{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,26]],"date-time":"2025-09-26T13:35:29Z","timestamp":1758893729482},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"8","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: A large fraction of eukaryotic proteins contain unstructured tails or linkers. The presence of flexible regions allows these systems to experience a high level of mobility facilitating their biological function. The complex nature of protein rotation in such flexible modular systems precludes a straightforward application of hydrodynamic methods to calculate their rotational motional properties. We describe the workflow of HYdrodynamic CoUpling of Domains (HYCUD), a program for prediction of effective rotational correlation times in multidomain proteins. The usage of HYCUD is demonstrated by its application to the ribosomal protein L7\/L12. Rotational correlation times predicted by HYCUD might be used to detect molecular switch events mediated by disorder\u2013order transitions in interdomain linkers.<\/jats:p>\n               <jats:p>Availability and implementation: The source code and documentation are available at www.mpibpc.mpg.de\/106144\/software.<\/jats:p>\n               <jats:p>Contact: \u00a0mzwecks@gwdg.de or nare@nmr.mpibpc.mpg.de<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary material is available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu824","type":"journal-article","created":{"date-parts":[[2014,12,14]],"date-time":"2014-12-14T01:33:54Z","timestamp":1418520834000},"page":"1319-1321","source":"Crossref","is-referenced-by-count":10,"title":["HYCUD: a computational tool for prediction of effective rotational correlation time in flexible proteins"],"prefix":"10.1093","volume":"31","author":[{"given":"Nasrollah","family":"Rezaei-Ghaleh","sequence":"first","affiliation":[{"name":"1 Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 G\u00f6ttingen, Germany, 2Structural Biology in Dementia, German Center for Neurodegenerative Diseases (DZNE), 37077 G\u00f6ttingen, Germany and 3Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center G\u00f6ttingen (UMG), 37075 G\u00f6ttingen, Germany"},{"name":"1 Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 G\u00f6ttingen, Germany, 2Structural Biology in Dementia, German Center for Neurodegenerative Diseases (DZNE), 37077 G\u00f6ttingen, Germany and 3Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center G\u00f6ttingen (UMG), 37075 G\u00f6ttingen, Germany"}]},{"given":"Frederik","family":"Klama","sequence":"additional","affiliation":[{"name":"1 Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 G\u00f6ttingen, Germany, 2Structural Biology in Dementia, German Center for Neurodegenerative Diseases (DZNE), 37077 G\u00f6ttingen, Germany and 3Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center G\u00f6ttingen (UMG), 37075 G\u00f6ttingen, Germany"}]},{"given":"Francesca","family":"Munari","sequence":"additional","affiliation":[{"name":"1 Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 G\u00f6ttingen, Germany, 2Structural Biology in Dementia, German Center for Neurodegenerative Diseases (DZNE), 37077 G\u00f6ttingen, Germany and 3Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center G\u00f6ttingen (UMG), 37075 G\u00f6ttingen, Germany"},{"name":"1 Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 G\u00f6ttingen, Germany, 2Structural Biology in Dementia, German Center for Neurodegenerative Diseases (DZNE), 37077 G\u00f6ttingen, Germany and 3Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center G\u00f6ttingen (UMG), 37075 G\u00f6ttingen, Germany"}]},{"given":"Markus","family":"Zweckstetter","sequence":"additional","affiliation":[{"name":"1 Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 G\u00f6ttingen, Germany, 2Structural Biology in Dementia, German Center for Neurodegenerative Diseases (DZNE), 37077 G\u00f6ttingen, Germany and 3Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center G\u00f6ttingen (UMG), 37075 G\u00f6ttingen, Germany"},{"name":"1 Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 G\u00f6ttingen, Germany, 2Structural Biology in Dementia, German Center for Neurodegenerative Diseases (DZNE), 37077 G\u00f6ttingen, Germany and 3Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center G\u00f6ttingen (UMG), 37075 G\u00f6ttingen, Germany"},{"name":"1 Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 G\u00f6ttingen, Germany, 2Structural Biology in Dementia, German Center for Neurodegenerative Diseases (DZNE), 37077 G\u00f6ttingen, Germany and 3Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center G\u00f6ttingen (UMG), 37075 G\u00f6ttingen, Germany"}]}],"member":"286","published-online":{"date-parts":[[2014,12,12]]},"reference":[{"key":"2023051309021445100_btu824-B1","doi-asserted-by":"crossref","first-page":"1678","DOI":"10.1021\/ct300948u","article-title":"Prediction of hydrodynamic and other solution properties of partially disordered proteins with a simple, coarse-grained model, J","volume":"9","author":"Amoros","year":"2013","journal-title":"Chem. Theory Comput."},{"key":"2023051309021445100_btu824-B2","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1016\/j.ymeth.2010.10.005","article-title":"Recent advances in macromolecular hydrodynamic modeling","volume":"54","author":"Aragon","year":"2011","journal-title":"Methods"},{"key":"2023051309021445100_btu824-B3","doi-asserted-by":"crossref","first-page":"6814","DOI":"10.1021\/ja809687r","article-title":"Prediction of the rotational tumbling time for proteins with disordered segments, J","volume":"131","author":"Bae","year":"2009","journal-title":"Am. Chem. Soc."},{"key":"2023051309021445100_btu824-B4","doi-asserted-by":"crossref","first-page":"5656","DOI":"10.1021\/ja069124n","article-title":"Structural characterization of flexible proteins using small-angle X-ray scattering, J","volume":"129","author":"Bernado","year":"2007","journal-title":"Am. Chem. Soc."},{"key":"2023051309021445100_btu824-B5","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1016\/S0014-5793(98)00121-5","article-title":"Conformational independence of N- and C-domains in ribosomal protein L7\/L12 and in the complex with protein L10","volume":"423","author":"Bocharov","year":"1998","journal-title":"FEBS Lett."},{"key":"2023051309021445100_btu824-B6","doi-asserted-by":"crossref","first-page":"17697","DOI":"10.1074\/jbc.M313384200","article-title":"From structure and dynamics of protein L7\/L12 to molecular switching in ribosome, J","volume":"279","author":"Bocharov","year":"2004","journal-title":"Biol. Chem."},{"key":"2023051309021445100_btu824-B7","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1016\/S0014-5793(97)00361-X","article-title":"The L7\/L12 ribosomal domain of the ribosome: structural and functional studies","volume":"407","author":"Gudkov","year":"1997","journal-title":"FEBS Lett."},{"key":"2023051309021445100_btu824-B8","first-page":"2830","article-title":"Intrinsic dynamics of the partly unstructured PX domain from the Sendai virus RNA polymerase cofactor P, Biophys","volume":"93","author":"Houben","year":"2007","journal-title":"J."},{"key":"2023051309021445100_btu824-B9","doi-asserted-by":"crossref","first-page":"7068","DOI":"10.1021\/ja502030n","article-title":"Transient electrostatic interactions dominate the conformational equilibrium sampled by multidomain splicing factor U2AF65: a combined NMR and SAXS study, J","volume":"136","author":"Huang","year":"2014","journal-title":"Am. Chem. Soc."},{"key":"2023051309021445100_btu824-B10","doi-asserted-by":"crossref","first-page":"665","DOI":"10.1002\/prot.22380","article-title":"REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks","volume":"76","author":"Li","year":"2009","journal-title":"Proteins"},{"key":"2023051309021445100_btu824-B11","doi-asserted-by":"crossref","first-page":"627","DOI":"10.1039\/b9pp00029a","article-title":"Measuring rotational diffusion of macromolecules by fluorescence correlation spectroscopy, Photochem","volume":"9","author":"Loman","year":"2010","journal-title":"Photobiol. Sci."},{"key":"2023051309021445100_btu824-B12","first-page":"892","article-title":"Prediction of hydrodynamic and other solution properties of rigid proteins from atomic- and residue-level models, Biophys","volume":"101","author":"Ortega","year":"2011","journal-title":"J."},{"key":"2023051309021445100_btu824-B13","doi-asserted-by":"crossref","first-page":"11410","DOI":"10.1002\/anie.201305094","article-title":"Predicting the rotational tumbling of dynamic multidomain proteins and supramolecular complexes, Angew","volume":"52","author":"Rezaei-Ghaleh","year":"2013","journal-title":"Chem. Int. Ed. Engl."},{"key":"2023051309021445100_btu824-B14","doi-asserted-by":"crossref","first-page":"8977","DOI":"10.1021\/bi970049q","article-title":"Structural and dynamical properties of a denatured protein. Heteronuclear 3D NMR experiments and theoretical simulations of lysozyme in 8 M urea","volume":"36","author":"Schwalbe","year":"1997","journal-title":"Biochemistry"},{"key":"2023051309021445100_btu824-B15","first-page":"509","article-title":"Intrinsically disordered proteins: a 10-year recap, Trends Biochem","volume":"37","author":"Tompa","year":"2012","journal-title":"Sci."},{"key":"2023051309021445100_btu824-B16","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1016\/j.jmr.2004.03.019","article-title":"Efficient and accurate determination of the overall rotational diffusion tensor of a molecule from (15)N relaxation data using computer program ROTDIF, J","volume":"168","author":"Walker","year":"2004","journal-title":"Magn. Reson."},{"key":"2023051309021445100_btu824-B17","doi-asserted-by":"crossref","first-page":"11016","DOI":"10.1073\/pnas.0809994106","article-title":"Influence of the coupling of interdomain and overall motions on NMR relaxation, Proc","volume":"106","author":"Wong","year":"2009","journal-title":"Natl. Acad. Sci."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/8\/1319\/50305901\/bioinformatics_31_8_1319.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/8\/1319\/50305901\/bioinformatics_31_8_1319.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,13]],"date-time":"2023-05-13T09:03:17Z","timestamp":1683968597000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/8\/1319\/213137"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,12,12]]},"references-count":17,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2015,4,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu824","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,4,15]]},"published":{"date-parts":[[2014,12,12]]}}}