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A server and database for dipole moments of proteins
Clifford E Felder1, Jaime Prilusky, Israel Silman
1Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel.
Nucleic Acids Research
|May 29, 2007
Summary
This study introduces a server for calculating protein electrostatic properties like net charge and dipole moment. Most proteins exhibit specific electrostatic profiles, with highly charged or dipolar chains interacting with nucleic acids and ribosomes.
Area of Science:
- Biophysics
- Computational Biology
- Structural Biology
Background:
- Proteins possess intrinsic electrostatic properties, including net charge and dipole moment.
- These properties can influence protein structure, function, and interactions.
- Understanding protein electrostatics is crucial for deciphering biological mechanisms.
Purpose of the Study:
- To develop and present an accessible computational tool for analyzing protein electrostatic properties.
- To investigate the distribution and characteristics of net charge and dipole moments across a large protein dataset.
- To explore potential correlations between electrostatic properties and protein structure/function.
Main Methods:
- Development of an internet server (http://bip.weizmann.ac.il/dipol) for calculating protein net charge, dipole moment, and mean radius.
- Analysis of approximately 12,000 non-homologous protein structures from the PISCES set.
- Examination of unique protein chains with lengths of 50 residues or longer.
- Visualization of dipole vectors and their angles relative to specific amino acid residues.
Main Results:
- The server successfully calculates and visualizes electrostatic properties for 3D protein structures.
- The majority of analyzed protein charges and dipoles fall within a narrow range, with notable outliers.
- No general correlation was found between a protein's charge/dipole moment and its overall structure or function.
- Proteins with very large positive charges or dipoles frequently interact with ribosomes or nucleic acids.
Conclusions:
- Protein electrostatic properties are highly specific to individual proteins.
- The developed server provides a valuable resource for researchers studying protein electrostatics.
- Specific electrostatic profiles, particularly high positive charge or dipole moments, are indicative of interactions with ribosomes and nucleic acids.
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