Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts:   Target Concepts:
Query: EC:3.1.31.1 (micrococcal nuclease)
 2,818 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

Metal-nucleus distances measured by paramagnetic effects on T1 and interproton distances measured by the nuclear Overhauser effect have been used to determine the conformations, arrangement, locations of enzyme-bound substrates with respect to specific amino acid residues, and to dock them into X-ray structures of enzymes. Synthetic peptide fragments of enzymes that range from 45 to 50 residues in length in some cases retain enough secondary and tertiary structure to bind substrates with affinities and in conformations similar to those found on the complete enzymes. The entire structure of peptides of this size can be determined in solution by 2-dimensional nuclear magnetic resonance (NMR) methods. The applications of NMR methods to enzymology are exemplified by studies of adenylate kinase, ketosteroid isomerase, staphylococcal nuclease, and DNA polymerase I.--Mildvan, A. S. NMR studies of the interactions of substrates with enzymes and their peptide fragments.
 ...
PMID:NMR studies of the interactions of substrates with enzymes and their peptide fragments. 264 1

The fast and accurate prediction of protein flexibility is one of the major challenges in protein science. Enzyme activity, signal transduction, and ligand binding are dynamic processes involving essential conformational changes ranging from small side chain fluctuations to reorientations of entire domains. In the present work, we describe a reimplementation of the CONCOORD approach, termed tCONCOORD, which allows a computationally efficient sampling of conformational transitions of a protein based on geometrical considerations. Moreover, it allows for the extraction of the essential degrees of freedom, which, in general, are the biologically relevant ones. The method rests on a reliable estimate of the stability of interactions observed in a starting structure, in particular those interactions that change during a conformational transition. Applications to adenylate kinase, calmodulin, aldose reductase, T4-lysozyme, staphylococcal nuclease, and ubiquitin show that experimentally known conformational transitions are faithfully predicted.
 ...
PMID:Geometry-based sampling of conformational transitions in proteins. 1799 73