Note: On the universality of proximal radial distribution functions of proteins

Bin Lin; B. Montgomery Pettitt

doi:10.1063/1.3565035

Note: On the universality of proximal radial distribution functions of proteins

Bin Lin, B. Montgomery Pettitt

Research output: Contribution to journal › Article › peer-review

22 Scopus citations

Abstract

Protein hydration is important to protein structure and function. Molecular distribution functions have been an invaluable tool to study protein hydration. Proximal radial distribution functions (pRDFs) have been postulated as being transferable across proteins based on evidence collected from two proteins V. A. Makarov, B. K. Andrews, and B. M. Pettitt, Biopolymers 45(7), 469 (1998). Here we selected nine proteins with different sizes as well as different secondary topologies. We show that pRDFs are universal for proteins with compact structures. We further compare these pRDFs with those calculated from polyglycines that have no defined structures to consider the extent of the validity of this approach.

Original language	English (US)
Article number	106101
Journal	Journal of Chemical Physics
Volume	134
Issue number	10
DOIs	https://doi.org/10.1063/1.3565035
State	Published - Mar 14 2011
Externally published	Yes

ASJC Scopus subject areas

General Physics and Astronomy
Physical and Theoretical Chemistry

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10.1063/1.3565035

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title = "Note: On the universality of proximal radial distribution functions of proteins",

abstract = "Protein hydration is important to protein structure and function. Molecular distribution functions have been an invaluable tool to study protein hydration. Proximal radial distribution functions (pRDFs) have been postulated as being transferable across proteins based on evidence collected from two proteins V. A. Makarov, B. K. Andrews, and B. M. Pettitt, Biopolymers 45(7), 469 (1998). Here we selected nine proteins with different sizes as well as different secondary topologies. We show that pRDFs are universal for proteins with compact structures. We further compare these pRDFs with those calculated from polyglycines that have no defined structures to consider the extent of the validity of this approach.",

author = "Bin Lin and Pettitt, {B. Montgomery}",

note = "Funding Information: The authors thank G. C. Lynch, K.-Y. Wong, H. Kokubo, and C. Y. Hu for many valuable discussions. We thank NIH (GM-037657) and the R. A. Welch Foundation (E-1024) for partial financial support. The computations were performed in part using the NSF metacenter facilities and the Molecular Science Computing Facility sponsored by DOE's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory, operated by Battelle.",

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N2 - Protein hydration is important to protein structure and function. Molecular distribution functions have been an invaluable tool to study protein hydration. Proximal radial distribution functions (pRDFs) have been postulated as being transferable across proteins based on evidence collected from two proteins V. A. Makarov, B. K. Andrews, and B. M. Pettitt, Biopolymers 45(7), 469 (1998). Here we selected nine proteins with different sizes as well as different secondary topologies. We show that pRDFs are universal for proteins with compact structures. We further compare these pRDFs with those calculated from polyglycines that have no defined structures to consider the extent of the validity of this approach.

AB - Protein hydration is important to protein structure and function. Molecular distribution functions have been an invaluable tool to study protein hydration. Proximal radial distribution functions (pRDFs) have been postulated as being transferable across proteins based on evidence collected from two proteins V. A. Makarov, B. K. Andrews, and B. M. Pettitt, Biopolymers 45(7), 469 (1998). Here we selected nine proteins with different sizes as well as different secondary topologies. We show that pRDFs are universal for proteins with compact structures. We further compare these pRDFs with those calculated from polyglycines that have no defined structures to consider the extent of the validity of this approach.

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Note: On the universality of proximal radial distribution functions of proteins

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