Principles for designing ideal protein structures

Article

关键词: DE-NOVO DESIGN;    TORSION ANGLE DYNAMICS;    COMPUTATIONAL DESIGN;    STRUCTURE PREDICTION;    NEGATIVE DESIGN;    NMR STRUCTURE;    LOCAL-STRUCTURE;    FOLDING FUNNEL;    REDESIGN;    REFINEMENT;   

DOI  :  10.1038/nature11600

来源: SCIE

【 摘 要 】

Unlike random heteropolymers, natural proteins fold into unique ordered structures. Understanding how these are encoded in amino-acid sequences is complicated by energetically unfavourable non-ideal features-for example kinked alpha-helices, bulged beta-strands, strained loops and buried polar groups-that arise in proteins from evolutionary selection for biological function or from neutral drift. Here we describe an approach to designing ideal protein structures stabilized by completely consistent local and non-local interactions. The approach is based on a set of rules relating secondary structure patterns to protein tertiary motifs, which make possible the design of funnel-shaped protein folding energy landscapes leading into the target folded state. Guided by these rules, we designed sequences predicted to fold into ideal protein structures consisting of alpha-helices, beta-strands and minimal loops. Designs for five different topologies were found to be monomeric and very stable and to adopt structures in solution nearly identical to the computational models. These results illuminate how the folding funnels of natural proteins arise and provide the foundation for engineering a new generation of functional proteins free from natural evolution.

【 授权许可】

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