Does helix dipole have any role in binding metal ions in protein structures?
Positions of metal-binding residues with respect to helical terminii in protein structures have been analyzed in order to determine if the location of these ligands is influenced by the helix dipole. Most ligands do not show any preference for the amino- or carboxy-terminus of a helix. For steric reasons, peptide ligands can be located only at the C-terminus. The availability of a second ligand residue closely placed along the sequence may be of more importance, rather than the electrostatic interaction involving helix dipole, in cases where ligands are found near the C-terminus. The location of heme-binding histidine residues at the C-terminus may be due to the steric requirements of the heme group and also the intrahelical hydrogen bond that the residues can form at this position. Considerations based on such geometrical features and not just the helix dipole may help us to understand the observed distribution of charged residues along alpha-helices and the favorable role these amino acids have on folding of isolated helices.
Division of Physical Chemistry, National Chemical Laboratory, Pune, India.
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Chakrabarti
D000595:Amino Acid Sequence; D001429:Bacteriochlorophylls / Q000737:chemistry; D002264:Carboxylic Acids / Q000737:chemistry; D006454:Hemoglobins / Q000737:chemistry; D006639:Histidine / Q000378:metabolism; D008024:Ligands; D008670:Metals / Q000737:chemistry*; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry*; D011485:Protein Binding; D011487:Protein Conformation
D001429:Bacteriochlorophylls; D002264:Carboxylic Acids; D006454:Hemoglobins; D008024:Ligands; D008670:Metals; D010455:Peptides; D006639:Histidine