From Beads on a String to the Pearls of Regulation: the Structure and Dynamics of Chromatin

2012 ◽  
Vol 40 (2) ◽  
pp. 331-334
Author(s):  
Richard P. Bowater ◽  
Ian C. Wood ◽  
Ben F. Luisi
Keyword(s):  
Structural Biology ◽  
Structural Organization ◽  
Regulation Of Gene Expression ◽  
Structure And Function ◽  
Research Field ◽  
Structure And Dynamics ◽  
Recent Conference ◽  
Eukaryotic Chromatin ◽  
Poster Presentations ◽  
And Function

The assembly of eukaryotic chromatin, and the bearing of its structural organization on the regulation of gene expression, were the central topics of a recent conference organized jointly by the Biochemical Society and Wellcome Trust. A range of talks and poster presentations covered topical aspects of this research field and illuminated recent advances in our understanding of the structure and function of chromatin. The two-day meeting had stimulating presentations complemented with lively discourse and interactions of participants. In the present paper, we summarize the topics presented at the meeting, in particular highlighting subjects that are reviewed in more detail within this issue of Biochemical Society Transactions. The reports bring to life the truly fascinating molecular and structural biology of chromatin.

scholarly journals Regulation of OmpA Translation and Shigella dysenteriae Virulence by an RNA Thermometer

2019 ◽  
Vol 88 (3) ◽  
Author(s):  
Erin R. Murphy ◽  
Johanna Roßmanith ◽  
Jacob Sieg ◽  
Megan E. Fris ◽  
Hebaallaha Hussein ◽  
...  
Keyword(s):  
In Silico ◽  
Bacterial Species ◽  
Regulation Of Gene Expression ◽  
Structure And Function ◽  
Shigella Dysenteriae ◽  
Content Type ◽  
Bacterial Physiology ◽  
Wide Range ◽  
Rna Thermometer ◽  
And Function

ABSTRACT RNA thermometers are cis-acting riboregulators that mediate the posttranscriptional regulation of gene expression in response to environmental temperature. Such regulation is conferred by temperature-responsive structural changes within the RNA thermometer that directly result in differential ribosomal binding to the regulated transcript. The significance of RNA thermometers in controlling bacterial physiology and pathogenesis is becoming increasingly clear. This study combines in silico, molecular genetics, and biochemical analyses to characterize both the structure and function of a newly identified RNA thermometer within the ompA transcript of Shigella dysenteriae. First identified by in silico structural predictions, genetic analyses have demonstrated that the ompA RNA thermometer is a functional riboregulator sufficient to confer posttranscriptional temperature-dependent regulation, with optimal expression observed at the host-associated temperature of 37°C. Structural studies and ribosomal binding analyses have revealed both increased exposure of the ribosomal binding site and increased ribosomal binding to the ompA transcript at permissive temperatures. The introduction of site-specific mutations predicted to alter the temperature responsiveness of the ompA RNA thermometer has predictable consequences for both the structure and function of the regulatory element. Finally, in vitro tissue culture-based analyses implicate the ompA RNA thermometer as a bona fide S. dysenteriae virulence factor in this bacterial pathogen. Given that ompA is highly conserved among Gram-negative pathogens, these studies not only provide insight into the significance of riboregulation in controlling Shigella virulence, but they also have the potential to facilitate further understanding of the physiology and/or pathogenesis of a wide range of bacterial species.

scholarly journals Structural Organization of Procaryotic and Eucaryotic Hsp90. INFLUENCE OF DIVALENT CATIONS ON STRUCTURE AND FUNCTION

1995 ◽  
Vol 270 (24) ◽  
pp. 14412-14419 ◽  
Author(s):  
Ursula Jakob ◽  
Ines Meyer ◽  
Hans Bügl ◽  
Stefanie André ◽  
James C. A. Bardwell ◽  
...  
Keyword(s):  
Structural Organization ◽  
Divalent Cations ◽  
Structure And Function ◽  
And Function

Native Mass Spectrometry: Recent Progress and Remaining Challenges

2022 ◽  
Vol 51 (1) ◽  
Author(s):  
Kelly R. Karch ◽  
Dalton T. Snyder ◽  
Sophie R. Harvey ◽  
Vicki H. Wysocki
Keyword(s):  
Mass Spectrometry ◽  
Gas Phase ◽  
Structural Biology ◽  
Recent Progress ◽  
Native Mass Spectrometry ◽  
Structure And Function ◽  
Annual Review ◽  
Publication Date ◽  
Analysis Software ◽  
And Function

Native mass spectrometry (nMS) has emerged as an important tool in studying the structure and function of macromolecules and their complexes in the gas phase. In this review, we cover recent advances in nMS and related techniques including sample preparation, instrumentation, activation methods, and data analysis software. These advances have enabled nMS-based techniques to address a variety of challenging questions in structural biology. The second half of this review highlights recent applications of these technologies and surveys the classes of complexes that can be studied with nMS. Complementarity of nMS to existing structural biology techniques and current challenges in nMS are also addressed. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals The ribosome and its role in protein folding: looking through a magnifying glass

2017 ◽  
Vol 73 (6) ◽  
pp. 509-521 ◽  
Author(s):  
Abid Javed ◽  
John Christodoulou ◽  
Lisa D. Cabrita ◽  
Elena V. Orlova
Keyword(s):  
Protein Folding ◽  
Structural Biology ◽  
Polypeptide Chain ◽  
Structure And Function ◽  
Cellular Activity ◽  
Cryo Electron Microscopy ◽  
Nascent Chain ◽  
Exit Tunnel ◽  
Dynamics Simulations ◽  
And Function

Protein folding, a process that underpins cellular activity, begins co-translationally on the ribosome. During translation, a newly synthesized polypeptide chain enters the ribosomal exit tunnel and actively interacts with the ribosome elements – the r-proteins and rRNA that line the tunnel – prior to emerging into the cellular milieu. While understanding of the structure and function of the ribosome has advanced significantly, little is known about the process of folding of the emerging nascent chain (NC). Advances in cryo-electron microscopy are enabling visualization of NCs within the exit tunnel, allowing early glimpses of the interplay between the NC and the ribosome. Once it has emerged from the exit tunnel into the cytosol, the NC (still attached to its parent ribosome) can acquire a range of conformations, which can be characterized by NMR spectroscopy. Using experimental restraints within molecular-dynamics simulations, the ensemble of NC structures can be described. In order to delineate the process of co-translational protein folding, a hybrid structural biology approach is foreseeable, potentially offering a complete atomic description of protein folding as it occurs on the ribosome.

scholarly journals Computer Simulations in Service of Biology

2021 ◽  
Vol 8 ◽  
Author(s):  
Michael Levitt
Keyword(s):  
Computer Simulation ◽  
Structural Biology ◽  
Computer Simulations ◽  
Virtual World ◽  
Computer Game ◽  
Structure And Function ◽  
Important Research ◽  
Scientific World ◽  
The World ◽  
And Function

Computer simulation is an important research tool in today’s scientific world. Computers allow us to perform computations that mimic the behavior of complex (biological) systems in ways that we could not otherwise achieve. You could think of these simulations as a computer game, in which a virtual world is created that works according to certain (e.g., physical) rules. While we play the game, we learn the rules governing this virtual world and its environment, and also the way that we affect this world as players. In this article, I will explain how we use computer simulations in the world of structural biology to study the structure and function of molecules. I will also describe how I think that we could use insights from the world of biology and computer simulations to advance the society that we live in.

Structure and function of nonorthodox chromatins: I. aggregation sensitivity of DNA is correlated to the Protein content of chromosomal material

1990 ◽  
Vol 48 (3) ◽  
pp. 120-121
Author(s):  
J. Pelzer ◽  
B. Bohrmann ◽  
R. Johansen ◽  
M. Maeder ◽  
R. Gyalog ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Protein Content ◽  
Organic Solvents ◽  
Soluble Proteins ◽  
Structure And Function ◽  
Living World ◽  
Eukaryotic Chromatin ◽  
And Function

Aggregation insensitive eukaryotic chromatin in which DNA is associated with histones can be crosslinked by all fixatives commonly used in electron microscopy. By crosslinking it becomes protected from aggregation during dehydration with organic solvents. This is not the case with most nonorthodox chromatins, where the ratio of protein to DNA is estimated to be 5 to 10 times lower and where the basic, acid-soluble proteins are rather different from the histones. The aggregation sensitivity of different chromatins is summarized in table 1.Nonorthodox aggregation sensitive chromatins were found in Eubacteria, bacteriophage- pools (fig. 1a,b), Cyanobacteria, mitochondria, and Dinoflagellates (fig. 2a,b). The latter organisms are of particular interest because of morphologic similarities to other flagellates like Euglena with its aggregation insensitive histone-containing chromosomes (fig. 3a,b). With respect to the distribution over the living world, nonorthodox chromatins might be more frequent than the histone-containing ones.

scholarly journals Rem2 signaling affects neuronal structure and function in part by regulation of gene expression

2017 ◽  
Vol 85 ◽  
pp. 190-201 ◽  
Author(s):  
Katelyn Kenny ◽  
Leandro Royer ◽  
Anna R. Moore ◽  
Xiao Chen ◽  
Michael T. Marr ◽  
...  
Keyword(s):  
Gene Expression ◽  
Regulation Of Gene Expression ◽  
Structure And Function ◽  
Neuronal Structure ◽  
And Function

scholarly journals MetaLab 2.0 enables accurate post-translational modifications profiling in metaproteomics

2019 ◽  
Author(s):  
Kai Cheng ◽  
Zhibin Ning ◽  
Xu Zhang ◽  
Leyuan Li ◽  
Bo Liao ◽  
...  
Keyword(s):  
Data Analysis ◽  
Microbial Communities ◽  
Search Strategy ◽  
Structure And Function ◽  
Research Field ◽  
Human Gut ◽  
Post Translational Modifications ◽  
Protein Functions ◽  
And Function

AbstractStudying the structure and function of microbiomes is an emerging research field. Metaproteomic approaches focusing on the characterization of expressed proteins and post-translational modifications (PTMs) provide a deeper understanding of microbial communities. Previous research has highlighted the value of examining microbiome-wide protein expression in studying the roles of the microbiome in human diseases. Nevertheless, the regulation of protein functions in complex microbiomes remains under-explored. This is mainly due to the lack of efficient bioinformatics tools to identify and quantify PTMs in the microbiome. We have developed a comprehensive software termed MetaLab for the data analysis of metaproteomic datasets. Here we build an open search workflow within MetaLab for unbiased identification and quantification of PTMs from microbiome samples. This bioinformatics platform provides information about proteins, PTMs, taxa, functions, and pathways of microbial communities. The performance of the workflow was evaluated using conventional proteomics, metaproteomics from mouse and human gut microbiomes, and modification-specific enriched datasets. Superior accuracy and sensitivity were obtained simultaneously by using our method comparing with the traditional closed search strategy.

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