Jan 24, 2014

Bayesian Energy Landscape Tilting: Towards Concordant Models of Molecular Ensembles

BioRxiv : the Preprint Server for Biology
Kyle BeauchampRhiju Das

Abstract

Predicting biological structure has remained challenging for systems such as disordered proteins that take on myriad conformations. Hybrid simulation/experiment strategies have been undermined by difficulties in evaluating errors from computa- tional model inaccuracies and data uncertainties. Building on recent proposals from maximum entropy theory and nonequilibrium thermodynamics, we address these issues through a Bayesian Energy Landscape Tilting (BELT) scheme for computing Bayesian “hyperensembles” over conformational ensembles. BELT uses Markov chain Monte Carlo to directly sample maximum-entropy conformational ensembles consistent with a set of input experimental observables. To test this framework, we apply BELT to model trialanine, starting from disagreeing simulations with the force fields ff96, ff99, ff99sbnmr-ildn, CHARMM27, and OPLS-AA. BELT incorporation of limited chemical shift and 3 J measurements gives convergent values of the peptide’s α , β , and PP II conformational populations in all cases. As a test of predictive power, all five BELT hyperensembles recover set-aside measurements not used in the fitting and report accu- rate errors, even when starting from highly inaccurate simulations. BELT’s principled ...Continue Reading

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Mentioned in this Paper

Anatomic Structures
Proline
Muscle Energy Technique
Molecular Target
Structure
Chemicals
Simulation
Accu
Alanyl-alanyl-alanine
Beta protein

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