51
|
Wang JQ, Cui Q, Lei ZN, Teng QX, Ji N, Lin L, Liu Z, Chen ZS. Insights on the structure-function relationship of human multidrug resistance protein 7 (MRP7/ABCC10) from molecular dynamics simulations and docking studies. MedComm (Beijing) 2021; 2:221-235. [PMID: 34766143 PMCID: PMC8491190 DOI: 10.1002/mco2.65] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/25/2021] [Accepted: 03/01/2021] [Indexed: 12/18/2022] Open
Abstract
ATP-binding cassette (ABC) transporters superfamily mediates multidrug resistance in cancer by extruding structurally distinct chemotherapeutic agents, causing failure in chemotherapy. Among the 49 ABC transporters, multidrug resistance protein 7 (MRP7 or ABCC10) is relatively new and has been identified as the efflux pump of multiple anticancer agents including Vinca alkaloids and taxanes. Herein, we construct and validate a homology model for human MRP7 based on the cryo-EM structures of MRP1. Structure-function relationship of MRP7 was obtained from molecular dynamics simulations and docking studies and was in accordance with previous studies of ABC transporters. The motion patterns correlated with efflux mechanism were discussed. Additionally, predicted substrate- and modulator-binding sites of MRP7 were described for the first time, which provided rational insights in understanding the drug binding and functional regulation in MRP7. Our findings will benefit the high-throughput virtual screening and development of MRP7 modulators in the future.
Collapse
Affiliation(s)
- Jing-Quan Wang
- Department of Pharmaceutical Sciences College of Pharmacy and Health Sciences St. John's University Queens New York USA
| | - Qingbin Cui
- Department of Pharmaceutical Sciences College of Pharmacy and Health Sciences St. John's University Queens New York USA.,School of Public Health Guangzhou Medical University Guangzhou China
| | - Zi-Ning Lei
- Department of Pharmaceutical Sciences College of Pharmacy and Health Sciences St. John's University Queens New York USA
| | - Qiu-Xu Teng
- Department of Pharmaceutical Sciences College of Pharmacy and Health Sciences St. John's University Queens New York USA
| | - Ning Ji
- Department of Pharmaceutical Sciences College of Pharmacy and Health Sciences St. John's University Queens New York USA
| | - Lusheng Lin
- Cell Research Center Shenzhen Bolun Institute of Biotechnology Shenzhen China
| | - Zhijun Liu
- Department of Medical Microbiology Weifang Medical University Weifang China
| | - Zhe-Sheng Chen
- Department of Pharmaceutical Sciences College of Pharmacy and Health Sciences St. John's University Queens New York USA
| |
Collapse
|
52
|
Fu T, Li F, Zhang Y, Yin J, Qiu W, Li X, Liu X, Xin W, Wang C, Yu L, Gao J, Zheng Q, Zeng S, Zhu F. VARIDT 2.0: structural variability of drug transporter. Nucleic Acids Res 2021; 50:D1417-D1431. [PMID: 34747471 PMCID: PMC8728241 DOI: 10.1093/nar/gkab1013] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/08/2021] [Accepted: 11/04/2021] [Indexed: 12/20/2022] Open
Abstract
The structural variability data of drug transporter (DT) are key for research on precision medicine and rational drug use. However, these valuable data are not sufficiently covered by the available databases. In this study, a major update of VARIDT (a database previously constructed to provide DTs' variability data) was thus described. First, the experimentally resolved structures of all DTs reported in the original VARIDT were discovered from PubMed and Protein Data Bank. Second, the structural variability data of each DT were collected by literature review, which included: (a) mutation-induced spatial variations in folded state, (b) difference among DT structures of human and model organisms, (c) outward/inward-facing DT conformations and (d) xenobiotics-driven alterations in the 3D complexes. Third, for those DTs without experimentally resolved structural variabilities, homology modeling was further applied as well-established protocol to enrich such valuable data. As a result, 145 mutation-induced spatial variations of 42 DTs, 1622 inter-species structures originating from 292 DTs, 118 outward/inward-facing conformations belonging to 59 DTs, and 822 xenobiotics-regulated structures in complex with 57 DTs were updated to VARIDT (https://idrblab.org/varidt/ and http://varidt.idrblab.net/). All in all, the newly collected structural variabilities will be indispensable for explaining drug sensitivity/selectivity, bridging preclinical research with clinical trial, revealing the mechanism underlying drug-drug interaction, and so on.
Collapse
Affiliation(s)
- Tingting Fu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, China
| | - Fengcheng Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yang Zhang
- Department of Pharmacology, Hebei Medical University, Shijiazhuang 050017, China
| | - Jiayi Yin
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wenqi Qiu
- Department of Surgery, HKU-SZH & Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Xuedong Li
- Department of Pharmacology, Hebei Medical University, Shijiazhuang 050017, China
| | - Xingang Liu
- Department of Pharmacology, Hebei Medical University, Shijiazhuang 050017, China
| | - Wenwen Xin
- Department of Pharmacology, Hebei Medical University, Shijiazhuang 050017, China
| | - Chengzhao Wang
- Department of Pharmacology, Hebei Medical University, Shijiazhuang 050017, China
| | - Lushan Yu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jianqing Gao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
| | - Qingchuan Zheng
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, China
| | - Su Zeng
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| |
Collapse
|
53
|
Matamoros‐Recio A, Franco‐Gonzalez JF, Perez‐Regidor L, Billod J, Guzman‐Caldentey J, Martin‐Santamaria S. Full-Atom Model of the Agonist LPS-Bound Toll-like Receptor 4 Dimer in a Membrane Environment. Chemistry 2021; 27:15406-15425. [PMID: 34569111 PMCID: PMC8596573 DOI: 10.1002/chem.202102995] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Indexed: 01/06/2023]
Abstract
The Toll-like receptor 4 (TLR4)/myeloid differentiation factor 2 (MD-2) innate immunity system is a membrane receptor of paramount importance as therapeutic target. Its assembly, upon binding of Gram-negative bacteria lipopolysaccharide (LPS), and also dependent on the membrane composition, finally triggers the immune response cascade. We have combined ab-initio calculations, molecular docking, all-atom molecular dynamics simulations, and thermodynamics calculations to provide the most realistic and complete 3D models of the active full TLR4 complex embedded into a realistic membrane to date. Our studies give functional and structural insights into the transmembrane domain behavior in different membrane environments, the ectodomain bouncing movement, and the dimerization patterns of the intracellular Toll/Interleukin-1 receptor domain. Our work provides TLR4 models as reasonable 3D structures for the (TLR4/MD-2/LPS)2 architecture accounting for the active (agonist) state of the TLR4, and pointing to a signal transduction mechanism across cell membrane. These observations unveil relevant molecular aspects involved in the TLR4 innate immune pathways and will promote the discovery of new TLR4 modulators.
Collapse
Affiliation(s)
- Alejandra Matamoros‐Recio
- Department of Structural and Chemical BiologyCentre for Biological Research Margarita Salas, CIB-CSICC/ Ramiro de Maeztu, 928040MadridSpain
| | - Juan Felipe Franco‐Gonzalez
- Department of Structural and Chemical BiologyCentre for Biological Research Margarita Salas, CIB-CSICC/ Ramiro de Maeztu, 928040MadridSpain
| | - Lucia Perez‐Regidor
- Department of Structural and Chemical BiologyCentre for Biological Research Margarita Salas, CIB-CSICC/ Ramiro de Maeztu, 928040MadridSpain
| | - Jean‐Marc Billod
- Department of Structural and Chemical BiologyCentre for Biological Research Margarita Salas, CIB-CSICC/ Ramiro de Maeztu, 928040MadridSpain
| | - Joan Guzman‐Caldentey
- Department of Structural and Chemical BiologyCentre for Biological Research Margarita Salas, CIB-CSICC/ Ramiro de Maeztu, 928040MadridSpain
| | - Sonsoles Martin‐Santamaria
- Department of Structural and Chemical BiologyCentre for Biological Research Margarita Salas, CIB-CSICC/ Ramiro de Maeztu, 928040MadridSpain
| |
Collapse
|
54
|
Modulating Glycoside Hydrolase Activity between Hydrolysis and Transfer Reactions Using an Evolutionary Approach. Molecules 2021; 26:molecules26216586. [PMID: 34770995 PMCID: PMC8587830 DOI: 10.3390/molecules26216586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 01/02/2023] Open
Abstract
The proteins within the CAZy glycoside hydrolase family GH13 catalyze the hydrolysis of polysaccharides such as glycogen and starch. Many of these enzymes also perform transglycosylation in various degrees, ranging from secondary to predominant reactions. Identifying structural determinants associated with GH13 family reaction specificity is key to modifying and designing enzymes with increased specificity towards individual reactions for further applications in industrial, chemical, or biomedical fields. This work proposes a computational approach for decoding the determinant structural composition defining the reaction specificity. This method is based on the conservation of coevolving residues in spatial contacts associated with reaction specificity. To evaluate the algorithm, mutants of α-amylase (TmAmyA) and glucanotransferase (TmGTase) from Thermotoga maritima were constructed to modify the reaction specificity. The K98P/D99A/H222Q variant from TmAmyA doubled the transglycosydation/hydrolysis (T/H) ratio while the M279N variant from TmGTase increased the hydrolysis/transglycosidation ratio five-fold. Molecular dynamic simulations of the variants indicated changes in flexibility that can account for the modified T/H ratio. An essential contribution of the presented computational approach is its capacity to identify residues outside of the active center that affect the reaction specificity.
Collapse
|
55
|
Yusof NA, Charles J, Wan Mahadi WNS, Abdul Murad AM, Mahadi NM. Characterization of Inducible HSP70 Genes in an Antarctic Yeast, Glaciozyma antarctica PI12, in Response to Thermal Stress. Microorganisms 2021; 9:microorganisms9102069. [PMID: 34683390 PMCID: PMC8540855 DOI: 10.3390/microorganisms9102069] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/01/2021] [Accepted: 09/06/2021] [Indexed: 11/17/2022] Open
Abstract
The induction of highly conserved heat shock protein 70 (HSP70) is often related to a cellular response due to harmful stress or adverse life conditions. In this study, we determined the expression of Hsp70 genes in the Antarctic yeast, Glaciozyma antarctica, under different several thermal treatments for several exposure periods. The main aims of the present study were (1) to determine if stress-induced Hsp70 could be used to monitor the exposure of the yeast species G. antarctica to various types of thermal stress; (2) to analyze the structures of the G. antarctica HSP70 proteins using comparative modeling; and (3) to evaluate the relationship between the function and structure of HSP70 in G. antarctica. In this study, we managed to amplify and clone 2 Hsp70 genes from G. antarctica named GaHsp70-1 and GaHsp70-2. The cells of G. antarctica expressed significantly inducible Hsp70 genes after the heat and cold shock treatments. Interestingly, GaHsp70-1 showed 2–6-fold higher expression than GaHsp70-2 after the heat and cold exposure. ATP hydrolysis analysis on both G. antarctica HSP70s proved that these psychrophilic chaperones can perform activities in a wide range of temperatures, such as at 37, 25, 15, and 4 °C. The 3D structures of both HSP70s revealed several interesting findings, such as the substitution of a β-sheet to loop in the N-terminal ATPase binding domain and some modest residue substitutions, which gave the proteins the flexibility to function at low temperatures and retain their functional activity at ambient temperatures. In conclusion, both analyzed HSP70s played important roles in the physiological adaptation of G. antarctica.
Collapse
Affiliation(s)
- Nur Athirah Yusof
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia; (J.C.); (W.N.S.W.M.)
- Correspondence: ; Tel.: +60-19-605-1219
| | - Jennifer Charles
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia; (J.C.); (W.N.S.W.M.)
| | - Wan Nur Shuhaida Wan Mahadi
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia; (J.C.); (W.N.S.W.M.)
| | - Abdul Munir Abdul Murad
- Faculty of Science and Technology, School of Biosciences and Biotechnology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia;
| | | |
Collapse
|
56
|
Zhao C, Pratelli R, Yu S, Shelley B, Collakova E, Pilot G. Detailed characterization of the UMAMIT proteins provides insight into their evolution, amino acid transport properties, and role in the plant. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6400-6417. [PMID: 34223868 DOI: 10.1093/jxb/erab288] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 06/11/2021] [Indexed: 05/02/2023]
Abstract
Amino acid transporters play a critical role in distributing amino acids within the cell compartments and between plant organs. Despite this importance, relatively few amino acid transporter genes have been characterized and their role elucidated with certainty. Two main families of proteins encode amino acid transporters in plants: the amino acid-polyamine-organocation superfamily, containing mostly importers, and the UMAMIT (usually multiple acids move in and out transporter) family, apparently encoding exporters, totaling 63 and 44 genes in Arabidopsis, respectively. Knowledge of UMAMITs is scarce, based on six Arabidopsis genes and a handful of genes from other species. To gain insight into the role of the members of this family and provide data to be used for future characterization, we studied the evolution of the UMAMITs in plants, and determined the functional properties, the structure, and localization of the 47 Arabidopsis UMAMITs. Our analysis showed that the AtUMAMITs are essentially localized at the tonoplast or the plasma membrane, and that most of them are able to export amino acids from the cytosol, confirming a role in intra- and intercellular amino acid transport. As an example, this set of data was used to hypothesize the role of a few AtUMAMITs in the plant and the cell.
Collapse
Affiliation(s)
- Chengsong Zhao
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Réjane Pratelli
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Shi Yu
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Brett Shelley
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Eva Collakova
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Guillaume Pilot
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| |
Collapse
|
57
|
Wang J, Zhang K, Goyal P, Grewer C. Mechanism and potential sites of potassium interaction with glutamate transporters. J Gen Physiol 2021; 152:152037. [PMID: 32835376 PMCID: PMC7537348 DOI: 10.1085/jgp.202012577] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 08/03/2020] [Indexed: 12/21/2022] Open
Abstract
In the mammalian glutamate transporters, countertransported intracellular K+ is essential for relocating the glutamate binding site to the extracellular side of the membrane. This K+-dependent process is believed to be rate limiting for the transport cycle. In contrast, extracellular K+ induces glutamate release upon transporter reversal. Here, we analyzed potential K+ binding sites using molecular dynamics (MD) simulations and site-directed mutagenesis. Two candidate sites were identified by spontaneous K+ binding in MD simulations, one site (K1 site) overlapping with the Na1 Na+ binding site and the K2 site being localized under hairpin loop 2 (HP2). Mutations to conserved amino acid residues in these sites resulted in several transporters that were defective in K+-induced reverse transport and which bound K+ with reduced apparent affinity compared with the wild-type transporter. However, external K+ interaction was abolished in only one mutant transporter EAAC1D454A in the K1 site. Our results, for the first time, directly demonstrate effects of K1-site mutations on K+ binding, in contrast to previous reports on K+ binding sites based on indirect evidence. We propose that K+ binding to the K1 site is responsible for catalyzing the relocation step, whereas binding to the K2 site may have an as-of-yet unidentified regulatory function.
Collapse
Affiliation(s)
- Jiali Wang
- Department of Chemistry, Binghamton University, Binghamton, NY
| | - Kaiqi Zhang
- Department of Chemistry, Binghamton University, Binghamton, NY
| | - Puja Goyal
- Department of Chemistry, Binghamton University, Binghamton, NY
| | - Christof Grewer
- Department of Chemistry, Binghamton University, Binghamton, NY
| |
Collapse
|
58
|
Shi S, Ma B, Sun F, Qu C, An H. Theaflavin binds to a druggable pocket of TMEM16A channel and inhibits lung adenocarcinoma cell viability. J Biol Chem 2021; 297:101016. [PMID: 34329684 PMCID: PMC8368026 DOI: 10.1016/j.jbc.2021.101016] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 12/22/2022] Open
Abstract
As a calcium-activated chloride channel regulated by the intracellular Ca2+ concentration and membrane potential, TMEM16A has attracted considerable attention and has been proposed as a novel anticancer drug target. We have previously reported that the pocket above the ion conductance pore could be a nonselective inhibitor-binding pocket. However, whether this pocket is druggable remains unexplored. In this study, we performed virtual screening to target the presumed inhibitor-binding pocket and identified a highly effective TMEM16A inhibitor, theaflavin (TF: a tea polyphenol in black tea). Molecular dynamics simulations revealed that theaflavin adopts a "wedge insertion mode" to block the ion conduction pore and induces pore closure. Moreover, the binding mode showed that the TF pedestal plays an important role in pore blockade, and R515, R535, T539, K603, E623, and E633 were determined to be most likely to interact directly with the pedestal. Mutagenesis experiment results corroborated the mechanism through which TF binds to this pocket. Combined with the quantitative calculation results, our data indicated that the three hydroxyl groups on the pedestal may be the most crucial pharmacophores for TMEM16A inhibition by TF. Finally, antitumor experiments revealed that TF could target TMEM16A to inhibit the proliferation and migration of LA795 cells, indicating the potential therapeutic effect of TF on the growth of lung adenocarcinoma with high TMEM16A expression. The successful application of drug screening strategies based on this binding pocket highlights new directions for discovering superior modulators and contributes to the development of novel therapeutics for lung adenocarcinoma.
Collapse
Affiliation(s)
- Sai Shi
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin, China; Key Laboratory of Electromagnetic Field and Electrical Apparatus Reliability of Hebei Province, Hebei University of Technology, Tianjin, China; Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Science, Hebei University of Technology, Tianjin, China
| | - Biao Ma
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin, China; Key Laboratory of Electromagnetic Field and Electrical Apparatus Reliability of Hebei Province, Hebei University of Technology, Tianjin, China; Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Science, Hebei University of Technology, Tianjin, China
| | - Fude Sun
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Science, Hebei University of Technology, Tianjin, China
| | - Chang Qu
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin, China; Key Laboratory of Electromagnetic Field and Electrical Apparatus Reliability of Hebei Province, Hebei University of Technology, Tianjin, China; Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Science, Hebei University of Technology, Tianjin, China
| | - Hailong An
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin, China; Key Laboratory of Electromagnetic Field and Electrical Apparatus Reliability of Hebei Province, Hebei University of Technology, Tianjin, China; Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Science, Hebei University of Technology, Tianjin, China.
| |
Collapse
|
59
|
Naqvi STQ, Yasmeen M, Ismail M, Muhammad SA, Nawazish-i-Husain S, Ali A, Munir F, Zhang Q. Designing of Potential Polyvalent Vaccine Model for Respiratory Syncytial Virus by System Level Immunoinformatics Approaches. BIOMED RESEARCH INTERNATIONAL 2021; 2021:9940010. [PMID: 34136576 PMCID: PMC8177976 DOI: 10.1155/2021/9940010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/18/2021] [Accepted: 05/10/2021] [Indexed: 11/25/2022]
Abstract
BACKGROUND Respiratory syncytial virus (RSV) infection is a public health epidemic, leading to around 3 million hospitalization and about 66,000 deaths each year. It is a life-threatening condition exclusive to children with no effective treatment. METHODS In this study, we used system-level and vaccinomics approaches to design a polyvalent vaccine for RSV, which could stimulate the immune components of the host to manage this infection. Our framework involves data accession, antigenicity and subcellular localization analysis, T cell epitope prediction, proteasomal and conservancy evaluation, host-pathogen-protein interactions, pathway studies, and in silico binding affinity analysis. RESULTS We found glycoprotein (G), fusion protein (F), and small hydrophobic protein (SH) of RSV as potential vaccine candidates. Of these proteins (G, F, and SH), we found 9 epitopes for multiple alleles of MHC classes I and II bear significant binding affinity. These potential epitopes were linked to form a polyvalent construct using AAY, GPGPG linkers, and cholera toxin B adjuvant at N-terminal with a 23.9 kDa molecular weight of 224 amino acid residues. The final construct was a stable, immunogenic, and nonallergenic protein containing cleavage sites, TAP transport efficiency, posttranslation shifts, and CTL epitopes. The molecular docking indicated the optimum binding affinity of RSV polyvalent construct with MHC molecules (-12.49 and -10.48 kcal/mol for MHC classes I and II, respectively). This interaction showed that a polyvalent construct could manage and control this disease. CONCLUSION Our vaccinomics and system-level investigation could be appropriate to trigger the host immune system to prevent RSV infection.
Collapse
Affiliation(s)
| | - Mamoona Yasmeen
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University Multan, Pakistan
| | - Mehreen Ismail
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University Multan, Pakistan
| | - Syed Aun Muhammad
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University Multan, Pakistan
| | | | - Amjad Ali
- ASAB, National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Fahad Munir
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, China
- Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - QiYu Zhang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, China
| |
Collapse
|
60
|
Saih A, Baba H, Bouqdayr M, Ghazal H, Hamdi S, Kettani A, Wakrim L. In Silico Analysis of High-Risk Missense Variants in Human ACE2 Gene and Susceptibility to SARS-CoV-2 Infection. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6685840. [PMID: 33884270 PMCID: PMC8040925 DOI: 10.1155/2021/6685840] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 03/08/2021] [Accepted: 03/18/2021] [Indexed: 11/18/2022]
Abstract
SARS-CoV-2 coronavirus uses for entry to human host cells a SARS-CoV receptor of the angiotensin-converting enzyme (ACE2) that catalyzes the conversion of angiotensin II into angiotensin (1-7). To understand the effect of ACE2 missense variants on protein structure, stability, and function, various bioinformatics tools were used including SIFT, PANTHER, PROVEAN, PolyPhen2.0, I. Mutant Suite, MUpro, SWISS-MODEL, Project HOPE, ModPred, QMEAN, ConSurf, and STRING. All twelve ACE2 nsSNPs were analyzed. Six ACE2 high-risk pathogenic nsSNPs (D427Y, R514G, R708W, R710C, R716C, and R768W) were found to be the most damaging by at least six software tools (cumulative score between 6 and 7) and exert deleterious effect on the ACE2 protein structure and likely function. Additionally, they revealed high conservation, less stability, and having a role in posttranslation modifications such a proteolytic cleavage or ADP-ribosylation. This in silico analysis provides information about functional nucleotide variants that have an impact on the ACE2 protein structure and function and therefore susceptibility to SARS-CoV-2.
Collapse
Affiliation(s)
- Asmae Saih
- Virology Unit, Immunovirology Laboratory, Institut Pasteur du Maroc, 20360 Casablanca, Morocco
- Laboratory of Biology and Health, URAC 34, Faculty of Sciences Ben M'Sik Hassan II University of Casablanca, Morocco
| | - Hana Baba
- Virology Unit, Immunovirology Laboratory, Institut Pasteur du Maroc, 20360 Casablanca, Morocco
- Laboratory of Biology and Health, URAC 34, Faculty of Sciences Ben M'Sik Hassan II University of Casablanca, Morocco
| | - Meryem Bouqdayr
- Virology Unit, Immunovirology Laboratory, Institut Pasteur du Maroc, 20360 Casablanca, Morocco
- Laboratory of Biology and Health, URAC 34, Faculty of Sciences Ben M'Sik Hassan II University of Casablanca, Morocco
| | - Hassan Ghazal
- National Center for Scientific Technical Research (CNRST), Rabat 10102, Morocco
- Department of Fundamental Sciences, School of Medicine, Mohammed VI University of Health Sciences, Casablanca, Morocco
| | - Salsabil Hamdi
- Environmental Health Laboratory, Institut Pasteur du Maroc, 20360 Casablanca, Morocco
| | - Anass Kettani
- Laboratory of Biology and Health, URAC 34, Faculty of Sciences Ben M'Sik Hassan II University of Casablanca, Morocco
| | - Lahcen Wakrim
- Virology Unit, Immunovirology Laboratory, Institut Pasteur du Maroc, 20360 Casablanca, Morocco
| |
Collapse
|
61
|
Liu Z, Gong Y, Guo Y, Zhang X, Lu C, Zhang L, Wang H. TMP- SSurface2: A Novel Deep Learning-Based Surface Accessibility Predictor for Transmembrane Protein Sequence. Front Genet 2021; 12:656140. [PMID: 33790952 PMCID: PMC8006303 DOI: 10.3389/fgene.2021.656140] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 02/22/2021] [Indexed: 12/13/2022] Open
Abstract
Transmembrane protein (TMP) is an important type of membrane protein that is involved in various biological membranes related biological processes. As major drug targets, TMPs’ surfaces are highly concerned to form the structural biases of their material-bindings for drugs or other biological molecules. However, the quantity of determinate TMP structures is still far less than the requirements, while artificial intelligence technologies provide a promising approach to accurately identify the TMP surfaces, merely depending on their sequences without any feature-engineering. For this purpose, we present an updated TMP surface residue predictor TMP-SSurface2 which achieved an even higher prediction accuracy compared to our previous version. The method uses an attention-enhanced Bidirectional Long Short Term Memory (BiLSTM) network, benefiting from its efficient learning capability, some useful latent information is abstracted from protein sequences, thus improving the Pearson correlation coefficients (CC) value performance of the old version from 0.58 to 0.66 on an independent test dataset. The results demonstrate that TMP-SSurface2 is efficient in predicting the surface of transmembrane proteins, representing new progress in transmembrane protein structure modeling based on primary sequences. TMP-SSurface2 is freely accessible at https://github.com/NENUBioCompute/TMP-SSurface-2.0.
Collapse
Affiliation(s)
- Zhe Liu
- School of Computer Science and Engineering, Changchun University of Technology, Changchun, China.,School of Information Science and Technology, Institute of Computational Biology, Northeast Normal University, Changchun, China.,Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yingli Gong
- College of Intelligence and Computing, Tianjin University, Tianjin, China
| | - Yuanzhao Guo
- School of Information Science and Technology, Institute of Computational Biology, Northeast Normal University, Changchun, China
| | - Xiao Zhang
- College of Computing and Software Engineering, Kennesaw State University, Kennesaw, GA, United States
| | - Chang Lu
- School of Information Science and Technology, Institute of Computational Biology, Northeast Normal University, Changchun, China
| | - Li Zhang
- School of Computer Science and Engineering, Changchun University of Technology, Changchun, China
| | - Han Wang
- School of Information Science and Technology, Institute of Computational Biology, Northeast Normal University, Changchun, China
| |
Collapse
|
62
|
The Interplay of Cholesterol and Ligand Binding in hTSPO from Classical Molecular Dynamics Simulations. Molecules 2021; 26:molecules26051250. [PMID: 33652554 PMCID: PMC7956637 DOI: 10.3390/molecules26051250] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/28/2021] [Accepted: 02/03/2021] [Indexed: 12/23/2022] Open
Abstract
The translocator protein (TSPO) is a 18kDa transmembrane protein, ubiquitously present in human mitochondria. It is overexpressed in tumor cells and at the sites of neuroinflammation, thus representing an important biomarker, as well as a promising drug target. In mammalian TSPO, there are cholesterol–binding motifs, as well as a binding cavity able to accommodate different chemical compounds. Given the lack of structural information for the human protein, we built a model of human (h) TSPO in the apo state and in complex with PK11195, a molecule routinely used in positron emission tomography (PET) for imaging of neuroinflammatory sites. To better understand the interactions of PK11195 and cholesterol with this pharmacologically relevant protein, we ran molecular dynamics simulations of the apo and holo proteins embedded in a model membrane. We found that: (i) PK11195 stabilizes hTSPO structural fold; (ii) PK11195 might enter in the binding site through transmembrane helices I and II of hTSPO; (iii) PK11195 reduces the frequency of cholesterol binding to the lower, N–terminal part of hTSPO in the inner membrane leaflet, while this impact is less pronounced for the upper, C–terminal part in the outer membrane leaflet, where the ligand binding site is located; (iv) very interestingly, cholesterol most frequently binds simultaneously to the so-called CRAC and CARC regions in TM V in the free form (residues L150–X–Y152–X(3)–R156 and R135–X(2)–Y138–X(2)–L141, respectively). However, when the protein is in complex with PK11195, cholesterol binds equally frequently to the CRAC–resembling motif that we observed in TM I (residues L17–X(2)–F20–X(3)–R24) and to CRAC in TM V. We expect that the CRAC–like motif in TM I will be of interest in future experimental investigations. Thus, our MD simulations provide insight into the structural features of hTSPO and the previously unknown interplay between PK11195 and cholesterol interactions with this pharmacologically relevant protein.
Collapse
|
63
|
Wada A, Prates ÉT, Hirano R, Werner AZ, Kamimura N, Jacobson DA, Beckham GT, Masai E. Characterization of aromatic acid/proton symporters in Pseudomonas putida KT2440 toward efficient microbial conversion of lignin-related aromatics. Metab Eng 2021; 64:167-179. [PMID: 33549838 DOI: 10.1016/j.ymben.2021.01.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/10/2020] [Accepted: 01/30/2021] [Indexed: 11/18/2022]
Abstract
Pseudomonas putida KT2440 (hereafter KT2440) is a well-studied platform bacterium for the production of industrially valuable chemicals from heterogeneous mixtures of aromatic compounds obtained from lignin depolymerization. KT2440 can grow on lignin-related monomers, such as ferulate (FA), 4-coumarate (4CA), vanillate (VA), 4-hydroxybenzoate (4HBA), and protocatechuate (PCA). Genes associated with their catabolism are known, but knowledge about the uptake systems remains limited. In this work, we studied the KT2440 transporters of lignin-related monomers and their substrate selectivity. Based on the inhibition by protonophores, we focused on five genes encoding aromatic acid/H+ symporter family transporters categorized into major facilitator superfamily that uses the proton motive force. The mutants of PP_1376 (pcaK) and PP_3349 (hcnK) exhibited significantly reduced growth on PCA/4HBA and FA/4CA, respectively, while no change was observed on VA for any of the five gene mutants. At pH 9.0, the conversion of these compounds by hcnK mutant (FA/4CA) and vanK mutant (VA) was dramatically reduced, revealing that these transporters are crucial for the uptake of the anionic substrates at high pH. Uptake assays using 14C-labeled substrates in Escherichia coli and biosensor-based assays confirmed that PcaK, HcnK, and VanK have ability to take up PCA, FA/4CA, and VA/PCA, respectively. Additionally, analyses of the predicted protein structures suggest that the size and hydropathic properties of the substrate-binding sites of these transporters determine their substrate preferences. Overall, this study reveals that at physiological pH, PcaK and HcnK have a major role in the uptake of PCA/4HBA and FA/4CA, respectively, and VanK is a VA/PCA transporter. This information can contribute to the engineering of strains for the efficient conversion of lignin-related monomers to value-added chemicals.
Collapse
Affiliation(s)
- Ayumu Wada
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Érica T Prates
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Ryo Hirano
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Allison Z Werner
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Naofumi Kamimura
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Daniel A Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Gregg T Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Eiji Masai
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan.
| |
Collapse
|
64
|
Esfandi B, Atabati M. Sequential Dihedral Angles (SDAs): A Method for Evaluating the 3D Structure of Proteins. Protein J 2021; 40:1-7. [PMID: 33442828 DOI: 10.1007/s10930-020-09961-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/31/2020] [Indexed: 11/29/2022]
Abstract
One of the most important steps in modeling three-dimensional (3D) structures of proteins is the evaluation of the constructed models. The present study suggests that the correctness of a structure may be tested by using the characteristics of sequential dihedral angles (SDAs) between adjacent alpha-carbons (Cα) in the main chains of proteins. From our studies on protein structures in the protein data bank (PDB), the SDAs between the Cα in the main chains are limited in their values. In addition, the sum of the absolute values of the three sequential dihedral angles (SDAs) can never be 0 degree. Moreover, 48 degrees is the lowest value existing for the sum of the absolute values of three sequential dihedral angles (SDAs). Thus, the SDAs between the alpha-carbons along the main chains of proteins may be a useful parameter for evaluating anomalies in protein structures.
Collapse
Affiliation(s)
- Babak Esfandi
- School of Chemistry, Damghan University, Damghan, Iran
| | | |
Collapse
|
65
|
Destiarani W, Mulyani R, Yusuf M, Maksum IP. Molecular Dynamics Simulation of T10609C and C10676G Mutations of Mitochondrial ND4L Gene Associated With Proton Translocation in Type 2 Diabetes Mellitus and Cataract Patients. Bioinform Biol Insights 2020; 14:1177932220978672. [PMID: 33402819 PMCID: PMC7747115 DOI: 10.1177/1177932220978672] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 11/14/2020] [Indexed: 11/17/2022] Open
Abstract
The mutation rate of mitochondrial DNA (mtDNA) is 17 times higher than nuclear DNA, and these mutations can cause mitochondrial disease in 1 of 10.000 people. The T10609C mutation was identified in type 2 diabetes mellitus (T2DM) patients and the C10676G mutation in cataract patients, with both mutations occurring in the ND4L gene of mtDNA that encodes ND4L protein. ND4L protein, a subunit of complex I in the respiratory complex, has been shown to play a role in the proton translocation process. The purpose of this study was to investigate the effect of both mutations on the proton translocation mechanism. Mutation mapping showed changes in amino acids M47T (T10609C) and C69W (C10676G). The 100 ns molecular dynamics (MD) simulations performed on native and mutants of ND4L-ND6 subunits. It is revealed that the native model had a similar proton translocation pathway to that of complex I from other organisms. Interestingly, the mutant M47T and C69W showed the interruption of the translocation pathway by a hydrogen bond formation between Glu34 and Tyr157. It is observed that the mutations were restricting the passage of water molecules through the transmembrane region. These results could help to develop the computational assay for the validation of a specific genetic biomarker for T2DM and cataracts.
Collapse
Affiliation(s)
- Wanda Destiarani
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang, Indonesia
| | - Rahmaniar Mulyani
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang, Indonesia
| | - Muhammad Yusuf
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang, Indonesia
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, Indonesia
| | - Iman Permana Maksum
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang, Indonesia
| |
Collapse
|
66
|
Zhao L, Barber LM, Hung A. Structural and dynamical effects of targeted mutations on μO-Conotoxin MfVIA: Molecular simulation studies. J Mol Graph Model 2020; 102:107777. [PMID: 33130390 DOI: 10.1016/j.jmgm.2020.107777] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/25/2020] [Accepted: 10/12/2020] [Indexed: 12/19/2022]
Abstract
Conotoxins are a group of cysteine-rich, neurotoxic peptides isolated from the venom of marine cone snails. MfVIA is a member of the μO-conotoxin family, and acts as an inhibitor of subtype 1.8 voltage-gated sodium ion channels (NaV1.8). The unique selectivity of MfVIA as an inhibitor of NaV1.8 makes it an ideal peptide for elucidation of the physiological functions of this voltage-gated ion channel. Previous experimental studies of point mutations of MfVIA showed that the double mutant [E5K,E8K] exhibited greater activity at NaV1.8 relative to the wild-type toxin. The present study employs molecular dynamics (MD) simulations to examine the effects of various mutations at these key residues (E5 and E8) on the structure and dynamics of MfVIA. Five double mutants were studied, in which the positions 5 and 8 residues were mutated to amino acids with a range of different physicochemical properties, namely [E5A,E8A], [E5D,E8D], [E5F,E8F], [E5K,E8K], and [E5R,E8R]. Except for [E5D,E8D], all of the mutants tend to show decreased contacts at the N-terminus owing to the loss of the R1-E5 salt bridge relative to that of the wild-type, which subsequently lead to greater exposure and flexibility of the N-terminus for most of the mutant peptides studied, potentially rendering them more able to interact with other species, including NaV1.8. Molecular docking studies of the peptides to NaV1.8 via different binding mechanisms suggest that the [E5R, E8R] mutant may be especially worthy of further investigation owing to its predicted binding mode, which differs markedly from those of the other peptides in this study.
Collapse
Affiliation(s)
- Lina Zhao
- School of Science, RMIT University, Melbourne, VIC, 3001, Australia
| | - Lisa M Barber
- School of Science, RMIT University, Melbourne, VIC, 3001, Australia
| | - Andrew Hung
- School of Science, RMIT University, Melbourne, VIC, 3001, Australia.
| |
Collapse
|
67
|
Evaluation of gene expression and protein structural modeling involved in persister cell formation in Salmonella Typhimurium. Braz J Microbiol 2020; 52:207-217. [PMID: 33125683 DOI: 10.1007/s42770-020-00388-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 10/16/2020] [Indexed: 10/23/2022] Open
Abstract
Persisters are phenotypic variants of the bacterial population that survive against lethal doses of bactericidal antibiotics.These phenotypes are created in numerous bacterial species, including those of clinical significance, such as Salmonella Typhimurium. Since persister cells are associated with the failure of antibiotic treatment and infection recurrence, it is crucial to identify the mechanisms that influence the formation of these cells. The aim of this study is to investigate the persister cell formation and expression analysis as well as to predict the 3D structure of the genes involved in the production of persister cells. The presence of persisters in S. Typhimurium was determined by time dependent killing of different types of bactericidal antibiotics and expression of genes associated with persister cell formation which was assessed five hours after the addition of antibiotics by the qRT-PCR. Indeed, the 3D structural model of the proteins studied was predicted by performing several computational methods of retrieved primary protein sequences. The results of the study showed that the S. Typhimurium produced high levels of persister cells in the exposure of bactericidal antibiotics. Furthermore, qRT-PCR resulted in the fact that the expression of related genes was different depending on the type of antibiotic. Overall, this study provides information on the creation of persister cells and the role of different genes in the formation of these cells and structure of proteins involved in the production of persister cells in S. Typhimurium.
Collapse
|
68
|
Toffano AA, Chiarot G, Zamuner S, Marchi M, Salvi E, Waxman SG, Faber CG, Lauria G, Giacometti A, Simeoni M. Computational pipeline to probe NaV1.7 gain-of-function variants in neuropathic painful syndromes. Sci Rep 2020; 10:17930. [PMID: 33087732 PMCID: PMC7578092 DOI: 10.1038/s41598-020-74591-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/30/2020] [Indexed: 01/09/2023] Open
Abstract
Applications of machine learning and graph theory techniques to neuroscience have witnessed an increased interest in the last decade due to the large data availability and unprecedented technology developments. Their employment to investigate the effect of mutational changes in genes encoding for proteins modulating the membrane of excitable cells, whose biological correlates are assessed at electrophysiological level, could provide useful predictive clues. We apply this concept to the analysis of variants in sodium channel NaV1.7 subunit found in patients with chronic painful syndromes, by the implementation of a dedicated computational pipeline empowering different and complementary techniques including homology modeling, network theory, and machine learning. By testing three templates of different origin and sequence identities, we provide an optimal condition for its use. Our findings reveal the usefulness of our computational pipeline in supporting the selection of candidates for cell electrophysiology assay and with potential clinical applications.
Collapse
Affiliation(s)
- Alberto A Toffano
- Dipartimento di Scienze Molecolari e Nanosistemi, Universitá Ca' Foscari Venezia, Venezia-Mestre, Italy
| | - Giacomo Chiarot
- Dipartimento di Scienze Ambientali, Informatica e Statistica, Universitá Ca' Foscari Venezia, Venezia-Mestre, Italy
| | - Stefano Zamuner
- Laboratory of Statistical Biophysics, Institute of Physics, School of Basic Sciences, Ècole Polytechnique Fèdèrale de Lausanne (EPFL), Lausanne, Switzerland
| | - Margherita Marchi
- Neuroalgology Unit, Fondazione IRCCS Istituto Neurologico "Carlo Besta", Milan, Italy
| | - Erika Salvi
- Neuroalgology Unit, Fondazione IRCCS Istituto Neurologico "Carlo Besta", Milan, Italy
| | - Stephen G Waxman
- Center for Neuroscience and Regeneration Research, VA Connecticut Healthcare System and Yale Medical School, West Haven, USA
| | - Catharina G Faber
- MHeNs school for Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands.,Department of Neurology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Giuseppe Lauria
- Neuroalgology Unit, Fondazione IRCCS Istituto Neurologico "Carlo Besta", Milan, Italy.,Department of Biomedical and Clinical Sciences "Luigi Sacco", University of Milan, Milan, Italy
| | - Achille Giacometti
- Dipartimento di Scienze Molecolari e Nanosistemi, Universitá Ca' Foscari Venezia, Venezia-Mestre, Italy.,European Centre for Living Technology (ECLT), Venice, Italy
| | - Marta Simeoni
- Dipartimento di Scienze Ambientali, Informatica e Statistica, Universitá Ca' Foscari Venezia, Venezia-Mestre, Italy. .,European Centre for Living Technology (ECLT), Venice, Italy.
| |
Collapse
|
69
|
Singh R, Gautam A, Chandel S, Ghosh A, Dey D, Roy S, Ravichandiran V, Ghosh D. Protease Inhibitory Effect of Natural Polyphenolic Compounds on SARS-CoV-2: An In Silico Study. Molecules 2020; 25:E4604. [PMID: 33050360 PMCID: PMC7587198 DOI: 10.3390/molecules25204604] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/19/2020] [Accepted: 09/23/2020] [Indexed: 01/07/2023] Open
Abstract
The current pandemic, caused by SARS-CoV-2 virus, is a severe challenge for human health and the world economy. There is an urgent need for development of drugs that can manage this pandemic, as it has already infected 19 million people and led to the death of around 711,277 people worldwide. At this time, in-silico studies are providing lots of preliminary data about potential drugs, which can be a great help in further in-vitro and in-vivo studies. Here, we have selected three polyphenolic compounds, mangiferin, glucogallin, and phlorizin. These compounds are isolated from different natural sources but share structural similarities and have been reported for their antiviral activity. The objective of this study is to analyze and predict the anti-protease activity of these compounds on SARS-CoV-2main protease (Mpro) and TMPRSS2 protein. Both the viral protein and the host protein play an important role in the viral life cycle, such as post-translational modification and viral spike protein priming. This study has been performed by molecular docking of the compounds using PyRx with AutoDock Vina on the two aforementioned targets chosen for this study, i.e., SARS-CoV-2 Mpro and TMPRSS2. The compounds showed good binding affinity and are further analyzed by (Molecular dynamic) MD and Molecular Mechanics Poisson-Boltzmann Surface Area MM-PBSA study. The MD-simulation study has predicted that these natural compounds will have a great impact on the stabilization of the binding cavity of the Mpro of SARS-CoV-2. The predicted pharmacokinetic parameters also show that these compounds are expected to have good solubility and absorption properties. Further predictions for these compounds also showed no involvement in drug-drug interaction and no toxicity.
Collapse
Affiliation(s)
- Rajveer Singh
- National Institute of Pharmaceutical Education and Research, Kolkata 70054, India; (R.S.); (S.C.); (D.D.); (S.R.); (V.R.)
| | - Anupam Gautam
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany;
- International Max Planck Research School ‘From Molecules to Organisms’, 72076 Tübingen, Germany
| | - Shivani Chandel
- National Institute of Pharmaceutical Education and Research, Kolkata 70054, India; (R.S.); (S.C.); (D.D.); (S.R.); (V.R.)
| | - Arijit Ghosh
- Department of Chemistry, University of Calcutta, Kolkata 700009, India;
| | - Dhritiman Dey
- National Institute of Pharmaceutical Education and Research, Kolkata 70054, India; (R.S.); (S.C.); (D.D.); (S.R.); (V.R.)
| | - Syamal Roy
- National Institute of Pharmaceutical Education and Research, Kolkata 70054, India; (R.S.); (S.C.); (D.D.); (S.R.); (V.R.)
| | - Velayutham Ravichandiran
- National Institute of Pharmaceutical Education and Research, Kolkata 70054, India; (R.S.); (S.C.); (D.D.); (S.R.); (V.R.)
| | - Dipanjan Ghosh
- National Institute of Pharmaceutical Education and Research, Kolkata 70054, India; (R.S.); (S.C.); (D.D.); (S.R.); (V.R.)
| |
Collapse
|
70
|
Studer G, Rempfer C, Waterhouse AM, Gumienny R, Haas J, Schwede T. QMEANDisCo-distance constraints applied on model quality estimation. Bioinformatics 2020; 36:1765-1771. [PMID: 31697312 PMCID: PMC7075525 DOI: 10.1093/bioinformatics/btz828] [Citation(s) in RCA: 527] [Impact Index Per Article: 105.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 10/24/2019] [Accepted: 11/06/2019] [Indexed: 01/13/2023] Open
Abstract
Motivation Methods that estimate the quality of a 3D protein structure model in absence of an experimental reference structure are crucial to determine a model’s utility and potential applications. Single model methods assess individual models whereas consensus methods require an ensemble of models as input. In this work, we extend the single model composite score QMEAN that employs statistical potentials of mean force and agreement terms by introducing a consensus-based distance constraint (DisCo) score. Results DisCo exploits distance distributions from experimentally determined protein structures that are homologous to the model being assessed. Feed-forward neural networks are trained to adaptively weigh contributions by the multi-template DisCo score and classical single model QMEAN parameters. The result is the composite score QMEANDisCo, which combines the accuracy of consensus methods with the broad applicability of single model approaches. We also demonstrate that, despite being the de-facto standard for structure prediction benchmarking, CASP models are not the ideal data source to train predictive methods for model quality estimation. For performance assessment, QMEANDisCo is continuously benchmarked within the CAMEO project and participated in CASP13. For both, it ranks among the top performers and excels with low response times. Availability and implementation QMEANDisCo is available as web-server at https://swissmodel.expasy.org/qmean. The source code can be downloaded from https://git.scicore.unibas.ch/schwede/QMEAN. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Gabriel Studer
- Biozentrum, University of Basel, Basel 4056, Switzerland.,SIB Swiss Institute of Bioinformatics, Basel 4056, Switzerland
| | - Christine Rempfer
- Biozentrum, University of Basel, Basel 4056, Switzerland.,SIB Swiss Institute of Bioinformatics, Basel 4056, Switzerland
| | - Andrew M Waterhouse
- Biozentrum, University of Basel, Basel 4056, Switzerland.,SIB Swiss Institute of Bioinformatics, Basel 4056, Switzerland
| | - Rafal Gumienny
- Biozentrum, University of Basel, Basel 4056, Switzerland.,SIB Swiss Institute of Bioinformatics, Basel 4056, Switzerland
| | - Juergen Haas
- Biozentrum, University of Basel, Basel 4056, Switzerland.,SIB Swiss Institute of Bioinformatics, Basel 4056, Switzerland
| | - Torsten Schwede
- Biozentrum, University of Basel, Basel 4056, Switzerland.,SIB Swiss Institute of Bioinformatics, Basel 4056, Switzerland
| |
Collapse
|
71
|
Muhammad SA, Ashfaq H, Zafar S, Munir F, Jamshed MB, Chen J, Zhang Q. Polyvalent therapeutic vaccine for type 2 diabetes mellitus: Immunoinformatics approach to study co-stimulation of cytokines and GLUT1 receptors. BMC Mol Cell Biol 2020; 21:56. [PMID: 32703184 PMCID: PMC7376330 DOI: 10.1186/s12860-020-00279-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 04/28/2020] [Indexed: 12/14/2022] Open
Abstract
Background Type 2 diabetes mellitus (T2DM) is a worldwide disease that have an impact on individuals of all ages causing micro and macro vascular impairments due to hyperglycemic internal environment. For ultimate treatment to cure T2DM, association of diabetes with immune components provides a strong basis for immunotherapies and vaccines developments that could stimulate the immune cells to minimize the insulin resistance and initiate gluconeogenesis through an insulin independent route. Methodology Immunoinformatics based approach was used to design a polyvalent vaccine for T2DM that involved data accession, antigenicity analysis, T-cell epitopes prediction, conservation and proteasomal evaluation, functional annotation, interactomic and in silico binding affinity analysis. Results We found the binding affinity of antigenic peptides with major histocompatibility complex (MHC) Class-I molecules for immune activation to control T2DM. We found 13-epitopes of 9 amino acid residues for multiple alleles of MHC class-I bears significant binding affinity. The downstream signaling resulted by T-cell activation is directly regulated by the molecular weight, amino acid properties and affinity of these epitopes. Each epitope has important percentile rank with significant ANN IC50 values. These high score potential epitopes were linked using AAY, EAAAK linkers and HBHA adjuvant to generate T-cell polyvalent vaccine with a molecular weight of 35.6 kDa containing 322 amino acids residues. In silico analysis of polyvalent construct showed the significant binding affinity (− 15.34 Kcal/mol) with MHC Class-I. This interaction would help to understand our hypothesis, potential activation of T-cells and stimulatory factor of cytokines and GLUT1 receptors. Conclusion Our system-level immunoinformatics approach is suitable for designing potential polyvalent therapeutic vaccine candidates for T2DM by reducing hyperglycemia and enhancing metabolic activities through the immune system.
Collapse
Affiliation(s)
- Syed Aun Muhammad
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University Multan, Multan, Pakistan.
| | - Hiba Ashfaq
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University Multan, Multan, Pakistan
| | - Sidra Zafar
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University Multan, Multan, Pakistan
| | - Fahad Munir
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, People's Republic of China
| | - Muhammad Babar Jamshed
- School of Pharmaceutical Sciences of Wenzhou Medical University, Wenzhou, 325000, People's Republic of China
| | - Jake Chen
- Informatics Institute, School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Qiyu Zhang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, People's Republic of China.
| |
Collapse
|
72
|
Bonito CA, Ferreira RJ, Ferreira MJU, Gillet JP, Cordeiro MNDS, Dos Santos DJVA. Theoretical insights on helix repacking as the origin of P-glycoprotein promiscuity. Sci Rep 2020; 10:9823. [PMID: 32555203 PMCID: PMC7300024 DOI: 10.1038/s41598-020-66587-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 04/27/2020] [Indexed: 12/14/2022] Open
Abstract
P-glycoprotein (P-gp, ABCB1) overexpression is, currently, one of the most important multidrug resistance (MDR) mechanisms in tumor cells. Thus, modulating drug efflux by P-gp has become one of the most promising approaches to overcome MDR in cancer. Yet, more insights on the molecular basis of drug specificity and efflux-related signal transmission mechanism between the transmembrane domains (TMDs) and the nucleotide binding domains (NBDs) are needed to develop molecules with higher selectivity and efficacy. Starting from a murine P-gp crystallographic structure at the inward-facing conformation (PDB ID: 4Q9H), we evaluated the structural quality of the herein generated human P-gp homology model. This initial human P-gp model, in the presence of the “linker” and inserted in a suitable lipid bilayer, was refined through molecular dynamics simulations and thoroughly validated. The best human P-gp model was further used to study the effect of four single-point mutations located at the TMDs, experimentally related with changes in substrate specificity and drug-stimulated ATPase activity. Remarkably, each P-gp mutation is able to induce transmembrane α-helices (TMHs) repacking, affecting the drug-binding pocket volume and the drug-binding sites properties (e.g. volume, shape and polarity) finally compromising drug binding at the substrate binding sites. Furthermore, intracellular coupling helices (ICH) also play an important role since changes in the TMHs rearrangement are shown to have an impact in residue interactions at the ICH-NBD interfaces, suggesting that identified TMHs repacking affect TMD-NBD contacts and interfere with signal transmission from the TMDs to the NBDs.
Collapse
Affiliation(s)
- Cátia A Bonito
- LAQV@REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - Ricardo J Ferreira
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, 75124, Uppsala, Sweden
| | - Maria-José U Ferreira
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
| | - Jean-Pierre Gillet
- Laboratory of Molecular Cancer Biology, Molecular Physiology Research Unit-URPhyM, Namur Research Institute for Life Sciences (NARILIS), Faculty of Medicine, University of Namur, B-5000, Namur, Belgium
| | - M Natália D S Cordeiro
- LAQV@REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - Daniel J V A Dos Santos
- LAQV@REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal. .,Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal.
| |
Collapse
|
73
|
Structural and evolutionary analyses of the Plasmodium falciparum chloroquine resistance transporter. Sci Rep 2020; 10:4842. [PMID: 32179795 PMCID: PMC7076037 DOI: 10.1038/s41598-020-61181-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 02/24/2020] [Indexed: 12/12/2022] Open
Abstract
Mutations in the Plasmodium falciparum chloroquine resistance transporter (PfCRT) confer resistance to several antimalarial drugs such as chloroquine (CQ) or piperaquine (PPQ), a partner molecule in current artemisinin-based combination therapies. As a member of the Drug/Metabolite Transporter (DMT) superfamily, the vacuolar transporter PfCRT may translocate substrate molecule(s) across the membrane of the digestive vacuole (DV), a lysosome-like organelle. However, the physiological substrate(s), the transport mechanism and the functional regions of PfCRT remain to be fully characterized. Here, we hypothesized that identification of evolutionary conserved sites in a tertiary structural context could help locate putative functional regions of PfCRT. Hence, site-specific substitution rates were estimated over Plasmodium evolution at each amino acid sites, and the PfCRT tertiary structure was predicted in both inward-facing (open-to-vacuole) and occluded states through homology modeling using DMT template structures sharing <15% sequence identity with PfCRT. We found that the vacuolar-half and membrane-spanning domain (and especially the transmembrane helix 9) of PfCRT were more conserved, supporting that its physiological substrate is expelled out of the parasite DV. In the PfCRT occluded state, some evolutionary conserved sites, including positions related to drug resistance mutations, participate in a putative binding pocket located at the core of the PfCRT membrane-spanning domain. Through structural comparison with experimentally-characterized DMT transporters, we identified several conserved PfCRT amino acid sites located in this pocket as robust candidates for mediating substrate transport. Finally, in silico mutagenesis revealed that drug resistance mutations caused drastic changes in the electrostatic potential of the transporter vacuolar entry and pocket, facilitating the escape of protonated CQ and PPQ from the parasite DV.
Collapse
|
74
|
Shi S, Li J, Sun F, Chen Y, Pang C, Geng Y, Qi J, Guo S, Wang X, Zhang H, Zhan Y, An H. Molecular Mechanisms and Structural Basis of Retigabine Analogues in Regulating KCNQ2 Channel. J Membr Biol 2020; 253:167-181. [DOI: 10.1007/s00232-020-00113-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 03/05/2020] [Indexed: 12/22/2022]
|
75
|
Lang SA, McIlroy P, Shain DH. Structural Evolution of the Glacier Ice Worm F o ATP Synthase Complex. Protein J 2020; 39:152-159. [PMID: 32112190 DOI: 10.1007/s10930-020-09889-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The segmented annelid worm, Mesenchytraeus solifugus, is a permanent resident of temperate, maritime glaciers in the Pacific northwestern region of North America, displaying atypically high intracellular ATP levels which have been linked to its unusual ability to thrive in hydrated glacier ice. We have shown previously that ice worms contain a highly basic, carboxy terminal extension on their ATP6 regulatory subunit, likely acquired by horizontal gene transfer from a microbial dietary source. Here we examine the full complement of F1F0 ATP synthase structural subunits with attention to non-conservative, ice worm-specific structural modifications. Our genomics analyses and molecular models identify putative proton shuttling domains on either side of the F0 hemichannel, which predictably function to enhance proton flow across the mitochondrial membrane. Other components of the ice worm ATP synthase complex have remained largely unchanged in the context of Metazoan evolution.
Collapse
Affiliation(s)
- Shirley A Lang
- Department of Biology, Haverford College, Haverford, PA, 19041, USA
| | - Patrick McIlroy
- Department of Biology and Center for Computational and Integrative Biology, Rutgers The State University of New Jersey, Camden, NJ, 08102, USA
| | - Daniel H Shain
- Department of Biology and Center for Computational and Integrative Biology, Rutgers The State University of New Jersey, Camden, NJ, 08102, USA.
| |
Collapse
|
76
|
Guzzi AF, Oliveira FSL, Amaro MMS, Tavares-Filho PF, Gabriel JE. In silico prediction of the functional and structural consequences of the non-synonymous single nucleotide polymorphism A122V in bovine CXC chemokine receptor type 1. BRAZ J BIOL 2020; 80:39-46. [DOI: 10.1590/1519-6984.188655] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 07/17/2018] [Indexed: 02/04/2023] Open
Abstract
Abstract The current study aimed to assess whether the A122V causal polymorphism promotes alterations in the functional and structural proprieties of the CXC chemokine receptor type 1 protein (CXCR1) of cattle Bos taurus by in silico analyses. Two amino acid sequences of bovine CXCR1 was selected from database UniProtKB/Swiss-Prot: a) non-polymorphic sequence (A7KWG0) with alanine (A) at position 122, and b) polymorphic sequence harboring the A122V polymorphism, substituting alanine by valine (V) at same position. CXCR1 sequences were submitted as input to different Bioinformatics’ tools to examine the effects of this polymorphism on functional and structural stabilities, to predict eventual alterations in the 3-D structural modeling, and to estimate the quality and accuracy of the predictive models. The A122V polymorphism exerted tolerable and non-deleterious effects on the polymorphic CXCR1, and the predictive structural model for polymorphic CXCR1 revealed an alpha helix spatial structure typical of a receptor transmembrane polypeptide. Although higher variations in the distances between pairs of amino acid residues at target-positions are detected in the polymorphic CXCR1 protein, more than 97% of the amino acid residues in both models were located in favored and allowed conformational regions in Ramachandran plots. Evidences has supported that the A122V polymorphism in the CXCR1 protein is associated with increased clinical mastitis incidence in dairy cows. Thus, the findings described herein prove that the replacement of the alanine by valine amino acids provokes local conformational changes in the A122V-harboring CXCR1 protein, which could directly affect its post-translational folding mechanisms and biological functionality.
Collapse
Affiliation(s)
- A. F. Guzzi
- Universidade Federal do Vale do São Francisco, Brasil
| | | | | | | | - J. E. Gabriel
- Universidade Federal do Vale do São Francisco, Brasil
| |
Collapse
|
77
|
Shanmugarajan D, P. P, Kumar BRP, Suresh B. Curcumin to inhibit binding of spike glycoprotein to ACE2 receptors: computational modelling, simulations, and ADMET studies to explore curcuminoids against novel SARS-CoV-2 targets. RSC Adv 2020; 10:31385-31399. [PMID: 35520671 PMCID: PMC9056388 DOI: 10.1039/d0ra03167d] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 08/08/2020] [Indexed: 11/21/2022] Open
Abstract
The significant role of curcumin against SARS-CoV-2 drug targets to thwart virus replication and binding into the host system using the computational biology paradigm approach.
Collapse
Affiliation(s)
- Dhivya Shanmugarajan
- Department of Pharmaceutical Chemistry
- JSS College of Pharmacy
- JSS Academy of Higher Education & Research
- Mysuru 570 015
- India
| | - Prabitha P.
- Department of Pharmaceutical Chemistry
- JSS College of Pharmacy
- JSS Academy of Higher Education & Research
- Mysuru 570 015
- India
| | - B. R. Prashantha Kumar
- Department of Pharmaceutical Chemistry
- JSS College of Pharmacy
- JSS Academy of Higher Education & Research
- Mysuru 570 015
- India
| | - B. Suresh
- JSS Academy of Higher Education & Research
- Mysuru 570 015
- India
| |
Collapse
|
78
|
Sharma M, Anirudh CR. In silico characterization of residues essential for substrate binding of human cystine transporter, xCT. J Mol Model 2019; 25:336. [PMID: 31705320 DOI: 10.1007/s00894-019-4233-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 10/14/2019] [Indexed: 02/06/2023]
Abstract
xCT is a sodium-independent amino acid antiporter that imports L-cystine and exports L-glutamate in a 1:1 ratio. It is a component of heterodimeric amino acid transporter system Xc- working at the cross-roads of maintaining neurological processes and regulating antioxidant defense. The transporter has 12 transmembrane domains with intracellular N- and C-termini, and like other transporter proteins can undergo various conformational changes while switching the ligand accessibilities from intracellular to extracellular site. In the present study, we generated two homology models of human xCT in two distinct conformations: inward-facing occluded state and outward-facing open state. Our results indicated the substrate translocation channel composed of transmembrane helices TMs 1, 3, 6, 8, and 10. We docked anionic L-cystine and L-glutamate within the cavities to assess the two distinct binding scenarios for xCT as antiporter. We also assessed the interactions between the ligands and transporter and observed that ligands bind to similar residues within the channel. Using MM-PBSA/MM-GBSA approach, we computed the binding energies of these ligands to different conformational states. Cystine and glutamate bind xCT with favorable binding energies, with more favorable binding observed in inward occluded state than in outward open state. We further computed the residue-wise decomposition of these binding energies and identified the residues as essential for substrate binding/permeation. Filtering the residues that form favorable energetic contributions to the ligand binding in both the states, our studies suggest T56, A60, R135, A138, V141, Y244, A247, F250, S330, L392, and R396 as critical residues for ligand binding as well as ligand transport for any conformational state adopted by xCT during its transport cycle. .Graphical Abstract.
Collapse
Affiliation(s)
- Monika Sharma
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Sector 81, Knowledge City, SAS, Nagar, Punjab, India.
| | - C R Anirudh
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Sector 81, Knowledge City, SAS, Nagar, Punjab, India
| |
Collapse
|
79
|
Rehan S, Shahid S, Salminen TA, Jaakola VP, Paavilainen VO. Current Progress on Equilibrative Nucleoside Transporter Function and Inhibitor Design. SLAS DISCOVERY 2019; 24:953-968. [PMID: 31503511 DOI: 10.1177/2472555219870123] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Physiological nucleosides are used for the synthesis of DNA, RNA, and ATP in the cell and serve as universal mammalian signaling molecules that regulate physiological processes such as vasodilation and platelet aggregation by engaging with cell surface receptors. The same pathways that allow uptake of physiological nucleosides mediate the cellular import of synthetic nucleoside analogs used against cancer, HIV, and other viral diseases. Physiological nucleosides and nucleoside drugs are imported by two families of nucleoside transporters: the SLC28 concentrative nucleoside transporters (CNTs) and SLC29 equilibrative nucleoside transporters (ENTs). The four human ENT paralogs are expressed in distinct tissues, localize to different subcellular sites, and transport a variety of different molecules. Here we provide an overview of the known structure-function relationships of the ENT family with a focus on ligand binding and transport in the context of a new hENT1 homology model. We provide a generic residue numbering system for the different ENTs to facilitate the interpretation of mutational data produced using different ENT homologs. The discovery of paralog-selective small-molecule modulators is highly relevant for the design of new therapies and for uncovering the functions of poorly characterized ENT family members. Here, we discuss recent developments in the discovery of new paralog-selective small-molecule ENT inhibitors, including new natural product-inspired compounds. Recent progress in the ability to heterologously produce functional ENTs will allow us to gain insight into the structure and functions of different ENT family members as well as the rational discovery of highly selective inhibitors.
Collapse
Affiliation(s)
- Shahid Rehan
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,HiLIFE, University of Helsinki, Helsinki, Finland
| | - Saman Shahid
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Tiina A Salminen
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Veli-Pekka Jaakola
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Ville O Paavilainen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,HiLIFE, University of Helsinki, Helsinki, Finland
| |
Collapse
|
80
|
Mbaye MN, Hou Q, Basu S, Teheux F, Pucci F, Rooman M. A comprehensive computational study of amino acid interactions in membrane proteins. Sci Rep 2019; 9:12043. [PMID: 31427701 PMCID: PMC6700154 DOI: 10.1038/s41598-019-48541-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 08/07/2019] [Indexed: 01/26/2023] Open
Abstract
Transmembrane proteins play a fundamental role in a wide series of biological processes but, despite their importance, they are less studied than globular proteins, essentially because their embedding in lipid membranes hampers their experimental characterization. In this paper, we improved our understanding of their structural stability through the development of new knowledge-based energy functions describing amino acid pair interactions that prevail in the transmembrane and extramembrane regions of membrane proteins. The comparison of these potentials and those derived from globular proteins yields an objective view of the relative strength of amino acid interactions in the different protein environments, and their role in protein stabilization. Separate potentials were also derived from α-helical and β-barrel transmembrane regions to investigate possible dissimilarities. We found that, in extramembrane regions, hydrophobic residues are less frequent but interactions between aromatic and aliphatic amino acids as well as aromatic-sulfur interactions contribute more to stability. In transmembrane regions, polar residues are less abundant but interactions between residues of equal or opposite charges or non-charged polar residues as well as anion-π interactions appear stronger. This shows indirectly the preference of the water and lipid molecules to interact with polar and hydrophobic residues, respectively. We applied these new energy functions to predict whether a residue is located in the trans- or extramembrane region, and obtained an AUC score of 83% in cross validation, which demonstrates their accuracy. As their application is, moreover, extremely fast, they are optimal instruments for membrane protein design and large-scale investigations of membrane protein stability.
Collapse
Affiliation(s)
- Mame Ndew Mbaye
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium.,Department of Mathematics and Informatics, Cheikh Anta Diop University, Dakar-Fann, Senegal
| | - Qingzhen Hou
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium
| | - Sankar Basu
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium
| | - Fabian Teheux
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium
| | - Fabrizio Pucci
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium.,John von Neumann Institute for Computing, Jülich Supercomputer Centre, Forschungszentrum Jülich, Jülich, Germany
| | - Marianne Rooman
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium.
| |
Collapse
|
81
|
Palazzotti D, Bissaro M, Bolcato G, Astolfi A, Felicetti T, Sabatini S, Sturlese M, Cecchetti V, Barreca ML, Moro S. Deciphering the Molecular Recognition Mechanism of Multidrug Resistance Staphylococcus aureus NorA Efflux Pump Using a Supervised Molecular Dynamics Approach. Int J Mol Sci 2019; 20:E4041. [PMID: 31430864 PMCID: PMC6719125 DOI: 10.3390/ijms20164041] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 08/09/2019] [Accepted: 08/15/2019] [Indexed: 12/01/2022] Open
Abstract
The use and misuse of antibiotics has resulted in critical conditions for drug-resistant bacteria emergency, accelerating the development of antimicrobial resistance (AMR). In this context, the co-administration of an antibiotic with a compound able to restore sufficient antibacterial activity may be a successful strategy. In particular, the identification of efflux pump inhibitors (EPIs) holds promise for new antibiotic resistance breakers (ARBs). Indeed, bacterial efflux pumps have a key role in AMR development; for instance, NorA efflux pump contributes to Staphylococcus aureus (S. aureus) resistance against fluoroquinolone antibiotics (e.g., ciprofloxacin) by promoting their active extrusion from the cells. Even though NorA efflux pump is known to be a potential target for EPIs development, the absence of structural information about this protein and the little knowledge available on its mechanism of action have strongly hampered rational drug discovery efforts in this area. In the present work, we investigated at the molecular level the substrate recognition pathway of NorA through a Supervised Molecular Dynamics (SuMD) approach, using a NorA homology model. Specific amino acids were identified as playing a key role in the efflux pump-mediated extrusion of its substrate, paving the way for a deeper understanding of both the mechanisms of action and the inhibition of such efflux pumps.
Collapse
Affiliation(s)
- Deborah Palazzotti
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, 35131 Padova, Italy
- Department of Pharmaceutical Sciences, “Department of excellence 2018-2022”, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Maicol Bissaro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, 35131 Padova, Italy
| | - Giovanni Bolcato
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, 35131 Padova, Italy
| | - Andrea Astolfi
- Department of Pharmaceutical Sciences, “Department of excellence 2018-2022”, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Tommaso Felicetti
- Department of Pharmaceutical Sciences, “Department of excellence 2018-2022”, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Stefano Sabatini
- Department of Pharmaceutical Sciences, “Department of excellence 2018-2022”, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Mattia Sturlese
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, 35131 Padova, Italy
| | - Violetta Cecchetti
- Department of Pharmaceutical Sciences, “Department of excellence 2018-2022”, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Maria Letizia Barreca
- Department of Pharmaceutical Sciences, “Department of excellence 2018-2022”, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Stefano Moro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, 35131 Padova, Italy
| |
Collapse
|
82
|
Cheng J, Choe MH, Elofsson A, Han KS, Hou J, Maghrabi AHA, McGuffin LJ, Menéndez-Hurtado D, Olechnovič K, Schwede T, Studer G, Uziela K, Venclovas Č, Wallner B. Estimation of model accuracy in CASP13. Proteins 2019; 87:1361-1377. [PMID: 31265154 DOI: 10.1002/prot.25767] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 06/04/2019] [Accepted: 06/15/2019] [Indexed: 12/28/2022]
Abstract
Methods to reliably estimate the accuracy of 3D models of proteins are both a fundamental part of most protein folding pipelines and important for reliable identification of the best models when multiple pipelines are used. Here, we describe the progress made from CASP12 to CASP13 in the field of estimation of model accuracy (EMA) as seen from the progress of the most successful methods in CASP13. We show small but clear progress, that is, several methods perform better than the best methods from CASP12 when tested on CASP13 EMA targets. Some progress is driven by applying deep learning and residue-residue contacts to model accuracy prediction. We show that the best EMA methods select better models than the best servers in CASP13, but that there exists a great potential to improve this further. Also, according to the evaluation criteria based on local similarities, such as lDDT and CAD, it is now clear that single model accuracy methods perform relatively better than consensus-based methods.
Collapse
Affiliation(s)
- Jianlin Cheng
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri
| | - Myong-Ho Choe
- Department of Life Science, University of Science, Pyongyang, DPR Korea
| | - Arne Elofsson
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Kun-Sop Han
- Department of Life Science, University of Science, Pyongyang, DPR Korea
| | - Jie Hou
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri
| | - Ali H A Maghrabi
- School of Biological Sciences, University of Reading, Reading, UK
| | - Liam J McGuffin
- School of Biological Sciences, University of Reading, Reading, UK
| | - David Menéndez-Hurtado
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Kliment Olechnovič
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Torsten Schwede
- Biozentrum, University of Basel, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Basel, Switzerland
| | - Gabriel Studer
- Biozentrum, University of Basel, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Basel, Switzerland
| | - Karolis Uziela
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Česlovas Venclovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Björn Wallner
- Department of Physics, Chemistry, and Biology, Bioinformatics Division, Linköping University, Linköping, Sweden
| |
Collapse
|
83
|
Chen IS, Liu C, Tateyama M, Karbat I, Uesugi M, Reuveny E, Kubo Y. Non-sedating antihistamines block G-protein-gated inwardly rectifying K + channels. Br J Pharmacol 2019; 176:3161-3179. [PMID: 31116876 DOI: 10.1111/bph.14717] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 04/19/2019] [Accepted: 05/02/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND AND PURPOSE A second-generation antihistamine, terfenadine, is known to induce arrhythmia by blocking hERG channels. In this study, we have shown that terfenadine also inhibits the activity of G-protein-gated inwardly rectifying K+ (GIRK) channels, which regulate the excitability of neurons and cardiomyocytes. To clarify the underlying mechanism(s), we examined the effects of several antihistamines on GIRK channels and identified the structural determinant for the inhibition. EXPERIMENTAL APPROACH Electrophysiological recordings were made in Xenopus oocytes and rat atrial myocytes to analyse the effects of antihistamines on various GIRK subunits (Kir 3.x). Mutagenesis analyses identified the residues critical for inhibition by terfenadine and the regulation of ion selectivity. The potential docking site of terfenadine was analysed by molecular docking. KEY RESULTS GIRK channels containing Kir 3.1 subunits heterologously expressed in oocytes and native GIRK channels in atrial myocytes were inhibited by terfenadine and other non-sedating antihistamines. In Kir 3.1 subunits, mutation of Phe137, located in the centre of the pore helix, to the corresponding Ser in Kir 3.2 subunits reduced the inhibition by terfenadine. Introduction of an amino acid with a large side chain in Kir 3.2 subunits at Ser148 increased the inhibition. When this residue was mutated to a non-polar amino acid, the channel became permeable to Na+ . Phosphoinositide-mediated activity was also decreased by terfenadine. CONCLUSION AND IMPLICATIONS The Phe137 residue in Kir 3.1 subunits is critical for inhibition by terfenadine. This study provides novel insights into the regulation of GIRK channels by the pore helix and information for drug design.
Collapse
Affiliation(s)
- I-Shan Chen
- Division of Biophysics and Neurobiology, Department of Molecular and Cellular Physiology, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Japan.,Department of Physiological Sciences, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Japan
| | - Chang Liu
- Division of Biophysics and Neurobiology, Department of Molecular and Cellular Physiology, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Japan.,Department of Physiological Sciences, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Japan
| | - Michihiro Tateyama
- Division of Biophysics and Neurobiology, Department of Molecular and Cellular Physiology, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Japan.,Department of Physiological Sciences, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Japan
| | - Izhar Karbat
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Motonari Uesugi
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Uji, Japan.,Institute for Chemical Research, Kyoto University, Uji, Japan
| | - Eitan Reuveny
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Yoshihiro Kubo
- Division of Biophysics and Neurobiology, Department of Molecular and Cellular Physiology, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Japan.,Department of Physiological Sciences, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Japan
| |
Collapse
|
84
|
Limeres MJ, Gomez ER, Noseda DG, Cerrudo CS, Ghiringhelli PD, Nusblat AD, Cuestas ML. Impact of hepatitis B virus genotype F on in vitro diagnosis: detection efficiency of HBsAg from Amerindian subgenotypes F1b and F4. Arch Virol 2019; 164:2297-2307. [PMID: 31267215 DOI: 10.1007/s00705-019-04332-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 05/31/2019] [Indexed: 02/06/2023]
Abstract
The influence of the high genetic variability of hepatitis B virus (HBV) on the sensitivity of serological assays has received little attention so far. A major source of variability is related to viral genotypes and subgenotypes. Their possible influence on diagnosis and prophylaxis is poorly known and has mostly been evaluated for genotypes A, B, C and D. Robust data showing the detection efficiency of HBsAg from genotype F is lacking. This study examined the effect of virus-like particles containing HBsAg from genotypes A and F (particularly, F1b and F4) produced in Pichia pastoris in relation to the anti-HBs antibodies used in the immunoassays for in vitro diagnosis and compared it with that exerted by the G145R S-escape mutant. The results showed that HBsAg detection rates for subgenotypes F1b and F4 differed significantly from those obtained for genotype A and that subgenotype F1b had a major impact on the sensitivity of the immunoassays tested. Prediction of the tertiary structure of subgenotypes F1b and F4 revealed changes inside and outside the major hydrophilic region (aa 101-160) of the HBsAg compared to genotype A and the G145R variant. A phosphorylation site (target for protein kinase C) produced by the G145R substitution might prevent recognition by anti-HBs antibodies. In conclusion, the use of different genotypes or variants for diagnosis could improve the rate of detection of HBV infection. The incorporation of a genotype-F-derived HBsAg vaccine in areas where this genotype is endemic should be evaluated, since this might also affect vaccination efficacy.
Collapse
Affiliation(s)
- María J Limeres
- CONICET, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Evangelina R Gomez
- Instituto de Agrobiotecnología y Biología Molecular, INTA-CONICET, Buenos Aires, Argentina
| | - Diego G Noseda
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín (UNSAM)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Carolina S Cerrudo
- Departamento de Ciencia y Tecnología, Laboratorio de Ingeniería Genética y Biología Celular y Molecular, Área Virosis de Insectos (LIGBCM-AVI), Instituto de Microbiología Básica y Aplicada (IMBA), Universidad Nacional de Quilmes, Bernal, Provincia de Buenos Aires, Argentina
| | - Pablo D Ghiringhelli
- Departamento de Ciencia y Tecnología, Laboratorio de Ingeniería Genética y Biología Celular y Molecular, Área Virosis de Insectos (LIGBCM-AVI), Instituto de Microbiología Básica y Aplicada (IMBA), Universidad Nacional de Quilmes, Bernal, Provincia de Buenos Aires, Argentina
| | - Alejandro D Nusblat
- Facultad de Farmacia y Bioquímica, Instituto de Nanobiotecnología (NANOBIOTEC), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - María L Cuestas
- CONICET, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM), Universidad de Buenos Aires, Buenos Aires, Argentina.
| |
Collapse
|
85
|
Wheeler S, Haberkant P, Bhardwaj M, Tongue P, Ferraz MJ, Halter D, Sprong H, Schmid R, Aerts JM, Sullo N, Sillence DJ. Cytosolic glucosylceramide regulates endolysosomal function in Niemann-Pick type C disease. Neurobiol Dis 2019; 127:242-252. [DOI: 10.1016/j.nbd.2019.03.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 03/06/2019] [Accepted: 03/09/2019] [Indexed: 12/22/2022] Open
|
86
|
Schott-Verdugo S, Müller L, Classen E, Gohlke H, Groth G. Structural Model of the ETR1 Ethylene Receptor Transmembrane Sensor Domain. Sci Rep 2019; 9:8869. [PMID: 31222090 PMCID: PMC6586836 DOI: 10.1038/s41598-019-45189-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 06/03/2019] [Indexed: 01/14/2023] Open
Abstract
The structure, mechanism of action and copper stoichiometry of the transmembrane sensor domain of the plant ethylene receptor ETR1 and homologs have remained elusive, hampering the understanding on how the perception of the plant hormone ethylene is transformed into a downstream signal. We generated the first structural model of the transmembrane sensor domain of ETR1 by integrating ab initio structure prediction and coevolutionary information. To refine and independently validate the model, we determined protein-related copper stoichiometries on purified receptor preparations and explored the helix arrangement by tryptophan scanning mutagenesis. All-atom molecular dynamics simulations of the dimeric model reveal how ethylene can bind proximal to the copper ions in the receptor, illustrating the initial stages of the ethylene perception process.
Collapse
Affiliation(s)
- Stephan Schott-Verdugo
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Centro de Bioinformática y Simulación Molecular (CBSM), Facultad de Ingeniería, Universidad de Talca, Talca, Chile
| | - Lena Müller
- Institute of Biochemical Plant Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Elisa Classen
- Institute of Biochemical Plant Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute of Hydraulic Engineering and Water Resources Management, RWTH Aachen University, Aachen, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC) & Institute for Complex Systems - Structural Biochemistry (ICS 6), Forschungszentrum Jülich GmbH, Jülich, Germany.
- Bioeconomy Science Center, Forschungszentrum Jülich GmbH, Jülich, Germany.
| | - Georg Groth
- Institute of Biochemical Plant Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
- Bioeconomy Science Center, Forschungszentrum Jülich GmbH, Jülich, Germany.
| |
Collapse
|
87
|
In Silico Insight into the Dominant Type II Toxin–Antitoxin Systems and Clp Proteases in Listeria monocytogenes and Designation of Derived Peptides as a Novel Approach to Interfere with this System. Int J Pept Res Ther 2019. [DOI: 10.1007/s10989-019-09868-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
88
|
Palomo-Ligas L, Gutiérrez-Gutiérrez F, Ochoa-Maganda VY, Cortés-Zárate R, Charles-Niño CL, Castillo-Romero A. Identification of a novel potassium channel (GiK) as a potential drug target in Giardia lamblia: Computational descriptions of binding sites. PeerJ 2019; 7:e6430. [PMID: 30834181 PMCID: PMC6397635 DOI: 10.7717/peerj.6430] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 01/10/2019] [Indexed: 12/12/2022] Open
Abstract
Background The protozoan Giardia lamblia is the causal agent of giardiasis, one of the main diarrheal infections worldwide. Drug resistance to common antigiardial agents and incidence of treatment failures have increased in recent years. Therefore, the search for new molecular targets for drugs against Giardia infection is essential. In protozoa, ionic channels have roles in their life cycle, growth, and stress response. Thus, they are promising targets for drug design. The strategy of ligand-protein docking has demonstrated a great potential in the discovery of new targets and structure-based drug design studies. Methods In this work, we identify and characterize a new potassium channel, GiK, in the genome of Giardia lamblia. Characterization was performed in silico. Because its crystallographic structure remains unresolved, homology modeling was used to construct the three-dimensional model for the pore domain of GiK. The docking virtual screening approach was employed to determine whether GiK is a good target for potassium channel blockers. Results The GiK sequence showed 24–50% identity and 50–90% positivity with 21 different types of potassium channels. The quality assessment and validation parameters indicated the reliability of the modeled structure of GiK. We identified 110 potassium channel blockers exhibiting high affinity toward GiK. A total of 39 of these drugs bind in three specific regions. Discussion The GiK pore signature sequence is related to the small conductance calcium-activated potassium channels (SKCa). The predicted binding of 110 potassium blockers to GiK makes this protein an attractive target for biological testing to evaluate its role in the life cycle of Giardia lamblia and potential candidate for the design of novel antigiardial drugs.
Collapse
Affiliation(s)
- Lissethe Palomo-Ligas
- Departamento de Fisiología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Filiberto Gutiérrez-Gutiérrez
- Departamento de Química, Centro Universitario de Ciencias Exactas e Ingenierías, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Verónica Yadira Ochoa-Maganda
- Departamento de Fisiología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Rafael Cortés-Zárate
- Departamento de Microbiología y Patología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Claudia Lisette Charles-Niño
- Departamento de Microbiología y Patología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Araceli Castillo-Romero
- Departamento de Microbiología y Patología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| |
Collapse
|
89
|
In silico prediction of prolactin molecules as a tool for equine genomics reproduction. Mol Divers 2019; 23:1019-1028. [PMID: 30740642 DOI: 10.1007/s11030-018-09914-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 12/31/2018] [Indexed: 10/27/2022]
Abstract
The prolactin hormone is involved in several biological functions, although its main role resides on reproduction. As it interferes on fertility changes, studies focused on human health have established a linkage of this hormone to fertility losses. Regarding animal research, there is still a lack of information about the structure of prolactin. In case of horse breeding, prolactin has a particular influence; once there is an individualization of these animals and equines are known for presenting several reproductive disorders. As there is no molecular structure available for the prolactin hormone and receptor, we performed several bioinformatics analyses through prediction and refinement softwares, as well as manual modifications. Aiming to elucidate the first computational structure of both molecules and analyse structural and functional aspects related to these proteins, here we provide the first known equine model for prolactin and prolactin receptor, which obtained high global quality scores in diverse software's for quality assessment. QMEAN overall score obtained for ePrl was (- 4.09) and QMEANbrane for ePrlr was (- 8.45), which proves the structures' reliability. This study will implement another tool in equine genomics in order to give light to interactions of these molecules, structural and functional alterations and therefore help diagnosing fertility problems, contributing in the selection of a high genetic herd.
Collapse
|
90
|
Wheeler S, Schmid R, Sillence DJ. Lipid⁻Protein Interactions in Niemann⁻Pick Type C Disease: Insights from Molecular Modeling. Int J Mol Sci 2019; 20:E717. [PMID: 30736449 PMCID: PMC6387118 DOI: 10.3390/ijms20030717] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 01/31/2019] [Accepted: 02/03/2019] [Indexed: 12/19/2022] Open
Abstract
The accumulation of lipids in the late endosomes and lysosomes of Niemann⁻Pick type C disease (NPCD) cells is a consequence of the dysfunction of one protein (usually NPC1) but induces dysfunction in many proteins. We used molecular docking to propose (a) that NPC1 exports not just cholesterol, but also sphingosine, (b) that the cholesterol sensitivity of big potassium channel (BK) can be traced to a previously unappreciated site on the channel's voltage sensor, (c) that transient receptor potential mucolipin 1 (TRPML1) inhibition by sphingomyelin is likely an indirect effect, and (d) that phosphoinositides are responsible for both the mislocalization of annexin A2 (AnxA2) and a soluble NSF (N-ethylmaleimide Sensitive Fusion) protein attachment receptor (SNARE) recycling defect. These results are set in the context of existing knowledge of NPCD to sketch an account of the endolysosomal pathology key to this disease.
Collapse
Affiliation(s)
- Simon Wheeler
- School of Pharmacy, De Montfort University, The Gateway, Leicester LE1 9BH, UK.
| | - Ralf Schmid
- Leicester Institute of Structural and Chemical Biology, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester LE1 7RH, UK.
| | - Dan J Sillence
- School of Pharmacy, De Montfort University, The Gateway, Leicester LE1 9BH, UK.
| |
Collapse
|
91
|
Dobrijevic D, Benhamou L, Aliev AE, Méndez-Sánchez D, Dawson N, Baud D, Tappertzhofen N, Moody TS, Orengo CA, Hailes HC, Ward JM. Metagenomic ene-reductases for the bioreduction of sterically challenging enones. RSC Adv 2019; 9:36608-36614. [PMID: 35539044 PMCID: PMC9075147 DOI: 10.1039/c9ra06088j] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 11/02/2019] [Indexed: 11/21/2022] Open
Abstract
Ene-reductases (ERs) of the Old Yellow Enzyme family catalyse asymmetric reduction of activated alkenes providing chiral products. They have become an important method in the synthetic chemists' toolbox offering a sustainable alternative to metal-catalysed asymmetric reduction. Development of new biocatalytic alkene reduction routes, however needs easy access to novel biocatalysts. A sequence-based functional metagenomic approach was used to identify novel ERs from a drain metagenome. From the ten putative ER enzymes initially identified, eight exhibited activities towards widely accepted mono-cyclic substrates with several of the ERs giving high reaction yields and stereoselectivities. Two highly performing enzymes that displayed excellent co-solvent tolerance were used for the stereoselective reduction of sterically challenging bicyclic enones where the reactions proceeded in high yields, which is unprecedented to date with wild-type ERs. On a preparative enzymatic scale, reductions of Hajos–Parish, Wieland–Miescher derivatives and a tricyclic ketone proceeded with good to excellent yields. Exceptional organic solvent tolerant ene-reductases mined from a drain metagenome library are highly versatile catalysts for difficult enones.![]()
Collapse
Affiliation(s)
- Dragana Dobrijevic
- Department of Biochemical Engineering
- University College London
- London WC1H 6BT
- UK
| | - Laure Benhamou
- Department of Chemistry
- University College London
- London
- UK
| | - Abil E. Aliev
- Department of Chemistry
- University College London
- London
- UK
| | | | - Natalie Dawson
- Structural and Molecular Biology
- University College London
- London
- UK
| | - Damien Baud
- Department of Chemistry
- University College London
- London
- UK
| | | | - Thomas S. Moody
- Almac
- Department of Biocatalysis & Isotope Chemistry
- Craigavon
- UK
| | | | | | - John M. Ward
- Department of Biochemical Engineering
- University College London
- London WC1H 6BT
- UK
| |
Collapse
|
92
|
FK506 Resistance of Saccharomyces cerevisiae Pdr5 and Candida albicans Cdr1 Involves Mutations in the Transmembrane Domains and Extracellular Loops. Antimicrob Agents Chemother 2018; 63:AAC.01146-18. [PMID: 30348662 DOI: 10.1128/aac.01146-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 10/10/2018] [Indexed: 12/14/2022] Open
Abstract
The 23-membered-ring macrolide tacrolimus, a commonly used immunosuppressant, also known as FK506, is a broad-spectrum inhibitor and an efflux pump substrate of pleiotropic drug resistance (PDR) ATP-binding cassette (ABC) transporters. Little, however, is known about the molecular mechanism by which FK506 inhibits PDR transporter drug efflux. Thus, to obtain further insights we searched for FK506-resistant mutants of Saccharomyces cerevisiae cells overexpressing either the endogenous multidrug efflux pump Pdr5 or its Candida albicans orthologue, Cdr1. A simple but powerful screen gave 69 FK506-resistant mutants with, between them, 72 mutations in either Pdr5 or Cdr1. Twenty mutations were in just three Pdr5/Cdr1 equivalent amino acid positions, T550/T540 and T552/S542 of extracellular loop 1 (EL1) and A723/A713 of EL3. Sixty of the 72 mutations were either in the ELs or the extracellular halves of individual transmembrane spans (TMSs), while 11 mutations were found near the center of individual TMSs, mostly in predicted TMS-TMS contact points, and only two mutations were in the cytosolic nucleotide-binding domains of Pdr5. We propose that FK506 inhibits Pdr5 and Cdr1 drug efflux by slowing transporter opening and/or substrate release, and that FK506 resistance of Pdr5/Cdr1 drug efflux is achieved by modifying critical intramolecular contact points that, when mutated, enable the cotransport of FK506 with other pump substrates. This may also explain why the 35 Cdr1 mutations that caused FK506 insensitivity of fluconazole efflux differed from the 13 Cdr1 mutations that caused FK506 insensitivity of cycloheximide efflux.
Collapse
|
93
|
Triantaphyllopoulos KA, Baltoumas FA, Hamodrakas SJ. Structural characterization and molecular dynamics simulations of the caprine and bovine solute carrier family 11 A1 (SLC11A1). J Comput Aided Mol Des 2018; 33:265-285. [PMID: 30543052 DOI: 10.1007/s10822-018-0179-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 12/03/2018] [Indexed: 12/22/2022]
Abstract
Natural Resistance-Associated Macrophage Proteins are a family of transmembrane divalent metal ion transporters, with important implications in life of both bacteria and mammals. Among them, the Solute Carrier family 11 member A1 (SLC11A1) has been implicated with susceptibility to infection by Mycobacterium avium subspecies paratuberculosis (MAP), potentially causing Crohn's disease in humans and paratuberculosis (PTB) in ruminants. Our previous research had focused on sequencing the mRNA of the caprine slc11a1 gene and pinpointed polymorphisms that contribute to caprine SLC11A1's susceptibility to infection by MAP in PTB. Despite its importance, little is known on the structural/dynamic features of mammalian SLC11A1 that may influence its function under normal or pathological conditions at the protein level. In this work we studied the structural architecture of SLC11A1 in Capra hircus and Bos taurus through molecular modeling, molecular dynamics simulations in different, functionally relevant configurations, free energy calculations of protein-metal interactions and sequence conservation analysis. The results of this study propose a three dimensional structure for SLC11A1 with conserved sequence and structural features and provide hints for a potential mechanism through which divalent metal ion transport is conducted. Given the importance of SLC11A1 in susceptibility to PTB, this study provides a framework for further studies on the structure and dynamics of SLC11A1 in other organisms, to gain 3D structural insight into the macromolecular arrangements of SLC11A1 but also suggesting a potential mechanism which divalent metal ion transport is conducted.
Collapse
Affiliation(s)
- Kostas A Triantaphyllopoulos
- Department of Animal Breeding and Husbandry, Faculty of Animal Science and Aquaculture, School of Agricultural Production, Infrastructure and Environment, Agricultural University of Athens, 75 Iera Odos St., 11855, Athens, Greece.
| | - Fotis A Baltoumas
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, Panepistimiopolis, 15701, Athens, Greece
| | - Stavros J Hamodrakas
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, Panepistimiopolis, 15701, Athens, Greece
| |
Collapse
|
94
|
Cardona SM, Kim SV, Church KA, Torres VO, Cleary IA, Mendiola AS, Saville SP, Watowich SS, Parker-Thornburg J, Soto-Ospina A, Araque P, Ransohoff RM, Cardona AE. Role of the Fractalkine Receptor in CNS Autoimmune Inflammation: New Approach Utilizing a Mouse Model Expressing the Human CX3CR1 I249/M280 Variant. Front Cell Neurosci 2018; 12:365. [PMID: 30386211 PMCID: PMC6199958 DOI: 10.3389/fncel.2018.00365] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 09/26/2018] [Indexed: 12/21/2022] Open
Abstract
Multiple sclerosis (MS), an inflammatory demyelinating disease of the central nervous system (CNS) is the leading cause of non-traumatic neurological disability in young adults. Immune mediated destruction of myelin and oligodendrocytes is considered the primary pathology of MS, but progressive axonal loss is the major cause of neurological disability. In an effort to understand microglia function during CNS inflammation, our laboratory focuses on the fractalkine/CX3CR1 signaling as a regulator of microglia neurotoxicity in various models of neurodegeneration. Fractalkine (FKN) is a transmembrane chemokine expressed in the CNS by neurons and signals through its unique receptor CX3CR1 present in microglia. During experimental autoimmune encephalomyelitis (EAE), CX3CR1 deficiency confers exacerbated disease defined by severe inflammation and neuronal loss. The CX3CR1 human polymorphism I249/M280 present in ∼20% of the population exhibits reduced adhesion for FKN conferring defective signaling whose role in microglia function and influence on neurons during MS remains unsolved. The aim of this study is to assess the effect of weaker signaling through hCX3CR1I249/M280 during EAE. We hypothesize that dysregulated microglial responses due to impaired CX3CR1 signaling enhance neuronal/axonal damage. We generated an animal model replacing the mouse CX3CR1 locus for the hCX3CR1I249/M280 variant. Upon EAE induction, these mice exhibited exacerbated EAE correlating with severe inflammation and neuronal loss. We also observed that mice with aberrant CX3CR1 signaling are unable to produce FKN and ciliary neurotrophic factor during EAE in contrast to wild type mice. Our results provide validation of defective function of the hCX3CR1I249/M280 variant and the foundation to broaden the understanding of microglia dysfunction during neuroinflammation.
Collapse
Affiliation(s)
- Sandra M Cardona
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States.,South Texas Center for Emerging Infectious Diseases, The University of Texas at San Antonio, San Antonio, TX, United States
| | - Sangwon V Kim
- Department of Microbiology and Immunology, Sidney Kimmel Medical College of Thomas Jefferson University, Philadelphia, PA, United States
| | - Kaira A Church
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States
| | - Vanessa O Torres
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Ian A Cleary
- Department of Biomedical Sciences, Grand Valley State University, Allendale, MI, United States
| | - Andrew S Mendiola
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States.,Gladstone Institute of Neurological Disease, San Francisco, CA, United States
| | - Stephen P Saville
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States.,South Texas Center for Emerging Infectious Diseases, The University of Texas at San Antonio, San Antonio, TX, United States
| | - Stephanie S Watowich
- Department of Immunology, Center for Inflammation and Cancer, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Jan Parker-Thornburg
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Alejandro Soto-Ospina
- Basic Sciences Department, Research and Innovation in Chemical Formulations, University EIA, Envigado, Colombia
| | - Pedronel Araque
- Basic Sciences Department, Research and Innovation in Chemical Formulations, University EIA, Envigado, Colombia
| | | | - Astrid E Cardona
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States.,South Texas Center for Emerging Infectious Diseases, The University of Texas at San Antonio, San Antonio, TX, United States
| |
Collapse
|
95
|
Kirsch SA, Kugemann A, Carpaneto A, Böckmann RA, Dietrich P. Phosphatidylinositol-3,5-bisphosphate lipid-binding-induced activation of the human two-pore channel 2. Cell Mol Life Sci 2018; 75:3803-3815. [PMID: 29705952 PMCID: PMC11105763 DOI: 10.1007/s00018-018-2829-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/29/2018] [Accepted: 04/23/2018] [Indexed: 11/24/2022]
Abstract
Mammalian two-pore channels (TPCs) are activated by the low-abundance membrane lipid phosphatidyl-(3,5)-bisphosphate (PI(3,5)P2) present in the endo-lysosomal system. Malfunction of human TPC1 or TPC2 (hTPC) results in severe organellar storage diseases and membrane trafficking defects. Here, we compared the lipid-binding characteristics of hTPC2 and of the PI(3,5)P2-insensitive TPC1 from the model plant Arabidopsis thaliana. Combination of simulations with functional analysis of channel mutants revealed the presence of an hTPC2-specific lipid-binding pocket mutually formed by two channel regions exposed to the cytosolic side of the membrane. We showed that PI(3,5)P2 is simultaneously stabilized by positively charged amino acids (K203, K204, and K207) in the linker between transmembrane helices S4 and S5 and by S322 in the cytosolic extension of S6. We suggest that PI(3,5)P2 cross links two parts of the channel, enabling their coordinated movement during channel gating.
Collapse
Affiliation(s)
- Sonja A Kirsch
- Computational Biology, Department of Biology, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Andreas Kugemann
- Molecular Plant Physiology, Department of Biology, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Armando Carpaneto
- Institute of Biophysics, National Research Council, Genoa, Italy
- Department of Earth, Environment and Life Sciences-DISTAV, University of Genoa, Genoa, Italy
| | - Rainer A Böckmann
- Computational Biology, Department of Biology, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany.
| | - Petra Dietrich
- Molecular Plant Physiology, Department of Biology, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany.
| |
Collapse
|
96
|
Salimi F, Forouzandeh Moghadam M, Rajabibazl M. Development of a novel anti-HER2 scFv by ribosome display and in silico evaluation of its 3D structure and interaction with HER2, alone and after fusion to LAMP2B. Mol Biol Rep 2018; 45:2247-2256. [DOI: 10.1007/s11033-018-4386-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 09/12/2018] [Indexed: 12/31/2022]
|
97
|
Zeng J, Guareschi R, Damre M, Cao R, Kless A, Neumaier B, Bauer A, Giorgetti A, Carloni P, Rossetti G. Structural Prediction of the Dimeric Form of the Mammalian Translocator Membrane Protein TSPO: A Key Target for Brain Diagnostics. Int J Mol Sci 2018; 19:E2588. [PMID: 30200318 PMCID: PMC6165245 DOI: 10.3390/ijms19092588] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 08/21/2018] [Accepted: 08/28/2018] [Indexed: 11/17/2022] Open
Abstract
Positron emission tomography (PET) radioligands targeting the human translocator membrane protein (TSPO) are broadly used for the investigations of neuroinflammatory conditions associated with neurological disorders. Structural information on the mammalian protein homodimers-the suggested functional state of the protein-is limited to a solid-state nuclear magnetic resonance (NMR) study and to a model based on the previously-deposited solution NMR structure of the monomeric mouse protein. Computational studies performed here suggest that the NMR-solved structure in the presence of detergents is not prone to dimer formation and is furthermore unstable in its native membrane environment. We, therefore, propose a new model of the functionally-relevant dimeric form of the mouse protein, based on a prokaryotic homologue. The model, fully consistent with solid-state NMR data, is very different from the previous predictions. Hence, it provides, for the first time, structural insights into this pharmaceutically-important target which are fully consistent with experimental data.
Collapse
Affiliation(s)
- Juan Zeng
- Institute for Advanced Simulations (IAS)-5/Institute for Neuroscience and Medicine (INM)-9, Forschungszentrum Jülich, 52428 Jülich, Germany.
- Laboratory of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, 518055 Shenzhen, China.
| | - Riccardo Guareschi
- Institute for Advanced Simulations (IAS)-5/Institute for Neuroscience and Medicine (INM)-9, Forschungszentrum Jülich, 52428 Jülich, Germany.
| | - Mangesh Damre
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy.
- Neurobiology, International School for Advanced Studies (SISSA), 34136 Trieste, Italy.
| | - Ruyin Cao
- Institute for Advanced Simulations (IAS)-5/Institute for Neuroscience and Medicine (INM)-9, Forschungszentrum Jülich, 52428 Jülich, Germany.
| | - Achim Kless
- Grünenthal Innovation, Translational Science & Intelligence, Grünenthal GmbH, 52078 Aachen, Germany.
| | - Bernd Neumaier
- Institute for Neuroscience and Medicine (INM)-5, Forschungszentrum Jülich, 52428 Jülich, Germany.
| | - Andreas Bauer
- Institute for Neuroscience and Medicine (INM)-2, Forschungszentrum Jülich, 52428 Jülich, Germany.
| | - Alejandro Giorgetti
- Institute for Advanced Simulations (IAS)-5/Institute for Neuroscience and Medicine (INM)-9, Forschungszentrum Jülich, 52428 Jülich, Germany.
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy.
| | - Paolo Carloni
- Institute for Advanced Simulations (IAS)-5/Institute for Neuroscience and Medicine (INM)-9, Forschungszentrum Jülich, 52428 Jülich, Germany.
- RWTH Aachen University, Department of Physics, 52078 Aachen, Germany.
| | - Giulia Rossetti
- Institute for Advanced Simulations (IAS)-5/Institute for Neuroscience and Medicine (INM)-9, Forschungszentrum Jülich, 52428 Jülich, Germany.
- Jülich Supercomputing Center (JSC), Forschungszentrum Jülich, 52428 Jülich, Germany.
- University Hospital Aachen, RWTH Aachen University, 52078 Aachen, Germany.
| |
Collapse
|
98
|
Zimmermann MT, Urrutia R, Cousin MA, Oliver GR, Klee EW. Assessing Human Genetic Variations in Glucose Transporter SLC2A10 and Their Role in Altering Structural and Functional Properties. Front Genet 2018; 9:276. [PMID: 30090112 PMCID: PMC6068234 DOI: 10.3389/fgene.2018.00276] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 07/05/2018] [Indexed: 11/13/2022] Open
Abstract
Purpose: Demand is increasing for clinical genomic sequencing to provide diagnoses for patients presenting phenotypes indicative of genetic diseases, but for whom routine genetic testing failed to yield a diagnosis. DNA-based testing using high-throughput technologies often identifies variants with insufficient evidence to determine whether they are disease-causal or benign, leading to categorization as variants of uncertain significance (VUS). Methods: We used molecular modeling and simulation to generate specific hypotheses for the molecular effects of variants in the human glucose transporter, GLUT10 (SLC2A10). Similar to many disease-relevant membrane proteins, no experimentally derived 3D structure exists. An atomic model was generated and used to evaluate multiple variants, including pathogenic, benign, and VUS. Results: These analyses yielded detailed mechanistic data, not currently predictable from sequence, including altered protein stability, charge distribution of ligand binding surfaces, and shifts toward or away from transport-competent conformations. Consideration of the two major conformations of GLUT10 was important as variants have conformation-specific effects. We generated detailed molecular hypotheses for the functional impact of variants in GLUT10 and propose means to determine their pathogenicity. Conclusion: The type of workflow we present here is valuable for increasing the throughput and resolution with which VUS effects can be assessed and interpreted.
Collapse
Affiliation(s)
- Michael T Zimmermann
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, United States.,Bioinformatics Research and Development Laboratory, Genomics Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Raul Urrutia
- Bioinformatics Research and Development Laboratory, Genomics Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, United States.,Laboratory of Epigenetics and Chromatin Dynamics, Department of Biochemistry and Molecular Biology, Epigenomics Translational Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States
| | - Margot A Cousin
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States
| | - Gavin R Oliver
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, United States.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States
| | - Eric W Klee
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, United States.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States
| |
Collapse
|
99
|
Palestro PH, Enrique N, Goicoechea S, Villalba ML, Sabatier LL, Martin P, Milesi V, Bruno Blanch LE, Gavernet L. Searching for New Leads To Treat Epilepsy: Target-Based Virtual Screening for the Discovery of Anticonvulsant Agents. J Chem Inf Model 2018; 58:1331-1342. [PMID: 29870230 DOI: 10.1021/acs.jcim.7b00721] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The purpose of this investigation is to contribute to the development of new anticonvulsant drugs to treat patients with refractory epilepsy. We applied a virtual screening protocol that involved the search into molecular databases of new compounds and known drugs to find small molecules that interact with the open conformation of the Nav1.2 pore. As the 3D structure of human Nav1.2 is not available, we first assembled 3D models of the target, in closed and open conformations. After the virtual screening, the resulting candidates were submitted to a second virtual filter, to find compounds with better chances of being effective for the treatment of P-glycoprotein (P-gp) mediated resistant epilepsy. Again, we built a model of the 3D structure of human P-gp, and we validated the docking methodology selected to propose the best candidates, which were experimentally tested on Nav1.2 channels by patch clamp techniques and in vivo by the maximal electroshock seizure (MES) test. Patch clamp studies allowed us to corroborate that our candidates, drugs used for the treatment of other pathologies like Ciprofloxacin, Losartan, and Valsartan, exhibit inhibitory effects on Nav1.2 channel activity. Additionally, a compound synthesized in our lab, N, N'-diphenethylsulfamide, interacts with the target and also triggers significant Na1.2 channel inhibitory action. Finally, in vivo studies confirmed the anticonvulsant action of Valsartan, Ciprofloxacin, and N, N'-diphenethylsulfamide.
Collapse
Affiliation(s)
- Pablo H Palestro
- Medicinal Chemistry, Department of Biological Sciences, Faculty of Exact Sciences , National University of La Plata , 47 and 115 , La Plata , Buenos Aires B1900BJW , Argentina
| | - Nicolas Enrique
- Instituto de Estudios Inmunológicos y Fisiopatológicos (IIFP, CONICET-Universidad Nacional de la Plata), Fac. de Ciencias Exactas , Universidad Nacional de La Plata , La Plata , Buenos Aires B1900BJW , Argentina
| | - Sofia Goicoechea
- Medicinal Chemistry, Department of Biological Sciences, Faculty of Exact Sciences , National University of La Plata , 47 and 115 , La Plata , Buenos Aires B1900BJW , Argentina
| | - Maria L Villalba
- Medicinal Chemistry, Department of Biological Sciences, Faculty of Exact Sciences , National University of La Plata , 47 and 115 , La Plata , Buenos Aires B1900BJW , Argentina
| | - Laureano L Sabatier
- Medicinal Chemistry, Department of Biological Sciences, Faculty of Exact Sciences , National University of La Plata , 47 and 115 , La Plata , Buenos Aires B1900BJW , Argentina
| | - Pedro Martin
- Instituto de Estudios Inmunológicos y Fisiopatológicos (IIFP, CONICET-Universidad Nacional de la Plata), Fac. de Ciencias Exactas , Universidad Nacional de La Plata , La Plata , Buenos Aires B1900BJW , Argentina
| | - Veronica Milesi
- Instituto de Estudios Inmunológicos y Fisiopatológicos (IIFP, CONICET-Universidad Nacional de la Plata), Fac. de Ciencias Exactas , Universidad Nacional de La Plata , La Plata , Buenos Aires B1900BJW , Argentina
| | - Luis E Bruno Blanch
- Medicinal Chemistry, Department of Biological Sciences, Faculty of Exact Sciences , National University of La Plata , 47 and 115 , La Plata , Buenos Aires B1900BJW , Argentina
| | - Luciana Gavernet
- Medicinal Chemistry, Department of Biological Sciences, Faculty of Exact Sciences , National University of La Plata , 47 and 115 , La Plata , Buenos Aires B1900BJW , Argentina
| |
Collapse
|
100
|
Jayaraman K, Morley AN, Szöllősi D, Wassenaar TA, Sitte HH, Stockner T. Dopamine transporter oligomerization involves the scaffold domain, but spares the bundle domain. PLoS Comput Biol 2018; 14:e1006229. [PMID: 29874235 PMCID: PMC6005636 DOI: 10.1371/journal.pcbi.1006229] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 06/18/2018] [Accepted: 05/24/2018] [Indexed: 12/11/2022] Open
Abstract
The human dopamine transporter (hDAT) is located on presynaptic neurons, where it plays an essential role in limiting dopaminergic signaling by temporarily curtailing high neurotransmitter concentration through rapid re-uptake. Transport by hDAT is energized by transmembrane ionic gradients. Dysfunction of this transporter leads to disease states, such as Parkinson’s disease, bipolar disorder or depression. It has been shown that hDAT and other members of the monoamine transporter family exist in oligomeric forms at the plasma membrane. Several residues are known to be involved in oligomerization, but interaction interfaces, oligomer orientation and the quarternary arrangement in the plasma membrane remain poorly understood. Here we examine oligomeric forms of hDAT using a direct approach, by following dimerization of two randomly-oriented hDAT transporters in 512 independent simulations, each being 2 μs in length. We employed the DAFT (docking assay for transmembrane components) approach, which is an unbiased molecular dynamics simulation method to identify oligomers, their conformations and populations. The overall ensemble of a total of >1 ms simulation time revealed a limited number of symmetric and asymmetric dimers. The identified dimer interfaces include all residues known to be involved in dimerization. Importantly, we find that the surface of the bundle domain is largely excluded from engaging in dimeric interfaces. Such an interaction would typically lead to inhibition by stabilization of one conformation, while substrate transport relies on a large scale rotation between the inward-facing and the outward-facing state. The human dopamine transporter efficiently removes the neurotransmitter dopamine from the synaptic cleft. Alteration of dopamine transporter function is associated with several neurological diseases, including mood disorders or attention-deficit hyperactivity disorder, but is also a major player in addiction and drug abuse. Functional studies have revealed that not only is transporter oligomerization involved in surface expression and endocytosis, but, more importantly, in reverse transport (efflux) of dopamine that is triggered by amphetamine-like drugs of abuse. Structural knowledge of transporter oligomerization is largely missing. We performed a large scale comprehensive computational study on transporter oligomerization to reveal dimer geometries and the residues involved in the interfaces. The dimer conformations we find in our dataset are fully consistent with all available experimental data in the literature, but also show novel interfaces. We further verified all dimer geometries by free energy calculations. Our results identified an unpredicted—but for the mechanism of substrate transport essential—property: the bundle domain, which moves during the transport cycle, is excluded from contributing to dimer interfaces, thereby allowing for unrestrained movements necessary to translocate substrates through the membrane.
Collapse
Affiliation(s)
- Kumaresan Jayaraman
- Medical University of Vienna Center for Physiology and Pharmacology, Institute of Pharmacology, Vienna, Austria
| | - Alex N. Morley
- Medical University of Vienna Center for Physiology and Pharmacology, Institute of Pharmacology, Vienna, Austria
| | - Daniel Szöllősi
- Medical University of Vienna Center for Physiology and Pharmacology, Institute of Pharmacology, Vienna, Austria
| | - Tsjerk A. Wassenaar
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Harald H. Sitte
- Medical University of Vienna Center for Physiology and Pharmacology, Institute of Pharmacology, Vienna, Austria
| | - Thomas Stockner
- Medical University of Vienna Center for Physiology and Pharmacology, Institute of Pharmacology, Vienna, Austria
- * E-mail:
| |
Collapse
|