TY - JOUR
T1 - Surface map comparison
T2 - Studying function diversity of homologous proteins
AU - Pawłowski, Krzysztof
AU - Godzik, Adam
N1 - Funding Information:
The authors were supported by NIH grant GM60049. The authors thank Drs J.C. Reed and J.M. Zapata for helpful discussions. The authors also thank Dr A. SÏali for making available the Modeller program.
PY - 2001/6/8
Y1 - 2001/6/8
N2 - A simplified protein surface cartography approach has been developed to assist in the analysis of surface features in homologous families, and thus to predict conservation or divergence of protein functions and protein-protein interaction patterns. A spherical approximation of protein surface was used, with a focus on charged and hydrophobic residues. The resulting surface map allows for qualitative analysis and comparison of surfaces of proteins, but can also be used to define a simple numerical measure of map similarity between two or more proteins. The latter was shown to be useful for function based classifications within large protein families. Surface map analysis was tested on several test cases: haemoglobins, death domains and TRAF domains. It was shown that surface map comparison allows a better function prediction than general sequence analysis methods and can reproduce known examples of functional variation within a divergent group of proteins. In another example, we predict novel, unexpected sets of common functional properties for seemingly distant members of a large group of divergent proteins. The method was also shown to be robust enough to allow using protein models from comparative modelling instead of experimental structures.
AB - A simplified protein surface cartography approach has been developed to assist in the analysis of surface features in homologous families, and thus to predict conservation or divergence of protein functions and protein-protein interaction patterns. A spherical approximation of protein surface was used, with a focus on charged and hydrophobic residues. The resulting surface map allows for qualitative analysis and comparison of surfaces of proteins, but can also be used to define a simple numerical measure of map similarity between two or more proteins. The latter was shown to be useful for function based classifications within large protein families. Surface map analysis was tested on several test cases: haemoglobins, death domains and TRAF domains. It was shown that surface map comparison allows a better function prediction than general sequence analysis methods and can reproduce known examples of functional variation within a divergent group of proteins. In another example, we predict novel, unexpected sets of common functional properties for seemingly distant members of a large group of divergent proteins. The method was also shown to be robust enough to allow using protein models from comparative modelling instead of experimental structures.
KW - Protein cartography
KW - Protein function prediction
KW - Protein structure prediction
KW - Protein surface maps
KW - Sequence analysis
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U2 - 10.1006/jmbi.2001.4630
DO - 10.1006/jmbi.2001.4630
M3 - Article
C2 - 11397097
AN - SCOPUS:0035827178
SN - 0022-2836
VL - 309
SP - 793
EP - 806
JO - Journal of Molecular Biology
JF - Journal of Molecular Biology
IS - 3
ER -