Spatial profiling of protein hydrophobicity: Native vs. Decoy structures
- 31 July 2003
- journal article
- research article
- Published by Wiley in Proteins-Structure Function and Bioinformatics
- Vol. 52 (4), 561-572
- https://doi.org/10.1002/prot.10419
Abstract
A recent study of 30 soluble globular protein structures revealed a quasi‐invariant called the hydrophobic ratio. This invariant, which is the ratio of the distance at which the second order hydrophobic moment vanished to the distance at which the zero order moment vanished, was found to be 0.75 ± 0.05 for 30 protein structures. This report first describes the results of the hydrophobic profiling of 5,387 non‐redundant globular protein domains of the Protein Data Bank, which yields a hydrophobic ratio of 0.71 ± 0.08. Then, a new hydrophobic score is defined based on the hydrophobic profiling to discriminate native‐like proteins from decoy structures. This is tested on three widely used decoy sets, namely the Holm and Sander decoys, Park and Levitt decoys, and Baker decoys. Since the hydrophobic moment profiling characterizes a global feature and requires reasonably good statistics, this imposes a constraint upon the size of the protein structures in order to yield relatively smooth moment profiles. We show that even subject to the limitations of protein size (both Park & Levitt and Baker sets are small protein decoys), the hydrophobic moment profiling and hydrophobic score can provide useful information that should be complementary to the information provided by force field calculations. Proteins 2003;52:561–572.Keywords
This publication has 25 references indexed in Scilit:
- Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all‐atom force field and the surface generalized born solvent modelProteins-Structure Function and Bioinformatics, 2002
- TOUCHSTONE: An ab initio protein structure prediction method that uses threading-based tertiary restraintsProceedings of the National Academy of Sciences, 2001
- Hydrophobic moments of protein structures: Spatially profiling the distributionProceedings of the National Academy of Sciences, 2001
- Improving the performance of rosetta using multiple sequence alignment information and global measures of hydrophobic core formationProteins-Structure Function and Bioinformatics, 2001
- Effective energy functions for protein structure predictionCurrent Opinion in Structural Biology, 2000
- Designing potential energy functions for protein foldingCurrent Opinion in Structural Biology, 1999
- Clustering of low-energy conformations near the native structures of small proteinsProceedings of the National Academy of Sciences, 1998
- Potential energy functions for threadingCurrent Opinion in Structural Biology, 1996
- Recognizing Native Folds by the Arrangement of Hydrophobic and Polar ResiduesJournal of Molecular Biology, 1995
- Evaluation of protein models by atomic solvation preferenceJournal of Molecular Biology, 1992