On the Use of the Discrete Constant pH Molecular Dynamics to Describe the Conformational Space of Peptides
Abstract
:1. Introduction
2. Materials and Methods
3. Results
3.1. Gibbs Free Energies in the Ramachandran Space
3.1.1. Basic pKa Amino Acids
3.1.2. Histidine
3.1.3. Acidic Amino Acids
3.2. Energetic Contributions
3.3. Side Chain Orientation and Atom Distances
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Residue | CMD | CpHMD | Prot. State. | Intrinsic pKa | ||
---|---|---|---|---|---|---|
pH 1 | pH 12 | pH 14 | ||||
ASP | ✓ | D | 4.0 | |||
ASH | ✓ | P | ||||
AS4 | ✓ | ✓ | T | |||
GLU | ✓ | D | 4.4 | |||
GLH | ✓ | P | ||||
GL4 | ✓ | ✓ | T | |||
HIE | ✓ | D | 7.1 (ε) 6.5 (δ) | |||
HID | ✓ | D | ||||
HIP | ✓ | ✓ | ✓ | P/T | ||
CYM | ✓ | D | 8.5 | |||
CYS | ✓ | ✓ | ✓ | P/T | ||
TYR | ✓ | ✓ | P/T | 9.6 | ||
LYN | ✓ | D | 10.4 | |||
LYS | ✓ | ✓ | ✓ | P/T |
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Privat, C.; Madurga, S.; Mas, F.; Rubio-Martínez, J. On the Use of the Discrete Constant pH Molecular Dynamics to Describe the Conformational Space of Peptides. Polymers 2021, 13, 99. https://doi.org/10.3390/polym13010099
Privat C, Madurga S, Mas F, Rubio-Martínez J. On the Use of the Discrete Constant pH Molecular Dynamics to Describe the Conformational Space of Peptides. Polymers. 2021; 13(1):99. https://doi.org/10.3390/polym13010099
Chicago/Turabian StylePrivat, Cristian, Sergio Madurga, Francesc Mas, and Jaime Rubio-Martínez. 2021. "On the Use of the Discrete Constant pH Molecular Dynamics to Describe the Conformational Space of Peptides" Polymers 13, no. 1: 99. https://doi.org/10.3390/polym13010099
APA StylePrivat, C., Madurga, S., Mas, F., & Rubio-Martínez, J. (2021). On the Use of the Discrete Constant pH Molecular Dynamics to Describe the Conformational Space of Peptides. Polymers, 13(1), 99. https://doi.org/10.3390/polym13010099