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"Ideal" Protein Structures Computational De Novo Design of Speaker: Dr. Nobuyasu Koga University of Washington ＜日時＞ 平成 23 年 6 月 21 日 ( 火 ) 14：00〜 ＜場所＞ 生物物理第 1 セミナー室 BP1（理学部 1 号館 106 号室） ７５３−４２２０ 高田 彰二 Nobuyasu Koga , Rie Koga , Gaohua Liu , Rong Xiao , Gaetano T. Montelione , David Baker 1. Biochemistry, Howard Hughes Medical Institute, University of Washington, Seattle, WA, United States. 2. Molecular Biology and Biochemistry, Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, NJ, United States. De novo design of an arbitrary protein structure is a stringent test of our understanding of the principles of protein folding: how do amino acid sequences determine protein tertiary structures? Native protein structures have irregular features such as long loops, bent helices and bulge of strands that can arise asa result of functional selection during evolution. Here, to shed light on the key issues underlying folding without these complications, we computationally designed “ideal” structures completely from scratch with Rosetta using only canonical secondary structure (SS) elements. We focused on 4 alpha+/beta topologies: Ferredoxin, Rossmann2x2, Flavodoxin, and Rossmann3x3. In folding calculations we found that the probability of folding to a desired target topology was strongly dependent on length of the SS elements. This led us to develop a principled and systematic approach for rationally designing structures for alpha+/beta topologies. By building backbone conformations with SS lengths that maximize foldability, and placing side-chains stabilizing the backbone conformations, we created proteins having smoothfunnel-like energy landscape in silico. The designed sequences range in length from 76 to 151 residues. To critically test our approach, we synthesized genes encoding these designs and expressed, purified, and characterized the proteins. Many of the designed proteins are monomeric and highly stable remaining folded even at 100C.The structures were solved by NMR (PDB ID: 2kl8, 2kpo, 2l69, 2lci, and 2l82). The NMR structures of designed proteins with less than 100 residues, 2kl8 and 2kpo, agree with the computational models to high accuracy, RMSD <1.3Å. For the more complex proteins with more than 100 residues, 2l69, 2lci and 2l82, the NMR and computational models were in agreement in the architecture level, but the neighboring 2 strands were swapped. These results show that we have advanced considerably towards the goal of rationally designing any single domain alpha+/beta protein, but there are still challenges and mysteries remaining. Computational De Novo Design of “Ideal” Protein Structures 1 1 1 2 2 2
