- Article -
| In Silico Biology 9, 0023 (2009); ©2009, Bioinformation Systems e.V. |
Conformational dynamics and thermal stabilities of the αβ-tubulin dimer: a molecular dynamics simulation study
Xiaomin Wu, Gang Yang*, Yuangang Zu*, Zhiwei Yang and Lijun Zhou
Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, P. R. China
* Corresponding author
Email: theobiochem@gmail.com
Edited by E. Wingender; received September 19, 2008; revised May 14, 2009; accepted May 21, 2009; published July 19, 2009
Abstract
Molecular dynamics simulations were employed to study the conformational dynamics and thermal stabilities of the large αβ-tubulin dimer systems under various conditions. The αβ-tubulin dimer at ambient and cryogenic temperatures remains stable around the native conformations, and the water solvent molecules tend to stabilize the native conformations through the formation of complex hydrogen-bonding networks. The elevation of temperature severely destroys the native conformations and the bioactivities, especially in aqueous solution. It was caused by the lack of intra- and inter-molecular interactions and the decrease of water polarity at higher temperatures. The conformational analysis of the selected segment (β15-QIGAKFWEVIS) provides detailed information on the whole proteins. It was revealed that the local structures of proteins at ambient and cryogenic temperatures have obvious differences albeit the overall structures are close to each other. The selected segments under high temperatures are dominated by random coils instead of native helix at ambient and cryogenic temperatures, accompanied by more diversities and faster conversions of conformations. In addition, the temperature or/and the solvent are capable of altering the secondary structures and further the conformations of the segments and the whole proteins. At ambient temperatures, the water solvent helps the proteins to achieve the native conformation with bioactivities. Different from the corresponding segments in proteins, the truncated peptides are endowed with higher structural flexibilities and characterized by random coils even at ambient temperatures, along with the disappearance of helical hydrogen bonds.
Keywords: protein structures, stability, solvent effects, tubulin segments, molecular dynamics