+ Site Statistics
References:
54,258,434
Abstracts:
29,560,870
PMIDs:
28,072,757
+ Search Articles
+ Subscribe to Site Feeds
Most Shared
PDF Full Text
+ PDF Full Text
Request PDF Full Text
+ Follow Us
Follow on Facebook
Follow on Twitter
Follow on LinkedIn
+ Translate
+ Recently Requested

Simulating activity of the bacterial ribosome



Simulating activity of the bacterial ribosome



Quarterly Reviews of Biophysics 42(4): 301-316



Computational modeling studies that investigate activity of the bacterial ribosome were reviewed. Computational approaches became possible with the availability of three-dimensional atomic resolution structures of the ribosomal subunits. However, due to the enormous size of the system, theoretical efforts to study the ribosome are few and challenging. For example, to extend the simulation timescales to biologically relevant ones, often, reduced models that require tedious parameterizations need to be applied. To that end, modeling of the ribosome focused on its internal dynamics, electrostatic properties, inhibition by antibiotics, polypeptide folding in the ribosome tunnel and assembly mechanisms driving the formation of the small ribosomal subunit.

(PDF emailed within 0-6 h: $19.90)

Accession: 055783425

Download citation: RISBibTeXText

PMID: 20450532

DOI: 10.1017/S0033583510000028


Related references

Dealing with stable structures at ribosome binding sites: bacterial translation and ribosome standby. Rna Biology 4(3): 113-117, 2007

The conserved GTPase HflX is a ribosome splitting factor that binds to the E-site of the bacterial ribosome. Nucleic Acids Research 44(4): 1952-1961, 2016

The bacterial ribosome responds like the eukaryote ribosome to the frameshift stimulatory signal of the human immunodeficiency virus type-1. Molecular & Cellular Proteomics 2(9): 884, September, 2003

Increased bacterial hemolytic activity is conferred by expression of TlyA methyltransferase but not by its 2'-O-methylation of the ribosome. Current Microbiology 67(1): 61-68, 2013

Bacterial expression and enzymatic activity analysis of ME1, a ribosome-inactivating protein from Mirabilis expansa. Protein Expression and Purification 40(1): 142-151, 2005

Bacterial activity in the rhizosphere analyzed at the single-cell level by monitoring ribosome contents and synthesis rates. Applied and Environmental Microbiology 66(2): 801-809, 2000

A high-throughput screen of the GTPase activity of Escherichia coli EngA to find an inhibitor of bacterial ribosome biogenesis. Journal of Biomolecular Screening 18(7): 830-836, 2014

Selective SecA association with signal sequences in ribosome-bound nascent chains: a potential role for SecA in ribosome targeting to the bacterial membrane. Journal of Biological Chemistry 280(45): 37930-37940, 2005

Simulating movement of tRNA into the ribosome during decoding. Proceedings of the National Academy of Sciences of the United States of America 102(44): 15854-9, 2005

68 Simulating mRNA-tRNA translocation through the ribosome. Journal of Biomolecular Structure & Dynamics 33 Suppl 1: 44-45, 2015

Ribosome recycling factor (ribosome releasing factor) is essential for bacterial growth. Proceedings of the National Academy of Sciences of the United States of America 91(10): 4249-4253, 1994

Ribosome-inactivating proteins from plants inhibit ribosome activity of Trypanosoma and Leishmania. Journal of Protozoology, 353: 384-387, 1988

YoeB-ribosome structure: a canonical RNase that requires the ribosome for its specific activity. Nucleic Acids Research 41(20): 9549-9556, 2014