Paper Citing NAMD - Abstract
Ding, Yanrui; Cai, Yujie
Conformational dynamics of xylanase a from Streptomyces lividans: Implications for TIM-barrel enzyme thermostability
BIOPOLYMERS, 99:594-604, SEP 2013
The conformational dynamics of xylanase A from Streptomyces lividans (Sl-XlnA) were studied using Molecular Dynamics (MD) simulation to identify the thermally sensitive regions. Sl-XlnA begins to unfold at loop4 and this unfolding expands to the loops near the N-terminus. The high flexibility of loop6 during the 300 K simulation is related to its function. The intense movements of the 310-helices also affect the structural stability. The interaction between the 45-loop and the neighboring 56-loop plays a crucial role in stabilizing the region from the 45-loop to 6. The most thermally sensitive region is from 3 to loop4. The high mobility of the long loop4 easily transfers to the adjacent 4 and 4 and causes 4 and 4 to fluctuate. And, salt bridges ASP124-ARG79, ASP200-ARG159, and ASP231-LYS166 formed a clamp to stabilize the region including 4, 4, 5, 6, and 7. (c) 2013 Wiley Periodicals, Inc. Biopolymers 99: 573-581, 2013.
