Local repulsion in protein structures as revealed by a charge distribution analysis of all amino acid sequences from the Saccharomyces cerevisiae genome

The structures and physical properties of individual protein molecules have been extensively studied, but the general features of all proteins in a cell have hardly been investigated. The distribution of net electric charges of all proteins from the Saccharomyces cerevisiae proteome agreed well with a Gaussian distribution. The shift in charge distribution caused by protonation of histidine suggested that the proteins in a cell are buffered against pH changes. A comparison between the amino acid sequences from the proteome and randomly generated sequences indicated that electric charges in the real sequences are clustered. Analysis of autocorrelation function of charged residues in the total proteome of S. cerevisiae showed a positive correlation of net charges in amino acid sequences with characteristic length as long as 81 residues, leading to the conclusion that the interactions within proteins is repulsive on average.