In vitro assembly of 30S and 70S bacterial ribosomes from 16S RNA containing single base substitutions, insertions, and deletions around the decoding site (C1400)

Biochemistry ◽  
1989 ◽  
Vol 28 (3) ◽  
pp. 1002-1011 ◽  
Author(s):  
Robert Denman ◽  
Carl Weitzmann ◽  
Philip R. Cunningham ◽  
Didier Negre ◽  
Kelvin Nurse ◽  
...  
Keyword(s):  
Single Base ◽  
Insertions And Deletions ◽  
Base Substitutions ◽  
16S Rna ◽  
In Vitro Assembly

scholarly journals SigProfilerMatrixGenerator: a tool for visualizing and exploring patterns of small mutational events

2019 ◽  
Author(s):  
Erik N. Bergstrom ◽  
Mi Ni Huang ◽  
Uma Mahto ◽  
Mark Barnes ◽  
Michael R. Stratton ◽  
...  
Keyword(s):  
Cancer Genome ◽  
Single Base ◽  
Insertions And Deletions ◽  
Link Type ◽  
Base Substitutions ◽  
Mutational Pattern ◽  
Comprehensive Classification ◽  
Single Matrix ◽  
Mutational Processes

ABSTRACTBackgroundCancer genomes are peppered with somatic mutations imprinted by different mutational processes. The mutational pattern of a cancer genome can be used to identify and understand the etiology of the underlying mutational processes. A plethora of prior research has focused on examining mutational signatures and mutational patterns from single base substitutions and their immediate sequencing context. We recently demonstrated that further classification of small mutational events (including substitutions, insertions, deletions, and doublet substitutions) can be used to provide a deeper understanding of the mutational processes that have molded a cancer genome. However, there has been no standard tool that allows fast, accurate, and comprehensive classification for all types of small mutational eventsResultsHere, we present SigProfilerMatrixGenerator, a computational tool designed for optimized exploration and visualization of mutational patterns for all types of small mutational events. SigProfilerMatrixGenerator is written in Python with an R wrapper package provided for users that prefer working in an R environment. SigProfilerMatrixGenerator produces fourteen distinct matrices by considering transcriptional strand bias of individual events and by incorporating distinct classifications for single base substitutions, doublet base substitutions, and small insertions and deletions. While the tool provides a comprehensive classification of mutations, SigProfilerMatrixGenerator is also faster and more memory efficient than existing tools that generate only a single matrix.ConclusionsSigProfilerMatrixGenerator provides a standardized method for classifying small mutational events that is both efficient and scalable to large datasets. In addition to extending the classification of single base substitutions, the tool is the first to provide support for classifying doublet base substitutions and small insertions and deletions. SigProfilerMatrixGenerator is freely available athttps://github.com/AlexandrovLab/SigProfilerMatrixGeneratorwith an extensive documentation athttps://osf.io/s93d5/wiki/home/.

In vitro assembly of 30S ribosomal particles from precursor 16S RNA of Escherichia coli

Nature ◽  
1974 ◽  
Vol 247 (5442) ◽  
pp. 552-554 ◽  
Author(s):  
JOHN W. WIREMAN ◽  
PAUL S. SYPHERD
Keyword(s):  
Escherichia Coli ◽  
16S Rna ◽  
In Vitro Assembly

In vitro assembly of 2-D crystals from partially purified EA1 protein secreted by Bacillus anthracis strain Delta Sterne-1

1994 ◽  
Vol 52 ◽  
pp. 276-277
Author(s):  
Mary Beth Downs ◽  
Wilson Ribot ◽  
Joseph W. Farchaus
Keyword(s):  
Cell Wall ◽  
Molecular Sieves ◽  
Cell Envelope ◽  
Single Species ◽  
Supporting Cell ◽  
Surface Layers ◽  
Rabbit Igg ◽  
In Vitro Assembly ◽  
Covalently Linked

Many bacteria possess surface layers (S-layers) that consist of a two-dimensional protein lattice external to the cell envelope. These S-layer arrays are usually composed of a single species of protein or glycoprotein and are not covalently linked to the underlying cell wall. When removed from the cell, S-layer proteins often reassemble into a lattice identical to that found on the cell, even without supporting cell wall fragments. S-layers exist at the interface between the cell and its environment and probably serve as molecular sieves that exclude destructive macromolecules while allowing passage of small nutrients and secreted proteins. Some S-layers are refractory to ingestion by macrophages and, generally, bacteria are more virulent when S-layers are present.When grown in rich medium under aerobic conditions, B. anthracis strain Delta Sterne-1 secretes large amounts of a proteinaceous extractable antigen 1 (EA1) into the growth medium. Immunocytochemistry with rabbit polyclonal anti-EAl antibody made against the secreted protein and gold-conjugated goat anti-rabbit IgG showed that EAI was localized at the cell surface (fig 1), which suggests its role as an S-layer protein.

scholarly journals In Vitro Assembly of l-Asparaginase Subunits

1974 ◽  
Vol 249 (13) ◽  
pp. 4175-4180 ◽  
Author(s):  
Sidney Shifrin ◽  
Catherine L. Parrott
Keyword(s):  
In Vitro Assembly

scholarly journals A Conformational Transition Observed in Single HIV-1 Gag Molecules during In Vitro Assembly of Virus-Like Particles

2014 ◽  
Vol 88 (6) ◽  
pp. 3577-3585 ◽  
Author(s):  
J. B. Munro ◽  
A. Nath ◽  
M. Farber ◽  
S. A. K. Datta ◽  
A. Rein ◽  
...  
Keyword(s):  
Conformational Transition ◽  
Virus Like Particles ◽  
In Vitro Assembly ◽  
Hiv 1

Application of the Peristaltic in Vitro Assembly to Gastric Acid Neutralization by Liquid Antacids: a Preliminary Report

1981 ◽  
Vol 7 (5) ◽  
pp. 621-632 ◽  
Author(s):  
D. L. Simmons ◽  
N. K. Patel ◽  
M. Chénier ◽  
A. A. Legore ◽  
F. Cesari ◽  
...  
Keyword(s):  
Gastric Acid ◽  
Preliminary Report ◽  
Acid Neutralization ◽  
In Vitro Assembly

scholarly journals In Vitro Assembly of the T=13 Procapsid of Bacteriophage T5 with Its Scaffolding Domain

2010 ◽  
Vol 84 (18) ◽  
pp. 9350-9358 ◽  
Author(s):  
Alexis Huet ◽  
James F. Conway ◽  
Lucienne Letellier ◽  
Pascale Boulanger
Keyword(s):  
Self Assembly ◽  
Scaffolding Protein ◽  
Accessory Proteins ◽  
Conformational Diversity ◽  
In Vitro Assembly ◽  
20 Nm ◽  
Head Protein ◽  
Bacteriophage T5 ◽  
Icosahedral Capsid

ABSTRACT The Siphoviridae coliphage T5 differs from other members of this family by the size of its genome (121 kbp) and by its large icosahedral capsid (90 nm), which is organized with T=13 geometry. T5 does not encode a separate scaffolding protein, but its head protein, pb8, contains a 159-residue aminoterminal scaffolding domain (Δ domain) that is the mature capsid. We have deciphered the early events of T5 shell assembly starting from purified pb8 with its Δ domain (pb8p). The self assembly of pb8p is regulated by salt conditions and leads to structures with distinct morphologies. Expanded tubes are formed in the presence of NaCl, whereas Ca2+ promotes the association of pb8p into contracted tubes and procapsids. Procapsids display an angular organization and 20-nm-long internal radial structures identified as the Δ domain. The T5 head maturation protease pb11 specifically cleaves the Δ domain of contracted and expanded tubes. Ca2+ is not required for proteolytic activity but for the organization of the Δ domain. Taken together, these data indicate that pb8p carries all of the information in its primary sequence to assemble in vitro without the requirement of the portal and accessory proteins. Furthermore, Ca2+ plays a key role in introducing the conformational diversity that permits the formation of a stable procapsid. Phage T5 is the first example of a viral capsid consisting of quasi-equivalent hexamers and pentamers whose assembly can be carried out in vitro, starting from the major head protein with its scaffolding domain, and whose endpoint is an icosahedral T=13 particle.

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