Proline puckering parameters for collagen structure simulations
- Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438 (China)
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.
- OSTI ID:
- 22454477
- Journal Information:
- AIP Advances, Vol. 5, Issue 3; Other Information: (c) 2015 Author(s); Country of input: International Atomic Energy Agency (IAEA); ISSN 2158-3226
- Country of Publication:
- United States
- Language:
- English
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