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Computational analyses of the surface properties of protein-protein interfaces.

Gruber J, Zawaira A, Saunders R, Barrett CP, Noble ME - Acta Crystallogr. D Biol. Crystallogr. (2006)

Bottom Line: Experiment remains the best way to answer this question, but computational tools can contribute where this fails.Using the CXXSurface toolkit, developed as a part of the CCP4MG program, a suite of tools to analyse the properties of surfaces and their interfaces in complexes has been prepared and applied.These tools have enabled the rapid analysis of known complexes to evaluate the distribution of (i) hydrophobicity, (ii) electrostatic complementarity and (iii) sequence conservation in authentic complexes, so as to assess the extent to which these properties may be useful indicators of probable biological function.

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Affiliation: Laboratory of Molecular Biophysics, Rex Richards Building, South Parks Road, Oxford OX1 3QU, England.

ABSTRACT
Several potential applications of structural biology depend on discovering how one macromolecule might recognize a partner. Experiment remains the best way to answer this question, but computational tools can contribute where this fails. In such cases, structures may be studied to identify patches of exposed residues that have properties common to interaction surfaces and the locations of these patches can serve as the basis for further modelling or for further experimentation. To date, interaction surfaces have been proposed on the basis of unusual physical properties, unusual propensities for particular amino-acid types or an unusually high level of sequence conservation. Using the CXXSurface toolkit, developed as a part of the CCP4MG program, a suite of tools to analyse the properties of surfaces and their interfaces in complexes has been prepared and applied. These tools have enabled the rapid analysis of known complexes to evaluate the distribution of (i) hydrophobicity, (ii) electrostatic complementarity and (iii) sequence conservation in authentic complexes, so as to assess the extent to which these properties may be useful indicators of probable biological function.

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Rank-ordered distribution of electrostatic complementarity. The linear correlation coefficient of electrostatic potentials for different interacting partners is presented for 72 structures. In the vast majority of cases there is an anticorrelation of potential consistent with a marked electrostatic complementarity.
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fig5: Rank-ordered distribution of electrostatic complementarity. The linear correlation coefficient of electrostatic potentials for different interacting partners is presented for 72 structures. In the vast majority of cases there is an anticorrelation of potential consistent with a marked electrostatic complementarity.

Mentions: This calculation was performed for the Lo Conte set of protein–protein interfaces. From Fig. 5 ▶, it can be seen that the vast majority of complexes demonstrate a marked electrostatic complementarity.


Computational analyses of the surface properties of protein-protein interfaces.

Gruber J, Zawaira A, Saunders R, Barrett CP, Noble ME - Acta Crystallogr. D Biol. Crystallogr. (2006)

Rank-ordered distribution of electrostatic complementarity. The linear correlation coefficient of electrostatic potentials for different interacting partners is presented for 72 structures. In the vast majority of cases there is an anticorrelation of potential consistent with a marked electrostatic complementarity.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2483497&req=5

fig5: Rank-ordered distribution of electrostatic complementarity. The linear correlation coefficient of electrostatic potentials for different interacting partners is presented for 72 structures. In the vast majority of cases there is an anticorrelation of potential consistent with a marked electrostatic complementarity.
Mentions: This calculation was performed for the Lo Conte set of protein–protein interfaces. From Fig. 5 ▶, it can be seen that the vast majority of complexes demonstrate a marked electrostatic complementarity.

Bottom Line: Experiment remains the best way to answer this question, but computational tools can contribute where this fails.Using the CXXSurface toolkit, developed as a part of the CCP4MG program, a suite of tools to analyse the properties of surfaces and their interfaces in complexes has been prepared and applied.These tools have enabled the rapid analysis of known complexes to evaluate the distribution of (i) hydrophobicity, (ii) electrostatic complementarity and (iii) sequence conservation in authentic complexes, so as to assess the extent to which these properties may be useful indicators of probable biological function.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratory of Molecular Biophysics, Rex Richards Building, South Parks Road, Oxford OX1 3QU, England.

ABSTRACT
Several potential applications of structural biology depend on discovering how one macromolecule might recognize a partner. Experiment remains the best way to answer this question, but computational tools can contribute where this fails. In such cases, structures may be studied to identify patches of exposed residues that have properties common to interaction surfaces and the locations of these patches can serve as the basis for further modelling or for further experimentation. To date, interaction surfaces have been proposed on the basis of unusual physical properties, unusual propensities for particular amino-acid types or an unusually high level of sequence conservation. Using the CXXSurface toolkit, developed as a part of the CCP4MG program, a suite of tools to analyse the properties of surfaces and their interfaces in complexes has been prepared and applied. These tools have enabled the rapid analysis of known complexes to evaluate the distribution of (i) hydrophobicity, (ii) electrostatic complementarity and (iii) sequence conservation in authentic complexes, so as to assess the extent to which these properties may be useful indicators of probable biological function.

Show MeSH