1
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Morgan D, DeMeo DL, Glass K. Using methylation data to improve transcription factor binding prediction. Epigenetics 2024; 19:2309826. [PMID: 38300850 PMCID: PMC10841018 DOI: 10.1080/15592294.2024.2309826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 01/01/2024] [Indexed: 02/03/2024] Open
Abstract
Modelling the regulatory mechanisms that determine cell fate, response to external perturbation, and disease state depends on measuring many factors, a task made more difficult by the plasticity of the epigenome. Scanning the genome for the sequence patterns defined by Position Weight Matrices (PWM) can be used to estimate transcription factor (TF) binding locations. However, this approach does not incorporate information regarding the epigenetic context necessary for TF binding. CpG methylation is an epigenetic mark influenced by environmental factors that is commonly assayed in human cohort studies. We developed a framework to score inferred TF binding locations using methylation data. We intersected motif locations identified using PWMs with methylation information captured in both whole-genome bisulfite sequencing and Illumina EPIC array data for six cell lines, scored motif locations based on these data, and compared with experimental data characterizing TF binding (ChIP-seq). We found that for most TFs, binding prediction improves using methylation-based scoring compared to standard PWM-scores. We also illustrate that our approach can be generalized to infer TF binding when methylation information is only proximally available, i.e. measured for nearby CpGs that do not directly overlap with a motif location. Overall, our approach provides a framework for inferring context-specific TF binding using methylation data. Importantly, the availability of DNA methylation data in existing patient populations provides an opportunity to use our approach to understand the impact of methylation on gene regulatory processes in the context of human disease.
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Affiliation(s)
- Daniel Morgan
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Dawn L. DeMeo
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Kimberly Glass
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biostatistics, Harvard Chan School of Public Health, Boston, MA, USA
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2
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Liu Z, Lu L, Jiang S. Receptor-binding domain-associated serotypes of SARS-CoV-2. Emerg Microbes Infect 2024; 13:2309968. [PMID: 38264798 PMCID: PMC10866045 DOI: 10.1080/22221751.2024.2309968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 01/19/2024] [Indexed: 01/25/2024]
Affiliation(s)
- Zezhong Liu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, School of Pharmacy, Shanghai Medical College, Fudan University, Shanghai, People’s Republic of China
| | - Lu Lu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, School of Pharmacy, Shanghai Medical College, Fudan University, Shanghai, People’s Republic of China
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, School of Pharmacy, Shanghai Medical College, Fudan University, Shanghai, People’s Republic of China
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3
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Yu Y, Fan C, Qi J, Zhao X, Yang H, Ye G, Zhang M, Liu D. Effect of ultrasound treatment on porcine myofibrillar protein binding furan flavor compounds at different salt concentrations. Food Chem 2024; 443:138427. [PMID: 38277938 DOI: 10.1016/j.foodchem.2024.138427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/05/2023] [Accepted: 01/10/2024] [Indexed: 01/28/2024]
Abstract
The effects of ultrasound (500 W) on the interaction of porcine myofibrillar protein (MP) with furan flavor compounds at different salt concentrations (0.6 %, 1.2 % and 2.4 %) were investigated. With the increase of salt concentration, the particle size of MP decreased, and the surface hydrophobicity and active sulfhydryl content increased due to the unfolding and depolymerization of MP. At the same time, ultrasound promoted the exposure of hydrophobic binding sites and hydrogen bonding sites of MP in different salt concentration systems, thus improving the binding ability of MP with furan compounds by 2 % to 22 %, among which MP had the strongest binding capacity of 2-pentylfuran. In conclusion, ultrasound could effectively promote the unfolding of the secondary structure of MP, which was beneficial to the combination of MP and furan flavor compounds under different salt concentrations.
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Affiliation(s)
- Ying Yu
- College of Food Science and Technology, Bohai University, Jinzhou 121013, China
| | - Chaoxia Fan
- College of Food Science and Technology, Bohai University, Jinzhou 121013, China
| | - Jun Qi
- Anhui Engineering Laboratory for Agro-products Processing, College of Tea & Food Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Xiaocao Zhao
- College of Food Science and Technology, Bohai University, Jinzhou 121013, China
| | - Hui Yang
- College of Food Science and Technology, Bohai University, Jinzhou 121013, China
| | - Guoqing Ye
- College of Food Science and Technology, Bohai University, Jinzhou 121013, China
| | - Mingcheng Zhang
- College of Food Science and Technology, Bohai University, Jinzhou 121013, China
| | - Dengyong Liu
- College of Food Science and Technology, Bohai University, Jinzhou 121013, China.
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4
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Hu ZY, Sui HY, Zhong QF, Hu L, Shi JH, Jiang SL, Han L. In vitro investigation of the binding characteristics of dacomitinib to human α 1-acid glycoprotein: Multispectral and computational modeling. Spectrochim Acta A Mol Biomol Spectrosc 2024; 314:124197. [PMID: 38554689 DOI: 10.1016/j.saa.2024.124197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 03/10/2024] [Accepted: 03/26/2024] [Indexed: 04/02/2024]
Abstract
Dacomitinib is a highly selective second-generation tyrosine kinase inhibitor that can irreversibly bind to tyrosine kinase and is mainly used in the treatment of lung cancer. The binding characteristics of dacomitinib with human α 1-acid glycoprotein (HAG) were analyzed by multispectral and computational simulation techniques. The fluorescence spectra showed that dacomitinib can quench the fluorescence of HAG by forming the HAG-dacomitinib complex with a molar ratio of 1:1 (static quenching). At the temperature similar to that of the human body, the affinity of dacomitinib to HAG (8.95 × 106 M-1) was much greater than that to BSA (3.39 × 104 M-1), indicating that dacomitinib will give priority to binding onto HAG. Thermodynamics parameters analysis and driving force competition experiments showed that hydrogen bonding and hydrophobic forces were the major sources for keeping the complex of HAG-dacomitinib stable. The experimental outcomes also showed that the binding of dacomitinib can lead to the loosening of the skeleton structure of HAG, which led to a slight change in the secondary structure, and also reduces the hydrophobicity of the microenvironment of Trp and Tyr residues. The binding sites of dacomitinib on HAG and the contribution of key amino acid residues to the binding reaction were determined by molecular docking and molecular dynamics (MD) simulation. In addition, it was found that there was a synergistic effect between dacomitinib and Mg2+ and Co2+ ions. Mg2+ and Co2+ could increase the Kb of dacomitinib to HAG and prolong the half-life of dacomitinib.
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Affiliation(s)
- Zhe-Ying Hu
- College of Pharmaceutic Science, Zhejiang University of Technology, Hangzhou 310032, China
| | - Huan-Yu Sui
- College of Pharmaceutic Science, Zhejiang University of Technology, Hangzhou 310032, China
| | - Qi-Feng Zhong
- College of Pharmaceutic Science, Zhejiang University of Technology, Hangzhou 310032, China
| | - Lu Hu
- College of Pharmaceutic Science, Zhejiang University of Technology, Hangzhou 310032, China
| | - Jie-Hua Shi
- College of Pharmaceutic Science, Zhejiang University of Technology, Hangzhou 310032, China
| | - Shao-Liang Jiang
- College of Pharmaceutic Science, Zhejiang University of Technology, Hangzhou 310032, China.
| | - Liang Han
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310032, China.
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5
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Duan M, Gao G, Lin A, Mackey EJ, Banfield DK, Merz AJ. SM protein Sly1 and a SNARE Habc domain promote membrane fusion through multiple mechanisms. J Cell Biol 2024; 223:e202001034. [PMID: 38478017 PMCID: PMC10943372 DOI: 10.1083/jcb.202001034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 12/20/2023] [Accepted: 02/22/2024] [Indexed: 03/17/2024] Open
Abstract
SM proteins including Sly1 are essential cofactors of SNARE-mediated membrane fusion. Using SNARE and Sly1 mutants and chemically defined in vitro assays, we separate and assess proposed mechanisms through which Sly1 augments fusion: (i) opening the closed conformation of the Qa-SNARE Sed5; (ii) close-range tethering of vesicles to target organelles, mediated by the Sly1-specific regulatory loop; and (iii) nucleation of productive trans-SNARE complexes. We show that all three mechanisms are important and operate in parallel, and that close-range tethering promotes trans-complex assembly when cis-SNARE assembly is a competing process. Further, we demonstrate that the autoinhibitory N-terminal Habc domain of Sed5 has at least two positive activities: it is needed for correct Sed5 localization, and it directly promotes Sly1-dependent fusion. "Split Sed5," with Habc presented solely as a soluble fragment, can function both in vitro and in vivo. Habc appears to facilitate events leading to lipid mixing rather than promoting opening or stability of the fusion pore.
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Affiliation(s)
- Mengtong Duan
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Guanbin Gao
- The Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Ariel Lin
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Emma J. Mackey
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - David K. Banfield
- The Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Alexey J. Merz
- Department of Biochemistry, University of Washington, Seattle, WA, USA
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Tsukamoto A, Jae Man L, Oyama K, Masuda A, Mon H, Ueda T, Kusakabe T. Effective expression and characterization of the receptor binding domains in SARS-CoV-2 Spike proteins from original strain and variants of concern using Bombyx mori nucleopolyhedrovirus in silkworm. Protein Expr Purif 2024; 218:106450. [PMID: 38395208 DOI: 10.1016/j.pep.2024.106450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 02/25/2024]
Abstract
A new coronavirus, known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is responsible for the global pandemic of COVID-19 in 2020. Through structural analysis, it was found that several amino acid residues in the human angiotensin-converting enzyme-2 (hACE2) receptor directly interact with those in the receptor binding domain (RBD) of the spike glycoprotein (S-protein). Various cell lines, including HEK293, HeLa cells, and the baculovirus expression vector system (BEVS) with the insect cell line Sf9, have been utilized to produce the RBD. In this study, we investigated the use of Bombyx mori nucleopolyhedrovirus (BmNPV) and BEVS. For efficient production of a highly pure recombinant RBD protein, we designed it with two tags (His tag and STREP tag) at the C-terminus and a solubilizing tag (SUMO) at the N-terminus. After expressing the protein using BmNPV and silkworm and purifying it with a HisTrap excel column, the eluted protein was digested with SUMO protease and further purified using a Strep-Tactin Superflow column. As a result, we obtained the RBD as a monomer with a yield of 2.6 mg/10 mL serum (equivalent to 30 silkworms). The RBD showed an affinity for the hACE2 receptor. Additionally, the RBDs from the Alpha, Beta, Gamma, Delta, and Omicron variants were expressed and purified using the same protocol. It was found that the RBD from the Alpha, Beta, Gamma, and Delta variants could be obtained with yields of 1.4-2.6 mg/10 mL serum and had an affinity to the hACE2 receptor.
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Affiliation(s)
- Akira Tsukamoto
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Lee Jae Man
- Laboratory of Creative Science for Insect Industries, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Kosuke Oyama
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Akitsu Masuda
- Laboratory of Creative Science for Insect Industries, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Hiroaki Mon
- Laboratory of Insect Genome Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Tadashi Ueda
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka, 812-8582, Japan.
| | - Takahiro Kusakabe
- Laboratory of Insect Genome Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan.
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7
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Shaffer KJ, Smith RAA, Daines AM, Luo X, Lu X, Tan TC, Le BQ, Schwörer R, Hinkley SFR, Tyler PC, Nurcombe V, Cool SM. Rational synthesis of a heparan sulfate saccharide that promotes the activity of BMP2. Carbohydr Polym 2024; 333:121979. [PMID: 38494232 DOI: 10.1016/j.carbpol.2024.121979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 03/19/2024]
Abstract
Heparan sulfate (HS) is a glycosaminoglycan (GAG) found throughout nature and is involved in a wide range of functions including modulation of cell signalling via sequestration of growth factors. Current consensus is that the specificity of HS motifs for protein binding are individual for each protein. Given the structural complexity of HS the synthesis of libraries of these compounds to probe this is not trivial. Herein we present the synthesis of an HS decamer, the design of which was undertaken rationally from previously published data for HS binding to the growth factor BMP-2. The biological activity of this HS decamer was assessed in vitro, showing that it had the ability to both bind BMP-2 and increase its thermal stability as well as enhancing the bioactivity of BMP-2 in vitro in C2C12 cells. At the same time no undesired anticoagulant effect was observed. This decamer was then analysed in vivo in a rabbit model where higher bone formation, bone mineral density (BMD) and trabecular thickness were observed over an empty defect or collagen implant alone. This indicated that the HS decamer was effective in promoting bone regeneration in vivo.
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Affiliation(s)
- Karl J Shaffer
- Ferrier Research Institute, Victoria University of Wellington, 69 Gracefield Road, Gracefield, Lower Hutt 5010, New Zealand
| | - Raymond A A Smith
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 138673, Singapore; School of Chemical Engineering, University of Queensland, Brisbane, Qld 4072, Australia
| | - Alison M Daines
- Ferrier Research Institute, Victoria University of Wellington, 69 Gracefield Road, Gracefield, Lower Hutt 5010, New Zealand.
| | - Xiaoman Luo
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 138673, Singapore
| | - Xiaohua Lu
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 138673, Singapore
| | - Tuan Chun Tan
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 138673, Singapore
| | - Bach Q Le
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 138673, Singapore
| | - Ralf Schwörer
- Ferrier Research Institute, Victoria University of Wellington, 69 Gracefield Road, Gracefield, Lower Hutt 5010, New Zealand
| | - Simon F R Hinkley
- Ferrier Research Institute, Victoria University of Wellington, 69 Gracefield Road, Gracefield, Lower Hutt 5010, New Zealand
| | - Peter C Tyler
- Ferrier Research Institute, Victoria University of Wellington, 69 Gracefield Road, Gracefield, Lower Hutt 5010, New Zealand
| | - Victor Nurcombe
- Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR), 138632, Singapore
| | - Simon M Cool
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 138673, Singapore; School of Chemical Engineering, University of Queensland, Brisbane, Qld 4072, Australia; Department of Orthopaedic Surgery, Yong Yoo Lin School of Medicine, National University of Singapore, Singapore
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8
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Kalashnyk O, Lykhmus O, Sullivan R, Komisarenko S, Skok M. Agonists or positive allosteric modulators of α7 nicotinic acetylcholine receptor prevent interaction of SARS-Cov-2 receptor-binding domain with astrocytoma cells. Biochem Biophys Res Commun 2024; 709:149825. [PMID: 38537599 DOI: 10.1016/j.bbrc.2024.149825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 03/24/2024] [Indexed: 04/13/2024]
Abstract
SARS-Cov-2, the virus causing COVID-19, penetrates host target cells via the receptor of angiotensin-converting enzyme 2 (ACE2). Disrupting the virus interaction with ACE2 affords a plausible mechanism for prevention of cell penetration and inhibiting dissemination of the virus. Our studies demonstrate that ACE2 interaction with the receptor binding domain of SARS-Cov-2 spike protein (RBD) can be impaired by modulating the α7 nicotinic acetylcholine receptor (α7 nAChR) contiguous with ACE2. U373 cells of human astrocytoma origin were shown to bind both ACE2-specific antibody and recombinant RBD in Cell-ELISA. ACE2 was found to interact with α7 nAChR in U373 cell lysates studied by Sandwich ELISA. Our studies demonstrate that inhibition of RBD binding to ACE2-expressing U373 cells were defined with α7 nAChR agonists choline and PNU282987, but not a competitive antagonist methyllicaconitine (MLA). Additionally, the type 2 positive allosteric modulator (PAM2) PNU120596 and hydroxyurea (HU) also inhibited the binding. Our studies demonstrate that activation of α7 AChRs has efficacy in inhibiting the SARS-Cov-2 interaction with the ACE2 receptor and in such a way can prevent virus target cell penetration. These studies also help to clarify the consistent efficacy and positive outcomes for utilizing HU in treating COVID-19.
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Affiliation(s)
- Olena Kalashnyk
- Palladin Institute of Biochemistry, NAS of Ukraine, 9, Leontovycha Str., 01054, Kyiv, Ukraine.
| | - Olena Lykhmus
- Palladin Institute of Biochemistry, NAS of Ukraine, 9, Leontovycha Str., 01054, Kyiv, Ukraine.
| | | | - Serhiy Komisarenko
- Palladin Institute of Biochemistry, NAS of Ukraine, 9, Leontovycha Str., 01054, Kyiv, Ukraine.
| | - Maryna Skok
- Palladin Institute of Biochemistry, NAS of Ukraine, 9, Leontovycha Str., 01054, Kyiv, Ukraine.
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9
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Yuan L, Liu T, Qi X, Zhang Y, Wang Q, Wang Q, Liu M. Multi-spectroscopic and molecular docking studies for the pH-dependent interaction of β-lactoglobulin with (-)-epicatechin gallate and/or piceatannol: Influence on antioxidant activity and stability. Spectrochim Acta A Mol Biomol Spectrosc 2024; 313:124090. [PMID: 38428163 DOI: 10.1016/j.saa.2024.124090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/03/2024]
Abstract
(-)-Epicatechin gallate (ECG) and piceatannol (PIC) are commonly polyphenols with excellent biological activities. β-Lactoglobulin (BLG) is a food-grade globule protein and its morphologies are sensitive to pH. This study used experimental and computational methods to determine the interaction of single or combined ECG and PIC with BLG at different pHs. The static quenching process was determined through fluorescence and ultraviolet-visible spectroscopy. Compared with ECG, PIC could significantly bind to BLG with higher affinity. Their binding affinity for BLG with different morphologies followed the tendency of monomer > dimer > tetramer. The negative contribution of van der Waals forces, electrostatic interactions, and hydrogen bonds to ΔHo exceeded the positive contribution of hydrophobic interactions in the spontaneous and exothermic process. The reduced binding affinity in the ternary systems demonstrated the competitive binding between ECG and PIC on BLG, and the hinder effect of ECG or PIC was enhanced with increasing pH. Molecular docking studies revealed the same binding sites of ECG and PIC on various conformations of BLG and identical driven forces as thermodynamic results. Tryptophan and tyrosine were the main participators in the BLG + ECG and BLG + PIC systems, respectively. The conformational changes in the binary and ternary systems could be ascertained through synchronous fluorescence, circular dichroism, and dynamic light scattering. Furthermore, the effects of pH and BLG encapsulation on the antioxidant capacity and stability of ECG or PIC were also implemented. ECG or PIC was the most stable in the (BLG + PIC) + ECG system at pH 6.0. This study could clarify the interaction mechanism between ECG/PIC and BLG and elucidate the pH effect on their binding information. The results will provide basic support for their usage in food processing and applications.
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Affiliation(s)
- Lixia Yuan
- Institute of BioPharmaceutical Research, Liaocheng University, Liaocheng 252059, People's Republic of China
| | - Tingting Liu
- School of Material Science and Engineering, Tiangong University, Tianjin 300387, People's Republic of China
| | - Xin Qi
- Institute of BioPharmaceutical Research, Liaocheng University, Liaocheng 252059, People's Republic of China
| | - Yanqing Zhang
- School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng 252059, People's Republic of China
| | - Qiulu Wang
- Institute of BioPharmaceutical Research, Liaocheng University, Liaocheng 252059, People's Republic of China
| | - Qingpeng Wang
- Institute of BioPharmaceutical Research, Liaocheng University, Liaocheng 252059, People's Republic of China
| | - Min Liu
- Institute of BioPharmaceutical Research, Liaocheng University, Liaocheng 252059, People's Republic of China; School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng 252059, People's Republic of China.
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10
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Fatima M, Nabi F, Khan RH, Naeem A. Investigating the binding interaction of quinoline yellow with bovine serum albumin and anti-amyloidogenic behavior of ferulic acid on QY-induced BSA fibrils. Spectrochim Acta A Mol Biomol Spectrosc 2024; 313:124076. [PMID: 38442614 DOI: 10.1016/j.saa.2024.124076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 01/30/2024] [Accepted: 02/21/2024] [Indexed: 03/07/2024]
Abstract
Protein aggregation induces profound changes in the structure along with the conformation of the protein, and is responsible for the pathogenesis of a number of neurodegenerative conditions such as Huntington's, Creutzfeldt-Jacob, Type II diabetes mellitus, Alzheimer's, etc. Numerous multi-spectroscopic approaches and in-silico experiments were utilized to investigate BSA's biomolecular interaction and aggregation in the presence of quinoline yellow. The present research investigation evaluated the interaction of BSA with the food colorant (QY) at two different pH (7.4 and 2.0). The development of the BSA-QY complex was established with UV visible and fluorescence spectroscopy. The quenching of fluorescence upon the interaction of BSA with QY revealed the static nature of quenching mechanism. The Kb value obtained from our result is 4. 54 × 10-4 M-1. The results from the competitive site marker study infer that quinoline yellow is binding with the sub-domain IB of bovine serum albumin, specifically on site III. Three-dimensional fluorescence and synchronous fluorescence spectroscopy were applied for monitoring the alterations in the microenvironment of BSA upon the addition of quinoline yellow. The results from turbidity and RLS studies showed that higher concentrations of QY (80-400 µM) triggered bovine serum albumin (BSA) aggregation at pH 2.0. At pH 7.4, QY couldn't manage to trigger bovine serum albumin aggregation, perhaps because of the repulsion between negatively charged dye (QY) and anionic bovine serum albumin. The results from far-UV CD, Congo Red, and scanning electron microscopy implicate that the QY-induced aggregates exhibit amyloid fibril-like structures. Molecular docking results revealed that hydrophobic interactions, hydrogen bonding, and Pi-Sulfur interactions contribute to QY-induced aggregation of BSA. Further, the amyloid inhibitory potential of ferulic acid (FA), a phenolic acid on QY-induced aggregation of BSA, has also been assessed. The QY-induced amyloid fibrils are FA-soluble, as confirmed by turbidity, RLS, and far-UV CD studies. Far-UV CD results showed that FA retains α helix and inhibits cross β sheet formation when the BSA samples were pre-incubated with increasing concentrations of FA (0-500 µM). Our findings conclude that QY dye successfully stimulates BSA aggregation, but ferulic acid inhibits QY-induced aggregation of BSA. Thus, FA can serve as a therapeutic agent and can help in the treatment of various amyloid-related conditions.
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Affiliation(s)
- Maham Fatima
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Faisal Nabi
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Aabgeena Naeem
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, U.P., India.
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11
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Vahedi SZ, Farhadian S, Shareghi B, Asgharzadeh S. Thermodynamic and functional changes of alpha-chymotrypsin after interaction with gallic acid. Spectrochim Acta A Mol Biomol Spectrosc 2024; 313:124109. [PMID: 38447443 DOI: 10.1016/j.saa.2024.124109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/24/2024] [Accepted: 03/02/2024] [Indexed: 03/08/2024]
Abstract
In the present study, the interaction mechanism between gallic acid (GA) and α-Chymotrypsin (α-CT) was investigated by employing a series ofspectroscopic methods, computational docking and molecular dynamic (MD) simulation. Fluorescence spectra analysis indicated the formation of a stable complex between GA and α-CT, where the quenching of the fluorescence emission was predominantly characterized by a static mechanism. TheCA obtained binding constants for the α-CT-GA complex were in the order of 103 M-1, indicating the moderate binding affinity of GA for α-CT. The corresponding CD findings showed that the interaction between GA and α-CT resulted in an alteration of the protein's secondary structure. The findings of the enzyme activity investigation clearly showed that the presence of GA led to a notable decline in the enzymatic activity of α-CT, highlighting GA's function as an effective inhibitor for α-CT. The molecular docking simulations revealed the optimal binding site for the GA molecule within the α-CT structure and MD simulations confirmed the stability of the α-CT-GA complex. This research expands our comprehension regarding the behavior of enzymes in the presence of small-molecule ligands and opens avenues for food safety.
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Affiliation(s)
- Seyedeh Zohreh Vahedi
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box.115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Sadegh Farhadian
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box.115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
| | - Behzad Shareghi
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box.115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Sanaz Asgharzadeh
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box.115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran
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12
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Duan X, Liu W, Liang J, Jing T, Liu Y, Wang X, Liu B. Modulation of protein-ligand interactions in the presence of ZIF-8: Spectroscopy and molecular dynamics simulation. Spectrochim Acta A Mol Biomol Spectrosc 2024; 312:124053. [PMID: 38422930 DOI: 10.1016/j.saa.2024.124053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 12/17/2023] [Accepted: 02/17/2024] [Indexed: 03/02/2024]
Abstract
In this paper, we investigated the protein-ligand interactions in the presence of ZIF-8 using multi-spectroscopic approaches and molecular dynamics simulation. Fluorescence experiments and molecular docking results showed that ZIF-8 did not change the type of quenching and interaction force between ciprofloxacin (CIP) and human serum albumin (HSA), but made the binding constant of HSA-CIP to be smaller, suggesting that ZIF-8 maybe accelerate the dissociation of CIP from HSA-CIP complex. Moreover, the effect of ZIF-8 on the physiological function of HSA was explored. Multi-spectroscopic methods revealed that ZIF-8 did not significantly alter the microenvironment of amino acid groups, but cause a slight decrease in the content of α-helical conformation, and a sparse and flexible structure of the protein backbone. These peculiarities might lead to the diminution of HSA's ability to control drugs. In short, ZIF-8 might enhance drug effect due to affecting the binding of drugs to proteins. However, the present study is only a preliminary investigation of the suitability of ZIF-8 as a drug carrier in vitro, and subsequent in vivo experimental studies will be required to further confirm the idea.
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Affiliation(s)
- Xinyue Duan
- School of Pharmaceutical Sciences, Liaoning University, Shenyang 110036, China
| | - Wei Liu
- School of Pharmaceutical Sciences, Liaoning University, Shenyang 110036, China
| | - Jiaqi Liang
- School of Pharmaceutical Sciences, Liaoning University, Shenyang 110036, China
| | - Tingyu Jing
- School of Pharmaceutical Sciences, Liaoning University, Shenyang 110036, China
| | - Yu Liu
- School of Pharmaceutical Sciences, Liaoning University, Shenyang 110036, China
| | - Xiao Wang
- Department of Gastroenterology, Central Hospital Affiliated to Shenyang Medical College, Shenyang 110075, China.
| | - Bin Liu
- School of Pharmaceutical Sciences, Liaoning University, Shenyang 110036, China.
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13
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Galván-Ojeda HJ, Acosta-Elias J, Saavedra-Alanis VM, Espinosa-Tanguma R, Del Carmen Rodríguez-Aranda M, Hernández-Arteaga AC, Navarro-Contreras HR. Raman spectroscopy study of 7,8-dihydrofolate inhibition on the Wuhan strain SARS-CoV-2 binding to human ACE2 receptor. Spectrochim Acta A Mol Biomol Spectrosc 2024; 312:124050. [PMID: 38402702 DOI: 10.1016/j.saa.2024.124050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/13/2024] [Accepted: 02/14/2024] [Indexed: 02/27/2024]
Abstract
Emerging evidence suggests that elevated levels of folic acid in the bloodstream may confer protection against Wuhan-SARS-CoV-2 infection and mitigate its associated symptoms. Notably, two comprehensive studies of COVID-19 patients in Israel and UK uncovered a remarkable trend, wherein individuals with heightened folic acid levels exhibited only mild symptoms and necessitated no ventilatory support. In parallel, research has underscored the potential connection between decreased folic acid levels and the severity of Covid-19 among hospitalized patients. Yet, the underlying mechanisms governing this intriguing inhibition remain elusive. In a quest to elucidate these mechanisms, we conducted a molecular dynamics simulation approach followed by a Raman spectroscopy study to delve into the intricate interplay between the folic acid metabolite, 7,8-dihydrofolate (DHF), and the angiotensin-converting enzyme ACE2 receptor, coupled with its interaction with the receptor-binding domain (RBD) of the Wuhan strain of SARS-CoV-2. Through a meticulous exploration, we scrutinized the transformation of the ACE2 + RBD complex, allowing these reactants to form bonds. This was juxtaposed with a similar investigation where ACE2 was initially permitted to react with DHF, followed by the exposure of the ACE2 + DHF complex to RBD. We find that DHF, when bonded to ACE2, functions as a physical barrier, effectively inhibiting the binding of the Wuhan strain RBD. This physicochemical process offers a cogent explanation for the observed inhibition of host cell infection in subjects receiving supplementary folic acid doses, as epidemiologically substantiated in multiple studies. This study not only sheds light on a potential avenue for mitigating SARS-CoV-2 infection but also underscores the crucial role of folic acid metabolites in host-virus interactions. This research paves the way for novel therapeutic strategies in the battle against COVID-19 and reinforces the significance of investigating the molecular mechanisms underlying the protective effects of folic acid in the context of viral infections.
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Affiliation(s)
- Hiram Joazet Galván-Ojeda
- Coordinación para la Innovación y la Aplicación de la Ciencia y la Tecnología, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona #550, Col. Lomas 2a, Sección, CP 78210 San Luis Potosí, SLP, Mexico
| | - Jesus Acosta-Elias
- Facultad de Ciencias, Universidad Autónoma de San Luís Potosí, Álvaro Obregón 64, San Luis Potosí, SLP 78000, Mexico
| | - Victor M Saavedra-Alanis
- Facultad de Medicina, Universidad Autónoma de San Luís Potosí, Álvaro Obregón 64, San Luis Potosí, SLP 78000, Mexico
| | - Ricardo Espinosa-Tanguma
- Facultad de Medicina, Universidad Autónoma de San Luís Potosí, Álvaro Obregón 64, San Luis Potosí, SLP 78000, Mexico
| | - Ma Del Carmen Rodríguez-Aranda
- Coordinación para la Innovación y la Aplicación de la Ciencia y la Tecnología, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona #550, Col. Lomas 2a, Sección, CP 78210 San Luis Potosí, SLP, Mexico
| | - Aida Catalina Hernández-Arteaga
- Coordinación para la Innovación y la Aplicación de la Ciencia y la Tecnología, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona #550, Col. Lomas 2a, Sección, CP 78210 San Luis Potosí, SLP, Mexico
| | - Hugo Ricardo Navarro-Contreras
- Coordinación para la Innovación y la Aplicación de la Ciencia y la Tecnología, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona #550, Col. Lomas 2a, Sección, CP 78210 San Luis Potosí, SLP, Mexico.
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14
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Silva PV, Nobre CN. Computational methods in the analysis of SARS-CoV-2 in mammals: A systematic review of the literature. Comput Biol Med 2024; 173:108264. [PMID: 38564853 DOI: 10.1016/j.compbiomed.2024.108264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 02/15/2024] [Accepted: 03/06/2024] [Indexed: 04/04/2024]
Abstract
SARS-CoV-2 is an enveloped RNA virus that causes severe respiratory illness in humans and animals. It infects cells by binding the Spike protein to the host's angiotensin-converting enzyme 2 (ACE2). The bat is considered the natural host of the virus, and zoonotic transmission is a significant risk and can happen when humans come into close contact with infected animals. Therefore, understanding the interconnection between human, animal, and environmental health is important to prevent and control future coronavirus outbreaks. This work aimed to systematically review the literature to identify characteristics that make mammals suitable virus transmitters and raise the main computational methods used to evaluate SARS-CoV-2 in mammals. Based on this review, it was possible to identify the main factors related to transmissions mentioned in the literature, such as the expression of ACE2 and proximity to humans, in addition to identifying the computational methods used for its study, such as Machine Learning, Molecular Modeling, Computational Simulation, between others. The findings of the work contribute to the prevention and control of future outbreaks, provide information on transmission factors, and highlight the importance of advanced computational methods in the study of infectious diseases that allow a deeper understanding of transmission patterns and can help in the development of more effective control and intervention strategies.
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Affiliation(s)
- Paula Vitória Silva
- Pontifical Catholic University of Minas Gerais - PUC Minas, 500 Dom José Gaspar Street, Building 41, Coração Eucarístico, Belo Horizonte, MG 30535-901, Brazil.
| | - Cristiane N Nobre
- Pontifical Catholic University of Minas Gerais - PUC Minas, 500 Dom José Gaspar Street, Building 41, Coração Eucarístico, Belo Horizonte, MG 30535-901, Brazil.
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15
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Haselhorst T. Studying the interaction of glycans with intact virions and virus-like particles by ligand-observed NMR spectroscopy. Magn Reson Chem 2024; 62:337-344. [PMID: 37776196 DOI: 10.1002/mrc.5399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 09/12/2023] [Accepted: 09/13/2023] [Indexed: 10/02/2023]
Abstract
Virus-glycan interactions play a crucial role in the infection process of many viruses. NMR spectroscopy has emerged as a powerful tool for studying these interactions at the molecular level. In this article, we review several published papers and reports that have highlighted the application of NMR spectroscopy in understanding the complex questions of how viruses engage with and bind to receptor glycans. The use of saturation transfer difference (STD) NMR spectroscopy has demonstrated itself as highly advantageous in investigating the interaction between glycans and intact virions or virus-like particles (VLPs). The broad NMR signal linewidth of virions and VLPs allows efficient saturation without affecting the glycan signals. The advantage of this approach is that the viral capsid environment in protein organization and function is not ignored and therefore provides a more biologically relevant model for exploring the interactions between the virus and the host cell glycans. We will review some examples of using NMR spectroscopy to study influenza cell tropism, rotaviruses, and noroviruses.
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Affiliation(s)
- Thomas Haselhorst
- Institute for Glycomics & School of Environment and Science, Griffith University, Southport, Queensland, Australia
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16
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Thines L, Jang H, Li Z, Sayedyahossein S, Maloney R, Nussinov R, Sacks DB. Disruption of Ca 2+/calmodulin:KSR1 interaction lowers ERK activation. Protein Sci 2024; 33:e4982. [PMID: 38591710 PMCID: PMC11002989 DOI: 10.1002/pro.4982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 02/22/2024] [Accepted: 03/16/2024] [Indexed: 04/10/2024]
Abstract
KSR1, a key scaffold protein for the MAPK pathway, facilitates ERK activation upon growth factor stimulation. We recently demonstrated that KSR1 binds the Ca2+-binding protein calmodulin (CaM), thereby providing an intersection between KSR1-mediated and Ca2+ signaling. In this study, we set out to generate a KSR1 point mutant with reduced Ca2+/CaM binding in order to unravel the functional implications of their interaction. To do so, we solved the structural determinants of complex formation. Using purified fragments of KSR1, we showed that Ca2+/CaM binds to the CA3 domain of KSR1. We then used in silico molecular modeling to predict contact residues for binding. This approach identified two possible modes of interaction: (1) binding of extended Ca2+/CaM to a globular conformation of KSR1-CA3 via electrostatic interactions or (2) binding of collapsed Ca2+/CaM to α-helical KSR1-CA3 via hydrophobic interactions. Experimentally, site-directed mutagenesis of the predicted contact residues for the two binding models favored that where collapsed Ca2+/CaM binds to the α-helical conformation of KSR1-CA3. Importantly, replacing KSR1-Phe355 with Asp reduces Ca2+/CaM binding by 76%. The KSR1-F355D mutation also significantly impairs the ability of EGF to activate ERK, which reveals that Ca2+/CaM binding promotes KSR1-mediated MAPK signaling. This work, by uncovering structural insight into the binding of KSR1 to Ca2+/CaM, identifies a KSR1 single-point mutant as a bioreagent to selectively study the crosstalk between Ca2+ and KSR1-mediated signaling.
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Affiliation(s)
- Louise Thines
- Department of Laboratory MedicineNational Institutes of HealthBethesdaMarylandUSA
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation LaboratoryNational Cancer InstituteFrederickMarylandUSA
| | - Zhigang Li
- Department of Laboratory MedicineNational Institutes of HealthBethesdaMarylandUSA
| | - Samar Sayedyahossein
- Department of Laboratory MedicineNational Institutes of HealthBethesdaMarylandUSA
| | - Ryan Maloney
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation LaboratoryNational Cancer InstituteFrederickMarylandUSA
| | - Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation LaboratoryNational Cancer InstituteFrederickMarylandUSA
- Department of Human Molecular Genetics and BiochemistrySackler School of Medicine, Tel Aviv UniversityTel AvivIsrael
| | - David B. Sacks
- Department of Laboratory MedicineNational Institutes of HealthBethesdaMarylandUSA
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17
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Singh P, Gopi P, Rani MSS, Singh S, Pandya P. Biophysical and structural characterization of tetramethrin serum protein complex and its toxicological implications. J Mol Recognit 2024; 37:e3076. [PMID: 38366770 DOI: 10.1002/jmr.3076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 02/18/2024]
Abstract
Tetramethrin (TMT) is a commonly used insecticide and has a carcinogenic and neurodegenerative effect on humans. The binding mechanism and toxicological implications of TMT to human serum albumin (HSA) were examined in this study employing a combination of biophysical and computational methods indicating moderate binding affinity and potential hepato and renal toxicity. Fluorescence quenching experiments showed that TMT binds to HSA with a moderate affinity, and the binding process was spontaneous and predominantly enthalpy-driven. Circular dichroism spectroscopy revealed that TMT binding did not induce any significant conformational changes in HSA, resulting in no changes in its alpha-helix content. The binding site and modalities of TMT interactions with HSA as computed by molecular docking and molecular dynamics simulations revealed that it binds to Sudlow site II of HSA via hydrophobic interactions through its dimethylcyclopropane carboxylate methyl propanyl group. The structural dynamics of TMT induce proper fit into the binding site creating increased and stabilizing interactions. Additionally, molecular mechanics-Poisson Boltzmann surface area calculations also indicated that non-polar and van der Waals were found to be the major contributors to the high binding free energy of the complex. Quantum mechanics (QM) revealed the conformational energies of the binding confirmation and the degree of deviation from the global minimum energy conformation of TMT. The results of this study provide a comprehensive understanding of the binding mechanism of TMT with HSA, which is important for evaluating the toxicity of this insecticide in humans.
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Affiliation(s)
- Pratik Singh
- Amity Institute of Forensic Sciences, Amity University, Noida, India
| | - Priyanka Gopi
- Amity Institute of Forensic Sciences, Amity University, Noida, India
| | | | - Shweta Singh
- Amity Institute of Forensic Sciences, Amity University, Noida, India
| | - Prateek Pandya
- Amity Institute of Forensic Sciences, Amity University, Noida, India
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18
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Thomas C, Byer-Alcorace A, Wang T. Human Serum Albumin Immobilized On Magnetizable Beads: A Rapid Method for Compound HSA Binding Study. J Pharm Sci 2024; 113:1359-1367. [PMID: 38325737 DOI: 10.1016/j.xphs.2024.01.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/30/2024] [Accepted: 01/30/2024] [Indexed: 02/09/2024]
Abstract
Immobilized human serum albumin (HSA) was developed by coupling His-tagged HSA onto Ni2+-coupled magnetizable beads (HSA-beads), allowing the HSA to be easily removed from incubation components. The HSA-beads system provides a rapid and convenient method to study HSA compound binding. In this study, the HSA-beads system was characterized and evaluated as a tool for assessing compound HSA binding properties. The free fraction (fu) values of test compounds measured using HSA-beads were comparable to those determined by equilibrium dialysis (ED), which is commonly used to evaluate albumin binding in vitro. The equilibrium dissociation constant (Kd) values determined for a series of compounds using the HSA-beads method demonstrated good correlation with literature data. This good correlation also suggests that the binding of His-HSA to the beads does not impact the conformations of the two compound binding sites of HSA, as the range of compounds tested encompassed binding to both sites. Furthermore, the Kd values of representative compounds itraconazole and BIRT2584 that were difficult to assess using ED, due to significant cellulose membrane adsorption, were successfully determined. The HSA-beads provide several advantages over ED, such as simple preparation, short assay incubation duration, and the ability to quantify both free and HSA-bound species of the test compound, facilitated by the simple separation of HSA-beads from the solution phase using a magnetic field. These properties render the HSA-beads method suitable for high-throughput studies on compound HSA binding.
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Affiliation(s)
- Cody Thomas
- Department of Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Rd., Ridgefield, CT 06877, USA
| | - Alexander Byer-Alcorace
- Department of Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Rd., Ridgefield, CT 06877, USA
| | - Ting Wang
- Department of Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Rd., Ridgefield, CT 06877, USA.
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19
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Kazakov AS, Rastrygina VA, Vologzhannikova AA, Zemskova MY, Bobrova LA, Deryusheva EI, Permyakova ME, Sokolov AS, Litus EA, Shevelyova MP, Uversky VN, Permyakov EA, Permyakov SE. Recognition of granulocyte-macrophage colony-stimulating factor by specific S100 proteins. Cell Calcium 2024; 119:102869. [PMID: 38484433 DOI: 10.1016/j.ceca.2024.102869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 03/01/2024] [Accepted: 03/03/2024] [Indexed: 04/05/2024]
Abstract
Granulocyte-macrophage colony-stimulating factor (GM-CSF) is a pleiotropic myelopoietic growth factor and proinflammatory cytokine, clinically used for multiple indications and serving as a promising target for treatment of many disorders, including cancer, multiple sclerosis, rheumatoid arthritis, psoriasis, asthma, COVID-19. We have previously shown that dimeric Ca2+-bound forms of S100A6 and S100P proteins, members of the multifunctional S100 protein family, are specific to GM-CSF. To probe selectivity of these interactions, the affinity of recombinant human GM-CSF to dimeric Ca2+-loaded forms of 18 recombinant human S100 proteins was studied by surface plasmon resonance spectroscopy. Of them, only S100A4 protein specifically binds to GM-CSF with equilibrium dissociation constant, Kd, values of 0.3-2 μM, as confirmed by intrinsic fluorescence and chemical crosslinking data. Calcium removal prevents S100A4 binding to GM-CSF, whereas monomerization of S100A4/A6/P proteins disrupts S100A4/A6 interaction with GM-CSF and induces a slight decrease in S100P affinity for GM-CSF. Structural modelling indicates the presence in the GM-CSF molecule of a conserved S100A4/A6/P-binding site, consisting of the residues from its termini, helices I and III, some of which are involved in the interaction with GM-CSF receptors. The predicted involvement of the 'hinge' region and F89 residue of S100P in GM-CSF recognition was confirmed by mutagenesis. Examination of S100A4/A6/P ability to affect GM-CSF signaling showed that S100A4/A6 inhibit GM-CSF-induced suppression of viability of monocytic THP-1 cells. The ability of the S100 proteins to modulate GM-CSF activity is relevant to progression of various neoplasms and other diseases, according to bioinformatics analysis. The direct regulation of GM-CSF signaling by extracellular forms of the S100 proteins should be taken into account in the clinical use of GM-CSF and development of the therapeutic interventions targeting GM-CSF or its receptors.
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Affiliation(s)
- Alexey S Kazakov
- Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institute for Biological Instrumentation, Institutskaya str., 7, Pushchino, Moscow Region 142290, Russia.
| | - Victoria A Rastrygina
- Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institute for Biological Instrumentation, Institutskaya str., 7, Pushchino, Moscow Region 142290, Russia
| | - Alisa A Vologzhannikova
- Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institute for Biological Instrumentation, Institutskaya str., 7, Pushchino, Moscow Region 142290, Russia
| | - Marina Y Zemskova
- Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institute for Biological Instrumentation, Institutskaya str., 7, Pushchino, Moscow Region 142290, Russia; Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, pr. Nauki, 5, Pushchino, Moscow Region 142290, Russia
| | - Lolita A Bobrova
- Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institute for Biological Instrumentation, Institutskaya str., 7, Pushchino, Moscow Region 142290, Russia
| | - Evgenia I Deryusheva
- Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institute for Biological Instrumentation, Institutskaya str., 7, Pushchino, Moscow Region 142290, Russia.
| | - Maria E Permyakova
- Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institute for Biological Instrumentation, Institutskaya str., 7, Pushchino, Moscow Region 142290, Russia
| | - Andrey S Sokolov
- Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institute for Biological Instrumentation, Institutskaya str., 7, Pushchino, Moscow Region 142290, Russia
| | - Ekaterina A Litus
- Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institute for Biological Instrumentation, Institutskaya str., 7, Pushchino, Moscow Region 142290, Russia
| | - Marina P Shevelyova
- Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institute for Biological Instrumentation, Institutskaya str., 7, Pushchino, Moscow Region 142290, Russia
| | - Vladimir N Uversky
- Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institute for Biological Instrumentation, Institutskaya str., 7, Pushchino, Moscow Region 142290, Russia; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
| | - Eugene A Permyakov
- Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institute for Biological Instrumentation, Institutskaya str., 7, Pushchino, Moscow Region 142290, Russia
| | - Sergei E Permyakov
- Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institute for Biological Instrumentation, Institutskaya str., 7, Pushchino, Moscow Region 142290, Russia.
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20
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Wang L, Wu H, Cao T, Li H, Shen P, Lu L, Zhang Z. Identification of structural origins of complex charge heterogeneity in therapeutic ACE2Fc fusion protein facilitated by free-flow isoelectric focusing. Eur J Pharm Biopharm 2024; 198:114248. [PMID: 38467335 DOI: 10.1016/j.ejpb.2024.114248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/26/2024] [Accepted: 03/06/2024] [Indexed: 03/13/2024]
Abstract
Fc Fusion protein represents a versatile molecular platform with considerable potential as protein therapeutics of which the charge heterogeneity should be well characterized according to regulatory guidelines. Angiotensin-converting enzyme 2 Fc fusion protein (ACE2Fc) has been investigated as a potential neutralizing agent to various coronaviruses, including the lingering SARS-CoV-2, as this coronavirus must bind to ACE2 to allow for its entry into host cells. ACE2Fc, an investigational new drug developed by Henlius (Shanghai China), has passed the Phase I clinical trial, but its huge amount of charge isoforms and complicated charge heterogeneity posed a challenge to charge variant investigation in pharmaceutical development. We employed offline free-flow isoelectric focusing (FF-IEF) fractionation, followed by detailed characterization of enriched ACE2Fc fractions, to unveil the structural origins of charge heterogeneity in ACE2Fc expressed by recombinant CHO cells. We adopted a well-tuned 3-component separation medium for ACE2Fc fractionation, the highest allowable voltage to maximize the FF-IEF separation window and a mild Protein A elution method for preservation of protein structural integrity. Through peptide mapping and other characterizations, we revealed that the intricate profiles of ACE2Fc charge heterogeneity are mainly caused by highly sialylated multi-antenna N-glycosylation. In addition, based on fraction characterization and in silico glycoprotein model analysis, we discovered that the large acidic glycans at N36, N73, and N305 of ACE2Fc were able to decrease the binding activity towards Spike (S) protein of SARS-CoV-2. Our study exemplifies the value of FF-IEF in highly complex fusion protein characterization and revealed a quantitative sialylation-activity relationship in ACE2Fc.
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Affiliation(s)
- Lingyu Wang
- Department of Analytical Science and Development, Shanghai Henlius Biologics Co., Ltd., Shanghai 201600, China
| | - Hai Wu
- Department of Analytical Science and Development, Shanghai Henlius Biologics Co., Ltd., Shanghai 201600, China
| | - Ting Cao
- Department of Analytical Science and Development, Shanghai Henlius Biologics Co., Ltd., Shanghai 201600, China
| | - Hongyang Li
- Department of Analytical Science and Development, Shanghai Henlius Biologics Co., Ltd., Shanghai 201600, China
| | - Pengcheng Shen
- Department of Analytical Science and Development, Shanghai Henlius Biologics Co., Ltd., Shanghai 201600, China
| | - Lihong Lu
- Department of Analytical Science and Development, Shanghai Henlius Biologics Co., Ltd., Shanghai 201600, China
| | - Zhongli Zhang
- Department of Analytical Science and Development, Shanghai Henlius Biologics Co., Ltd., Shanghai 201600, China.
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21
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Mohammed RDS, Piell KM, Maurer MC. Identification of Factor XIII β-Sandwich Residues Mediating Glutamine Substrate Binding and Activation Peptide Cleavage. Thromb Haemost 2024; 124:408-422. [PMID: 38040030 DOI: 10.1055/a-2220-7544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2023]
Abstract
BACKGROUND Factor XIII (FXIII) forms covalent crosslinks across plasma and cellular substrates and has roles in hemostasis, wound healing, and bone metabolism. FXIII activity is implicated in venous thromboembolism (VTE) and is a target for developing pharmaceuticals, which requires understanding FXIII - substrate interactions. Previous studies proposed the β-sandwich domain of the FXIII A subunit (FXIII-A) exhibits substrate recognition sites. MATERIAL AND METHODS Recombinant FXIII-A proteins (WT, K156E, F157L, R158Q/E, R171Q, and R174E) were generated to identify FXIII-A residues mediating substrate recognition. Proteolytic (FXIII-A*) and non-proteolytic (FXIII-A°) forms were analyzed for activation and crosslinking activities toward physiological substrates using SDS-PAGE and MALDI-TOF MS. RESULTS All FXIII-A* variants displayed reduced crosslinking abilities compared to WT for Fbg αC (233 - 425), fibrin, and actin. FXIII-A* WT activity was greater than A°, suggesting the binding site is more exposed in FXIII-A*. With Fbg αC (233 - 425), FXIII-A* variants R158Q/E, R171Q, and R174E exhibited decreased activities approaching those of FXIII-A°. However, with a peptide substrate, FXIII-A* WT and variants showed similar crosslinking suggesting the recognition site is distant from the catalytic site. Surprisingly, FXIII-A R158E and R171Q displayed slower thrombin activation than WT, potentially due to loss of crucial H-bonding with neighboring activation peptide (AP) residues. CONCLUSION In conclusion, FXIII-A residues K156, F157, R158, R171, and R174 are part of a binding site for physiological substrates [fibrin (α and γ) and actin]. Moreover, R158 and R171 control AP cleavage during thrombin activation. These investigations provide new molecular details on FXIII - substrate interactions that control crosslinking abilities.
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Affiliation(s)
| | - Kellianne M Piell
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, Kentucky, United States
| | - Muriel C Maurer
- Department of Chemistry, University of Louisville, Louisville, Kentucky, United States
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22
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Huszenicza Z, Gilmour BC, Koll L, Kjelstrup H, Chan H, Sundvold V, Granum S, Spurkland A. Interaction of T-cell-specific adapter protein with Src- and Tec-family kinases. Scand J Immunol 2024; 99:e13358. [PMID: 38605535 DOI: 10.1111/sji.13358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 04/13/2024]
Abstract
Adapter proteins are flexible and dynamic modulators of cellular signalling that are important for immune cell function. One of these, the T-cell-specific adapter protein (TSAd), interacts with the non-receptor tyrosine kinases Src and Lck of the Src family kinases (SFKs) and Itk of the Tec family kinases (TFKs). Three tyrosine residues in the TSAd C-terminus are phosphorylated by Lck and serve as docking sites for the Src homology 2 (SH2) domains of Src and Lck. The TSAd proline-rich region (PRR) binds to the Src homology 3 (SH3) domains found in Lck, Src and Itk. Despite known interactors, the role TSAd plays in cellular signalling remains largely unknown. TSAd's ability to bind both SFKs and TFKs may point to its function as a general scaffold for both kinase families. Using GST-pulldown as well as peptide array experiments, we found that both the SH2 and SH3 domains of the SFKs Fyn and Hck, as well as the TFKs Tec and Txk, interact with TSAd. This contrasts with Itk, which interacts with TSAd only through its SH3 domain. Although our analysis showed that TSAd is both co-expressed and may interact with Fyn, we were unable to co-precipitate Fyn with TSAd from Jurkat cells, as detected by Western blotting and affinity purification mass spectrometry. This may suggest that TSAd-Fyn interaction in intact cells may be limited by other factors, such as the subcellular localization of the two molecules or the co-expression of competing binding partners.
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Affiliation(s)
- Zsuzsa Huszenicza
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Brian C Gilmour
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Lise Koll
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Hanna Kjelstrup
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Hanna Chan
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Vibeke Sundvold
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Stine Granum
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Anne Spurkland
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
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23
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Tang J, Hu R, Liu Y, Liu J, Wang G, Lv J, Cheng L, He T, Liu Y, Shao PL, Zhang B. Deciphering ACE2-RBD binding affinity through peptide scanning: A molecular dynamics simulation approach. Comput Biol Med 2024; 173:108325. [PMID: 38513389 DOI: 10.1016/j.compbiomed.2024.108325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 03/15/2024] [Accepted: 03/15/2024] [Indexed: 03/23/2024]
Abstract
Rapid discovery of target information for protein-protein interactions (PPIs) is significant in drug design, diagnostics, vaccine development, antibody therapy, etc. Peptide microarray is an ideal tool for revealing epitope information of PPIs. In this work, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) spike receptor-binding domain (RBD) and the host cell receptor angiotensin-converting enzyme 2 (ACE2) were introduced as a model to study the epitope information of RBD-specific binding to ACE2 via a combination of theoretical calculations and experimental validation. Through dock and molecular dynamics simulations, it was found that among the 22 peptide fragments that consist of RBD, #14 (YNYLYRLFRKSNLKP) has the highest binding strength. Subsequently, the experiments of peptide microarray constructed based on plasmonic materials chip also confirmed the theoretical calculation data. Compared to other methods, such as phage display technology and surface plasmon resonance (SPR), this method is rapid and cost-effective, providing insights into the investigation of pathogen invasion processes and the timely development of peptide drugs and other fields.
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Affiliation(s)
- Jiahu Tang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055, China; Key Laboratory of Molecular Target & Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, China
| | - Ruibin Hu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055, China; Xianghu Laboratory, Hangzhou, 311231, China
| | - Yiyi Liu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jingchao Liu
- Institute of Forestry and Pomology, Tianjin Academy of Agricultural Sciences, Tianjin, 300384, China
| | - Guanghui Wang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jiahui Lv
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Li Cheng
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Tingzhen He
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Ying Liu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Pan-Lin Shao
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, China.
| | - Bo Zhang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055, China.
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24
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Pagán OR. The complexities of ligand/receptor interactions: Exploring the role of molecular vibrations and quantum tunnelling. Bioessays 2024; 46:e2300195. [PMID: 38459808 DOI: 10.1002/bies.202300195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/19/2024] [Accepted: 02/19/2024] [Indexed: 03/10/2024]
Abstract
Molecular vibrations and quantum tunneling may link ligand binding to the function of pharmacological receptors. The well-established lock-and-key model explains a ligand's binding and recognition by a receptor; however, a general mechanism by which receptors translate binding into activation, inactivation, or modulation remains elusive. The Vibration Theory of Olfaction was proposed in the 1930s to explain this subset of receptor-mediated phenomena by correlating odorant molecular vibrations to smell, but a mechanism was lacking. In the 1990s, inelastic electron tunneling was proposed as a plausible mechanism for translating molecular vibration to odorant physiology. More recently, studies of ligands' vibrational spectra and the use of deuterated ligand analogs have provided helpful information to study this admittedly controversial hypothesis in metabotropic receptors other than olfactory receptors. In the present work, based in part on published experiments from our laboratory using planarians as an experimental organism, I will present a rationale and possible experimental approach for extending this idea to ligand-gated ion channels.
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Affiliation(s)
- Oné R Pagán
- Department of Biology, West Chester University, West Chester, Pennsylvania, USA
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25
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Zhou S, Wu X, Song Y, Li L, Shi C, Lai Z, Ding Q, Wu W, Dai J, Wang X, Lu Y. Ser252Asn Mutation Introduces a New N-Linked Glycosylation Site and Causes Type IIb Protein C Deficiency. Thromb Haemost 2024; 124:459-470. [PMID: 38011863 DOI: 10.1055/s-0043-1777133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
BACKGROUND Protein C (PC) is a vitamin K-dependent anticoagulant serine protease zymogen which upon activation by the thrombin-thrombomodulin (TM) complex downregulates the coagulation cascade by degrading cofactors Va and VIIIa by limited proteolysis. We identified a thrombosis patient who carried a heterozygous mutation c.881G > A, p.Ser252Asn (S252N) in PROC. This mutation was originally described in a report of novel mutations in patients presenting with defective PC anticoagulant activity in Paris. The research identified PC-S252N (the "Paris" mutation) in a propositus and her family members and highlighted the critical role of Ser252 in the anticoagulation process of activated PC (APC). MATERIAL AND METHODS We expressed the PC-S252N mutant in mammalian cells and characterized the properties in coagulation assays to decipher the molecular basis of anticoagulant defect of this mutation. RESULTS We demonstrated that PC-S252N had a diminished ability to TM binding, which resulted in its impaired activation by the thrombin-TM complex. However, APC-S252N exhibited a slightly stronger cleavage capacity for the chromogenic substrate. Meanwhile, the catalytic activity of APC-S252N toward FVa was significantly reduced. Sequence analysis revealed that Ser252 to Asn substitution introduced a new potential N-linked glycosylation site (252NTT254) in the catalytic domain of PC, which adversely affected both the activation process of PC and anticoagulant activity of APC. CONCLUSION The new N-glycosylation site (252NTT254) resulting from the mutation of Ser252 to Asn252 in PROC affects the overall structure of the protease, thereby adversely affecting the anticoagulant function of protein C. This modification has a negative impact on both TM-promoted activation of protein C and APC cleavage of FVa, ultimately leading to thrombosis in the patient.
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Affiliation(s)
- Shijie Zhou
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xi Wu
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Ying Song
- Department of Clinical Hematology and osology, Shanghai Center of Clinical Laboratory, Shanghai, China
| | - Lei Li
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Chunli Shi
- Department of Molecular Biology, Shanghai Center of Clinical Laboratory, Shanghai, China
| | - Zhe Lai
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Qiulan Ding
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Wenman Wu
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jing Dai
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xuefeng Wang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yeling Lu
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
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26
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Asgharzadeh S, Shareghi B, Farhadian S. Probing the toxic effect of chlorpyrifos as an environmental pollutant on the structure and biological activity of lysozyme under physiological conditions. Chemosphere 2024; 355:141724. [PMID: 38499074 DOI: 10.1016/j.chemosphere.2024.141724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/04/2024] [Accepted: 03/13/2024] [Indexed: 03/20/2024]
Abstract
The pervasive use of pesticides like chlorpyrifos (CPY) has been associated with deleterious effects on biomolecules, posing significant risks to environmental integrity, public health, and overall ecosystem equilibrium. Accordingly, in this study, we investigated the potential binding interaction between the well-conserved enzyme, lysozyme (LSZ), and CPY through various spectroscopic techniques and molecular modeling. The UV-vis absorption and fluorescence experiments confirmed the complex formation and static quenching of the intrinsic fluorescence intensity. LSZ revealed a singular binding site for CPY, with binding constants around 105 M-1 across different temperature ranges. Analysis of thermodynamic parameters showed the spontaneous nature of the complexation process, while also revealing the pivotal role of hydrophobic interactions in stabilizing the LSZ-CPY system. According to circular dichroism and Fourier transform infrared studies, CPY binding changed the secondary structure of LSZ by boosting α-helix presence and reducing the levels of β-sheet and β-turn content. Further, CPY decreased the stability and activity of LSZ. Computational docking delineated the specific and highly preferred binding site of CPY within the structure of LSZ. Molecular dynamic simulation indicated the enduring stability of the LSZ/CPY complex and revealed structural modifications in the LSZ after binding with CPY. This research provides a detailed understanding of the intermolecular dynamics between CPY and LSZ, concurrently elucidating the molecular-level implications for the potential hazards of pesticides in the natural environment.
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Affiliation(s)
- Sanaz Asgharzadeh
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box.115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Behzad Shareghi
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box.115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
| | - Sadegh Farhadian
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box.115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
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27
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Kumar RS, Datta T, Sinha H, Trivedi PK. Light-dependent expression and accumulation of miR408-encoded peptide, miPEP408, is regulated by HY5 in Arabidopsis. Biochem Biophys Res Commun 2024; 706:149764. [PMID: 38484569 DOI: 10.1016/j.bbrc.2024.149764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 03/07/2024] [Indexed: 03/24/2024]
Abstract
Recent studies propose that primary transcripts of miRNAs (pri-miRNAs) contain small Open Reading Frames (ORFs) capable of encoding miRNA-encoded peptides (miPEPs). These miPEPs can function as transcriptional regulators for their corresponding pri-miRNAs, ultimately enhancing mature miRNA accumulation. Notably, pri-miR408 encodes the functional peptide miPEP408, regulating expression of miR408 and its target genes, providing plant tolerance to stresses. While miPEPs are crucial regulators, the factors governing them are have not been studied in detail. Here, we explored the light-dependent regulation of miPEP408 in Arabidopsis. Expression analysis during dark-light transitions revealed light-induced transcription and accumulation of the miPEP408. As the promoter of miR408 contains cis-acting elements responsible for binding to the bZIP-type transcription factor ELONGATED HYPOCOTYL5 (HY5), known for light-mediated regulation in plants, we studied its involvement in the regulation of miR408. Analysis of HY5 mutant (hy5-215), complemented line (HY5OX/hy5), and CONSTITUTIVE PHOTOMORPHOGENIC 1 mutant (cop1-4) plants supported HY5's positive regulation of miPEP408. Grafting and GUS assays further suggested the role of HY5 as a shoot-root mobile signal inducing light-dependent miPEP408 expression. This study underscores the regulatory impact of light on small peptides, exemplified by miPEP408, mediated by the key transcription factor HY5.
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Affiliation(s)
- Ravi Shankar Kumar
- CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, India; CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Tapasya Datta
- CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, India
| | - Hiteshwari Sinha
- CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, India; CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Prabodh Kumar Trivedi
- CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, India; CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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28
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Hellsberg E, Boytsov D, Chen Q, Niello M, Freissmuth M, Rudnick G, Zhang YW, Sandtner W, Forrest LR. Identification of the potassium-binding site in serotonin transporter. Proc Natl Acad Sci U S A 2024; 121:e2319384121. [PMID: 38652746 DOI: 10.1073/pnas.2319384121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 03/11/2024] [Indexed: 04/25/2024] Open
Abstract
Clearance of serotonin (5-hydroxytryptamine, 5-HT) from the synaptic cleft after neuronal signaling is mediated by serotonin transporter (SERT), which couples this process to the movement of a Na+ ion down its chemical gradient. After release of 5-HT and Na+ into the cytoplasm, the transporter faces a rate-limiting challenge of resetting its conformation to be primed again for 5-HT and Na+ binding. Early studies of vesicles containing native SERT revealed that K+ gradients can provide an additional driving force, via K+ antiport. Moreover, under appropriate conditions, a H+ ion can replace K+. Intracellular K+ accelerates the resetting step. Structural studies of SERT have identified two binding sites for Na+ ions, but the K+ site remains enigmatic. Here, we show that K+ antiport can drive substrate accumulation into vesicles containing SERT extracted from a heterologous expression system, allowing us to study the residues responsible for K+ binding. To identify candidate binding residues, we examine many cation binding configurations using molecular dynamics simulations, predicting that K+ binds to the so-called Na2 site. Site-directed mutagenesis of residues in this site can eliminate the ability of both K+ and H+ to drive 5-HT accumulation into vesicles and, in patch clamp recordings, prevent the acceleration of turnover rates and the formation of a channel-like state by K+ or H+. In conclusion, the Na2 site plays a pivotal role in orchestrating the sequential binding of Na+ and then K+ (or H+) ions to facilitate 5-HT uptake in SERT.
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Affiliation(s)
- Eva Hellsberg
- Computational Structural Biology Section, National Institutes of Neurological Disorders and Stroke, NIH, Bethesda, MD 20892
| | - Danila Boytsov
- Center of Physiology and Pharmacology, Department of Pharmacology, Medical University of Vienna, Vienna 1090, Austria
| | - Qingyang Chen
- School of Life Sciences, Higher Education Mega Center, Guangzhou University, Guangzhou 510006, China
| | - Marco Niello
- Center of Physiology and Pharmacology, Department of Pharmacology, Medical University of Vienna, Vienna 1090, Austria
| | - Michael Freissmuth
- Center of Physiology and Pharmacology, Department of Pharmacology, Medical University of Vienna, Vienna 1090, Austria
| | - Gary Rudnick
- Department of Pharmacology, Yale University, New Haven, CT 06510
| | - Yuan-Wei Zhang
- School of Life Sciences, Higher Education Mega Center, Guangzhou University, Guangzhou 510006, China
| | - Walter Sandtner
- Center of Physiology and Pharmacology, Department of Pharmacology, Medical University of Vienna, Vienna 1090, Austria
| | - Lucy R Forrest
- Computational Structural Biology Section, National Institutes of Neurological Disorders and Stroke, NIH, Bethesda, MD 20892
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29
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Nordin A, Pagella P, Zambanini G, Cantù C. Exhaustive identification of genome-wide binding events of transcriptional regulators. Nucleic Acids Res 2024; 52:e40. [PMID: 38499482 DOI: 10.1093/nar/gkae180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 02/20/2024] [Accepted: 02/29/2024] [Indexed: 03/20/2024] Open
Abstract
Genome-wide binding assays aspire to map the complete binding pattern of gene regulators. Common practice relies on replication-duplicates or triplicates-and high stringency statistics to favor false negatives over false positives. Here we show that duplicates and triplicates of CUT&RUN are not sufficient to discover the entire activity of transcriptional regulators. We introduce ICEBERG (Increased Capture of Enrichment By Exhaustive Replicate aGgregation), a pipeline that harnesses large numbers of CUT&RUN replicates to discover the full set of binding events and chart the line between false positives and false negatives. We employed ICEBERG to map the full set of H3K4me3-marked regions, the targets of the co-factor β-catenin, and those of the transcription factor TBX3, in human colorectal cancer cells. The ICEBERG datasets allow benchmarking of individual replicates, comparing the performance of peak calling and replication approaches, and expose the arbitrary nature of strategies to identify reproducible peaks. Instead of a static view of genomic targets, ICEBERG establishes a spectrum of detection probabilities across the genome for a given factor, underlying the intrinsic dynamicity of its mechanism of action, and permitting to distinguish frequent from rare regulation events. Finally, ICEBERG discovered instances, undetectable with other approaches, that underlie novel mechanisms of colorectal cancer progression.
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Affiliation(s)
- Anna Nordin
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Pierfrancesco Pagella
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Gianluca Zambanini
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Claudio Cantù
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
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30
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Saotome M, Poduval DB, Grimm SA, Nagornyuk A, Gunarathna S, Shimbo T, Wade PA, Takaku M. Genomic transcription factor binding site selection is edited by the chromatin remodeling factor CHD4. Nucleic Acids Res 2024; 52:3607-3622. [PMID: 38281186 DOI: 10.1093/nar/gkae025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 12/19/2023] [Accepted: 01/04/2024] [Indexed: 01/30/2024] Open
Abstract
Biologically precise enhancer licensing by lineage-determining transcription factors enables activation of transcripts appropriate to biological demand and prevents deleterious gene activation. This essential process is challenged by the millions of matches to most transcription factor binding motifs present in many eukaryotic genomes, leading to questions about how transcription factors achieve the exquisite specificity required. The importance of chromatin remodeling factors to enhancer activation is highlighted by their frequent mutation in developmental disorders and in cancer. Here, we determine the roles of CHD4 in enhancer licensing and maintenance in breast cancer cells and during cellular reprogramming. In unchallenged basal breast cancer cells, CHD4 modulates chromatin accessibility. Its depletion leads to redistribution of transcription factors to previously unoccupied sites. During cellular reprogramming induced by the pioneer factor GATA3, CHD4 activity is necessary to prevent inappropriate chromatin opening. Mechanistically, CHD4 promotes nucleosome positioning over GATA3 binding motifs to compete with transcription factor-DNA interaction. We propose that CHD4 acts as a chromatin proof-reading enzyme that prevents unnecessary gene expression by editing chromatin binding activities of transcription factors.
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Affiliation(s)
- Mika Saotome
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, USA
| | - Deepak B Poduval
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, USA
| | - Sara A Grimm
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Aerica Nagornyuk
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, USA
| | - Sakuntha Gunarathna
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, USA
| | - Takashi Shimbo
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Paul A Wade
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Motoki Takaku
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, USA
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31
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Hong Q, Zhou G, Qin Y, Shen J, Li H. SadNet: a novel multimodal fusion network for protein-ligand binding affinity prediction. Phys Chem Chem Phys 2024; 26:12880-12891. [PMID: 38625412 DOI: 10.1039/d3cp05664c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Protein-ligand binding affinity prediction plays an important role in the field of drug discovery. Existing deep learning-based approaches have significantly improved the efficiency of protein-ligand binding affinity prediction through their excellent inductive bias capability. However, these methods only focus on fragmented three-dimensional data, which truncates the integrity of pocket data, leading to the neglect of potential long-range interactions. In this paper, we propose a dual-stream framework, with amino acid sequence assisting the atomic data fusion for graph neural network (termed SadNet), to fuse both 3D atomic data and sequence data for more accurate prediction results. In detail, SadNet consists of a pocket module and a sequence module. The sequence module expands the "receptive field" of the pocket module through a mid-term virtual node fusion. To better integrate sequence-level information from the sequence module and 3D structural information from the pocket module, we incorporate structural information for each amino acid within the sequence module. Besides, to better understand the intrinsic relationship between sequences and 3D atomic information, our SadNet utilizes information stacking from both the early stage and later stage. Experimental results on publicly available benchmark datasets demonstrate the superiority of the proposed dual-stream approach over the state-of-the-art alternatives. The code of this work is available online at https://github.com/wardhong/SadNet.
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Affiliation(s)
- Qiansen Hong
- Nanjing University of Posts and Telecommunications, NanJing, China.
| | - Guoqiang Zhou
- Nanjing University of Posts and Telecommunications, NanJing, China.
| | - Yuke Qin
- Nanjing University of Posts and Telecommunications, NanJing, China.
| | - Jun Shen
- University of Wollongong, Australia
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Lu Z, Xie S, Su H, Han S, Huang H, Zhou X. Identification of G-quadruplex-interacting proteins in living cells using an artificial G4-targeting biotin ligase. Nucleic Acids Res 2024; 52:e37. [PMID: 38452210 DOI: 10.1093/nar/gkae126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 01/30/2024] [Accepted: 02/11/2024] [Indexed: 03/09/2024] Open
Abstract
G-quadruplexes (G4s) are noncanonical nucleic acid structures pivotal to cellular processes and disease pathways. Deciphering G4-interacting proteins is imperative for unraveling G4's biological significance. In this study, we developed a G4-targeting biotin ligase named G4PID, meticulously assessing its binding affinity and specificity both in vitro and in vivo. Capitalizing on G4PID, we devised a tailored approach termed G-quadruplex-interacting proteins specific biotin-ligation procedure (PLGPB) to precisely profile G4-interacting proteins. Implementing this innovative strategy in live cells, we unveiled a cohort of 149 potential G4-interacting proteins, which exhibiting multifaceted functionalities. We then substantiate the directly binding affinity of 7 candidate G4-interacting-proteins (SF3B4, FBL, PP1G, BCL7C, NDUV1, ILF3, GAR1) in vitro. Remarkably, we verified that splicing factor 3B subunit 4 (SF3B4) binds preferentially to the G4-rich 3' splice site and the corresponding splicing sites are modulated by the G4 stabilizer PDS, indicating the regulating role of G4s in mRNA splicing procedure. The PLGPB strategy could biotinylate multiple proteins simultaneously, which providing an opportunity to map G4-interacting proteins network in living cells.
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Affiliation(s)
- Ziang Lu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei 430072, P.R. China
| | - Shengjie Xie
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei 430072, P.R. China
| | - Haomiao Su
- Department of Chemistry, Yale University, 600 West Campus Drive West Haven, West Haven, CT 06516, USA
| | - Shaoqing Han
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei 430072, P.R. China
| | - Haiyan Huang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei 430072, P.R. China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei 430072, P.R. China
- Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei 430072, P.R. China
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Raimer Young HM, Hou PC, Bartosik AR, Atkin ND, Wang L, Wang Z, Ratan A, Zang C, Wang YH. DNA fragility at topologically associated domain boundaries is promoted by alternative DNA secondary structure and topoisomerase II activity. Nucleic Acids Res 2024; 52:3837-3855. [PMID: 38452213 DOI: 10.1093/nar/gkae164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 02/03/2024] [Accepted: 02/23/2024] [Indexed: 03/09/2024] Open
Abstract
CCCTC-binding factor (CTCF) binding sites are hotspots of genome instability. Although many factors have been associated with CTCF binding site fragility, no study has integrated all fragility-related factors to understand the mechanism(s) of how they work together. Using an unbiased, genome-wide approach, we found that DNA double-strand breaks (DSBs) are enriched at strong, but not weak, CTCF binding sites in five human cell types. Energetically favorable alternative DNA secondary structures underlie strong CTCF binding sites. These structures coincided with the location of topoisomerase II (TOP2) cleavage complex, suggesting that DNA secondary structure acts as a recognition sequence for TOP2 binding and cleavage at CTCF binding sites. Furthermore, CTCF knockdown significantly increased DSBs at strong CTCF binding sites and at CTCF sites that are located at topologically associated domain (TAD) boundaries. TAD boundary-associated CTCF sites that lost CTCF upon knockdown displayed increased DSBs when compared to the gained sites, and those lost sites are overrepresented with G-quadruplexes, suggesting that the structures act as boundary insulators in the absence of CTCF, and contribute to increased DSBs. These results model how alternative DNA secondary structures facilitate recruitment of TOP2 to CTCF binding sites, providing mechanistic insight into DNA fragility at CTCF binding sites.
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Affiliation(s)
- Heather M Raimer Young
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908-0733, USA
| | - Pei-Chi Hou
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908-0733, USA
| | - Anna R Bartosik
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908-0733, USA
| | - Naomi D Atkin
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908-0733, USA
| | - Lixin Wang
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
| | - Zhenjia Wang
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA 22908-0717, USA
| | - Aakrosh Ratan
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908-0733, USA
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA 22908-0717, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
- University of Virginia Comprehensive Cancer Center, Charlottesville, VA 22908, USA
| | - Chongzhi Zang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908-0733, USA
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA 22908-0717, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
- University of Virginia Comprehensive Cancer Center, Charlottesville, VA 22908, USA
| | - Yuh-Hwa Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908-0733, USA
- University of Virginia Comprehensive Cancer Center, Charlottesville, VA 22908, USA
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Hawley SA, Russell FM, Hardie DG. AMP-activated protein kinase can be allosterically activated by ADP but AMP remains the key activating ligand. Biochem J 2024; 481:587-599. [PMID: 38592738 DOI: 10.1042/bcj20240082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/02/2024] [Accepted: 04/09/2024] [Indexed: 04/10/2024]
Abstract
The AMP-activated protein kinase (AMPK) is a sensor of cellular energy status. When activated by increases in ADP:ATP and/or AMP:ATP ratios (signalling energy deficit), AMPK acts to restore energy balance. Binding of AMP to one or more of three CBS repeats (CBS1, CBS3, CBS4) on the AMPK-γ subunit activates the kinase complex by three complementary mechanisms: (i) promoting α-subunit Thr172 phosphorylation by the upstream kinase LKB1; (ii) protecting against Thr172 dephosphorylation; (iii) allosteric activation. Surprisingly, binding of ADP has been reported to mimic the first two effects, but not the third. We now show that at physiologically relevant concentrations of Mg.ATP2- (above those used in the standard assay) ADP binding does cause allosteric activation. However, ADP causes only a modest activation because (unlike AMP), at concentrations just above those where activation becomes evident, ADP starts to cause competitive inhibition at the catalytic site. Our results cast doubt on the physiological relevance of the effects of ADP and suggest that AMP is the primary activator in vivo. We have also made mutations to hydrophobic residues involved in binding adenine nucleotides at each of the three γ subunit CBS repeats of the human α2β2γ1 complex and examined their effects on regulation by AMP and ADP. Mutation of the CBS3 site has the largest effects on all three mechanisms of AMP activation, especially at lower ATP concentrations, while mutation of CBS4 reduces the sensitivity to AMP. All three sites appear to be required for allosteric activation by ADP.
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Affiliation(s)
- Simon A Hawley
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, U.K
| | - Fiona M Russell
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, U.K
| | - D Grahame Hardie
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, U.K
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Hao MS, Mazurkewich S, Li H, Kvammen A, Saha S, Koskela S, Inman AR, Nakajima M, Tanaka N, Nakai H, Brändén G, Bulone V, Larsbrink J, McKee LS. Structural and biochemical analysis of family 92 carbohydrate-binding modules uncovers multivalent binding to β-glucans. Nat Commun 2024; 15:3429. [PMID: 38653764 DOI: 10.1038/s41467-024-47584-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 04/08/2024] [Indexed: 04/25/2024] Open
Abstract
Carbohydrate-binding modules (CBMs) are non-catalytic proteins found appended to carbohydrate-active enzymes. Soil and marine bacteria secrete such enzymes to scavenge nutrition, and they often use CBMs to improve reaction rates and retention of released sugars. Here we present a structural and functional analysis of the recently established CBM family 92. All proteins analysed bind preferentially to β-1,6-glucans. This contrasts with the diversity of predicted substrates among the enzymes attached to CBM92 domains. We present crystal structures for two proteins, and confirm by mutagenesis that tryptophan residues permit ligand binding at three distinct functional binding sites on each protein. Multivalent CBM families are uncommon, so the establishment and structural characterisation of CBM92 enriches the classification database and will facilitate functional prediction in future projects. We propose that CBM92 proteins may cross-link polysaccharides in nature, and might have use in novel strategies for enzyme immobilisation.
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Affiliation(s)
- Meng-Shu Hao
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311215, China
| | - Scott Mazurkewich
- Department of Life Sciences, Chalmers University of Technology, 41296, Gothenburg, Sweden
- Wallenberg Wood Science Center, Teknikringen 56-58, 10044, Stockholm, Sweden
| | - He Li
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden
| | - Alma Kvammen
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden
| | - Srijani Saha
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden
| | - Salla Koskela
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden
- Wallenberg Wood Science Center, Teknikringen 56-58, 10044, Stockholm, Sweden
| | - Annie R Inman
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden
| | - Masahiro Nakajima
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Nobukiyo Tanaka
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Hiroyuki Nakai
- Faculty of Agriculture, Niigata University, Niigata, 950-2181, Japan
| | - Gisela Brändén
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-405 30, Gothenburg, Sweden
| | - Vincent Bulone
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden
- College of Medicine and Public Health, Flinders University, Bedford Park Campus, Sturt Road, SA, 5042, Australia
| | - Johan Larsbrink
- Department of Life Sciences, Chalmers University of Technology, 41296, Gothenburg, Sweden
- Wallenberg Wood Science Center, Teknikringen 56-58, 10044, Stockholm, Sweden
| | - Lauren S McKee
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden.
- Wallenberg Wood Science Center, Teknikringen 56-58, 10044, Stockholm, Sweden.
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36
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Nguyen DM, Rath DH, Devost D, Pétrin D, Rizk R, Ji AX, Narayanan N, Yong D, Zhai A, Kuntz DA, Mian MUQ, Pomroy NC, Keszei AFA, Benlekbir S, Mazhab-Jafari MT, Rubinstein JL, Hébert TE, Privé GG. Structure and dynamics of a pentameric KCTD5/CUL3/Gβγ E3 ubiquitin ligase complex. Proc Natl Acad Sci U S A 2024; 121:e2315018121. [PMID: 38625940 DOI: 10.1073/pnas.2315018121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 03/07/2024] [Indexed: 04/18/2024] Open
Abstract
Heterotrimeric G proteins can be regulated by posttranslational modifications, including ubiquitylation. KCTD5, a pentameric substrate receptor protein consisting of an N-terminal BTB domain and a C-terminal domain, engages CUL3 to form the central scaffold of a cullin-RING E3 ligase complex (CRL3KCTD5) that ubiquitylates Gβγ and reduces Gβγ protein levels in cells. The cryo-EM structure of a 5:5:5 KCTD5/CUL3NTD/Gβ1γ2 assembly reveals a highly dynamic complex with rotations of over 60° between the KCTD5BTB/CUL3NTD and KCTD5CTD/Gβγ moieties of the structure. CRL3KCTD5 engages the E3 ligase ARIH1 to ubiquitylate Gβγ in an E3-E3 superassembly, and extension of the structure to include full-length CUL3 with RBX1 and an ARIH1~ubiquitin conjugate reveals that some conformational states position the ARIH1~ubiquitin thioester bond to within 10 Å of lysine-23 of Gβ and likely represent priming complexes. Most previously described CRL/substrate structures have consisted of monovalent complexes and have involved flexible peptide substrates. The structure of the KCTD5/CUL3NTD/Gβγ complex shows that the oligomerization of a substrate receptor can generate a polyvalent E3 ligase complex and that the internal dynamics of the substrate receptor can position a structured target for ubiquitylation in a CRL3 complex.
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Affiliation(s)
- Duc Minh Nguyen
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Deanna H Rath
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Dominic Devost
- Department of Pharmacology and Therapeutics, McGill University, Montréal, QC H3G 1Y6, Canada
| | - Darlaine Pétrin
- Department of Pharmacology and Therapeutics, McGill University, Montréal, QC H3G 1Y6, Canada
| | - Robert Rizk
- Department of Pharmacology and Therapeutics, McGill University, Montréal, QC H3G 1Y6, Canada
| | - Alan X Ji
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Naveen Narayanan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Darren Yong
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Andrew Zhai
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Douglas A Kuntz
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Maha U Q Mian
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Neil C Pomroy
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Alexander F A Keszei
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Samir Benlekbir
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Mohammad T Mazhab-Jafari
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - John L Rubinstein
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - Terence E Hébert
- Department of Pharmacology and Therapeutics, McGill University, Montréal, QC H3G 1Y6, Canada
| | - Gilbert G Privé
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
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37
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Xiao T, Li X, Felsenfeld G. The Myc-associated zinc finger protein epigenetically controls expression of interferon-γ-stimulated genes by recruiting STAT1 to chromatin. Proc Natl Acad Sci U S A 2024; 121:e2320938121. [PMID: 38635637 DOI: 10.1073/pnas.2320938121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 03/22/2024] [Indexed: 04/20/2024] Open
Abstract
The MYC-Associated Zinc Finger Protein (MAZ) plays important roles in chromatin organization and gene transcription regulation. Dysregulated expression of MAZ causes diseases, such as glioblastoma, breast cancer, prostate cancer, and liposarcoma. Previously, it has been reported that MAZ controls the proinflammatory response in colitis and colon cancer via STAT3 signaling, suggesting that MAZ is involved in regulating immunity-related pathways. However, the molecular mechanism underlying this regulation remains elusive. Here, we investigate the regulatory effect of MAZ on interferon-gamma (IFN-γ)-stimulated genes via STAT1, a protein that plays an essential role in immune responses to viral, fungal, and mycobacterial pathogens. We demonstrate that about 80% of occupied STAT1-binding sites colocalize with occupied MAZ-binding sites in HAP1/K562 cells after IFN-γ stimulation. MAZ depletion significantly reduces STAT1 binding in the genome. By analyzing genome-wide gene expression profiles in the RNA-Seq data, we show that MAZ depletion significantly suppresses a subset of the immune response genes, which include the IFN-stimulated genes IRF8 and Absent in Melanoma 2. Furthermore, we find that MAZ controls expression of the immunity-related genes by changing the epigenetic landscape in chromatin. Our study reveals an important role for MAZ in regulating immune-related gene expression.
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Affiliation(s)
- Tiaojiang Xiao
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH
| | - Xin Li
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH
| | - Gary Felsenfeld
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH
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Peters CH, Singh RK, Langley AA, Nichols WG, Ferris HR, Jeffrey DA, Proenza C, Bankston JR. LRMP inhibits cAMP potentiation of HCN4 channels by disrupting intramolecular signal transduction. eLife 2024; 12:RP92411. [PMID: 38652113 DOI: 10.7554/elife.92411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024] Open
Abstract
Lymphoid restricted membrane protein (LRMP) is a specific regulator of the hyperpolarization-activated cyclic nucleotide-sensitive isoform 4 (HCN4) channel. LRMP prevents cAMP-dependent potentiation of HCN4, but the interaction domains, mechanisms of action, and basis for isoform-specificity remain unknown. Here, we identify the domains of LRMP essential for this regulation, show that LRMP acts by disrupting the intramolecular signal transduction between cyclic nucleotide binding and gating, and demonstrate that multiple unique regions in HCN4 are required for LRMP isoform-specificity. Using patch clamp electrophysiology and Förster resonance energy transfer (FRET), we identified the initial 227 residues of LRMP and the N-terminus of HCN4 as necessary for LRMP to associate with HCN4. We found that the HCN4 N-terminus and HCN4-specific residues in the C-linker are necessary for regulation of HCN4 by LRMP. Finally, we demonstrated that LRMP-regulation can be conferred to HCN2 by addition of the HCN4 N-terminus along with mutation of five residues in the S5 region and C-linker to the cognate HCN4 residues. Taken together, these results suggest that LRMP inhibits HCN4 through an isoform-specific interaction involving the N-terminals of both proteins that prevents the transduction of cAMP binding into a change in channel gating, most likely via an HCN4-specific orientation of the N-terminus, C-linker, and S4-S5 linker.
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Affiliation(s)
- Colin H Peters
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical Campus, Aurora, United States
| | - Rohit K Singh
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical Campus, Aurora, United States
- Skaggs School of Pharmacy, Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, United States
| | - Avery A Langley
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical Campus, Aurora, United States
| | - William G Nichols
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical Campus, Aurora, United States
| | - Hannah R Ferris
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical Campus, Aurora, United States
| | - Danielle A Jeffrey
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical Campus, Aurora, United States
| | - Catherine Proenza
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical Campus, Aurora, United States
- Department of Medicine, Division of Cardiology, University of Colorado Anschutz Medical Campus, Aurora, United States
| | - John R Bankston
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical Campus, Aurora, United States
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39
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Feng Y, Gong C, Zhu J, Liu G, Tang Y, Li W. Unraveling the Ligand-Binding Sites of CYP3A4 by Molecular Dynamics Simulations with Solvent Probes. J Chem Inf Model 2024; 64:3451-3464. [PMID: 38593186 DOI: 10.1021/acs.jcim.4c00089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Cytochrome P450 3A4 (CYP3A4) is one of the most important drug-metabolizing enzymes in the human body and is well known for its complicated, atypical kinetic characteristics. The existence of multiple ligand-binding sites in CYP3A4 has been widely recognized as being capable of interfering with the active pocket through allosteric effects. The identification of ligand-binding sites other than the canonical active site above the heme is especially important for understanding the atypical kinetic characteristics of CYP3A4 and the intriguing association between the ligand and the receptor. In this study, we first employed mixed-solvent molecular dynamics (MixMD) simulations coupled with the online computational predictive tools to explore potential ligand-binding sites in CYP3A4. The MixMD approach demonstrates better performance in dealing with the receptor flexibility compared with other computational tools. From the sites identified by MixMD, we then picked out multiple sites for further exploration using ensemble docking and conventional molecular dynamics (cMD) simulations. Our results indicate that three extra sites are suitable for ligand binding in CYP3A4, including one experimentally confirmed site and two novel sites.
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Affiliation(s)
- Yanjun Feng
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Changda Gong
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Jieyu Zhu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Guixia Liu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Yun Tang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Weihua Li
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
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40
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Tao L, Zhou T, Wu Z, Hu F, Yang S, Kong X, Li C. ESPDHot: An Effective Machine Learning-Based Approach for Predicting Protein-DNA Interaction Hotspots. J Chem Inf Model 2024; 64:3548-3557. [PMID: 38587997 DOI: 10.1021/acs.jcim.3c02011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
Protein-DNA interactions are pivotal to various cellular processes. Precise identification of the hotspot residues for protein-DNA interactions holds great significance for revealing the intricate mechanisms in protein-DNA recognition and for providing essential guidance for protein engineering. Aiming at protein-DNA interaction hotspots, this work introduces an effective prediction method, ESPDHot based on a stacked ensemble machine learning framework. Here, the interface residue whose mutation leads to a binding free energy change (ΔΔG) exceeding 2 kcal/mol is defined as a hotspot. To tackle the imbalanced data set issue, the adaptive synthetic sampling (ADASYN), an oversampling technique, is adopted to synthetically generate new minority samples, thereby rectifying data imbalance. As for molecular characteristics, besides traditional features, we introduce three new characteristic types including residue interface preference proposed by us, residue fluctuation dynamics characteristics, and coevolutionary features. Combining the Boruta method with our previously developed Random Grouping strategy, we obtained an optimal set of features. Finally, a stacking classifier is constructed to output prediction results, which integrates three classical predictors, Support Vector Machine (SVM), XGBoost, and Artificial Neural Network (ANN) as the first layer, and Logistic Regression (LR) algorithm as the second one. Notably, ESPDHot outperforms the current state-of-the-art predictors, achieving superior performance on the independent test data set, with F1, MCC, and AUC reaching 0.571, 0.516, and 0.870, respectively.
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Affiliation(s)
- Lianci Tao
- College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Tong Zhou
- College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Zhixiang Wu
- College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Fangrui Hu
- College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Shuang Yang
- College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Xiaotian Kong
- College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Chunhua Li
- College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China
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41
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Bhattacharya S, Satpati P. Why Does the E1219V Mutation Expand T-Rich PAM Recognition in Cas9 from Streptococcus pyogenes? J Chem Inf Model 2024; 64:3237-3247. [PMID: 38600752 DOI: 10.1021/acs.jcim.3c01515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
Popular RNA-guided DNA endonuclease Cas9 from Streptococcus pyogenes (SpCas9) recognizes the canonical 5'-NGG-3' protospacer adjacent motif (PAM) and triggers double-stranded DNA cleavage activity. Mutations in SpCas9 were demonstrated to expand the PAM readability and hold promise for therapeutic and genome editing applications. However, the energetics of the PAM recognition and its relation to the atomic structure remain unknown. Using the X-ray structure (precatalytic SpCas9:sgRNA:dsDNA) as a template, we calculated the change in the PAM binding affinity in response to SpCas9 mutations using computer simulations. The E1219V mutation in SpCas9 fine-tunes the water accessibility in the PAM binding pocket and promotes new interactions in the SpCas9:noncanonical T-rich PAM, thus weakening the PAM stringency. The nucleotide-specific interaction of two arginine residues (i.e., R1333 and R1335 of SpCas9) ensured stringent 5'-NGG-3' PAM recognition. R1335A substitution (SpCas9R1335A) completely disrupts the direct interaction between SpCas9 and PAM sequences (canonical or noncanonical), accounting for the loss of editing activity. Interestingly, the double mutant (SpCas9R1335A,E1219V) boosts DNA binding affinity by favoring protein:PAM electrostatic contact in a desolvated pocket. The underlying thermodynamics explain the varied DNA cleavage activity of SpCas9 variants. A direct link between the energetics, structures, and activity is highlighted, which can aid in the rational design of improved SpCas9-based genome editing tools.
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Affiliation(s)
- Shreya Bhattacharya
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Priyadarshi Satpati
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
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42
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Kuroiwa F, Suda H, Yabuki M, Atsuzawa K, Yamaguchi H, Toyota M, Kaneko Y, Yamashita S, Takahashi S, Tozawa Y. Cell-free translation system with artificial lipid-monolayer particles as a unique tool for characterizing lipid-monolayer binding proteins. Biosci Biotechnol Biochem 2024; 88:555-560. [PMID: 38444196 DOI: 10.1093/bbb/zbae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 02/20/2024] [Indexed: 03/07/2024]
Abstract
Methods for functional analysis of proteins specifically localizing to lipid monolayers such as rubber particles and lipid droplets are limited. We have succeeded in establishing a system in which artificially prepared lipid monolayer particles are added to a cell-free translation system to confirm the properties of proteins that specifically bind to lipid monolayers in a translation-coupled manner.
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Affiliation(s)
- Fu Kuroiwa
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Hiraku Suda
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Maho Yabuki
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Kimie Atsuzawa
- Comprehensive Analysis Center for Science, Saitama University, Saitama, Japan
| | | | - Masatsugu Toyota
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Yasuko Kaneko
- Department of Natural Science in the Faculty of Education, Saitama University, Saitama, Japan
| | - Satoshi Yamashita
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Japan
| | - Seiji Takahashi
- Graduate School of Engineering, Tohoku University, Sendai, Miyagi, Japan
| | - Yuzuru Tozawa
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
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43
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Macaya L, González D, Vöhringer-Martinez E. Nonbonded Force Field Parameters from MBIS Partitioning of the Molecular Electron Density Improve Binding Affinity Predictions of the T4-Lysozyme Double Mutant. J Chem Inf Model 2024; 64:3269-3277. [PMID: 38546407 DOI: 10.1021/acs.jcim.3c01912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The use of computer simulation for binding affinity prediction is growing in drug discovery. However, its wider use is constrained by the accuracy of the free energy calculations. The key sources of error are the force fields used to depict molecular interactions and insufficient sampling of the configurational space. To improve the quality of the force field, we developed a Python-based computational workflow. The workflow described here uses the minimal basis iterative stockholder (MBIS) method to determine atomic charges and Lennard-Jones parameters from the polarized molecular density. This is done by performing electronic structure calculations on various configurations of the ligand when it is both bound and unbound. In addition, we validated a simulation procedure that accounts for the protein and ligand degrees of freedom to precisely calculate binding free energies. This was achieved by comparing the self-adjusted mixture sampling and nonequilibrium thermodynamic integration methods using various protein and ligand conformations. The accuracy of predicting binding affinity is improved by using MBIS-derived force field parameters and a validated simulation procedure. This improvement surpasses the chemical precision for the eight aromatic ligands, reaching a root-mean-square error of 0.7 kcal/mol.
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Affiliation(s)
- Luis Macaya
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, 4070386 Concepción, Chile
| | - Duván González
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, 4070386 Concepción, Chile
| | - Esteban Vöhringer-Martinez
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, 4070386 Concepción, Chile
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44
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Graef J, Ehrt C, Reim T, Rarey M. Database-Driven Identification of Structurally Similar Protein-Protein Interfaces. J Chem Inf Model 2024; 64:3332-3349. [PMID: 38470439 DOI: 10.1021/acs.jcim.3c01462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Analyzing the similarity of protein interfaces in protein-protein interactions gives new insights into protein function and assists in discovering new drugs. Usually, tools that assess the similarity focus on the interactions between two protein interfaces, while sometimes we only have one predicted interface. Herein, we present PiMine, a database-driven protein interface similarity search. It compares interface residues of one or two interacting chains by calculating and searching tetrahedral geometric patterns of α-carbon atoms and calculating physicochemical and shape-based similarity. On a dedicated, tailor-made dataset, we show that PiMine outperforms commonly used comparison tools in terms of early enrichment when considering interfaces of sequentially and structurally unrelated proteins. In an application example, we demonstrate its usability for protein interaction partner prediction by comparing predicted interfaces to known protein-protein interfaces.
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Affiliation(s)
- Joel Graef
- Universität Hamburg, ZBH─Center for Bioinformatics , Albert-Einstein-Ring 8-10, 22761 Hamburg, Germany
| | - Christiane Ehrt
- Universität Hamburg, ZBH─Center for Bioinformatics , Albert-Einstein-Ring 8-10, 22761 Hamburg, Germany
| | - Thorben Reim
- Universität Hamburg, ZBH─Center for Bioinformatics , Albert-Einstein-Ring 8-10, 22761 Hamburg, Germany
| | - Matthias Rarey
- Universität Hamburg, ZBH─Center for Bioinformatics , Albert-Einstein-Ring 8-10, 22761 Hamburg, Germany
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45
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Samanta R, Zhuang X, Varney KM, Weber DJ, Matysiak S. Deciphering S100B Allosteric Signaling: The Role of a Peptide Target, TRTK-12, as an Ensemble Modulator. J Chem Inf Model 2024; 64:3477-3487. [PMID: 38605537 DOI: 10.1021/acs.jcim.4c00116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
Allostery is an essential biological phenomenon in which perturbation at one site in a biomolecule elicits a functional response at a distal location(s). It is integral to biological processes, such as cellular signaling, metabolism, and transcription regulation. Understanding allostery is also crucial for rational drug discovery. In this work, we focus on an allosteric S100B protein that belongs to the S100 class of EF-hand Ca2+-binding proteins. The Ca2+-binding affinity of S100B is modulated allosterically by TRTK-12 peptide binding 25 Å away from the Ca2+-binding site. We investigated S100B allostery by carrying out nuclear magnetic resonance (NMR) measurements along with microsecond-long molecular dynamics (MD) simulations on S100B/Ca2+ with/without TRTK-12 at different NaCl salt concentrations. NMR HSQC results show that TRTK-12 reorganizes how S100B/Ca2+ responds to different salt concentrations at both orthosteric and allosteric sites. The MD data suggest that TRTK-12 breaks the dynamic aromatic and hydrogen-bond interactions (not observed in X-ray crystallographic structures) between the hinge/helix and Ca2+-binding EF-hand loop of the two subunits in the homodimeric protein. This triggers rearrangement in the protein network architectures and leads to allosteric communication. Finally, computational studies of S100B at distinct ionic strengths suggest that ligand-bound species are more robust to the changing environment relative to the S100B/Ca2+ complex.
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Affiliation(s)
- Riya Samanta
- Biophysics Graduate Program, University of Maryland, College Park, Maryland 20742, United States
| | - Xinhao Zhuang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Kristen M Varney
- Department of Biochemistry and Molecular Biology, University of Maryland, Baltimore, Maryland 20742, United States
| | - David J Weber
- IBBR, Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Silvina Matysiak
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
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46
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Ovek D, Keskin O, Gursoy A. ProInterVal: Validation of Protein-Protein Interfaces through Learned Interface Representations. J Chem Inf Model 2024; 64:2979-2987. [PMID: 38526504 DOI: 10.1021/acs.jcim.3c01788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
Proteins are vital components of the biological world and serve a multitude of functions. They interact with other molecules through their interfaces and participate in crucial cellular processes. Disruption of these interactions can have negative effects on organisms, highlighting the importance of studying protein-protein interfaces for developing targeted therapies for diseases. Therefore, the development of a reliable method for investigating protein-protein interactions is of paramount importance. In this work, we present an approach for validating protein-protein interfaces using learned interface representations. The approach involves using a graph-based contrastive autoencoder architecture and a transformer to learn representations of protein-protein interaction interfaces from unlabeled data and then validating them through learned representations with a graph neural network. Our method achieves an accuracy of 0.91 for the test set, outperforming existing GNN-based methods. We demonstrate the effectiveness of our approach on a benchmark data set and show that it provides a promising solution for validating protein-protein interfaces.
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Affiliation(s)
- Damla Ovek
- KUIS AI Center, Koç University, Istanbul 34450, Turkey
- Computer Engineering, Koç University, Istanbul 34450, Turkey
| | - Ozlem Keskin
- Chemical and Biological Engineering, Koç University, Istanbul 34450, Turkey
| | - Attila Gursoy
- Computer Engineering, Koç University, Istanbul 34450, Turkey
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47
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Wang TH, Shao HP, Zhao BQ, Zhai HL. Molecular Insights into the Variability in Infection and Immune Evasion Capabilities of SARS-CoV-2 Variants: A Sequence and Structural Investigation of the RBD Domain. J Chem Inf Model 2024; 64:3503-3523. [PMID: 38517012 DOI: 10.1021/acs.jcim.3c01730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
As severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants continuously emerge, an increasing number of mutations are accumulating in the Spike protein receptor-binding domain (RBD) region. Through sequence analysis of various Variants of Concern (VOC), we identified that they predominantly fall within the ο lineage although recent variants introduce any novel mutations in the RBD. Molecular dynamics simulations were employed to compute the binding free energy of these variants with human Angiotensin-converting enzyme 2 (ACE2). Structurally, the binding interface of the ο RBD displays a strong positive charge, complementing the negatively charged binding interface of ACE2, resulting in a significant enhancement in the electrostatic potential energy for the ο variants. Although the increased potential energy is partially offset by the rise in polar solvation free energy, enhanced electrostatic potential contributes to the long-range recognition between the ο variant's RBD and ACE2. We also conducted simulations of glycosylated ACE2-RBD proteins. The newly emerged ο (JN.1) variant has added a glycosylation site at N-354@RBD, which significantly weakened its binding affinity with ACE2. Further, our interaction studies with three monoclonal antibodies across multiple SARS-CoV-2 strains revealed a diminished neutralization efficacy against the ο variants, primarily attributed to the electrostatic repulsion between the antibodies and RBD interface. Considering the characteristics of the ο variant and the trajectory of emerging strains, we propose that newly developed antibodies against SARS-CoV-2 RBD should have surfaces rich in negative potential and, postbinding, exhibit strong van der Waals interactions. These findings provide invaluable guidance for the formulation of future therapeutic strategies.
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Affiliation(s)
- Tian Hua Wang
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou 730000, P. R. China
| | - Hai Ping Shao
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou 730000, P. R. China
| | - Bing Qiang Zhao
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou 730000, P. R. China
| | - Hong Lin Zhai
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou 730000, P. R. China
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48
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Gu Z, Yan Y, Liu H, Wu D, Yao H, Lin K, Li X. Discovery of Covalent Lead Compounds Targeting 3CL Protease with a Lateral Interactions Spiking Neural Network. J Chem Inf Model 2024; 64:3047-3058. [PMID: 38520328 DOI: 10.1021/acs.jcim.3c01900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2024]
Abstract
Covalent drugs exhibit advantages in that noncovalent drugs cannot match, and covalent docking is an important method for screening covalent lead compounds. However, it is difficult for covalent docking to screen covalent compounds on a large scale because covalent docking requires determination of the covalent reaction type of the compound. Here, we propose to use deep learning of a lateral interactions spiking neural network to construct a covalent lead compound screening model to quickly screen covalent lead compounds. We used the 3CL protease (3CL Pro) of SARS-CoV-2 as the screen target and constructed two classification models based on LISNN to predict the covalent binding and inhibitory activity of compounds. The two classification models were trained on the covalent complex data set targeting cysteine (Cys) and the compound inhibitory activity data set targeting 3CL Pro, respected, with good prediction accuracy (ACC > 0.9). We then screened the screening compound library with 6 covalent binding screening models and 12 inhibitory activity screening models. We tested the inhibitory activity of the 32 compounds, and the best compound inhibited SARS-CoV-2 3CL Pro with an IC50 value of 369.5 nM. Further assay implied that dithiothreitol can affect the inhibitory activity of the compound to 3CL Pro, indicating that the compound may covalently bind 3CL Pro. The selectivity test showed that the compound had good target selectivity to 3CL Pro over cathepsin L. These correlation assays can prove the rationality of the covalent lead compound screening model. Finally, covalent docking was performed to demonstrate the binding conformation of the compound with 3CL Pro. The source code can be obtained from the GitHub repository (https://github.com/guzh970630/Screen_Covalent_Compound_by_LISNN).
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Affiliation(s)
- Zhihao Gu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yong Yan
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Hanwen Liu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Di Wu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Hequan Yao
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Kejiang Lin
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Xuanyi Li
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
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49
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Zou Y, Guan L, Tan J, Qi B, Sun Y, Huang F, Zhang Q. Molecular Insights into the Differential Effects of Acetylation on the Aggregation of Tau Microtubule-Binding Repeats. J Chem Inf Model 2024; 64:3386-3399. [PMID: 38489841 DOI: 10.1021/acs.jcim.3c01929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2024]
Abstract
Aggregation of tau protein into intracellular fibrillary inclusions is characterized as the hallmark of tauopathies, including Alzheimer's disease and chronic traumatic encephalopathy. The microtubule-binding (MTB) domain of tau, containing either three or four repeats with sequence similarities, plays an important role in determining tau's aggregation. Previous studies have reported that abnormal acetylation of lysine residues displays a distinct effect on the formation of pathological tau aggregates. However, the underlying molecular mechanism remains mostly elusive. In this study, we performed extensive replica exchange molecular dynamics (REMD) simulations of 144 μs in total to systematically investigate the dimerization of four tau MTB repeats and explore the impacts of Lys280 (K280) or Lys321 (K321) acetylation on the conformational ensembles of the R2 or R3 dimer. Our results show that R3 is the most prone to aggregation among the four repeats, followed by R2 and R4, while R1 displays the weakest aggregation propensity with a disordered structure. Acetylation of K280 could promote the aggregation of R2 peptides by increasing the formation of β-sheet structures and strengthening the interchain interaction. However, K321 acetylation decreases the β-sheet content of the R3 dimer, reduces the ability of R3 peptides to form long β-strands, and promotes the stable helix structure formation. The salt bridge and Y310-Y310 π-π stacking interactions of the R3 dimer are greatly weakened by K321 acetylation, resulting in the inhibition of dimerization. This study uncovers the structural ensembles of tau MTB repeats and provides mechanistic insights into the influences of acetylation on tau aggregation, which may deepen the understanding of the pathogenesis of tauopathies.
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Affiliation(s)
- Yu Zou
- Department of Sport and Exercise Science, College of Education, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, Zhejiang, P. R. China
| | - Lulu Guan
- Department of Sport and Exercise Science, College of Education, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, Zhejiang, P. R. China
| | - Jingwang Tan
- Department of Sport and Exercise Science, College of Education, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, Zhejiang, P. R. China
| | - Bote Qi
- Department of Sport and Exercise Science, College of Education, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, Zhejiang, P. R. China
| | - Yunxiang Sun
- Department of Physics, Ningbo University, 818 Fenghua Road, Ningbo 315211, Zhejiang, P. R. China
| | - Fengjuan Huang
- Ningbo Institute of Innovation for Combined Medicine and Engineering (NIIME), Ningbo Medical Center Lihuili Hospital, Ningbo 315211, Zhejiang, P. R. China
| | - Qingwen Zhang
- College of Physical Education, Shanghai University of Sport, 399 Changhai Road, Shanghai 200438, P. R. China
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50
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Wu X, Hou W, Zhao Z, Huang L, Sheng N, Yang Q, Zhang S, Wang Y. MMGAT: a graph attention network framework for ATAC-seq motifs finding. BMC Bioinformatics 2024; 25:158. [PMID: 38643066 PMCID: PMC11031952 DOI: 10.1186/s12859-024-05774-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/10/2024] [Indexed: 04/22/2024] Open
Abstract
BACKGROUND Motif finding in Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) data is essential to reveal the intricacies of transcription factor binding sites (TFBSs) and their pivotal roles in gene regulation. Deep learning technologies including convolutional neural networks (CNNs) and graph neural networks (GNNs), have achieved success in finding ATAC-seq motifs. However, CNN-based methods are limited by the fixed width of the convolutional kernel, which makes it difficult to find multiple transcription factor binding sites with different lengths. GNN-based methods has the limitation of using the edge weight information directly, makes it difficult to aggregate the neighboring nodes' information more efficiently when representing node embedding. RESULTS To address this challenge, we developed a novel graph attention network framework named MMGAT, which employs an attention mechanism to adjust the attention coefficients among different nodes. And then MMGAT finds multiple ATAC-seq motifs based on the attention coefficients of sequence nodes and k-mer nodes as well as the coexisting probability of k-mers. Our approach achieved better performance on the human ATAC-seq datasets compared to existing tools, as evidenced the highest scores on the precision, recall, F1_score, ACC, AUC, and PRC metrics, as well as finding 389 higher quality motifs. To validate the performance of MMGAT in predicting TFBSs and finding motifs on more datasets, we enlarged the number of the human ATAC-seq datasets to 180 and newly integrated 80 mouse ATAC-seq datasets for multi-species experimental validation. Specifically on the mouse ATAC-seq dataset, MMGAT also achieved the highest scores on six metrics and found 356 higher-quality motifs. To facilitate researchers in utilizing MMGAT, we have also developed a user-friendly web server named MMGAT-S that hosts the MMGAT method and ATAC-seq motif finding results. CONCLUSIONS The advanced methodology MMGAT provides a robust tool for finding ATAC-seq motifs, and the comprehensive server MMGAT-S makes a significant contribution to genomics research. The open-source code of MMGAT can be found at https://github.com/xiaotianr/MMGAT , and MMGAT-S is freely available at https://www.mmgraphws.com/MMGAT-S/ .
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Affiliation(s)
- Xiaotian Wu
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, 130012, China
- School of Artificial Intelligence, Jilin University, Changchun, 130012, China
| | - Wenju Hou
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, 130012, China
| | - Ziqi Zhao
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, 130012, China
| | - Lan Huang
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, 130012, China
| | - Nan Sheng
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, 130012, China
| | - Qixing Yang
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, 130012, China
| | - Shuangquan Zhang
- School of Cyber Science and Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China.
| | - Yan Wang
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, 130012, China.
- School of Artificial Intelligence, Jilin University, Changchun, 130012, China.
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