Potts Hamiltonian models of protein sequence co-variation are statistical models constructed from the pair correlations observed in a multiple sequence alignment (MSA) of a protein family. These models are powerful because they capture higher order correlations induced by mutations evolving under constraints and help quantify the connections between protein sequence, structure, and function mai...

Minisatellite isoallelism, i.e. the occurrence of minisatellite alleles with different internal sequence composition but indistinguishable length, is a common limitation of minisatellite allele length analysis. Internal sequence variation can be used to distinguish such isoalleles, provided that detailed sequence knowledge of its basis is available. We now show that minisatellite isoalleles can...

The deposition of protein aggregates is a unifying feature of a large class of diseases known as protein conformational disorders, which includes Alzheimer disease and prion diseases. One of the most fascinating and puzzling aspects of such diseases is the phenomenon of amyloid polymorphism, whereby a single diseaseassociated protein forms different types of ordered aggregate structures. This i...

The deuterium nuclear magnetic resonance (2H NMR) spectrum of perdeuterated tetradecanol in a mixture of 1-palmitoyl-2-oleoyl-phosphatidylethanolamine (POPE) and water was used to compare the variation of the acyl chain orientational order parameter, S(n), with carbon position, n, in the liquid crystalline lamellar (La) and hexagonal (HI,) phases. The characteristic independence of S(n) with n ...

Ribonucleic acid (RNA) molecules are known to undergo conformational changes in response various environmental stimuli including temperature, pH, and ligands.

We report a comprehensive electron crystallographic analysis of conformational changes in the photocycle of wild-type bacteriorhodopsin and in a variety of mutant proteins with kinetic defects in the photocycle. Specific intermediates that accumulate in the late stages of the photocycle of wild-type bacteriorhodopsin, the single mutants D38R, D96N, D96G, T46V, L93A and F219L, and the triple mut...

A secondary structure has been predicted for the heat shock protein HSP90 family from an aligned set of homologous protein sequences by using a transparent method in both manual and automated implementation that extracts conformational information from patterns of variation and conservation within the family. No statistically significant sequence similarity relates this family to any protein wi...

MOTIVATION Organic enzyme cofactors are involved in many enzyme reactions. Therefore, the analysis of cofactors is crucial to gain a better understanding of enzyme catalysis. To aid this, we have created the CoFactor database. RESULTS CoFactor provides a web interface to access hand-curated data extracted from the literature on organic enzyme cofactors in biocatalysis, as well as automaticall...

A kernel method enables the comprehensive characterization of conformational ensembles oligosaccharides in association with free-energy landscape.

A comprehensive conformational search and high-level composite ab initio computations provide benchmark proton affinities gas-phase basicities for glycine.