No data available.
Please log in to see this content.
You have no subscription access to this content.
No metrics data to plot.
The attempt to load metrics for this article has failed.
The attempt to plot a graph for these metrics has failed.
The full text of this article is not currently available.
The puckering free-energy surface of proline
6. K. Kawahara, Y. Nishi, S. Nakamura, S. Uchiyama, Y. Nishiuchi, T. Nakazawa, T. Ohkubo, and Y. Kobayashi, Biochemistry 44, 15812 (2005);
13. M. A. Sahai, T. A. K. Kehoe, J. C. P. Koo, D. H. Setiadi, G. A. Chass, B. Viskolcz, B. Penke, E. F. Pai, and I. G. Csizmadia, J. Phys. Chem. A 109, 2660 (2005).
22. D. Hamelberg, T. Shen, and J. A. McCammon, J. Am. Chem. Soc. 127, 1969 (2005);
22.T. Y. Shen, D. Hamelberg, and J. A. McCammon, Phys. Rev. E 73 (2006);
27. A. D. MacKerell, D. Bashford, M. Bellott, R. L. Dunbrack, J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus, J. Phys. Chem. B 102, 3586 (1998).
38. E. F. Pettersen, T. D. Goddard, C. C. Huang, G. S. Couch, D. M. Greenblatt, E. C. Meng, and T. E. Ferrin, J. Comput. Chem. 25, 1605 (2004).
Article metrics loading...
Proline has two preferred puckering states, which are often characterized by the pseudorotation phase angle and amplitude. Although proline's five endocyclic torsion angles can be utilized to calculate the phase angle and amplitude, it is not clear if there is any direct correlation between each torsion angle and the proline-puckering pathway. Here we have designed five proline puckering pathways utilizing each torsion angle χ j (j = 1∼5) as the reaction coordinate. By examining the free-energy surfaces of the five puckering pathways, we find they can be categorized into two groups. The χ 2 pathway (χ 2 is about the C β —C γ bond) is especially meaningful in describing proline puckering: it changes linearly with the puckering amplitude and symmetrically with the phase angle. Our results show that this conclusion applies to both trans and cis proline conformations. We have also analyzed the correlations of proline puckering and its backbone torsion angles ϕ and ψ. We show proline has preferred puckering states at the specific regions of ϕ, ψ angles. Interestingly, the shapes of ψ-χ 2 free-energy surfaces are similar among the trans proline in water, cis proline in water and cis proline in the gas phase, but they differ substantially from that of the trans proline in the gas phase. Our calculations are conducted using molecular simulations; we also verify our results using the proline conformations selected from the Protein Data Bank. In addition, we have compared our results with those calculated by the quantum mechanical methods.
Full text loading...
Most read this month