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Modeling unfolded states of proteins and peptides. II. Backbone solvent accessibility
T P Creamer1, R Srinivasan, G D Rose
1Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.
Biochemistry
|March 11, 1997
Summary
Most protein backbone surface area is buried within local structures in the unfolded state. This study refines calculations of unfolded state surface area, improving models of protein folding and the hydrophobic effect.
Area of Science:
- Protein structure and folding
- Biophysics
- Computational biology
Background:
- Buried surface area quantifies the hydrophobic effect in protein folding.
- Calculating unfolded state surface area is model-dependent.
- Previous work established models for side-chain surface area extremes.
Purpose of the Study:
- To investigate backbone surface area in the unfolded state of proteins.
- To refine models for estimating unfolded state surface area.
- To understand the contribution of backbone surface area to protein folding.
Main Methods:
- Developed models to bracket unfolded state backbone surface area between limiting extrema.
- Extended previous work on side-chain surface area to backbone contributions.
- Analyzed protein structures to determine buried surface area.
Main Results:
- Most protein backbone surface area is buried within local structures in the unfolded state.
- The study provides refined estimates for unfolded state backbone surface area.
- Identified limitations of previous models in accounting for backbone contributions.
Conclusions:
- Local structure plays a significant role in burying backbone surface area.
- Accurate estimation of unfolded state surface area is crucial for understanding protein folding.
- This research advances the quantitative understanding of the hydrophobic effect in proteins.