Dataset Information

Configurational entropy in protein-peptide binding: computational study of Tsg101 ubiquitin E2 variant domain with an HIV-derived PTAP nonapeptide.

ABSTRACT: Configurational entropy is thought to influence biomolecular processes, but there are still many open questions about this quantity, including its magnitude, its relationship to molecular structure, and the importance of correlation. The mutual information expansion (MIE) provides a novel and systematic approach to extracting configurational entropy changes due to correlated motions from molecular simulations. We present the first application of the MIE method to protein-ligand binding using multiple molecular dynamics simulations to study the association of the ubiquitin E2 variant domain of the protein Tsg101 and an HIV-derived nonapeptide. This investigation utilizes the second-order MIE approximation, which accounts for correlations between all pairs of degrees of freedom. The computed change in configurational entropy is large and has a major contribution from changes in pairwise correlation. The results also reveal intricate structure-entropy relationships. Thus, the present analysis suggests that in order for a model of binding to be accurate, it must include a careful accounting of configurational entropy changes.

SUBMITTER: Killian BJ

PROVIDER: S-EPMC2758778 | biostudies-literature | 2009 Jun

REPOSITORIES: biostudies-literature

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Publications

Configurational entropy in protein-peptide binding: computational study of Tsg101 ubiquitin E2 variant domain with an HIV-derived PTAP nonapeptide.

Killian Benjamin J BJ Kravitz Joslyn Yudenfreund JY Somani Sandeep S Dasgupta Paramita P Pang Yuan-Ping YP Gilson Michael K MK

Journal of molecular biology 20090409 2

Configurational entropy is thought to influence biomolecular processes, but there are still many open questions about this quantity, including its magnitude, its relationship to molecular structure, and the importance of correlation. The mutual information expansion (MIE) provides a novel and systematic approach to extracting configurational entropy changes due to correlated motions from molecular simulations. We present the first application of the MIE method to protein-ligand binding using mul ...[more]

PMID: 19362095

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Project description:Entropy and the second law of thermodynamics are fundamental concepts that underlie all natural processes and patterns. Recent research has shown how the entropy of a landscape mosaic can be calculated using the Boltzmann equation, with the entropy of a lattice mosaic equal to the logarithm of the number of ways a lattice with a given dimensionality and number of classes can be arranged to produce the same total amount of edge between cells of different classes. However, that work seemed to also suggest that the feasibility of applying this method to real landscapes was limited due to intractably large numbers of possible arrangements of raster cells in large landscapes. Here I extend that work by showing that: (1) the proportion of arrangements rather than the number with a given amount of edge length provides a means to calculate unbiased relative configurational entropy, obviating the need to compute all possible configurations of a landscape lattice; (2) the edge lengths of randomized landscape mosaics are normally distributed, following the central limit theorem; and (3) given this normal distribution it is possible to fit parametric probability density functions to estimate the expected proportion of randomized configurations that have any given edge length, enabling the calculation of configurational entropy on any landscape regardless of size or number of classes. I evaluate the boundary limits (4) for this normal approximation for small landscapes with a small proportion of a minority class and show it holds under all realistic landscape conditions. I further (5) demonstrate that this relationship holds for a sample of real landscapes that vary in size, patch richness, and evenness of area in each cover type, and (6) I show that the mean and standard deviation of the normally distributed edge lengths can be predicted nearly perfectly as a function of the size, patch richness and diversity of a landscape. Finally, (7) I show that the configurational entropy of a landscape is highly related to the dimensionality of the landscape, the number of cover classes, the evenness of landscape composition across classes, and landscape heterogeneity. These advances provide a means for researchers to directly estimate the frequency distribution of all possible macrostates of any observed landscape, and then directly calculate the relative configurational entropy of the observed macrostate, and to understand the ecological meaning of different amounts of configurational entropy. These advances enable scientists to take configurational entropy from a concept to an applied tool to measure and compare the disorder of real landscapes with an objective and unbiased measure based on entropy and the second law.

Dataset Information

Configurational entropy in protein-peptide binding: computational study of Tsg101 ubiquitin E2 variant domain with an HIV-derived PTAP nonapeptide.

Publications

Configurational entropy in protein-peptide binding: computational study of Tsg101 ubiquitin E2 variant domain with an HIV-derived PTAP nonapeptide.

Similar Datasets

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