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Choi JY, Chung E. Molecular Dynamics Simulations of Matrix Metalloproteinase 13 and the Analysis of the Specificity Loop and the S1'-Site. Int J Mol Sci 2023; 24:10577. [PMID: 37445757 PMCID: PMC10342107 DOI: 10.3390/ijms241310577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 05/05/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
The specificity loop of Matrix Metalloproteinases (MMPs) is known to regulate recognition of their substrates, and the S1'-site surrounded by the loop is a unique place to address the selectivity of ligands toward each MMP. Molecular dynamics (MD) simulations of apo-MMP-13 and its complex forms with various ligands were conducted to identify the role of the specificity loop for the ligand binding to MMP-13. The MD simulations showed the dual role of T247 as a hydrogen bond donor to the ligand, as well as a contributor to the formation of the van der Waal surface area, with T245 and K249 on the S1'-site. The hydrophobic surface area mediated by T247 blocks the access of water molecules to the S1'-site of MMP-13 and stabilizes the ligand in the site. The F252 residue is flexible in order to search for the optimum location in the S1'-site of the apo-MMP-13, but once a ligand binds to the S1'-site, it can form offset π-π or edge-to-π stacking interactions with the ligand. Lastly, H222 and Y244 provide the offset π-π and π-CH(Cβ) interactions on each side of the phenyl ring of the ligand, and this sandwiched interaction could be critical for the ligand binding to MMP-13.
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Affiliation(s)
- Jun Yong Choi
- Department of Chemistry and Biochemistry, Queens College, Flushing, NY 11367, USA
- Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
| | - Eugene Chung
- Department of Chemistry and Biochemistry, Queens College, Flushing, NY 11367, USA
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Kim DH, Kim MJ, Kwak SY, Jeong J, Choi D, Choi SW, Ryu J, Kang KS. Bioengineered liver crosslinked with nano-graphene oxide enables efficient liver regeneration via MMP suppression and immunomodulation. Nat Commun 2023; 14:801. [PMID: 36781854 PMCID: PMC9925774 DOI: 10.1038/s41467-023-35941-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 01/09/2023] [Indexed: 02/15/2023] Open
Abstract
Decellularized extracellular matrix scaffold, widely utilized for organ engineering, often undergoes matrix decomposition after transplantation and produces byproducts that cause inflammation, leading to clinical failure. Here we propose a strategy using nano-graphene oxide to modify the biophysical properties of decellularized liver scaffolds. Notably, we demonstrate that scaffolds crosslinked with nano-graphene oxide show high resistance to enzymatic degradation via direct inhibition of matrix metalloproteinase activity and increased mechanical rigidity. We find that M2-like macrophage polarization is promoted within the crosslinked scaffolds, which reduces graft-elicited inflammation. Moreover, we show that low activities of matrix metalloproteinases, attributed to both nano-graphene oxide and tissue inhibitors of metalloproteinases expressed by M2c, can protect the crosslinked scaffolds against in vivo degradation. Lastly, we demonstrate that bioengineered livers fabricated with the crosslinked scaffolds remain functional, thereby effectively regenerating damaged livers after transplantation into liver failure mouse models. Overall, nano-graphene oxide crosslinking prolongs allograft survival and ultimately improves therapeutic effects of bioengineered livers, which offer an alternative for donor organs.
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Affiliation(s)
- Da-Hyun Kim
- Adult Stem Cell Research Center and Research Institute for Veterinary Medicine, College of Veterinary Medicine, Seoul National University, Seoul, 08826, Republic of Korea
| | - Min-Ji Kim
- Adult Stem Cell Research Center and Research Institute for Veterinary Medicine, College of Veterinary Medicine, Seoul National University, Seoul, 08826, Republic of Korea
| | - Seon-Yeong Kwak
- Department of Agriculture, Forestry and Life Science, College of Agriculture and Life Science, Seoul National University, Seoul, 08826, Republic of Korea.,Bio-MAX Institute, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jaemin Jeong
- Department of Surgery, Hanyang University College of Medicine, Seoul, 04763, Republic of Korea
| | - Dongho Choi
- Department of Surgery, Hanyang University College of Medicine, Seoul, 04763, Republic of Korea
| | - Soon Won Choi
- Adult Stem Cell Research Center and Research Institute for Veterinary Medicine, College of Veterinary Medicine, Seoul National University, Seoul, 08826, Republic of Korea.,Institute of Bio & Nano Convergence, Biogo Co., LTD, Seoul, 08826, Republic of Korea
| | - Jaechul Ryu
- Adult Stem Cell Research Center and Research Institute for Veterinary Medicine, College of Veterinary Medicine, Seoul National University, Seoul, 08826, Republic of Korea.,Institute of Bio & Nano Convergence, Biogo Co., LTD, Seoul, 08826, Republic of Korea
| | - Kyung-Sun Kang
- Adult Stem Cell Research Center and Research Institute for Veterinary Medicine, College of Veterinary Medicine, Seoul National University, Seoul, 08826, Republic of Korea. .,Bio-MAX Institute, Seoul National University, Seoul, 08826, Republic of Korea.
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Antonia AL, Barnes AB, Martin AT, Wang L, Ko DC. Variation in Leishmania chemokine suppression driven by diversification of the GP63 virulence factor. PLoS Negl Trop Dis 2021; 15:e0009224. [PMID: 34710089 PMCID: PMC8577781 DOI: 10.1371/journal.pntd.0009224] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 11/09/2021] [Accepted: 10/17/2021] [Indexed: 11/18/2022] Open
Abstract
Leishmaniasis is a neglected tropical disease with diverse outcomes ranging from self-healing lesions, to progressive non-healing lesions, to metastatic spread and destruction of mucous membranes. Although resolution of cutaneous leishmaniasis is a classic example of type-1 immunity leading to self-healing lesions, an excess of type-1 related inflammation can contribute to immunopathology and metastatic spread. Leishmania genetic diversity can contribute to variation in polarization and robustness of the immune response through differences in both pathogen sensing by the host and immune evasion by the parasite. In this study, we observed a difference in parasite chemokine suppression between the Leishmania (L.) subgenus and the Viannia (V.) subgenus, which is associated with severe immune-mediated pathology such as mucocutaneous leishmaniasis. While Leishmania (L.) subgenus parasites utilize the virulence factor and metalloprotease glycoprotein-63 (gp63) to suppress the type-1 associated host chemokine CXCL10, L. (V.) panamensis did not suppress CXCL10. To understand the molecular basis for the inter-species variation in chemokine suppression, we used in silico modeling to identify a putative CXCL10-binding site on GP63. The putative CXCL10 binding site is in a region of gp63 under significant positive selection, and it varies from the L. major wild-type sequence in all gp63 alleles identified in the L. (V.) panamensis reference genome. Mutating wild-type L. (L.) major gp63 to the L. (V.) panamensis sequence at the putative binding site impaired cleavage of CXCL10 but not a non-specific protease substrate. Notably, Viannia clinical isolates confirmed that L. (V.) panamensis primarily encodes non-CXCL10-cleaving gp63 alleles. In contrast, L. (V.) braziliensis has an intermediate level of activity, consistent with this species having more equal proportions of both alleles. Our results demonstrate how parasite genetic diversity can contribute to variation in immune responses to Leishmania spp. infection that may play critical roles in the outcome of infection. Leishmaniasis is a neglected tropical disease caused by Leishmania parasites and spread by the bites of infected sand flies. Most cases of leishmaniasis present as self-healing sores that are resolved by a balanced immune response. Other cases of leishmaniasis involve spread to sites distant from the original bite, including damage of the inner surfaces of the mouth and nose. These cases of leishmaniasis involve an excessive immune response. Leishmania parasites produce virulence factor proteins, such as GP63, to trick the immune system into mounting a weaker response. GP63 specifically degrades signaling proteins that attract and activate certain immune cells. Here, we demonstrate that Leishmania parasite species have evolved to differ in their ability to degrade signaling proteins. In Leishmania species known to cause more immune-mediated tissue damage, the GP63 virulence factor has evolved to not degrade specific immune signaling proteins, thus attracting, and activating more immune cells. Our results demonstrate how diversity among Leishmania parasite species can contribute to variation in immune responses that may play critical roles in the outcome of infection.
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Affiliation(s)
- Alejandro L. Antonia
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, North Carolina, United States of America
| | - Alyson B. Barnes
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, North Carolina, United States of America
| | - Amelia T. Martin
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, North Carolina, United States of America
| | - Liuyang Wang
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, North Carolina, United States of America
| | - Dennis C. Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, North Carolina, United States of America
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, North Carolina, United States of America
- * E-mail:
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Kumar L, Nash A, Harms C, Planas-Iglesias J, Wright D, Klein-Seetharaman J, Sarkar SK. Allosteric Communications between Domains Modulate the Activity of Matrix Metalloprotease-1. Biophys J 2020; 119:360-374. [PMID: 32585130 PMCID: PMC7376139 DOI: 10.1016/j.bpj.2020.06.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 05/30/2020] [Accepted: 06/09/2020] [Indexed: 11/23/2022] Open
Abstract
An understanding of the structure-dynamics relationship is essential for understanding how a protein works. Prior research has shown that the activity of a protein correlates with intradomain dynamics occurring at picosecond to millisecond timescales. However, the correlation between interdomain dynamics and the function of a protein is poorly understood. Here, we show that communications between the catalytic and hemopexin domains of matrix metalloprotease-1 (MMP1) on type 1 collagen fibrils correlate with its activity. Using single-molecule Förster resonance energy transfer, we identified functionally relevant open conformations in which the two MMP1 domains are well separated, which were significantly absent for catalytically inactive point mutant (E219Q) of MMP1 and could be modulated by an inhibitor or an enhancer of activity. The observed relevance of open conformations resolves the debate about the roles of open and closed MMP1 structures in function. We fitted the histograms of single-molecule Förster resonance energy transfer values to a sum of two Gaussians and the autocorrelations to an exponential and power law. We used a two-state Poisson process to describe the dynamics and calculate the kinetic rates from the fit parameters. All-atom and coarse-grained simulations reproduced some of the experimental features and revealed substrate-dependent MMP1 dynamics. Our results suggest that an interdomain separation facilitates opening up the catalytic pocket so that the collagen chains come closer to the MMP1 active site. Coordination of functional conformations at different parts of MMP1 occurs via allosteric communications that can take place via interactions mediated by collagen even if the linker between the domains is absent. Modeling dynamics as a Poisson process enables connecting the picosecond timescales of molecular dynamics simulations with the millisecond timescales of single-molecule measurements. Water-soluble MMP1 interacting with water-insoluble collagen fibrils poses challenges for biochemical studies that the single-molecule tracking can overcome for other insoluble substrates. Interdomain communications are likely important for multidomain proteins.
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Affiliation(s)
- Lokender Kumar
- Department of Physics, Colorado School of Mines, Golden, Colorado
| | - Anthony Nash
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Chase Harms
- Department of Physics, Colorado School of Mines, Golden, Colorado
| | - Joan Planas-Iglesias
- Warwick Medical School, University of Warwick, Coventry, United Kingdom; Loschmidt Laboratories, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Derek Wright
- Department of Physics, Colorado School of Mines, Golden, Colorado
| | - Judith Klein-Seetharaman
- Warwick Medical School, University of Warwick, Coventry, United Kingdom; Department of Chemistry, Colorado School of Mines, Golden, Colorado
| | - Susanta K Sarkar
- Department of Physics, Colorado School of Mines, Golden, Colorado.
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Xie WQ, Zhao YJ, Li F, Shu B, Lin SR, Sun L, Wang YJ, Zheng HX. Velvet antler polypeptide partially rescue facet joint osteoarthritis-like phenotype in adult β-catenin conditional activation mice. BMC COMPLEMENTARY AND ALTERNATIVE MEDICINE 2019; 19:191. [PMID: 31362725 PMCID: PMC6668128 DOI: 10.1186/s12906-019-2607-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 07/22/2019] [Indexed: 01/23/2023]
Abstract
BACKGROUND Wnt/β-catenin signaling pathway is closely related to osteoarthritis. In our preliminary study, β-catenin conditional activation (cAct) mice that specifically over-express β-catenin gene in cartilage chondrocyte exhibits osteoarthritis-like phenotype in the lumbar disc and knee joint. Therefore, we used the mice to model FJ-OA and test the potential curative effect of Velvet Antler Polypeptide (VAP) on this mice model. METHODS We tested the effect of VAP on β-catenin conditional activation mice, and used Cre negative littermates as controls. Micro-CT, histology and histomorphometry analysis were performed to evaluate the curative effect of VAP on mice facet joint-like phenotype. Expression of β-catenin and collagen II was detected by immunohistochemistry (IHC) and western-blot., MMP13, ADAMTS4 and ADAMTS5 was detected by immunofluorescence (IF). RT-PCR analysis was preformed to detect mRNA expression of cartilage degrading enzymes, such as MMP13, ADAMTS4 and ADAMTS5. RESULTS Results of micro-CT (μCT) analysis showed that VAP could partially reverse lumbar disc osteophyte formation observed in β-catenin(ex3)Col2ER mice. Histology data revealed VAP partially improved facet joint cartilage tissue invades. Histomorphometry analysis showed an increase in total cartilage area after VAP treatment. IHC show that VAP reduced β-catenin protein levels and moderately up-regulated collagen II protein levels. RT-PCR and IF data showed that VAP down-regulated the expression of extracellular matrix synthesis (ECM) degradation enzymes MMP13, ADAMTS4 and ADAMTS5. CONCLUSION Taken together, VAP may modulate ECM by inhibits MMP13, ADAMTS4 and ADAMTS5 via Wnt /β-catenin signaling pathway. Velvet Antler Polypeptide may be a potential medicine for FJ-OA.
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Ramya Chandar Charles M, Hsieh HP, Selvaraj Coumar M. Delineating the active site architecture of G9a lysine methyltransferase through substrate and inhibitor binding mode analysis: a molecular dynamics study. J Biomol Struct Dyn 2018; 37:2581-2592. [PMID: 30047835 DOI: 10.1080/07391102.2018.1491422] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Mono- and di-methylation of the H3K9 residue in the histone tail by G9a lysine methyltransferase is associated with transcriptional suppression of genes. Here, we use molecular dynamics simulation and free energy calculations of five different modified/mutated G9a substrate peptides to elucidate the rationale behind the substrate binding to G9a. We also investigated the binding energy contribution based architecture of the active site of G9a to understand substrate and inhibitor binding. Wild-type peptide (H3K9) shows better binding affinity than mono- and di-methylated lysine (K9) and other modified peptides (K9A and R8A). Arg8 of the substrate peptide is crucial for determining the degree of conformational freedom/stability of the wild-type substrate peptide, as well as binding to G9a. Our results also suggest that the G9a active site is segregated into energy rich and low regions, and the energy rich region alone is used by the inhibitors for binding. These insights into the active site architecture should be taken into consideration in virtual screening experiments designed to discover novel inhibitors for G9a. In particular, compounds that could interact with the six residues of G9a - Asp1074, Asp1083, Leu1086, Asp1088, Tyr1154 and Phe1158 - should be preferentially tested in G9a inhibition biological assays. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Hsing-Pang Hsieh
- b Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan , Taiwan , ROC
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Jana S, Singh SK. Identification of selective MMP-9 inhibitors through multiple e-pharmacophore, ligand-based pharmacophore, molecular docking, and density functional theory approaches. J Biomol Struct Dyn 2018; 37:944-965. [DOI: 10.1080/07391102.2018.1444510] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Srabanti Jana
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Sushil K. Singh
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
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Wang Y, Yang L, Hou J, Zou Q, Gao Q, Yao W, Yao Q, Zhang J. Hierarchical virtual screening of the dual MMP-2/HDAC-6 inhibitors from natural products based on pharmacophore models and molecular docking. J Biomol Struct Dyn 2018; 37:649-670. [PMID: 29380672 DOI: 10.1080/07391102.2018.1434833] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The dual-target inhibitors tend to improve the response rate in treating tumors, comparing with the single-target inhibitors. Matrix metalloproteinase-2 (MMP-2) and histone deacetylase-6 (HDAC-6) are attractive targets for cancer therapy. In this study, the hierarchical virtual screening of dual MMP-2/HDAC-6 inhibitors from natural products is investigated. The pharmacophore model of MMP-2 inhibitors is built based on ligands, but the pharmacophore model of HDAC-6 inhibitors is built based on the experimental crystal structures of multiple receptor-ligand complexes. The reliability of these two pharmacophore models is validated subsequently. The hierarchical virtual screening, combining these two different pharmacophore models of MMP-2 and HDAC-6 inhibitors with molecular docking, is carried out to identify the dual MMP-2/HDAC-6 inhibitors from a database of natural products. The four potential dual MMP-2/HDAC-6 inhibitors of natural products, STOCK1 N-46177, STOCK1 N-52245, STOCK1 N-55477, and STOCK1 N-69706, are found. The studies of binding modes show that the screened four natural products can simultaneously well bind with the MMP-2 and HDAC-6 active sites by different kinds of interactions, to inhibit the MMP-2 and HDAC-6 activities. In addition, the ADMET properties of screened four natural products are assessed. These found dual MMP-2/HDAC-6 inhibitors of natural products could serve as the lead compounds for designing the new dual MMP-2/HDAC-6 inhibitors having higher biological activities by carrying out structural modifications and optimizations in the future studies.
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Affiliation(s)
- Yijun Wang
- a Department of Physical Chemistry , China Pharmaceutical University , Nanjing , 210009 , People's Republic of China
| | - Limei Yang
- a Department of Physical Chemistry , China Pharmaceutical University , Nanjing , 210009 , People's Republic of China
| | - Jiaying Hou
- a Department of Physical Chemistry , China Pharmaceutical University , Nanjing , 210009 , People's Republic of China
| | - Qing Zou
- a Department of Physical Chemistry , China Pharmaceutical University , Nanjing , 210009 , People's Republic of China
| | - Qi Gao
- a Department of Physical Chemistry , China Pharmaceutical University , Nanjing , 210009 , People's Republic of China
| | - Wenhui Yao
- a Department of Physical Chemistry , China Pharmaceutical University , Nanjing , 210009 , People's Republic of China
| | - Qizheng Yao
- c School of Pharmacy , China Pharmaceutical University , Nanjing , 210009 , People's Republic of China
| | - Ji Zhang
- a Department of Physical Chemistry , China Pharmaceutical University , Nanjing , 210009 , People's Republic of China.,b State Key Laboratory of Natural Medicines , China Pharmaceutical University , Nanjing , 210009 , People's Republic of China
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Nash A, Collier T, Birch HL, de Leeuw NH. ForceGen: atomic covalent bond value derivation for Gromacs. J Mol Model 2017; 24:5. [PMID: 29214361 PMCID: PMC5719132 DOI: 10.1007/s00894-017-3530-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 11/14/2017] [Indexed: 01/07/2023]
Abstract
A large number of crystallographic protein structures include ligands, small molecules and post-translational modifications. Atomic bond force values for computational atomistic models of post-translational or non-standard amino acids, metal binding active sites, small molecules and drug molecules are not readily available in most simulation software packages. We present ForceGen, a Java tool that extracts the bond stretch and bond angle force values and equilibrium values from the Hessian of a Gaussian vibrational frequency analysis. The parameters are compatible with force fields derived using the second order tensor of the Hessian. The output is formatted with the Gromacs topology in mind. This study further demonstrates the use of ForceGen over the quantum mechanically derived structures of a small organic solvent, a naturally occurring protein crosslink derived from two amino acids following post-translational modification and the amino acid ligands of a zinc ion. We then derive Laplacian bond orders to understand how the resulting force values relate back to the quantum mechanical model. The parameterisation of the organic solvent, toluene, was verified using Molecular Mechanics simulations. The structural data from the simulation compared well with the quantum mechanical structure and the system density compared well with experimental values.
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Affiliation(s)
- Anthony Nash
- Department of Physiology, Genetics, and Anatomy, University of Oxford, Oxford, UK.
| | - Thomas Collier
- Institute of Natural and Mathematical Sciences, Massey University, Palmerston North, New Zealand
| | - Helen L Birch
- Institute of Orthopaedics and Musculoskeletal Science, Stanmore Campus, University College London, London, UK
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Wang S, Liu Q, Li X, Zhao X, Qiu L, Lin J. Possible binding sites and interactions of propanidid and AZD3043 within the γ-aminobutyric acid type A receptor (GABAAR). J Biomol Struct Dyn 2017; 36:3926-3937. [DOI: 10.1080/07391102.2017.1403959] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Shanshan Wang
- School of Chemical and Material Engineering, Jiangnan University, Wuxi 214122, P.R China
- Key Laboratory of Nuclear Medicine, Ministry of Health & Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, P.R. China
| | - Qingzhu Liu
- Key Laboratory of Nuclear Medicine, Ministry of Health & Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, P.R. China
| | - Xi Li
- School of Chemical and Material Engineering, Jiangnan University, Wuxi 214122, P.R China
- Key Laboratory of Nuclear Medicine, Ministry of Health & Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, P.R. China
| | - Xueyu Zhao
- School of Chemical and Material Engineering, Jiangnan University, Wuxi 214122, P.R China
- Key Laboratory of Nuclear Medicine, Ministry of Health & Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, P.R. China
| | - Ling Qiu
- School of Chemical and Material Engineering, Jiangnan University, Wuxi 214122, P.R China
- Key Laboratory of Nuclear Medicine, Ministry of Health & Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, P.R. China
| | - Jianguo Lin
- Key Laboratory of Nuclear Medicine, Ministry of Health & Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, P.R. China
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Karabencheva-Christova TG, Christov CZ, Fields GB. Collagenolytic Matrix Metalloproteinase Structure–Function Relationships: Insights From Molecular Dynamics Studies. STRUCTURAL AND MECHANISTIC ENZYMOLOGY 2017; 109:1-24. [DOI: 10.1016/bs.apcsb.2017.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Othman H, Wieninger SA, ElAyeb M, Nilges M, Srairi-Abid N. In Silico prediction of the molecular basis of ClTx and AaCTx interaction with matrix metalloproteinase-2 (MMP-2) to inhibit glioma cell invasion. J Biomol Struct Dyn 2016; 35:2815-2829. [DOI: 10.1080/07391102.2016.1231633] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Houcemeddine Othman
- Laboratory of venoms and therapeutic biomolecules (LR11IPT08), Institut Pasteur de Tunis, Tunis, Tunisia
- Faculté des Sciences de Bizerte, Université de Carthage, Bizerte, Tunisia
| | - Silke Andrea Wieninger
- Département de Biologie Structurale et Chimie, Institut Pasteur, Unité de Bioinformatique Structurale, Paris, France
| | - Mohamed ElAyeb
- Laboratory of venoms and therapeutic biomolecules (LR11IPT08), Institut Pasteur de Tunis, Tunis, Tunisia
| | - Michael Nilges
- Département de Biologie Structurale et Chimie, Institut Pasteur, Unité de Bioinformatique Structurale, Paris, France
| | - Najet Srairi-Abid
- Laboratory of venoms and therapeutic biomolecules (LR11IPT08), Institut Pasteur de Tunis, Tunis, Tunisia
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