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Jalalypour F, Sensoy O, Atilgan C. Perturb-Scan-Pull: A Novel Method Facilitating Conformational Transitions in Proteins. J Chem Theory Comput 2020; 16:3825-3841. [PMID: 32324386 DOI: 10.1021/acs.jctc.9b01222] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Conformational transitions in proteins facilitate precise physiological functions. Therefore, it is crucial to understand the mechanisms underlying these processes to modulate protein function. Yet, studying structural and dynamical properties of proteins is notoriously challenging due to the complexity of the underlying potential energy surfaces (PES). We have previously developed the perturbation-response scanning (PRS) method to identify key residues that participate in the communication network responsible for specific conformational transitions. PRS is based on a residue-by-residue scan of the protein to determine the subset of residues/forces which provide the closest conformational change leading to a target conformational state, inasmuch as linear response theory applies to these motions. Here, we develop a novel method to further evaluate if conformational transitions may be triggered on the PES. We aim to study functionally relevant conformational transitions in proteins by using results obtained from PRS and feeding them as inputs to steered molecular dynamics simulations. The success and the transferability of the method are evaluated on three protein systems having different complexities of motion on the PES: calmodulin, adenylate kinase, and bacterial ferric binding protein. We find that the method captures the target conformation, while providing key residues and the optimum paths with relatively low free energy profiles.
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Affiliation(s)
- Farzaneh Jalalypour
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Istanbul, Turkey
| | - Ozge Sensoy
- School of Engineering and Natural Sciences, Istanbul Medipol University, 34810, Istanbul, Turkey
| | - Canan Atilgan
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Istanbul, Turkey.,Sabanci University Nanotechnology Research and Application Center, SUNUM, 34956, Istanbul, Turkey
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The effect of calcium binding on the unfolding force of mutated and healthy titin I10 domain: A steered molecular dynamics simulation study. J Mol Graph Model 2020; 96:107534. [DOI: 10.1016/j.jmgm.2020.107534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 12/03/2019] [Accepted: 01/08/2020] [Indexed: 01/03/2023]
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Pan Y, Qi R, Li M, Wang B, Huang H, Han W. Random acceleration and steered molecular dynamics simulations reveal the (un)binding tunnels in adenosine deaminase and critical residues in tunnels. RSC Adv 2020; 10:43994-44002. [PMID: 35517169 PMCID: PMC9058408 DOI: 10.1039/d0ra07796h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 11/27/2020] [Indexed: 11/21/2022] Open
Abstract
Adenosine deaminase (ADA), an important enzyme related to purine nucleoside metabolism, can be divided into open conformation and closed conformation according to the inhibitors of binding.
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Affiliation(s)
- Yue Pan
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education
- School of Life Science
- Jilin University
- Changchun 130012
- China
| | - Renrui Qi
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education
- School of Life Science
- Jilin University
- Changchun 130012
- China
| | - Minghao Li
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education
- School of Life Science
- Jilin University
- Changchun 130012
- China
| | - Bingda Wang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education
- School of Life Science
- Jilin University
- Changchun 130012
- China
| | - Honglan Huang
- Department of Pathobiology
- College of Basic Medical Sciences
- Jilin University
- Changchun
- China
| | - Weiwei Han
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education
- School of Life Science
- Jilin University
- Changchun 130012
- China
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Prajapati GK, Pandey B, Mishra AK, Baek KH, Pandey DM. Identification of GCC-box and TCC-box motifs in the promoters of differentially expressed genes in rice (Oryza sativa L.): Experimental and computational approaches. PLoS One 2019; 14:e0214964. [PMID: 31026257 PMCID: PMC6485614 DOI: 10.1371/journal.pone.0214964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/23/2019] [Indexed: 01/22/2023] Open
Abstract
The transcription factor selectively binds with the cis-regulatory elements of the promoter and regulates the differential expression of genes. In this study, we aimed to identify and validate the presence of GCC-box and TCC-box motifs in the promoters of upregulated differentially expressed genes (UR-DEGs) and downregulated differentially expressed genes (DR-DEGs) under anoxia using molecular beacon probe (MBP) based real-time PCR. The GCC-box motif was detected in UR-DEGs (DnaJ and 60S ribosomal protein L7 genes), whereas, the TCC-box was detected in DR-DEGs (DnaK and CPuORF11 genes). In addition, the mechanism of interaction of AP2/EREBP family transcription factor (LOC_Os03g22170) with GCC-box promoter motif present in DnaJ gene (LOC_Os06g09560) and 60S ribosomal protein L7 gene (LOC_Os08g42920); and TCC-box promoter motif of DnaK gene (LOC_Os02g48110) and CPuORF11 gene (LOC_Os02g01240) were explored using molecular dynamics (MD) simulations analysis including binding free energy calculations, principal component analyses, and free energy landscapes. The binding free energy analysis revealed that AP2/EREBP model residues such as Arg68, Arg72, Arg83, Lys87, and Arg90 were commonly involved in the formation of hydrogen bonds with GCC and TCC-box promoter motifs, suggesting that these residues are critical for strong interaction. The movement of the entire protein bound to DNA was restricted, confirming the stability of the complex. This study provides comprehensive binding information and a more detailed view of the dynamic interaction between proteins and DNA.
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Affiliation(s)
- Gopal Kumar Prajapati
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India
| | - Bharati Pandey
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India
| | - Awdhesh Kumar Mishra
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, Republic of Korea
| | - Kwang-Hyun Baek
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, Republic of Korea
- * E-mail: (DP); (KB)
| | - Dev Mani Pandey
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India
- * E-mail: (DP); (KB)
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Alaybeyoglu B, Sariyar Akbulut B, Ozkirimli E. Insights into membrane translocation of the cell-penetrating peptide pVEC from molecular dynamics calculations. J Biomol Struct Dyn 2016; 34:2387-98. [DOI: 10.1080/07391102.2015.1117396] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Begum Alaybeyoglu
- Chemical Engineering Department, Bogazici University, Bebek, 34342 Istanbul, Turkey
| | | | - Elif Ozkirimli
- Chemical Engineering Department, Bogazici University, Bebek, 34342 Istanbul, Turkey
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Gu J, Li H, Wang X. A Self-Adaptive Steered Molecular Dynamics Method Based on Minimization of Stretching Force Reveals the Binding Affinity of Protein-Ligand Complexes. Molecules 2015; 20:19236-51. [PMID: 26506335 PMCID: PMC6332444 DOI: 10.3390/molecules201019236] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 10/14/2015] [Accepted: 10/14/2015] [Indexed: 01/22/2023] Open
Abstract
Binding affinity prediction of protein–ligand complexes has attracted widespread interest. In this study, a self-adaptive steered molecular dynamics (SMD) method is proposed to reveal the binding affinity of protein–ligand complexes. The SMD method is executed through adjusting pulling direction to find an optimum trajectory of ligand dissociation, which is realized by minimizing the stretching force automatically. The SMD method is then used to simulate the dissociations of 19 common protein–ligand complexes which are derived from two homology families, and the binding free energy values are gained through experimental techniques. Results show that the proposed SMD method follows a different dissociation pathway with lower a rupture force and energy barrier when compared with the conventional SMD method, and further analysis indicates the rupture forces of the complexes in the same protein family correlate well with their binding free energy, which reveals the possibility of using the proposed SMD method to identify the active ligand.
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Affiliation(s)
- Junfeng Gu
- State Key Laboratory of Structural Analysis for Industrial Equipment, Department of Engineering Mechanics, Dalian University of Technology, Dalian 116023, China.
| | - Hongxia Li
- School of Mechanical Engineering, Dalian University of Technology, Dalian 116023, China.
| | - Xicheng Wang
- State Key Laboratory of Structural Analysis for Industrial Equipment, Department of Engineering Mechanics, Dalian University of Technology, Dalian 116023, China.
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Santamaria R, Jones K, Arroyo M, González-García T. Polymer folding via external potentials in ab-initio calculations. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2015.06.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Identifying key interactions stabilizing DOF zinc finger-DNA complexes using in silico approaches. J Theor Biol 2015; 382:150-9. [PMID: 26092376 DOI: 10.1016/j.jtbi.2015.06.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 05/09/2015] [Accepted: 06/06/2015] [Indexed: 11/21/2022]
Abstract
DOF (DNA-binding with one finger) proteins, a family of DNA-binding transcription factors, are members of zinc fingers unique to plants. They are associated with different plant specific phenomena including germination, dormancy, light and defense responses. Until now, there is no report of experimentally solved structure for DOF proteins, making empirical investigation of DOF-DNA interaction more challenging. It has been shown that comparative modeling can be used to reliably predict the three-dimensional (3D) model of structurally unknown proteins whenever a suitable template is available. Furthermore, current molecular mechanics force fields allow prediction of interaction energies for macromolecular complexes. Therefore, the approaches considered in this work were to model the 3D structures of DOF zinc fingers (ZFs) from Arabidopsis thaliana complexed with DNA molecule, to calculate their binding energies, to identify key interactions established between ZFs and DNA, and to determine the impact of the different interactions on the binding energies. The results were used to predict the binding affinities for the novel designed ZFs and may be used in engineering DNA binding proteins.
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Bung N, Pradhan M, Srinivasan H, Bulusu G. Structural insights into E. coli porphobilinogen deaminase during synthesis and exit of 1-hydroxymethylbilane. PLoS Comput Biol 2014; 10:e1003484. [PMID: 24603363 PMCID: PMC3945110 DOI: 10.1371/journal.pcbi.1003484] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 01/08/2014] [Indexed: 11/19/2022] Open
Abstract
Porphobilinogen deaminase (PBGD) catalyzes the formation of 1-hydroxymethylbilane (HMB), a crucial intermediate in tetrapyrrole biosynthesis, through a step-wise polymerization of four molecules of porphobilinogen (PBG), using a unique dipyrromethane (DPM) cofactor. Structural and biochemical studies have suggested residues with catalytic importance, but their specific role in the mechanism and the dynamic behavior of the protein with respect to the growing pyrrole chain remains unknown. Molecular dynamics simulations of the protein through the different stages of pyrrole chain elongation suggested that the compactness of the overall protein decreases progressively with addition of each pyrrole ring. Essential dynamics showed that domains move apart while the cofactor turn region moves towards the second domain, thus creating space for the pyrrole rings added at each stage. Residues of the flexible active site loop play a significant role in its modulation. Steered molecular dynamics was performed to predict the exit mechanism of HMB from PBGD at the end of the catalytic cycle. Based on the force profile and minimal structural changes the proposed path for the exit of HMB is through the space between the domains flanking the active site loop. Residues reported as catalytically important, also play an important role in the exit of HMB. Further, upon removal of HMB, the structure of PBGD gradually relaxes to resemble its initial stage structure, indicating its readiness to resume a new catalytic cycle. Heme is the prosthetic group at the core of the oxygen carrier metalloprotein hemoglobin. Heme consists of a tetrapyrrole called porphyrin bound to an iron ion. It is synthesized by the heme biosynthetic pathway, which is common to all eukaryotes and most prokaryotes. Porphobilinogen deaminase, an enzyme in the heme biosynthetic pathway, catalyzes the formation of a linear tetrapyrrole product, 1-hydroxymethylbilane, from four units of porphobilinogen. In this study we carried out molecular dynamics simulations to understand the structural changes that the enzyme undergoes while catalyzing this reaction. There are three segments to the study: 1) understanding the changes in the enzyme when the porphobilinogen units get attached to the dipyrromethane cofactor, thereby forming a polypyrrole chain; 2) exit of the product from the active site of the enzyme via steered molecular dynamics; and 3) the relaxation of the enzyme to the initial stage to resume its catalytic cycle. Molecular dynamics simulations of the protein through the different stages of pyrrole chain elongation gives insight into the motions of domains, active site loop and role of conserved active site residues in facilitating the accommodation of the polypyrrole chain. In addition to this, we propose a possible exit path for the product and demonstrate the relaxation of the enzyme after the exit of the product to resume the catalytic cycle.
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Affiliation(s)
- Navneet Bung
- TCS Innovation Labs-Hyderabad (Life Sciences Division), Tata Consultancy Services Limited, Hyderabad, India
| | - Meenakshi Pradhan
- TCS Innovation Labs-Hyderabad (Life Sciences Division), Tata Consultancy Services Limited, Hyderabad, India
| | - Harini Srinivasan
- TCS Innovation Labs-Hyderabad (Life Sciences Division), Tata Consultancy Services Limited, Hyderabad, India
| | - Gopalakrishnan Bulusu
- TCS Innovation Labs-Hyderabad (Life Sciences Division), Tata Consultancy Services Limited, Hyderabad, India
- * E-mail:
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Mai BK, Viet MH, Li MS. Top Leads for Swine Influenza A/H1N1 Virus Revealed by Steered Molecular Dynamics Approach. J Chem Inf Model 2010; 50:2236-47. [DOI: 10.1021/ci100346s] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Binh Khanh Mai
- Institute for Computational Science and Technology, 6 Quarter, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam, and Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Man Hoang Viet
- Institute for Computational Science and Technology, 6 Quarter, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam, and Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Mai Suan Li
- Institute for Computational Science and Technology, 6 Quarter, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam, and Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
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Fishelovitch D, Shaik S, Wolfson HJ, Nussinov R. Theoretical characterization of substrate access/exit channels in the human cytochrome P450 3A4 enzyme: involvement of phenylalanine residues in the gating mechanism. J Phys Chem B 2010; 113:13018-25. [PMID: 19728720 PMCID: PMC2750738 DOI: 10.1021/jp810386z] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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The human cytochrome P450 3A4 mono-oxygenates ∼50% of all drugs. Its substrates/products enter/leave the active site by access/exit channels. Here, we perform steered molecular dynamics simulations, pulling the products temazepam and testosterone-6βOH out of the P450 3A4 enzyme in order to identify the preferred substrate/product pathways and their gating mechanism. We locate six different egress pathways of products from the active site with different exit preferences for the two products and find that there is more than just one access/exit channel in CYP3A4. The so-called solvent channel manifests the largest opening for both tested products, thereby identifying this channel as a putative substrate channel. Most channels consist of one or two π-stacked phenylalanine residues that serve as gate keepers. The oxidized drug breaks the hydrophobic interactions of the gating residues and forms mainly hydrophobic contacts with the gate. We argue that product exit preferences in P450s are regulated by protein−substrate specificity.
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Affiliation(s)
- Dan Fishelovitch
- Department of Human Molecular Genetics and Biochemistry, Sackler Institute of Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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Peplowski L, Kubiak K, Nowak W. Mechanical aspects of nitrile hydratase enzymatic activity. Steered molecular dynamics simulations of Pseudonocardia thermophila JCM 3095. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.10.072] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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