title: Analysis of the structure and dynamics of human serum albumin.
abstract: Human serum albumin (HSA) is a biologically relevant protein that binds a variety of drugs and other small molecules. No less than 50 structures are deposited in the RCSB Protein Data Bank (PDB). Based on these structures, we first performed a clustering analysis. Despite the diversity of ligands, only two well defined conformations are detected, with a deviation of 0.46 nm between the average structures of the two clusters, while deviations within each cluster are smaller than 0.08 nm. Those two conformations are representative of the apoprotein and the HSA-myristate complex already identified in previous literature. Considering the structures within each cluster as a representative sample of the dynamical states of the corresponding conformation, we scrutinize the structural and dynamical differences between both conformations. Analysis of the fluctuations within each cluster set reveals that domain II is the most rigid one and better matches both structures. Then, taking this domain as reference, we show that the structural difference between both conformations can be expressed in terms of twist and hinge motions of domains I and III, respectively. We also characterize the dynamical difference between conformations by computing correlations and principal components for each set of dynamical states. The two conformations display different collective motions. The results are compared with those obtained from the trajectories of short molecular dynamics simulations, giving consistent outcomes. Let us remark that, beyond the relevance of the results for the structural and dynamical characterization of HAS conformations, the present methodology could be extended to other proteins in the PDB archive.
authors.affiliation: Physics Department, Pontifical Catholic University of Rio de Janeiro, Rio de Janeiro, Brazil, trcuyag@gmail.com.br.
authors.forename: T R Cuya
authors.initials: TR
authors.lastname: Guizado
mesh_terms: D001665:Binding Sites; D016000:Cluster Analysis; D030562:Databases, Protein; D006801:Humans; D008024:Ligands; D056004:Molecular Dynamics Simulation; D025341:Principal Component Analysis; D011485:Protein Binding; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D012709:Serum Albumin / Q000737:chemistry* / Q000378:metabolism; D000075462:Serum Albumin, Human; D013329:Structure-Activity Relationship
chemical_list: C422455:ALB protein, human; D008024:Ligands; D012709:Serum Albumin; D000075462:Serum Albumin, Human