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Baruah I, Borgohain G. Structural and functional changes of the protein β-lactoglobulin under thermal and electrical processing conditions. Biophys Chem 2020; 267:106479. [PMID: 33027745 DOI: 10.1016/j.bpc.2020.106479] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 09/15/2020] [Accepted: 09/15/2020] [Indexed: 10/23/2022]
Abstract
In the present study we have tried to explore the effect of static external electric field of strength 3.0 V/nm on the conformational changes adopted by the protein β-lactoglobulin. We have chosen different temperatures viz. 300 K, 400 K and 450 K to evaluate the temperature dependent effect of electric field. We have observed that combined effect of high temperature and static external electric field show significant changes on the structural conformation of the protein which in turn may affect the functional properties of the protein. Calculations of root mean square deviations reveal that both helical and β-sheet regions of the protein are noticeably affected at high temperature. We have used solvent accessible surface area (SASA) and dipole moment values to explain that there is changes in hydrophobicity of the protein surface due to presence of external electric field. The study reveals that electric field in combination with high temperature can be used to alter the conformation of the protein and the effect of external electric field is more pronounced at high temperature than that of low temperature. The study provides a better understanding of the conformational changes adopted by the protein under the stress of external electric field and high temperature and provide guidance to choose optimum conditions for processing without loss of nutritional properties.
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Affiliation(s)
- Indrani Baruah
- Department of Chemistry, Cotton University, Guwahati, Assam 781001, India
| | - Gargi Borgohain
- Department of Chemistry, Cotton University, Guwahati, Assam 781001, India.
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2
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Barazorda-Ccahuana HL, Theiss-De-Rosso V, Valencia DE, Gómez B. Heat-Stable Hazelnut Profilin: Molecular Dynamics Simulations and Immunoinformatics Analysis. Polymers (Basel) 2020; 12:E1742. [PMID: 32764224 PMCID: PMC7464029 DOI: 10.3390/polym12081742] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 07/23/2020] [Accepted: 07/23/2020] [Indexed: 01/21/2023] Open
Abstract
Heat treatment can modify the allergenic potential, reducing allergenicity in specific proteins. Profilins are one of the important hazelnut allergens; these proteins are considered panallergens due to their high capacity for cross-reactivity with other allergens. In the present work, we evaluated the thermostability of hazelnut profilin, combining molecular dynamics simulation and immunoinformatic techniques. This approach helped us to have reliable results in immunogenicity studies. We modeled Cor a 2 profilin and applied annealing simulation, equilibrium, and production simulation at constant temperatures ranging from 300 to 500 K using Gromacs software. Despite the hazelnut profilins being able to withstand temperatures of up to 400 K, this does not seem to reduce its allergenicity. We have found that profilin subjected to temperatures of 450 and 500 K could generate cross-reactivity with other food allergens. In conclusion, we note a remarkable thermostability of Cor a 2 at 400 K which avoids its structural unfolding.
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Affiliation(s)
- Haruna L. Barazorda-Ccahuana
- Centro de Investigación en Ingeniería Molecular—CIIM, Vicerrectorado de Investigación, Universidad Católica de Santa María, Urb. San José s/n—Umacollo, Arequipa 04000, Peru; (D.E.V.); (B.G.)
| | | | - Diego Ernesto Valencia
- Centro de Investigación en Ingeniería Molecular—CIIM, Vicerrectorado de Investigación, Universidad Católica de Santa María, Urb. San José s/n—Umacollo, Arequipa 04000, Peru; (D.E.V.); (B.G.)
| | - Badhin Gómez
- Centro de Investigación en Ingeniería Molecular—CIIM, Vicerrectorado de Investigación, Universidad Católica de Santa María, Urb. San José s/n—Umacollo, Arequipa 04000, Peru; (D.E.V.); (B.G.)
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3
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Pandey B, Aarthy M, Sharma M, Singh SK, Kumar V. Computational analysis identifies druggable mutations in human rBAT mediated Cystinuria. J Biomol Struct Dyn 2020; 39:5058-5067. [PMID: 32602810 DOI: 10.1080/07391102.2020.1784792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Culex quinquefasciatus Cqm1 protein acts as the receptor for Lysinibacillus sphaericus mosquito-larvicidal binary (BinAB) toxin that is used worldwide for mosquito control. We found amino acid transporter protein, rBAT, as phylogenetically closest Cqm1 homolog in humans. The present study reveals large evolutionary distance between Cqm1 and rBAT, and rBAT ectodomain lacks the sequence motif which serves as binding-site for the BinAB toxin. Thus, BinAB toxin can be expected to remain safe for humans. rBAT (heavy subunit; SLC3A1) and catalytic b0,+AT (light subunit; SLC7A9), linked by single disulfide bond, mediate renal reabsorption of cystine and dibasic amino acids in Na+ independent manner. Mutations in rBAT cause type I Cystinuria disease which shows global prevalence, and rBAT can be thought as an important pharmacological target. However, 3D structures of rBAT and b0,+AT, the two components of b0,+ heteromeric amino acid transporter systems, are not available. We constructed a reliable homology model of rBAT using Cqm1 coordinates and that of transmembrane b0,+AT subunit using LAT1 coordinates. Mapping of pathogenic mutations onto rBAT ectodomain revealed their scattered distribution throughout the rBAT protein. Further, our computational simulations-based scoring of several known deleterious mutations of rBAT revealed that mutations those do not compromise the protein fold and stability, are localized on the same face of the molecule. These residues are expected to interact with the b0,+AT transporter. The present study thus identifies druggable sites on rBAT that could be targeted for the treatment of type I Cystinuria.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bharati Pandey
- Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Murali Aarthy
- Computer-aided drug design Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
| | - Mahima Sharma
- Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Sanjeev Kumar Singh
- Computer-aided drug design Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
| | - Vinay Kumar
- Homi Bhabha National Institute, Mumbai, India
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4
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Determinants of Thermostability in Serine Hydroxymethyltransferase Identified by Principal Component Analysis. Sci Rep 2017; 7:46463. [PMID: 28422151 PMCID: PMC5396068 DOI: 10.1038/srep46463] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 03/20/2017] [Indexed: 01/29/2023] Open
Abstract
Protein thermostability has received growing attention in recent years. Little is known about the determinants of thermal resistance in individual protein families. However, it is known that the mechanism is family-dependent and not identical for all proteins. We present a multivariate statistical analysis to find the determinants of thermostability in one protein family, the serine hydroxymethyltransferase family. Based on principal component analysis, we identified three amino acid fragments as the potential determinants of thermostability. The correlation coefficients between all the putative fragments and the protein thermostability were significant according to multivariable linear regression. Within the fragments, four critical amino acid positions were identified, and they indicated the contributions of Leu, Val, Lys, Asp, Glu, and Phe to thermostability. Moreover, we analyzed the insertions/deletions of amino acids in the sequence, which showed that thermophilic SHMTs tend to insert or delete residues in the C-terminal domain rather than the N-terminal domain. Our study provided a promising approach to perform a preliminary search for the determinants of thermophilic proteins. It could be extended to other protein families to explore their own strategies for adapting to high temperature.
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5
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Tych KM, Batchelor M, Hoffmann T, Wilson MC, Hughes ML, Paci E, Brockwell DJ, Dougan L. Differential Effects of Hydrophobic Core Packing Residues for Thermodynamic and Mechanical Stability of a Hyperthermophilic Protein. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:7392-7402. [PMID: 27338140 DOI: 10.1021/acs.langmuir.6b01550] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Proteins from organisms that have adapted to environmental extremes provide attractive systems to explore and determine the origins of protein stability. Improved hydrophobic core packing and decreased loop-length flexibility can increase the thermodynamic stability of proteins from hyperthermophilic organisms. However, their impact on protein mechanical stability is not known. Here, we use protein engineering, biophysical characterization, single-molecule force spectroscopy (SMFS), and molecular dynamics (MD) simulations to measure the effect of altering hydrophobic core packing on the stability of the cold shock protein TmCSP from the hyperthermophilic bacterium Thermotoga maritima. We make two variants of TmCSP in which a mutation is made to reduce the size of aliphatic groups from buried hydrophobic side chains. In the first, a mutation is introduced in a long loop (TmCSP L40A); in the other, the mutation is introduced on the C-terminal β-strand (TmCSP V62A). We use MD simulations to confirm that the mutant TmCSP L40A shows the most significant increase in loop flexibility, and mutant TmCSP V62A shows greater disruption to the core packing. We measure the thermodynamic stability (ΔGD-N) of the mutated proteins and show that there is a more significant reduction for TmCSP L40A (ΔΔG = 63%) than TmCSP V62A (ΔΔG = 47%), as might be expected on the basis of the relative reduction in the size of the side chain. By contrast, SMFS measures the mechanical stability (ΔG*) and shows a greater reduction for TmCSP V62A (ΔΔG* = 8.4%) than TmCSP L40A (ΔΔG* = 2.5%). While the impact on the mechanical stability is subtle, the results demonstrate the power of tuning noncovalent interactions to modulate both the thermodynamic and mechanical stability of a protein. Such understanding and control provide the opportunity to design proteins with optimized thermodynamic and mechanical properties.
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Affiliation(s)
- Katarzyna M Tych
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
| | - Matthew Batchelor
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
| | - Toni Hoffmann
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
| | - Michael C Wilson
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
| | - Megan L Hughes
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
| | - Emanuele Paci
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
| | - David J Brockwell
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
| | - Lorna Dougan
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
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6
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Zhang PP, Zhao L, Long SY, Tian P. The effect of ligands on the thermal stability of sulfotransferases: a molecular dynamics simulation study. J Mol Model 2015; 21:72. [PMID: 25750022 DOI: 10.1007/s00894-015-2625-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Accepted: 02/15/2015] [Indexed: 11/24/2022]
Abstract
Human cytosolic sulfotransferases (hSULTs) are important phase II metabolic enzymes. They catalyze transfer of the sulfuryl-group (-SO3) from 3'-phosphoadenosine 5'-phosphosulfate (PAPS) to the hydroxyl or primary amine moieties of a large number of endogenous and xenobiotic substrates. Broad selectivity and specificity of binding and activity within the sulfortransferases family could be detected by thermal denaturation assays, which have been made more and more suitable for high throughput screening based on recent technical advances. Here molecular dynamics simulations were used to explore the effect of the cofactor (PAPS) and substrate (LCA) on the thermal stability of the enzyme. It was found that the apo-enzyme unfolded fastest upon heating. The holo-enzyme with bound substrate LCA unfolded slowest. This thermo-denaturation order is consistent with that observed in experiments. Further it was found that the cofactor and substrate will pronouncedly increase the thermal stability of the active pocket regions that interact directly with the ligands. In addition, cofactor and substrate show noticeable synergy effect on the thermal stability of the enzyme.
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Affiliation(s)
- Pu-pu Zhang
- School of Life Sciences, Jilin University, Changchun, China
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7
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Li H, Xie Y, Liu C, Liu S. Physicochemical bases for protein folding, dynamics, and protein-ligand binding. SCIENCE CHINA-LIFE SCIENCES 2014; 57:287-302. [PMID: 24554472 DOI: 10.1007/s11427-014-4617-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 09/27/2013] [Indexed: 01/02/2023]
Abstract
Proteins are essential parts of living organisms and participate in virtually every process within cells. As the genomic sequences for increasing number of organisms are completed, research into how proteins can perform such a variety of functions has become much more intensive because the value of the genomic sequences relies on the accuracy of understanding the encoded gene products. Although the static three-dimensional structures of many proteins are known, the functions of proteins are ultimately governed by their dynamic characteristics, including the folding process, conformational fluctuations, molecular motions, and protein-ligand interactions. In this review, the physicochemical principles underlying these dynamic processes are discussed in depth based on the free energy landscape (FEL) theory. Questions of why and how proteins fold into their native conformational states, why proteins are inherently dynamic, and how their dynamic personalities govern protein functions are answered. This paper will contribute to the understanding of structure-function relationship of proteins in the post-genome era of life science research.
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Affiliation(s)
- HuiMin Li
- School of Mathematics and Computer Science, Yunnan University of Nationalities, Kunming, 650500, China
- Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of Ministry of Education, Yunnan University, Kunming, 650091, China
| | - YueHui Xie
- Teaching and Research Section of Computer, Department of Basic Medical, Kunming Medical University, Kunming, 650031, China
- Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of Ministry of Education, Yunnan University, Kunming, 650091, China
| | - CiQuan Liu
- Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of Ministry of Education, Yunnan University, Kunming, 650091, China
- Southwest Biological Diversity Laboratory, Kunming Branch of Chinese Academy of Sciences, Kunming, 650223, China
| | - ShuQun Liu
- Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of Ministry of Education, Yunnan University, Kunming, 650091, China.
- Southwest Biological Diversity Laboratory, Kunming Branch of Chinese Academy of Sciences, Kunming, 650223, China.
- Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, Kunming, 650091, China.
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8
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Chu WT, Zheng QC. Conformational changes of enzymes and DNA in molecular dynamics: influenced by pH, temperature, and ligand. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2013; 92:179-217. [PMID: 23954102 DOI: 10.1016/b978-0-12-411636-8.00005-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Protein conformation, which has been a research hotspot for human diseases, is an important factor of protein properties. Recently, a series of approaches have been utilized to investigate the conformational changes under different conditions. Some of them have gained promising achievements, but it is still deficient in the detail researches at the atomic level. In this chapter, a series of computational examples of protein conformational changes under different pH environment, temperature, and ligand binding are described. We further show some useful methods, such as constant pH molecular dynamics simulations, molecular docking, and molecular mechanics Poisson-Boltzmann surface area/generalized Born surface area calculations. In comparison with the experimental results, the methods mentioned above are reasonable to detect and predict the interaction between residue and residue, residue and DNA, and residue and ligand. Additionally, some crucial interactions that cause protein conformational changes are discovered and discussed in this chapter. In summary, our work can give penetrating information to understand the pH-, temperature-, and ligand-induced conformational change mechanisms.
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Affiliation(s)
- Wen-Ting Chu
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, PR China
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9
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Molecular dynamics simulation of temperature induced unfolding of animal prion protein. J Mol Model 2013; 19:4433-41. [DOI: 10.1007/s00894-013-1955-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Accepted: 07/22/2013] [Indexed: 01/22/2023]
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10
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Chin IS, Murad AMA, Mahadi NM, Nathan S, Bakar FDA. Thermal stability engineering of Glomerella cingulata cutinase. Protein Eng Des Sel 2013; 26:369-75. [DOI: 10.1093/protein/gzt007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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11
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Chen L, Zhang JL, Yu LY, Zheng QC, Chu WT, Xue Q, Zhang HX, Sun CC. Influence of hyperthermophilic protein Cren7 on the stability and conformation of DNA: insights from molecular dynamics simulation and free energy analysis. J Phys Chem B 2012; 116:12415-25. [PMID: 23013198 DOI: 10.1021/jp305860h] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cren7, a novel chromatin protein highly conserved among crenarchaea, plays an important role in genome packaging and gene regulation. However, the detail dynamical structural characteristic of the Cren7-DNA complex and the detail study of the DNA in the complex have not been done. Focused on two specific Cren7-DNA complexes (PDB codes 3LWH and 3LWI ), we applied molecular dynamics (MD) simulations at four different temperatures (300, 350, 400, and 450 K) and the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) free energy calculation at 300 and 350 K to examine the role of Cren7 protein in enhancing the stability of DNA duplexes via protein-DNA interactions, and to study the structural transition in DNA. The simulation results indicate that Cren7 stabilizes DNA duplex in a certain temperature range in the binary complex compared with the unbound DNA molecules. At the same time, DNA molecules were found to undergo B-like to A-like form transitions with increased temperature. The results of statistical analyses of the H-bond and hydrophobic contacts show that some residues have significant influence on the structure of DNA molecules. Our work can give important information to understand the interactions of proteins with nucleic acids and other ligands.
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Affiliation(s)
- Lin Chen
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, People's Republic of China
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12
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Li CH, Zuo ZC, Su JG, Xu XJ, Wang CX. The interactions and recognition of cyclic peptide mimetics of Tat with HIV-1 TAR RNA: a molecular dynamics simulation study. J Biomol Struct Dyn 2012; 31:276-87. [PMID: 22943434 DOI: 10.1080/07391102.2012.698248] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The interaction of HIV-1 trans-activator protein Tat with its cognate trans-activation response element (TAR) RNA is critical for viral transcription and replication. Therefore, it has long been considered as an attractive target for the development of antiviral compounds. Recently, the conformationally constrained cyclic peptide mimetics of Tat have been tested to be a promising family of lead peptides. Here, we focused on two representative cyclic peptides termed as L-22 and KP-Z-41, both of which exhibit excellent inhibitory potency against Tat and TAR interaction. By means of molecular dynamics simulations, we obtained a detailed picture of the interactions between them and HIV-1 TAR RNA. In results, it is found that the binding modes of the two cyclic peptides to TAR RNA are almost identical at or near the bulge regions, whereas the binding interfaces at the apical loop exhibit large conformational heterogeneity. In addition, it is revealed that electrostatic interaction energy contributes much more to KP-Z-41 complex formation than to L-22 complex, which is the main source of energy that results in a higher binding affinity of KP-Z-41 over-22 for TAR RNA. Furthermore, we identified a conserved motif RRK (Arg-Arg-Lys) that is shown to be essential for specific binding of this class of cyclic peptides to TAR RNA. This work can provide a useful insight into the design and modification of cyclic peptide inhibitors targeting the association of HIV-1 Tat and TAR RNA.
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Affiliation(s)
- Chun Hua Li
- College of Life Science and Bioengineering, Beijing University of Technology, Pingleyuan 100, Chaoyang District, Beijing 100124, China.
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13
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Hu JP, He HQ, Tang DY, Sun GF, Zhang YQ, Fan J, Chang S. Study on the interactions between diketo-acid inhibitors and prototype foamy virus integrase-DNA complex via molecular docking and comparative molecular dynamics simulation methods. J Biomol Struct Dyn 2012; 31:734-47. [PMID: 22913375 DOI: 10.1080/07391102.2012.709458] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Human immunodeficiency virus type 1 (HIV-1) integrase (IN) is an important drug target for anti-acquired immune deficiency disease (AIDS) treatment and diketo-acid (DKA) inhibitors are potent and selective inhibitors of HIV-1 IN. Due to lack of three-dimensional structures including detail interactions between HIV-1 IN and its substrate viral DNA, the drug design and screening platform remains incompleteness and deficient. In addition, the action mechanism of DKA inhibitors with HIV-1 IN is not well understood. In view of the high homology between the structure of prototype foamy virus (PFV) IN and that of HIV-1 IN, we used PFV IN as a surrogate model for HIV-1 IN to investigate the inhibitory mechanism of raltegravir (RLV) and the binding modes with a series of DKA inhibitors. Firstly, molecular dynamics simulations of PFV IN, IN-RLV, IN-DNA, and IN-DNA-RLV systems were performed for 10 ns each. The interactions and inhibitory mechanism of RLV to PFV IN were explored through overall dynamics behaviors, catalytic loop conformation distribution, and hydrogen bond network analysis. The results show that the coordinated interactions of RLV with IN and viral DNA slightly reduce the flexibility of catalytic loop region of IN, and remarkably restrict the mobility of the CA end of viral DNA, which may lead to the partial loss of the inhibitory activity of IN. Then, we docked a series of DKA inhibitors into PFV IN-DNA receptor and obtained the IN-DNA-inhibitor complexes. The docking results between PFV IN-DNA and DKA inhibitors agree well with the corresponding complex of HIV-1 IN, which proves the dependability of PFV IN-DNA used for the anti-AIDS drug screening. Our study may help to make clear some theoretical questions and to design anti-AIDS drug based on the structure of IN.
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Affiliation(s)
- Jian-Ping Hu
- Department of Chemistry and Life Science, Leshan Normal University, Leshan, China.
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14
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Misra N, Patra MC, Panda PK, Sukla LB, Mishra BK. Homology modeling and docking studies of FabH (β-ketoacyl-ACP synthase III) enzyme involved in type II fatty acid biosynthesis of Chlorella variabilis: a potential algal feedstock for biofuel production. J Biomol Struct Dyn 2012; 31:241-57. [PMID: 22830394 DOI: 10.1080/07391102.2012.698247] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The concept of using microalgae as an alternative renewable source of biofuel has gained much importance in recent years. However, its commercial feasibility is still an area of concern for researchers. Unraveling the fatty acid metabolic pathway and understanding structural features of various key enzymes regulating the process will provide valuable insights to target microalgae for augmented oil content. FabH (β-ketoacyl-acyl carrier protein synthase; KAS III) is a condensing enzyme catalyzing the initial elongation step of type II fatty acid biosynthetic process and acyl carrier protein (ACP) facilitates the shuttling of the fatty acyl intermediates to the active site of the respective enzymes in the pathway. In the present study, a reliable three-dimensional structure of FabH from Chlorella variabilis, an oleaginous green microalga was modeled and subsequently the key residues involved in substrate binding were determined by employing protein-protein docking and molecular dynamics (MD) simulation protocols. The FabH-ACP complex having the lowest docking energy score showed the binding of ACP to the electropositive FabH surface with strong hydrogen bond interactions. The MD simulation results indicated that the substrate-complexed FabH adopted a more stable conformation than the free enzyme. Further, the FabH structure retained its stability throughout the simulation although noticeable displacements were observed in the loop regions. Molecular simulation studies suggested the importance of crucial hydrogen bonding of the conserved Arg(91) of FabH with Glu(53) and Asp(56) of ACP for exhibiting high affinity between the enzyme and substrate. The molecular modeling results are consistent with available experimental results on the flexibility of FabH and the present study provides first in silico insights into the structural and dynamical aspect of catalytic mechanism of FabH, which could be used for further site-specific mutagenic experiments to develop engineered high oil-yielding microalgal strains for biofuel production.
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Affiliation(s)
- Namrata Misra
- Bioresources Engineering Department, CSIR-Institute of Minerals and Materials Technology, Bhubaneswar, 751 013 Odisha, India
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15
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Liu M, Wang S, Sun T, Su J, Zhang Y, Yue J, Sun Z. Insight into the structure, dynamics and the unfolding property of amylosucrases: implications of rational engineering on thermostability. PLoS One 2012; 7:e40441. [PMID: 22792323 PMCID: PMC3391273 DOI: 10.1371/journal.pone.0040441] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Accepted: 06/07/2012] [Indexed: 11/19/2022] Open
Abstract
Amylosucrase (AS) is a kind of glucosyltransferases (E.C. 2.4.1.4) belonging to the Glycoside Hydrolase (GH) Family 13. In the presence of an activator polymer, in vitro, AS is able to catalyze the synthesis of an amylose-like polysaccharide composed of only α-1,4-linkages using sucrose as the only energy source. Unlike AS, other enzymes responsible for the synthesis of such amylose-like polymers require the addition of expensive nucleotide-activated sugars. These properties make AS an interesting enzyme for industrial applications. In this work, the structures and topology of the two AS were thoroughly investigated for the sake of explaining the reason why Deinococcus geothermalis amylosucrase (DgAS) is more stable than Neisseria polysaccharea amylosucrase (NpAS). Based on our results, there are two main factors that contribute to the superior thermostability of DgAS. On the one hand, DgAS holds some good structural features that may make positive contributions to the thermostability. On the other hand, the contacts among residues of DgAS are thought to be topologically more compact than those of NpAS. Furthermore, the dynamics and unfolding properties of the two AS were also explored by the gauss network model (GNM) and the anisotropic network model (ANM). According to the results of GNM and ANM, we have found that the two AS could exhibit a shear-like motion, which is probably associated with their functions. What is more, with the discovery of the unfolding pathway of the two AS, we can focus on the weak regions, and hence designing more appropriate mutations for the sake of thermostability engineering. Taking the results on structure, dynamics and unfolding properties of the two AS into consideration, we have predicted some novel mutants whose thermostability is possibly elevated, and hopefully these discoveries can be used as guides for our future work on rational design.
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Affiliation(s)
- Ming Liu
- Beijing Institute of Biotechnology, Beijing, China
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Genor Biopharma Co., Ltd, Shanghai, China
| | - Shuang Wang
- Beijing Institute of Biotechnology, Beijing, China
| | - Tingguang Sun
- Department of Biological and Chemical Engineering, Guangxi University of Technology, Liuzhou, China
| | - Jiguo Su
- College of Science, Yanshan University, Qinhuangdao, China
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- * E-mail: (ZS) (YZ); (JY) (JY); (YZ) (ZS)
| | - Junjie Yue
- Beijing Institute of Biotechnology, Beijing, China
- * E-mail: (ZS) (YZ); (JY) (JY); (YZ) (ZS)
| | - Zhiwei Sun
- Beijing Institute of Biotechnology, Beijing, China
- * E-mail: (ZS) (YZ); (JY) (JY); (YZ) (ZS)
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16
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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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17
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Chang S, He HQ, Hu JP, Jiao X, Tian XH. Network models reveal stability and structural rearrangement of signal recognition particle. J Biomol Struct Dyn 2012; 30:150-9. [PMID: 22702726 DOI: 10.1080/07391102.2012.677765] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The signal recognition particle (SRP) and its receptors (SR) mediate the cotranslational targeting of the membrane and secretory proteins in all cells. In Escherichia coli, SRP is composed of the Ffh protein and the 4.5S SRP RNA. Ffh is a multidomain protein comprising a methionine-rich (M) domain, a helical N domain, and a Ras-like guanine triphosphatase (GTPase) (G) domain. The N and G domains are commonly referred to as one structural unit, the NG domain. In this article, the complex structure of SRP and SR is investigated with the Gaussian network model (GNM) and anisotropic network model (ANM). GNM provides the information of structure stability. It is found that the intermolecular interactions between SRP and SR can obviously decrease the fluctuation of NG domains. Nevertheless, the large structural rearrangement will take place during the cotranslational protein targeting cycle. Hence, the moving directions of fluctuation regions are further ascertained by using cross-correlation analysis and the ANM. The NG domain of Ffh undergoes a clockwise rotation around the GM linker and the M domain of Ffh shows an opposite direction to the NG domain. These functional movements will facilitate the SRP structure to transform into the free form and the sequence-bound form. These simple coarse-grained analyses can be used as a general and quick method for the mechanism studies of protein assembly and supramolecular systems.
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Affiliation(s)
- Shan Chang
- College of Informatics, South China Agricultural University, Guangzhou, 510642, China.
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18
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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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19
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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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20
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Hamza A, Wei NN, Johnson-Scalise T, Naftolin F, Cho H, Zhan CG. Unveiling the Unfolding Pathway of F5F8D Disorder-Associated D81H/V100D Mutant of MCFD2viaMultiple Molecular Dynamics Simulations. J Biomol Struct Dyn 2012; 29:699-714. [DOI: 10.1080/07391102.2012.10507410] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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21
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Ramakrishnan V, Jagannathan S, Shaikh AR, Rajagopalan R. Dynamic and Structural Changes in the Minimally Restructuring EcoRI Bound to a Minimally Mutated DNA Chain. J Biomol Struct Dyn 2012; 29:743-56. [DOI: 10.1080/073911012010525020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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