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ABSTRACT Molecular dynamics simulations are used to analyze the relationship between NMR‐derived squared generalized order parameters of amide NH groups and backbone entropy. Amide order parameters (O2NH) are largely determined by the secondary structure and average values appear unrelated to...
ABSTRACT Accurate prediction of protein function in humans is important for understanding biological processes at the molecular level in biomedicine and drug design. Over a third of proteins are commonly held to bind metal, and ∼10% of human proteins, to bind zinc. Therefore, an initial step in...
ABSTRACT Protein structures are often thought of as static objects, and indeed, the bulk of a protein's sequence forms α‐helices, β‐sheets, and other generally well‐ordered substructures. These portions of the molecule pre‐pay the entropic price of maintaining a globally unique fold,...
ABSTRACT Binding of a ligand on a protein changes the flexibility of certain parts of the protein, which directly affects its function. These changes are not the same at each point, some parts become more flexible and some others become stiffer. Here, an equation is derived that gives the...
ABSTRACT Signal transduction mediated by Ser/Thr phosphorylation in Mycobacterium tuberculosis has been intensively studied in the last years, as its genome harbors eleven genes coding for eukaryotic‐like Ser/Thr kinases. Here we describe the crystal structure and the autophosphorylation sites...
The initiation of microtubule assembly within cells is guided by a cone shaped multi‐protein complex, γ‐tubulin ring complex (γTuRC) containing γ‐tubulin and atleast five other γ‐tubulin‐complex proteins (GCPs), i.e., GCP2, GCP3, GCP4, GCP5, and GCP6. The rim of γTuRC is a ring of...
ABSTRACT We have used probe‐based molecular dynamics (pMD) simulations to search for interaction hotspots on the surface of the therapeutically highly relevant oncogenic K‐Ras G12D. Combining the probe‐based query with an ensemble‐based pocket identification scheme and an analysis of...
ABSTRACT Structural characterization of protein–protein interactions is essential for our ability to understand life processes. However, only a fraction of known proteins have experimentally determined structures. Such structures provide templates for modeling of a large part of the proteome,...
How to compare the structures of an ensemble of protein conformations is a fundamental problem in structural biology. As has been previously observed, the widely used RMSD measure due to Kabsch, in which a rigid‐body superposition minimizing the least‐squares positional deviations is...
Heme‐containing catalases and catalase‐peroxidases catalyze the dismutation of hydrogen peroxide as their predominant catalytic activity, but in addition, individual enzymes support low levels of peroxidase and oxidase activities, produce superoxide, and activate isoniazid as an...
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