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Title: Proline puckering parameters for collagen structure simulations

Abstract

Collagen is made of triple helices rich in proline residues, and hence is influenced by the conformational motions of prolines. Because the backbone motions of prolines are restricted by the helical structures, the only side chain motion—proline puckering—becomes an influential factor that may affect the stability of collagen structures. In molecular simulations, a proper proline puckering population is desired so to yield valid results of the collagen properties. Here we design the proline puckering parameters in order to yield suitable proline puckering populations as demonstrated in the experimental results. We test these parameters in collagen and the proline dipeptide simulations. Compared with the results of the PDB and the quantum calculations, we propose the proline puckering parameters for the selected collagen model simulations.

Authors:
 [1]
  1. Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438 (China)
Publication Date:
OSTI Identifier:
22454477
Resource Type:
Journal Article
Resource Relation:
Journal Name: AIP Advances; Journal Volume: 5; Journal Issue: 3; Other Information: (c) 2015 Author(s); Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United States
Language:
English
Subject:
36 MATERIALS SCIENCE; COLLAGEN; COMPARATIVE EVALUATIONS; DESIGN; PROLINE; RESIDUES; SIMULATION; STABILITY

Citation Formats

Wu, Di, E-mail: diwu@fudan.edu.cn. Proline puckering parameters for collagen structure simulations. United States: N. p., 2015. Web. doi:10.1063/1.4915295.
Wu, Di, E-mail: diwu@fudan.edu.cn. Proline puckering parameters for collagen structure simulations. United States. doi:10.1063/1.4915295.
Wu, Di, E-mail: diwu@fudan.edu.cn. Sun . "Proline puckering parameters for collagen structure simulations". United States. doi:10.1063/1.4915295.
@article{osti_22454477,
title = {Proline puckering parameters for collagen structure simulations},
author = {Wu, Di, E-mail: diwu@fudan.edu.cn},
abstractNote = {Collagen is made of triple helices rich in proline residues, and hence is influenced by the conformational motions of prolines. Because the backbone motions of prolines are restricted by the helical structures, the only side chain motion—proline puckering—becomes an influential factor that may affect the stability of collagen structures. In molecular simulations, a proper proline puckering population is desired so to yield valid results of the collagen properties. Here we design the proline puckering parameters in order to yield suitable proline puckering populations as demonstrated in the experimental results. We test these parameters in collagen and the proline dipeptide simulations. Compared with the results of the PDB and the quantum calculations, we propose the proline puckering parameters for the selected collagen model simulations.},
doi = {10.1063/1.4915295},
journal = {AIP Advances},
number = 3,
volume = 5,
place = {United States},
year = {Sun Mar 15 00:00:00 EDT 2015},
month = {Sun Mar 15 00:00:00 EDT 2015}
}