201
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Chaugule VK, Arkinson C, Rennie ML, Kämäräinen O, Toth R, Walden H. Allosteric mechanism for site-specific ubiquitination of FANCD2. Nat Chem Biol 2019; 16:291-301. [PMID: 31873223 PMCID: PMC7035956 DOI: 10.1038/s41589-019-0426-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 11/05/2019] [Indexed: 01/31/2023]
Abstract
DNA damage repair is implemented by proteins that are coordinated by specialised molecular signals. One such signal in the Fanconi Anemia (FA) DNA-interstrand crosslink repair pathway is the site-specific monoubiquitination of FANCD2 and FANCI. The signal is mediated by a multi-protein FA core complex (FA-CC) however, the mechanics for precise ubiquitination remain elusive. We show that FANCL, the RING-bearing module in FA-CC, allosterically activates its cognate E2 Ube2T to drive site-specific FANCD2 ubiquitination. Unlike typical RING E3 ligases, FANCL catalyses ubiquitination by rewiring Ube2T’s intra-residue network to influence the active site. Consequently, a basic triad unique to Ube2T engages a structured acidic patch near the target lysine on FANCD2. This three-dimensional complementarity, between the E2 active site and substrate surface, induced by FANCL is central to site-specific monoubiquitination in the FA pathway. Furthermore, the allosteric network of Ube2T can be engineered to enhance FANCL catalysed FANCD2-FANCI di-monoubiquitination without compromising site-specificity.
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Affiliation(s)
- Viduth K Chaugule
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK. .,MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, UK.
| | - Connor Arkinson
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.,MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, UK
| | - Martin L Rennie
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Outi Kämäräinen
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Rachel Toth
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, UK
| | - Helen Walden
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK. .,MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, UK.
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202
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Liu H, Zhong H, Liu X, Zhou S, Tan S, Liu H, Yao X. Disclosing the Mechanism of Spontaneous Aggregation and Template-Induced Misfolding of the Key Hexapeptide (PHF6) of Tau Protein Based on Molecular Dynamics Simulation. ACS Chem Neurosci 2019; 10:4810-4823. [PMID: 31661961 DOI: 10.1021/acschemneuro.9b00488] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The microtubule-associated protein tau is critical for the development and maintenance of the nervous system. Tau dysfunction is associated with a variety of neurodegenerative diseases called tauopathies, which are characterized by neurofibrillary tangles formed by abnormally aggregated tau protein. Studying the aggregation mechanism of tau protein is of great significance for elucidating the etiology of tauopathies. The hexapeptide 306VQIVYK311 (PHF6) of R3 has been shown to play a vital role in promoting tau aggregation. In this study, long-term all-atom molecular dynamics simulations in explicit solvent were performed to investigate the mechanisms of spontaneous aggregation and template-induced misfolding of PHF6, and the dimerization at the early stage of nucleation was further specifically analyzed by the Markov state model (MSM). Our results show that PHF6 can spontaneously aggregate to form multimers enriched with β-sheet structure and the β-sheets in multimers prefer to exist in a parallel way. It is observed that PHF6 monomer can be induced to form a β-sheet structure on either side of the template but in a different way. In detail, the β-sheet structure is easier to form on the left side but does not extend well, but on the right side, the monomer can form the extended β-sheet structure. Furthermore, MSM analysis shows that the formation of dimer mainly occurs in three steps. First, the separated monomers collide with each other at random orientations, and then a dimer with short β-sheet structure at the N-terminal forms; finally, β-sheets elongate to form an extended parallel β-sheet dimer. During these processes, multiple intermediate states are identified and multiple paths can form a parallel β-sheet dimer from the disordered coil structure. Moreover, the residues I308, V309, and Y310 play an essential role in the dimerization. In a word, our results uncover the aggregation and misfolding mechanism of PHF6 from the atomic level, which can provide useful theoretical guidance for rational design of effective therapeutic drugs against tauopathies.
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Affiliation(s)
| | | | | | - Shuangyan Zhou
- Chongqing Key Laboratory on Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | | | | | - Xiaojun Yao
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau 999078, China
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203
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Human Rhinovirus Inhibition Through Capsid “Canyon” Perturbation: Structural Insights into The Role of a Novel Benzothiophene Derivative. Cell Biochem Biophys 2019; 78:3-13. [DOI: 10.1007/s12013-019-00896-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 12/04/2019] [Indexed: 02/07/2023]
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204
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Zhang Q, An X, Liu H, Wang S, Xiao T, Liu H. Uncovering the Resistance Mechanism of Mycobacterium tuberculosis to Rifampicin Due to RNA Polymerase H451D/Y/R Mutations From Computational Perspective. Front Chem 2019; 7:819. [PMID: 31850310 PMCID: PMC6902089 DOI: 10.3389/fchem.2019.00819] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 11/12/2019] [Indexed: 11/13/2022] Open
Abstract
Tuberculosis is still one of the top 10 causes of deaths worldwide, especially with the emergence of multidrug-resistant tuberculosis. Rifampicin, as the most effective first-line antituberculosis drug, also develops resistance due to the mutation on Mycobacterium tuberculosis (Mtb) RNA polymerase. Among these mutations, three mutations at position 451 (H451D, H451Y, H451R) are associated with high-level resistance to rifampicin. However, the resistance mechanism of Mtb to rifampicin is still unclear. In this work, to explore the resistance mechanism of Mtb to rifampicin due to H451D/Y/R mutations, we combined the molecular dynamics simulation, molecular mechanics generalized-Born surface area calculation, dynamic network analysis, and residue interactions network analysis to compare the interaction change of rifampicin with wild-type RNA polymerase and three mutants. The results of molecular mechanics generalized-Born surface area calculations indicate that the binding free energy of rifampicin with three mutants decreases. In addition, the dynamic network analysis and residue interaction network analysis show that when H451 was mutated, the interactions of residue 451 with its adjacent residues such as Q438, F439, M440, D441, and S447 disappeared or weakened, increasing the flexibility of binding pocket. At the same time, the disappearance of hydrogen bonds between R613 and rifampicin caused by the flipping of R613 is another important reason for the reduction of binding ability of rifampicin in H451D/Y mutants. In H451R mutant, the mutation causes the binding pocket change too much so that the position of rifampicin has a large movement in the binding pocket. In this study, the resistance mechanism of rifampicin at the atomic level is proposed. The proposed drug-resistance mechanism will provide the valuable guidance for the design of antituberculosis drugs.
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Affiliation(s)
| | - Xiaoli An
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
| | - Hongli Liu
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Shuo Wang
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Tong Xiao
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Huanxiang Liu
- School of Pharmacy, Lanzhou University, Lanzhou, China
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205
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Williamson A, Leiros HKS. Structural intermediates of a DNA-ligase complex illuminate the role of the catalytic metal ion and mechanism of phosphodiester bond formation. Nucleic Acids Res 2019; 47:7147-7162. [PMID: 31312841 PMCID: PMC6698739 DOI: 10.1093/nar/gkz596] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 06/24/2019] [Accepted: 07/05/2019] [Indexed: 01/17/2023] Open
Abstract
DNA ligases join adjacent 5' phosphate (5'P) and 3' hydroxyl (3'OH) termini of double-stranded DNA via a three-step mechanism requiring a nucleotide cofactor and divalent metal ion. Although considerable structural detail is available for the first two steps, less is known about step 3 where the DNA-backbone is joined or about the cation role at this step. We have captured high-resolution structures of an adenosine triphosphate (ATP)-dependent DNA ligase from Prochlorococcus marinus including a Mn-bound pre-ternary ligase-DNA complex poised for phosphodiester bond formation, and a post-ternary intermediate retaining product DNA and partially occupied AMP in the active site. The pre-ternary structure unambiguously identifies the binding site of the catalytic metal ion and confirms both its role in activating the 3'OH terminus for nucleophilic attack on the 5'P group and stabilizing the pentavalent transition state. The post-ternary structure indicates that DNA distortion and most enzyme-AMP contacts remain after phosphodiester bond formation, implying loss of covalent linkage to the DNA drives release of AMP, rather than active site rearrangement. Additionally, comparisons of this cyanobacterial DNA ligase with homologs from bacteria and bacteriophage pose interesting questions about the structural origin of double-strand break joining activity and the evolution of these ATP-dependent DNA ligase enzymes.
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Affiliation(s)
- Adele Williamson
- Department of Chemistry, UiT The Arctic University of Norway, Tromsø, N-9037, Norway.,School of Science, University of Waikato, Hamilton 3240, New Zealand
| | - Hanna-Kirsti S Leiros
- Department of Chemistry, UiT The Arctic University of Norway, Tromsø, N-9037, Norway
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206
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Structural insights into the binding mechanism of Plasmodium falciparum exported Hsp40-Hsp70 chaperone pair. Comput Biol Chem 2019; 83:107099. [DOI: 10.1016/j.compbiolchem.2019.107099] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 07/11/2019] [Accepted: 08/06/2019] [Indexed: 11/21/2022]
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207
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Santos YLDL, Chew-Fajardo YL, Brault G, Doucet N. Dissecting the evolvability landscape of the CalB active site toward aromatic substrates. Sci Rep 2019; 9:15588. [PMID: 31666622 PMCID: PMC6821916 DOI: 10.1038/s41598-019-51940-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 10/07/2019] [Indexed: 01/17/2023] Open
Abstract
A key event in the directed evolution of enzymes is the systematic use of mutagenesis and selection, a process that can give rise to mutant libraries containing millions of protein variants. To this day, the functional analysis and identification of active variants among such high numbers of mutational possibilities is not a trivial task. Here, we describe a combinatorial semi-rational approach to partly overcome this challenge and help design smaller and smarter mutant libraries. By adapting a liquid medium transesterification assay in organic solvent conditions with a combination of virtual docking, iterative saturation mutagenesis, and residue interaction network (RIN) analysis, we engineered lipase B from P. antarctica (CalB) to improve enzyme recognition and activity against the bulky aromatic substrates and flavoring agents methyl cinnamate and methyl salicylate. Substrate-imprinted docking was used to target active-site positions involved in enzyme-substrate and enzyme-product complexes, in addition to identifying 'hot spots' most likely to yield active variants. This iterative semi-rational design strategy allowed selection of CalB variants exhibiting increased activity in just two rounds of site-saturation mutagenesis. Beneficial replacements were observed by screening only 0.308% of the theoretical library size, illustrating how semi-rational approaches with targeted diversity can quickly facilitate the discovery of improved activity variants relevant to a number of biotechnological applications.
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Affiliation(s)
- Yossef López de Los Santos
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, QC, H7V 1B7, Canada
| | - Ying Lian Chew-Fajardo
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, QC, H7V 1B7, Canada
| | - Guillaume Brault
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, QC, H7V 1B7, Canada
| | - Nicolas Doucet
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, QC, H7V 1B7, Canada.
- PROTEO, the Québec Network for Research on Protein Function, Engineering, and Applications, 1045 Avenue de la Médecine, Université Laval, Quebec City, QC, G1V 0A6, Canada.
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208
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Gheibi N, Ghorbani M, Shariatifar H, Farasat A. In silico assessment of human Calprotectin subunits (S100A8/A9) in presence of sodium and calcium ions using Molecular Dynamics simulation approach. PLoS One 2019; 14:e0224095. [PMID: 31622441 PMCID: PMC6797115 DOI: 10.1371/journal.pone.0224095] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/04/2019] [Indexed: 11/19/2022] Open
Abstract
Calprotectin is a heterodimeric protein complex which consists of two subunits including S100A8 and S100A9. This protein has a major role in different inflammatory disease and various types of cancers. In current study we aimed to evaluate the structural and thermodynamic changes of the subunits and the complex in presence of sodium and calcium ions using molecular dynamics (MD) simulation. Therefore, the residue interaction network (RIN) was visualized in Cytoscape program. In next step, to measure the binding free energy, the potential of mean force (PMF) method was performed. Finally, the molecular mechanics Poisson-Boltzmann surface area (MMPBSA) method was applied as an effective tool to calculate the molecular model affinities. The MD simulation results of the subunits represented their structural changes in presence of Ca2+. Moreover, the RIN and Hydrogen bond analysis demonstrated that cluster interactions between Calprotectin subunits in presence of Ca2+ were greater in comparison with Na+. Our findings indicated that the binding free energy of the subunits in presence of Ca2+ was significantly greater than Na+. The results revealed that Ca2+ has the ability to induce structural changes in subunits in comparison with Na+ which lead to create stronger interactions between. Hence, studying the physical characteristics of the human proteins could be considered as a powerful tool in theranostics and drug design purposes.
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Affiliation(s)
- Nematollah Gheibi
- Cellular and Molecular Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Mohammad Ghorbani
- Department of Nanobiotechnology/ Biophysics, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran
| | - Hanifeh Shariatifar
- Young Researchers and Elite Club, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Alireza Farasat
- Cellular and Molecular Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
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209
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DistAA: Database of amino acid distances in proteins and web application for statistical review of distances. Comput Biol Chem 2019; 83:107130. [PMID: 31593887 DOI: 10.1016/j.compbiolchem.2019.107130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 09/07/2019] [Accepted: 09/17/2019] [Indexed: 11/22/2022]
Abstract
Three-dimensional structure of a protein chain is determined by its amino acid interactions. One approach to the analysis of amino acid interactions refers to geometric distances of amino acid pairs in polypeptide chains. For a detailed analysis of the amino acid distances, the database with three types of amino acid distances in a set of chains was created. Web application Distances of Amino Acids has also been developed to enable scientists to explore interactions of amino acids with different properties based on distances stored in the database. Web application calculates and displays descriptive statistics and graphs of amino acid pair distances with selected properties, such as geometric distance threshold, corresponding SCOP class of proteins and secondary structure types. In addition to the analysis of pre-calculated distances stored in the database, the amino acid distances of a single protein with the specified PDB identifier can also be analyzed. The web application is available at http://andromeda.matf.bg.ac.rs/aadis_dynamic/.
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210
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Buthelezi NM, Mhlongo NN, Amoako DG, Somboro AM, Sosibo SC, Shunmugam L, Machaba KE, Kumalo HM. Exploring the impact of H5N1 neuraminidase (H274Y) mutation on Peramivir: a bio-computational study from a molecular perspective. J Biomol Struct Dyn 2019; 38:4344-4352. [PMID: 31588851 DOI: 10.1080/07391102.2019.1677501] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ndumiso M Buthelezi
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
| | - Ndumiso N Mhlongo
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
| | - Daniel G Amoako
- Infection Genomics and Applied Bioinformatics Division, Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.,Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Anou M Somboro
- Infection Genomics and Applied Bioinformatics Division, Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.,Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Sphelele C Sosibo
- School of Physical and Chemical Sciences, Department of Chemistry, North West University, Mmabatho, South Africa
| | - Letitia Shunmugam
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
| | - Kgothatso E Machaba
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
| | - Hezekiel M Kumalo
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
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211
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Perera KD, Rathnayake AD, Liu H, Pedersen NC, Groutas WC, Chang KO, Kim Y. Characterization of amino acid substitutions in feline coronavirus 3C-like protease from a cat with feline infectious peritonitis treated with a protease inhibitor. Vet Microbiol 2019; 237:108398. [PMID: 31585653 PMCID: PMC6779346 DOI: 10.1016/j.vetmic.2019.108398] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/21/2019] [Accepted: 08/21/2019] [Indexed: 12/26/2022]
Abstract
Feline infectious peritonitis (FIP) is a highly fatal disease caused by a virulent feline coronavirus in domestic and wild cats. We have previously reported the synthesis of potent coronavirus 3C-like protease (3CLpro) inhibitors and the efficacy of a protease inhibitor, GC376, in client-owned cats with FIP. In this study, we studied the effect of the amino acid changes in 3CLpro of feline coronavirus from a feline patient who received antiviral treatment for prolonged duration. We generated recombinant 3CLpro containing the identified amino acid changes (N25S, A252S or K260 N) and determined their susceptibility to protease inhibitors in the fluorescence resonance energy transfer assay. The assay showed that N25S in 3CLpro confers a small change (up to 1.68-fold increase in the 50% inhibitory concentration) in susceptibility to GC376, but other amino acid changes do not affect susceptibility. Modelling of 3CLpro carrying the amino acid changes was conducted to probe the structural basis for these findings. The results of this study may explain the observed absence of clinical resistance to the long-term antiviral treatment in the patients.
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Affiliation(s)
- Krishani Dinali Perera
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | | | - Hongwei Liu
- Center for Companion Animal Health, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Niels C Pedersen
- Center for Companion Animal Health, School of Veterinary Medicine, University of California, Davis, CA, USA
| | | | - Kyeong-Ok Chang
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Yunjeong Kim
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA.
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212
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Exploring the effect of aplidin on low molecular weight protein tyrosine phosphatase by molecular docking and molecular dynamic simulation study. Comput Biol Chem 2019; 83:107123. [PMID: 31561070 DOI: 10.1016/j.compbiolchem.2019.107123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 07/26/2019] [Accepted: 09/04/2019] [Indexed: 12/24/2022]
Abstract
The low molecular weight protein tyrosine phosphatase (LMW-PTP) could regulate many signaling pathways, and it had drawn attention as a potential target for cancer. As previous report has indicated that the aplidin could inhibit the LMW-PTP, and thus, the relevant cancer caused by the abnormal regulation of the LMW-PTP could be remission. However, the molecular mechanism of inhibition of the LMW-PTP by the aplidin had not been fully understood. In this study, various computational approaches, namely molecular docking, MDs and post-dynamic analyses were utilized to explore the effect of the aplidin on the LMW-PTP. The results suggested that the intramolecular interactions of the residues in the two sides of the active site (Ser43-Ala55 and Pro121-Asn134) and the P-loop region (Leu13-Ser19) in the LMW-PTP was disturbed owing to the aplidin, meanwhile, the π-π interaction between Tyr131 and Tyr132 might be broken. The Asn15 might be the key residue to break the residues interactions. In a word, this study may provide more information for understanding the effect of inhibition of the aplidin on the LMW-PTP.
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213
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Analysis of mutations leading to para-aminosalicylic acid resistance in Mycobacterium tuberculosis. Sci Rep 2019; 9:13617. [PMID: 31541138 PMCID: PMC6754364 DOI: 10.1038/s41598-019-48940-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 07/31/2019] [Indexed: 12/18/2022] Open
Abstract
Thymidylate synthase A (ThyA) is the key enzyme involved in the folate pathway in Mycobacterium tuberculosis. Mutation of key residues of ThyA enzyme which are involved in interaction with substrate 2′-deoxyuridine-5′-monophosphate (dUMP), cofactor 5,10-methylenetetrahydrofolate (MTHF), and catalytic site have caused para-aminosalicylic acid (PAS) resistance in TB patients. Focusing on R127L, L143P, C146R, L172P, A182P, and V261G mutations, including wild-type, we performed long molecular dynamics (MD) simulations in explicit solvent to investigate the molecular principles underlying PAS resistance due to missense mutations. We found that these mutations lead to (i) extensive changes in the dUMP and MTHF binding sites, (ii) weak interaction of ThyA enzyme with dUMP and MTHF by inducing conformational changes in the structure, (iii) loss of the hydrogen bond and other atomic interactions and (iv) enhanced movement of protein atoms indicated by principal component analysis (PCA). In this study, MD simulations framework has provided considerable insight into mutation induced conformational changes in the ThyA enzyme of Mycobacterium.
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214
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Minervini G, Quaglia F, Tabaro F, Tosatto SCE. Insights into the molecular features of the von Hippel-Lindau-like protein. Amino Acids 2019; 51:1461-1474. [PMID: 31485743 DOI: 10.1007/s00726-019-02781-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 08/28/2019] [Indexed: 12/19/2022]
Abstract
We present an in silico characterization of the von Hippel-Lindau-like protein (VLP), the only known human paralog of the von Hippel-Lindau tumor suppressor protein (pVHL). Phylogenetic investigation showed VLP to be mostly conserved in upper mammals and specifically expressed in brain and testis. Structural analysis and molecular dynamics simulations show VLP to be very similar to pVHL three-dimensional organization and binding dynamics. In particular, conservation of elements at the protein interfaces suggests VLP to be a functional pVHL homolog potentially possessing multiple functions beyond HIF-1α-dependent binding activity. Our findings show that VLP may share at least seven interactors with pVHL, suggesting novel functional roles for this understudied human protein. These may occur at precise hypoxia levels where functional overlap with pVHL may permit a finer modulation of pVHL functions.
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Affiliation(s)
- Giovanni Minervini
- Department of Biomedical Sciences, University of Padova, Viale G. Colombo 3, 35121, Padua, Italy
| | - Federica Quaglia
- Department of Biomedical Sciences, University of Padova, Viale G. Colombo 3, 35121, Padua, Italy
| | - Francesco Tabaro
- Department of Biomedical Sciences, University of Padova, Viale G. Colombo 3, 35121, Padua, Italy.,Institute of Biosciences and Medical Technology, Tampere, Finland
| | - Silvio C E Tosatto
- Department of Biomedical Sciences, University of Padova, Viale G. Colombo 3, 35121, Padua, Italy. .,CNR Institute of Neuroscience, Padua, Italy.
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215
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Wu J, Sun Y, Zhou H, Ma Y, Wang R. Design, synthesis, biological evaluation and molecular dynamics simulation studies of (R)-5-methylthiazolidin-4-One derivatives as megakaryocyte protein tyrosine phosphatase 2 (PTP-MEG2) inhibitors for the treatment of type 2 diabetes. J Biomol Struct Dyn 2019; 38:3156-3165. [PMID: 31402760 DOI: 10.1080/07391102.2019.1654410] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
PTP-MEG2 plays a significant role in insulin production and is able to enhance insulin signaling and improve insulin sensitivity. So, PTP-MEG2 inhibitors are closely associated with type 2 diabetes therapy. A series of novel (R)-5-methylthiazolidin-4-one derivatives were designed and synthesized, and their PTP-MEG2 inhibitory activities (IC50) were determined. Among the desired compounds, 1h shares the highest inhibitory activity (IC50 = 1.34 μM) against PTP-MEG2. Additionally, various post-dynamic analyses confirmed that when compound 1h bound to the PTP-MEG2, the protein conformations became unstable and the function of the pTyr recognition loop (Asn331-Cys338) would be disturbed. And thus, the ideal conformations needed for the catalytic activity was difficult to be maintained. In brief, these might be how the compound 1h worked. Furthermore, we also found that the key residues Arg332 would play a critical role in disturbing the residue interactions. AbbreviationsDCCMdynamic cross-correlation mappingDMFN,N-dimethylformamideDSSPdefinition of secondary structure of proteinsFOXOforkhead transcription factorsMDmolecular dynamicsPCAprincipal component analysisPDBprotein data bankPTKsprotein tyrosine kinasesPTPsprotein tyrosine phosphatasesPTP-MEG2megakaryocyte protein tyrosine phosphatase 2RINresidue interaction networkRINGResidue Interaction Network GeneratorRMSDroot means square deviationRMSFroot mean square fluctuationCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jingwei Wu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Yingzhan Sun
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Hui Zhou
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Ying Ma
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Runling Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
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216
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Piovesan D, Tabaro F, Paladin L, Necci M, Micetic I, Camilloni C, Davey N, Dosztányi Z, Mészáros B, Monzon AM, Parisi G, Schad E, Sormanni P, Tompa P, Vendruscolo M, Vranken WF, Tosatto SCE. MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins. Nucleic Acids Res 2019; 46:D471-D476. [PMID: 29136219 PMCID: PMC5753340 DOI: 10.1093/nar/gkx1071] [Citation(s) in RCA: 156] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 10/19/2017] [Indexed: 01/30/2023] Open
Abstract
The MobiDB (URL: mobidb.bio.unipd.it) database of protein disorder and mobility annotations has been significantly updated and upgraded since its last major renewal in 2014. Several curated datasets for intrinsic disorder and folding upon binding have been integrated from specialized databases. The indirect evidence has also been expanded to better capture information available in the PDB, such as high temperature residues in X-ray structures and overall conformational diversity. Novel nuclear magnetic resonance chemical shift data provides an additional experimental information layer on conformational dynamics. Predictions have been expanded to provide new types of annotation on backbone rigidity, secondary structure preference and disordered binding regions. MobiDB 3.0 contains information for the complete UniProt protein set and synchronization has been improved by covering all UniParc sequences. An advanced search function allows the creation of a wide array of custom-made datasets for download and further analysis. A large amount of information and cross-links to more specialized databases are intended to make MobiDB the central resource for the scientific community working on protein intrinsic disorder and mobility.
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Affiliation(s)
- Damiano Piovesan
- Department of Biomedical Sciences, University of Padua, via U. Bassi 58/b, 35131 Padua, Italy
| | - Francesco Tabaro
- Department of Biomedical Sciences, University of Padua, via U. Bassi 58/b, 35131 Padua, Italy.,Institute of Biosciences and Medical Technology, Arvo Ylpön katu 34, 33520 Tampere, Finland
| | - Lisanna Paladin
- Department of Biomedical Sciences, University of Padua, via U. Bassi 58/b, 35131 Padua, Italy
| | - Marco Necci
- Department of Biomedical Sciences, University of Padua, via U. Bassi 58/b, 35131 Padua, Italy.,Department of Agricultural Sciences, University of Udine, via Palladio 8, 33100 Udine, Italy.,Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, Italy
| | - Ivan Micetic
- Department of Biomedical Sciences, University of Padua, via U. Bassi 58/b, 35131 Padua, Italy
| | - Carlo Camilloni
- Department of Biosciences, University of Milan, 20133 Milano, Italy
| | - Norman Davey
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland.,UCD School of Medicine & Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Zsuzsanna Dosztányi
- MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, 1/c Pázmány Péter sétány, H-1117, Budapest, Hungary
| | - Bálint Mészáros
- MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, 1/c Pázmány Péter sétány, H-1117, Budapest, Hungary.,Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7, H-1518 Budapest, Hungary
| | - Alexander M Monzon
- Structural Bioinformatics Group, Department of Science and Technology, National University of Quilmes, CONICET, Roque Saenz Pena 182, Bernal B1876BXD, Argentina
| | - Gustavo Parisi
- Structural Bioinformatics Group, Department of Science and Technology, National University of Quilmes, CONICET, Roque Saenz Pena 182, Bernal B1876BXD, Argentina
| | - Eva Schad
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7, H-1518 Budapest, Hungary
| | - Pietro Sormanni
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Peter Tompa
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7, H-1518 Budapest, Hungary.,Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium.,VIB-VUB Center for Structural Biology, Flanders Institute for Biotechnology (VIB), Brussels 1050, Belgium
| | | | - Wim F Vranken
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium.,VIB-VUB Center for Structural Biology, Flanders Institute for Biotechnology (VIB), Brussels 1050, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, ULB/VUB, 1050 Brussels, Belgium
| | - Silvio C E Tosatto
- Department of Biomedical Sciences, University of Padua, via U. Bassi 58/b, 35131 Padua, Italy.,CNR Institute of Neuroscience, via U. Bassi 58/b, 35131 Padua, Italy
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217
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Singh S, Dodt J, Volkers P, Hethershaw E, Philippou H, Ivaskevicius V, Imhof D, Oldenburg J, Biswas A. Structure functional insights into calcium binding during the activation of coagulation factor XIII A. Sci Rep 2019; 9:11324. [PMID: 31383913 PMCID: PMC6683118 DOI: 10.1038/s41598-019-47815-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 07/24/2019] [Indexed: 01/25/2023] Open
Abstract
The dimeric FXIII-A2, a pro-transglutaminase is the catalytic part of the heterotetrameric coagulation FXIII-A2B2 complex that upon activation by calcium binding/thrombin cleavage covalently cross-links preformed fibrin clots protecting them from premature fibrinolysis. Our study characterizes the recently disclosed three calcium binding sites of FXIII-A concerning evolution, mutual crosstalk, thermodynamic activation profile, substrate binding, and interaction with other similarly charged ions. We demonstrate unique structural aspects within FXIII-A calcium binding sites that give rise to functional differences making FXIII unique from other transglutaminases. The first calcium binding site showed an antagonistic relationship towards the other two. The thermodynamic profile of calcium/thrombin-induced FXIII-A activation explains the role of bulk solvent in transitioning its zymogenic dimeric form to an activated monomeric form. We also explain the indirect effect of solvent ion concentration on FXIII-A activation. Our study suggests FXIII-A calcium binding sites could be putative pharmacologically targetable regions.
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Affiliation(s)
- Sneha Singh
- Institute of Experimental Hematology and Transfusion medicine, University Hospital of Bonn, Bonn, 53127, Germany
| | | | | | - Emma Hethershaw
- Discovery and Translational Science Department, University of Leeds, Leeds, LS29JT, United Kingdom
| | - Helen Philippou
- Discovery and Translational Science Department, University of Leeds, Leeds, LS29JT, United Kingdom
| | - Vytautus Ivaskevicius
- Institute of Experimental Hematology and Transfusion medicine, University Hospital of Bonn, Bonn, 53127, Germany
| | - Diana Imhof
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, Bonn, 53121, Germany
| | - Johannes Oldenburg
- Institute of Experimental Hematology and Transfusion medicine, University Hospital of Bonn, Bonn, 53127, Germany
| | - Arijit Biswas
- Institute of Experimental Hematology and Transfusion medicine, University Hospital of Bonn, Bonn, 53127, Germany.
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218
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Valdez‐Camacho JR, Cortés‐Guzmán KP, Torres‐Gómez H, Flores R, Leyva MA, Escalante J. Kinetics, Thermodynamics, and Theoretical Studies in a Diels‐Alder Dimerization Process of 3‐Vinylindole Derivative of the 3‐Indoleacetic Acid: An Auxin. ChemistrySelect 2019. [DOI: 10.1002/slct.201901141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jonathan Román Valdez‐Camacho
- Centro de Investigaciones Químicas-IICBAUniversidad Autónoma del Estado de Morelos, Cuernavaca Av. Universidad 1001 C.P. 62210 México
| | - Karen Paola Cortés‐Guzmán
- Centro de Investigaciones Químicas-IICBAUniversidad Autónoma del Estado de Morelos, Cuernavaca Av. Universidad 1001 C.P. 62210 México
| | - Héctor Torres‐Gómez
- Institut für Pharmazeutische und Medizinische ChemieHeinrich-Heine-Universität Düsseldorf Universitätsstraße 40225 Düsseldorf Germany
| | - Roberto Flores
- Facultad de Ciencias Químicas e IngenieríaUniversidad Autónoma del Estado de Morelos
| | - Marco A. Leyva
- CINVESTAV−I.P.N.Chemistry Department, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco C.P. 07000 Ciudad de México Mexico
| | - Jaime Escalante
- Centro de Investigaciones Químicas-IICBAUniversidad Autónoma del Estado de Morelos, Cuernavaca Av. Universidad 1001 C.P. 62210 México
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219
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Xu Z, Zhang Q, Shi J, Zhu W. Underestimated Noncovalent Interactions in Protein Data Bank. J Chem Inf Model 2019; 59:3389-3399. [PMID: 31294978 DOI: 10.1021/acs.jcim.9b00258] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Noncovalent interactions (NCIs) play essential roles in the structure and function of biomacromolecules. There are various NCIs, e.g., hydrogen bonds (HBs), cation-π and π-π interactions, and ionic bonds, among which HBs are the most widespread and well-studied. By utilizing the ratio of the observed HBs over pseudo HBs (1.0 Å longer than the HB distance criteria without angle constraints), we demonstrated that HBs in both protein-ligand and protein-protein interfaces are overlooked in structures deposited in PDB. After the QM/MM optimization of 12 protein-ligand complexes, we showed that the overlooked HBs could be recovered. With a systematic search in the PDB, we found that the HB number per residue (NHB/R) in proteins decreases as structural resolution becomes lower, implying that HBs are overlooked even today, regardless of the type of refinement approach used. Similarly, cation-π, π-π, and ionic interactions were found to be significantly lost, manifesting the universal underestimation of various NCIs. Considering the vital role of NCIs, it is important to recover the NCIs to facilitate drug design, to explore protein-protein interaction, and to study protein structure and function.
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Affiliation(s)
- Zhijian Xu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203 , China
| | - Qian Zhang
- Department of Computer Science and Technology , East China Normal University , Shanghai 200241 , China
| | - Jiye Shi
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203 , China
| | - Weiliang Zhu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203 , China.,Open Studio for Druggability Research of Marine Natural Products , Pilot National Laboratory for Marine Science and Technology (Qingdao) , Qingdao 266237 , China
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220
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Williamson A, Grgic M, Leiros HKS. DNA binding with a minimal scaffold: structure-function analysis of Lig E DNA ligases. Nucleic Acids Res 2019; 46:8616-8629. [PMID: 30007325 PMCID: PMC6144786 DOI: 10.1093/nar/gky622] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 06/28/2018] [Indexed: 11/13/2022] Open
Abstract
DNA ligases join breaks in the phosphodiester backbone of DNA by catalysing the formation of bonds between opposing 5′P and 3′OH ends in an adenylation-dependent manner. Catalysis is accompanied by reorientation of two core domains to provide access to the active site for cofactor utilization and enable substrate binding and product release. The general paradigm is that DNA ligases engage their DNA substrate through complete encirclement of the duplex, completed by inter-domain kissing contacts via loops or additional domains. The recent structure of a minimal Lig E-type DNA ligase, however, implies it must use a different mechanism, as it lacks any domains or loops appending the catalytic core which could complete encirclement. In the present study, we have used a structure-guided mutagenesis approach to investigate the role of conserved regions in the Lig E proteins with respect to DNA binding. We report the structure of a Lig-E type DNA ligase bound to the nicked DNA-adenylate reaction intermediate, confirming that complete encirclement is unnecessary for substrate engagement. Biochemical and biophysical measurements of point mutants to residues implicated in binding highlight the importance of basic residues in the OB domain, and inter-domain contacts to the linker.
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Affiliation(s)
- Adele Williamson
- Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Miriam Grgic
- Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
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221
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Hockenberry AJ, Wilke CO. Evolutionary couplings detect side-chain interactions. PeerJ 2019; 7:e7280. [PMID: 31328041 PMCID: PMC6622159 DOI: 10.7717/peerj.7280] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 06/09/2019] [Indexed: 12/19/2022] Open
Abstract
Patterns of amino acid covariation in large protein sequence alignments can inform the prediction of de novo protein structures, binding interfaces, and mutational effects. While algorithms that detect these so-called evolutionary couplings between residues have proven useful for practical applications, less is known about how and why these methods perform so well, and what insights into biological processes can be gained from their application. Evolutionary coupling algorithms are commonly benchmarked by comparison to true structural contacts derived from solved protein structures. However, the methods used to determine true structural contacts are not standardized and different definitions of structural contacts may have important consequences for interpreting the results from evolutionary coupling analyses and understanding their overall utility. Here, we show that evolutionary coupling analyses are significantly more likely to identify structural contacts between side-chain atoms than between backbone atoms. We use both simulations and empirical analyses to highlight that purely backbone-based definitions of true residue–residue contacts (i.e., based on the distance between Cα atoms) may underestimate the accuracy of evolutionary coupling algorithms by as much as 40% and that a commonly used reference point (Cβ atoms) underestimates the accuracy by 10–15%. These findings show that co-evolutionary outcomes differ according to which atoms participate in residue–residue interactions and suggest that accounting for different interaction types may lead to further improvements to contact-prediction methods.
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Affiliation(s)
- Adam J Hockenberry
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Claus O Wilke
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
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222
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Li R, Li X, Jiang J, Tian Y, Liu D, Zhangsun D, Fu Y, Wu Y, Luo S. Interaction of rat α9α10 nicotinic acetylcholine receptor with α-conotoxin RgIA and Vc1.1: Insights from docking, molecular dynamics and binding free energy contributions. J Mol Graph Model 2019; 92:55-64. [PMID: 31330438 DOI: 10.1016/j.jmgm.2019.06.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 06/25/2019] [Accepted: 06/27/2019] [Indexed: 12/12/2022]
Abstract
The α9α10 nicotinic acetylcholine receptor (nAChR) is an effective therapeutic target for neuropathic pain. α-Conotoxin RgIA and Vc1.1 are two well-known peptides blocking α9α10 nAChR potently and selectively, which have been extensively investigated as drug candidates. Several key residues were established in previous experimental research. However, the mechanism of the specific interaction still needs to be elucidated in more detail. In this work, we explored the interaction mechanism between RgIA/Vc1.1 and rat α9α10 nAChR using docking and molecular dynamics (MD) simulations. Energy and network analysis programs were used to reveal key residues responsible for their interaction. Our results indicated that the most critical residues were in accord with previous studies. Importantly, several novel residues, including Tyr95, Trp151 in α9 (+)α10 (-) interface as well as Tyr196, Arg59in α10 (+)α9 (-) interface, were found in our models. Furthermore, we analyzed noncovalent interaction energies between RgIA/Vc1.1 and rat α9α10 nAChR. The results showed that three negatively charged residues (Glu197 in α10 subunit, Asp168 in α9 subunit and Asp205 in α10 subunit) were involved in the interaction between RgIA and rat α9α10 nAChR. In contrast, the interaction between Vc1.1 and rat α9α10 nAChR was mediated by the positively charged residues Arg59, Arg81 in α9 (-) subunit. These findings provided further insights into the molecular mechanisms of interaction between RgIA and Vc1.1 and rat α9α10 nAChR.
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Affiliation(s)
- Rui Li
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Key Lab for Marine Drugs of Haikou, Hainan University, Haikou, Hainan, 570228, China
| | - Xincan Li
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Key Lab for Marine Drugs of Haikou, Hainan University, Haikou, Hainan, 570228, China
| | - Jiemei Jiang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Key Lab for Marine Drugs of Haikou, Hainan University, Haikou, Hainan, 570228, China
| | - Yuanyuan Tian
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Key Lab for Marine Drugs of Haikou, Hainan University, Haikou, Hainan, 570228, China
| | - Danrui Liu
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Key Lab for Marine Drugs of Haikou, Hainan University, Haikou, Hainan, 570228, China
| | - Donting Zhangsun
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Key Lab for Marine Drugs of Haikou, Hainan University, Haikou, Hainan, 570228, China
| | - Ying Fu
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Key Lab for Marine Drugs of Haikou, Hainan University, Haikou, Hainan, 570228, China
| | - Yong Wu
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Key Lab for Marine Drugs of Haikou, Hainan University, Haikou, Hainan, 570228, China.
| | - Sulan Luo
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Key Lab for Marine Drugs of Haikou, Hainan University, Haikou, Hainan, 570228, China.
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223
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Shcherbinin D, Veselovsky A, Rubtsova M, Grigorenko V, Egorov A. The impact of long-distance mutations on the Ω-loop conformation in TEM type β-lactamases. J Biomol Struct Dyn 2019; 38:2369-2376. [PMID: 31241429 DOI: 10.1080/07391102.2019.1634642] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
β-lactamases are hydrolytic enzymes primarily responsible for occurrence and abundance of bacteria resistant to β-lactam antibiotics. TEM type β-lactamases are formed by the parent enzyme TEM-1 and more than two hundred of its mutants. Positions for the known amino acid substitutions cover ∼30% of TEM type enzyme's sequence. These substitutions are divided into the key mutations that lead to changes in catalytic properties of β-lactamases, and the secondary ones, which role is poorly understood. In this study, Residue Interaction Networks were constructed from molecular dynamic trajectories of β-lactamase TEM-1 and its variants with two key substitutions, G238S and E240K, and their combinations with secondary ones (M182T and Q39K). Particular attention was paid to a detailed analysis of the interactions that affect conformation and mobility of the Ω-loop, representing a part of the β-lactamase active site. It was shown that key mutations weakened the stability of contact inside the Ω-loop thus increasing its mobility. Combination of three amino acid substitutions, including the 182 residue, leads to the release of R65 promoting its new contacts with N175 and D176. As a result, Ω-loop is fixed on the protein globule. The second distal mutation Q39K prevents changes in spatial position of R65, which lead to the weakening of the effect of M182T substitution and the recovery of the Ω-loop mobility. Thus, the distal secondary mutations are directed for recovering the mobility of enzyme disturbed by the key mutations responsible for expansion of substrate specificity. AbbreviationsESBLextended spectrum beta-lactamasesIRinhibitor resistant beta-lactamasesMDmolecular dynamicsRINresidue interaction networksRMSDroot mean square deviationRMSFroot mean square fluctuations.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dmitrii Shcherbinin
- Institute of Biomedical Chemistry, Moscow, Russia.,Department of Molecular Technologies, Pirogov Russian National Research Medical University, Moscow, Russia
| | | | - Maya Rubtsova
- Chemistry Faculty, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Vitaly Grigorenko
- Chemistry Faculty, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Alexey Egorov
- Chemistry Faculty, M.V. Lomonosov Moscow State University, Moscow, Russia
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224
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Saldaño TE, Tosatto SCE, Parisi G, Fernandez-Alberti S. Network analysis of dynamically important residues in protein structures mediating ligand-binding conformational changes. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2019; 48:559-568. [PMID: 31273390 DOI: 10.1007/s00249-019-01384-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 05/31/2019] [Accepted: 07/01/2019] [Indexed: 11/26/2022]
Abstract
According to the generalized conformational selection model, ligand binding involves the co-existence of at least two conformers with different ligand-affinities in a dynamical equilibrium. Conformational transitions between them should be guaranteed by intramolecular vibrational dynamics associated to each conformation. These motions are, therefore, related to the biological function of a protein. Positions whose mutations are found to alter these vibrations the most can be defined as key positions, that is, dynamically important residues that mediate the ligand-binding conformational change. In a previous study, we have shown that these positions are evolutionarily conserved. They correspond to buried aliphatic residues mostly localized in regular structured regions of the protein like β-sheets and α-helices. In the present paper, we perform a network analysis of these key positions for a large dataset of paired protein structures in the ligand-free and ligand-bound form. We observe that networks of interactions between these key positions present larger and more integrated networks with faster transmission of the information. Besides, networks of residues result that are robust to conformational changes. Our results reveal that the conformational diversity of proteins seems to be guaranteed by a network of strongly interconnected key positions rather than individual residues.
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Affiliation(s)
- Tadeo E Saldaño
- Universidad Nacional de Quilmes/CONICET, Roque Saenz Peña 352, B1876BXD, Bernal, Argentina
| | - Silvio C E Tosatto
- Department of Biomedical Sciences, University of Padova, Viale G. Colombo 3, 5131, Padua, Italy
| | - Gustavo Parisi
- Universidad Nacional de Quilmes/CONICET, Roque Saenz Peña 352, B1876BXD, Bernal, Argentina
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225
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Aydınkal RM, Serçinoğlu O, Ozbek P. ProSNEx: a web-based application for exploration and analysis of protein structures using network formalism. Nucleic Acids Res 2019; 47:W471-W476. [PMID: 31114881 PMCID: PMC6602423 DOI: 10.1093/nar/gkz390] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/17/2019] [Accepted: 05/09/2019] [Indexed: 01/14/2023] Open
Abstract
ProSNEx (Protein Structure Network Explorer) is a web service for construction and analysis of Protein Structure Networks (PSNs) alongside amino acid flexibility, sequence conservation and annotation features. ProSNEx constructs a PSN by adding nodes to represent residues and edges between these nodes using user-specified interaction distance cutoffs for either carbon-alpha, carbon-beta or atom-pair contact networks. Different types of weighted networks can also be constructed by using either (i) the residue-residue interaction energies in the format returned by gRINN, resulting in a Protein Energy Network (PEN); (ii) the dynamical cross correlations from a coarse-grained Normal Mode Analysis (NMA) of the protein structure; (iii) interaction strength. Upon construction of the network, common network metrics (such as node centralities) as well as shortest paths between nodes and k-cliques are calculated. Moreover, additional features of each residue in the form of conservation scores and mutation/natural variant information are included in the analysis. By this way, tool offers an enhanced and direct comparison of network-based residue metrics with other types of biological information. ProSNEx is free and open to all users without login requirement at http://prosnex-tool.com.
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Affiliation(s)
- Rasim Murat Aydınkal
- Department of Bioengineering, Faculty of Engineering, Marmara University, Kadikoy, Istanbul 34722, Turkey
- Ali Nihat Gokyigit Foundation, Etiler, Istanbul 34340, Turkey
| | - Onur Serçinoğlu
- Department of Bioengineering, Faculty of Engineering, Marmara University, Kadikoy, Istanbul 34722, Turkey
- Department of Bioengineering, Faculty of Engineering, Recep Tayyip Erdoğan University, Rize 53100, Turkey
| | - Pemra Ozbek
- Department of Bioengineering, Faculty of Engineering, Marmara University, Kadikoy, Istanbul 34722, Turkey
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226
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Xia Q, Ding Y. Thermostability of Lipase A and Dynamic Communication Based on Residue Interaction Network. Protein Pept Lett 2019; 26:702-716. [PMID: 31215367 DOI: 10.2174/0929866526666190617091812] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 04/10/2019] [Accepted: 04/25/2019] [Indexed: 11/22/2022]
Abstract
OBJECTIVE Dynamic communication caused by mutation affects protein stability. The main objective of this study is to explore how mutations affect communication and to provide further insight into the relationship between heat resistance and signal propagation of Bacillus subtilis lipase (Lip A). METHODS The relationship between dynamic communication and Lip A thermostability is studied by long-time MD simulation and residue interaction network. The Dijkstra algorithm is used to get the shortest path of each residue pair. Subsequently, time-series frequent paths and spatio-temporal frequent paths are mined through an Apriori-like algorithm. RESULTS Time-series frequent paths show that the communication between residue pairs, both in wild-type lipase (WTL) and mutant 6B, becomes chaotic with an increase in temperature; however, more residues in 6B can maintain stable communication at high temperature, which may be associated with the structural rigidity. Furthermore, spatio-temporal frequent paths reflect the interactions among secondary structures. For WTL at 300K, β7, αC, αB, the longest loop, αA and αF contact frequently. The 310-helix between β3 and αA is penetrated by spatio-temporal frequent paths. At 400K, only αC can be frequently transmitted. For 6B, when at 300K, αA and αF are in more tight contact by spatio-temporal frequent paths though I157M and N166Y. Moreover, the rigidity of the active site His156 and the C-terminal of Lip A are increased, as reflected by the spatio-temporal frequent paths. At 400K, αA and αF, 310-helix between β3 and αA, the longest loop, and the loop where the active site Asp133 is located can still maintain stable communication. CONCLUSION From the perspective of residue dynamic communication, it is obviously found that mutations cause changes in interactions between secondary structures and enhance the rigidity of the structure, contributing to the thermal stability and functional activity of 6B.
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Affiliation(s)
- Qian Xia
- Laboratory of Media Design and Software Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Yanrui Ding
- Laboratory of Media Design and Software Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China.,Key Laboratory of Industrial Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
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227
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Wu H, Liu Q, Casas-Pastor D, Dürr F, Mascher T, Fritz G. The role of C-terminal extensions in controlling ECF σ factor activity in the widely conserved groups ECF41 and ECF42. Mol Microbiol 2019; 112:498-514. [PMID: 30990934 DOI: 10.1111/mmi.14261] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2019] [Indexed: 01/01/2023]
Abstract
The activity of extracytoplasmic function σ-factors (ECFs) is typically regulated by anti-σ factors. In a number of highly abundant ECF groups, including ECF41 and ECF42, σ-factors contain fused C-terminal protein domains, which provide the necessary regulatory function instead. Here, we identified the contact interface between the C-terminal extension and the core σ-factor regions required for controlling ECF activity. We applied direct coupling analysis (DCA) to infer evolutionary covariation between contacting amino acid residues for groups ECF41 and ECF42. Mapping the predicted interactions to a recently solved ECF41 structure demonstrated that DCA faithfully identified an important contact interface between the SnoaL-like extension and the linker between the σ2 and σ4 domains. Systematic alanine substitutions of contacting residues support this model and suggest that this interface stabilizes a compact conformation of ECF41 with low transcriptional activity. For group ECF42, DCA supports a structural homology model for their C-terminal tetratricopeptide repeat (TPR) domains and predicts an intimate contact between the first TPR-helix and the σ4 domain. Mutational analyses demonstrate the essentiality of the predicted interactions for ECF42 activity. These results indicate that C-terminal extensions indeed bind and regulate the core ECF regions, illustrating the potential of DCA for discovering regulatory motifs in the ECF subfamily.
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Affiliation(s)
- Hao Wu
- LOEWE-Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, 35032, Marburg, Germany
| | - Qiang Liu
- Institute of Microbiology, Technische Universität (TU) Dresden, 01062, Dresden, Germany.,Department Biology I, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Delia Casas-Pastor
- LOEWE-Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, 35032, Marburg, Germany
| | - Franziska Dürr
- Institute of Microbiology, Technische Universität (TU) Dresden, 01062, Dresden, Germany
| | - Thorsten Mascher
- Institute of Microbiology, Technische Universität (TU) Dresden, 01062, Dresden, Germany
| | - Georg Fritz
- LOEWE-Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, 35032, Marburg, Germany
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Tounsi S, Kamoun Y, Feki K, Jemli S, Saïdi MN, Ziadi H, Alcon C, Brini F. Localization and expression analysis of a novel catalase from Triticum monococcum TmCAT1 involved in response to different environmental stresses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 139:366-378. [PMID: 30954019 DOI: 10.1016/j.plaphy.2019.03.039] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 03/26/2019] [Accepted: 03/27/2019] [Indexed: 05/09/2023]
Abstract
Catalase proteins play a crucial role in detoxifying hydrogen peroxide, generated during plant growth, and in response to various environmental stresses. Despite their importance, little is known about their localization and expression in wheat. In this study, we identified and characterized a novel peroxisomal catalase gene from Triticum monococcum, designated as TmCAT1. Phylogenetic analysis revealed that TmCAT1 shared high identity with TdCAT1 and other plant catalases belonging to subfamily 1. We predicted the 3D structure model and the oligomerization arrangement of TmCAT1. Besides, we displayed an arrangement in asymmetric unit, which involved interactions including, mainly, residues from N-terminal domain. Interestingly, sequence analysis indicated that TmCAT1, like TdCAT1, had the peroxisomal targeting signal (PTS1) around its C-terminus. Transient expression of TmCAT1-GFP and TdCAT1-GFP in tobacco leaves revealed that the two fused proteins are targeted into peroxisomes. However, the truncated forms lacking the tripeptide QKL remained in the cytosol. Concerning the expression profile analysis, TmCAT1 is expressed especially in leaves in normal condition. On the other hand, it is up-regulated by different stress incorporating salt, osmotic, oxidative, heavy metal and hormones stresses. Functional analysis by heterologous expression in yeast cells showed that TmCAT1 improved tolerance to multiple abiotic stresses. The presence of important cis-regulatory elements in the promoter region of TmCAT1 strongly reinforces the interest of this gene in plant adaptation to various stresses.
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Affiliation(s)
- Sana Tounsi
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax (CBS)/University of Sfax, B.P ''1177'', 3018, Sfax, Tunisia
| | - Yosra Kamoun
- Laboratory of Molecular Biotechnology of Eukaryotes, Centre of Biotechnology of Sfax, B.P ''1177'', 3018, Sfax, Tunisia
| | - Kaouthar Feki
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax (CBS)/University of Sfax, B.P ''1177'', 3018, Sfax, Tunisia; Laboratory of Legumes, Centre of Biotechnology Bordj Cedria, BP 901, 2050, Hammam Lif, Tunisia
| | - Sonia Jemli
- Laboratory of Microbial Biotechnology and Enzymes Engineering, Centre of Biotechnology of Sfax, B.P ''1177'', 3018, Sfax, Tunisia
| | - Mohamed Najib Saïdi
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax (CBS)/University of Sfax, B.P ''1177'', 3018, Sfax, Tunisia
| | - Hajer Ziadi
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax (CBS)/University of Sfax, B.P ''1177'', 3018, Sfax, Tunisia
| | - Carine Alcon
- Biochimie & Physiologie Moléculaire des Plantes, PHIV Platform, UMR 5004 CNRS/386 INRA/Supagro Montpellier / Université Montpellier 2, Campus Supagro-INRA, 34060, Montpellier Cedex 2, France
| | - Faiçal Brini
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax (CBS)/University of Sfax, B.P ''1177'', 3018, Sfax, Tunisia.
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229
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Naqvi AAT, Alajmi MF, Rehman T, Hussain A, Hassan I. Effects of Pro1266Leu mutation on structure and function of glycoprotein Ib binding domain of von Willebrand factor. J Cell Biochem 2019; 120:17847-17857. [PMID: 31135071 DOI: 10.1002/jcb.29052] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 04/26/2019] [Accepted: 04/30/2019] [Indexed: 02/06/2023]
Abstract
Glycoprotein Ibα (GpIbα) binding ability of A1 domain of von Willebrand factor (vWF) facilitates platelet adhesion that plays a crucial role in maintaining hemostasis and thrombosis at the site of vascular damage. There are both "loss as well as gain of function" mutations observed in this domain. Naturally occurring "gain of function" mutations leave self-activating impacts on the A1 domain which turns the normal binding to characteristic constitutive binding with GPIbα. These "gain of function" mutations are associated with the von Willebrand disease type 2B. In recent years, studies focused on understanding the mechanism and conformational patterns attached to these phenomena have been conducted, but the conformational pathways leading to such binding patterns are poorly understood as of now. To obtain a microscopic picture of such events for the better understanding of pathways, we used molecular dynamics (MD) simulations along with principal component analysis and normal mode analysis to study the effects of Pro1266Leu (Pro503Leu in structural context) mutation on the structure and function of A1 domain of vWF. MD simulations have provided atomic-level details of intermolecular motions as a function of time to understand the dynamic behavior of A1 domain of vWF. Comparative analysis of the trajectories obtained from MD simulations of both the wild type and Pro503Leu mutant suggesting appreciable conformational changes in the structure of mutant which might provide a basis for assuming the "gain of function" effects of these mutations on the A1 domain of vWF, resulting in the constitutive binding with GpIbα.
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Affiliation(s)
- Ahmad Abu Turab Naqvi
- Center for Interdisciplinary Research in Basic Science, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
| | - Mohamed F Alajmi
- Department of Pharmacognosy College of Pharmacy, King Saud University, Riyadh, KSA
| | - Tabish Rehman
- Department of Pharmacognosy College of Pharmacy, King Saud University, Riyadh, KSA
| | - Afzal Hussain
- Department of Pharmacognosy College of Pharmacy, King Saud University, Riyadh, KSA
| | - Imtaiyaz Hassan
- Center for Interdisciplinary Research in Basic Science, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
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230
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Liu WS, Wang RR, Sun YZ, Li WY, Li HL, Liu CL, Ma Y, Wang RL. Exploring the effect of inhibitor AKB-9778 on VE-PTP by molecular docking and molecular dynamics simulation. J Cell Biochem 2019; 120:17015-17029. [PMID: 31125141 DOI: 10.1002/jcb.28963] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/03/2019] [Accepted: 03/15/2019] [Indexed: 01/02/2023]
Abstract
Diabetic macular edema, also known as diabetic eye disease, is mainly caused by the overexpression of vascular endothelial protein tyrosine phosphatase (VE-PTP) at hypoxia/ischemic. AKB-9778 is a known VE-PTP inhibitor that can effectively interact with the active site of VE-PTP to inhibit the activity of VE-PTP. However, the binding pattern of VE-PTP with AKB-9778 and the dynamic implications of AKB-9778 on VE-PTP system at the molecular level are poorly understood. Through molecular docking, it was found that the AKB-9778 was docked well in the binding pocket of VE-PTP by the interactions of hydrogen bond and Van der Waals. Furthermore, after molecular dynamic simulations on VE-PTP system and VE-PTP AKB-9778 system, a series of postdynamic analyses found that the flexibility and conformation of the active site undergone an obvious transition after VE-PTP binding with AKB-9778. Moreover, by constructing the RIN, it was found that the different interactions in the active site were the detailed reasons for the conformational differences between these two systems. Thus, the finding here might provide a deeper understanding of AKB-9778 as VE-PTP Inhibitor.
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Affiliation(s)
- Wen-Shan Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Rui-Rui Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Ying-Zhan Sun
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Wei-Ya Li
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Hong-Lian Li
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Chi-Lu Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Ying Ma
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Run-Ling Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
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231
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Prediction and characterisation of lantibiotic structures with molecular modelling and molecular dynamics simulations. Sci Rep 2019; 9:7169. [PMID: 31073133 PMCID: PMC6509333 DOI: 10.1038/s41598-019-42963-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 04/08/2019] [Indexed: 11/08/2022] Open
Abstract
Lantibiotics are lanthionine-containing bactericidal peptides produced by gram-positive bacteria as a defence mechanism against other bacterial species. Lantipeptides disrupt the integrity of target cells by forming pores in their cell membranes, or by preventing cell wall biosynthesis, which subsequently results in cell death. Lantibiotics are of immense importance to the food preservation and pharmaceutical industries. The rise in multidrug resistance demands the discovery of novel antimicrobials, and several authors advocate that lantibiotics hold the future of antimicrobial drug discovery. Owing to their amenability to structural modifications, novel lantibiotics with higher efficacy and antimicrobial activity can be constructed by bioengineering and nanoengineering strategies, and is opined to have immense therapeutic success in combating the rise in multidrug resistance. Understanding the structure and dynamics of lantibiotics is therefore crucial for the development of novel lantipeptides, and this study aimed to study the structural properties and dynamics of 37 lantibiotics using computational strategies. The structures of these 37 lantibiotics were constructed from homology, and their structural stability and compactness were analysed by molecular dynamics simulations. The phylogenetic relationships, physicochemical properties, disordered regions, pockets, intramolecular bonds and interactions, and structural diversity of the 37 lantipeptides were studied. The structures of the 37 lantipeptides constructed herein remained stable throughout simulation. The study revealed that the structural diversity of lantibiotics is not significantly correlated to sequence diversity, and this property could be exploited for designing novel lantipeptides with higher efficacy.
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232
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Astl L, Verkhivker GM. Atomistic Modeling of the ABL Kinase Regulation by Allosteric Modulators Using Structural Perturbation Analysis and Community-Based Network Reconstruction of Allosteric Communications. J Chem Theory Comput 2019; 15:3362-3380. [PMID: 31017783 DOI: 10.1021/acs.jctc.9b00119] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In this work, we have examined the molecular mechanisms of allosteric regulation of the ABL tyrosine kinase at the atomic level. Atomistic modeling of the ABL complexes with a panel of allosteric modulators has been performed using a combination of molecular dynamics simulations, structural residue perturbation scanning, and a novel community analysis of the residue interaction networks. Our results have indicated that allosteric inhibitors and activators may exert a differential control on allosteric signaling between the kinase binding sites and functional regions. While the inhibitor binding can strengthen the closed ABL state and induce allosteric communications directed from the allosteric pocket to the ATP binding site, the DPH activator may induce a more dynamic open form and activate allosteric couplings between the ATP and substrate binding sites. By leveraging a network-centric theoretical framework, we have introduced a novel community analysis method and global topological parameters that have unveiled the hierarchical modularity and the intercommunity bridging sites in the residue interaction network. We have found that allosteric functional hotspots responsible for the kinase regulation may serve the intermodular bridges in the global interaction network. The central conclusion from this analysis is that the regulatory switch centers play a fundamental role in the modular network organization of ABL as the unique intercommunity bridges that connect the SH2 and SH3 domains with the catalytic core into a functional kinase assembly. The hierarchy of network organization in the ABL regulatory complexes may allow for the synergistic action of dense intercommunity links required for the robust signal transfer in the catalytic core and sparse network bridges acting as the regulatory control points that orchestrate allosteric transitions between the inhibited and active kinase forms.
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Affiliation(s)
- Lindy Astl
- Graduate Program in Computational and Data Sciences, Keck Center for Science and Engineering, Schmid College of Science and Technology , Chapman University , One University Drive , Orange , California 92866 , United States
| | - Gennady M Verkhivker
- Graduate Program in Computational and Data Sciences, Keck Center for Science and Engineering, Schmid College of Science and Technology , Chapman University , One University Drive , Orange , California 92866 , United States.,Department of Biomedical and Pharmaceutical Sciences , Chapman University School of Pharmacy , Irvine , California 92618 , United States
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233
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Smith IN, Thacker S, Seyfi M, Cheng F, Eng C. Conformational Dynamics and Allosteric Regulation Landscapes of Germline PTEN Mutations Associated with Autism Compared to Those Associated with Cancer. Am J Hum Genet 2019; 104:861-878. [PMID: 31006514 PMCID: PMC6506791 DOI: 10.1016/j.ajhg.2019.03.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 03/08/2019] [Indexed: 01/07/2023] Open
Abstract
Individuals with germline PTEN tumor-suppressor variants have PTEN hamartoma tumor syndrome (PHTS). Clinically, PHTS has variable presentations; there are distinct subsets of PHTS-affected individuals, such as those diagnosed with autism spectrum disorder (ASD) or cancer. It remains unclear why mutations in one gene can lead to such seemingly disparate phenotypes. Therefore, we sought to determine whether it is possible to predict a given PHTS-affected individual's a priori risk of ASD, cancer, or the co-occurrence of both phenotypes. By integrating network proximity analysis performed on the human interactome, molecular simulations, and residue-interaction networks, we demonstrate the role of conformational dynamics in the structural communication and long-range allosteric regulation of germline PTEN variants associated with ASD or cancer. We show that the PTEN interactome shares significant overlap with the ASD and cancer interactomes, providing network-based evidence that PTEN is a crucial player in the biology of both disorders. Importantly, this finding suggests that a germline PTEN variant might perturb the ASD or cancer networks differently, thus favoring one disease outcome at any one time. Furthermore, protein-dynamic structural-network analysis reveals small-world structural communication mediated by highly conserved functional residues and potential allosteric regulation of PTEN. We identified a salient structural-communication pathway that extends across the inter-domain interface for cancer-only mutations. In contrast, the structural-communication pathway is predominantly restricted to the phosphatase domain for ASD-only mutations. Our integrative approach supports the prediction and potential modulation of the relevant conformational states that influence structural communication and long-range perturbations associated with mutational effects that lead to PTEN-ASD or PTEN-cancer phenotypes.
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Affiliation(s)
- Iris Nira Smith
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Stetson Thacker
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
| | - Marilyn Seyfi
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Feixiong Cheng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA; Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA; Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
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234
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Pook NP, Adam A, Gjikaj M. Crystal structure and Hirshfeld surface analysis of (μ-2-{4-[(carboxyl-atometh-yl)carbamo-yl]benz-amido}-acetato-κ 2 O: O')bis-[bis-(1,10-phenanthroline-κ 2 N, N')copper(II)] dinitrate N, N'-(1,4-phenyl-enedicarbon-yl)diglycine monosolvate octa-hydrate. Acta Crystallogr E Crystallogr Commun 2019; 75:667-674. [PMID: 31110808 PMCID: PMC6505584 DOI: 10.1107/s2056989019005164] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 04/15/2019] [Indexed: 11/10/2022]
Abstract
The centrosymmetric binuclear complex cation of the title compound, [Cu2(C12H10N2O6)(C12H8N2)4](NO3)2·C12H12N2O6·8H2O, is composed of a CuII atom with a distorted trigonal-bipyramidal coordination environment defined by four N atoms from two bidentate 1,10-phenanthroline ligands and one oxygen atom from one-half of the monodentate N,N'-(1,4-phenyl-enedicarbon-yl)diglycinate anion. The asymmetric unit is completed by one-half of the N,N'-(1,4-phenyl-enedicarbon-yl)diglycine solvent mol-ecule, which is located on a centre of inversion, by one nitrate counter-anion and four water mol-ecules. In the crystal, the cationic complexes are linked via inter-molecular π-π stacking and through lone-pair⋯π inter-actions involving the N,N'-(1,4-phenyl-enedicarbon-yl)diglycinate anion and the phenanthroline ligands. The N,N'-(1,4-phenyl-enedicarbon-yl)diglycine solvent mol-ecule is involved in classical and non-classical hydrogen-bonding inter-actions, as well as π-π stacking inter-actions. The centroid-to-centroid distances between aromatic entities are in the range 3.5402 (5)-4.3673 (4) Å. The crystal structure is stabilized by further C-H⋯O contacts as well as by O-H⋯O and N-H⋯O hydrogen bonds between water mol-ecules, the nitrate anions, the N,N'-(1,4-phenyl-enedicarbon-yl)diglycinate ligands, N,N'-(1,4-phenyl-enedicarbon-yl)diglycine solvent mol-ecules and phenanthroline ligands, giving rise to a supra-molecular framework. A Hirshfeld surface analysis was carried out to qu-antify these inter-actions.
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Affiliation(s)
- Niels-Patrick Pook
- Institute of Inorganic and Analytical Chemistry, Clausthal University of Technology, Paul-Ernst-Str. 4, D-38678, Clausthal-Zellerfeld, Germany
| | - Arnold Adam
- Institute of Inorganic and Analytical Chemistry, Clausthal University of Technology, Paul-Ernst-Str. 4, D-38678, Clausthal-Zellerfeld, Germany
| | - Mimoza Gjikaj
- Institute of Inorganic and Analytical Chemistry, Clausthal University of Technology, Paul-Ernst-Str. 4, D-38678, Clausthal-Zellerfeld, Germany
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235
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Minervini G, Quaglia F, Tabaro F, Tosatto SCE. Genotype-phenotype relations of the von Hippel-Lindau tumor suppressor inferred from a large-scale analysis of disease mutations and interactors. PLoS Comput Biol 2019; 15:e1006478. [PMID: 30943211 PMCID: PMC6464237 DOI: 10.1371/journal.pcbi.1006478] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 04/15/2019] [Accepted: 02/25/2019] [Indexed: 02/06/2023] Open
Abstract
Familiar cancers represent a privileged point of view for studying the complex cellular events inducing tumor transformation. Von Hippel-Lindau syndrome, a familiar predisposition to develop cancer is a clear example. Here, we present our efforts to decipher the role of von Hippel-Lindau tumor suppressor protein (pVHL) in cancer insurgence. We collected high quality information about both pVHL mutations and interactors to investigate the association between patient phenotypes, mutated protein surface and impaired interactions. Our data suggest that different phenotypes correlate with localized perturbations of the pVHL structure, with specific cell functions associated to different protein surfaces. We propose five different pVHL interfaces to be selectively involved in modulating proteins regulating gene expression, protein homeostasis as well as to address extracellular matrix (ECM) and ciliogenesis associated functions. These data were used to drive molecular docking of pVHL with its interactors and guide Petri net simulations of the most promising alterations. We predict that disruption of pVHL association with certain interactors can trigger tumor transformation, inducing metabolism imbalance and ECM remodeling. Collectively taken, our findings provide novel insights into VHL-associated tumorigenesis. This highly integrated in silico approach may help elucidate novel treatment paradigms for VHL disease.
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Affiliation(s)
| | - Federica Quaglia
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Francesco Tabaro
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Silvio C. E. Tosatto
- Department of Biomedical Sciences, University of Padova, Padova, Italy
- CNR Institute of Neuroscience, Padova, Padova, Italy
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236
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Liang Z, Verkhivker GM, Hu G. Integration of network models and evolutionary analysis into high-throughput modeling of protein dynamics and allosteric regulation: theory, tools and applications. Brief Bioinform 2019; 21:815-835. [DOI: 10.1093/bib/bbz029] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 02/04/2019] [Accepted: 02/21/2019] [Indexed: 12/24/2022] Open
Abstract
Abstract
Proteins are dynamical entities that undergo a plethora of conformational changes, accomplishing their biological functions. Molecular dynamics simulation and normal mode analysis methods have become the gold standard for studying protein dynamics, analyzing molecular mechanism and allosteric regulation of biological systems. The enormous amount of the ensemble-based experimental and computational data on protein structure and dynamics has presented a major challenge for the high-throughput modeling of protein regulation and molecular mechanisms. In parallel, bioinformatics and systems biology approaches including genomic analysis, coevolution and network-based modeling have provided an array of powerful tools that complemented and enriched biophysical insights by enabling high-throughput analysis of biological data and dissection of global molecular signatures underlying mechanisms of protein function and interactions in the cellular environment. These developments have provided a powerful interdisciplinary framework for quantifying the relationships between protein dynamics and allosteric regulation, allowing for high-throughput modeling and engineering of molecular mechanisms. Here, we review fundamental advances in protein dynamics, network theory and coevolutionary analysis that have provided foundation for rapidly growing computational tools for modeling of allosteric regulation. We discuss recent developments in these interdisciplinary areas bridging computational biophysics and network biology, focusing on promising applications in allosteric regulations, including the investigation of allosteric communication pathways, protein–DNA/RNA interactions and disease mutations in genomic medicine. We conclude by formulating and discussing future directions and potential challenges facing quantitative computational investigations of allosteric regulatory mechanisms in protein systems.
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Affiliation(s)
- Zhongjie Liang
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Gennady M Verkhivker
- Department of Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA, USA
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA, USA
| | - Guang Hu
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
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Liu H, Liu X, Zhou S, An X, Liu H, Yao X. Disclosing the Template-Induced Misfolding Mechanism of Tau Protein by Studying the Dissociation of the Boundary Chain from the Formed Tau Fibril Based on a Steered Molecular Dynamics Simulation. ACS Chem Neurosci 2019; 10:1854-1865. [PMID: 30665304 DOI: 10.1021/acschemneuro.8b00732] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The level of tau aggregation into neurofibrillary tangles, including paired helical filament (PHF) and straight filament (SF), is closely associated with Alzheimer's disease. Despite the pathological importance of misfolding and aggregation of tau, the corresponding mechanism remains unclear. Therefore, to uncover the misfolding mechanism of the tau monomer upon induction of formed PHF and SF, in this study, a conventional molecular dynamics simulation combined with a steered molecular dynamics simulation was performed to study the dissociation of the boundary chain. Interestingly, our results show that the dissociation mechanisms of the boundary chain in PHF and SF are different. In PHF, the boundary chain begins to dissociate from regions β2 and β3 and ends at β8. However, in SF, it is simultaneously dissociated from β1 and β8 and ends at β5. The dissociation of the boundary chain is the reverse of template-induced misfolding of the monomer. Therefore, we can deduce the misfolding mechanism of the monomer upon induction of the template. For PHF, β8 first interacts with the template by hydrophobic interaction. Then β7, β6, β5, β4, and β1 sequentially bind to the template by electrostatic and hydrophobic interactions. After β1 binds to the template, β2 and β3 very quickly bind to the template through hydrophobic interaction. For SF, β5 of the monomer first interacts with the template by electrostatic attraction. Then β4 and β6, β3 and β7, and β2 and β8 bind to the template in turn. Finally, β1 and β8 are fully bound to the template by hydrophobic interaction. The obtained results will be vital for understanding the earlier events during misfolding and aggregation of tau.
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Affiliation(s)
- Hongli Liu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Xuewei Liu
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, China
| | - Shuangyan Zhou
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Xiaoli An
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, China
| | - Huanxiang Liu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Xiaojun Yao
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, China
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau 999078, China
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238
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Bjij I, Khan S, Ramharak P, Cherqaoui D, Soliman MES. Distinguishing the optimal binding mechanism of an E3 ubiquitin ligase: Covalent versus noncovalent inhibition. J Cell Biochem 2019; 120:12859-12869. [DOI: 10.1002/jcb.28556] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 01/07/2019] [Accepted: 01/14/2019] [Indexed: 01/18/2023]
Affiliation(s)
- Imane Bjij
- Molecular Bio‐Computation & Drug Design Lab, School of Health Sciences University of KwaZulu‐Natal Durban South Africa
- Université Cadi Ayyad, Faculté des Sciences Semlalia, Département de Chimie Marrakech Morocco
| | - Shama Khan
- Molecular Bio‐Computation & Drug Design Lab, School of Health Sciences University of KwaZulu‐Natal Durban South Africa
| | - Pritika Ramharak
- Molecular Bio‐Computation & Drug Design Lab, School of Health Sciences University of KwaZulu‐Natal Durban South Africa
| | - Driss Cherqaoui
- Université Cadi Ayyad, Faculté des Sciences Semlalia, Département de Chimie Marrakech Morocco
| | - Mahmoud E. S. Soliman
- Molecular Bio‐Computation & Drug Design Lab, School of Health Sciences University of KwaZulu‐Natal Durban South Africa
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239
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Tang H, Shu C, Chen H, Zhang X, Zang Z, Deng C. Constitutively active BRS3 is a genuinely orphan GPCR in placental mammals. PLoS Biol 2019; 17:e3000175. [PMID: 30840614 PMCID: PMC6422423 DOI: 10.1371/journal.pbio.3000175] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 03/18/2019] [Accepted: 02/19/2019] [Indexed: 11/19/2022] Open
Abstract
G protein-coupled receptors (GPCRs) play an important role in physiology and disease and represent the most productive drug targets. Orphan GPCRs, with their endogenous ligands unknown, were considered a source of drug targets and consequently attract great interest to identify their endogenous cognate ligands for deorphanization. However, a contrary view to the ubiquitous existence of endogenous ligands for every GPCR is that there might be a significant overlooked fraction of orphan GPCRs that function constitutively in a ligand-independent manner only. Here, we investigated the evolution of the bombesin receptor-ligand family in vertebrates in which one member-bombesin receptor subtype-3 (BRS3)-is a potential orphan GPCR. With analysis of 17 vertebrate BRS3 structures and 10 vertebrate BRS3 functional data, our results demonstrated that nonplacental vertebrate BRS3 still connects to the original ligands-neuromedin B (NMB) and gastrin-releasing peptide (GRP)-because of adaptive evolution, with significantly changed protein structure, especially in three altered key residues (Q127R, P205S, and R294H) originally involved in ligand binding/activation, whereas the placental mammalian BRS3 lost the binding affinity to NMB/GRP and constitutively activates Gs/Gq/G12 signaling in a ligand-independent manner. Moreover, the N terminus of placental mammalian BRS3 underwent positive selection, exhibiting significant structural differences compared to nonplacental vertebrate BRS3, and this domain plays an important role in constitutive activity of placental mammalian BRS3. In conclusion, constitutively active BRS3 is a genuinely orphan GPCR in placental mammals, including human. To our knowledge, this study identified the first example that might represent a new group of genuinely orphan GPCRs that will never be deorphanized by the discovery of a natural ligand and provided new perspectives in addition to the current ligand-driven GPCR deorphanization.
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Affiliation(s)
- Huihao Tang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Chuanjun Shu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
- Department of Bioinformatics, College of Biomedical Engineering and Information, Nanjing Medical University, Nanjing, China
| | - Haidi Chen
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaojing Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Zhuqing Zang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Cheng Deng
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
- * E-mail:
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240
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Ge HH, Qiu Y, Yi ZW, Zeng RY, Zhang GY. π-π stacking interaction is a key factor for the stability of GH11 xylanases at low pH. Int J Biol Macromol 2019; 124:895-902. [DOI: 10.1016/j.ijbiomac.2018.11.282] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 11/30/2018] [Accepted: 11/30/2018] [Indexed: 01/05/2023]
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241
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Ensembles from Ordered and Disordered Proteins Reveal Similar Structural Constraints during Evolution. J Mol Biol 2019; 431:1298-1307. [DOI: 10.1016/j.jmb.2019.01.031] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 01/23/2019] [Accepted: 01/24/2019] [Indexed: 01/08/2023]
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242
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Tan LY, Tsuchido Y, Osakada K, Cai Z, Takahashi Y, Takeuchi D. Synthesis and Aggregation Behavior of Poly(arylene alkenylene)s and Poly(arylene alkylene)s Having Dialkoxyphenylene and Aromatic Diimide Groups. Macromolecules 2019. [DOI: 10.1021/acs.macromol.8b02468] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Li Yi Tan
- Laboratory for Chemistry and Life Science, Tokyo Institute of Technology, R1-03, 4259 Nagatsuta, Yokohama 226-8503, Japan
| | - Yoshitaka Tsuchido
- Laboratory for Chemistry and Life Science, Tokyo Institute of Technology, R1-03, 4259 Nagatsuta, Yokohama 226-8503, Japan
| | - Kohtaro Osakada
- Laboratory for Chemistry and Life Science, Tokyo Institute of Technology, R1-03, 4259 Nagatsuta, Yokohama 226-8503, Japan
| | - Zhengguo Cai
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai 201620, P. R. China
| | - Yoshiaki Takahashi
- Institute for Materials Chemistry and Engineering and Department of Molecular and Materials Sciences, Kyushu University, 6-1 Kasuga-koen, Kasuga, Fukuoka 816-8580, Japan
| | - Daisuke Takeuchi
- Laboratory for Chemistry and Life Science, Tokyo Institute of Technology, R1-03, 4259 Nagatsuta, Yokohama 226-8503, Japan
- Department of Frontier Materials Chemistry, Graduate School of Science and Technology, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan
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243
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Molecular Dynamics Simulations of A27S and K120A Mutated PTP1B Reveals Selective Binding of the Bidentate Inhibitor. BIOMED RESEARCH INTERNATIONAL 2019; 2019:9852897. [PMID: 30729132 PMCID: PMC6341276 DOI: 10.1155/2019/9852897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 12/09/2018] [Accepted: 12/24/2018] [Indexed: 11/26/2022]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) is considered a potential target for the treatment of type II diabetes and obesity due to its critical negative role in the insulin signaling pathway. However, improving the selectivity of PTP1B inhibitors over the most closely related T-cell protein tyrosine phosphatase (TCPTP) remains a major challenge for inhibitor development. Lys120 at the active site and Ser27 at the second pTyr binding site are distinct in PTP1B and TCPTP, which may bring differences in binding affinity. To explore the determinant of selective binding of inhibitor, molecular dynamics simulations with binding free energy calculations were performed on K120A and A27S mutated PTP1B, and the internal changes induced by mutations were investigated. Results reveal that the presence of Lys120 induces a conformational change in the WPD-loop and YRD-motif and has a certain effect on the selective binding at the active site. Ser27 weakens the stability of the inhibitor at the second pTyr binding site by altering the orientation of the Arg24 and Arg254 side chains via hydrogen bonds. Further comparison of alanine scanning demonstrates that the reduction in the energy contribution of Arg254 caused by A27S mutation leads to a different inhibitory activity. These observations provide novel insights into the selective binding mechanism of PTP1B inhibitors to TCPTP.
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244
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Molina M, Moulis C, Monties N, Pizzut-Serin S, Guieysse D, Morel S, Cioci G, Remaud-Siméon M. Deciphering an Undecided Enzyme: Investigations of the Structural Determinants Involved in the Linkage Specificity of Alternansucrase. ACS Catal 2019. [DOI: 10.1021/acscatal.8b04510] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Manon Molina
- LISBP (Laboratoire d’Ingénierie des Systèmes Biologiques et des Procédés), Université de Toulouse, CNRS (Centre National de la Recherche Scientifique), INRA (Institut National de la Recherche Agronomique), INSA (Institut National des Sciences Appliquées), F-31077 Toulouse, France
| | - Claire Moulis
- LISBP (Laboratoire d’Ingénierie des Systèmes Biologiques et des Procédés), Université de Toulouse, CNRS (Centre National de la Recherche Scientifique), INRA (Institut National de la Recherche Agronomique), INSA (Institut National des Sciences Appliquées), F-31077 Toulouse, France
| | - Nelly Monties
- LISBP (Laboratoire d’Ingénierie des Systèmes Biologiques et des Procédés), Université de Toulouse, CNRS (Centre National de la Recherche Scientifique), INRA (Institut National de la Recherche Agronomique), INSA (Institut National des Sciences Appliquées), F-31077 Toulouse, France
| | - Sandra Pizzut-Serin
- LISBP (Laboratoire d’Ingénierie des Systèmes Biologiques et des Procédés), Université de Toulouse, CNRS (Centre National de la Recherche Scientifique), INRA (Institut National de la Recherche Agronomique), INSA (Institut National des Sciences Appliquées), F-31077 Toulouse, France
| | - David Guieysse
- LISBP (Laboratoire d’Ingénierie des Systèmes Biologiques et des Procédés), Université de Toulouse, CNRS (Centre National de la Recherche Scientifique), INRA (Institut National de la Recherche Agronomique), INSA (Institut National des Sciences Appliquées), F-31077 Toulouse, France
| | - Sandrine Morel
- LISBP (Laboratoire d’Ingénierie des Systèmes Biologiques et des Procédés), Université de Toulouse, CNRS (Centre National de la Recherche Scientifique), INRA (Institut National de la Recherche Agronomique), INSA (Institut National des Sciences Appliquées), F-31077 Toulouse, France
| | - Gianluca Cioci
- LISBP (Laboratoire d’Ingénierie des Systèmes Biologiques et des Procédés), Université de Toulouse, CNRS (Centre National de la Recherche Scientifique), INRA (Institut National de la Recherche Agronomique), INSA (Institut National des Sciences Appliquées), F-31077 Toulouse, France
| | - Magali Remaud-Siméon
- LISBP (Laboratoire d’Ingénierie des Systèmes Biologiques et des Procédés), Université de Toulouse, CNRS (Centre National de la Recherche Scientifique), INRA (Institut National de la Recherche Agronomique), INSA (Institut National des Sciences Appliquées), F-31077 Toulouse, France
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245
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Dey S, Wayland BB, Zdilla MJ. Solution and Solid State Properties for Low-Spin Cobalt(II) Dibenzotetramethyltetraaza[14]annulene [(tmtaa)Co II] and the Monopyridine Complex. Inorg Chem 2019; 58:1224-1233. [PMID: 30618250 DOI: 10.1021/acs.inorgchem.8b02644] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The single-crystal X-ray structure of solvent-free (tmtaa)CoII reveals three different π-π intermacrocyclic interactions between tmtaa units (tmtaa = dibenzotetramethyltetraaza[14]annulene). Pairs of inequivalent (tmtaa)CoII units in the unit cell link into a one-dimensional π-π stacked array in the solid state. Magnetic susceptibility (χ) studies from 300 to 2 K reveal the effects of intermolecular interactions between (tmtaa)CoII units in the solid state. The effective magnetic moment per CoII center is constant at 2.83 μB from 300 to 100 K and begins to significantly decrease at lower temperatures. The magnetic data are fit to a singlet ( S = 0) ground state with a triplet ( S = 1) excited state that is 13 cm-1 higher in energy (-2 J = 13 cm-1). Toluene solutions of (tmtaa)CoII have 1H nuclear magnetic resonance (NMR) paramagnetic shifts, a solution-phase magnetic moment μeff (295 K) of 2.1 μB, and toluene glass electron paramagnetic resonance spectra that are most consistent with a low-spin ( S = 1/2) CoII with the unpaired electron located in the d yz orbital. Pyridine interacts with (tmtaa)CoII to form a five-coordinate monopyridine complex in which the unpaired electron is in the d z2 orbital. The five-coordinate complex has been structurally characterized by single-crystal X-ray diffraction, and the equilibrium constant for pyridine binding at 295 K has been evaluated by both electronic and 1H NMR spectra. Density functional theory computation using the UB3LYP hybrid functional places the unpaired electron for (tmtaa)CoII in the d yz orbital and that for the monopyridine complex in the d z2 orbital, consistent with spectroscopic observations.
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Affiliation(s)
- Soumyajit Dey
- Department of Chemistry , Temple University , 1901 Northy 13th Street , Philadelphia , Pennsylvania 19122 , United States
| | - Bradford B Wayland
- Department of Chemistry , Temple University , 1901 Northy 13th Street , Philadelphia , Pennsylvania 19122 , United States
| | - Michael J Zdilla
- Department of Chemistry , Temple University , 1901 Northy 13th Street , Philadelphia , Pennsylvania 19122 , United States
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246
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Liu Y, Ebalunode JO, Briggs JM. Insights into the substrate binding specificity of quorum-quenching acylase PvdQ. J Mol Graph Model 2019; 88:104-120. [PMID: 30703686 DOI: 10.1016/j.jmgm.2019.01.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 01/09/2019] [Accepted: 01/10/2019] [Indexed: 01/19/2023]
Abstract
Quorum sensing is a cell to cell signaling mechanism that enables them to coordinate their behaviors in a density-dependent manner mediated by small diffusible signaling molecules, which can control the virulence and biofilm gene expression in many Gram-negative and positive bacteria. N-acyl homoserine lactone acylase PvdQ from human opportunistic pathogen Pseudomonas aeruginosa is a quorum-quenching enzyme that can hydrolyze the amide bond of the quorum signaling N-acyl homoserine lactones (AHLs) thereby degrading the signaling molecules, turning off the biofilm phenotype and resulting in a reduction of bacterial virulence. Previous studies demonstrated that PvdQ has different preferences for N-acyl substrates with different acyl chain lengths and substituents. However, the substrate binding specificity determinants of the quorum-quenching enzyme PvdQ with the different bacterial ligands are unknown and unintuitive. Further, elucidation of these determinants can lead to mutants with efficiency and broader substrate promiscuity. To investigate this question, a computational study was carried out combining multiple molecular docking methods, molecular dynamics simulations, residue interaction network analysis, and binding free energy calculations. The main findings are: firstly, the results from pKa predictions support that the pKa of the N-terminus of Serβ1 was depressed due to the surrounding residues. Multiple molecular docking studies provide useful information about the detailed binding modes and binding affinities. Secondly, 300 ns molecular dynamics simulations were carried out to analyze the overall molecular motions of substrate-bound and substrate-free PvdQ. The specific interactions between the active site of PvdQ and different ligands revealed the determinants for the preference among the ligands. A systematic comparison and analysis of the protein dynamic fingerprint of each complex demonstrated that binding of the most favorable ligand, C12-homoserine lactone (C12-HSL), reduced the global motions of the complex and maintained the correct arrangement of the catalytic site. Further, the residue interaction network analysis of each system illustrated that there are more communication contacts and pathways between the residues in the C12-HSL complex as compared to complexes with the other ligands. The binding of the C12-HSL ligand facilitates structural communication between the two knobs and the active site. While the binding of the other ligands tend to impair specific communication pathways between the two knobs and the active site, and lead to a catalytically inefficient state. Finally, simulation results from free energy landscape and binding free energy analysis revealed that the C12-HSL ligand has the lowest binding free energy and greater stability than the less favored ligands. Each of the following residues: Serβ1, Hisβ23, Pheβ24, Metβ30, Pheβ32, Leuβ50, Asnβ57, Thrβ69, Valβ70, Trpβ162, Trpβ186, Asnβ269, Argβ297 and Leuα146, play different roles in substrate binding specificity. This is the first computational study that provides molecular information for structure-dynamic-function relationships of PvdQ with different ligands and demonstrates determinants of bacterial substrate binding specificity.
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Affiliation(s)
- Yanyun Liu
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204-5001, USA
| | - Jerry O Ebalunode
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204-5001, USA
| | - James M Briggs
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204-5001, USA.
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247
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Doh CY, Li J, Mamidi R, Stelzer JE. The HCM-causing Y235S cMyBPC mutation accelerates contractile function by altering C1 domain structure. Biochim Biophys Acta Mol Basis Dis 2019; 1865:661-677. [PMID: 30611859 DOI: 10.1016/j.bbadis.2019.01.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 12/18/2018] [Accepted: 01/02/2019] [Indexed: 12/20/2022]
Abstract
Mutations in cardiac myosin binding protein C (cMyBPC) are a major cause of hypertrophic cardiomyopathy (HCM). In particular, a single amino acid substitution of tyrosine to serine at residue 237 in humans (residue 235 in mice) has been linked to HCM with strong disease association. Although cMyBPC truncations, deletions and insertions, and frame shift mutations have been studied, relatively little is known about the functional consequences of missense mutations in cMyBPC. In this study, we characterized the functional and structural effects of the HCM-causing Y235S mutation by performing mechanical experiments and molecular dynamics simulations (MDS). cMyBPC null mouse myocardium was virally transfected with wild-type (WT) or Y235S cMyBPC (KOY235S). We found that Y235S cMyBPC was properly expressed and incorporated into the cardiac sarcomere, suggesting that the mechanism of disease of the Y235S mutation is not haploinsufficiency or poison peptides. Mechanical experiments in detergent-skinned myocardium isolated from KOY235S hearts revealed hypercontractile behavior compared to KOWT hearts, evidenced by accelerated cross-bridge kinetics and increased Ca2+ sensitivity of force generation. In addition, MDS revealed that the Y235S mutation causes alterations in important intramolecular interactions, surface conformations, and electrostatic potential of the C1 domain of cMyBPC. Our combined in vitro and in silico data suggest that the Y235S mutation directly disrupts internal and surface properties of the C1 domain of cMyBPC, which potentially alters its ligand-binding interactions. These molecular changes may underlie the mechanism for hypercontractile cross-bridge behavior, which ultimately results in the development of cardiac hypertrophy and in vivo cardiac dysfunction.
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Affiliation(s)
- Chang Yoon Doh
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Jiayang Li
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Ranganath Mamidi
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Julian E Stelzer
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
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248
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Characterizing early drug resistance-related events using geometric ensembles from HIV protease dynamics. Sci Rep 2018; 8:17938. [PMID: 30560871 PMCID: PMC6298995 DOI: 10.1038/s41598-018-36041-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 11/14/2018] [Indexed: 02/07/2023] Open
Abstract
The use of antiretrovirals (ARVs) has drastically improved the life quality and expectancy of HIV patients since their introduction in health care. Several millions are still afflicted worldwide by HIV and ARV resistance is a constant concern for both healthcare practitioners and patients, as while treatment options are finite, the virus constantly adapts via complex mutation patterns to select for resistant strains under the pressure of drug treatment. The HIV protease is a crucial enzyme for viral maturation and has been a game changing drug target since the first application. Due to similarities in protease inhibitor designs, drug cross-resistance is not uncommon across ARVs of the same class. It is known that resistance against protease inhibitors is associated with a wider active site, but results from our large scale molecular dynamics simulations combined with statistical tests and network analysis further show, for the first time, that there are regions of local expansions and compactions associated with high levels of resistance conserved across eight different protease inhibitors visible in their complexed form within closed receptor conformations. The observed conserved expansion sites may provide an alternative drug-targeting site. Further, the method developed here is novel, supplementary to methods of variation analysis at sequence level, and should be applicable in analysing the structural consequences of mutations in other contexts using molecular ensembles.
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249
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Exploiting correlated molecular-dynamics networks to counteract enzyme activity-stability trade-off. Proc Natl Acad Sci U S A 2018; 115:E12192-E12200. [PMID: 30530661 PMCID: PMC6310800 DOI: 10.1073/pnas.1812204115] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rigidifying flexible sites is a powerful method to improve enzyme stability. However, if the highly flexible regions form the active site, modifying them risks losing activity due to the activity–stability trade-off. We hypothesized here that regions outside the active site whose dynamics were highly correlated to flexible active sites, would provide good targets for stabilizing mutations. To test this hypothesis, six variants were constructed in the 3M variant of Escherichia coli transketolase. The best variant had a 10.8-fold improved half-life at 55 °C, and increased the Tm and Tagg by 3 °C and 4.3 °C, respectively. The variants even increased the activity, by up to threefold. This study highlights how protein engineering strategies could be potentially improved by considering long-range dynamics. The directed evolution of enzymes for improved activity or substrate specificity commonly leads to a trade-off in stability. We have identified an activity–stability trade-off and a loss in unfolding cooperativity for a variant (3M) of Escherichia coli transketolase (TK) engineered to accept aromatic substrates. Molecular dynamics simulations of 3M revealed increased flexibility in several interconnected active-site regions that also form part of the dimer interface. Mutating the newly flexible active-site residues to regain stability risked losing the new activity. We hypothesized that stabilizing mutations could be targeted to residues outside of the active site, whose dynamics were correlated with the newly flexible active-site residues. We previously stabilized WT TK by targeting mutations to highly flexible regions. These regions were much less flexible in 3M and would not have been selected a priori as targets using the same strategy based on flexibility alone. However, their dynamics were highly correlated with the newly flexible active-site regions of 3M. Introducing the previous mutations into 3M reestablished the WT level of stability and unfolding cooperativity, giving a 10.8-fold improved half-life at 55 °C, and increased midpoint and aggregation onset temperatures by 3 °C and 4.3 °C, respectively. Even the activity toward aromatic aldehydes increased up to threefold. Molecular dynamics simulations confirmed that the mutations rigidified the active-site via the correlated network. This work provides insights into the impact of rigidifying mutations within highly correlated dynamic networks that could also be useful for developing improved computational protein engineering strategies.
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250
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Brysbaert G, Mauri T, de Ruyck J, Lensink MF. Identification of Key Residues in Proteins Through Centrality Analysis and Flexibility Prediction with RINspector. ACTA ACUST UNITED AC 2018; 65:e66. [PMID: 30489695 DOI: 10.1002/cpbi.66] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Protein structures inherently contain information that can be used to decipher their functions, but the exploitation of this knowledge is not trivial. We recently developed an app for the Cytoscape network visualization and analysis program, called RINspector, the goal of which is to integrate two different approaches that identify key residues in a protein structure or complex. The first approach consists of calculating centralities on a residue interaction network (RIN) generated from the three-dimensional structure; the second consists of predicting backbone flexibility and needs only the primary sequence. The identified residues are highly correlated with functional relevance and constitute a good set of targets for mutagenesis experiments. Here we present a protocol that details in a step-by-step fashion how to create a RIN from a structure and then calculate centralities and predict flexibilities. We also discuss how to understand and use the results of the analyses. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Guillaume Brysbaert
- University of Lille, CNRS UMR8576 UGSF, Institute for Structural and Functional Glycobiology, F-59000 Lille, France
| | - Théo Mauri
- University of Lille, CNRS UMR8576 UGSF, Institute for Structural and Functional Glycobiology, F-59000 Lille, France
| | - Jérôme de Ruyck
- University of Lille, CNRS UMR8576 UGSF, Institute for Structural and Functional Glycobiology, F-59000 Lille, France
| | - Marc F Lensink
- University of Lille, CNRS UMR8576 UGSF, Institute for Structural and Functional Glycobiology, F-59000 Lille, France
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