Dataset Information

Comparative Molecular Dynamics Analysis of RNase-S Complex Formation.

ABSTRACT: Limited proteolysis of RNase-A yields a short N-terminal S-peptide segment and the larger S-protein. Binding of S-peptide to S-protein results in the formation of an enzymatically active RNase-S protein. S-peptide undergoes a transition from intrinsic disorder to an ordered helical state upon association with S-protein to form RNase-S and is an excellent model system to study coupled folding and binding. To better understand the dynamics of the RNases-S complex and its isolated partners, comparative molecular dynamics simulations have been performed. In agreement with experiment, we find significant conformational fluctuations of the isolated S-peptide compatible with a disordered regime and only little residual helical structure. In the RNase-S complex, the N-terminal helix of S-peptide unfolds and refolds repeatedly on the microsecond timescale, indicating that the ?-helical structure is only part of the equilibrium regime for these residues whereas the C-terminal residues are confined to the helical conformation that is found in the x-ray structure. This is also in line with systematic, in silico Alanine scanning free-energy simulations, which indicate that the major contribution to complex stability emerges from the C-terminal helical turn, consisting of residues 8-13 in S-peptide whereas the N-terminal S-peptide residues 1-7 make only minor contributions. Comparative simulations of S-protein in the presence and absence of S-peptide reveal that the isolated S-protein is significantly more flexible than in the complex, and undergoes a global pincerlike conformational change that narrows the S-peptide binding cleft. The narrowed binding cleft adds a barrier for complex formation likely influencing the binding kinetics. This conformational change is reversed by S-peptide association, which also stabilizes conformational fluctuations in S-protein. Such global motions associated with binding are also likely to play a role for other coupled peptide folding and binding processes at peptide binding regions on protein surfaces.

SUBMITTER: Luitz MP

PROVIDER: S-EPMC5627186 | biostudies-literature | 2017 Oct

REPOSITORIES: biostudies-literature

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Publications

Comparative Molecular Dynamics Analysis of RNase-S Complex Formation.

Luitz Manuel P MP Bomblies Rainer R Zacharias Martin M

Biophysical journal 20171001 7

Limited proteolysis of RNase-A yields a short N-terminal S-peptide segment and the larger S-protein. Binding of S-peptide to S-protein results in the formation of an enzymatically active RNase-S protein. S-peptide undergoes a transition from intrinsic disorder to an ordered helical state upon association with S-protein to form RNase-S and is an excellent model system to study coupled folding and binding. To better understand the dynamics of the RNases-S complex and its isolated partners, compara ...[more]

PMID: 28978440

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Project description:In Bacillus subtilis , the RicT (YaaT), RicA (YmcA) and RicF (YlbF) proteins, which form a stable ternary complex, are needed together with RNase Y (Rny), to cleave and thereby stabilize several key transcripts encoding enzymes of intermediary metabolism. We show here that RicT, but not RicA or RicF, forms a stable complex with Rny, and that this association requires the presence of RicA and RicF. We propose that RicT is handed off from the ternary complex to Rny. We show further that the two iron-sulfur clusters carried by the ternary Ric complex are required for the formation of the stable RicT-Rny complex. We demonstrate that proteins of the degradosome-like network of B. subtilis , which also interact with Rny, are dispensable for processing of the gapA operon. Thus, Rny participates in distinct RNA-related processes, determined by its binding partners, and a RicT-Rny complex is likely the functional entity for gapA mRNA maturation.ImportanceThe action of nucleases on RNA is universal and essential for all forms of life and includes processing steps that lead to the mature and functional forms of certain transcripts. In B. subtilis it has been shown that key transcripts for energy producing steps of glycolysis, for nitrogen assimilation and for oxidative phosphorylation, all of them crucial processes of intermediary metabolism, are cleaved at specific locations, resulting in mRNA stabilization. The proteins required for these cleavages in B. subtilis (Rny (RNase Y), RicA (YmcA), RicF (YlbF) and RicT (YaaT)) are broadly conserved among the firmicutes, including in several important pathogens, hinting that regulatory mechanisms they control may also be conserved. Several aspects of these regulatory events have been explored: phenotypes associated with the absence of these proteins have been described, the impact of these absences on the transcriptome has been documented, and there has been significant exploration of the biochemistry and structural biology of Rny and the Ric proteins. The present study further advances our understanding of the association of Ric proteins and Rny and shows that a complex of Rny with RicT is probably the entity that carries out mRNA maturation.

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Dataset Information

Comparative Molecular Dynamics Analysis of RNase-S Complex Formation.

Publications

Comparative Molecular Dynamics Analysis of RNase-S Complex Formation.

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