Why not ? Look at the partner protein is there a similar charge reversal present? The function is preserved (interaction of both proteins) in different species but the charges have swapped over time in evolution while the backbone scaffold (fold) of the protein was maintained.
Just as an example P.falciparum aldolase versus human aldolase share only 50% identical residues per subunit but the fold of the subunits is within 0.8 Å r.m.s.d . If you only consider the conservation of the active site then 45/46 residues are identical. ...................... Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742<tel:%2B1-410-614-4742> Lab: +1-410-614-4894<tel:%2B1-410-614-4894> Fax: +1-410-955-2926<tel:%2B1-410-955-2926> http://lupo.jhsph.edu On May 10, 2015, at 6:37 AM, Andre Godoy <[email protected]<mailto:[email protected]>> wrote: Dear users. I'm comparing surface charge of a structure with its homologous (85% seq ID), and noted that APBS suggest completely opposite charge distribution (exactly what I expected, since despite its similarity molecules have opposite biochemical profile) But since molecules are quite similar, I'm not convinced that charge distribution can be that different. Considering that AA is basically the same, what other factors can be influencing APBS charge calculations? (Ex: rotamers position, crystal packing, crystallization conditions, etc) best, Andre Godoy IFSC - University of Sao Paulo - Brazil
