Exploring the common dynamics of homologous proteins. Application to the globin family.
We present a procedure to explore the global dynamics shared between members of the same protein family. The method allows the comparison of patterns of vibrational motion obtained by Gaussian network model analysis. After the identification of collective coordinates that were conserved during evolution, we quantify the common dynamics within a family. Representative vectors that describe these dynamics are defined using a singular value decomposition approach. As a test case, the globin heme-binding family is considered. The two lowest normal modes are shown to be conserved within this family. Our results encourage the development of models for protein evolution that take into account the conservation of dynamical features.
Maguid
Sandra
S
Universidad Nacional de Quilmes, B1876BXD Bernal, Argentina.
Fernandez-Alberti
Sebastian
S
Ferrelli
Leticia
L
Echave
Julian
J
D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D001703:Biophysics / Q000379:methods*; D002384:Catalysis; D017124:Conserved Sequence; D030562:Databases, Protein; D005914:Globins / Q000737:chemistry*; D006418:Heme / Q000737:chemistry; D006454:Hemoglobins / Q000737:chemistry; D006801:Humans; D007798:Lampreys; D046911:Macromolecular Substances / Q000737:chemistry; D008958:Models, Molecular; D015233:Models, Statistical; D008962:Models, Theoretical; D008969:Molecular Sequence Data; D009211:Myoglobin / Q000737:chemistry; D016011:Normal Distribution; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry; D017386:Sequence Homology, Amino Acid; D012984:Software; D013696:Temperature
D006454:Hemoglobins; D046911:Macromolecular Substances; D009211:Myoglobin; D011506:Proteins; D006418:Heme; D005914:Globins