A Peptide Potential Based on a Bond Dipole Representation of Electrostatics
Abstract
:1. Introduction
2. Theoretical Model
3. Parameterization
3.1. Parameters for Electrostatics
3.2. Parameters for Van Der Waals
3.3. Parameters for Bonded Terms
3.4. Scale Factors for Intramolecular Dipole–Dipole Interactions
4. Applications
4.1. Conformational Energy
4.2. Intermolecular Interaction Energy
4.3. Structures
4.4. Efficiency
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Parameters for Electrostatics | μ0 (Debye) | c | q0 |
---|---|---|---|
C=O | 2.65 | 1.80 | −0.3800 |
C=O(Ac) | 2.65 | 1.80 | −0.3720 |
N-H | 1.51 | 1.00 | 0.2690 |
N-H(NHMe), NA-H | 1.51 | 1.00 | 0.2360 |
N-HQ | 1.31 | 1.80 | 0.2373 |
CT-H1 | 0.70 | 1.00 | 0.1150 |
CT-OH | 0.70 | 0.00 | -- |
CA-OH | 0.70 | 0.00 | -- |
OW-HW | 1.51 | 1.86 | 0.1942 |
OH-HO | 1.51 | 1.00 | 0.2164 |
CT-SH | 0.90 | 0.00 | -- |
CT-S | 0.90 | 0.00 | -- |
SH-HS | 0.65 | 1.00 | 0.0304 |
Scale factors for intramolecular dipole-dipole interactions | |||
two dipoles separated by 3 bonds | 0.75 | ||
two dipoles separated by 4 bonds | 0.90 | ||
Parameters for van der Waals | R*(Å) | ε (kcal/mol) | |
C, CA, CB, CC, C*, CN, CW, CV, CR | 1.9080 | 0.0860 | |
CT | 1.9080 | 0.1094 | |
N, NA, NB | 1.6240 | 0.1700 | |
O, O(Ac) | 1.6612 | 0.2100 | |
OH | 1.7210 | 0.2104 | |
S, SH | 2.0000 | 0.6500 | |
H, HQ, H(NHMe) | 0.8000 | 0.0157 | |
H1, H2, HC | 1.3000 | 0.0157 | |
HA | 1.4590 | 0.0150 | |
HO | 0.0000 | 0.0000 | |
H4 | 1.4090 | 0.0150 | |
H5 | 1.3590 | 0.0150 | |
HS | 0.6000 | 0.0157 |
X | Conformer | M06-2X/cc-pVTZ | AMBER99sb | Δ | AMOEBAbio18 | Δ | This Work | Δ |
---|---|---|---|---|---|---|---|---|
Val | helix | −17.76 | −23.91 | −6.15 | −24.84 | −7.08 | −15.77 | 1.98 |
C5 | 7.87 | 9.39 | 1.51 | −6.96 | −14.83 | 10.68 | 2.81 | |
Ile | helix | −19.07 | −24.82 | −5.75 | −27.55 | −8.48 | −16.62 | 2.46 |
C5 | 6.71 | 8.18 | 1.47 | −10.84 | −17.55 | 9.03 | 2.32 | |
Leu | helix | −17.20 | −24.53 | −7.33 | −25.51 | −8.31 | −15.84 | 1.36 |
C5 | 9.28 | 9.32 | 0.04 | −10.88 | −20.16 | 9.80 | 0.52 | |
Phe | helix | −16.32 | −23.40 | −7.08 | −24.46 | −8.14 | −15.94 | 0.38 |
C5 | 7.48 | 8.34 | 0.86 | −11.79 | −19.27 | 8.01 | 0.53 | |
Asn | helix | −18.65 | −26.42 | −7.77 | −27.27 | −8.62 | −17.84 | 0.81 |
C5 | 9.19 | 9.91 | 0.72 | −8.97 | −18.16 | 7.25 | −1.95 | |
Gln | helix | −22.50 | −30.17 | −7.67 | −32.62 | −10.12 | −19.23 | 3.27 |
C5 | 9.56 | 11.27 | 1.71 | −10.74 | −20.30 | 10.93 | 1.37 | |
Ser | helix | −11.48 | −17.86 | −6.38 | −19.04 | −7.56 | −12.52 | −1.04 |
C5 | 11.29 | 11.75 | 0.46 | −6.02 | −17.31 | 11.42 | 0.13 | |
Thr | helix | −11.46 | −18.09 | −6.63 | −17.64 | −6.18 | −12.25 | −0.79 |
C5 | 11.34 | 13.27 | 1.93 | −1.85 | −13.19 | 12.75 | 1.41 | |
Tyr | helix | −16.14 | −22.80 | −6.66 | −24.26 | −8.12 | −15.59 | 0.55 |
C5 | 7.62 | 10.10 | 2.48 | −8.79 | −16.41 | 10.83 | 3.21 | |
Cys | helix | −16.11 | −22.79 | −6.68 | −23.57 | −7.46 | −14.67 | 1.44 |
C5 | 8.85 | 10.35 | 1.50 | −9.16 | −18.01 | 10.88 | 2.03 | |
Hid | helix | −17.85 | −27.27 | −9.42 | −28.55 | −10.70 | −16.53 | 1.32 |
C5 | -- | -- | -- | -- | -- | -- | -- | |
Hie | helix | −18.51 | −24.19 | −5.68 | −26.98 | −8.47 | −13.80 | 4.71 |
C5 | 7.70 | 8.06 | 0.36 | −10.78 | −18.48 | 8.21 | 0.51 | |
Met | helix | −19.47 | −25.47 | −6.00 | −27.61 | −8.14 | −16.10 | 3.37 |
C5 | 7.46 | 7.16 | −0.30 | −13.08 | −20.54 | 8.18 | 0.72 | |
Trp | helix | −19.38 | −28.34 | −8.97 | −29.24 | −9.87 | −15.87 | 3.51 |
C5 | 4.37 | 1.36 | −3.01 | −17.42 | −21.79 | 4.06 | −0.32 | |
Max Absolute Error | 9.42 | 21.79 | 4.71 | |||||
RMSE | 5.22 | 14.08 | 2.04 |
Conformer | QM | AMBER99sb | Δ | AMOEBAbio18 | Δ | This Work | Δ | |
---|---|---|---|---|---|---|---|---|
AcAla13NH2 | helix | −34.73 | −46.57 | −11.84 | −48.05 | −13.32 | −32.73 | 2.00 |
C5 | 12.33 | 14.91 | 2.58 | −15.06 | −27.39 | 13.86 | 1.53 | |
Ac(Ala2GlnAla2)3NH2 | helix | −49.72 | −62.99 | −13.27 | −57.51 | −7.79 | −48.25 | 1.47 |
C5 | 16.38 | 15.75 | −0.63 | −9.51 | −25.89 | 15.96 | −0.42 |
Hydrogen-Bonded Dimer | QM a | AMBER99sb | Δ | AMOEBAbio18 | Δ | This Work | Δ |
---|---|---|---|---|---|---|---|
antiparallel glycine tripeptide | −21.65 | −21.77 (84.4%) | −0.12 | −21.54 (106.0%) | 0.11 | −22.62 (83.4%) | −0.97 |
parallel glycine tripeptide | −16.80 | −15.31 (96.5%) | 1.49 | −15.61 (98.2%) | 1.19 | −17.25(88.7%) | −0.45 |
antiparallel glycine pentapeptide | −33.69 | −36.08 (81.8%) | −2.39 | −36.10 (104.3%) | −2.41 | −36.26 (81.0%) | −2.57 |
parallel glycine pentapeptide | −27.18 | −25.34 (93.6%) | 1.84 | −26.42 (95.8%) | 0.76 | −27.30 (87.3%) | −0.12 |
antiparallel alanine tripeptide | −25.22 | −23.34 (85.4%) | 1.88 | −23.10 (113.9%) | 2.12 | −24.61 (86.2%) | 0.61 |
parallel alanine tripeptide | −24.54 | −22.92 (85.0%) | 1.62 | −21.17 (112.4%) | 3.37 | −24.88 (85.5%) | −0.34 |
antiparallel alanine tetrapeptide | −30.07 | −29.12 (81.0%) | 0.95 | −29.60 (109.5%) | 0.47 | −30.12 (81.9%) | −0.05 |
parallel alanine tetrapeptide | −32.38 | −30.20 (85.4%) | 2.18 | −28.47 (111.9%) | 3.91 | −32.46 (85.0%) | −0.08 |
RMSE | 1.70 | 2.21 | 1.02 |
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Li, Y.-M.; Zheng, X.-H.; Li, C.-M.; Liu, Q.; Wang, L.; Hao, Q.; Wang, C.-S. A Peptide Potential Based on a Bond Dipole Representation of Electrostatics. Processes 2023, 11, 1291. https://doi.org/10.3390/pr11041291
Li Y-M, Zheng X-H, Li C-M, Liu Q, Wang L, Hao Q, Wang C-S. A Peptide Potential Based on a Bond Dipole Representation of Electrostatics. Processes. 2023; 11(4):1291. https://doi.org/10.3390/pr11041291
Chicago/Turabian StyleLi, Yan-Min, Xiao-Han Zheng, Chao-Ming Li, Qi Liu, Lei Wang, Qiang Hao, and Chang-Sheng Wang. 2023. "A Peptide Potential Based on a Bond Dipole Representation of Electrostatics" Processes 11, no. 4: 1291. https://doi.org/10.3390/pr11041291
APA StyleLi, Y.-M., Zheng, X.-H., Li, C.-M., Liu, Q., Wang, L., Hao, Q., & Wang, C.-S. (2023). A Peptide Potential Based on a Bond Dipole Representation of Electrostatics. Processes, 11(4), 1291. https://doi.org/10.3390/pr11041291