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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

A topological measurement of protein compressibility

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Author(s):
Gameiro, Marcio [1] ; Hiraoka, Yasuaki [2] ; Izumi, Shunsuke [3] ; Kramar, Miroslav [4] ; Mischaikow, Konstantin [5] ; Nanda, Vidit [6]
Total Authors: 6
Affiliation:
[1] Univ Sao Paulo, Inst Ciencias Matemat & Comp, BR-13560970 Sao Carlos, SP - Brazil
[2] Kyushu Univ, Inst Math Ind, Nishi Ku, Fukuoka 8190395 - Japan
[3] Hiroshima Univ, Dept Math & Life Sci, Higashihiroshima 7398526 - Japan
[4] Rutgers State Univ, Dept Math, Piscataway, NJ 08854 - USA
[5] Rutgers State Univ, Dept Math & BioMaPS, Piscataway, NJ 08854 - USA
[6] Univ Penn, Dept Math, Philadelphia, PA 19104 - USA
Total Affiliations: 6
Document type: Journal article
Source: JAPAN JOURNAL OF INDUSTRIAL AND APPLIED MATHEMATICS; v. 32, n. 1, p. 1-17, MAR 2015.
Web of Science Citations: 34
Abstract

In this paper we partially clarify the relation between the compressibility of a protein and its molecular geometric structure. To identify and understand the relevant topological features within a given protein, we model its molecule as an alpha filtration and hence obtain multi-scale insight into the structure of its tunnels and cavities. The persistence diagrams of this alpha filtration capture the sizes and robustness of such tunnels and cavities in a compact and meaningful manner. From these persistence diagrams, we extract a measure of compressibility derived from those topological features whose relevance is suggested by physical and chemical properties. Due to recent advances in combinatorial topology, this measure is efficiently and directly computable from information found in the Protein Data Bank (PDB). Our main result establishes a clear linear correlation between the topological measure and the experimentally-determined compressibility of most proteins for which both PDB information and experimental compressibility data are available. Finally, we establish that both the topological measurement and the linear correlation are stable with respect to small perturbations in the input data, such as those arising from experimental errors in compressibility and X-ray crystallography experiments. (AU)

FAPESP's process: 10/00875-9 - Topological methods and rigorous numerics for bifurcations of dynamical systems
Grantee:Marcio Fuzeto Gameiro
Support Opportunities: Regular Research Grants
FAPESP's process: 13/07460-7 - Rigorous computations for PDEs
Grantee:Marcio Fuzeto Gameiro
Support Opportunities: Regular Research Grants