Interaction of Classical Platinum Agents with the Monomeric and Dimeric Atox1 Proteins: A Molecular Dynamics Simulation Study
Abstract
:1. Introduction
2. Results
2.1. The Characteristics of Platinum Agents Combining with a Monomeric Atox1 Protein
2.1.1. The Structure Characteristics of Platinum + Atox1 Complexes
2.1.2. Free Energy and Interaction Analysis of Platinum + Atox1 Complexes
2.1.3. Dynamical Fluctuation Analysis for Platinum + Atox1 Complexes
2.2. The Characteristics of Platinum Agents Combining with a Dimeric Atox1 Protein
3. Discussion
3.1. The Structure Analysis of Platinum Agents Combining with the Monomeric and Dimeric Atox1 Protein
3.2. Comparison on the Structural Characteristics of the Oxaliplatin + Atox1 and Oxaliplatin + 2Atox1 Models
4. Models and Methods
4.1. Initial Structures
4.2. Force Field Parameter Preparation
4.3. Molecular Dynamics Simulation Protocols
4.4. Free-Energy Analyses
4.5. Fluctuation Analyses
4.6. Calculation of Angle between Two Helices
4.7. DynDom and Surface Analyses
5. Conclusions
Supplementary Information
ijms-15-00075-s001.pdfAcknowledgments
Conflicts of Interest
References
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Component | CisPt + Atox1 | TransPt + Atox1 | OxaliPt + Atox1 |
---|---|---|---|
Receptor | Atox1 | Atox1 | Atox1 |
Ligand | Cisplatin ligand | Transplatin ligand | Oxaliplatin ligand |
ΔEele | −46.47 | 11.24 | −35.54 |
ΔEvdw | −0.64 | −2.47 | −9.09 |
ΔEint | 0.00 | 0.00 | 0.00 |
ΔGnp/solv | −8.86 | −11.10 | −14.93 |
ΔGpb/solv | 45.06 | −0.39 | 41.56 |
ΔGnp | −9.50 | −13.57 | −24.02 |
ΔGpb | −1.41 | 10.85 | 6.02 |
ΔHbinding | −10.91 | −2.73 | −18.00 |
TΔS | −16.19 | −15.14 | −13.87 |
ΔGbinding | 5.28 | 12.41 | −4.13 |
Hydrogen bond | OxaliPt + Atox1 |
---|---|
(Cys15)CB H–N1 | 99.0 |
(Cys15)CA H–N2 | 77.6 |
N1 H–CA(Cys15) | 30.6 |
Hydrophobic contact | |
(Val8)CG1 C4(oxaliplatin) | 65.4 |
(Val8)CG1 C5(oxaliplatin) | 88.7 |
(Val8)CG1 C3(oxaliplatin) | 47.2 |
(Asp9)CB C5(oxaliplatin) | 90.3 |
(Cys15)CA/CB C1(oxaliplatin) | 197.2 |
(Ala18)CB C2(oxaliplatin) | 76.3 |
(Thr58)CB C4(oxaliplatin) | 50.9 |
(Thr58)CB/CG2 C3(oxaliplatin) | 126.5 |
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Wang, X.; Li, C.; Wang, Y.; Chen, G. Interaction of Classical Platinum Agents with the Monomeric and Dimeric Atox1 Proteins: A Molecular Dynamics Simulation Study. Int. J. Mol. Sci. 2014, 15, 75-99. https://doi.org/10.3390/ijms15010075
Wang X, Li C, Wang Y, Chen G. Interaction of Classical Platinum Agents with the Monomeric and Dimeric Atox1 Proteins: A Molecular Dynamics Simulation Study. International Journal of Molecular Sciences. 2014; 15(1):75-99. https://doi.org/10.3390/ijms15010075
Chicago/Turabian StyleWang, Xiaolei, Chaoqun Li, Yan Wang, and Guangju Chen. 2014. "Interaction of Classical Platinum Agents with the Monomeric and Dimeric Atox1 Proteins: A Molecular Dynamics Simulation Study" International Journal of Molecular Sciences 15, no. 1: 75-99. https://doi.org/10.3390/ijms15010075