Protein structure solvent accessibility

If no remote homolog can be detected for U, we are forced to simplify the prediction problem. There is a pay-off from making this simplification using the rich diversity of information in current databases, it is possible to make very accurate ID predictions from the sequence alone. Automatic prediction services are readily available for secondary structure, solvent accessibility, location and topology for transmembrane helices, and the location of helices for the special class of coiled-coil proteins, ... 

The rich information contained in the growing sequence and structure databases has been used to improve the accuracy of predictions of some aspects of protein structure. Evolutionary information is successfully used for predictions of secondary structure, solvent accessibility, and transmembrane helices. These predictions of protein structure in ID are significantly more accurate, and more useful than five years ago. Some methods have indicated that ID predictions can be useful as an intermediate step on the way to predicting 3D structure (inter-strand contacts prediction-based threading). Another advantage of predictions in ID is that they are not very CPU-intensive, i.e., ID structure can be predicted for the... 

Figure 4 Sample spatial restraint m Modeller. A restraint on a given C -C , distance, d, is expressed as a conditional probability density function that depends on two other equivalent distances (d = 17.0 and d" = 23.5) p(dld, d"). The restraint (continuous line) is obtained by least-squares fitting a sum of two Gaussian functions to the histogram, which in turn is derived from many triple alignments of protein structures. In practice, more complicated restraints are used that depend on additional information such as similarity between the proteins, solvent accessibility, and distance from a gap m the alignment.

JU Bowie, ND Clarke, CO Paho, RT Sauer. Identification of protein folds Matching hydro-phohicity patterns of sequence sets with solvent accessibility patterns of known structures. Proteins Struct Func Genet 7 257-264, 1990. 

The second major class of protein structures contains structures based around parallel or mixed j8-sheets. Parallel /3-sheet arrays, as previously discussed, distribute hydrophobic side chains on both sides of the sheet. This means that neither side of parallel /3-sheets can be exposed to solvent. Parallel /3-sheets are thus typically found as core structures in proteins, with little access to solvent. 

DOMpro Protein Domain Prediction Using Profiles, Secondary Structure, Relative Solvent Accessibility and Recursive Neural Networks. 

Woods V.L. Jr Methods for the high-resolution identification of solvent-accessible ami,kde hydrogens in polypeptides or proteins and for the characterization of the fine structure of protein binding sites. U.S. Patent 6 291 189, 2001. 

The surface traced out by the center of a solvent probe molecule as it is rolled over the surface of a protein whose three-dimensional structure has been determined at the atomic level. Solvent-accessible surface areas can be calculated by various computer algorithms, and differences in solvent-accessible areas can be used to characterize the energetics of surface hydration as a function of changes in protein conformation, oligomerization, and complexation. 

High-potential iron proteins, 45 313-314, 344 cluster stability, 45 324-332 function, 45 315-316 residues, 45 322-344 structure and, 45 317-322 redox properties, 45 333-344 solvent accessibility, 45 330, 332-333 source and function, 45 314-316 structure, 45 316-322 hydrogen bonding and, 45 321-322 intermolecular aggregation, 45 322 primary, 45 317-318 secondary and tertiary, 45 318-321... 

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