Dynamical Behavior of β-Lactamases and Penicillin- Binding Proteins in Different Functional States and Its Potential Role in Evolution
Abstract
:1. Introduction
2. Materials and Methods
2.1. Molecular Dynamic Simulations
2.2. Root-Mean-Square Fluct+uation (RMSF)
2.3. Principal Component Analysis (PCA)
2.4. Configurational Entropy
2.5. Time-Structure-Based Independent Component Analysis (t-ICA)
2.6. Markov State Models (MSMs)
2.7. Hidden Markov Model (HMM)
2.8. Transition-Path Theory
3. Results
3.1. Hidden Markov State Models Analysis of Overall Structures
3.2. Analysis of Active Site Structures Using Markov State Models
3.3. Atomic Distance
3.4. Configurational Entropy
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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TEM-1 | TOHO-1 | PBP-A | DD-Transpeptidase |
---|---|---|---|
S70 | S70 | S61 | S62 |
K73 | K73 | K64 | K65 |
S130 | S130 | S122 | Y159 |
N132 | N132 | N124 | N161 |
N166 | A166 | L158 | A237 |
K234 | K234 | K219 | H298 |
S235 | T235 | T220 | T299 |
A237 | S237 | D222 | T301 |
G244 | N245 | G228 | T307 |
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Wang, F.; Zhou, H.; Wang, X.; Tao, P. Dynamical Behavior of β-Lactamases and Penicillin- Binding Proteins in Different Functional States and Its Potential Role in Evolution. Entropy 2019, 21, 1130. https://doi.org/10.3390/e21111130
Wang F, Zhou H, Wang X, Tao P. Dynamical Behavior of β-Lactamases and Penicillin- Binding Proteins in Different Functional States and Its Potential Role in Evolution. Entropy. 2019; 21(11):1130. https://doi.org/10.3390/e21111130
Chicago/Turabian StyleWang, Feng, Hongyu Zhou, Xinlei Wang, and Peng Tao. 2019. "Dynamical Behavior of β-Lactamases and Penicillin- Binding Proteins in Different Functional States and Its Potential Role in Evolution" Entropy 21, no. 11: 1130. https://doi.org/10.3390/e21111130