Recognition of T-rich single-stranded DNA by the cold shock protein Bs-CspB in solution.
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 beta1-beta2 and beta3-beta4 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 beta3-beta4.
Zeeb
Markus
M
Laboratorium für Biochemie, Universität Bayreuth, D-95440 Bayreuth, Germany.
Max
Klaas E A
KE
Weininger
Ulrich
U
Löw
Christian
C
Sticht
Heinrich
H
Balbach
Jochen
J
D001412:Bacillus subtilis; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D004252:DNA Mutational Analysis; D004277:DNA, Single-Stranded / Q000737:chemistry* / Q000378:metabolism; D041961:Deuterium Exchange Measurement; D007700:Kinetics; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D011487:Protein Conformation; D013816:Thermodynamics; D013936:Thymidine / Q000737:chemistry*
D001426:Bacterial Proteins; D004277:DNA, Single-Stranded; C077188:cold-shock protein CspB, Bacteria; D013936:Thymidine