Nucleic Acids Research Advance Access originally published online on September 6, 2006
Nucleic Acids Research 2006 34(16):4561-4571; doi:10.1093/nar/gkl376
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Nucleic Acids Research, 2006, Vol. 34, No. 16 4561-4571
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Structural Biology |
Recognition of T-rich single-stranded DNA by the cold shock protein Bs-CspB in solution
Laboratorium für Biochemie, Universität Bayreuth D-95440 Bayreuth, Germany 1 Max-Delbrück-Centrum für Molekulare Medizin 13125 Berlin, Germany 2 Institut für Biochemie, Emil-Fischer-Zentrum, Universität Erlangen–Nürnberg 91054 Erlangen, Germany
*To whom correspondence should be addressed. Tel: +49 345 55 25353; Fax: +49 345 55 27383; Email: jochen.balbach{at}physik.uni-halle.de
Received December 6, 2005. Revised February 28, 2006. Accepted April 30, 2006.
Cold shock proteins (CSP) belong to the family of single-stranded nucleic acid binding proteins with OB-fold. CSP are believed to function as ‘RNA chaperones’ and during anti-termination. We determined the solution structure of Bs-CspB bound to the single-stranded DNA (ssDNA) fragment heptathymidine (dT7) by NMR spectroscopy. Bs-CspB reveals an almost invariant conformation when bound to dT7 with only minor reorientations in loop ß1–ß2 and ß3–ß4 and of few aromatic side chains involved in base stacking. Binding studies of protein variants and mutated ssDNA demonstrated that Bs-CspB associates with ssDNA at almost diffusion controlled rates and low sequence specificity consistent with its biological function. A variation of the ssDNA affinity is accomplished solely by changes of the dissociation rate. 15N NMR relaxation and H/D exchange experiments revealed that binding of dT7 increases the stability of Bs-CspB and reduces the sub-nanosecond dynamics of the entire protein and especially of loop ß3–ß4.
Present addresses: Markus Zeeb, Department of Molecular Biology, The Scripps Research Institute, La Jolla, USA
Ulrich Weininger, Christian Löw and Jochen Balbach, Fachbereich Physik, Fachgruppe Biophysik, Martin-Luther-Universität Halle-Wittenberg, D-06099 Halle(Saale), Germany
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