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Albany 2013: Book of Abstracts

category image Albany 2013
Conversation 18
June 11-15 2013
©Adenine Press (2012)

Wonderful roles of the entropy in protein dynamics, binding and folding

The entropy, which is central to the second law of thermodynamics, determines that the thermal energy always flows spontaneously from regions of higher temperature to regions of lower temperature. In the protein-solvent thermodynamic system, the entropy is defined as a measure of how evenly the thermal energy would distribute over the entire system (Liu, et al., 2012). Such tendency to distribute energy as evenly as possible will reduce the state of order of the initial system, and hence the entropy can be regarded as an expression of the disorder or randomness of the system (Yang, et al., 2012).

For a protein-solvent system under a constant solvent condition, the origin of entropy is the thermal energy stored in atoms, which makes atoms jostle around and bump onto one another, thus leading to vibrations of the covalent bonds connecting two atoms (occurring on the fs timescale) and the rotational and translational motions of amino acid side chain groups (occurring on ps timescale) and water molecules. These motions break the noncovalent bonds around the structural regions that are weakest constrained, thus triggering the competitive interactions among residues or between residues and water molecules, leading ultimately to the loop motions (occurring on ns timescale) around the protein surface. The loop motions can further transmit either through the water network around the protein surface or via specific structural components (such as the hinge-bending regions) over the entire protein molecule, thus leading to the large concerted motions (occurring on μs to s timescales) that are most relevant to protein functions (Amadei, Linssen & Berendsen, 1993; Tao, Rao & Liu, 2010). Thus, the multiple hierarchies of the protein dynamics on distinct timescales (Henzler-Wildman & Kern, 2007) are a consequence of the cascade amplification of the microscopic motions of atoms and groups, for which the entropy originating from atomic thermal energy is most fundamental.

In the case of protein-ligand binding, the importance of the entropy is embodied in the following aspects. (i) The release of the water molecule kinetic energy (which is a process of the solvent entropy maximization) will cause Brownian motions of individual water molecules, which result in strong Brownian bombardments to solute molecules causing molecule wanders/diffusions and subsequent accident contacts/collisions between proteins and ligands. (ii) Such collisions will inevitably cause water molecule displacement and, if the contact interfaces are properly complementary, the requirement to increase the solvent entropy would further displace the water network around the binding interfaces, thus leading to the formation the initial protein-ligand complex. (iii) In the initial complex, the loose association of the two partners provide the opportunity for protein to increase conformational entropy, thus triggering the conformational adjustments through competitive interaction between protein residues and ligand, leading ultimately to the formation of tightly associated complex (Liu, et al., 2012).

In the protein folding process, the first stage, i.e., the rapid hydrophobic collapse (Agashe, Shastry & Udgaonkar, 1995; Dill, 1985), is in fact driven by the effect of the solvent entropy maximization. Specifically, the requirement to maintain as many as possible the dynamic hydrogen bonds among the water molecules will squeeze/sequestrate the hydrophobic amino acid side chains into the interior of the folding intermediates and expose the polar/charged side chains onto the intermediate surface. This will minimize the solvent accessible surface area of the folding intermediates and as thus maximize the entropy of the solvent. The resulting molten globule states (Ohgushi & Wada, 1983) may contain a few secondary structural components and native tertiary contacts, while many native contacts, or close residue-residue interactions present in the native state, have not yet formed. However, the nature to increase the protein conformational entropy can trigger a further conformational adjustment process, i.e., the conformational entropy increase breaks the transient secondary or tertiary contacts and triggers the competitive interactions among protein residues and between residues and water. This process may repeat many rounds until the negative enthalpy change resulting from the noncovalent formations can overcompensate for protein conformational entropy loss.

In summary, we consider that the tendency to maximize the entropy of the protein-solvent system, which originates from the atomic thermal energy, is the most fundamental driving factor for protein folding, binding and dynamics, whereas the enthalpy reduction, an opposing factor that tends to make the system become ordered, can compensate for the effect of entropy loss to ultimately allow the system to reach equilibrium at the free energy minima, either global or local.

This research is supported by NSFC (No. 31160181 and 30860011) and project of innovation term of Yunnan province (2011CI123).

References

    Agashe, V. R., Shastry, M. C. R., & Udgaonkar, J. B. (1995). Initial hydrophobic collapse in the folding of barstar. Nature, 377, 754-757.

    Amadei, A., Linssen, A. B. M., & Berendsen, H. J. C. (1993). Essential dynamics of proteins. Proteins: Structure, Function, and Genetics, 17, 412-425.

    Dill, K. A. (1985). Theory for the folding and stability of globular proteins. Biochemistry, 24, 1501-1509.

    Henzler-Wildman, K. A., & Kern, D. (2007). Dynamic personalities of proteins. Nature, 450, 964-972.

    Liu, S. Q., Xie, Y. H., Ji, X. L., Tao, Y., Tan, D. Y., Zhang, K. Q., & Fu, Y. X. (2012). Protein folding, binding and energy landscape: A synthesis. In P. T. P. Kaumaya (Ed.), Protein engineering (pp. 207-252). Rijeka: Intech.

    Ohgushi, M., & Wada, A. (1983). 'Molten-globule state': a compact form of globular proteins with mobile side-chains. FEBS Letters, 164, 21-24.

    Tao, Y., Rao, Z. H., & Liu, S. Q. (2010). Insight derived from molecular dynamics simulation into substrate-induced changes in protein motions of proteinase K. Journal of Biomolecular Structure and Dynamics, 28, 143-157.

    Yang, L. Q., Sang, P., Xie, Y. H., Tao, Y., Fu, Y. X., Zhang, K. Q., & Liu, S. Q. (2013). Protein dynamics and motions in relation to their functions: several case studies and the underlying mechanisms. Journal of Biomolecular Structure and Dynamics, In press.


Yue-Hui Xie a
Yan Tao b
Shu-Qun Liu b*

aTeaching and Research Section of computer
Department of Basic Medical Kunming Medical College
Kunming 650031, P.R. China
bLaboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education
Yunnan University
Kunming 650091, P. R. China

*Corresponding author
Ph: (86)871-5035257
shuqunliu@gmail.com