Protein Folding and Structure Prediction from the Ground Up II: AAWSEM for alpha/beta Proteins

MC Chen and XC Lin and W Lu and JN Onuchic and PG Wolynes, JOURNAL OF PHYSICAL CHEMISTRY B, 121, 3473-3482 (2017).

DOI: 10.1021/acs.jpcb.6b09347

The atomistic associative memory) water Mediated, structure and energy model (AAWSEM) is an efficient. coarse-grained force field with transferable tertiary interactions that incorporates local in sequence energetic biases using structural information derived from all-atom simulations of long segments of the protein. For alpha helical proteins, the accuracy of structure prediction using AAWSEM has been established previously. In this article, we examine the capability of AAWSEM to predict the structure of alpha/beta proteins. We also elaborate on an iterative approach that uses the structures from a first round of AAWSEM simulation as fragment memories. This iterative scheme improves the quality of the structure predietion and makes the free energy profile more funneled toward native configurations. We explore the use of clustering,analyses as a way of evaluating the confidence in various structure prediction models. Clustering using a local relative order parameter (mutual Q) of the predicted structural ensemble turns out to be optimal. The tightest cluster according to mutual Q generally has the most correctly folded structure. Since there is no bioinformatic input, AAWSEM amounts to an ab initio protein structure prediction method, that combines the efficiency of coarse-grained simulations with the local structural accuracy that can be achieved from all-atom simulations.

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