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

Bioinformatics

Volumn 31, Issue 8, 2015, Pages 1319-1321

  Rezaei Ghaleh, Nasrollah ^a,b   Klama, Frederik ^a   Munari, Francesca ^a,b   Zweckstetter, Markus ^a,b,c  

^a MAX PLANCK INSTITUTE FOR BIOPHYSICAL CHEMISTRY   (Germany)

^b GERMAN CENTER FOR NEURODEGENERATIVE DISEASES DZNE   (Germany)

^c UNIVERSITY MEDICAL CENTER GÖTTINGEN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EUKARYOTA;

RIBOSOMAL PROTEIN L7-L12; RIBOSOME PROTEIN;

BIOLOGY; CHEMISTRY; COMPUTER PROGRAM; PROCEDURES; PROTEIN TERTIARY STRUCTURE; ROTATION;

COMPUTATIONAL BIOLOGY; PROTEIN STRUCTURE, TERTIARY; RIBOSOMAL PROTEINS; ROTATION; SOFTWARE;

EID: 84927725796     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu824     Document Type: Article

References (17)

1. Amoros, D. et al. (2013) Prediction of hydrodynamic and other solution properties of partially disordered proteins with a simple, coarse-grained model, J. Chem. Theory Comput., 9, 1678-1685.
2. Aragon, S. R. (2011) Recent advances in macromolecular hydrodynamic modeling, Methods, 54, 101-114.
3. Bae, S. H. et al. (2009) Prediction of the rotational tumbling time for proteins with disordered segments, J. Am. Chem. Soc., 131, 6814-6821.
4. Bernado, P. et al. (2007) Structural characterization of flexible proteins using small-angle X-ray scattering, J. Am. Chem. Soc., 129, 5656-5664.
5. Bocharov, E. V. et al. (1998) Conformational independence of N-and Cdomains in ribosomal protein L7/L12 and in the complex with protein L10, FEBS Lett., 423, 347-350.
6. Bocharov, E. V. et al. (2004) From structure and dynamics of protein L7/L12 to molecular switching in ribosome, J. Biol. Chem., 279, 17697-17706.
7. Gudkov, A. T. (1997) The L7/L12 ribosomal domain of the ribosome: structural and functional studies, FEBS Lett., 407, 253-256.
8. Houben, K. et al. (2007) Intrinsic dynamics of the partly unstructured PX domain from the Sendai virus RNA polymerase cofactor P, Biophys. J., 93, 2830-2844.
9. Huang, J. R. et al. (2014) Transient electrostatic interactions dominate the conformational equilibrium sampled by multidomain splicing factor U2AF65: a combined NMR and SAXS study, J. Am. Chem. Soc., 136, 7068-7076.
10. Li, Y. and Zhang, Y. (2009) REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks, Proteins, 76, 665-676.
11. Loman, A. et al. (2010) Measuring rotational diffusion of macromolecules by fluorescence correlation spectroscopy, Photochem. Photobiol. Sci., 9, 627-636.
12. Ortega, A. et al. (2011) Prediction of hydrodynamic and other solution properties of rigid proteins from atomic-and residue-level models, Biophys. J., 101, 892-898.
13. Rezaei-Ghaleh, N. et al. (2013) Predicting the rotational tumbling of dynamic multidomain proteins and supramolecular complexes, Angew. Chem. Int. Ed. Engl., 52, 11410-11414.
14. Schwalbe, H. et al. (1997) Structural and dynamical properties of a denatured protein. Heteronuclear 3D NMR experiments and theoretical simulations of lysozyme in 8Murea, Biochemistry, 36, 8977-8991.
15. Tompa, P. (2012) Intrinsically disordered proteins: a 10-year recap, Trends Biochem. Sci., 37, 509-516.
16. Walker, O. et al. (2004) Efficient and accurate determination of the overall rotational diffusion tensor of a molecule from (15)N relaxation data using computer program ROTDIF, J. Magn. Reson., 168, 336-345.
17. Wong, V. et al. (2009) Influence of the coupling of interdomain and overall motions on NMR relaxation, Proc. Natl. Acad. Sci., 106, 11016-11021.