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Graziano G. On the molecular origin of cold denaturation of globular proteins. Phys Chem Chem Phys 2010; 12:14245-52. [PMID: 20882232 DOI: 10.1039/c0cp00945h] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A polypeptide chain can adopt very different conformations, a fundamental distinguishing feature of which is the water accessible surface area, WASA, that is a measure of the layer around the polypeptide chain where the center of water molecules cannot physically enter, generating a solvent-excluded volume effect. The large WASA decrease associated with the folding of a globular protein leads to a large decrease in the solvent-excluded volume, and so to a large increase in the configurational/translational freedom of water molecules. The latter is a quantity that depends upon temperature. Simple calculations over the -30 to 150 °C temperature range, where liquid water can exist at 1 atm, show that such a gain decreases significantly on lowering the temperature below 0 °C, paralleling the decrease in liquid water density. There will be a temperature where the destabilizing contribution of the polypeptide chain conformational entropy exactly matches the stabilizing contribution of the water configurational/translational entropy, leading to cold denaturation.
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Affiliation(s)
- Giuseppe Graziano
- Dipartimento di Scienze Biologiche ed Ambientali, Università del Sannio, Via Port'Arsa 11, 82100 Benevento, Italy.
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Noé F, Daidone I, Smith JC, di Nola A, Amadei A. Solvent Electrostriction-Driven Peptide Folding Revealed by Quasi-Gaussian Entropy Theory and Molecular Dynamics Simulation. J Phys Chem B 2008; 112:11155-63. [DOI: 10.1021/jp801391t] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Frank Noé
- DFG Research Center Matheon, Free University of Berlin, Arnimallee 6, 14159 Berlin, Germany, Interdisciplinary Center for Scientific Computing, University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany, Center for Molecular Biophysics, University of Tennessee/Oak Ridge National Laboratory, One Bethel Valley Road, P.O. Box 2008, Oak Ridge, Tennessee 37831-6255, Department of Chemistry, University of Rome “La Sapienza”, P. le Aldo Moro 5, 00185 Rome, Italy, and Department of Chemical
| | - Isabella Daidone
- DFG Research Center Matheon, Free University of Berlin, Arnimallee 6, 14159 Berlin, Germany, Interdisciplinary Center for Scientific Computing, University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany, Center for Molecular Biophysics, University of Tennessee/Oak Ridge National Laboratory, One Bethel Valley Road, P.O. Box 2008, Oak Ridge, Tennessee 37831-6255, Department of Chemistry, University of Rome “La Sapienza”, P. le Aldo Moro 5, 00185 Rome, Italy, and Department of Chemical
| | - Jeremy C. Smith
- DFG Research Center Matheon, Free University of Berlin, Arnimallee 6, 14159 Berlin, Germany, Interdisciplinary Center for Scientific Computing, University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany, Center for Molecular Biophysics, University of Tennessee/Oak Ridge National Laboratory, One Bethel Valley Road, P.O. Box 2008, Oak Ridge, Tennessee 37831-6255, Department of Chemistry, University of Rome “La Sapienza”, P. le Aldo Moro 5, 00185 Rome, Italy, and Department of Chemical
| | - Alfredo di Nola
- DFG Research Center Matheon, Free University of Berlin, Arnimallee 6, 14159 Berlin, Germany, Interdisciplinary Center for Scientific Computing, University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany, Center for Molecular Biophysics, University of Tennessee/Oak Ridge National Laboratory, One Bethel Valley Road, P.O. Box 2008, Oak Ridge, Tennessee 37831-6255, Department of Chemistry, University of Rome “La Sapienza”, P. le Aldo Moro 5, 00185 Rome, Italy, and Department of Chemical
| | - Andrea Amadei
- DFG Research Center Matheon, Free University of Berlin, Arnimallee 6, 14159 Berlin, Germany, Interdisciplinary Center for Scientific Computing, University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany, Center for Molecular Biophysics, University of Tennessee/Oak Ridge National Laboratory, One Bethel Valley Road, P.O. Box 2008, Oak Ridge, Tennessee 37831-6255, Department of Chemistry, University of Rome “La Sapienza”, P. le Aldo Moro 5, 00185 Rome, Italy, and Department of Chemical
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Dolenc J, Baron R, Oostenbrink C, Koller J, van Gunsteren WF. Configurational entropy change of netropsin and distamycin upon DNA minor-groove binding. Biophys J 2006; 91:1460-70. [PMID: 16731550 PMCID: PMC1518646 DOI: 10.1529/biophysj.105.074617] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2005] [Accepted: 03/31/2006] [Indexed: 11/18/2022] Open
Abstract
Binding of a small molecule to a macromolecular target reduces its conformational freedom, resulting in a negative entropy change that opposes the binding. The goal of this study is to estimate the configurational entropy change of two minor-groove-binding ligands, netropsin and distamycin, upon binding to the DNA duplex d(CGCGAAAAACGCG).d(CGCGTTTTTCGCG). Configurational entropy upper bounds based on 10-ns molecular dynamics simulations of netropsin and distamycin in solution and in complex with DNA in solution were estimated using the covariance matrix of atom-positional fluctuations. The results suggest that netropsin and distamycin lose a significant amount of configurational entropy upon binding to the DNA minor groove. The estimated changes in configurational entropy for netropsin and distamycin are -127 J K(-1) mol(-1) and -104 J K(-1) mol(-1), respectively. Estimates of the configurational entropy contributions of parts of the ligands are presented, showing that the loss of configurational entropy is comparatively more pronounced for the flexible tails than for the relatively rigid central body.
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Affiliation(s)
- Jozica Dolenc
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
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