Utilize este identificador para referenciar este registo: http://hdl.handle.net/10362/5791
Título: Computational design with flexible backbone sampling for protein remodeling and scaffolding of complex binding sites
Autor: Correia, Bruno Emanuel Ferreira de Sousa
Orientador: Schief, Bill
Baker, David
Data de Defesa: Out-2010
Editora: Universidade Nova de Lisboa. Instituto de Tecnologia Química e Biológica
Resumo: Computational protein design has achieved several milestones, including the design of a new protein fold, the design of enzymes for reactions that lack natural catalysts, and the re-engineering of protein-protein and protein-DNA binding speci city. These achievements have spurred demand to apply protein design methods to a wider array of research problems. However, the existing computational methods have largely relied on xed-backbone approaches that may limit the scope of problems that can be tackled. Here, we describe four computational protocols - side chain grafting, exible backbone remodeling, backbone grafting, and de novo sca old design - that expand the methodological protein design repertoire, three of which incorporate backbone exibility. Brie y, in the side chain grafting method, side chains of a structural motif are transplanted to a protein with a similar backbone conformation; in exible backbone remodeling, de novo segments of backbone are built and designed; in backbone grafting, structural motifs are explicitly grafted onto other proteins; and in de novo sca olding, a protein is folded and designed around a structural motif. We developed these new methods for the design of epitope-sca old vaccines in which viral neutralization epitopes of known three-dimensional structure were transplanted onto nonviral sca old proteins for conformational stabilization and immune presentation.(...)
Descrição: Dissertation presented to obtain the Doutoramento (Ph.D.) degree in Biochemistry at the Instituto de Tecnologia Qu mica e Biol ogica da Universidade Nova de Lisboa
URI: http://hdl.handle.net/10362/5791
Aparece nas colecções:ITQB: LA - PhD Theses

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