The Experts below are selected from a list of 31350 Experts worldwide ranked by ideXlab platform
Chaitali Mukhopadhyay - One of the best experts on this subject based on the ideXlab platform.
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Urea-mediated Protein Denaturation: a consensus view.
The journal of physical chemistry. B, 2009Co-Authors: Atanu Das, Chaitali MukhopadhyayAbstract:We have performed all-atom molecular dynamics simulations of three structurally similar small globular Proteins in 8 M urea and compared the results with pure aqueous simulations. Protein Denaturation is preceded by an initial loss of water from the first solvation shell and consequent in-flow of urea toward the Protein. Urea reaches the first solvation shell of the Protein mainly due to electrostatic interaction with a considerable contribution coming from the dispersion interaction. Urea shifts the equilibrium from the native to denatured ensemble by making the Protein-Protein contact less stable than Protein-urea contact, which is just the reverse of the condition in pure water, where Protein-Protein contact is more stable than Protein-water contact. We have also seen that water follows urea and reaches the Protein interior at later stages of Denaturation, while urea preferentially and efficiently solvates different parts of the Protein. Solvation of the Protein backbone via hydrogen bonding, favorable electrostatic interaction with hydrophilic residues, and dispersion interaction with hydrophobic residues are the key steps through which urea intrudes the core of the Protein and denatures it. Why urea is preferred over water for binding to the Protein backbone and how urea orients itself toward the Protein backbone have been identified comprehensively. All the key components of intermolecular forces are found to play a significant part in urea-induced Protein Denaturation and also toward the stability of the denatured state ensemble. Changes in water network/structure and dynamical properties and higher degree of solvation of the hydrophobic residues validate the presence of "indirect mechanism" along with the "direct mechanism" and reinforce the effect of urea on Protein.
Bruce J. Berne - One of the best experts on this subject based on the ideXlab platform.
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Comment on "urea-mediated Protein Denaturation: a consensus view".
The journal of physical chemistry. B, 2011Co-Authors: Ruhong Zhou, Zaixing Yang, Lan Hua, Bruce J. BerneAbstract:Urea has been widely used as a Protein denaturant for more than a hundred years; however, its chemical Denaturation mechanism still remains controversial, despite the extensive studies from both experimental and theoretical approaches in last several decades.1–19 The denaturing power of urea has been explained by two very different mechanisms: the “indirect” and “direct” mechanisms. The indirect mechanism suggests that urea denatures Proteins by disrupting the water structure, which in turn weakens the hydrophobic interaction and makes the Protein hydrophobic residues less compact and more readily solvated.4 The direct mechanism, on the other hand, indicates that urea unfolds Proteins through direct interactions with Protein, either through stronger electrostatic interactions10,11,13,16 with backbone and/or polar residues or through preferential van der Waals attractions14,15,18 with Protein residues. Most of the concurrent studies support the direct mechanism involving urea's preferential binding to Protein backbone or side chains,10,11,13–15,18 although some recent studies also indicate that the indirect mechanism can also play a role in the urea-induced Protein Denaturation.8,16,19
Abani K Huya - One of the best experts on this subject based on the ideXlab platform.
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on the mechanism of sds induced Protein Denaturation
Biopolymers, 2010Co-Authors: Abani K HuyaAbstract:To understand the mechanism of ionic detergent-induced Protein Denaturation, this study examines the action of sodium dodecyl sulfate on ferrocytochrome c conformation under neutral and strongly alkaline conditions. Equilibrium and stopped-flow kinetic results consistently suggest that tertiary structure unfolding in the submicellar and chain expansion in the micellar range of SDS concentrations are the two major and discrete events in the perturbation of Protein structure. The nature of interaction between the detergent and the Protein is predominantly hydrophobic in the submicellar and exclusively hydrophobic at micellar levels of SDS concentration. The observation that SDS also interacts with a highly denatured and negatively charged form of ferrocytochrome c suggests that the interaction is independent of structure, conformation, and ionization state of the Protein. The expansion of the Protein chain at micellar concentration of SDS is driven by coulombic repulsion between the Protein-bound micelles, and the micelles and anionic amino acid side chains.
Per Ertbjerg - One of the best experts on this subject based on the ideXlab platform.
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Mimicking myofibrillar Protein Denaturation in frozen-thawed meat: Effect of pH at high ionic strength
Food chemistry, 2020Co-Authors: Yuemei Zhang, Eero Puolanne, Per ErtbjergAbstract:Abstract This study aims at providing new insight on Protein Denaturation in freezing-thawing. Freezing-thawing minced pork reduced water-holding of myofibrils and increased surface hydrophobicity. One additional freezing-thawing cycle at slow freezing rate caused appearance of a 160 kDa myosin-4 fragment in SDS-PAGE, further decreased water-holding of myofibrils and increased surface hydrophobicity. Fresh minced pork was exposed to either high salt (2 M KCl) only or high salt with lower pH to mimic conditions in freezing. Exposure to high salt only increased water-holding of myofibrils and hence did not reproduce myofibrillar Protein changes in freezing. Exposure to combinations of lower pHs and high salt decreased water-holding and increased surface hydrophobicity, suggesting myofibrillar Protein Denaturation occurred by a comparable mechanism as in freezing-thawing. We propose that exposure to decreased pH combined with high solute concentrations in the unfrozen water of frozen meat is the primary cause of myofibrillar Protein Denaturation in frozen-thawed meat.
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On the origin of thaw loss: Relationship between freezing rate and Protein Denaturation.
Food chemistry, 2019Co-Authors: Yuemei Zhang, Per ErtbjergAbstract:Abstract The role of Protein Denaturation in formation of thaw loss is currently not well understood. This study investigated Denaturation of myofibrillar and sarcoplasmic Proteins of pork loins caused by freezing-thawing in relation to freezing rate. Compared to fast freezing, slow freezing caused 28% larger thaw loss, decreased water-holding capacity of myofibrils and increased surface hydrophobicity, indicating more pronounced Denaturation of myofibrillar Proteins. We here propose a model: In slow freezing protons are concentrated in the unfrozen water resulting in reduced pH in proximity of structural Proteins causing Protein Denaturation. In parallel, large ice crystals are formed outside of muscle fibers resulting in transversal shrinkage. In fast freezing small ice crystals trap protons and cause less severe Protein Denaturation and reduced thaw loss. Differential scanning calorimetry and tryptophan fluorescence spectra indicated sarcoplasmic Protein Denaturation in drip due to freezing-thawing. However, sarcoplasmic Protein Denaturation was independent of freezing rate.
Atanu Das - One of the best experts on this subject based on the ideXlab platform.
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Urea-mediated Protein Denaturation: a consensus view.
The journal of physical chemistry. B, 2009Co-Authors: Atanu Das, Chaitali MukhopadhyayAbstract:We have performed all-atom molecular dynamics simulations of three structurally similar small globular Proteins in 8 M urea and compared the results with pure aqueous simulations. Protein Denaturation is preceded by an initial loss of water from the first solvation shell and consequent in-flow of urea toward the Protein. Urea reaches the first solvation shell of the Protein mainly due to electrostatic interaction with a considerable contribution coming from the dispersion interaction. Urea shifts the equilibrium from the native to denatured ensemble by making the Protein-Protein contact less stable than Protein-urea contact, which is just the reverse of the condition in pure water, where Protein-Protein contact is more stable than Protein-water contact. We have also seen that water follows urea and reaches the Protein interior at later stages of Denaturation, while urea preferentially and efficiently solvates different parts of the Protein. Solvation of the Protein backbone via hydrogen bonding, favorable electrostatic interaction with hydrophilic residues, and dispersion interaction with hydrophobic residues are the key steps through which urea intrudes the core of the Protein and denatures it. Why urea is preferred over water for binding to the Protein backbone and how urea orients itself toward the Protein backbone have been identified comprehensively. All the key components of intermolecular forces are found to play a significant part in urea-induced Protein Denaturation and also toward the stability of the denatured state ensemble. Changes in water network/structure and dynamical properties and higher degree of solvation of the hydrophobic residues validate the presence of "indirect mechanism" along with the "direct mechanism" and reinforce the effect of urea on Protein.