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Wu Q, Wang XZ, Tang YY, Yu HT, Ding YF, De Yang C, Cui FG, Zhang JC, Wang CT. Molecular cloning and characterization of NPR1 gene from Arachis hypogaea. Mol Biol Rep 2014; 41:5247-56. [PMID: 24842264 DOI: 10.1007/s11033-014-3395-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 05/02/2014] [Indexed: 10/25/2022]
Abstract
The NPR1 gene was an important regulator for a plant disease resistance. The cDNA of NPR1 gene was cloned from peanut cultivar Ri Hua 1 by rapid amplification of cDNA ends-polymerase chain reaction (RACE-PCR). The full length cDNA of Arachis hypogaea NPR1 consisted of 2,078 base pairs with a 1,446 bp open-reading frame encoding 481 amino acids. The predicted NPR1 contained the highly conserved functional domains (BTB/POZ domain from M1 to D116), protein-protein interaction domains (three ankyrin repeats from K158 to L186; N187 to L217 and R221 to D250) and one NPR1-like domain (C262 to S469). The DNA sequence of the NPR1 gene was 2,332 or 2,223 bp. Both two sequences contained three introns and four exons. The NPR1 transcripts were expressed mainly in roots and leaves, while fewer signals were detected in the stems. Amount of the NPR1 transcript was significantly increased 1 h after salicylic acid challenge and was eventually 5.3 times greater than that in the control group. Both the DNA sequence and the coding sequence were obtained from eight cultivars and nine wild species of Arachis. Maximum likelihood analyses of d N/d S ratios for 25 sequences from different species showed that different selection pressures may have acted on different branches.
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Affiliation(s)
- Qi Wu
- Shandong Peanut Research Institute (SPRI), 126 Fushan Rd., Qingdao, 266100, People's Republic of China,
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2
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John S, Thangapandian S, Lee KW. Potential human cholesterol esterase inhibitor design: benefits from the molecular dynamics simulations and pharmacophore modeling studies. J Biomol Struct Dyn 2012; 29:921-36. [PMID: 22292952 DOI: 10.1080/07391102.2012.10507419] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Human pancreatic cholesterol esterase (hCEase) is one of the lipases found to involve in the digestion of large and broad spectrum of substrates including triglycerides, phospholipids, cholesteryl esters, etc. The presence of bile salts is found to be very important for the activation of hCEase. Molecular dynamic simulations were performed for the apoform and bile salt complexed form of hCEase using the co-ordinates of two bile salts from bovine CEase. The stability of the systems throughout the simulation time was checked and two representative structures from the highly populated regions were selected using cluster analysis. These two representative structures were used in pharmacophore model generation. The generated pharmacophore models were validated and used in database screening. The screened hits were refined for their drug-like properties based on Lipinski's rule of five and ADMET properties. The drug-like compounds were further refined by molecular docking simulation using GOLD program based on the GOLD fitness score, mode of binding, and molecular interactions with the active site amino acids. Finally, three hits of novel scaffolds were selected as potential leads to be used in novel and potent hCEase inhibitor design. The stability of binding modes and molecular interactions of these final hits were re-assured by molecular dynamics simulations.
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Affiliation(s)
- Shalini John
- Division of Applied Life Science_(BK21 Program), Systems and Synthetic Agrobiotech Center (SSAC) Gyeongsang National University (GNU), 501 Jinju-daero, Gazha-dong, Jinju 660-701, Republic of Korea
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3
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Cao J. The pectin lyases in Arabidopsis thaliana: evolution, selection and expression profiles. PLoS One 2012; 7:e46944. [PMID: 23056537 PMCID: PMC3467278 DOI: 10.1371/journal.pone.0046944] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 09/06/2012] [Indexed: 11/22/2022] Open
Abstract
Pectin lyases are a group of enzymes that are thought to contribute to many biological processes, such as the degradation of pectin. However, until this study, no comprehensive study incorporating phylogeny, chromosomal location, gene duplication, gene organization, functional divergence, adaptive evolution, expression profiling and functional networks has been reported for Arabidopsis. Sixty-seven pectin lyase genes have been identified, and most of them possess signal sequences targeting the secretory pathway. Phylogenetic analyses identified five gene groups with considerable conservation among groups. Pectin lyase genes were non-randomly distributed across chromosomes and clustering was evident. Functional divergence and adaptive evolution analyses suggested that purifying selection was the main force driving pectin lyase evolution, although some critical sites responsible for functional divergence might be the consequence of positive selection. A stigma- and receptacle-specific expression promoter was identified, and it had increased expression in response to wounding. Two hundred and eighty-eight interactions were identified by functional network analyses, and most of these were involved in cellular metabolism, cellular transport and localization, and stimulus responses. This investigation contributes to an improved understanding of the complexity of the Arabidopsis pectin lyase gene family.
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Affiliation(s)
- Jun Cao
- Institute of Life Science, Jiangsu University, Zhenjiang, Jiangsu, P.R. China.
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4
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Chen L, Zheng QC, Yu LY, Chu WT, Zhang JL, Xue Q, Zhang HX, Sun CC. Insights into the thermal stabilization and conformational transitions of DNA by hyperthermophile protein Sso7d: molecular dynamics simulations and MM-PBSA analysis. J Biomol Struct Dyn 2012; 30:716-27. [PMID: 22731116 DOI: 10.1080/07391102.2012.689702] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In the assembly of DNA-protein complex, the DNA kinking plays an important role in nucleoprotein structures and gene regulation. Molecular dynamics (MD) simulations were performed on specific protein-DNA complexes in this study to investigate the stability and structural transitions of DNA depending on temperature. Furthermore, we introduced the molecular mechanics/Poisson-Boltzmann surface area (MM-PBSA) approach to analyze the interactions between DNA and protein in hyperthermophile. Focused on two specific Sso7d-DNA complexes (PDB codes: 1BNZ and 1BF4), we performed MD simulations at four temperatures (300, 360, 420, and 480 K) and MM-PBSA at 300 and 360 K to illustrate detailed information on the changes of DNA. Our results show that Sso7d stabilizes DNA duplex over a certain temperature range and DNA molecules undergo B-like to A-like form transitions in the binary complex with the temperature increasing, which are consistent with the experimental data. Our work will contribute to a better understanding of protein-DNA interaction.
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Affiliation(s)
- Lin Chen
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, 130023, P.R. China
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Wang ZJ, Si YX, Oh S, Yang JM, Yin SJ, Park YD, Lee J, Qian GY. The effect of fucoidan on tyrosinase: computational molecular dynamics integrating inhibition kinetics. J Biomol Struct Dyn 2012; 30:460-73. [PMID: 22694253 DOI: 10.1080/07391102.2012.682211] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Fucoidan is a complex sulfated polysaccharide extracted from brown seaweed and has a wide variety of biological activities. In this study, we investigated the inhibitory effect of fucoidan on tyrosinase via a combination of inhibition kinetics and computational simulations. Fucoidan reversibly inhibited tyrosinase in a mixed-type manner. Time-interval kinetics showed that the inhibition was processed as first order with biphasic processes. For further insight, we simulated dockings with various sizes of molecular models (monomer to decamer) of fucoidan and showed that the best binding energy change results were obtained from the pentamer (-1.89 kcal/mol) and the hexamer (-1.97 kcal/mol) models of AutoDock Vina. The molecular dynamics simulation confirmed the binding mechanisms between tyrosinase and fucoidan and suggested that fucoidan mostly interacts with several residues including copper ions located in the active site. Our study suggests that fucoidan might be a potential natural antipigment agent.
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Affiliation(s)
- Zhi-Jiang Wang
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, 315100, P.R. China
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6
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Majumder R, Roy S, Thakur AR. Analysis of Delta–Notch interaction by molecular modeling and molecular dynamic simulation studies. J Biomol Struct Dyn 2012; 30:13-29. [DOI: 10.1080/07391102.2012.674184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Thangapandian S, John S, Lee KW. Molecular Dynamics Simulation Study Explaining Inhibitor Selectivity in Different Class of Histone Deacetylases. J Biomol Struct Dyn 2012; 29:677-98. [DOI: 10.1080/07391102.2012.10507409] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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8
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Serikov R, Petyuk V, Vorobijev Y, Koval V, Fedorova O, Vlassov V, Zenkova M. Mechanism of antisense oligonucleotide interaction with natural RNAs. J Biomol Struct Dyn 2011; 29:27-50. [PMID: 21696224 DOI: 10.1080/073911011010524987] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Oligonucleotides find several numbers of applications: as diagnostic probes, RT and PCR primers and antisense agents due to their ability of forming specific interactions with complementary nucleotide sequences within nucleic acids. These interactions are strongly affected by accessibility of the target sequence in the RNA structure. In the present work the mechanism of invasion of RNA structure by oligonucleotide was investigated using a model system: yeast tRNA(Phe) and oligonucleotides complementary to the 3'-part of this molecule. Kinetics of interaction of oligonucleotides with in vitro transcript of yeast tRNAPhe was studied using stopped-flow technique with fluorescence quenching detection, 5'-DABCYL labeled oligonucleotide was hybridized with 3'-fluorescein labeled tRNA(Phe). The results evidence for a four-step invasion process of the oligonucleotide-RNA complex formation. The process is initiated by formation of transition complexes with nucleotides in the T-loop and ACCA sequence. This complex formation is followed by RNA unfolding and formation of an extended heteroduplex with the oligonucleotide via strand displacement process. Computer modeling of oligonucleotide-tRNA(Phe) interaction revealed potential factors that could favor transition complexes formation and confirmed the proposed mechanism, showing the oligonucleotide to be a molecular "wedge". Our data evidence that oligonucleotide invasion into structured RNA is initiated by loop-single strand interactions, similar to the initial step of the antisense RNA-RNA interactions. The obtained results can be used for choosing efficient oligonucleotide probes.
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Affiliation(s)
- R Serikov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev Ave., 630090 Novosibirsk, Russian Federation
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Jurkowski W, Kułaga T, Roterman I. Geometric parameters defining the structure of proteins--relation to early-stage folding step. J Biomol Struct Dyn 2011; 29:79-104. [PMID: 21696227 DOI: 10.1080/07391102.2011.10507376] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Two geometrical parameters describing the structure of a polypeptide: V-dihedral angle between two sequential peptide bond planes and R-radius of curvature are used for structural classification of polypeptide structure in proteins. The relation between these two parameters was the basis for the definition of the conformational sub-space for early-stage structural forms. The cluster analysis of V and lnR, applied to the selected proteins of well-defined secondary structure (according to DSSP classification) and to proteins without any introductory classified analysis, revealed that several of the discriminated groups of proteins agree with the assumed model of early-stage conformational sub-space. This analysis shows that protein structures may be represented in VR space instead of Phi, Psi angles space, thus lowering the conformational space dimensionality. The VR model allows classification of traditional secondary structure elements as well as different Random Coil motifs, which broadens the range of recognized structural categories (compared to standard secondary structure elements).
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Affiliation(s)
- W Jurkowski
- Department of Bioinformatics and Telemedicine, Jagiellonian University-Medical College, Department of Bioinformatics and Telemedicine, Lazarza 16, 31-530 Krakow, Poland
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Dey R, Chen L. In search of allosteric modulators of a7-nAChR by solvent density guided virtual screening. J Biomol Struct Dyn 2011; 28:695-715. [PMID: 21294583 DOI: 10.1080/07391102.2011.10508600] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Nicotinic acetylcholine receptors (nAChR) are pentameric ligand gated ion channels whose activity can be modulated by endogenous neurotransmitters as well as by synthetic ligands that bind the same or distinct sites from the natural ligand. The subtype of α7 nAChR has been considered as a potenial therapeutic target for Alzheimer's disease, schizophrenia and other neurological and psychiatric disorders. Here we have developed a homology model of α7 nAChR based on two high resolution crystal structures with Brookhaven Protein Data Bank (PDB) codes 2QC1 and 2WN9 for threading on one monomer and then for building a pentamer, respectively. A number of small molecule binding sites are identified using Pocket Finder (J. An, M. Tortov, and R. Abagyan, Molecular & Cellular Proteomics, 4.6, 752-761 (2005)) of Internal Coordinate Mechanics (ICM). Remarkably, these computer-identified sites match perfectly with ordered solvent densities found in the high-resolution crystal structure of α1 nAChR, suggesting that the surface cavities in the α7 nAChR model are likely binding sites of small molecules. A high throughput virtual screening by flexible ligand docking of 5008 small molecule compounds was performed at three potential allosteric modulator (AM) binding sites of α7 nAChR using Molsoft ICM software (R. Abagyan, M. Tortov and D. Kuznetsov, J Comput Chem 15, 488-506, (1994)). Some experimentally verified allosteric modulators of α7 like CCMI comp-6, LY 7082101, 5-HI, TQS, PNU-120596, genistein, and NS-1738 ranked among top 100 compounds, while the rest of the compounds in the list could guide further search for new allosteric modulators.
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Affiliation(s)
- Raja Dey
- Molecular and Computational Biology, Department of Biological Sciences,University of Southern California, Los Angeles, CA 90089, USA.
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Semighini EP, Resende JA, de Andrade P, Morais PAB, Carvalho I, Taft CA, Silva CHTP. Using computer-aided drug design and medicinal chemistry strategies in the fight against diabetes. J Biomol Struct Dyn 2011; 28:787-96. [PMID: 21294589 DOI: 10.1080/07391102.2011.10508606] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The aim of this work is to present a simple, practical and efficient protocol for drug design, in particular Diabetes, which includes selection of the illness, good choice of a target as well as a bioactive ligand and then usage of various computer aided drug design and medicinal chemistry tools to design novel potential drug candidates in different diseases. We have selected the validated target dipeptidyl peptidase IV (DPP-IV), whose inhibition contributes to reduce glucose levels in type 2 diabetes patients. The most active inhibitor with complex X-ray structure reported was initially extracted from the BindingDB database. By using molecular modification strategies widely used in medicinal chemistry, besides current state-of-the-art tools in drug design (including flexible docking, virtual screening, molecular interaction fields, molecular dynamics, ADME and toxicity predictions), we have proposed 4 novel potential DPP-IV inhibitors with drug properties for Diabetes control, which have been supported and validated by all the computational tools used herewith.
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Affiliation(s)
- Evandro P Semighini
- Departamento de Ciencias Farmaceuticas, Faculdade de Ciencias Farmaceuticas de Ribeirao Preto, Universidade de Sao Paulo, Av. do Cafe, s/n, Monte Alegre, 14040-903, Ribeirao Preto-SP, Brazil
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12
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Chang TT, Sun MF, Chen HY, Tsai FJ, Fisher M, Lin JG, Chen CYC. Screening from the world's largest TCM database against H1N1 virus. J Biomol Struct Dyn 2011; 28:773-86. [PMID: 21294588 DOI: 10.1080/07391102.2011.10508605] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The swine influenza virus (H1N1) 2009 pandemic highlights the importance of having effective anti-viral strategies. Recently, oseltamivir (Tamiflu) resistant influenza viruses are identified; which further emphasizes the urgency in developing new antiviral agents. In influenza virus replication cycle, viral surface glycoprotein, hemagglutinin, is responsible for viral entry into host cells. Hence, a potentially effective antiviral strategy is to inhibit viral entry mechanism. To develop novel antiviral agent that inhibits viral entry, we analyzed 20,000 traditional Chinese medicine (TCM) ingredients in hemagglutinin subtype H1 sialic acid binding site found on H1N1 virus. We then performed molecular dynamics simulations to investigate receptor-ligand interaction of the candidates obtained from docking. Here, we report three TCM derivatives that have high binding affinities to H1 sialic acid binding site residues based on structure-based calculations. The top three derivatives, xylopine_2, rosmaricine_14 and rosmaricine_15, all have an amine group that interact with Glu83 and a pyridinium group that interact with Asp103. Molecular dynamics simulations show that these derivatives form strong hydrogen bonding with Glu83 but interact transiently with Asp103. We therefore suggest that an enhanced hemagglutinin inhibitor, based on our scaffold, should be designed to bind both Glu83 and Asp103 with high affinity.
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Affiliation(s)
- Tung-Ti Chang
- Laboratory of Computational and Systems Biology, School of Chinese Medicine, China Medical University, Taichung, 40402, Taiwan
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Xu X, Su J, Chen W, Wang C. Thermal stability and unfolding pathways of Sso7d and its mutant F31A: insight from molecular dynamics simulation. J Biomol Struct Dyn 2011; 28:717-27. [PMID: 21294584 DOI: 10.1080/07391102.2011.10508601] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The thermo-stability and unfolding behaviors of a small hyperthermophilic protein Sso7d as well as its single-point mutation F31A are studied by molecular dynamics simulation at temperatures of 300 K, 371 K and 500 K. Simulations at 300 K show that the F31A mutant displays a much larger flexibility than the wild type, which implies that the mutation obviously decreases the protein's stability. In the simulations at 371 K, although larger fluctuations were observed, both of these two maintain their stable conformations. High temperature simulations at 500 K suggest that the unfolding of these two proteins evolves along different pathways. For the wild-type protein, the C-terminal alpha-helix is melted at the early unfolding stage, whereas it is destroyed much later in the unfolding process of the F31A mutant. The results also show that the mutant unfolds much faster than its parent protein. The deeply buried aromatic cluster in the F31A mutant dissociates quickly relative to the wild-type protein at high temperature. Besides, it is found that the triple-stranded antiparallel β-sheet in the wild-type protein plays an important role in maintaining the stability of the entire structure.
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Affiliation(s)
- Xianjin Xu
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China
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Majumder R, Roy S, Thakur AR. Molecular Modeling and Molecular Dynamics Simulation Studies of Delta-Notch Complex. J Biomol Struct Dyn 2011; 29:297-310. [DOI: 10.1080/07391102.2011.10507386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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15
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Behmard E, Abdolmaleki P, Asadabadi EB, Jahandideh S. Prevalent Mutations of Human Prion Protein: A Molecular Modeling and Molecular Dynamics Study. J Biomol Struct Dyn 2011; 29:379-89. [DOI: 10.1080/07391102.2011.10507392] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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16
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Jani V, Sonavane UB, Joshi R. Microsecond scale replica exchange molecular dynamic simulation of villin headpiece: an insight into the folding landscape. J Biomol Struct Dyn 2011; 28:845-60. [PMID: 21469746 DOI: 10.1080/07391102.2011.10508612] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Reaching the experimental time scale of millisecond is a grand challenge for protein folding simulations. The development of advanced Molecular Dynamics techniques like Replica Exchange Molecular Dynamics (REMD) makes it possible to reach these experimental timescales. In this study, an attempt has been made to reach the multi microsecond simulation time scale by carrying out folding simulations on a three helix bundle protein, Villin, by combining REMD and Amber United Atom model. Twenty replicas having different temperatures ranging from 295 K to 390 K were simulated for 1.5 µs each. The lowest Root Mean Square Deviation (RMSD) structure of 2.5 Å was obtained with respect to native structure (PDB code 1VII), with all the helices formed. The folding population landscapes were built using segment-wise RMSD and Principal Components as reaction coordinates. These analyses suggest the two-stage folding for Villin. The combination of REMD and Amber United Atom model may be useful to understand the folding mechanism of various fast folding proteins.
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Affiliation(s)
- Vinod Jani
- Bioinformatics Team, Scientific and Engineering Computing Group, Centre for Development of Advanced Computing, Pune University Campus, Ganeshkhind, Pune - 411007, Maharashtra, India
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Su JG, Xu XJ, Li CH, Chen WZ, Wang CX. An Analysis of the Influence of Protein Intrinsic Dynamical Properties on its Thermal Unfolding Behavior. J Biomol Struct Dyn 2011; 29:105-21. [DOI: 10.1080/07391102.2011.10507377] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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18
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Purohit R, Rajendran V, Sethumadhavan R. Studies on Adaptability of Binding Residues Flap Region of TMC-114 Resistance HIV-1 Protease Mutants. J Biomol Struct Dyn 2011; 29:137-52. [DOI: 10.1080/07391102.2011.10507379] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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19
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Ji XL, Liu SQ. Is stoichiometry-driven protein folding getting out of thermodynamic control? J Biomol Struct Dyn 2011; 28:621-3; discussion 669-674. [PMID: 21142237 DOI: 10.1080/07391102.2011.10508598] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Xing-Lai Ji
- Laboratory for Conservation and Utilization of Bio-Resources, Ministry of Education, Yunnan University, Kunming 650091, PR China
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Solov'eva TF, Likhatskaya GN, Khomenko VA, Stenkova AM, Kim NY, Portnyagina OY, Novikova OD, Trifonov EV, Nurminski EA, Isaeva MP. A novel OmpY porin from Yersinia pseudotuberculosis: structure, channel-forming activity and trimer thermal stability. J Biomol Struct Dyn 2011; 28:517-33. [PMID: 21142221 DOI: 10.1080/07391102.2011.10508592] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
A novel OmpY porin was predicted based on the Yersinia pseudotuberculosis genome analysis. Whereas it has the different genomic annotation such as "outer membrane protein N" (ABS46310.1) in str. IP 31758 or "outer membrane protein C2, porin" (YP_070481.1) in str. IP32953, it might be warranted to rename the OmpN/OmpC2 to OmpY, "outer membrane protein Y", where letter "Y" pertained to Yersinia. Both phylogenetic analysis and genomic localization clearly support that the OmpY porin belongs to a new group of general bacterial porins. The recombinant OmpY protein with its signal sequence was overexpressed in porin-deficient Escherichia coli strain. The mature rOmpY was shown to insert into outer membrane as a trimer. The OmpY porin, isolated from the outer membrane, was studied employing spectroscopic, electrophoretic and bilayer lipid membranes techniques. The far UV CD spectrum of rOmpY was essentially identical to that of Y. pseudotuberculosis OmpF. The near UV CD spectrum of rOmpY was weaker and smoother than that of OmpF. The rOmpY single-channel conductance was 180 ± 20 pS in 0.1 M NaCl and was lower than that of the OmpF porin. As was shown by electrophoretic and bilayer lipid membrane experiments, the rOmpY trimers were less thermostable than the OmpF trimers. The porins differed in the trimer-monomer transition temperature by about 20°C. The three-dimensional structural models of the Y. pseudotuberculosis OmpY and OmpF trimers were generated and the intra- and intermonomeric interactions stabilizing the porins were investigated. The difference in the thermal stability of OmpY and OmpF trimers was established to correlate with the difference in intermonomeric polar contacts.
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Affiliation(s)
- T F Solov'eva
- Pacific Institute of Bioorganic Chemistry FEBRAS, prospect 100-let Vladivostoku 159, Vladivostok 690022, Russia
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Zhou ZL, Zhao JH, Liu HL, Wu JW, Liu KT, Chuang CK, Tsai WB, Ho Y. The Possible Structural Models for Polyglutamine Aggregation: A Molecular Dynamics Simulations Study. J Biomol Struct Dyn 2011; 28:743-58. [DOI: 10.1080/07391102.2011.10508603] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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22
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Olmez EO, Alakent B. Alpha7 Helix Plays an Important Role in the Conformational Stability of PTP1B. J Biomol Struct Dyn 2011; 28:675-93. [DOI: 10.1080/07391102.2011.10508599] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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23
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Roy S, Thakur AR. Two models of Smad4 and Hoxa9 Complex are Proposed: Structural and Interactional Perspective. J Biomol Struct Dyn 2011; 28:729-42. [DOI: 10.1080/07391102.2011.10508602] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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24
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Zhao Y, Gong Z, Xiao Y. Improvements of the Hierarchical Approach for Predicting RNA Tertiary Structure. J Biomol Struct Dyn 2011; 28:815-26. [DOI: 10.1080/07391102.2011.10508609] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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25
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26
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Bryce RA. Stoichiometry and Folding of Linear Polypeptides—Reading Between the Lines. J Biomol Struct Dyn 2011; 28:647-8; discussion 669-674. [DOI: 10.1080/073911011010524976] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Galzitskaya OV, Lobanov MY, Finkelstein AV. Cunning Simplicity of a Stoichiometry Driven Protein Folding Thesis. J Biomol Struct Dyn 2011; 28:595-8; discussion 669-674. [DOI: 10.1080/073911011010524958] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Mittal A, Jayaram B. Backbones of Folded Proteins Reveal Novel Invariant Amino Acid Neighborhoods. J Biomol Struct Dyn 2011; 28:443-54. [DOI: 10.1080/073911011010524954] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Mishra S. ‘Chargaff's Rules’ for Protein Folding: Stoichiometric Leitmotif Made Visible. J Biomol Struct Dyn 2011; 28:649-52; discussion 669-674. [DOI: 10.1080/073911011010524977] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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31
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Chan HS. Short-Range Contact Preferences and Long-Range Indifference: Is Protein Folding Stoichiometry Driven? J Biomol Struct Dyn 2011; 28:603-5; discussion 669-674. [DOI: 10.1080/073911011010524960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Mezei M. Discriminatory Power of Stoichiometry-Driven Protein Folding? J Biomol Struct Dyn 2011; 28:625-6; discussion 669-674. [DOI: 10.1080/073911011010524966] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Berka K, Otyepka M. Insenstivity to Close Contacts and Inability to Predict Protein Foldability. J Biomol Struct Dyn 2011; 28:633-4; discussion 669-674. [DOI: 10.1080/073911011010524969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Silva CH, Taft CA. Stoichiometry of Amino acids Drives Protein Folding? J Biomol Struct Dyn 2011; 28:635-6; discussion 669-674. [DOI: 10.1080/073911011010524970] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Burnett JC, Nguyen TL. Is Stoichiometry a New Metric for Evaluating Folded Proteins? J Biomol Struct Dyn 2011; 28:641-2; discussion 669-674. [DOI: 10.1080/073911011010524973] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Agutter PS. Stoichiometry-driven Protein Folding: A Comment. J Biomol Struct Dyn 2011; 28:643-4; discussion 669-674. [DOI: 10.1080/073911011010524974] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Ramanathan R, Verma A. Are there Still Surprises Buried Inside Statistical Analysis of Protein Structure? J Biomol Struct Dyn 2011; 28:661-2; discussion 669-674. [DOI: 10.1080/073911011010524981] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Song Y, Song Y, Chen X. The Yeast Prion Case: Could There be a Uniform Concept Underlying Complex Protein Folding? J Biomol Struct Dyn 2011; 28:663-5; discussion 669-674. [DOI: 10.1080/073911011010524982] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Wang J, Cao Z, Yu J. Protein Structures-based Neighborhood Analysis vs Preferential Interactions Between the Special Pairs of Amino acids? J Biomol Struct Dyn 2011; 28:629-32; discussion 669-674. [DOI: 10.1080/073911011010524968] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Bagchi A, Ghosh TC. New Direction to the Solution of Protein Folding Problem. J Biomol Struct Dyn 2011; 28:653-4; discussion 669-674. [DOI: 10.1080/073911011010524978] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Mukhopadhyay BP, Bairagya HR. Protein Folding: Grand Challenge of Nature. J Biomol Struct Dyn 2011; 28:637-8; discussion 669-674. [DOI: 10.1080/073911011010524971] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Ma BG, Zhang HY. Stoichiometry and Preferential Interaction: Two Components of the Principle for Protein Structure Organization. J Biomol Struct Dyn 2011; 28:619-20; discussion 669-674. [DOI: 10.1080/073911011010524965] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Joshi R. Stoichiometry in Protein Folding?: Deeper Insights may be Useful. J Biomol Struct Dyn 2011; 28:667-8; discussion 669-674. [DOI: 10.1080/073911011010524983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Mitternacht S, Berezovsky IN. On the Importance of Amino Acid Sequence and Spatial Proximity of Interacting Residues for Protein Folding. J Biomol Struct Dyn 2011; 28:607-9; discussion 669-674. [DOI: 10.1080/073911011010524961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Chakrabarti B, Bairagya HR, Mallik P, Mukhopadhyay BP, Bera AK. An Insight to Conserved Water Molecular Dynamics of Catalytic and Structural Zn+2ions in Matrix Metalloproteinase 13 of Human. J Biomol Struct Dyn 2011; 28:503-16. [DOI: 10.1080/07391102.2011.10508591] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Ramalho TC, da Cunha EF. Thermodynamic Framework of the Interaction between Protein and Solvent Drives Protein Folding. J Biomol Struct Dyn 2011; 28:645-6; discussion 669-674. [DOI: 10.1080/073911011010524975] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Florová P, Sklenovský P, Banáš P, Otyepka M. Explicit Water Models Affect the Specific Solvation and Dynamics of Unfolded Peptides While the Conformational Behavior and Flexibility of Folded Peptides Remain Intact. J Chem Theory Comput 2010; 6:3569-79. [PMID: 26617103 DOI: 10.1021/ct1003687] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Conventional molecular dynamics simulations on 50 ns to 1 μs time scales were used to study the effects of explicit solvent models on the conformational behavior and solvation of two oligopeptide solutes: α-helical EK-peptide (14 amino acids) and a β-hairpin chignolin (10 amino acids). The widely used AMBER force fields (ff99, ff99SB, and ff03) were combined with four of the most commonly used explicit solvent models (TIP3P, TIP4P, TIP5P, and SPC/E). Significant differences in the specific solvation of chignolin among the studied water models were identified. Chignolin was highly solvated in TIP5P, whereas reduced specific solvation was found in the TIP4P, SPC/E, and TIP3P models for kinetic, thermodynamic, and both kinetic and thermodynamic reasons, respectively. The differences in specific solvation did not influence the dynamics of structured parts of the folded peptide. However, substantial differences between TIP5P and the other models were observed in the dynamics of unfolded chignolin, stability of salt bridges, and specific solvation of the backbone carbonyls of EK-peptide. Thus, we conclude that the choice of water model may affect the dynamics of flexible parts of proteins that are solvent-exposed. On the other hand, all water models should perform similarly for well-structured folded protein regions. The merits of the TIP3P model include its high and overestimated mobility, which accelerates simulation processes and thus effectively increases sampling.
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Affiliation(s)
- Petra Florová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, tr. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Petr Sklenovský
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, tr. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, tr. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, tr. 17 listopadu 12, 771 46 Olomouc, Czech Republic
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