marzolo 5 35131 Padova Italy
| | - Alice Sosic
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova via Marzolo 5 35131 Padova Italy
| | - Martina Volpiana
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova via Marzolo 5 35131 Padova Italy
| | - Angela Lugato
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova via Marzolo 5 35131 Padova Italy
| | - Marco Barone
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova via Marzolo 5 35131 Padova Italy
| | - Barbara Gatto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova via Marzolo 5 35131 Padova Italy
| | - Maria Ludovica Macchia
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova via Marzolo 5 35131 Padova Italy
| | - Massimo Bellanda
- Department of Chemistry, University of Padova via Marzolo 1 35131 Padova Italy
| | - Roberto Battistutta
- Department of Chemistry, University of Padova via Marzolo 1 35131 Padova Italy
| | - Cristiano Salata
- Department of Molecular Medicine, University of Padua via Gabelli 63 35121 Padova Italy
| | | | - Rustam Iminov
- Enamine Ltd 78 Chervonotkats'ka Str. Kyiv 02094 Ukraine
| | | | | | | | | | - Iaroslava Kos
- Enamine Ltd 78 Chervonotkats'ka Str. Kyiv 02094 Ukraine
| | - Stefano Moro
- Molecular Modeling Section, Department of Pharmaceutical and Pharmacological Sciences, University of Padua via F. Marzolo 5 35131 Padova Italy
| | - Matthieu Montes
- Laboratoire GBCM, EA7528, Conservatoire National des Arts et Métiers, Hesam Université 2 Rue Conte 75003 Paris France
| | - Pengyu Ren
- University of Texas at Austin, Department of Biomedical Engineering TX 78712 USA
| | - Jay W Ponder
- Department of Chemistry, Washington University in Saint Louis MO 63130 USA.,Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine MO 63110 USA
| | - Louis Lagardère
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS 75005 Paris France
| | - Jean-Philip Piquemal
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS 75005 Paris France .,Institut Universitaire de France 75005 Paris France
| | - Davide Sabbadin
- Qubit Pharmaceuticals, Incubateur Paris Biotech Santé 24 Rue du Faubourg Saint Jacques 75014 Paris France
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He X, Walker B, Man VH, Ren P, Wang J. Recent progress in general force fields of small molecules. Curr Opin Struct Biol 2022; 72:187-193. [PMID: 34942567 PMCID: PMC8860847 DOI: 10.1016/j.sbi.2021.11.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 09/10/2021] [Accepted: 11/16/2021] [Indexed: 02/03/2023]
Abstract
Recent advances in computational hardware and free energy algorithms enable a broader application of molecular simulation of binding interactions between receptors and small-molecule ligands. The underlying molecular mechanics force fields (FFs) for small molecules have also achieved advancements in accuracy, user-friendliness, and speed during the past several years (2018-2020). Besides the expansion of chemical space coverage of ligand-like molecules among major popular classical additive FFs and polarizable FFs, new charge models have been proposed for better accuracy and transferability, new chemical perception of avoiding predefined atom types have been applied, and new automated parameterization toolkits, including machine learning approaches, have been developed for users' convenience.
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Affiliation(s)
- Xibing He
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
| | - Brandon Walker
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Viet H. Man
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA,Corresponding authors: Pengyu Ren (), Junmei Wang ()
| | - Junmei Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA,Corresponding authors: Pengyu Ren (), Junmei Wang ()
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Abstract
Thole-style mutual induction models for molecular polarization have been adopted by several popular polarizable force fields (FFs) for their simplicity and transferability. The atomic polarizability parameters of these models are typically derived by fitting to ab initio or/and experimental molecular polarizabilities. In this work, we improve upon Thole polarizability parameters by employing both high-level quantum mechanics molecular polarizabilities and electrostatic potential (ESP) responses on three-dimensional grids. Our results indicate that the two approaches to derive atomic polarizability parameters are both effective, while the ESP approaches can also capture the polarization for the atoms with lone pair electrons. The resulting polarizability parameters have been validated on a set of over 7200 molecules covering the most common elements found in organic molecules (C, H, O, N, P, S, F, Cl, Br, and I). These parameters have also been tested on the experimentally measured molecular polarizabilities of 422 molecules. The final set of parameters derived in this work show notable improvement over the current AMOEBA set. The result is a highly transferable, expanded set of atomic polarizabilities defined by the local chemical environment in the form of SMARTS patterns. These parameters can be used directly in molecular mechanics polarizable potential energy functions such as AMOEBA, AMOEBA+, and other Thole-style models.
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Affiliation(s)
| | | | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
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Cao F, Zhang J, Li D, Wang M, Lai C, Xu T, Bouakaz A, Ren P, Wan M, Han J, Zhang S. Non-invasive ultrasound modulation of solitary tract nucleus exerts a sustainable antihypertensive effect in spontaneously hypertensive rats. IEEE Trans Biomed Eng 2022; 70:1869-1878. [PMID: 37015531 DOI: 10.1109/tbme.2022.3231343] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
GOAL We applied the method of non-invasive ultrasound (US) neuromodulation to regulate blood pressure (BP) by stimulating the solitary tract nucleus (NTS) of spontaneously hypertensive rats (SHRs). METHODS The rats were exposed to US stimulation for 20 mins every day for two months. Morphology and function of the hypertensive target organs (heart and kidney) were then examined by echocardiography and immunohistochemical staining. C-fos immunofluorescence assays were used to evaluate neuronal activity in the US stimulated areas and to explore related neural pathways. Moreover, the effects of US stimulation on biochemical indicators (ANGII, Aldo, ANF, ET-1, and Cor) in SHRs were detected. In addition, HE, TUNEL, and Nissl staining were performed to evaluate the safety of long-term transcranial US stimulation. RESULTS After two months of US stimulation, systolic blood pressure (SBP) decreased from 170±1.1 mmHg to 158±5.3 mmHg, p<0.01. What's more, US stimulation effectively inhibited the pathological process of target organs from both morphological and functional levels. With US stimulation, neuronal activities were also significantly enhanced in the NTS, ventrolateral periaqueductal gray (vlPAG), and the caudal ventrolateral medulla (CVLM) region. And US stimulation did not cause brain tissue damage. Meanwhile, the plasma levels of ANF, ATCH, and Cor content were inhibited. CONCLUSION US stimulation of the NTS could significantly lower BP in SHRs. SIGNIFICANCE Non-invasive transcranial US stimulation acting on the NTS might be a potential therapeutic intervention due to its efficacy and safety.
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Affiliation(s)
- Fangyuan Cao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Department of Biomedical Engineering, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Jingjing Zhang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Department of Biomedical Engineering, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Dapeng Li
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Department of Biomedical Engineering, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Mengke Wang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Department of Biomedical Engineering, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Chunhao Lai
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Department of Biomedical Engineering, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Tianqi Xu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Department of Biomedical Engineering, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | | | - Pengyu Ren
- Institute of Medical Artificial Intelligence, the Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Mingxi Wan
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Department of Biomedical Engineering, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Jie Han
- Department of Cardiology, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Siyuan Zhang
- Research Institute of Xi'an Jiaotong University, Zhejiang, China
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Ren P, Cao J, Ma FX, Zhou S, Yu Z, Zhao CY. [Application effects of free transplantation of autologous omentum in treating maxillofacial infection complicated with complex sinus tract]. Zhonghua Shao Shang Za Zhi 2021; 37:953-958. [PMID: 34689465 DOI: 10.3760/cma.j.cn501120-20200721-00354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To investigate the application effects of free transplantation of autologous omentum in treating maxillofacial infection complicated with complex sinus tract. Methods: The retrospective observational study method was used. Four patients with maxillofacial infection complicated with complex sinus tract were admitted to Department of Burns and Plastic Surgery of the Second Affiliated Hospital of Air Force Medical University from July 2017 to the December 2019, including 3 males and 1 female aged 36-60 years. Preoperative facial computed tomography (CT) was performed on patients for calculating the volume of sinus tract. During the operation, the sinus tract was thoroughly debrided, and the volume of the tissue defect was about 5 cm×3 cm×2 cm-10 cm×5 cm×3 cm after debridement. The tissue defect area was filled with omentum of 100-300 mL which was cut under laparoscopy. The artery and vein on the right side of the omentum were reserved as the vascular pedicle of the donor area, which were anastomosed with the facial artery and external jugular vein of the recipient area. The survival of omentum, and the occurrences of reinfection and complication were observed after operation, respectively. On the 10th day and in 1 month after the operation, the blood supply of omentum was examined by colored Doppler ultrasound and CT angiography, and the filling of tissue defect area was examined by head and face CT. During follow-up after the operation, the recoveries of face appearance and function and scar hyperplasia in the donor area. Results: The transplanted omentums in 4 patients survived after the operation with no reinfection and complication. On the 10th day and in 1 month after the operation, the transplanted omentums had good blood supply, and the filled area with omentum was in good shape, without formation of dead cavity. During follow-up of 6-10 months after surgery, the appearance and function of face recovered well, and there was no obvious scar hyperplasia in the donor area. Conclusions: After free transplantation of omentum in treating maxillofacial infection with complex sinus tract, the patients have good facial appearance and function, and the application of laparoscopy results in little damage to the patients and quick postoperative recovery.
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Affiliation(s)
- P Ren
- Department of Burns and Plastic Surgery, the Second Affiliated Hospital of Air Force Medical University, Xi'an 710038, China
| | - J Cao
- Department of Burns and Plastic Surgery, the Second Affiliated Hospital of Air Force Medical University, Xi'an 710038, China
| | - F X Ma
- Department of Burns and Plastic Surgery, the Second Affiliated Hospital of Air Force Medical University, Xi'an 710038, China
| | - S Zhou
- Department of General Surgery, the Second Affiliated Hospital of Air Force Medical University, Xi'an 710038, China
| | - Z Yu
- Department of Burns and Plastic Surgery, the Second Affiliated Hospital of Air Force Medical University, Xi'an 710038, China
| | - C Y Zhao
- Department of Burns and Plastic Surgery, the Second Affiliated Hospital of Air Force Medical University, Xi'an 710038, China
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Abstract
We present E2EDNA, a simulation protocol and accompanying code for the molecular biophysics and materials science communities. This protocol is both easy to use and sufficiently efficient to simulate single-stranded (ss)DNA and small analyte systems that are important to cellular processes and nanotechnologies such as DNA aptamer-based sensors. Existing computational tools used for aptamer design focus on cost-effective secondary structure prediction and motif analysis in the large data sets produced by SELEX experiments. As a rule, they do not offer flexibility with respect to the choice of the theoretical engine or direct access to the simulation platform. Practical aptamer optimization often requires higher accuracy predictions for only a small subset of sequences suggested, e.g., by SELEX experiments, but in the absence of a streamlined procedure, this task is extremely time and expertise intensive. We address this gap by introducing E2EDNA, a computational framework that accepts a DNA sequence in the FASTA format and the structures of the desired ligands and performs approximate folding followed by a refining step, analyte complexation, and molecular dynamics sampling at the desired level of accuracy. As a case study, we simulate a DNA-UTP (uridine triphosphate) complex in water using the state-of-the-art AMOEBA polarizable force field. The code is available at https://github.com/InfluenceFunctional/E2EDNA.
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Affiliation(s)
- Michael Kilgour
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Tao Liu
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Brandon D Walker
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Lena Simine
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
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Stier AC, Goth W, Hurley A, Brown T, Feng X, Zhang Y, Lopes FCPS, Sebastian KR, Ren P, Fox MC, Reichenberg JS, Markey MK, Tunnell JW. Imaging sub-diffuse optical properties of cancerous and normal skin tissue using machine learning-aided spatial frequency domain imaging. J Biomed Opt 2021; 26:JBO-210048RR. [PMID: 34558235 PMCID: PMC8459901 DOI: 10.1117/1.jbo.26.9.096007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 08/27/2021] [Indexed: 05/28/2023]
Abstract
SIGNIFICANCE Sub-diffuse optical properties may serve as useful cancer biomarkers, and wide-field heatmaps of these properties could aid physicians in identifying cancerous tissue. Sub-diffuse spatial frequency domain imaging (sd-SFDI) can reveal such wide-field maps, but the current time cost of experimentally validated methods for rendering these heatmaps precludes this technology from potential real-time applications. AIM Our study renders heatmaps of sub-diffuse optical properties from experimental sd-SFDI images in real time and reports these properties for cancerous and normal skin tissue subtypes. APPROACH A phase function sampling method was used to simulate sd-SFDI spectra over a wide range of optical properties. A machine learning model trained on these simulations and tested on tissue phantoms was used to render sub-diffuse optical property heatmaps from sd-SFDI images of cancerous and normal skin tissue. RESULTS The model accurately rendered heatmaps from experimental sd-SFDI images in real time. In addition, heatmaps of a small number of tissue samples are presented to inform hypotheses on sub-diffuse optical property differences across skin tissue subtypes. CONCLUSION These results bring the overall process of sd-SFDI a fundamental step closer to real-time speeds and set a foundation for future real-time medical applications of sd-SFDI such as image guided surgery.
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Affiliation(s)
- Andrew C. Stier
- The University of Texas at Austin, Department of Electrical and Computer Engineering, Austin, Texas, United States
| | - Will Goth
- The University of Texas at Austin, Department of Biomedical Engineering, Austin, Texas, United States
| | - Aislinn Hurley
- The University of Texas at Austin, Department of Biomedical Engineering, Austin, Texas, United States
| | - Treshayla Brown
- The University of Texas at Austin, Department of Biomedical Engineering, Austin, Texas, United States
| | - Xu Feng
- The University of Texas at Austin, Department of Biomedical Engineering, Austin, Texas, United States
| | - Yao Zhang
- The University of Texas at Austin, Department of Biomedical Engineering, Austin, Texas, United States
| | - Fabiana C. P. S. Lopes
- The University of Texas at Austin, Dell Medical School, Department of Internal Medicine, Austin, Texas, United States
| | - Katherine R. Sebastian
- The University of Texas at Austin, Dell Medical School, Department of Internal Medicine, Austin, Texas, United States
| | - Pengyu Ren
- The University of Texas at Austin, Department of Biomedical Engineering, Austin, Texas, United States
| | - Matthew C. Fox
- The University of Texas at Austin, Dell Medical School, Department of Internal Medicine, Austin, Texas, United States
| | - Jason S. Reichenberg
- The University of Texas at Austin, Dell Medical School, Department of Internal Medicine, Austin, Texas, United States
| | - Mia K. Markey
- The University of Texas at Austin, Department of Biomedical Engineering, Austin, Texas, United States
- The University of Texas MD Anderson Cancer Center, Imaging Physics Residency Program, Houston, Texas, United States
| | - James W. Tunnell
- The University of Texas at Austin, Department of Biomedical Engineering, Austin, Texas, United States
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48
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Walker B, Jing Z, Ren P. Molecular dynamics free energy simulations of ATP:Mg 2+ and ADP:Mg 2+ using the polarizable force field AMOEBA. Mol Simul 2021; 47:439-448. [PMID: 34421214 DOI: 10.1080/08927022.2020.1725003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
ATPases and GTPases are two important classes of protein that play critical roles in energy transduction, cellular signaling, gene regulation and catalysis. These proteins use cofactors such as nucleoside di and tri-phosphates (NTP, NDP) and can detect the difference between NDP and NTP which then induce different protein conformations. Mechanisms that drive proteins into the NTP or NDP conformation may depend on factors such as ligand structure and how Mg2+ coordinates with the ligand, amino acids in the pocket and water molecules. Here, we have used the advanced electrostatic and polarizable force field AMOEBA and molecular dynamics free energy simulations (MDFE) to examine the various binding mechanisms of ATP:Mg2+ and ADP:Mg2+.We compared the ATP:Mg2+ binding with previous studies using non-polarizable force fields and experimental data on the binding affinity. It was found that the total free energy of binding for ATP:Mg2+ (-7.00 ± 2.13 kcal/mol) is in good agreement with experimental values (-8.6 ± .2 kcal/mol)1. In addition, parameters for relevant protonation states of ATP, ADP, GTP and GDP have been derived. These parameters will allow for researchers to investigate biochemical phenomena involving NTP's and NDP's with greater accuracy than previous studies involving non-polarizable force fields.
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Affiliation(s)
- Brandon Walker
- Department of Biomedical Engineering at The University of Texas at Austin, Austin, Texas 78712, United States
| | - Zhifeng Jing
- Department of Biomedical Engineering at The University of Texas at Austin, Austin, Texas 78712, United States
| | - Pengyu Ren
- Department of Biomedical Engineering at The University of Texas at Austin, Austin, Texas 78712, United States
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El Ahdab D, Lagardère L, Inizan TJ, Célerse F, Liu C, Adjoua O, Jolly LH, Gresh N, Hobaika Z, Ren P, Maroun RG, Piquemal JP. Interfacial Water Many-Body Effects Drive Structural Dynamics and Allosteric Interactions in SARS-CoV-2 Main Protease Dimerization Interface. J Phys Chem Lett 2021; 12:6218-6226. [PMID: 34196568 PMCID: PMC8262171 DOI: 10.1021/acs.jpclett.1c01460] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/10/2021] [Indexed: 05/27/2023]
Abstract
Following our previous work ( Chem. Sci. 2021, 12, 4889-4907), we study the structural dynamics of the SARS-CoV-2 Main Protease dimerization interface (apo dimer) by means of microsecond adaptive sampling molecular dynamics simulations (50 μs) using the AMOEBA polarizable force field (PFF). This interface is structured by a complex H-bond network that is stable only at physiological pH. Structural correlations analysis between its residues and the catalytic site confirms the presence of a buried allosteric site. However, noticeable differences in allosteric connectivity are observed between PFFs and non-PFFs. Interfacial polarizable water molecules are shown to appear at the heart of this discrepancy because they are connected to the global interface H-bond network and able to adapt their dipole moment (and dynamics) to their diverse local physicochemical microenvironments. The water-interface many-body interactions appear to drive the interface volume fluctuations and to therefore mediate the allosteric interactions with the catalytic cavity.
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Affiliation(s)
- Dina El Ahdab
- Sorbonne Université, LCT, UMR 7616 CNRS, 75005 Paris, France
- Université Saint-Joseph de Beyrouth, UR EGP, Centre d'Analyses et de Recherche, Faculté des Sciences, 1104 2020 Beirut, Lebanon
| | - Louis Lagardère
- Sorbonne Université, LCT, UMR 7616 CNRS, 75005 Paris, France
- Sorbonne Université, IP2CT, FR 2622 CNRS, 75005 Paris, France
| | | | - Fréderic Célerse
- Sorbonne Université, LCT, UMR 7616 CNRS, 75005 Paris, France
- Sorbonne Université, IPCM, UMR 8232 CNRS, 75005 Paris, France
| | - Chengwen Liu
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Olivier Adjoua
- Sorbonne Université, LCT, UMR 7616 CNRS, 75005 Paris, France
| | - Luc-Henri Jolly
- Sorbonne Université, IP2CT, FR 2622 CNRS, 75005 Paris, France
| | - Nohad Gresh
- Sorbonne Université, LCT, UMR 7616 CNRS, 75005 Paris, France
| | - Zeina Hobaika
- Université Saint-Joseph de Beyrouth, UR EGP, Centre d'Analyses et de Recherche, Faculté des Sciences, 1104 2020 Beirut, Lebanon
| | - Pengyu Ren
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Richard G Maroun
- Université Saint-Joseph de Beyrouth, UR EGP, Centre d'Analyses et de Recherche, Faculté des Sciences, 1104 2020 Beirut, Lebanon
| | - Jean-Philip Piquemal
- Sorbonne Université, LCT, UMR 7616 CNRS, 75005 Paris, France
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
- Institut Universitaire de France, 75005 Paris, France
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50
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Jing Z, Rackers JA, Pratt LR, Liu C, Rempe SB, Ren P. Thermodynamics of ion binding and occupancy in potassium channels. Chem Sci 2021; 12:8920-8930. [PMID: 34257893 PMCID: PMC8246295 DOI: 10.1039/d1sc01887f] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/01/2021] [Indexed: 12/15/2022] Open
Abstract
Potassium channels modulate various cellular functions through efficient and selective conduction of K+ ions. The mechanism of ion conduction in potassium channels has recently emerged as a topic of debate. Crystal structures of potassium channels show four K+ ions bound to adjacent binding sites in the selectivity filter, while chemical intuition and molecular modeling suggest that the direct ion contacts are unstable. Molecular dynamics (MD) simulations have been instrumental in the study of conduction and gating mechanisms of ion channels. Based on MD simulations, two hypotheses have been proposed, in which the four-ion configuration is an artifact due to either averaged structures or low temperature in crystallographic experiments. The two hypotheses have been supported or challenged by different experiments. Here, MD simulations with polarizable force fields validated by ab initio calculations were used to investigate the ion binding thermodynamics. Contrary to previous beliefs, the four-ion configuration was predicted to be thermodynamically stable after accounting for the complex electrostatic interactions and dielectric screening. Polarization plays a critical role in the thermodynamic stabilities. As a result, the ion conduction likely operates through a simple single-vacancy and water-free mechanism. The simulations explained crystal structures, ion binding experiments and recent controversial mutagenesis experiments. This work provides a clear view of the mechanism underlying the efficient ion conduction and demonstrates the importance of polarization in ion channel simulations. Polarization shapes the energy landscape of ion conduction in potassium channels.![]()
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Affiliation(s)
- Zhifeng Jing
- Department of Biomedical Engineering, The University of Texas at Austin Austin Texas 78712 USA
| | - Joshua A Rackers
- Center for Integrated Nanotechnologies, Sandia National Laboratories Albuquerque New Mexico 87185 USA
| | - Lawrence R Pratt
- Department of Chemical and Biomolecular Engineering, Tulane University New Orleans Louisiana 70118 USA
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin Austin Texas 78712 USA
| | - Susan B Rempe
- Center for Integrated Nanotechnologies, Sandia National Laboratories Albuquerque New Mexico 87185 USA
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin Austin Texas 78712 USA
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