title: Tandem repeats in proteins: from sequence to structure.
abstract: The bioinformatics analysis of proteins containing tandem repeats requires special computer programs and databases, since the conventional approaches predominantly developed for globular domains have limited success. Here, I survey bioinformatics tools which have been developed recently for identification and proteome-wide analysis of protein repeats. The last few years have also been marked by an emergence of new 3D structures of these proteins. Appraisal of the known structures and their classification uncovers a straightforward relationship between their architecture and the length of the repetitive units. This relationship and the repetitive character of structural folds suggest rules for better prediction of the 3D structures of such proteins. Furthermore, bioinformatics approaches combined with low resolution structural data, from biophysical techniques, especially, the recently emerged cryo-electron microscopy, lead to reliable prediction of the protein repeat structures and their mode of binding with partners within molecular complexes. This hybrid approach can actively be used for structural and functional annotations of proteomes.
authors: Centre de Recherches de Biochimie Macromoléculaire, CNRS, Université Montpellier 1 et 2, 1919 Route de Mende, 34293 Montpellier, Cedex 5, France. andrey.kajava@crbm.cnrs.fr
authors: Andrey V
authors: AV
authors: Kajava
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry / Q000235:genetics; D019295:Computational Biology; D003198:Computer Simulation; D030562:Databases, Protein; D024022:Fibrillar Collagens / Q000737:chemistry / Q000235:genetics; D005583:Fourier Analysis; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011099:Polyglutamic Acid / Q000737:chemistry / Q000235:genetics; D011487:Protein Conformation; D011506:Proteins; D020449:Repetitive Sequences, Amino Acid; D010566:Virulence Factors, Bordetella / Q000737:chemistry / Q000235:genetics
chemical_list: D001425:Bacterial Outer Membrane Proteins; D024022:Fibrillar Collagens; D011506:Proteins; D010566:Virulence Factors, Bordetella; D011099:Polyglutamic Acid; C068929:pertactin