The free energy landscape of protein folding and dynamics: a global view

Yang, Liquan; Ji, Xinglai; Liu, Shu-Qun

doi:10.1080/07391102.2012.748536

Cited by 30 publications

(43 citation statements)

References 25 publications

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“…This process will lead finally to an equilibrium that has a lower system free energy than that of the hydrophobic group-water solvent system. Similarly, the protein denaturation process in nonpolar solvents is also driven by the lowering of the total Gibbs free energy of the protein-nonpolar solvent system, in which both the entropy gain and enthalpy reduction make favorable contributions to the lowering of the system free energy, although the final shape of the FEL exhibits a relatively flat surface [41]. This, from an opposite side, shows that liquid water is an idea solvent that allows the formation and stabilization of the functional conformational states of proteins through its entropy maximization and enthalpy effect (e.g., the formation of hydrogen bonds between the exposed electrostatically charged/polar side chains and the water molecules).…”

Section: Why Is the Solvent Entropy Effect (The Hydrophobic Force) Immentioning

confidence: 99%

“…In the protein-solvent system, the water molecules have an absolute advantage in both quantity and mass compared to the protein molecules [41]. The requirement for the solvent entropy maximization will retain as much as possible the highly dynamic hydrogen bonds among water molecules.…”

Section: Distinct Contribution Of Entropic and Enthalpic Components Tmentioning

confidence: 99%

“…In fact, the free energy is a systemic concept that ap-proximates the overall chemical potential of the protein-solvent system but not merely the solvation free energy of the protein. Furthermore, not only can the conformational change in the protein (i.e., the conformational entropy change of the protein) lead to a change in system free energy, but also the solvent entropy change and the formations and breakages of noncovalent bonds between atoms within the protein and from the protein and solvent (i.e., the enthalpy change), or any change of the solvent condition, e.g., the addition of acid, base, denaturant, cofactor, ligand, substrate or other compounds into the solution, can change the system free energy [41]. The steeper the free energy gradient is, the stronger the force exerted on the protein will be, and the higher the probability that the protein will move towards the lower region of the FEL of the protein-solvent system.…”

Section: Distinct Contribution Of Entropic and Enthalpic Components Tmentioning

confidence: 99%

“…Furthermore, because the protein folding process is very complex, changes in entropy and enthalpy dominate different stages of this process by contributing differentially to the lowering of the system free energy [41].…”

Section: Thermodynamics Of Protein Foldingmentioning

confidence: 99%

“…To address the kinetic question, the forces that drive and guide the protein folding process have to be ascertained and elucidated, thus invoking the thermodynamic question, the folding code and its action mechanism. Clearly, these two questions are closely related and both need to be solved to obtain a complete understanding of the protein folding mechanism [6,41].…”

Section: The Protein Folding Problemmentioning

confidence: 99%

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Physicochemical bases for protein folding, dynamics, and protein-ligand binding

Xie

Liu

et al. 2014

Sci. China Life Sci.

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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. free energy landscape, entropy-enthalpy non-complementarity, ruggedness, driving force, thermodynamics, kinetics Citation:Li HM, Xie YH, Liu CQ, Liu SQ. Physicochemical bases for protein folding, dynamics, and protein-ligand binding.

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Section: Why Is the Solvent Entropy Effect (The Hydrophobic Force) Immentioning

confidence: 99%

Section: Distinct Contribution Of Entropic and Enthalpic Components Tmentioning

confidence: 99%

Section: Distinct Contribution Of Entropic and Enthalpic Components Tmentioning

confidence: 99%

Section: Thermodynamics Of Protein Foldingmentioning

confidence: 99%

Section: The Protein Folding Problemmentioning

confidence: 99%

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