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Bioinformatics. 2015 Apr 15;31(8):1319-21. doi: 10.1093/bioinformatics/btu824. Epub 2014 Dec 12.

HYCUD: a computational tool for prediction of effective rotational correlation time in flexible proteins.

Author information

1
Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany, Structural Biology in Dementia, German Center for Neurodegenerative Diseases (DZNE), 37077 Göttingen, Germany and Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen (UMG), 37075 Göttingen, Germany Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany, Structural Biology in Dementia, German Center for Neurodegenerative Diseases (DZNE), 37077 Göttingen, Germany and Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen (UMG), 37075 Göttingen, Germany.
2
Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany, Structural Biology in Dementia, German Center for Neurodegenerative Diseases (DZNE), 37077 Göttingen, Germany and Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen (UMG), 37075 Göttingen, Germany.
3
Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany, Structural Biology in Dementia, German Center for Neurodegenerative Diseases (DZNE), 37077 Göttingen, Germany and Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen (UMG), 37075 Göttingen, Germany Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany, Structural Biology in Dementia, German Center for Neurodegenerative Diseases (DZNE), 37077 Göttingen, Germany and Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen (UMG), 37075 Göttingen, Germany Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany, Structural Biology in Dementia, German Center for Neurodegenerative Diseases (DZNE), 37077 Göttingen, Germany and Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen (UMG), 37075 Göttingen, Germany.

Abstract

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-order transitions in interdomain linkers.

AVAILABILITY AND IMPLEMENTATION:

The source code and documentation are available at www.mpibpc.mpg.de/106144/software.

CONTACT:

mzwecks@gwdg.de or nare@nmr.mpibpc.mpg.de

SUPPLEMENTARY INFORMATION:

Supplementary material is available at Bioinformatics online.

PMID:
25505088
DOI:
10.1093/bioinformatics/btu824
[Indexed for MEDLINE]

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