Sequence conservation and correlation measures in protein structure prediction

The rapid elucidation of protein sequences has allowed multiple sequence alignments to be calculated for a wide variety of proteins. Such alignments reveal positions that exhibit amino acid conservation--either of specific chemical groups in active and binding sites or of the more chemically inert hydrophobic residues that contribute to the protein core. The latter can provide constraints on the position of the protein chain and any local periodicity can suggest the type of secondary structure. Conservation measures, however, cannot provide specific pairwise packing information (each conserved hydrophobic position might pack against any other). However, if correlated changes between positions were observed then specific pairs of residue could be identified as interacting and therefore probably spatially adjacent. Most 'observations' of correlated changes have been anecdotal and of the few systematic studies that have been made, most have mistakenly incorporated a strong bias towards selecting conserved positions. When the conservation effect is separated (as best as possible) then little correlation signal remains to help identify adjacent positions.