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Flexibility and packing in proteins.

¹Department of Biophysical Chemistry, Lund University, Box 124, SE-22100 Lund, Sweden. bertil.halle@bpc.lu.se

Proceedings of the National Academy of Sciences of the United States of America

|January 31, 2002

Summary

This summary is machine-generated.

Protein flexibility, measured by atomic mean-square displacements (AMSDs), is directly linked to local packing density. This finding simplifies understanding protein dynamics and reduces the need for complex energy landscape calculations.

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Area of Science:

Structural biology
Biophysics
Computational biology

Background:

Protein structural flexibility is crucial for biological function.
X-ray crystallography provides atomic mean-square displacements (AMSDs), or B factors, to study protein flexibility.
Interpreting AMSD profiles traditionally involves complex energy landscapes.

Purpose of the Study:

To establish a direct relationship between protein flexibility and local packing density.
To develop a simplified model for predicting protein flexibility profiles.
To investigate the influence of local atomic environment on protein dynamics.

Main Methods:

Utilized elementary statistical mechanics and atomic distribution features in proteins.
Developed a local density model predicting inverse proportionality between AMSD and contact density.
Validated the model against high-quality crystal structures of 38 diverse proteins.

Main Results:

The local density model accurately reproduces prominent and minor features in AMSD profiles.
Periodic AMSD variations within alpha helices were captured by the model.
The model's prediction of a rigidifying effect from crystal contacts aligns with experimental data.

Conclusions:

Protein flexibility (AMSD) is primarily determined by local packing density, not solely by dynamics.
The local density model offers superior accuracy and computational efficiency compared to previous methods.
AMSDs offer limited independent information beyond mean atomic coordinates, as flexibility is intrinsically linked to packing.