Covariance analysis of protein families: The case of the variable domains of antibodies

A nonrestrictive method for identifying covariance in protein families is d escribed and applied to human and mouse germline V kappa and VH sequence al ignments. Amino acids that occur at each position in a sequence alignment a re divided into two sets, called sword, by generating all possible combinat ions of alternative amino acids. Each word is associated with a pattern of changes. Words with identical patterns identify covariant positions. In ant ibody variable domains, the number of words generated ranged between 1103 a nd 2195 depending on the alignment, of which 4 to 12 % occurred in covarian t pairs. Despite the nonrestrictive character of pattern generation, covari ant residues did not reflect a random selection with respect to the nature of amino acid changers and/or their spatial proximity in a reference crysta llographic structure. This approach allowed the identification of a covaria nce signal for positions with high variability, mostly located in the outer part of the common structural framework of antibody variable domains. Cova riance in these regions may reflect the existence of alternative and mutual ly exclusive atomic arrangements that are compatible with antibody function . The method may be of general applicability to rationalize residue variabi lity in protein families. Proteins 2000;41:475-484. (C) 2000 Wiley-Liss, In c.