101
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Schummel PH, Gao M, Winter R. Modulation of the Polymerization Kinetics of α/β-Tubulin by Osmolytes and Macromolecular Crowding. Chemphyschem 2016; 18:189-197. [DOI: 10.1002/cphc.201601032] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Indexed: 12/30/2022]
Affiliation(s)
- Paul Hendrik Schummel
- Faculty of Chemistry and Chemical Biology, Physical Chemistry-Biophysical Chemistry; TU Dortmund University; Otto-Hahn-Str. 4a 44227 Dortmund Germany
| | - Mimi Gao
- Faculty of Chemistry and Chemical Biology, Physical Chemistry-Biophysical Chemistry; TU Dortmund University; Otto-Hahn-Str. 4a 44227 Dortmund Germany
| | - Roland Winter
- Faculty of Chemistry and Chemical Biology, Physical Chemistry-Biophysical Chemistry; TU Dortmund University; Otto-Hahn-Str. 4a 44227 Dortmund Germany
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102
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Son I, Chalikian TV. Volumetrically Derived Thermodynamic Profile of Interactions of Urea with a Native Protein. Biochemistry 2016; 55:6475-6483. [PMID: 27933780 DOI: 10.1021/acs.biochem.6b00805] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ikbae Son
- Department of Pharmaceutical
Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Tigran V. Chalikian
- Department of Pharmaceutical
Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
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103
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Matubayasi N. Free-energy analysis of protein solvation with all-atom molecular dynamics simulation combined with a theory of solutions. Curr Opin Struct Biol 2016; 43:45-54. [PMID: 27835803 DOI: 10.1016/j.sbi.2016.10.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 10/07/2016] [Indexed: 11/25/2022]
Abstract
The structure of a protein is strongly influenced by solvation. In the present review, the solvation effect is treated within the framework of statistical thermodynamics. The key quantity is the solvation free energy of protein and a fast method for its computation with explicit solvent is introduced. The applications of the method to the structural fluctuation of protein in water, structure determination of protein-protein complex, and urea effect on protein structure are then described, and the roles of solvent water and cosolvent are discussed from the standpoint of energetics.
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Affiliation(s)
- Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan; Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto 615-8520, Japan.
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104
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E Lacerda RR, do Nascimento ES, de Lacerda JTJG, Pinto LDS, Rizzi C, Bezerra MM, Pinto IR, Filho SMP, Pinto VDPT, Filho GC, Gadelha CADA, Gadelha TS. Lectin from seeds of a Brazilian lima bean variety (Phaseolus lunatus L. var. cascavel) presents antioxidant, antitumour and gastroprotective activities. Int J Biol Macromol 2016; 95:1072-1081. [PMID: 27984144 DOI: 10.1016/j.ijbiomac.2016.10.097] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 09/28/2016] [Accepted: 10/27/2016] [Indexed: 12/29/2022]
Abstract
Lectins are proteins able to interact specifically and reversibly with carbohydrates. They are present in all living beings, particularly in legume seeds, which have many biological functions. The aim of this study was to isolate, characterize and verify antioxidant, anti-hemolytic, antitumor and gastroprotective activities in a lectin present in seeds of Phaseolus lunatus L. var. cascavel (PLUN). The isolation of lectin was performed by size exclusion chromatography on Sephadex G-100, which was isolated from a protein capable of agglutinating only human erythrocytes type A, being this the only inhibited haemagglutination n-acetyl-d-galactosamine. Its weight was estimated by PAGE is 128kDa. The lectin is thermostable up to 80°C and is active between pH 2-11. As 8M urea was able to denature the lectin. PLUN is a glycoprotein consisting of 2% carbohydrate and has antioxidant action with ascorbic acid equivalent antioxidant capacity (μMAA/g) of 418.20, 326 and 82.9 for total antioxidant activity, ABTS radical capture and capture of DPPH radical, respectively. The lectin has antitumor activity against melanoma derived cells at doses of 100 and 50mg/ml, reducing up to 83% tumor cells, and gastroprotective action, reducing up to 63% damaged area of the stomach induced by ethanol.
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Affiliation(s)
- Rodrigo Rodrigues E Lacerda
- Master by the Graduate Programme in Cellular and Molecular Biology at the Federal University of Paraíba (Universidade Federal da Paraíba), João Pessoa, Brazil.
| | | | | | | | - Caroline Rizzi
- Federal University of Pelotas (Universidade Federal de Pelotas), Pelotas, Brazil.
| | | | | | | | | | | | | | - Tatiane Santi Gadelha
- Federal University of Paraíba (Universidade Federal da Paraíba), João Pessoa, Brazil.
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105
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Molecular basis of the osmolyte effect on protein stability: a lesson from the mechanical unfolding of lysozyme. Biochem J 2016; 473:3705-3724. [DOI: 10.1042/bcj20160604] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 08/16/2016] [Indexed: 01/08/2023]
Abstract
Osmolytes are a class of small organic molecules that shift the protein folding equilibrium. For this reason, they are accumulated by organisms under environmental stress and find applications in biotechnology where proteins need to be stabilized or dissolved. However, despite years of research, debate continues over the exact mechanisms underpinning the stabilizing and denaturing effect of osmolytes. Here, we simulated the mechanical denaturation of lysozyme in different solvent conditions to study the molecular mechanism by which two biologically relevant osmolytes, denaturing (urea) and stabilizing (betaine), affect the folding equilibrium. We found that urea interacts favorably with all types of residues via both hydrogen bonds and dispersion forces, and therefore accumulates in a diffuse solvation shell around the protein. This not only provides an enthalpic stabilization of the unfolded state, but also weakens the hydrophobic effect, as hydrophobic forces promote the association of urea with nonpolar residues, facilitating the unfolding. In contrast, we observed that betaine is excluded from the protein backbone and nonpolar side chains, but is accumulated near the basic residues, yielding a nonuniform distribution of betaine molecules at the protein surface. Spatially resolved solvent–protein interaction energies further suggested that betaine behaves in a ligand- rather than solvent-like manner and its exclusion from the protein surface arises mostly from the scarcity of favorable binding sites. Finally, we found that, in the presence of betaine, the reduced ability of water molecules to solvate the protein results in an additional enthalpic contribution to the betaine-induced stabilization.
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106
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Borgohain G, Paul S. Temperature-mediated switching of protectant-denaturant behavior of trimethylamine-N-oxide and consequences on protein stability from a replica exchange molecular dynamics simulation study. MOLECULAR SIMULATION 2016. [DOI: 10.1080/08927022.2016.1233546] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Gargi Borgohain
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, India
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, India
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107
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Zheng W, Borgia A, Buholzer K, Grishaev A, Schuler B, Best RB. Probing the Action of Chemical Denaturant on an Intrinsically Disordered Protein by Simulation and Experiment. J Am Chem Soc 2016; 138:11702-13. [PMID: 27583687 DOI: 10.1021/jacs.6b05443] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Chemical denaturants are the most commonly used agents for unfolding proteins and are thought to act by better solvating the unfolded state. Improved solvation is expected to lead to an expansion of unfolded chains with increasing denaturant concentration, providing a sensitive probe of the denaturant action. However, experiments have so far yielded qualitatively different results concerning the effects of chemical denaturation. Studies using Förster resonance energy transfer (FRET) and other methods found an increase in radius of gyration with denaturant concentration, but most small-angle X-ray scattering (SAXS) studies found no change. This discrepancy therefore challenges our understanding of denaturation mechanism and more generally the accuracy of these experiments as applied to unfolded or disordered proteins. Here, we use all-atom molecular simulations to investigate the effect of urea and guanidinium chloride on the structure of the intrinsically disordered protein ACTR, which can be studied by experiment over a wide range of denaturant concentration. Using unbiased molecular simulations with a carefully calibrated denaturant model, we find that the protein chain indeed swells with increasing denaturant concentration. This is due to the favorable association of urea or guanidinium chloride with the backbone of all residues and with the side-chains of almost all residues, with denaturant-water transfer free energies inferred from this association in reasonable accord with experimental estimates. Interactions of the denaturants with the backbone are dominated by hydrogen bonding, while interactions with side-chains include other contributions. By computing FRET efficiencies and SAXS intensities at each denaturant concentration, we show that the simulation trajectories are in accord with both experiments on this protein, demonstrating that there is no fundamental inconsistency between the two types of experiment. Agreement with experiment also supports the picture of chemical denaturation described in our simulations, driven by weak association of denaturant with the protein. Our simulations support some assumptions needed for each experiment to accurately reflect changes in protein size, namely, that the commonly used FRET chromophores do not qualitatively alter the results and that possible effects such as preferential solvent partitioning into the interior of the chain do not interfere with the determination of radius of gyration from the SAXS experiments.
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Affiliation(s)
- Wenwei Zheng
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0520, United States
| | - Alessandro Borgia
- Department of Biochemistry, University of Zurich , Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Karin Buholzer
- Department of Biochemistry, University of Zurich , Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Alexander Grishaev
- National Institute of Standards and Technology and the Institute for Bioscience and Biotechnology Research , Rockville, Maryland 20850, United States
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich , Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0520, United States
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108
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Ganguly P, van der Vegt NFA, Shea JE. Hydrophobic Association in Mixed Urea-TMAO Solutions. J Phys Chem Lett 2016; 7:3052-9. [PMID: 27440555 DOI: 10.1021/acs.jpclett.6b01344] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The formation of a hydrophobic core is key to the folding and resulting function of most proteins in the cell. In several organisms, as well as in many in vitro experiments, protein folding is modulated by the presence of osmolytes, but the mechanism by which hydrophobic association occurs is not well understood. We present a study of the solvation thermodynamics of hydrophobic self-association in mixed-osmolyte urea-TMAO solutions, with neopentane as a model hydrophobic molecule. Using molecular dynamics simulations and the Kirkwood-Buff theory of solutions, we show that a sensitive balance between the TMAO-water and the TMAO-urea interactions governs the osmolyte-induced changes in hydrophobic association in mixed urea-TMAO solutions. This balance must be correctly incorporated in force-field parametrization because hydrophobic association can be either enhanced or prevented all together by slightly increasing or decreasing the osmolyte-water affinity and osmolyte-osmolyte self-affinity of TMAO molecules.
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Affiliation(s)
- Pritam Ganguly
- Department of Chemistry and Biochemistry, University of California at Santa Barbara , Santa Barbara, California 93106, United States
- Department of Physics, University of California at Santa Barbara , Santa Barbara, California 93106, United States
| | - Nico F A van der Vegt
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie and Center of Smart Interfaces, Technische Universität Darmstadt , Alarich-Weiss-Straße 10, Darmstadt 64287, Germany
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California at Santa Barbara , Santa Barbara, California 93106, United States
- Department of Physics, University of California at Santa Barbara , Santa Barbara, California 93106, United States
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109
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Chiba S, Furuta T, Shimizu S. Kirkwood–Buff Integrals for Aqueous Urea Solutions Based upon the Quantum Chemical Electrostatic Potential and Interaction Energies. J Phys Chem B 2016; 120:7714-23. [DOI: 10.1021/acs.jpcb.6b05611] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Shuntaro Chiba
- Education
Academy of Computational Life Sciences, Tokyo Institute of Technology, J3-141 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Tadaomi Furuta
- School
of Life Science and Technology, Tokyo Institute of Technology, B-62 4259
Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Seishi Shimizu
- York
Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
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110
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Jas GS, Middaugh CR, Kuczera K. Probing Selection Mechanism of the Most Favorable Conformation of a Dipeptide in Chaotropic and Kosmotropic Solution. J Phys Chem B 2016; 120:6939-50. [DOI: 10.1021/acs.jpcb.6b04528] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gouri S. Jas
- Department
of Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas 66047, United States
| | - C. Russell Middaugh
- Department
of Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas 66047, United States
| | - Krzysztof Kuczera
- Department
of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
- Department
of Molecular Biosciences, The University of Kansas, Lawrence, Kansas 66045, United States
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111
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Mondal T, Sarkar J, Ghosh S. Fluorescent PEGulated Oligourethane Nanoparticles for Long-Term Cellular Tracing. Chemistry 2016; 22:10930-6. [DOI: 10.1002/chem.201601718] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Indexed: 01/14/2023]
Affiliation(s)
- Tathagata Mondal
- Indian Association for the Cultivation of Science; Polymer Science Unit; 2A & 2B Raja S. C. Mullick Road Kolkata 700032 India
| | - Jayita Sarkar
- Indian Association for the Cultivation of Science; Polymer Science Unit; 2A & 2B Raja S. C. Mullick Road Kolkata 700032 India
| | - Suhrit Ghosh
- Indian Association for the Cultivation of Science; Polymer Science Unit; 2A & 2B Raja S. C. Mullick Road Kolkata 700032 India
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112
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Austerberry JI, Belton DJ. The aggregation of cytochrome C may be linked to its flexibility during refolding. 3 Biotech 2016; 6:33. [PMID: 28330101 PMCID: PMC4713397 DOI: 10.1007/s13205-015-0345-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 08/03/2015] [Indexed: 11/29/2022] Open
Abstract
Large-scale expression of biopharmaceutical proteins in cellular hosts results in production of large insoluble mass aggregates. In order to generate functional product, these aggregates require further processing through refolding with denaturant, a process in itself that can result in aggregation. Using a model folding protein, cytochrome C, we show how an increase in final denaturant concentration decreases the propensity of the protein to aggregate during refolding. Using polarised fluorescence anisotropy, we show how reduced levels of aggregation can be achieved by increasing the period of time the protein remains flexible during refolding, mediated through dilution ratios. This highlights the relationship between the flexibility of a protein and its propensity to aggregate. We attribute this behaviour to the preferential urea-residue interaction, over self-association between molecules.
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Affiliation(s)
- James I Austerberry
- Manchester Institute of Biotechnology, University of Manchester, 121 Princess Street, Manchester, M1 7DN, UK.
| | - Daniel J Belton
- Department of Chemical Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
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113
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Borgohain G, Paul S. Model Dependency of TMAO’s Counteracting Effect Against Action of Urea: Kast Model versus Osmotic Model of TMAO. J Phys Chem B 2016; 120:2352-61. [DOI: 10.1021/acs.jpcb.5b10968] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gargi Borgohain
- Department of Chemistry, Indian Institute of Technology, Guwahati 781039, India
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati 781039, India
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114
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Yamamori Y, Ishizuka R, Karino Y, Sakuraba S, Matubayasi N. Interaction-component analysis of the hydration and urea effects on cytochrome c. J Chem Phys 2016; 144:085102. [DOI: 10.1063/1.4941945] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yu Yamamori
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Ryosuke Ishizuka
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Yasuhito Karino
- RIKEN Quantitative Biology Center, Kobe, Hyogo 650-0047, Japan
| | - Shun Sakuraba
- Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8568, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
- Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto 615-8520, Japan
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115
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Tang C, Lew S, He D. Using a second-order differential model to fit data without baselines in protein isothermal chemical denaturation. Protein Sci 2016; 25:898-904. [PMID: 26757366 DOI: 10.1002/pro.2878] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 12/21/2015] [Accepted: 12/23/2015] [Indexed: 11/06/2022]
Abstract
In vitro protein stability studies are commonly conducted via thermal or chemical denaturation/renaturation of protein. Conventional data analyses on the protein unfolding/(re)folding require well-defined pre- and post-transition baselines to evaluate Gibbs free-energy change associated with the protein unfolding/(re)folding. This evaluation becomes problematic when there is insufficient data for determining the pre- or post-transition baselines. In this study, fitting on such partial data obtained in protein chemical denaturation is established by introducing second-order differential (SOD) analysis to overcome the limitations that the conventional fitting method has. By reducing numbers of the baseline-related fitting parameters, the SOD analysis can successfully fit incomplete chemical denaturation data sets with high agreement to the conventional evaluation on the equivalent completed data, where the conventional fitting fails in analyzing them. This SOD fitting for the abbreviated isothermal chemical denaturation further fulfills data analysis methods on the insufficient data sets conducted in the two prevalent protein stability studies.
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Affiliation(s)
- Chuanning Tang
- Key Laboratory of Cell Proliferation and Regulation of Ministry of Education, Beijing Normal University, Beijing, 100875, China
| | - Scott Lew
- Neotein Therapeutics, New York, New York, 10706, USA
| | - Dacheng He
- Key Laboratory of Cell Proliferation and Regulation of Ministry of Education, Beijing Normal University, Beijing, 100875, China
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116
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Yang Y, Mu Y, Li W. Microscopic significance of hydrophobic residues in the protein-stabilizing effect of trimethylamine N-oxide (TMAO). Phys Chem Chem Phys 2016; 18:22081-8. [DOI: 10.1039/c6cp01205a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Proteins with a higher hydrophobic content are better protected by TMAO against the deleterious effect of urea.
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Affiliation(s)
- Yanmei Yang
- School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions
- Soochow University
- Suzhou
- China
| | - Yuguang Mu
- School of Biological Sciences
- Nanyang Technological University
- Singapore
| | - Weifeng Li
- School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions
- Soochow University
- Suzhou
- China
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117
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Zheng W, Borgia A, Borgia MB, Schuler B, Best RB. Empirical Optimization of Interactions between Proteins and Chemical Denaturants in Molecular Simulations. J Chem Theory Comput 2015; 11:5543-53. [PMID: 26574341 PMCID: PMC6139257 DOI: 10.1021/acs.jctc.5b00778] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Chemical denaturants are the most commonly used perturbation applied to study protein stability and folding kinetics as well as the properties of unfolded polypeptides. We build on recent work balancing the interactions of proteins and water, and accurate models for the solution properties of urea and guanidinium chloride, to develop a combined force field that is able to capture the strength of interactions between proteins and denaturants. We use solubility data for a model tetraglycine peptide in each denaturant to tune the protein-denaturant interaction by a novel simulation methodology. We validate the results against data for more complex sequences: single-molecule Förster resonance energy transfer data for a 34-residue fragment of the globular protein CspTm and photoinduced electron transfer quenching data for the disordered peptides C(AGQ)nW in denaturant solution as well as the chemical denaturation of the mini-protein Trp cage. The combined force field model should aid our understanding of denaturation mechanisms and the interpretation of experiment.
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Affiliation(s)
- Wenwei Zheng
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, 20892
| | - Alessandro Borgia
- Department of Biochemistry, University of Zürich, Zürich, Switzerland
| | | | - Ben Schuler
- Department of Biochemistry, University of Zürich, Zürich, Switzerland
| | - Robert B. Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, 20892
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118
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Kamo F, Ishizuka R, Matubayasi N. Correlation analysis for heat denaturation of Trp-cage miniprotein with explicit solvent. Protein Sci 2015; 25:56-66. [PMID: 26189564 DOI: 10.1002/pro.2754] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 07/15/2015] [Indexed: 11/10/2022]
Abstract
Energetics was analyzed for Trp-cage miniprotein in water to elucidate the solvation effect in heat denaturation. The solvation free energy was computed for a set of protein structures at room and high temperatures with all-atom molecular dynamics simulation combined with the solution theory in the energy representation, and its correlations were investigated against the intramolecular (structural) energy of the protein and the average interaction energy of the protein with the solvent water. It was observed both at room and high temperatures that the solvation free energy is anticorrelated to the structural energy and varies in parallel to the electrostatic component of the protein-water interaction energy without correlations to the van der Waals and excluded-volume components. When the set of folded structures sampled at room temperature was compared with the set of unfolded ones at high temperature, it was found that the preference order of the two sets is in correspondence to the van der Waals and excluded-volume components in the sum of the protein intramolecular and protein-water intermolecular interactions and is not distinguished by the electrostatic component.
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Affiliation(s)
- Fumitaka Kamo
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, 560-8531, Japan
| | - Ryosuke Ishizuka
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, 560-8531, Japan.,Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto, 615-8520, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, 560-8531, Japan.,Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto, 615-8520, Japan
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119
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Bandyopadhyay D, Bhanja K, Mohan S, Ghosh SK, Choudhury N. Effects of Concentration on Like-Charge Pairing of Guanidinium Ions and on the Structure of Water: An All-Atom Molecular Dynamics Simulation Study. J Phys Chem B 2015; 119:11262-74. [DOI: 10.1021/acs.jpcb.5b03064] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dibyendu Bandyopadhyay
- Heavy Water Division and ‡Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - K. Bhanja
- Heavy Water Division and ‡Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Sadhana Mohan
- Heavy Water Division and ‡Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Swapan K. Ghosh
- Heavy Water Division and ‡Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Niharendu Choudhury
- Heavy Water Division and ‡Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
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120
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English CA, García AE. Charged Termini on the Trp-Cage Roughen the Folding Energy Landscape. J Phys Chem B 2015; 119:7874-81. [DOI: 10.1021/acs.jpcb.5b02040] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Charles A. English
- Department of Physics and Astronomy and The Center for
Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Angel E. García
- Department of Physics and Astronomy and The Center for
Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
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121
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Heat, Acid and Chemically Induced Unfolding Pathways, Conformational Stability and Structure-Function Relationship in Wheat α-Amylase. PLoS One 2015; 10:e0129203. [PMID: 26053142 PMCID: PMC4460087 DOI: 10.1371/journal.pone.0129203] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 05/07/2015] [Indexed: 11/19/2022] Open
Abstract
Wheat α-amylase, a multi-domain protein with immense industrial applications, belongs to α+β class of proteins with native molecular mass of 32 kDa. In the present study, the pathways leading to denaturation and the relevant unfolded states of this multi-domain, robust enzyme from wheat were discerned under the influence of temperature, pH and chemical denaturants. The structural and functional aspects along with thermodynamic parameters for α-amylase unfolding were probed and analyzed using fluorescence, circular dichroism and enzyme assay methods. The enzyme exhibited remarkable stability up to 70°C with tendency to aggregate at higher temperature. Acid induced unfolding was also incomplete with respect to the structural content of the enzyme. Strong ANS binding at pH 2.0 suggested the existence of a partially unfolded intermediate state. The enzyme was structurally and functionally stable in the pH range 4.0–9.0 with 88% recovery of hydrolytic activity. Careful examination of biophysical properties of intermediate states populated in urea and GdHCl induced denaturation suggests that α-amylase unfolding undergoes irreversible and non-coincidental cooperative transitions, as opposed to previous reports of two-state unfolding. Our investigation highlights several structural features of the enzyme in relation to its catalytic activity. Since, α-amylase has been comprehensively exploited for use in a range of starch-based industries, in addition to its physiological significance in plants and animals, knowledge regarding its stability and folding aspects will promote its biotechnological applications.
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122
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Sapir L, Harries D. Macromolecular Stabilization by Excluded Cosolutes: Mean Field Theory of Crowded Solutions. J Chem Theory Comput 2015; 11:3478-90. [DOI: 10.1021/acs.jctc.5b00258] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Liel Sapir
- Institute of Chemistry and
The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
| | - Daniel Harries
- Institute of Chemistry and
The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
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123
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Ploetz EA, Smith PE. Particle and Energy Pair and Triplet Correlations in Liquids and Liquid Mixtures from Experiment and Simulation. J Phys Chem B 2015; 119:7761-77. [DOI: 10.1021/acs.jpcb.5b00741] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Elizabeth A. Ploetz
- Department
of Chemistry, Kansas State University, 213 CBC Building, Manhattan, Kansas 66506, United States
| | - Paul E. Smith
- Department
of Chemistry, Kansas State University, 213 CBC Building, Manhattan, Kansas 66506, United States
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124
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A hypothesis to reconcile the physical and chemical unfolding of proteins. Proc Natl Acad Sci U S A 2015; 112:E2775-84. [PMID: 25964355 DOI: 10.1073/pnas.1500352112] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
High pressure (HP) or urea is commonly used to disturb folding species. Pressure favors the reversible unfolding of proteins by causing changes in the volumetric properties of the protein-solvent system. However, no mechanistic model has fully elucidated the effects of urea on structure unfolding, even though protein-urea interactions are considered to be crucial. Here, we provide NMR spectroscopy and 3D reconstructions from X-ray scattering to develop the "push-and-pull" hypothesis, which helps to explain the initial mechanism of chemical unfolding in light of the physical events triggered by HP. In studying MpNep2 from Moniliophthora perniciosa, we tracked two cooperative units using HP-NMR as MpNep2 moved uphill in the energy landscape; this process contrasts with the overall structural unfolding that occurs upon reaching a threshold concentration of urea. At subdenaturing concentrations of urea, we were able to trap a state in which urea is preferentially bound to the protein (as determined by NMR intensities and chemical shifts); this state is still folded and not additionally exposed to solvent [fluorescence and small-angle X-ray scattering (SAXS)]. This state has a higher susceptibility to pressure denaturation (lower p1/2 and larger ΔVu); thus, urea and HP share concomitant effects of urea binding and pulling and water-inducing pushing, respectively. These observations explain the differences between the molecular mechanisms that control the physical and chemical unfolding of proteins, thus opening up new possibilities for the study of protein folding and providing an interpretation of the nature of cooperativity in the folding and unfolding processes.
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125
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Sikder A, Das A, Ghosh S. Hydrogen-Bond-Regulated Distinct Functional-Group Display at the Inner and Outer Wall of Vesicles. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201500971] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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126
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Sikder A, Das A, Ghosh S. Hydrogen-Bond-Regulated Distinct Functional-Group Display at the Inner and Outer Wall of Vesicles. Angew Chem Int Ed Engl 2015; 54:6755-60. [DOI: 10.1002/anie.201500971] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 03/13/2015] [Indexed: 12/19/2022]
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127
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Gallo E, Snyder AC, Jarvik JW. Engineering tandem single-chain Fv as cell surface reporters with enhanced properties of fluorescence detection. Protein Eng Des Sel 2015; 28:327-37. [PMID: 25843939 DOI: 10.1093/protein/gzv016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 02/20/2015] [Indexed: 12/13/2022] Open
Abstract
A recently described fluorescence biosensor platform utilizes single-chain Fv (scFvs) that selectively bind and activate fluorogen molecules. In this report we investigated the display of tandem scFv biosensors at the surface of mammalian cells with the aim of advancing current fluorescence detection strategies. We initially screened different peptide linkers to separate each scFv unit, and discovered that tandem proteins joined by either flexible or α-helical linkers properly fold and display at the surface of mammalian cells. Accordingly, we performed a combinatorial scFv-dimer study and identified that fluorescence activation correlated with the cellular location (membrane distal versus proximal) and selections of the different scFvs. Furthermore, in vitro measurements showed that the stability of each scFv monomer unit influenced the folding and cell surface activities of tandem scFvs. Additionally, we investigated the absence or poor signals from some scFv-dimer combinations and discovered that intramolecular and intermolecular scFv chain mispairings led to protein misfolding and/or secretory-pathway-mediated degradation. Furthermore, when tandem scFvs were utilized as fluorescence reporter tags with surface receptors, the biosensor unit and target protein showed independent activities. Thus, the live cell application of tandem scFvs permitted advanced detection of target proteins via fluorescence signal amplification, Förster resonance energy transfer resulting in the increase of Stokes shift and multi-color vesicular traffic of surface receptors.
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Affiliation(s)
- Eugenio Gallo
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Avin C Snyder
- Molecular Biosensor and Imaging Center, Pittsburgh, PA 15213, USA
| | - Jonathan W Jarvik
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA Molecular Biosensor and Imaging Center, Pittsburgh, PA 15213, USA
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128
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Kasavajhala K, Bikkina S, Patil I, MacKerell AD, Priyakumar UD. Dispersion interactions between urea and nucleobases contribute to the destabilization of RNA by urea in aqueous solution. J Phys Chem B 2015; 119:3755-61. [PMID: 25668757 DOI: 10.1021/jp512414f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Urea has long been used to investigate protein folding and, more recently, RNA folding. Studies have proposed that urea denatures RNA by participating in stacking interactions and hydrogen bonds with nucleic acid bases. In this study, the ability of urea to form unconventional stacking interactions with RNA bases is investigated using ab initio calculations (RI-MP2 and CCSD(T) methods with the aug-cc-pVDZ basis set). A total of 29 stable nucleobase-urea stacked complexes are identified in which the intermolecular interaction energies (up to -14 kcal/mol) are dominated by dispersion effects. Natural bond orbital (NBO) and atoms in molecules (AIM) calculations further confirm strong interactions between urea and nucleobases. Calculations on model systems with multiple urea and water molecules interacting with a guanine base lead to a hypothesis that urea molecules along with water are able to form cage-like structures capable of trapping nucleic acid bases in extrahelical states by forming both hydrogen-bonded and dispersion interactions, thereby contributing to the unfolding of RNA in the presence of urea in aqueous solution.
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Affiliation(s)
- Koushik Kasavajhala
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology , Hyderabad, 500032, India
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129
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Ganguly P, Hajari T, Shea JE, van der Vegt NFA. Mutual Exclusion of Urea and Trimethylamine N-Oxide from Amino Acids in Mixed Solvent Environment. J Phys Chem Lett 2015; 6:581-5. [PMID: 26262470 DOI: 10.1021/jz502634k] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
We study the solvation of amino acids in pure-osmolyte and mixed-osmolyte urea and trimethylamine N-oxide (TMAO) solutions using molecular dynamics simulations. Analysis of Kirkwood-Buff integrals between the solution components provides evidence that in the mixed osmolytic solution, both urea and TMAO are mutually excluded from the amino acid surface, accompanied by an increase in osmolyte-osmolyte aggregation. Similar observations are made in simulations of a model protein backbone, represented by triglycine, and suggest that TMAO stabilizes proteins under urea denaturation conditions by effectively removing urea from the protein surface. The effects of the mixed osmolytes on the solvation of the amino acids and the backbone are found to be highly nonlinear in terms of the effects of the individual osmolytes and independent of differences in the strength of the TMAO-water interactions, as observed with different TMAO force fields.
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Affiliation(s)
- Pritam Ganguly
- §Eduard-Zintl-Institut für Anorganische und Physikalische Chemie and Center of Smart Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, Darmstadt 64287, Germany
| | - Timir Hajari
- §Eduard-Zintl-Institut für Anorganische und Physikalische Chemie and Center of Smart Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, Darmstadt 64287, Germany
| | | | - Nico F A van der Vegt
- §Eduard-Zintl-Institut für Anorganische und Physikalische Chemie and Center of Smart Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, Darmstadt 64287, Germany
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130
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Sapir L, Harries D. Is the depletion force entropic? Molecular crowding beyond steric interactions. Curr Opin Colloid Interface Sci 2015. [DOI: 10.1016/j.cocis.2014.12.003] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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131
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Porter JL, Collyer CA, Ollis DL. Compensatory Stabilizing Role of Surface Mutations During the Directed Evolution of Dienelactone Hydrolase for Enhanced Activity. Protein J 2015; 34:82-9. [DOI: 10.1007/s10930-015-9600-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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132
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Cui D, Ou SC, Patel S. Protein denaturants at aqueous-hydrophobic interfaces: self-consistent correlation between induced interfacial fluctuations and denaturant stability at the interface. J Phys Chem B 2015; 119:164-78. [PMID: 25536388 PMCID: PMC4291035 DOI: 10.1021/jp507203g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 10/21/2014] [Indexed: 01/16/2023]
Abstract
The notion of direct interaction between denaturing cosolvent and protein residues has been proposed in dialogue relevant to molecular mechanisms of protein denaturation. Here we consider the correlation between free energetic stability and induced fluctuations of an aqueous-hydrophobic interface between a model hydrophobically associating protein, HFBII, and two common protein denaturants, guanidinium cation (Gdm(+)) and urea. We compute potentials of mean force along an order parameter that brings the solute molecule close to the known hydrophobic region of the protein. We assess potentials of mean force for different relative orientations between the protein and denaturant molecule. We find that in both cases of guanidinium cation and urea relative orientations of the denaturant molecule that are parallel to the local protein-water interface exhibit greater stability compared to edge-on or perpendicular orientations. This behavior has been observed for guanidinium/methylguanidinium cations at the liquid-vapor interface of water, and thus the present results further corroborate earlier findings. Further analysis of the induced fluctuations of the aqueous-hydrophobic interface upon approach of the denaturant molecule indicates that the parallel orientation, displaying a greater stability at the interface, also induces larger fluctuations of the interface compared to the perpendicular orientations. The correlation of interfacial stability and induced interface fluctuation is a recurring theme for interface-stable solutes at hydrophobic interfaces. Moreover, observed correlations between interface stability and induced fluctuations recapitulate connections to local hydration structure and patterns around solutes as evidenced by experiment (Cooper et al., J. Phys. Chem. A 2014, 118, 5657.) and high-level ab initio/DFT calculations (Baer et al., Faraday Discuss 2013, 160, 89).
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Affiliation(s)
- Di Cui
- Department of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Shu-Ching Ou
- Department of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Sandeep Patel
- Department of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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133
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Rodríguez-Ropero F, van der Vegt NFA. On the urea induced hydrophobic collapse of a water soluble polymer. Phys Chem Chem Phys 2015; 17:8491-8. [DOI: 10.1039/c4cp05314a] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Polymer collapse despite cosolvent binding: solvation of extended coil conformations is entropically penalized, therefore stabilizing compact globular conformations in the coil-globule equilibrium of poly(N-isopropylacrylamide) in aqueous urea solution.
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Affiliation(s)
- Francisco Rodríguez-Ropero
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie and Center of Smart Interfaces
- Technische Universität Darmstadt
- Darmstadt
- Germany
| | - Nico F. A. van der Vegt
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie and Center of Smart Interfaces
- Technische Universität Darmstadt
- Darmstadt
- Germany
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134
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Son I, Shek YL, Tikhomirova A, Baltasar EH, Chalikian TV. Interactions of Urea with Native and Unfolded Proteins: A Volumetric Study. J Phys Chem B 2014; 118:13554-63. [DOI: 10.1021/jp509356k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ikbae Son
- Department
of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Yuen Lai Shek
- Department
of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Anna Tikhomirova
- Department
of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Eduardo Hidalgo Baltasar
- Department
of Physical Chemistry, Faculty of Chemistry, University Complutense of Madrid, 28040 Madrid, Spain
| | - Tigran V. Chalikian
- Department
of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
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135
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Ploetz EA, Smith PE. Infinitely dilute partial molar properties of proteins from computer simulation. J Phys Chem B 2014; 118:12844-54. [PMID: 25325571 PMCID: PMC4234426 DOI: 10.1021/jp508632h] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A detailed understanding of temperature and pressure effects on an infinitely dilute protein's conformational equilibrium requires knowledge of the corresponding infinitely dilute partial molar properties. Established molecular dynamics methodologies generally have not provided a way to calculate these properties without either a loss of thermodynamic rigor, the introduction of nonunique parameters, or a loss of information about which solute conformations specifically contributed to the output values. Here we implement a simple method that is thermodynamically rigorous and possesses none of the above disadvantages, and we report on the method's feasibility and computational demands. We calculate infinitely dilute partial molar properties for two proteins and attempt to distinguish the thermodynamic differences between a native and a denatured conformation of a designed miniprotein. We conclude that simple ensemble average properties can be calculated with very reasonable amounts of computational power. In contrast, properties corresponding to fluctuating quantities are computationally demanding to calculate precisely, although they can be obtained more easily by following the temperature and/or pressure dependence of the corresponding ensemble averages.
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Affiliation(s)
- Elizabeth A Ploetz
- Department of Chemistry, Kansas State University , 213 CBC Building, Manhattan, Kansas 66506-0401, United States
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136
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Bandyopadhyay D, Mohan S, Ghosh SK, Choudhury N. Molecular Dynamics Simulation of Aqueous Urea Solution: Is Urea a Structure Breaker? J Phys Chem B 2014; 118:11757-68. [DOI: 10.1021/jp505147u] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dibyendu Bandyopadhyay
- Heavy water Division and ‡Theoretical Chemistry
Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Sadhana Mohan
- Heavy water Division and ‡Theoretical Chemistry
Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Swapan K. Ghosh
- Heavy water Division and ‡Theoretical Chemistry
Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Niharendu Choudhury
- Heavy water Division and ‡Theoretical Chemistry
Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
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137
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Parimal S, Cramer SM, Garde S. Application of a Spherical Harmonics Expansion Approach for Calculating Ligand Density Distributions around Proteins. J Phys Chem B 2014; 118:13066-76. [DOI: 10.1021/jp506849k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Siddharth Parimal
- Howard
P. Isermann Department
of Chemical and Biological Engineering and Center for Biotechnology
and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States
| | - Steven M. Cramer
- Howard
P. Isermann Department
of Chemical and Biological Engineering and Center for Biotechnology
and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States
| | - Shekhar Garde
- Howard
P. Isermann Department
of Chemical and Biological Engineering and Center for Biotechnology
and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States
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138
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On the influence of the mixture of denaturants on protein structure stability: A molecular dynamics study. Chem Phys 2014. [DOI: 10.1016/j.chemphys.2014.07.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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139
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Bogár F, Bartha F, Násztor Z, Fábián L, Leitgeb B, Dér A. On the Hofmeister Effect: Fluctuations at the Protein–Water Interface and the Surface Tension. J Phys Chem B 2014; 118:8496-504. [DOI: 10.1021/jp502505c] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ferenc Bogár
- MTA-SZTE
Supramolecular and Nanostructured Materials Research Group of Hungarian
Academy of Sciences, University of Szeged, H-6720 Szeged, Hungary
| | - Ferenc Bartha
- Department
of Medical Chemistry, University of Szeged, H-6720 Szeged, Hungary
| | - Zoltán Násztor
- Department
of Medical Chemistry, University of Szeged, H-6720 Szeged, Hungary
- Institute
of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, H-6726 Szeged, Hungary
| | - László Fábián
- Institute
of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, H-6726 Szeged, Hungary
| | - Balázs Leitgeb
- Institute
of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, H-6726 Szeged, Hungary
- Department
of Microbiology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary
| | - András Dér
- Institute
of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, H-6726 Szeged, Hungary
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140
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Budkov YA, Kolesnikov AL, Georgi N, Kiselev MG. A statistical theory of cosolvent-induced coil-globule transitions in dilute polymer solution. J Chem Phys 2014; 141:014902. [DOI: 10.1063/1.4884958] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yu. A. Budkov
- Institute of Solution Chemistry of the Russian Academy of Sciences, Ivanovo, Russia
| | - A. L. Kolesnikov
- Ivanovo State University, Ivanovo, Russia
- Institut für Nichtklassische Chemie e.V., Universitat Leipzig, Leipzig, Germany
| | - N. Georgi
- Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany
| | - M. G. Kiselev
- Institute of Solution Chemistry of the Russian Academy of Sciences, Ivanovo, Russia
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141
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Singh P, Sarkar SK, Bandyopadhyay P. Wang-Landau density of states based study of the folding-unfolding transition in the mini-protein Trp-cage (TC5b). J Chem Phys 2014; 141:015103. [DOI: 10.1063/1.4885726] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Priya Singh
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi - 110 067, India
| | - Subir K. Sarkar
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi - 110 067, India
| | - Pradipta Bandyopadhyay
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi - 110 067, India
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142
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Mondal T, Ghosh S. One pot synthesis and gelation studies of amphiphilic triblock polyurethanes. ACTA ACUST UNITED AC 2014. [DOI: 10.1002/pola.27263] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Tathagata Mondal
- Polymer Science Unit, Indian Association for the Cultivation of Science; 2A and 2B Raja S. C. Mullick Road Kolkata India 700032
| | - Suhrit Ghosh
- Polymer Science Unit, Indian Association for the Cultivation of Science; 2A and 2B Raja S. C. Mullick Road Kolkata India 700032
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143
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Keshwani N, Banerjee S, Brodsky B, Makhatadze GI. The role of cross-chain ionic interactions for the stability of collagen model peptides. Biophys J 2014; 105:1681-8. [PMID: 24094409 DOI: 10.1016/j.bpj.2013.08.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 07/18/2013] [Accepted: 08/09/2013] [Indexed: 11/25/2022] Open
Abstract
The contribution of ionic interactions to the stability of the collagen triple helix was studied using molecular dynamics (MD) simulations and biophysical methods. To this end, we examined the stability of a host-guest collagen model peptide, Ac-GPOGPOGPYGXOGPOGPO-NH2, substituting KGE, KGD, EGK, and DGK for the YGX sequence. All-atom, implicit solvent MD simulations show that the fraction of cross-chain ionic interactions formed is different, with the most pronounced in the KGE and KGD sequences, and the least in the DGK sequence. To test whether the fraction of cross-chain ionic interactions correlates with the stability, experimental measurements of thermostability were done using differential scanning calorimetry and circular dichroism spectroscopy. It was found that the melting temperature is very similar for KGE and KGD peptides, whereas the EGK peptide has lower thermostability and the DGK peptide is the least thermostable. A novel, to our knowledge, computational protocol termed temperature-scan MD was applied to estimate the relative stabilities of the peptides from MD simulations. We found an excellent correlation between transition temperatures obtained from temperature-scan MD and those measured experimentally. These results suggest the importance of cross-chain ionic interactions for the stability of collagen triple helix and confirm the utility of MD simulations in predicting interactions and stability in this system.
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Affiliation(s)
- Neelam Keshwani
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts
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144
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Dasgupta A, Udgaonkar JB, Das P. Multistage Unfolding of an SH3 Domain: An Initial Urea-Filled Dry Molten Globule Precedes a Wet Molten Globule with Non-Native Structure. J Phys Chem B 2014; 118:6380-92. [DOI: 10.1021/jp410019f] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Amrita Dasgupta
- National
Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Jayant B. Udgaonkar
- National
Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Payel Das
- Computational
Biology Center, IBM Thomas J. Watson Research Center, 1101 Kitchawan
Road, Yorktown Heights, New
York 10598, United States
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145
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Rajdev P, Molla MR, Ghosh S. Understanding the role of H-bonding in aqueous self-assembly of two naphthalene diimide (NDI)-conjugated amphiphiles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:1969-1976. [PMID: 24494820 DOI: 10.1021/la500089b] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Supramolecular architectures with the synchronized combination of various directional noncovalent forces are ubiquitous in biological systems. However, reports of such abiotic synthetic systems involving H-bonding in aqueous medium are rare due to the challenge faced in the formation of such structures by overcoming the competition from the water molecules. In this paper we have studied self-assembly of two structurally related naphthalene-diimide (NDI) conjugated bola-amphiphiles (NDI-1 and NDI-2) in water with an aim to realize the specific role of H-bonding among the hydrazide units present in one of the two building blocks (NDI-2) on the self-assembly. Both chromophores showed vesicular assembly in aqueous solution driven primarily by π-stacking among the NDI chromophores, which could be probed by UV-vis absorption spectra. Contrary to common belief, the lack of an H-bonding group in NDI-1 was found to be a boon in disguise in terms of the stability of the aggregates. Whereas NDI-2 aggregates showed LCST around 65-70 °C owing to the breaking of the H-bonds with increased temperature, the NDI-1 aggregates were found to be structurally intact until 90 °C, which may be attributed to the increased hydrophobicity introduced by the absence of the polar hydrazide group. Further concentration- and solvent-dependent UV-vis studies showed that NDI-1 formed assembled structure at greatly dilute solution and also in a solvent such as THF, confirming greater propensity for its self-assembly. As both bola-amphiphiles contain an electron-deficient NDI chromophore, interaction of their vesicles was studied with an externally added electron-rich pyrene derivative. Surprisingly, NDI-1 did not show any charge-transfer interaction with the donor, whereas NDI-2 could effectively intercalate, leading to a functional membrane with tunable surface functionalities. This was attributed to the additional stability of the intercalated state by H-bonding among the hydrazide units.
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Affiliation(s)
- Priya Rajdev
- Polymer Science Unit, Indian Association for the Cultivation of Science , Kolkata, India 700032
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146
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Malpiedi LP, Nerli BB, Abdalla DSP, Pessoa A. Assessment of the effect of triton X-114 on the physicochemical properties of an antibody fragment. Biotechnol Prog 2014; 30:554-61. [DOI: 10.1002/btpr.1882] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Revised: 01/29/2014] [Indexed: 01/05/2023]
Affiliation(s)
- Luciana P. Malpiedi
- Biochemical and Pharmaceutical Technology Dept./FCF; University of São Paulo. Av. Prof. Lineu Prestes; 580-Bloco 16 CEP 05508-000 São Paulo Brazil
- Physical Chemistry Dept., Faculty of Biochemistry and Pharmaceutical Sciences; National University of Rosario; Suipacha 570 S2002LRK Rosario Argentina
| | - Bibiana B. Nerli
- Physical Chemistry Dept., Faculty of Biochemistry and Pharmaceutical Sciences; National University of Rosario; Suipacha 570 S2002LRK Rosario Argentina
| | | | - Adalberto Pessoa
- Biochemical and Pharmaceutical Technology Dept./FCF; University of São Paulo. Av. Prof. Lineu Prestes; 580-Bloco 16 CEP 05508-000 São Paulo Brazil
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147
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Sengupta A, Singh RK, Gavvala K, Koninti RK, Mukherjee A, Hazra P. Urea induced unfolding dynamics of flavin adenine dinucleotide (FAD): spectroscopic and molecular dynamics simulation studies from femto-second to nanosecond regime. J Phys Chem B 2014; 118:1881-90. [PMID: 24456234 DOI: 10.1021/jp412339a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Here, we investigate the effect of urea in the unfolding dynamics of flavin adenine dinucleotide (FAD), an important enzymatic cofactor, through steady state, time-resolved fluorescence spectroscopic and molecular dynamics (MD) simulation studies. Steady state results indicate the possibility of urea induced unfolding of FAD, inferred from increasing emission intensity of FAD with urea. The TCSPC and up-conversion results suggest that the stack-unstack dynamics of FAD severely gets affected in the presence of urea and leads to an increase in the unstack conformation population from 15% in pure water to 40% in 12 M urea. Molecular dynamics simulation was employed to understand the nature of the interaction between FAD and urea at the molecular level. Results depict that urea molecules replace many of the water molecules around adenine and isoalloxazine rings of FAD. However, the major driving force for the stability of this unstack conformations arises from the favorable stacking interaction of a significant fraction of the urea molecules with adenine and isoalloxazine rings of FAD, which overcomes the intramolecular stacking interaction between themselves observed in pure water.
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Affiliation(s)
- Abhigyan Sengupta
- Department of Chemistry, Indian Institute of Science Education and Research (IISER)-Pune , Pune (411008), Maharashtra, India
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148
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English CA, García AE. Folding and unfolding thermodynamics of the TC10b Trp-cage miniprotein. Phys Chem Chem Phys 2014; 16:2748-57. [PMID: 24448113 DOI: 10.1039/c3cp54339k] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
We examine the folding-unfolding of a variant of the Trp-cage, known as TC10b, and compare structural stability, dynamics, and thermodynamics with that of the TC5b variant, using replica exchange molecular dynamics (REMD). The TC10b variant was designed to have larger helical stability by the substitution of amino acids with greater alpha helical propensities in the N-terminal region. Experiments have shown TC10b to possess larger overall stability than TC5b. Simulations starting from unbiased, unfolded initial conditions are run for 1 μs per replica. The calculations show a higher melting temperature for TC10b than TC5b, and suggest a more ordered folded structure through the elimination of a substate found in the folded ensemble of TC5b. We model the difference in Gibbs free energy, ΔG(P,T), of folding using the bootstrap statistical method, which is used to calculate uncertainties associated with the thermodynamic parameters for both variants of the Trp-cage. We find that while the shape of the area for which the protein is stability folded is elliptical for TC5b, there is a degree of uncertainty associated with that of TC10b, with one model suggesting elliptical and another suggesting hyperbolic. This model suggests that at high pressures, TC5b can experience pressure denaturation, but TC10b may not.
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Affiliation(s)
- Charles A English
- Department of Physics, Applied Physics and Astronomy, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
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149
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Monhemi H, Housaindokht MR, Moosavi-Movahedi AA, Bozorgmehr MR. How a protein can remain stable in a solvent with high content of urea: insights from molecular dynamics simulation of Candida antarctica lipase B in urea : choline chloride deep eutectic solvent. Phys Chem Chem Phys 2014; 16:14882-93. [DOI: 10.1039/c4cp00503a] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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150
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Mandal M, Mukhopadhyay C. Microsecond molecular dynamics simulation of guanidinium chloride induced unfolding of ubiquitin. Phys Chem Chem Phys 2014; 16:21706-16. [DOI: 10.1039/c4cp01657b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
All atom molecular dynamics simulations have been used to explore the atomic detail mechanism of guanidinium induced unfolding of the protein ubiquitin.
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Affiliation(s)
- Manoj Mandal
- Department of Chemistry
- University of Calcutta
- Kolkata – 700 009, India
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