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Protein Science (2007), 16:2140-2152. Published by Cold Spring Harbor Laboratory Press. Copyright © 2007 The Protein Society
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Optimization of linear disorder predictors yields tight association between crystallographic disorder and hydrophobicity

Nathan B. Holladay1,2, Lisa N. Kinch3, and Nick V. Grishin1,3

1 Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9050, USA
2 Medical Scientist Training Program, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9050, USA
3 Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9050, USA

(RECEIVED May 4, 2007; FINAL REVISION July 2, 2007; ACCEPTED July 3, 2007)

X-ray crystallographic protein structures often contain disordered regions that are observed as missing electron density. Diffraction data may give little or no direct evidence as to the specific nature of disordered regions. We have developed a weighted window-based disorder predictor optimized using crystallographic data. Performance of a predictor is strongly influenced by chain termini. Optimized score adjustment values for amino- and carboxy-terminal positions demonstrate a simple, monotonic relationship between disorder and residue distance from termini. This optimized disorder predictor performs similarly to DISOPRED2 on crystallographically disordered regions. Data-optimized residue disorder propensities show strong linear correlation with experimentally determined amino acid transfer energies between water and hydrogen-bonding organic solvents, which primarily reflect residue hydrophobicity (exemplified by the Nozaki-Tanford hydrophobicity scale). Disorder propensities do not correlate as well with transfer energies between water and apolar solvents, which primarily reflect a different hydropathic property: residue hydrophilicity (also reflected by the Kyte-Doolittle hydropathy scale). Our results suggest that while hydrophobic side-chain interactions are primarily involved in determining stability of the folded conformation, hydrogen bonding, and similar polar interactions are primarily involved in conformational and interaction specificity.

Keywords: X-ray crystallography; protein disorder; protein structure; hydrophobicity; hydrophilicity; simulated annealing; predictor optimization


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