Multi-State Computational Design and Experimental Characterization of Triosephosphate Isomerase Flexible Hinges

JACKSON CAHN; BERNARDO SOSA PADILLA ARAUJO; STEPHEN MAYO

San Diego, California

Conferencia; The 26th Annual Symposium of The Protein Society; 2012

The Protein Society

Traditional computational protein design calculationsenable the evaluation and selection of protein sequencesin the context of a single native structure. However manyproteins natively require multiple distinct conformationsfor functionality. Recently, a novel algorithm has beendeveloped which considers several structures in a singleoptimization calculation. This new method could beuseful for designing proteins that need to accommodateseveral conformations. We sought to test this algorithmon triosephosphate isomerase (TIM). Loop 6 in TIM isa lid with open and closed conformations that facilitatesubstrate binding, product diffusion, and catalysis. Ituses two 3-amino acid hinges that provide the flexibilityfor the open-closed transition. In the present work we usemulti-state design (MSD) methods to design the flexiblehinges in TIM. We are in the process of assessing theapplicability of MSD for the design of flexible proteinhinges by exhaustive screening of computationallydesigned libraries. The results will suggest whether,by considering both conformations of the enzymeinstead of purely the open or closed conformations,our methods provide libraries enriched in catalyticallyactive TIMs. This work supported by a DARPA ProteinDesign Processes grant and a National Security Scienceand Engineering Faculty Fellowship award to S.L.M.