Literature DB >> 21685361

Biological mechanisms, one molecule at a time.

Ignacio Tinoco1, Ruben L Gonzalez.   

Abstract

The last 15 years have witnessed the development of tools that allow the observation and manipulation of single molecules. The rapidly expanding application of these technologies for investigating biological systems of ever-increasing complexity is revolutionizing our ability to probe the mechanisms of biological reactions. Here, we compare the mechanistic information available from single-molecule experiments with the information typically obtained from ensemble studies and show how these two experimental approaches interface with each other. We next present a basic overview of the toolkit for observing and manipulating biology one molecule at a time. We close by presenting a case study demonstrating the impact that single-molecule approaches have had on our understanding of one of life's most fundamental biochemical reactions: the translation of a messenger RNA into its encoded protein by the ribosome.

Mesh:

Year:  2011        PMID: 21685361      PMCID: PMC3127425          DOI: 10.1101/gad.2050011

Source DB:  PubMed          Journal:  Genes Dev        ISSN: 0890-9369            Impact factor:   11.361


  138 in total

1.  Single molecule emission characteristics in near-field microscopy.

Authors: 
Journal:  Phys Rev Lett       Date:  1995-12-25       Impact factor: 9.161

2.  Force-fluorescence spectroscopy at the single-molecule level.

Authors:  Ruobo Zhou; Michael Schlierf; Taekjip Ha
Journal:  Methods Enzymol       Date:  2010       Impact factor: 1.600

3.  Dwell-time distribution analysis of polyprotein unfolding using force-clamp spectroscopy.

Authors:  Jasna Brujic; Rodolfo I Z Hermans; Sergi Garcia-Manyes; Kirstin A Walther; Julio M Fernandez
Journal:  Biophys J       Date:  2007-01-26       Impact factor: 4.033

4.  Force unfolding kinetics of RNA using optical tweezers. I. Effects of experimental variables on measured results.

Authors:  Jin-Der Wen; Maria Manosas; Pan T X Li; Steven B Smith; Carlos Bustamante; Felix Ritort; Ignacio Tinoco
Journal:  Biophys J       Date:  2007-02-09       Impact factor: 4.033

5.  Thiostrepton inhibition of tRNA delivery to the ribosome.

Authors:  Ruben L Gonzalez; Steven Chu; Joseph D Puglisi
Journal:  RNA       Date:  2007-10-19       Impact factor: 4.942

6.  GTP hydrolysis by IF2 guides progression of the ribosome into elongation.

Authors:  R Andrew Marshall; Colin Echeverría Aitken; Joseph D Puglisi
Journal:  Mol Cell       Date:  2009-07-10       Impact factor: 17.970

7.  Backtracking determines the force sensitivity of RNAP II in a factor-dependent manner.

Authors:  Eric A Galburt; Stephan W Grill; Anna Wiedmann; Lucyna Lubkowska; Jason Choy; Eva Nogales; Mikhail Kashlev; Carlos Bustamante
Journal:  Nature       Date:  2007-03-14       Impact factor: 49.962

8.  The mechanism for activation of GTP hydrolysis on the ribosome.

Authors:  Rebecca M Voorhees; T Martin Schmeing; Ann C Kelley; V Ramakrishnan
Journal:  Science       Date:  2010-11-05       Impact factor: 47.728

9.  Cell-substrate contacts illuminated by total internal reflection fluorescence.

Authors:  D Axelrod
Journal:  J Cell Biol       Date:  1981-04       Impact factor: 10.539

Review 10.  Ribosome gymnastics--degree of difficulty 9.5, style 10.0.

Authors:  J F Atkins; R B Weiss; R F Gesteland
Journal:  Cell       Date:  1990-08-10       Impact factor: 41.582

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  41 in total

Review 1.  Modeling stochastic kinetics of molecular machines at multiple levels: from molecules to modules.

Authors:  Debashish Chowdhury
Journal:  Biophys J       Date:  2013-06-04       Impact factor: 4.033

Review 2.  smFRET studies of the 'encounter' complexes and subsequent intermediate states that regulate the selectivity of ligand binding.

Authors:  Colin D Kinz-Thompson; Ruben L Gonzalez
Journal:  FEBS Lett       Date:  2014-07-24       Impact factor: 4.124

Review 3.  Probing the mechanisms of translation with force.

Authors:  Christian M Kaiser; Ignacio Tinoco
Journal:  Chem Rev       Date:  2014-01-09       Impact factor: 60.622

4.  Riboswitch structure and dynamics by smFRET microscopy.

Authors:  Krishna C Suddala; Nils G Walter
Journal:  Methods Enzymol       Date:  2014       Impact factor: 1.600

5.  Bayesian-Estimated Hierarchical HMMs Enable Robust Analysis of Single-Molecule Kinetic Heterogeneity.

Authors:  Jason Hon; Ruben L Gonzalez
Journal:  Biophys J       Date:  2019-04-02       Impact factor: 4.033

6.  Nonfluorescent quenchers to correlate single-molecule conformational and compositional dynamics.

Authors:  Jin Chen; Albert Tsai; Alexey Petrov; Joseph D Puglisi
Journal:  J Am Chem Soc       Date:  2012-03-23       Impact factor: 15.419

Review 7.  Towards physiological complexity with in vitro single-molecule biophysics.

Authors:  Daniel Duzdevich; Eric C Greene
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2012-12-24       Impact factor: 6.237

Review 8.  Bacterial replication, transcription and translation: mechanistic insights from single-molecule biochemical studies.

Authors:  Andrew Robinson; Antoine M van Oijen
Journal:  Nat Rev Microbiol       Date:  2013-04-03       Impact factor: 60.633

9.  The ribosome uses cooperative conformational changes to maximize and regulate the efficiency of translation.

Authors:  Wei Ning; Jingyi Fei; Ruben L Gonzalez
Journal:  Proc Natl Acad Sci U S A       Date:  2014-08-01       Impact factor: 11.205

Review 10.  Biophysical highlights from 54 years of macromolecular crystallography.

Authors:  Jane S Richardson; David C Richardson
Journal:  Biophys J       Date:  2014-02-04       Impact factor: 4.033

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