scholarly journals The Secondary Structure of Calcineurin Regulatory Region and Conformational Change Induced by Calcium/Calmodulin Binding

2008 ◽  
Vol 283 (17) ◽  
pp. 11407-11413 ◽  
Author(s):  
Xianrong Shen ◽  
Huiming Li ◽  
Yan Ou ◽  
Wenbing Tao ◽  
Aichun Dong ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Conformational Change ◽  
Regulatory Region ◽  
Calmodulin Binding

scholarly journals Light and heat control over secondary structure and amyloid-like fiber formation in an overcrowded-alkene-modified Trp zipper

2015 ◽  
Vol 6 (12) ◽  
pp. 7311-7318 ◽  
Author(s):  
Claudia Poloni ◽  
Marc C. A. Stuart ◽  
Pieter van der Meulen ◽  
Wiktor Szymanski ◽  
Ben L. Feringa
Keyword(s):  
Secondary Structure ◽  
Conformational Change ◽  
Fiber Formation ◽  
Major Influence ◽  
Heat Control ◽  
Large Conformational Change

The use of an overcrowded alkene photoswitch to control a model β-hairpin peptide is described. The light-induced, large conformational change has major influence on the secondary structure and the aggregation of the peptide, permitting the triggered formation of amyloid-like fibrils.

Characterization of the secondary structure of calmodulin in complex with a calmodulin-binding domain peptide

Biochemistry ◽  
1992 ◽  
Vol 31 (5) ◽  
pp. 1443-1451 ◽  
Author(s):  
Sharon M. Roth ◽  
Diane M. Schneider ◽  
Laura A. Strobel ◽  
Mark F. A. Van Berkum ◽  
Anthony R. Means ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Binding Domain ◽  
Calmodulin Binding ◽  
Domain Peptide

scholarly journals Correcting a SHAPE-directed RNA structure by a mutate-map-rescue approach

2014 ◽  
Author(s):  
Siqi Tian ◽  
Pablo Cordero ◽  
Wipapat Kladwang ◽  
Rhiju Das
Keyword(s):  
Secondary Structure ◽  
Conformational Change ◽  
High Throughput ◽  
Rna Structure ◽  
Three Dimensional ◽  
Dynamic Structure ◽  
Chemical Mapping ◽  
Computational Support ◽  
Shape Inference ◽  
Shape Selective

ABSTRACTThe three-dimensional conformations of non-coding RNAs underpin their biochemical functions but have largely eluded experimental characterization. Here, we report that integrating a classic mutation/rescue strategy with high-throughput chemical mapping enables rapid RNA structure inference with unusually strong validation. We revisit a paradigmatic 16S rRNA domain for which SHAPE (selective 2′-hydroxyl acylation with primer extension) suggested a conformational change between apo-and holo-ribosome conformations. Computational support estimates, data from alternative chemical probes, and mutate-and-map (M2) experiments expose limitations of prior methodology and instead give a near-crystallographic secondary structure. Systematic interrogation of single base pairs via a high-throughput mutation/rescue approach then permits incisive validation and refinement of the M2-based secondary structure and further uncovers the functional conformation as an excited state (25±5% population) accessible via a single-nucleotide register shift. These results correct an erroneous SHAPE inference of a ribosomal conformational change and suggest a general mutate-map-rescue approach for dissecting RNA dynamic structure landscapes.

scholarly journals MODELING CLASSIC ATTENUATION REGULATION OF GENE EXPRESSION IN BACTERIA

2007 ◽  
Vol 05 (01) ◽  
pp. 155-180 ◽  
Author(s):  
VASSILY A. LYUBETSKY ◽  
SERGEY A. PIROGOV ◽  
LEV I. RUBANOV ◽  
ALEXANDER V. SELIVERSTOV
Keyword(s):  
Gene Expression ◽  
Secondary Structure ◽  
Rna Polymerase ◽  
Rna Secondary Structure ◽  
Transcription Termination ◽  
Regulation Of Gene Expression ◽  
Regulatory Region ◽  
Model Parameters ◽  
Batch Mode ◽  
Adequate Model

A model is proposed primarily for the classical RNA attenuation regulation of gene expression through premature transcription termination. The model is based on the concept of the RNA secondary structure macrostate within the regulatory region between the ribosome and RNA-polymerase, on hypothetical equation describing deceleration of RNA-polymerase by a macrostate and on views of transcription and translation initiation and elongation, under different values of the four basic model parameters which were varied. A special effort was made to select adequate model parameters. We first discuss kinetics of RNA folding and define the concept of the macrostate as a specific parentheses structure used to construct a conventional set of hairpins. The originally developed software that realizes the proposed model offers functionality to fully model RNA secondary folding kinetics. Its performance is compared to that of a public server described in Ref. 1. We then describe the delay in RNA-polymerase shifting to the next base or its premature termination caused by an RNA secondary structure or, herefrom, a macrostate. In this description, essential concepts are the basic and excited states of the polymerase first introduced in Ref. 2: the polymerase shifting to the next base can occur only in the basic state, and its detachment from DNA strand — only in excited state. As to the authors' knowledge, such a model incorporating the above-mentioned attenuation characteristics is not published elsewhere. The model was implemented in an application with command line interface for running in batch mode in Windows and Linux environments, as well as a public web server.3The model was tested with a conventional Monte Carlo procedure. In these simulations, the estimate of correlation between the premature transcription termination probability p and concentration c of charged amino acyl-tRNA was obtained as function p(c) for many regulatory regions in many bacterial genomes, as well as for local mutations in these regions.

Prion Protein α-to-β Transition Monitored by Time-Resolved Fourier Transform Infrared Spectroscopy

2007 ◽  
Vol 61 (10) ◽  
pp. 1025-1031 ◽  
Author(s):  
Julian Ollesch ◽  
Eva Künnemann ◽  
Rudi Glockshuber ◽  
Klaus Gerwert
Keyword(s):  
Fourier Transform ◽  
Secondary Structure ◽  
Conformational Change ◽  
Prion Protein ◽  
Fourier Transform Infrared ◽  
Dimensional Structure ◽  
Transmissible Spongiform Encephalopathies ◽  
The Novel ◽  
Time Resolved ◽  
Β Sheet

The conformational change of the recombinant, murine prion protein (PrP) from an α-helical to a β-sheet enriched state was monitored by time-resolved Fourier transform infrared (FT-IR) spectroscopy. The α-to-β transition is induced by reduction of the single disulfide bond in PrP. This transition is believed to generate the scrapie form PrPSc, the supposed infectious agent of transmissible spongiform encephalopathies. We followed the kinetics of this conformational change using a novel method for amide I band analysis of the infrared (IR) spectra. The amide I analysis provides the secondary structure. The amide I decomposition was calibrated with the three dimensional structure of cellular PrP solved by nuclear magnetic resonance (NMR). The novel secondary structure analysis provides a root mean squared deviation (RMSD) of only 3% as compared to the NMR structure. Reduction of α-helical PrP caused the transient accumulation of a partially unfolded intermediate, followed by formation of a state with higher β-sheet than α-helical structure contents. The novel approach allows us to now determine the secondary structure of the β-sheet conformation. This was not determined by either NMR or X-ray. The experiments were performed in a double-sealed security cuvette developed for IR analysis of potentially infectious PrP samples outside the biosafety laboratory.

Metal ions induced secondary structure rearrangements: mechanically interlocked lassovs.unthreaded branched-cyclic topoisomers

The Analyst ◽  
2018 ◽  
Vol 143 (10) ◽  
pp. 2323-2333 ◽  
Author(s):  
Kevin Jeanne Dit Fouque ◽  
Javier Moreno ◽  
Julian D. Hegemann ◽  
Séverine Zirah ◽  
Sylvie Rebuffat ◽  
...  
Keyword(s):  
Protein Folding ◽  
Secondary Structure ◽  
Metal Ions ◽  
Conformational Change ◽  
Structural Stability ◽  
Significant Role

Metal ions can play a significant role in a variety of important functions in protein systems including cofactor for catalysis, protein folding, assembly, structural stability and conformational change.

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