Protein Engineering vol.9 no.9 pp.745-754, 19% Alternating charge clusters of side chains: new surface structural invariants observed in calf eye lens gamma-crystallins

Abstract

A detailed stereochemical analysis of the oppositely charged side chains of amino acid residues on the surface of calf eye lens protein gamma-crystallin B has been carried out. The refined structural data of very high quality obtained at 1.47 A resolution have been used. Charge—charge interactions were considered to be valuable for all the charged oxygen and nitrogen atoms situated at distances, d, between 2.4 and 7.0 A. This means we consider short contact ion pairs as those with interchange distances 2.4 < d ^s 4.0 A and distant contact ion pairs as those with distances 4.0 < d = £ 7.0 A. JHydrogen bonding of the charged atomic groups with the structural water molecules also has been considered. We have not looked at the side groups of histidines which are charged only partially at neutral pH. Five clusters of charged side chains which were large enough were observed. The clusters are comprised of four to six residues which compose 543 % of the total charged residues in the protein. The clusters contain from eight to 12 charged atoms and look like the bent chains of oppositely charged atoms. All clusters are of plane geometry and their maximal linear dimensions are from 11 to 18 A. The root mean square deviations of charged atoms from the cluster plane varied from 0.63 to 0.86 A for four clusters and was only 1.85 A for the largest cluster. All clusters include a number of water molecules situated on the cluster boundary and grouped near the cluster plane. It was shown that the amino acid sequence positions of charged residues are conservative for all the proteins of the gamma-crystallin family of vertebrates including fish, frog, mouse, rat, calf and human. The cluster properties were discussed both in their functional aspect for gamma-crystallins and in other aspects common for globular proteins. As a result, the alternating charge clusters should be considered as newly recognized surface structural invariants. The importance of the charged side chain clusters is claimed for the updated concept of the protein surface