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Pan Y, Zhao C, Fu W, Yang S, Lv S. Comparative analysis of structural dynamics and allosteric mechanisms of RecA/Rad51 family proteins: Integrated atomistic MD simulation and network-based analysis. Int J Biol Macromol 2024; 261:129843. [PMID: 38302027 DOI: 10.1016/j.ijbiomac.2024.129843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 01/26/2024] [Accepted: 01/27/2024] [Indexed: 02/03/2024]
Abstract
Homologous recombination plays a key role in double-strand break repair, stalled replication fork repair, and meiosis. The RecA/Rad51 family recombinases catalyze the DNA strand invasion reaction that occurs during homologous recombination. However, the high sequence differences between homologous groups have hindered the thoroughly studies of this ancient protein family. The dynamic mechanisms of the family, particularly at the residual level, remain poorly understood. In this work, five representative RecA/Rad51 recombinase family members from all major kingdoms of living organisms: prokaryotes, eukaryotes, archaea, and viruses, were selected to explore the molecular mechanisms behind their conserved biological significance. A variety of techniques, including all-atom molecular dynamics simulation, perturbation response scanning, and protein structure network analysis, were used to examine the flexibility and correlation of protein domains, distribution of sensors and effectors and conserved hub residues. Furthermore, the potential communication routes between the ATP-binding region and the DNA-binding region of each recombinase were identified. Our results demonstrate the conserved molecular dynamics of these recombinases in the early stage of homologous recombination, including cooperative motions between regions, conserved sensing and effecting functional residue distribution, and conserved hub residues. Meanwhile, the unique ATP-DNA communication routes of each recombinase was also revealed. These results provide new insights into the mechanism of RecA/Rad51 family proteins, and provide new theoretical guidance for the development of allosteric inhibitors and the application of RecA/Rad51 family proteins.
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Affiliation(s)
- Yue Pan
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Chong Zhao
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Wenyu Fu
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Shuo Yang
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, China.
| | - Shaowu Lv
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, China; Bioarchaeology Laboratory, Jilin University, 2699 Qianjin Street, Changchun 130012, China.
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Burra VLSP, Sahoo PS, Dhankhar A, Jhajj J, Kasamuthu PS, K SSVK, Macha SKR. Understanding the structural basis of the binding specificity of c-di-AMP to M. smegmatis RecA using computational biology approach. J Biomol Struct Dyn 2024; 42:2043-2057. [PMID: 38093709 DOI: 10.1080/07391102.2023.2227709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 04/09/2023] [Indexed: 02/21/2024]
Abstract
Mycobacterium tuberculosis RecA (MtRecA), a protein involved in DNA repair, homologous recombination and SOS pathway, contributes to the development of multidrug resistance. ATP binding-site in RecA has been a drug target to disable RecA dependent DNA repair. For the first time, experiments have shown the existence and binding of c-di-AMP to a novel allosteric site in the C-terminal-Domain (CTD) of Mycobacterium smegmatis RecA (MsRecA), a close homolog of MtRecA. In addition, it was observed that the c-di-AMP was not binding to Escherichia coli RecA (EcRecA). This article analyses the possible interactions of the three RecA homologs with the various c-di-AMP conformations to gain insights into the structural basis of the natural preference of c-di-AMP to MsRecA and not to EcRecA, using the structural biology tools. The comparative analysis, based on amino acid composition, homology, motifs, residue types, docking, molecular dynamics simulations and binding free energy calculations, indeed, conclusively indicates strong binding of c-di-AMP to MsRecA. Having very similar results as MsRecA, it is highly plausible for c-di-AMP to strongly bind MtRecA as well. These insights from the in-silico studies adds a new therapeutic approach against TB through design and development of novel allosteric inhibitors for the first time against MtRecA.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- V L S Prasad Burra
- Centre for Advanced Research and Innovation in Structural Biology of Diseases, K L E F (Deemed to be) University, Vaddeswaram, Andhra Pradesh, India
| | - Partha Sarathi Sahoo
- Centre for Advanced Research and Innovation in Structural Biology of Diseases, K L E F (Deemed to be) University, Vaddeswaram, Andhra Pradesh, India
| | - Amit Dhankhar
- Centre for Advanced Research and Innovation in Structural Biology of Diseases, K L E F (Deemed to be) University, Vaddeswaram, Andhra Pradesh, India
| | - Jatinder Jhajj
- Centre for Advanced Research and Innovation in Structural Biology of Diseases, K L E F (Deemed to be) University, Vaddeswaram, Andhra Pradesh, India
| | - Prasanna Sudharson Kasamuthu
- Centre for Advanced Research and Innovation in Structural Biology of Diseases, K L E F (Deemed to be) University, Vaddeswaram, Andhra Pradesh, India
| | - S S V Kiran K
- Centre for Advanced Research and Innovation in Structural Biology of Diseases, K L E F (Deemed to be) University, Vaddeswaram, Andhra Pradesh, India
| | - Samuel Krupa Rakshan Macha
- Centre for Advanced Research and Innovation in Structural Biology of Diseases, K L E F (Deemed to be) University, Vaddeswaram, Andhra Pradesh, India
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3
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Kumar P, Bhardwaj T, Kumar A, Garg N, Giri R. One microsecond MD simulations of the SARS-CoV-2 main protease and hydroxychloroquine complex reveal the intricate nature of binding. J Biomol Struct Dyn 2022; 40:10763-10770. [PMID: 34320905 DOI: 10.1080/07391102.2021.1948447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Currently, several vaccines and antivirals across the globe are in clinical trials. Hydroxychloroquine (HCQ) was reported to inhibit the SARS-CoV-2 virus in antiviral assays. Here, it raises the curiosity about the molecular target of HCQ inside the cell. It may inhibit some of the viral targets, or some other complex mechanisms must be at disposal towards action mechanisms. In some of the viruses, proteases are experimentally reported to be a potential target of HCQ. However, no in-depth investigations are available in the literature yet. Henceforth, we have carried out extensive, one-microsecond long molecular dynamics simulations of the bound complex of hydroxychloroquine with main protease (Mpro) of SARS-CoV-2. Our analysis found that HCQ binds within the catalytic pocket of Mpro and remains stable upto one-third of simulation time but further causes increased fluctuations in simulation parameters. In the end, the HCQ does not possess any pre-formed hydrogen bond, other non-covalent interactions with Mpro, ultimately showing the unsteadiness in binding at catalytic binding pocket and may suggest that HCQ may not inhibit the Mpro. In the future, this study would require experimental validation on enzyme assays against Mpro, and that may be the final say. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Prateek Kumar
- School of Basic Sciences, VPO Kamand, Indian Institute of Technology, Mandi, Mandi, India
| | - Taniya Bhardwaj
- School of Basic Sciences, VPO Kamand, Indian Institute of Technology, Mandi, Mandi, India
| | - Ankur Kumar
- School of Basic Sciences, VPO Kamand, Indian Institute of Technology, Mandi, Mandi, India
| | - Neha Garg
- Faculty of Ayurveda, Department of Medicinal Chemistry, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Rajanish Giri
- School of Basic Sciences, VPO Kamand, Indian Institute of Technology, Mandi, Mandi, India
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4
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Rola A, Potok P, Wieczorek R, Mos M, Gumienna-Kontecka E, Potocki S. Coordination Properties of the Zinc Domains of BigR4 and SmtB Proteins in Nickel Systems─Designation of Key Donors. Inorg Chem 2022; 61:9454-9468. [PMID: 35696675 PMCID: PMC9241078 DOI: 10.1021/acs.inorgchem.2c00319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
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The increasing number
of antibiotic-resistant pathogens has become
one of the foremost health problems of modern times. One of the most
lethal and multidrug-resistant bacteria is Mycobacterium
tuberculosis (Mtb), which causes tuberculosis (TB).
TB continues to engulf health systems due to the significant development
of bacterial multidrug-resistant strains. Mammalian immune system
response to mycobacterial infection includes, but is not limited to,
increasing the concentration of zinc(II) and other divalent metal
ions in phagosome vesicles up to toxic levels. Metal ions are necessary
for the survival and virulence of bacteria but can be highly toxic
to organisms if their concentrations are not strictly controlled.
Therefore, understanding the mechanisms of how bacteria use metal
ions to maintain their optimum concentrations and survive under lethal
environmental conditions is essential. The mycobacterial SmtB protein,
one of the metal-dependent transcription regulators of the ArsR/SmtB
family, dissociates from DNA in the presence of high concentrations
of metals, activating the expression of metal efflux proteins. In
this work, we explore the properties of α5 metal-binding domains
of SmtB/BigR4 proteins (the latter being the SmtB homolog from nonpathogenic Mycobacterium smegmatis), and two mutants of BigR4
as ligands for nickel(II) ions. The study focuses on the specificity
of metal–ligand interactions and describes the effect of mutations
on the coordination properties of the studied systems. The results
of this research reveal that the Ni(II)-BigR4 α5 species are
more stable than the Ni(II)-SmtB α5 complexes. His mutations,
exchanging one of the histidines for alanine, cause a decrease in
the stability of Ni(II) complexes. Surprisingly, the lack of His102
resulted also in increased involvement of acidic amino acids in the
coordination. The results of this study may help to understand the
role of critical mycobacterial virulence factor—SmtB in metal
homeostasis. Although SmtB prefers Zn(II) binding, it may also bind
metal ions that prefer other coordination modes, for example, Ni(II).
We characterized the properties of such complexes in order to understand
the nature of mycobacterial SmtB when acting as a ligand for metal
ions, given that nickel and zinc ArsR family proteins possess analogous
metal-binding motifs. This may provide an introduction to the design
of a new antimicrobial strategy against the pathogenic bacterium M. tuberculosis. The
histidine-rich α5 domains of SmtB (L4, Mycobacterium
tuberculosis) and BigR4 (L1, Mycobacterium
smegmatis) were studied as ligands
for Ni(II). Point mutation analysis of L1 revealed that His102 and
106 preferably bind metal ions. The general Ni(II)-binding motif for
both of the ligands was established as HX3HX3DX3HX2ED. L1 forms more
stable complexes than L4 due to the stabilizing effect of arginine
residues.
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Affiliation(s)
- Anna Rola
- Faculty of Chemistry, University of Wroclaw, 14 Joliot-Curie Street, Wroclaw 50-383, Poland
| | - Paulina Potok
- Faculty of Chemistry, University of Wroclaw, 14 Joliot-Curie Street, Wroclaw 50-383, Poland
| | - Robert Wieczorek
- Faculty of Chemistry, University of Wroclaw, 14 Joliot-Curie Street, Wroclaw 50-383, Poland
| | - Magdalena Mos
- WMG, International Manufacturing Centre, University of Warwick, Coventry CV4 7AL, U.K
| | | | - Sławomir Potocki
- Faculty of Chemistry, University of Wroclaw, 14 Joliot-Curie Street, Wroclaw 50-383, Poland
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5
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Iqbal S, Potharaju R, Naveen S, Lokanath NK, Mohanakrishnan AK, Gunasekaran K. Design, crystal structure determination, molecular dynamic simulation and MMGBSA calculations of novel p38-alpha MAPK inhibitors for combating Alzheimer's disease. J Biomol Struct Dyn 2021; 40:6114-6127. [PMID: 33522434 DOI: 10.1080/07391102.2021.1877197] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The hallmark of the Alzheimer's disease (AD) is the accumulation of aggregated, misfolded proteins. The cause for this accumulation is increased production of misfolded proteins and impaired clearance of them. Amyloid aggregation and tau hyperphosphorylation are the two proteinopathies which accomplish deprivation of cell and tissue hemostasis during neuropathological process of the AD, as a result of which progressive neuronal degeneration and the loss of cognitive functions. p38 mitogen-activated protein kinase (p38 MAPK) has been implicated in both the events associated with AD: tau protein phosphorylation and inflammation. p38α MAPK pathway is activated by a dual phosphorylation at Thr180 and Tyr182 residues. Clinical and preclinical evidence implicates the stress related kinase p38α MAPK as a potential neurotherapeutic target. Drug design of p38α MAPK inhibitors is mainly focused on small molecules that compete for Adenosine triphosphate in the catalytic site. Here we have carried out the synthesis of phenyl sulfonamide derivatives Sulfo (I) and Sulfo (II). Crystal structures of Sulfo (I) and Sulfo (II) were solved by direct methods using SHELXS-97. Sulfo (I) and Sulfo (II) have Rint values of 0.0283 and 0.0660, respectively, indicating good quality of crystals and investigated their ability against p38α MAPK. Docking studies revealed that the Sulfo (I) had better binding affinity (-62.24 kcal/mol) as compared to Sulfo (II) and cocrystal having binding affinity of -54.61 kcal/mol and -59.84 kcal/mol, respectively. Molecular dynamics simulation studies of Sulfo (I) and cocrystal of p38α MAPK suggest that during the course of 30 ns simulation run, compound Sulfo (I) attained stability, substantiating the consistency of its binding to p38α MAPK compared to cocrystal. Binding free energy analysis suggests that the compound Sulfo (I) is better than the cocrystal. Thus, this study corroborates the therapeutic potential of synthesized Sulfo (I) in combatting AD.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Saleem Iqbal
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, India.,Centre of Advanced Study in Crystallography & Biophysics, University of Madras, Chennai, India
| | - Raju Potharaju
- Department of Organic Chemistry, University of Madras, Chennai, India.,Escientia Bio Pharma Private Limited Turkapally, Hyderabad, India
| | - S Naveen
- Department of Physics, Faculty of Engineering & Technology, JAIN (Deemed-to-be University), Bangalore, India
| | - N K Lokanath
- Department of Studies in Physics, University of Mysore, Mysore, India
| | - Arasambattu K Mohanakrishnan
- Department of Organic Chemistry, University of Madras, Chennai, India.,Escientia Bio Pharma Private Limited Turkapally, Hyderabad, India
| | - Krishnasamy Gunasekaran
- Centre of Advanced Study in Crystallography & Biophysics, University of Madras, Chennai, India
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6
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Chandran AV, Srikalaivani R, Paul A, Vijayan M. Biochemical characterization of Mycobacterium tuberculosisLexA and structural studies of its C-terminal segment. Acta Crystallogr D Struct Biol 2019; 75:41-55. [DOI: 10.1107/s2059798318016066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 11/13/2018] [Indexed: 03/21/2023] Open
Abstract
LexA is a protein that is involved in the SOS response. The protein fromMycobacterium tuberculosisand its mutants have been biochemically characterized and the structures of their catalytic segments have been determined. The protein is made up of an N-terminal segment, which includes the DNA-binding domain, and a C-terminal segment encompassing much of the catalytic domain. The two segments are defined by a cleavage site. Full-length LexA, the two segments, two point mutants involving changes in the active-site residues (S160A and K197A) and another mutant involving a change at the cleavage site (G126D) were cloned and purified. The wild-type protein autocleaves at basic pH, while the mutants do not. The wild-type and the mutant proteins dimerize and bind DNA with equal facility. The C-terminal segment also dimerizes, and it also shows a tendency to form tetramers. The C-terminal segment readily crystallized. The crystals obtained from attempts involving the full-length protein and its mutants contained only the C-terminal segment including the catalytic core and a few residues preceding it, in a dimeric or tetrameric form, indicating protein cleavage during the long period involved in crystal formation. Modes of tetramerization of the full-length protein similar to those observed for the catalytic core are feasible. A complex ofM. tuberculosisLexA and the cognate SOS box could be modeled in which the mutual orientation of the two N-terminal domains differs from that in theEscherichia coliLexA–DNA complex. These results represent the first thorough characterization ofM. tuberculosisLexA and provide definitive information on its structure and assembly. They also provide leads for further exploration of this important protein.
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Yamada H, Yamaguchi M, Igarashi Y, Chikamatsu K, Aono A, Murase Y, Morishige Y, Takaki A, Chibana H, Mitarai S. Mycolicibacterium smegmatis, Basonym Mycobacterium smegmatis, Expresses Morphological Phenotypes Much More Similar to Escherichia coli Than Mycobacterium tuberculosis in Quantitative Structome Analysis and CryoTEM Examination. Front Microbiol 2018; 9:1992. [PMID: 30258411 PMCID: PMC6145149 DOI: 10.3389/fmicb.2018.01992] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 08/07/2018] [Indexed: 01/05/2023] Open
Abstract
A series of structome analyses, that is, quantitative and three-dimensional structural analysis of a whole cell at the electron microscopic level, have already been achieved individually in Exophiala dermatitidis, Saccharomyces cerevisiae, Mycobacterium tuberculosis, Myojin spiral bacteria, and Escherichia coli. In these analyses, sample cells were processed through cryo-fixation and rapid freeze-substitution, resulting in the exquisite preservation of ultrastructures on the serial ultrathin sections examined by transmission electron microscopy. In this paper, structome analysis of non pathogenic Mycolicibacterium smegmatis, basonym Mycobacterium smegmatis, was performed. As M. smegmatis has often been used in molecular biological experiments and experimental tuberculosis as a substitute of highly pathogenic M. tuberculosis, it has been a task to compare two species in the same genus, Mycobacterium, by structome analysis. Seven M. smegmatis cells cut into serial ultrathin sections, and, totally, 220 serial ultrathin sections were examined by transmission electron microscopy. Cell profiles were measured, including cell length, diameter of cell and cytoplasm, surface area of outer membrane and plasma membrane, volume of whole cell, periplasm, and cytoplasm, and total ribosome number and density per 0.1 fl cytoplasm. These data are based on direct measurement and enumeration of exquisitely preserved single cell structures in the transmission electron microscopy images, and are not based on the calculation or assumptions from biochemical or molecular biological indirect data. All measurements in M. smegmatis, except cell length, are significantly higher than those of M. tuberculosis. In addition, these data may explain the more rapid growth of M. smegmatis than M. tuberculosis and contribute to the understanding of their structural properties, which are substantially different from M. tuberculosis, relating to the expression of antigenicity, acid-fastness, and the mechanism of drug resistance in relation to the ratio of the targets to the corresponding drugs. In addition, data obtained from cryo-transmission electron microscopy examination were used to support the validity of structome analysis. Finally, our data strongly support the most recent establishment of the novel genus Mycolicibacterium, into which basonym Mycobacterium smegmatis has been classified.
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Affiliation(s)
- Hiroyuki Yamada
- Department of Mycobacterium Reference and Research, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Japan
| | | | - Yuriko Igarashi
- Department of Mycobacterium Reference and Research, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Japan
| | - Kinuyo Chikamatsu
- Department of Mycobacterium Reference and Research, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Japan
| | - Akio Aono
- Department of Mycobacterium Reference and Research, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Japan
| | - Yoshiro Murase
- Department of Mycobacterium Reference and Research, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Japan
| | - Yuta Morishige
- Department of Mycobacterium Reference and Research, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Japan
| | - Akiko Takaki
- Department of Mycobacterium Reference and Research, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Japan
| | - Hiroji Chibana
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Satoshi Mitarai
- Department of Mycobacterium Reference and Research, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Japan
- Department of Basic Mycobacteriology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
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8
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Kumar R, Maurya R, Saran S. Introducing a simple model system for binding studies of known and novel inhibitors of AMPK: a therapeutic target for prostate cancer. J Biomol Struct Dyn 2018; 37:781-795. [PMID: 29447108 DOI: 10.1080/07391102.2018.1441069] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Prostate cancer (PC) is one of the leading cancers in men, raising a serious health issue worldwide. Due to lack of suitable biomarker, their inhibitors and the platform for testing those inhibitors result in poor prognosis of PC. AMP-activated protein kinase (AMPK) is a highly conserved protein kinase found in eukaryotes that is involved in growth and development, and also acts as a therapeutic target for PC. The aim of the present study is to identify novel potent inhibitors of AMPK and propose a simple cellular model system for understanding its biology. Structural modelling and MD simulations were performed to construct and refine the 3D models of Dictyostelium and human AMPK. Binding mechanisms of different drug compounds were studied by performing molecular docking, molecular dynamics and MM-PBSA methods. Two novel drugs were isolated having higher binding affinity over the known drugs and hydrophobic forces that played a key role during protein-ligand interactions. The study also explored the simple cellular model system for drug screening and understanding the biology of a therapeutic target by performing in vitro experiments.
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Affiliation(s)
- Rakesh Kumar
- a School of Life Sciences , Jawaharlal Nehru University , New Delhi 110067 , India
| | - Ranjana Maurya
- a School of Life Sciences , Jawaharlal Nehru University , New Delhi 110067 , India
| | - Shweta Saran
- a School of Life Sciences , Jawaharlal Nehru University , New Delhi 110067 , India
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9
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Paul A, Kumar P, Surolia A, Vijayan M. Biochemical and structural studies of mutants indicate concerted movement of the dimer interface and ligand-binding region of Mycobacterium tuberculosis pantothenate kinase. Acta Crystallogr F Struct Biol Commun 2017; 73:635-643. [PMID: 29095158 PMCID: PMC5683034 DOI: 10.1107/s2053230x17015667] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 10/27/2017] [Indexed: 11/11/2022] Open
Abstract
Two point mutants and the corresponding double mutant of Mycobacterium tuberculosis pantothenate kinase have been prepared and biochemically and structurally characterized. The mutants were designed to weaken the affinity of the enzyme for the feedback inhibitor CoA. The mutants exhibit reduced activity, which can be explained in terms of their structures. The crystals of the mutants are not isomorphous to any of the previously analysed crystals of the wild-type enzyme or its complexes. The mycobacterial enzyme and its homologous Escherichia coli enzyme exhibit structural differences in their nucleotide complexes in the dimer interface and the ligand-binding region. In three of the four crystallographically independent mutant molecules the structure is similar to that in the E. coli enzyme. Although the mutants involve changes in the CoA-binding region, the dimer interface and the ligand-binding region move in a concerted manner, an observation which might be important in enzyme action. This work demonstrates that the structure of the mycobacterial enzyme can be transformed into a structure similar to that of the E. coli enzyme through minor perturbations without external influences such as those involving ligand binding.
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Affiliation(s)
- A. Paul
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - P. Kumar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - A. Surolia
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - M. Vijayan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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10
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Arif SM, Varshney U, Vijayan M. Hydrolysis of diadenosine polyphosphates. Exploration of an additional role of Mycobacterium smegmatis MutT1. J Struct Biol 2017; 199:165-176. [PMID: 28705712 DOI: 10.1016/j.jsb.2017.07.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 07/06/2017] [Accepted: 07/08/2017] [Indexed: 10/19/2022]
Abstract
Diadenosine polyphosphates (ApnA, n=2-6), particularly Ap4A, are involved in several important physiological processes. The substantial sequence identity of the Nudix hydrolase domain (domain 1) of Mycobacterium smegmatis MutT1 (MsMutT1) with a known Ap4A hydrolase suggested that MsMutT1 could also hydrolyse diadenosine polyphosphates. Biochemical experiments yielded results in conformity with this suggestion, with Ap4A as the best among the substrates. ATP is a product in all experiments; small amounts of ADP were also observed in the experiments involving Ap4A and Ap6A. Hydrolysis was inhibited by fluoride ions in all cases. The mechanism of action and its inhibition in relation to ApnA were explored through the X-ray analysis of the crystals of the MsMutT1 complexes with Ap5A; Ap5A and MnCl2; Ap4A; ATP; and ATP.NaF.MgCl2. The aggregation pattern of molecules in the first four crystals is similar to that found in a majority of MsMutT1-NTP crystals. Substrate molecules occupy the primary binding site and ATP occupies a site at an intermolecular interface, in the first two. ATP occupies both the sites in the third and fourth crystal. The protein-ligand interactions observed in these crystal structures lead to an explanation of the molecular mechanism of hydrolysis of ApnA by MsMutT1. The fifth crystal exhibits a new packing arrangement. The structure of the complex provides an explanation for the fluoride inhibition of the activity of the enzyme. It would thus appear that MutT1 has a major role involving the hydrolysis of diadenosine polyphosphates, which could be elucidated at the molecular level.
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Affiliation(s)
- S M Arif
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - U Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
| | - M Vijayan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.
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