Topic
Structural biology
About: Structural biology is a research topic. Over the lifetime, 2206 publications have been published within this topic receiving 126070 citations.
Papers published on a yearly basis
Papers
More filters
TL;DR: Comprehensive sets of structural superimpositions reveal that both CK2α and CK2β are relatively rigid molecules, suggesting an alternative mode of activity control.
Abstract: Within the last decade, 40 crystal structures corresponding to protein kinase CK2 (former name 'casein kinase 2'), to its catalytic subunit CK2α and to its regulatory subunit CK2β were published. Together they provide a valuable, yet by far not complete basis to rationalize the biochemical features of the enzyme, such as its constitutive activity, acidophilic substrate specificity, dual-cosubstrate specificity and its hetero-tetrameric quarternary structure. Comprehensive sets of structural superimpositions reveal that both CK2α and CK2β are relatively rigid molecules. In CK2β the critical region of CK2α recruitment is pre-formed in the unbound state. In CK2α the activation segment ― a key element of protein kinase regulation ― adapts invariably the typical conformation of the active enzymes. Recent structures of human CK2α revealed a surprising plasticity in the ATP-binding region, suggesting an alternative mode of activity control.
67 citations
TL;DR: It is shown here that the Structural Classification of Proteins (SCOP) database can be effectively used to enhance the sensitivity of the distant homology recognition methods to rival the “threading” methods.
Abstract: Protein structure prediction is arguably the biggest unsolved problem of structural biology. The notion of the number of naturally occurring different protein folds being limited allows partial solution of this problem by the use of fold recognition methods, which "thread" the sequence in question through a library of known protein folds. The fold recognition methods were thought to be superior to the distant homology recognition methods when there is no significant sequence similarity to known structures. We show here that the Structural Classification of Proteins (SCOP) database, organizing all known protein folds according their structural and evolutionary relationships, can be effectively used to enhance the sensitivity of the distant homology recognition methods to rival the "threading" methods. In the CASP2 experiment, our approach correctly assigned into existing SCOP superfamilies all of the six "fold recognition" targets we attempted. For each of the six targets, we correctly predicted the homologous protein with a very similar structure; often, it was the most similar structure. We correctly predicted local alignments of the sequence features that we found to be characteristic for the protein superfamily containing a given target. Our global alignments, extended manually from these local alignments, also appeared to be rather accurate.
66 citations
TL;DR: The secondary structure prediction system used combines the information from several algorithms and trains the data to offer an optimized prediction of the known P450cam, and assign full secondary structure to the target protein.
66 citations
TL;DR: Recent advances in structural biology and biophysical approaches that explore the underlying mechanism by which PDIs fulfil their distinct functions to promote productive protein folding and scavenge misfolded proteins in the ER, the primary factory for efficient production of the secretome are reviewed.
66 citations
TL;DR: Comparing the interactions of different peptides shows that an intricate network of water molecules have a key role in dictating specificity, and the use of mass spectrometry to quantify tightly bound water molecules may prove of general use in structural biology, where an independent determination of the water molecules associated with a structure would be advantageous.
66 citations