CABS-flex predictions of protein flexibility compared with NMR ensembles

Motivation: Identification of flexible regions of protein structures is important for understanding of their biological functions. Recently, we have developed a fast approach for predicting protein structure fluctuations from a single protein model: the CABS-flex. CABS-flex was shown to be an efficient alternative to conventional all-atom molecular dynamics (MD). In this work, we evaluate CABS-flex and MD predictions by comparison with protein structural variations within NMR ensembles. Results: Based on a benchmark set of 140 proteins, we show that the relative fluctuations of protein residues obtained from CABS-flex are well correlated to those of NMR ensembles. On average, this correlation is stronger than that between MD and NMR ensembles. In conclusion, CABS-flex is useful and complementary to MD in predicting of protein regions that undergo conformational changes and the extent of such changes

A hierarchical approach to the prediction of the quaternary structure of GCN4 and its mutants

First published in DIMACS Series in Discrete Mathematics and Theoretical Computer Science, 23 (1996) published by the American Mathematical Society.Presented at DIMACS Workshop on Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding, March 20-21, 1995.A hierarchical approach to protein folding is employed to examine the folding pathway and predict the quaternary structure of the GCN4 leucine zipper. Structures comparable in quality to experiment have been predicted. In addition, the equilibrium between dimers, trimers and tetramers of a number of GCN4 mutants has been examined. In five out of eight cases, the simulation results are in accordance with the experimental studies of Harbury, et al

Stone Bar-handled Bowls: Characteristics and Values

Stone bar-handled bowls are refined bowls displaying a characteristic bar-handle under the rim. They are typical of the Iron Age stone vessels assemblage, and were considerably widespread during Iron Age II and III throughout the Levant and Mesopotamia. In some archaeological reports, they are considered as possible witnesses of the process of Assyrianisation in the Levant, even though the basis for such a hypothesis remains unclear. Other questions concerning their origin, their relation with pottery, and the reasons for their spread have so far been left unanswered.This paper aims at filling these gaps trying to ultimately define the social value of this peculiar class of stone bowl

A simple technique to estimate partition functions and equilibrium constants from Monte Carlo simulations

©1995 American Institute of PhysicsThe electronic version of this article is the complete one and can be found online at: http://link.aip.org/link/?JCPSA6/102/6189/1DOI:10.1063/1.469063A combined Monte Carlo (MC) simulation-statistical mechanical treatment is proposed to calculate the internal partition function and equilibrium constant. The method has been applied to a number of one and multidimensional analytical functions. When sampling is incomplete, various factorization approximations for estimating the partition function are discussed. The resulting errors are smaller when the ratios of the partition functions are calculated (as in the determination of equilibrium constants) as opposed to the partition function itself

Coarse-Grained Simulations of Membrane Insertion and Folding of Small Helical Proteins Using the CABS Model

The CABS coarse-grained model is a well-established tool for modeling globular proteins (predicting their structure, dynamics, and interactions). Here we introduce an extension of the CABS representation and force field (CABS-membrane) to the modeling of the effect of the biological membrane environment on the structure of membrane proteins. We validate the CABS-membrane model in folding simulations of 10 short helical membrane proteins not using any knowledge about their structure. The simulations start from random protein conformations placed outside the membrane environment and allow for full flexibility of the modeled proteins during their spontaneous insertion into the membrane. In the resulting trajectories, we have found models close to the experimental membrane structures. We also attempted to select the correctly folded models using simple filtering followed by structural clustering combined with reconstruction to the all-atom representation and all-atom scoring. The CABS-membrane model is a promising approach for further development toward modeling of large protein–membrane systems