title: Metal recognition of septapeptides via polypod molecular architecture.
abstract: The understanding of the nature of recognition of inorganic materials by proteins is one of the core elements of and has profound implications in biological materials science and engineering. Using combinatorial display methods, a considerable number of short polypeptides have recently been selected with affinity to engineering materials. During these selections, more than several polypeptides are identified with binding specificity to a chosen inorganic material. Understanding the nature of surface recognition of materials by polypeptides is essential for rational design and biomimetic engineering of these inorganic-binding polypeptides for use as linkers, catalyzers, and growth modifiers in nanotechnology and nanobiotechnology. Although there may not be direct homology among the amino acids constituting the polypeptides, their function may come from conserved molecular architecture. Here we study crystallographic surface recognition of platinum metal-binding septapeptides by conformational analysis. We find that the septapeptides conform into certain molecular architectures containing multiple protrusions (polypods) that spatially match with the crystallographic metal surfaces. While the physical recognition may originate from how well the molecular polypods spatially match a given crystallographic surface, the degree of binding may be due to the reactive groups that form the polypods, e.g., charged or polar groups (e.g., hydroxyl and amine). These results are highly consistent with the experimental binding characteristics of the Pt binders with various degrees of affinities.
authors.affiliation: Materials Science & Engineering and Chemical Engineering, University of Washington, Seattle, Washington 98195, USA.
authors.forename: Ersin Emre
authors.initials: EE
authors.lastname: Oren
authors.forename: Candan
authors.initials: C
authors.lastname: Tamerler
authors.forename: Mehmet
authors.initials: M
authors.lastname: Sarikaya
mesh_terms: D001665:Binding Sites; D003198:Computer Simulation; D003460:Crystallization / Q000379:methods*; D007700:Kinetics; D046911:Macromolecular Substances / Q000032:analysis / Q000737:chemistry; D008670:Metals / Q000737:chemistry; D008956:Models, Chemical; D008958:Models, Molecular; D008968:Molecular Conformation; D049329:Nanostructures / Q000737:chemistry* / Q000648:ultrastructure*; D010455:Peptides / Q000032:analysis / Q000737:chemistry*; D010984:Platinum / Q000737:chemistry*; D011485:Protein Binding; D011487:Protein Conformation
chemical_list: D046911:Macromolecular Substances; D008670:Metals; D010455:Peptides; D010984:Platinum