Molecular Dynamics Investigation of Phenolic Oxidative Coupling Protein Hyp-1 Derived from Hypericum perforatum
Abstract
:1. Introduction
2. Materials and Methods
2.1. Hyp-1 Structure Model
2.2. Molecular Dynamics Simulation
2.3. Comparison between Experimental and Simulated Structure Model
2.4. Application of MD Nanoscale Simulation to Calculate ADPs Distribution
2.5. Stereochemical Constraints of Main- and Side-Chain Conformations
2.6. Comparison between Experimental and Calculated Distributions of Side-Chain Dihedral Angles
3. Results and Discussion
3.1. Impact of MD Simulation Parameters and Possible Artifacts
3.2. Accuracy of Experimental and Simulated Hyp-1 Structure Model
3.3. Actual and Experimental ADPs Comparison
3.4. Side-Chain Angles Probability Distribution P(χ1) for Pro, Ser, Cys
3.5. Val and Thr
3.6. Leu, Phe, Tyr, His
3.7. Asp, Asn
3.8. Glu, Gln
3.9. Met
3.10. Lys, Arg
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Correction Statement
References
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Simulation Step | ID | Number of Steps/Time Step (fs) |
---|---|---|
Energy minimization | EM | 100,000/1 |
NVT equilibration | NVT | 100,000/1 |
NPT equilibration | NPT | 1,000,000/1 |
Simulation of rotamer 1 | ROT1 | 100/200 |
Simulation of rotamer 2 | ROT2 | 10/20 |
Simulation of rotamer 3 | ROT3 | 1/2 |
Cooling down | CD | 1,200,000/1 |
RMSF gathering | RMSF | 1,000,000/1 |
Initial Torsion Angle | Intermediate Torsion Angles | Terminal Torsion Angle | |
---|---|---|---|
Arg | N-CA-CB-CG | CA-CB-CG-CD CB-CG-CD-NE | CG-CD-NE-CZ |
Asn | N-CA-CB-CG | CA-CB-CG-OD1 | |
Asp | N-CA-CB-CG | CA-CB-CG-OD1 | |
Cys | N-CA-CB-SG | ||
Gln | N-CA-CB-CG | CA-CB-CG-CD | CB-CG-CD-OE1 |
Glu | N-CA-CB-CG | CA-CB-CG-CD | CB-CG-CD-OE1 |
His | N-CA-CB-CG | CA-CB-CG-ND1 | |
Leu | N-CA-CB-CG | CA-CB-CG-CD1 | |
Lys | N-CA-CB-CG | CA-CB-CG-CD CB-CG-CD-CE | CG-CD-CE-NZ |
Met | N-CA-CB-CG | CA-CB-CG-SD | CB-CG-SD-CE |
Phe | N-CA-CB-CG | CA-CB-CG-CD1 | |
Pro | N-CA-CB-CG | ||
Ser | N-CA-CB-OG | ||
Thr | N-CA-CB-OG1 | ||
Tyr | N-CA-CB-CG | CA-CB-CG-CD1 | |
Val | N-CA-CB-CG1 |
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Smietanska, J.; Kozik, T.; Strzalka, R.; Buganski, I.; Wolny, J. Molecular Dynamics Investigation of Phenolic Oxidative Coupling Protein Hyp-1 Derived from Hypericum perforatum. Crystals 2021, 11, 43. https://doi.org/10.3390/cryst11010043
Smietanska J, Kozik T, Strzalka R, Buganski I, Wolny J. Molecular Dynamics Investigation of Phenolic Oxidative Coupling Protein Hyp-1 Derived from Hypericum perforatum. Crystals. 2021; 11(1):43. https://doi.org/10.3390/cryst11010043
Chicago/Turabian StyleSmietanska, Joanna, Tomasz Kozik, Radoslaw Strzalka, Ireneusz Buganski, and Janusz Wolny. 2021. "Molecular Dynamics Investigation of Phenolic Oxidative Coupling Protein Hyp-1 Derived from Hypericum perforatum" Crystals 11, no. 1: 43. https://doi.org/10.3390/cryst11010043