Biology – Quantitative Biology – Biomolecules
Scientific paper
2004-02-19
J. Mol. Biol. 336: 1223-1238 (2004)
Biology
Quantitative Biology
Biomolecules
28 pages, 7 figs, 2 tables
Scientific paper
The simplest approximation of interaction potential between amino-acids in proteins is the contact potential, which defines the effective free energy of a protein conformation by a set of amino acid contacts formed in this conformation. Finding a contact potential capable of predicting free energies of protein states across a variety of protein families will aid protein folding and engineering in silico on a computationally tractable time-scale. We test the ability of contact potentials to accurately and transferably (across various protein families) predict stability changes of proteins upon mutations. We develop a new methodology to determine the contact potentials in proteins from experimental measurements of changes in protein thermodynamic stabilities (ddG) upon mutations. We apply our methodology to derive sets of contact interaction parameters for a hierarchy of interaction models including solvation and multi-body contact parameters. We test how well our models reproduce experimental measurements by statistical tests. We evaluate the maximum accuracy of predictions obtained by using contact potentials and the correlation between parameters derived from different data-sets of experimental ddG values. We argue that it is impossible to reach experimental accuracy and derive fully transferable contact parameters using the contact models of potentials. However, contact parameters can yield reliable predictions of ddG for datasets of mutations confined to specific amino-acid positions in the sequence of a single protein.
Dokholyan Nikolay V.
Kahtun Jainab
Khare Sagar D.
No associations
LandOfFree
Can contact potentials reliably predict stability of proteins? does not yet have a rating. At this time, there are no reviews or comments for this scientific paper.
If you have personal experience with Can contact potentials reliably predict stability of proteins?, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Can contact potentials reliably predict stability of proteins? will most certainly appreciate the feedback.
Profile ID: LFWR-SCP-O-709594