A simple way to compute protein dynamics without a mechanical model.
We found that in proteins the average atomic fluctuation is linearly related to the square of the atomic distance from the center of mass of the protein. Using this simple relation, we can accurately compute the temperature factors of proteins of a wide range of sizes and folds, and the correlation of the fluctuations in proteins. This simple relation provides a direct link between protein dynamics and the static protein's geometrical shape and offers a simple way to compute protein dynamics without either long time trajectory integration or any matrix operations.
Shih
Chien-Hua
CH
Institute of Bioinformatics, National Chiao Tung University, HsinChu 30050, Taiwan, Republic of China.
Huang
Shao-Wei
SW
Yen
Shih-Chung
SC
Lai
Yan-Long
YL
Yu
Sung-Huan
SH
Hwang
Jenn-Kang
JK
D000465:Algorithms; D007700:Kinetics; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D013329:Structure-Activity Relationship; D013696:Temperature
D011506:Proteins