Towards identification of hydrophobic core in globular proteins

Fačkovec Boris¹, Vondrášek Jiří, Hobza Pavel

Institute of Organic Chemistry AS CR

Center for Biomolecules and Complex Molecular Systems

Flemingovo nám. 2.
166 10 Praha 6

¹borislavujo@gmail.com

Keywords: protein, hydrophobic core, thermostability, surface area, computational chemistry, biophysics

The concept of hydrophobic core is a contributory paradigm, which is successfully used when studying a protein deeper. A core has remarkable properties that might shed light on problems related to thermostability of proteins and protein folding kinetics.

However, there is not yet any exact definition of core that would integrate different physical models and would be transferable and definite.

The present study aims at integrated algorithm of searching for protein residues, that takes into account more core identification criteria and definitely determines whether residue belongs or does not belong to core set.

Analysis is theoretical based on PDB structures. Mainly empirical force field (Amber ff03) computations are employed, what makes method fast and feasible.

References

1. Hobza P., Müller-Dethlefs K.: Non-Covalent Interactions: Theory and Experiment, RSC Publishing, 2010.

Berka K., Hobza P., Vondrášek J.: Analysis of energy stabilization inside the hydrophobic core of rubredoxin. Chemphyschem. 10, 543 (2009).