title: De novo self-assembling collagen heterotrimers using explicit positive and negative design.
abstract: We sought to computationally design model collagen peptides that specifically associate as heterotrimers. Computational design has been successfully applied to the creation of new protein folds and functions. Despite the high abundance of collagen and its key role in numerous biological processes, fibrous proteins have received little attention as computational design targets. Collagens are composed of three polypeptide chains that wind into triple helices. We developed a discrete computational model to design heterotrimer-forming collagen-like peptides. Stability and specificity of oligomerization were concurrently targeted using a combined positive and negative design approach. The sequences of three 30-residue peptides, A, B, and C, were optimized to favor charge-pair interactions in an ABC heterotrimer, while disfavoring the 26 competing oligomers (i.e., AAA, ABB, BCA). Peptides were synthesized and characterized for thermal stability and triple-helical structure by circular dichroism and NMR. A unique A:B:C-type species was not achieved. Negative design was partially successful, with only A + B and B + C competing mixtures formed. Analysis of computed versus experimental stabilities helps to clarify the role of electrostatics and secondary-structure propensities determining collagen stability and to provide important insight into how subsequent designs can be improved.
authors.affiliation: Department of Biochemistry, Robert Wood Johnson Medical School, UMDNJ, and Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey 08854, USA.
authors.forename: Fei
authors.initials: F
authors.lastname: Xu
authors.forename: Lei
authors.initials: L
authors.lastname: Zhang
authors.forename: Ronald L
authors.initials: RL
authors.lastname: Koder
authors.forename: Vikas
authors.initials: V
authors.lastname: Nanda
mesh_terms: D000595:Amino Acid Sequence; D003094:Collagen / Q000737:chemistry* / Q000378:metabolism*; D003198:Computer Simulation; D015195:Drug Design; D006863:Hydrogen-Ion Concentration; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry / Q000378:metabolism; D017510:Protein Folding; D055503:Protein Multimerization; D055550:Protein Stability; D020836:Protein Structure, Quaternary; D055672:Static Electricity; D013379:Substrate Specificity; D013816:Thermodynamics
chemical_list: D010455:Peptides; D003094:Collagen