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Insights into the Interactions of Amino Acids and Peptides with Inorganic Materials Using Single-Molecule Force Spectroscopy
Published on: March 6, 2017
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All-Hydrocarbon Staples and Their Effect over Peptide Conformation under Different Force Fields
Bianca Villavicencio1, Rodrigo Ligabue-Braun1, Hugo Verli1
1Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia , Universidade Federal do Rio Grande do Sul (UFRGS) , 91500-970 Porto Alegre - RS , Brazil.
Journal of Chemical Information and Modeling
|August 11, 2018
Summary
Computational simulations can predict how hydrocarbon staples affect peptide structure. The GROMOS54A7 force field shows promise for this, aiding in cost-effective drug design.
Area of Science:
- Biophysical Chemistry
- Computational Chemistry
- Medicinal Chemistry
Background:
- Olefinic staples stabilize peptide secondary structures, mimicking protein surfaces for therapeutic applications.
- Accurate computational prediction of staple effects can reduce drug design costs.
Purpose of the Study:
- To evaluate the accuracy of different molecular dynamics force fields in simulating the impact of all-hydrocarbon staples on peptide conformation.
- To compare simulation results with experimental circular dichroism data.
Main Methods:
- Utilized AMBER99SB-ILDN, CHARMM36, and GROMOS54A7 force fields for molecular dynamics simulations.
- Employed two distinct initial peptide conformations for simulations.
- Validated simulation outcomes against experimental circular dichroism measurements.
Main Results:
- The GROMOS54A7 united-atom force field demonstrated higher accuracy than all-atom force fields in reproducing staple effects.
- GROMOS54A7 was not consistently accurate across all simulated systems.
- Discrepancies were observed between simulated and experimental data in certain cases.
Conclusions:
- Molecular dynamics simulations, particularly with improved force fields like GROMOS54A7, show potential for predicting the conformational impact of hydrocarbon staples in peptides.
- Further advancements in force field development are needed for reliable anticipation of staple-induced conformational changes in peptide drug design.
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