Tuyển tập các báo cáo nghiên cứu về y học được đăng trên tạp chí y học quốc tế cung cấp cho các bạn kiến thức về ngành y đề tài: High-Temperature unfolding of a trp-Cage mini-protein: a molecular dynamics simulation study | Theoretical Biology and Medical Modelling BioMed Central Research High-Temperature unfolding of a trp-Cage mini-protein a molecular dynamics simulation study Aswin Sai Narain Seshasayee Open Access Address Centre for Biotechnology Anna University Chennai 600025 India Email Aswin Sai Narain Seshasayee - Corresponding author Published II March 2005 Received 09 October 2004 Theoretical Biology and Medical Modelling 2005 2 7 doi 1742-4682-2-7 Accepted 11 March 2005 This article is available from http content 2 1 7 2005 Seshasayee licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License http licenses by which permits unrestricted use distribution and reproduction in any medium provided the original work is properly cited. Abstract Background Trp cage is a recently-constructed fast-folding miniprotein. It consists of a short helix a 3 10 helix and a C-terminal poly-proline that packs against a Trp in the alpha helix. It is known to fold within 4 ns. Results High-temperature unfolding molecular dynamics simulations of the Trp cage miniprotein have been carried out in explicit water using the OPLS-AA force-field incorporated in the program GROMACS. The radius of gyration Rg and Root Mean Square Deviation RMSD have been used as order parameters to follow the unfolding process. Distributions of Rg were used to identify ensembles. Conclusion Three ensembles could be identified. While the native-state ensemble shows an Rg distribution that is slightly skewed the second ensemble which is presumably the Transition State Ensemble TSE shows an excellent fit. The denatured ensemble shows large fluctuations but a Gaussian curve could be fitted. This means that the unfolding process is two-state. Representative structures from each of these ensembles are presented here. Background Understanding the mechanisms behind protein folding which is one
