Single-molecule imaging of non-equilibrium molecular ensembles on the millisecond timescale

Single-molecule fluorescence microscopy is uniquely suited for detecting transient molecular recognition events, yet achieving the time resolution and statistics needed to realize this potential has proven challenging. Here we present a single-molecule imaging and analysis platform using scientific complementary metal-oxide semiconductor (sCMOS) detectors that enables imaging of 15,000 individual molecules simultaneously at millisecond rates. This system enabled the detection of previously obscured processes relevant to the fidelity mechanism in protein synthesis.

[1]  M. Rodnina,et al.  Fidelity of aminoacyl-tRNA selection on the ribosome: kinetic and structural mechanisms. , 2001, Annual review of biochemistry.

[2]  Daniel S. Terry,et al.  Functional Dynamics within the Human Ribosome Regulate the Rate of Active Protein Synthesis. , 2015, Molecular cell.

[3]  Michael W. Davidson,et al.  Video-rate nanoscopy enabled by sCMOS camera-specific single-molecule localization algorithms , 2013, Nature Methods.

[4]  M. Rodnina,et al.  Kinetic mechanism of elongation factor Ts-catalyzed nucleotide exchange in elongation factor Tu. , 2002, Biochemistry.

[5]  W. B. Caldwell,et al.  Single-molecule fluorescence spectroscopy of enzyme conformational dynamics and cleavage mechanism. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[6]  Colin Echeverría Aitken,et al.  An oxygen scavenging system for improvement of dye stability in single-molecule fluorescence experiments. , 2008, Biophysical journal.

[7]  Daniel S. Terry,et al.  The bright future of single-molecule fluorescence imaging. , 2014, Current opinion in chemical biology.

[8]  Daniel S. Terry,et al.  Structural basis for potent inhibitory activity of the antibiotic tigecycline during protein synthesis , 2013, Proceedings of the National Academy of Sciences.

[9]  Clay M Armstrong,et al.  Life among the axons. , 2007, Annual review of physiology.

[10]  F. Young Biochemistry , 1955, The Indian Medical Gazette.

[11]  R. Rosenfeld Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.

[12]  Nils G Walter,et al.  Provided for Non-commercial Research and Educational Use Only. Not for Reproduction, Distribution or Commercial Use. Analysis of Complex Single-molecule Fret Time Trajectories Author's Personal Copy , 2022 .

[13]  Kevin J. McHale,et al.  Single-Molecule Fluorescence Experiments Determine Protein Folding Transition Path Times , 2012, Science.

[14]  L. Joshua-Tor,et al.  Dynamic look at DNA unwinding by a replicative helicase , 2014, Proceedings of the National Academy of Sciences.

[15]  K. Weninger,et al.  Optimizing methods to recover absolute FRET efficiency from immobilized single molecules. , 2010, Biophysical journal.

[16]  Magnus Johansson,et al.  Rate and accuracy of bacterial protein synthesis revisited. , 2008, Current opinion in microbiology.

[17]  P. Nissen,et al.  The sarcoplasmic Ca2+-ATPase: design of a perfect chemi-osmotic pump , 2010, Quarterly Reviews of Biophysics.

[18]  Michael B. Feldman,et al.  Conformational sampling of aminoacyl-tRNA during selection on the bacterial ribosome. , 2010, Journal of molecular biology.

[19]  Peter G Schultz,et al.  Systematic chromosomal deletion of bacterial ribosomal protein genes. , 2011, Journal of molecular biology.

[20]  Feng Qin Principles of single-channel kinetic analysis. , 2007, Methods in molecular biology.

[21]  Daniel S. Terry,et al.  Transport domain unlocking sets the uptake rate of an aspartate transporter , 2015, Nature.

[22]  L. Christophorou Science , 2018, Emerging Dynamics: Science, Energy, Society and Values.

[23]  Hak-Sung Kim,et al.  A single-molecule dissection of ligand binding to a protein with intrinsic dynamics. , 2013, Nature chemical biology.

[24]  Nathan O'Connor,et al.  Identification of two distinct hybrid state intermediates on the ribosome. , 2007, Molecular cell.

[25]  James B. Munro,et al.  Mitigating unwanted photophysical processes for improved single-molecule fluorescence imaging. , 2009, Biophysical journal.

[26]  Jonathan A Javitch,et al.  Cyanine fluorophore derivatives with enhanced photostability , 2011, Nature Methods.

[27]  Chris H Wiggins,et al.  Learning rates and states from biophysical time series: a Bayesian approach to model selection and single-molecule FRET data. , 2009, Biophysical journal.

[28]  S. McKinney,et al.  Analysis of single-molecule FRET trajectories using hidden Markov modeling. , 2006, Biophysical journal.

[29]  David Yadin,et al.  Defining the limits of single-molecule FRET resolution in TIRF microscopy. , 2010, Biophysical journal.

[30]  Benjamin Schuler,et al.  Microfluidic mixer designed for performing single-molecule kinetics with confocal detection on timescales from milliseconds to minutes , 2013, Nature Protocols.

[31]  Elio A. Abbondanzieri,et al.  Dynamic binding orientations direct activity of HIV reverse transcriptase , 2008, Nature.

[32]  A. McMahon,et al.  An eight residue fragment of an acyl carrier protein suffices for post-translational introduction of fluorescent pantetheinyl arms in protein modification in vitro and in vivo. , 2008, Journal of the American Chemical Society.

[33]  Dmitri S. Pavlichin,et al.  Single Molecule Analysis Research Tool (SMART): An Integrated Approach for Analyzing Single Molecule Data , 2012, PloS one.

[34]  J. Pawley,et al.  Handbook of Biological Confocal Microscopy , 1990, Springer US.

[35]  Jin Chen,et al.  High-throughput platform for real-time monitoring of biological processes by multicolor single-molecule fluorescence , 2013, Proceedings of the National Academy of Sciences.

[36]  Paul J. Besl,et al.  A Method for Registration of 3-D Shapes , 1992, IEEE Trans. Pattern Anal. Mach. Intell..

[37]  宁北芳,et al.  疟原虫var基因转换速率变化导致抗原变异[英]/Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A , 2005 .

[38]  Lasse L. Hildebrandt,et al.  iSMS: single-molecule FRET microscopy software , 2015, Nature Methods.

[39]  Rahul Roy,et al.  A practical guide to single-molecule FRET , 2008, Nature Methods.

[40]  J. Puglisi,et al.  tRNA selection and kinetic proofreading in translation , 2004, Nature Structural &Molecular Biology.

[41]  D. Kern,et al.  Dynamic personalities of proteins , 2007, Nature.

[42]  S. Blanchard,et al.  Chemically related 4,5-linked aminoglycoside antibiotics drive subunit rotation in opposite directions , 2015, Nature Communications.

[43]  E. Westhof,et al.  Nucleic Acids and Molecular Biology , 1988, Nucleic Acids and Molecular Biology.

[44]  Wei Zhang,et al.  GTPase activation of elongation factor EF‐Tu by the ribosome during decoding , 2009, The EMBO journal.

[45]  E. Greene,et al.  DNA Dynamics and Single-Molecule Biology , 2014, Chemical reviews.

[46]  D. Labuda,et al.  Mechanism of codon recognition by transfer RNA studied with oligonucleotides larger than triplets. , 1985, Nucleic acids research.

[47]  Michael B. Feldman,et al.  Allosteric control of the ribosome by small-molecule antibiotics , 2012, Nature Structural &Molecular Biology.