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枯草芽孢杆菌冷休克蛋白CspB的单链DNA结合:核磁共振图谱分析与突变特征研究

Single-stranded DNA binding of the cold-shock protein CspB from Bacillus subtilis: NMR mapping and mutational characterization.

作者信息

Zeeb Markus, Balbach Jochen

机构信息

Laboratorium für Biochemie, Universität Bayreuth, D-95440 Bayreuth, Germany.

出版信息

Protein Sci. 2003 Jan;12(1):112-23. doi: 10.1110/ps.0219703.

Abstract

Cold-shock proteins (CSPs) bind to single-stranded nucleic acids, thereby acting as a "RNA chaperone." To gain deeper insights into the rather unspecific nature of ssDNA/RNA binding, we characterized the binding interface of CspB from Bacillus subtilis to a 25-mer of ssDNA (Y-Box25) using heteronuclear 2D NMR spectroscopy. Seventeen residues, including eight out of nine aromatic amino acids, are directly involved in the Y-Box25 interaction and were identified by extreme line broadening of their cross-peaks. Eight residues belong to the earlier proposed RNP binding motifs. A second set of seven backbone amides becomes evident by major chemical shift perturbations reporting remote conformational rearrangements upon binding. These residues are located in loop beta3-beta4 and loopbeta4-beta5, and include Ile18. The individual contributions of the so-identified residues were examined by fluorescence titration experiments of 15 CspB variants. Phenylalanine substitutions in- and outside the RNP motifs significantly reduce the binding affinity. Unrestricted possible backbone conformations of loop beta3-beta4 also markedly contribute to binding. Stopped-flow fluorescence kinetics revealed that the different binding affinities of CspB variants are determined by the dissociation rate, whereas the association rate remains unchanged. This might be of importance for the "RNA chaperone" activity of CspB.

摘要

冷休克蛋白(CSPs)可与单链核酸结合,从而起到“RNA伴侣”的作用。为了更深入地了解单链DNA/RNA结合的非特异性本质,我们利用异核二维核磁共振光谱对枯草芽孢杆菌的CspB与一条25聚体单链DNA(Y-Box25)的结合界面进行了表征。17个残基,包括9个芳香族氨基酸中的8个,直接参与了与Y-Box25的相互作用,并通过其交叉峰的极度谱线展宽得以鉴定。8个残基属于先前提出的RNP结合基序。另一组7个主链酰胺通过结合后报告远程构象重排的主要化学位移扰动而变得明显。这些残基位于β3-β4环和β4-β5环中,包括Ile18。通过对15个CspB变体进行荧光滴定实验,研究了这些已鉴定残基的各自贡献。RNP基序内外的苯丙氨酸取代显著降低了结合亲和力。β3-β4环不受限制的可能主链构象也对结合有显著贡献。停流荧光动力学表明,CspB变体的不同结合亲和力由解离速率决定,而缔合速率保持不变。这可能对CspB的“RNA伴侣”活性具有重要意义。

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