Albany 2013: Book of Abstracts

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

Protein folding and binding funnels: a common driving force and a common mechanism

Under the free energy landscape theory, both the protein folding and protein-ligand binding processes are driven by the decrease in total Gibbs free energy of the protein-solvent or protein-ligand-solvent system, which involves the non-complementary changes between the entropy and enthalpy, ultimately leading to a global free energy minimization of these thermodynamic systems (Ji & Liu, 2011; Liu, et al., 2012; Yang, Ji & Liu, 2012).

In the case of protein folding, the lowering of the system free energy coupled with the gradual reduction in conformational degree of freedom of the folding intermediates determines that the shape of the free energy landscape for protein folding must be funnel-like (Dill & Chan, 1997), rather than non-funneled shapes (Ben-Naim, 2012). In the funnel-like free energy landscape, protein folding can be viewed as going down the hill via multiple parallel routes from a vast majority of individual non-native states on surface outside the funnel to the native states located around the bottom of the funnel. The first stage of folding, i.e., the rapid hydrophobic collapse process, is driven by the solvent entropy maximization. Concretely, the water molecules squeeze and sequestrate the hydrophobic amino acid side chains within the interior of the folding intermediates while exposing the polar and electrostatically charged side chains on the intermediate surface so as to minimize the solvent accessible surface area of the solute and thus, the minimal contacts between the folding intermediates and the water molecules. This will maximize the entropy of the solvent, thus contributing substantially to lowering of the system free energy due to an absolute advantage of the solvent in both quantity and mass (Yang, Ji & Liu, 2012). The resulting molten globule states (Ohgushi & Wada, 1983), within which a few transient secondary structural components and tertiary contacts have been formed but many native contacts or close residue-residue interactions has yet to form, need to be further sculptured into the native states. This is a relatively slow “bottleneck” process because the competitive interactions between protein residues within the folding intermediates and between residues and water molecules may repeat many rounds to accumulate a large enough number of stable noncovalent bonds capable of counteracting the conformational entropy loss of the intermediates, thus putting this bottleneck stage under the enthalpy control (i.e., negative enthalpy change), contributing further to the lowering of the system free energy.

Although the protein-ligand association occurs around the rugged bottom of the free energy landscape, the exclusion of water from the binding interfaces and the formation of noncovalent bonds between the two partners can still lower the system free energy. In conjunction with the loss of the rotational and translational degrees of freedom of the two partners as well as the loss of the conformational entropy of the protein, these processes could merge, downwards expand, and further narrow the free energy wells within which the protein-ligand binding process takes place, thereby making them look like a funnel, which we term the binding funnel. In this funnel, the free energy downhill process follows a similar paradigm to the protein folding process. For example, if the initial collisions/contacts occur between the properly complementary interfaces of the protein and ligand, a large amount of water molecules (which usually form a water network around the solute surface) will be displaced to suit the need for maximizing the solvent entropy. This process is similar to that of the hydrophobic collapse during protein folding, resulting in a loosely associated protein-ligand complex that needs also to be further adapted into a tight complex, i.e., the second step which is mainly driven by the negative enthalpy change through intermolecular competitive interactions to gradually accumulate the noncovalent bonds and ultimately, to stabilize the complex at a tightly bound state. Taken together, we conclude that, whether in the protein folding or in the protein-ligand binding process, both the entropy-driven first step and the enthalpy-driven second step contribute to the lowering of the system free energy, resulting in the funnel-like folding or binding free energy landscape.

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


    Ben-Naim, A. (2012). Levinthal’s question revisited, and answered. Journal of Biomolecular Structure and Dynamics, 30, 113-124.

    Dill, K. A., & Chan, H. S. (1997). From Levinthal to pathways to funnels. Nature Structural Biology, 4, 10-19.

    Ji, X. L., & Liu, S. Q. (2011). Thinking into mechanism of protein folding and molecular binding. Journal of Biomolecular Structure and Dynamics, 28, 995-996.

    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.

    Yang, L. Q., Ji, X. L., & Liu, S. Q. (2012). The free energy landscape of protein folding and dynamics - a global view. Journal of Biomolecular Structure and Dynamics, in press.

Yue-Hui Xie a
Peng Sangb
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