2000/12/01 by Leonid Mirny, Mirny, Leonid, Eugene Shakhnovich +1
Biochemistry, Genetics and Molecular Biology · Physics and Astronomy · #Biological Physics (physics.bio-ph) #Chemical Physics (physics.chem-ph) #FOS: Biological sciences #FOS: Physical sciences #Quantitative Biology (q-bio) #Statistical Mechanics (cond-mat.stat-mech) #cond-mat.stat-mech #physics.bio-ph #physics.chem-ph #q-bio
paper · pdf · doi:10.48550/arxiv.physics/0012003
submitted to Journal of Molecular Biology
arxiv created 2000/12/01 · arxiv updated 2009/11/30
In this Communication we present statistical analysis of conservation profiles in families of homologous sequences for nine proteins whose folding nucleus was determined by protein engineering methods. We show that in all but one protein (AcP) folding nucleus residues are significantly more conserved than the rest of the protein. Two aspects of our study are especially important: 1) grouping of amino acids into classes according to their physical-chemical properties and 2) proper normalization of amino acid probabilities that reflects the fact that evolutionary pressure to conserve some amino acid types may itself affect concentration of various amino acid types in protein families. Neglect of any of those two factors may make physical and biological ``signals'' from conservation profiles disappear.