Allosteric Communication Pathways and Thermal Rectification in PDZ-2 Protein: A Computational Study

Author(s)

Mino-Galaz, German A. ^[1]

Affiliation

^[1] Univ Chile, Fac Ciencias, Dept Fis, Grp Nanomat, Santiago - Chile

• Document type: Journal article
• Source: Journal of Physical Chemistry B; v. 119, n. 20, p. 6179-6189, MAY 21 2015.
• Web of Science Citations: 19

Abstract

Allosteric communication in proteins is a fundamental and yet unresolved problem of structural biochemistry. Previous findings, from computational biology (Ota, N.; Agard, D. A. J. Mol. Biol. 2005, 351, 345-354), have proposed that heat diffuses in a protein through cognate protein allosteric pathways. This work studied heat diffusion in the well-known PDZ-2 protein, and confirmed that this protein has two cognate allosteric pathways and that heat flows preferentially through these. Also, a new property was also observed for protein structures: heat diffuses asymmetrically through the structures. The underling structure of this asymmetrical heat flow was a normal length hydrogen bond (similar to 2.85 angstrom) that acted as a thermal rectifier. In contrast, thermal rectification was compromised in short hydrogen bonds (similar to 2.60 angstrom), giving rise to symmetrical thermal diffusion. Asymmetrical heat diffusion was due, on a higher scale, to the local, structural organization of residues that, in turn, was also mediated by hydrogen bonds. This asymmetrical/symmetrical energy flow may be relevant for allosteric signal communication directionality in proteins and for the control of heat flow in materials science. (AU)

• FAPESP's process: 13/05475-7 - Computational methods in optimization
• Grantee: Sandra Augusta Santos
• Support type: Research Projects - Thematic Grants
• FAPESP's process: 10/16947-9 - Correlations between dynamics, structure and function in protein: computer simulations and algorithms
• Grantee: Leandro Martinez
• Support type: Regular Research Grants