Structural Insight of the Full-Length Ros Protein: A Prototype of the Prokaryotic Zinc-Finger Family

Abstract

is a widespread family of bacterial zinc-finger (ZF) containing proteins that integrate multiple functions such as virulence, symbiosis and/or cell cycle transcription. NMR solution structure of Ros DNA-binding domain (region 56-142, i.e. Ros87) has been solved by our group and shows that the prokaryotic ZF domain shows interesting structural and functional features that differentiate it from its eukaryotic counterpart as it folds in a significantly larger zinc-binding globular domain. We have recently proposed a novel functional model for this family of proteins suggesting that they may act as H-NS-'like' gene silencers. Indeed, the N-terminal region of this family of proteins appears to be responsible for the formation of functional oligomers. No structural characterization of the Ros N-terminal domain (region 1-55) is available to date, mainly because of serious solubility problems of the full-length protein. Here we report the first structural characterization of the N-terminal domain of the prokaryotic Zf family examining by means of MD and nMR the structural preferences of the fulllength Ros protein from Agrobacterium tumefaciens.

Ancestral zinc-finger bearing protein MucR in alpha-proteobacteria: A novel xenogeneic silencer?

“…However, several questions remain unexplored for MucR. The zinc-finger of MucR family protein is proposed as an ancestral version of eukaryotic zinc-finger structure [20] , [73] , but the structure of intact MucR protein is challenging to be resolved due to its serious solubility problems [74] . We know nothing about the MucR nucleoprotein complex, the dynamic structure of which is essential for understanding the adaptive regulatory mechanisms of MucR responding to environmental changes.…”

Screening a Molecular Fragment Library to Modulate the PED/PEA15-Phospholipase D1 Interaction in Cellular Lysate Environments

“…All NMR data were processed with the software VNMRJ 1.1.D (Varian Inc) and analyzed by using CARA (Computer Aided Resonance Assignment) software (downloaded from cara.nmr.ch). 44 For CSP studies, starting from the amide resonances for free PED/PEA15, 14 average combined chemical shift changes for bound PED/PEA15 were determined using the following equation: 45 Δδ HNav = sqrt-[((Δδ H ) 2 + (Δδ N /5) 2 )/ 2 ], where Δδ H and Δδ N are the chemical shift variations of the amide proton and nitrogen resonances, respectively. Molecular Docking.…”

Polystyrene nanoplastics affect the human ubiquitin structure and ubiquitination in cells: a high-resolution study

“…A standard set of triple-resonance NMR experiments was performed as previously reported to enable the assignment of the sequence-specic backbone and Cb resonances; 25 1 H- 13 C HSQC was used to assign H a s and H b s. NMR spectra were processed by using TopSpin 4.1.0 (Bruker) and analyzed using SPARKY 26 and CARA soware. 27 Protein structures were visualized and evaluated using CHIMERA soware.…”