51
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Chen KC, Sun MF, Yang SC, Chang SS, Chen HY, Tsai FJ, Chen CYC. Investigation into potent inflammation inhibitors from traditional Chinese medicine. Chem Biol Drug Des 2011; 78:679-88. [PMID: 21801310 DOI: 10.1111/j.1747-0285.2011.01202.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Microsomal prostaglandin E synthase-1 (mPGES-1) is the key enzyme for prostaglandin E2 (PGE2) generation during inflammation and is a potential target for designing anti-inflammatory drugs. Potential inhibitors of m-PGES-1 were selected from traditional Chinese medicine (TCM Database@Taiwan) based on the pharmacophore map generated by the top HypoGen hypothesis and validated using structure- and ligand-based analysis. Key features for potential m-PGES-1 inhibitors include pi-interactions and H-bond donors. TCM compounds, shanciol B, shanciol A, castilliferol, and aurantiamide acetate, contoured to the quantitative structure-activity relationship pharmacophore and exhibited high docking scores and binding stability with m-PGES-1. Bioactivity models multiple linear regression (MLR) and support vector machine also supported activity predictions for the candidate compounds. Our results indicate that the investigated TCM compounds could be of use for development into mPGES-1 inhibitors.
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Affiliation(s)
- Kuan-Chung Chen
- Laboratory of Computational and Systems Biology, School of Chinese Medicine, China Medical University, Taichung 40402, Taiwan
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52
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Havelka D, Cifra M, Kučera O, Pokorný J, Vrba J. High-frequency electric field and radiation characteristics of cellular microtubule network. J Theor Biol 2011; 286:31-40. [PMID: 21782830 DOI: 10.1016/j.jtbi.2011.07.007] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2011] [Revised: 07/10/2011] [Accepted: 07/11/2011] [Indexed: 01/11/2023]
Abstract
Microtubules are important structures in the cytoskeleton, which organizes the cell. Since microtubules are electrically polar, certain microtubule normal vibration modes efficiently generate oscillating electric field. This oscillating field may be important for the intracellular organization and intercellular interaction. There are experiments which indicate electrodynamic activity of variety of cells in the frequency region from kHz to GHz, expecting the microtubules to be the source of this activity. In this paper, results from the calculation of intensity of electric field and of radiated electromagnetic power from the whole cellular microtubule network are presented. The subunits of microtubule (tubulin heterodimers) are approximated by elementary electric dipoles. Mechanical oscillation of microtubule is represented by the spatial function which modulates the dipole moment of subunits. The field around oscillating microtubules is calculated as a vector superposition of contributions from all modulated elementary electric dipoles which comprise the cellular microtubule network. The electromagnetic radiation and field characteristics of the whole cellular microtubule network have not been theoretically analyzed before. For the perspective experimental studies, the results indicate that macroscopic detection system (antenna) is not suitable for measurement of cellular electrodynamic activity in the radiofrequency region since the radiation rate from single cells is very low (lower than 10⁻²⁰ W). Low noise nanoscopic detection methods with high spatial resolution which enable measurement in the cell vicinity are desirable in order to measure cellular electrodynamic activity reliably.
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Affiliation(s)
- D Havelka
- Department of Electromagnetic Field, Faculty of Electrical Engineering, Czech Technical University in Prague, Czech Republic.
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53
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Yao Y, Zhang T, Xiong Y, Li L, Huo J, Wei DQ. Mutation probability of cytochrome P450 based on a genetic algorithm and support vector machine. Biotechnol J 2011; 6:1367-76. [DOI: 10.1002/biot.201000450] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Revised: 02/21/2011] [Accepted: 04/20/2011] [Indexed: 11/08/2022]
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54
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Roterman I, Konieczny L, Jurkowski W, Prymula K, Banach M. Two-intermediate model to characterize the structure of fast-folding proteins. J Theor Biol 2011; 283:60-70. [PMID: 21635900 DOI: 10.1016/j.jtbi.2011.05.027] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2010] [Revised: 05/17/2011] [Accepted: 05/18/2011] [Indexed: 01/15/2023]
Abstract
This paper introduces a new model that enables researchers to conduct protein folding simulations. A two-step in silico process is used in the course of structural analysis of a set of fast-folding proteins. The model assumes an early stage (ES) that depends solely on the backbone conformation, as described by its geometrical properties--specifically, by the V-angle between two sequential peptide bond planes (which determines the radius of curvature, also called R-radius, according to a second-degree polynomial form). The agreement between the structure under consideration and the assumed model is measured in terms of the magnitude of dispersion of both parameters with respect to idealized values. The second step, called late-stage folding (LS), is based on the "fuzzy oil drop" model, which involves an external hydrophobic force field described by a three-dimensional Gauss function. The degree of conformance between the structure under consideration and its idealized model is expressed quantitatively by means of the Kullback-Leibler entropy, which is a measure of disparity between the observed and expected hydrophobicity distributions. A set of proteins, representative of the fast-folding group - specifically, cold shock proteins - is shown to agree with the proposed model.
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Affiliation(s)
- I Roterman
- Department of Bioinformatics and Telemedicine, Jagiellonian University-Medical College, Lazarza 16, 31-530 Krakow, Poland.
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55
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Lian P, Wei DQ, Wang JF, Chou KC. An allosteric mechanism inferred from molecular dynamics simulations on phospholamban pentamer in lipid membranes. PLoS One 2011; 6:e18587. [PMID: 21525996 PMCID: PMC3078132 DOI: 10.1371/journal.pone.0018587] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2010] [Accepted: 03/10/2011] [Indexed: 11/18/2022] Open
Abstract
Phospholamban functions as a regulator of Ca(2+) concentration of cardiac muscle cells by triggering the bioactivity of sarcoplasmic reticulum Ca(2+)-ATPase. In order to understand its dynamic mechanism in the environment of bilayer surroundings, we performed long time-scale molecular dynamic simulations based on the high-resolution NMR structure of phospholamban pentamer. It was observed from the molecular dynamics trajectory analyses that the conformational transitions between the "bellflower" and "pinwheel" modes were detected for phospholamban. Particularly, the two modes became quite similar to each other after phospholamban was phosphorylated at Ser16. Based on these findings, an allosteric mechanism was proposed to elucidate the dynamic process of phospholamban interacting with Ca(2+)-ATPase.
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Affiliation(s)
- Peng Lian
- College of Life Science and Biotechnology and Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of Systems Biomedicine, Ministry of Education, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Dong-Qing Wei
- College of Life Science and Biotechnology and Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
- Gordon Life Science Institute, San Diego, California, United States of America
- * E-mail: (DQW); (JFW)
| | - Jing-Fang Wang
- Key Laboratory of Systems Biomedicine, Ministry of Education, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Center for Bioinformation and Technology, Shanghai, China
- * E-mail: (DQW); (JFW)
| | - Kuo-Chen Chou
- Gordon Life Science Institute, San Diego, California, United States of America
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56
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Wang JF, Chou KC. Insights from modeling the 3D structure of New Delhi metallo-β-lactamse and its binding interactions with antibiotic drugs. PLoS One 2011; 6:e18414. [PMID: 21494599 PMCID: PMC3073942 DOI: 10.1371/journal.pone.0018414] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Accepted: 03/04/2011] [Indexed: 11/18/2022] Open
Abstract
New Delhi metallo-beta-lactamase (NDM-1) is an enzyme that makes bacteria resistant to a broad range of beta-lactam antibiotic drugs. This is because it can inactivate most beta-lactam antibiotic drugs by hydrolyzing them. For in-depth understanding of the hydrolysis mechanism, the three-dimensional structure of NDM-1 was developed. With such a structural frame, two enzyme-ligand complexes were derived by respectively docking Imipenem and Meropenem (two typical beta-lactam antibiotic drugs) to the NDM-1 receptor. It was revealed from the NDM-1/Imipenem complex that the antibiotic drug was hydrolyzed while sitting in a binding pocket of NDM-1 formed by nine residues. And for the case of NDM-1/Meropenem complex, the antibiotic drug was hydrolyzed in a binding pocket formed by twelve residues. All these constituent residues of the two binding pockets were explicitly defined and graphically labeled. It is anticipated that the findings reported here may provide useful insights for developing new antibiotic drugs to overcome the resistance problem.
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Affiliation(s)
- Jing-Fang Wang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Center for Bioinformation and Technology, Shanghai, China
- Gordon Life Science Institute, San Diego, California, United States of America
- * E-mail: (J-FW); (K-CC)
| | - Kuo-Chen Chou
- Gordon Life Science Institute, San Diego, California, United States of America
- * E-mail: (J-FW); (K-CC)
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57
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Zhang J. Comparison studies of the structural stability of rabbit prion protein with human and mouse prion proteins. J Theor Biol 2011; 269:88-95. [DOI: 10.1016/j.jtbi.2010.10.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2010] [Revised: 09/07/2010] [Accepted: 10/15/2010] [Indexed: 11/16/2022]
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58
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Wang Y, Wei DQ, Wang JF. Molecular dynamics studies on T1 lipase: insight into a double-flap mechanism. J Chem Inf Model 2010; 50:875-8. [PMID: 20443585 DOI: 10.1021/ci900458u] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
T1 lipase is isolated from the palm Geobacillus zalihae strain T1 in Malaysia, functioning as a secreted protein responsible for the catalyzing hydrolysis of long-chain triglycerides into fatty acids and glycerol at high temperatures. In the current study, using 30 ns molecular dynamics simulations at different temperatures, an aqueous activation was detected for T1 lipase. This aqueous activation in T1 lipase was mainly caused by a double-flap movement mechanism. The double flaps were constituted by the hydrophobic helices 6 and 9. Helix 6 employed two major components with the hydrophilic part at the surface and the hydrophobic part inside. In the aqueous solution, the hydrophobic part could provide enough power for helix 6 to move away, driving the protein into an open configuration and exposing the catalytic triad. Our findings could provide structural evidence to support the double-flap movement, revealing the catalytic mechanism for T1 lipase.
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Affiliation(s)
- Ying Wang
- College of Life Science and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China
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59
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Gu H, Chen H, Wei D, Wang J. Molecular dynamics simulations exploring drug resistance in HIV-1 proteases. ACTA ACUST UNITED AC 2010. [DOI: 10.1007/s11434-010-3257-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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60
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Wang JF, Chou KC. Insights from studying the mutation-induced allostery in the M2 proton channel by molecular dynamics. Protein Eng Des Sel 2010; 23:663-6. [PMID: 20571121 DOI: 10.1093/protein/gzq040] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
As an essential component of the viral envelope, M2 proton channel plays a central role in the virus replications and has been a key target for drug design against the influenza A viruses. The adamantadine-based drugs, such as amantadine and rimantadine, were developed for blocking the channel so as to suppress the replication of viruses. However, patients, especially those infected by the H1N1 influenza A viruses, are increasingly suffering from the drug-resistance problem. According to the findings revealed recently by the high-resolution NMR studies, the drug-resistance problem is due to the structural allostery caused by some mutations, such as L26F, V27A and S31N, in the four-helix bundle of the channel. In this study, we are to address this problem from a dynamic point of view by conducting molecular dynamics (MD) simulations on both the open and the closed states of the wild-type (WT) and S31N mutant M2 channels in the presence of rimantadine. It was observed from the MD simulated structures that the mutant channel could still keep open even if binding with rimantadine, but the WT channel could not. This was because the mutation would destabilize the helix bundle and trigger it from a compact packing state to a loose one. It is anticipated that the findings may provide useful insights for in-depth understanding the action mechanism of the M2 channel and developing more-effective drugs against influenza A viruses.
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Affiliation(s)
- Jing-Fang Wang
- Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, 800 Dongchuan, Shanghai 200240, China.
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61
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Huang T, Shi XH, Wang P, He Z, Feng KY, Hu L, Kong X, Li YX, Cai YD, Chou KC. Analysis and prediction of the metabolic stability of proteins based on their sequential features, subcellular locations and interaction networks. PLoS One 2010; 5:e10972. [PMID: 20532046 PMCID: PMC2881046 DOI: 10.1371/journal.pone.0010972] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Accepted: 05/14/2010] [Indexed: 11/19/2022] Open
Abstract
The metabolic stability is a very important idiosyncracy of proteins that is related to their global flexibility, intramolecular fluctuations, various internal dynamic processes, as well as many marvelous biological functions. Determination of protein's metabolic stability would provide us with useful information for in-depth understanding of the dynamic action mechanisms of proteins. Although several experimental methods have been developed to measure protein's metabolic stability, they are time-consuming and more expensive. Reported in this paper is a computational method, which is featured by (1) integrating various properties of proteins, such as biochemical and physicochemical properties, subcellular locations, network properties and protein complex property, (2) using the mRMR (Maximum Relevance & Minimum Redundancy) principle and the IFS (Incremental Feature Selection) procedure to optimize the prediction engine, and (3) being able to identify proteins among the four types: “short”, “medium”, “long”, and “extra-long” half-life spans. It was revealed through our analysis that the following seven characters played major roles in determining the stability of proteins: (1) KEGG enrichment scores of the protein and its neighbors in network, (2) subcellular locations, (3) polarity, (4) amino acids composition, (5) hydrophobicity, (6) secondary structure propensity, and (7) the number of protein complexes the protein involved. It was observed that there was an intriguing correlation between the predicted metabolic stability of some proteins and the real half-life of the drugs designed to target them. These findings might provide useful insights for designing protein-stability-relevant drugs. The computational method can also be used as a large-scale tool for annotating the metabolic stability for the avalanche of protein sequences generated in the post-genomic age.
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Affiliation(s)
- Tao Huang
- Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
- Shanghai Center for Bioinformation Technology, Shanghai, People's Republic of China
| | - Xiao-He Shi
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Ping Wang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Zhisong He
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Kai-Yan Feng
- Shanghai Center for Bioinformation Technology, Shanghai, People's Republic of China
| | - LeLe Hu
- Institute of Systems Biology, Shanghai University, Shanghai, People's Republic of China
| | - Xiangyin Kong
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
- State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiaotong University, Shanghai, People's Republic of China
- * E-mail: (XYK); (YXL); (YDC); (KCC)
| | - Yi-Xue Li
- Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
- Shanghai Center for Bioinformation Technology, Shanghai, People's Republic of China
- * E-mail: (XYK); (YXL); (YDC); (KCC)
| | - Yu-Dong Cai
- Institute of Systems Biology, Shanghai University, Shanghai, People's Republic of China
- Centre for Computational Systems Biology, Fudan University, Shanghai, People's Republic of China
- Gordon Life Science Institute, San Diego, California, United States of America
- * E-mail: (XYK); (YXL); (YDC); (KCC)
| | - Kuo-Chen Chou
- Gordon Life Science Institute, San Diego, California, United States of America
- * E-mail: (XYK); (YXL); (YDC); (KCC)
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62
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Zhang J. Studies on the structural stability of rabbit prion probed by molecular dynamics simulations of its wild-type and mutants. J Theor Biol 2010; 264:119-22. [PMID: 20109469 DOI: 10.1016/j.jtbi.2010.01.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2009] [Revised: 01/08/2010] [Accepted: 01/19/2010] [Indexed: 10/19/2022]
Abstract
Prion diseases are invariably fatal and highly infectious neurodegenerative diseases that affect humans and animals. Rabbits are the only mammalian species reported to be resistant to infection from prion diseases isolated from other species (Vorberg et al., 2003). Fortunately, the NMR structure of rabbit prion (124-228) (PDB entry 2FJ3), the NMR structure of rabbit prion protein mutation S173N (PDB entry 2JOH) and the NMR structure of rabbit prion protein mutation I214V (PDB entry 2JOM) were released recently. This paper studies these NMR structures by molecular dynamics simulations. Simulation results confirm the structural stability of wild-type rabbit prion, and show that the salt bridge between D177 and R163 greatly contributes to the structural stability of rabbit prion protein.
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Affiliation(s)
- Jiapu Zhang
- Victorian Life Sciences Computation Initiative, The University of Melbourne, 1 Hull Road, Croydon, VIC 3136, Australia.
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