Hydrophobic moment of multi-domain proteins

Details Hydrophobic moment of multi-domain proteins Hydrophobic moment of multi-domain proteins

2011-01-25

2011-01-25

DeJong, Eric S (Department: 1631)

Data processing: measuring, calibrating, or testing

Measurement system in a specific environment

Chemical analysis

C703S011000

Reexamination Certificate

active

07877214

ABSTRACT:
Techniques for protein structure analysis are provided. In one aspect, a method of analyzing a multi-domain protein structure comprises the following steps. For at least one domain, a hydrophobic dipole, e.g., defined as a first-order hydrophobic moment of the domain, is calculated. A score representing the orientation of the hydrophobic dipole of the at least one domain relative to a hydrophobic dipole of one or more other domains of the multi-domain protein structure is then calculated.

REFERENCES:
Eisenberg et al. “Hydrophobic Moments and Protein Structure” Faraday Symp. Chem. Soc. (1982), vol. 17, pp. 109-120.
Karplus, “Hydrophobicity regained” Protein Science (1997) vol. 6, pp. 1302-1307.
R. Jaenicke, Stability and Folding of Domain Proteins, 71 Prog, Biophys. & Mol. Biol. 155-241 (1999).
C. Anselmi, et al., Identification of Protein Domains on Topological Basis, 58 Biopolymers 218-229 (2001).
S J. Wheelan et al., Domain Size Distributions Can Predict Domain Boundaries, 16 Bioinformatics 613-618 (2000).
A G. Murzin et al,, SCOP: A Structural Classification of Protein Database for the Investigation of Sequences and Structures, 247 J. Mol. Biol, 536-540 (1995).
B D. Silverman, Hydrophobic Moments of Protein Structures: Spatially Profiling the Distribution, 98 Proc.. Natl, Acad. Sci. USA 4996-5001 (2001).
R. Zhou et al., Spatial Profiling of Protein Hydrophobicity: Native vs. Decoy Structures, 52 Proteins: Struc. Funct. & Genetics 561-572 (2003).
D Eisenberg et al., The Helical Hydrophobic Moment: A Measure of the Amphiphilicity of a Helix, 299 Nature 371-374 (1982).
D. Eisenberg et al., Analysis of Membrane Protein Sequences with the Hydrophobic Moment Plot, 179 J. Mol. Biol. 125-142 (1984).
H.J. Pownall et al., Helical Amphipathic Moment: Application to Plasma Lipoproteins, 159 FEBS 17-23 (1983).
I. Tsigelny et al , Mechanism of Action of Chromogranin A on Catecholamine Release: Molecular Modeling of the Catestatin Region Reveals a -strand/loop/ -strand Structure Secured by Hydrophobic Interactions and Predictive of Activity 77 Regulatory Peptides 43-53 (1998).
J P Pardo et al., An Alternative Model for the Transmembrane Segments of the Yeast H+-ATPase, 15 Yeast 1585-1593 (1999).
P W. Mobley et al., Membrane Interactions of the Synthetic N-Terminal Peptide of HIV-1 gp41 and Its Structural Analogs, 1418 Biochimica et Biophysica Acta 1-18 (1999).
L Thong et al., Flexible Programs for the Prediction of Average Amphiphilicity of Multiply Aligned Homologous Proteins: Application to Integral Membrane Transport Proteins 16 Molecular Membrane Biology 173-179 (1999).
X Gallet et al., A Fast Method to Predict Protein Interaction Sites from Sequences, 302 J. Mol. Biol. 917-926 (2000).
D.A. Phoenix et al , The Hydrophobic Moment and Its Use in the Classification of Amphiphilic Structures (Review), 19 Molecular Membrane Biology 1-10 (2002).
H Zhou et al., The Stability Scale and Atomic Solvation Parameters Extracted From 1023 Mutation Experiments, 49 Proteins: Struc Funct & Genetics 483-492 (2002).

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