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Fully Autonomous Characterization and Data Collection from Crystals of Biological Macromolecules
Published on: March 22, 2019
Molecular modeling of calmodulin: a comparison with crystallographic data
1Roswell Park Memorial Institute, Buffalo, New York 14263, USA.
International Journal of Quantum Chemistry. Quantum Biology Symposium : Proceedings of the International Symposium on Quantum Biology and Quantum Pharmacology. International Symposium on Quantum Biology and Quantum Pharmacology
|January 1, 1989
Summary
Protein modeling side-chain placement significantly impacts molecular structure. Initial side-chain choices affect both main-chain conformation and supersecondary structure, influencing protein modeling accuracy.
Area of Science:
- Computational biology
- Structural bioinformatics
- Molecular modeling
Background:
- Accurate protein side-chain placement is crucial for reliable molecular modeling.
- Previous methods often overlook the influence of initial side-chain conformations on overall protein structure.
Purpose of the Study:
- To compare two distinct methods for protein side-chain placement in molecular modeling.
- To evaluate the impact of initial side-chain conformations on protein backbone and supersecondary structure.
- To refine methodologies for more accurate protein modeling.
Main Methods:
- Construction of two calmodulin molecular models with differing side-chain placement strategies.
- Utilized a virtual bond analysis program for backbone conformation determination.
- Employed a conformational grid search technique for side-chain placement.
- Explicitly included calcium ions during energy optimization using CHARMM.
Main Results:
- Initial side-chain placement choices demonstrably influenced protein main-chain conformation.
- Significant effects on supersecondary structure were observed based on initial side-chain configurations.
- Comparison with a refined crystal structure highlighted the importance of side-chain treatment.
Conclusions:
- The method of side-chain placement is a critical determinant in protein modeling.
- A refined methodology for side-chain placement can improve the accuracy of modeled protein structures.
- Further analysis can lead to more robust protein modeling protocols.
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