Michael T Woodside

Summary

Affiliation: National Research Council
Country: Canada

Publications

  1. pmc Determining intrachain diffusion coefficients for biopolymer dynamics from single-molecule force spectroscopy measurements
    Michael T Woodside
    Department of Physics, University of Alberta, Edmonton AB, T6G 2E1 Canada National Institute for Nanotechnology, National Research Council, Edmonton AB, T6G 2M9 Canada Electronic address
    Biophys J 107:1647-53. 2014
  2. pmc Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins
    Michael T Woodside
    National Institute for Nanotechnology, National Research Council of Canada, Edmonton, AB, Canada T6G 2V4
    Proc Natl Acad Sci U S A 103:6190-5. 2006
  3. pmc Energy landscape analysis of native folding of the prion protein yields the diffusion constant, transition path time, and rates
    Hao Yu
    Department of Physics, University of Alberta, Edmonton, AB, Canada T6G 2E1
    Proc Natl Acad Sci U S A 109:14452-7. 2012
  4. ncbi request reprint Transition path times for nucleic Acid folding determined from energy-landscape analysis of single-molecule trajectories
    Krishna Neupane
    Department of Physics, University of Alberta, Edmonton, Alberta, Canada
    Phys Rev Lett 109:068102. 2012
  5. ncbi request reprint Single-molecule force spectroscopy of rapidly fluctuating, marginally stable structures in the intrinsically disordered protein α-synuclein
    Allison Solanki
    Department of Physics, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
    Phys Rev Lett 112:158103. 2014
  6. doi request reprint Direct observation of transition paths during the folding of proteins and nucleic acids
    Krishna Neupane
    Department of Physics, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada
    Science 352:239-42. 2016
  7. pmc Protein misfolding occurs by slow diffusion across multiple barriers in a rough energy landscape
    Hao Yu
    Department of Physics, University of Alberta, Edmonton, AB, T6G 2E1, Canada
    Proc Natl Acad Sci U S A 112:8308-13. 2015
  8. pmc Single-molecule approaches to prion protein misfolding
    Hao Yu
    Department of Physics, University of Alberta, Edmonton, AB Canada
    Prion 7:140-6. 2013
  9. pmc Direct measurement of the full, sequence-dependent folding landscape of a nucleic acid
    Michael T Woodside
    National Institute for Nanotechnology, National Research Council of Canada, Edmonton AB, Canada, T6G 2M9
    Science 314:1001-4. 2006
  10. pmc Direct observation of multiple misfolding pathways in a single prion protein molecule
    Hao Yu
    Department of Physics, University of Alberta, Edmonton AB, T6G 2G7 Canada
    Proc Natl Acad Sci U S A 109:5283-8. 2012

Collaborators

  • Feng Wang
  • Daniel Herschlag
  • Valerie L Sim
  • Krishna Neupane
  • Hao Yu
  • Dustin B Ritchie
  • Derek R Dee
  • Daniel A N Foster
  • Amar Nath Gupta
  • Iveta Sosova
  • William J Greenleaf
  • Allison Solanki
  • Angela M Brigley
  • Armin Hoffmann
  • Ajay P Manuel
  • Xia Liu
  • Steven M Block
  • John Lambert
  • Megan C Engel
  • Leonardo M Cortez
  • Negar Rezajooei
  • Miro Belov
  • Kevin S D Beach
  • Jingchyuan Soong
  • William K A Sikkema
  • Abhilash Vincent
  • Elena Grandi
  • Laura Rivera
  • Max Anikovskiy
  • Nils O Petersen
  • Kirsten L Frieda
  • Elio A Abbondanzieri

Detail Information

Publications30

  1. pmc Determining intrachain diffusion coefficients for biopolymer dynamics from single-molecule force spectroscopy measurements
    Michael T Woodside
    Department of Physics, University of Alberta, Edmonton AB, T6G 2E1 Canada National Institute for Nanotechnology, National Research Council, Edmonton AB, T6G 2M9 Canada Electronic address
    Biophys J 107:1647-53. 2014
    ..Deconvolution of the finite compliance effects on the measurement allowed the intrinsic value to be recovered. These results were supported by Brownian dynamics simulations of the effects of force-probe compliance and bead size. ..
  2. pmc Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins
    Michael T Woodside
    National Institute for Nanotechnology, National Research Council of Canada, Edmonton, AB, Canada T6G 2V4
    Proc Natl Acad Sci U S A 103:6190-5. 2006
    ..We find quantitative agreement over the entire range of measurements with a hybrid landscape model that combines thermodynamic nearest-neighbor free energies and nanomechanical DNA stretching energies...
  3. pmc Energy landscape analysis of native folding of the prion protein yields the diffusion constant, transition path time, and rates
    Hao Yu
    Department of Physics, University of Alberta, Edmonton, AB, Canada T6G 2E1
    Proc Natl Acad Sci U S A 109:14452-7. 2012
    ..These results demonstrate how advances in single-molecule theory and experiment are harnessing the power of landscape formalisms to describe quantitatively the mechanics of folding...
  4. ncbi request reprint Transition path times for nucleic Acid folding determined from energy-landscape analysis of single-molecule trajectories
    Krishna Neupane
    Department of Physics, University of Alberta, Edmonton, Alberta, Canada
    Phys Rev Lett 109:068102. 2012
    ..These results show how energy-landscape analysis can be harnessed to characterize brief but critical events during folding reactions...
  5. ncbi request reprint Single-molecule force spectroscopy of rapidly fluctuating, marginally stable structures in the intrinsically disordered protein α-synuclein
    Allison Solanki
    Department of Physics, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
    Phys Rev Lett 112:158103. 2014
    ..The barriers were small, only a few kBT, but the diffusion was slow, revealing a landscape that is flat but rough. ..
  6. doi request reprint Direct observation of transition paths during the folding of proteins and nucleic acids
    Krishna Neupane
    Department of Physics, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada
    Science 352:239-42. 2016
    ..These measurements provide a first look at the critical microscopic events that occur during folding, opening exciting new avenues for investigating folding phenomena. ..
  7. pmc Protein misfolding occurs by slow diffusion across multiple barriers in a rough energy landscape
    Hao Yu
    Department of Physics, University of Alberta, Edmonton, AB, T6G 2E1, Canada
    Proc Natl Acad Sci U S A 112:8308-13. 2015
    ..These results open a new window onto the microscopic mechanisms governing protein misfolding. ..
  8. pmc Single-molecule approaches to prion protein misfolding
    Hao Yu
    Department of Physics, University of Alberta, Edmonton, AB Canada
    Prion 7:140-6. 2013
    ..Although single-molecule approaches to misfolding are relatively young, they have a promising future in prion science...
  9. pmc Direct measurement of the full, sequence-dependent folding landscape of a nucleic acid
    Michael T Woodside
    National Institute for Nanotechnology, National Research Council of Canada, Edmonton AB, Canada, T6G 2M9
    Science 314:1001-4. 2006
    ....
  10. pmc Direct observation of multiple misfolding pathways in a single prion protein molecule
    Hao Yu
    Department of Physics, University of Alberta, Edmonton AB, T6G 2G7 Canada
    Proc Natl Acad Sci U S A 109:5283-8. 2012
    ..These measurements of individual misfolding trajectories demonstrate the power of single-molecule approaches for characterizing misfolding directly by mapping out nonnative folding pathways...
  11. pmc Programmed -1 frameshifting efficiency correlates with RNA pseudoknot conformational plasticity, not resistance to mechanical unfolding
    Dustin B Ritchie
    Department of Physics, University of Alberta, Edmonton, AB, Canada T6G 2E1
    Proc Natl Acad Sci U S A 109:16167-72. 2012
    ....
  12. doi request reprint Transition-Path Probability as a Test of Reaction-Coordinate Quality Reveals DNA Hairpin Folding Is a One-Dimensional Diffusive Process
    Krishna Neupane
    Department of Physics, University of Alberta, 4 181 CCIS, Edmonton, Alberta T6G 2E1, Canada
    J Phys Chem Lett 6:1005-10. 2015
    ..This work establishes transition-path analysis as a powerful new tool for testing experimental reaction-coordinate quality. ..
  13. pmc Folding and unfolding single RNA molecules under tension
    Michael T Woodside
    National Institute for Nanotechnology, National Research Council of Canada, Edmonton AB T6G 2M9, Canada
    Curr Opin Chem Biol 12:640-6. 2008
    ....
  14. pmc Single-molecule force spectroscopy of the add adenine riboswitch relates folding to regulatory mechanism
    Krishna Neupane
    Department of Physics, University of Alberta, Edmonton, Alberta, Canada
    Nucleic Acids Res 39:7677-87. 2011
    ..Comparison of the folding of these riboswitches revealed many similarities arising from shared structural features but also essential differences related to their different regulatory mechanisms...
  15. ncbi request reprint Reconstructing folding energy landscape profiles from nonequilibrium pulling curves with an inverse Weierstrass integral transform
    Megan C Engel
    Department of Physics, University of Alberta, Edmonton, Alberta, T6G 2E1 Canada
    Phys Rev Lett 113:238104. 2014
    ..The IWT method is thus best for analyzing data from stiff force probes such as atomic force microscopes. ..
  16. doi request reprint Single-molecule assays for investigating protein misfolding and aggregation
    Armin Hoffmann
    Department of Physics, University of Alberta, Edmonton, AB, Canada
    Phys Chem Chem Phys 15:7934-48. 2013
    ..We describe some of the technical challenges involved in studying aggregation at the single-molecule level and discuss what has been learned about aggregation mechanisms from the different approaches...
  17. doi request reprint Phthalocyanine tetrasulfonates bind to multiple sites on natively-folded prion protein
    Derek R Dee
    Department of Physics, University of Alberta, Edmonton AB, Canada
    Biochim Biophys Acta 1824:826-32. 2012
    ..The binding isotherms indicated the presence of at least two different binding sites with micromolar affinities and a total stoichiometry of ~4-5 PcTS molecules per PrP molecule...
  18. pmc Diverse metastable structures formed by small oligomers of α-synuclein probed by force spectroscopy
    Krishna Neupane
    Department of Physics, University of Alberta, Edmonton, Alberta, Canada
    PLoS ONE 9:e86495. 2014
    ..These results provide a new window onto the complex α-synuclein aggregation landscape, characterizing the microscopic structural heterogeneity and kinetics of different pathways. ..
  19. pmc Pharmacological chaperone reshapes the energy landscape for folding and aggregation of the prion protein
    Amar Nath Gupta
    Department of Physics, University of Alberta, Edmonton, Alberta, Canada T6G 2E1
    Nat Commun 7:12058. 2016
    ..The ligand thus promotes native folding by stabilizing the native state while also suppressing interactions driving aggregation. ..
  20. pmc Direct measurement of sequence-dependent transition path times and conformational diffusion in DNA duplex formation
    Krishna Neupane
    Department of Physics, University of Alberta, Edmonton, AB T6G 2E1, Canada
    Proc Natl Acad Sci U S A . 2017
    ....
  21. pmc Quantifying Instrumental Artifacts in Folding Kinetics Measured by Single-Molecule Force Spectroscopy
    Krishna Neupane
    Department of Physics, University of Alberta, Edmonton, Alberta, Canada
    Biophys J 111:283-6. 2016
    ..These results indicate that typical optical trap measurements of kinetics reflect the dynamics of the molecule fairly well, and suggest practical limitations on experimental design to ensure reliable kinetic measurements. ..
  22. pmc Comparing the energy landscapes for native folding and aggregation of PrP
    Derek R Dee
    a Department of Physics, University of Alberta, Edmonton, AB, Canada
    Prion 10:207-20. 2016
    ..Here we describe the importance of characterizing free-energy landscapes for aggregation and the challenges involved in doing so, and we discuss how single-molecule studies can help test proposed structural models for PrP aggregates. ..
  23. doi request reprint Probing the structural dynamics of proteins and nucleic acids with optical tweezers
    Dustin B Ritchie
    Department of Physics, University of Alberta, Edmonton, AB T6G2E1 Canada
    Curr Opin Struct Biol 34:43-51. 2015
    ..We also review the development of assays probing the dynamics of complex protein-nucleic acid and protein-protein assemblies that reveal the dynamic interactions between biomolecular machines and their substrates. ..
  24. pmc Reconstructing folding energy landscapes from splitting probability analysis of single-molecule trajectories
    Ajay P Manuel
    Department of Physics, University of Alberta, Edmonton, AB, Canada T6G 2E1
    Proc Natl Acad Sci U S A 112:7183-8. 2015
    ..This work confirms that the molecular extension is a good reaction coordinate for these measurements, and validates a powerful yet simple method for reconstructing landscapes from single-molecule trajectories...
  25. pmc Reconstructing folding energy landscapes by single-molecule force spectroscopy
    Michael T Woodside
    Department of Physics, University of Alberta, Edmonton, Alberta T6G2E1, Canada Email
    Annu Rev Biophys 43:19-39. 2014
    ..We also discuss issues that complicate measurement and interpretation, including the possibility of multiple states or pathways and the effects of projecting multiple dimensions onto a single coordinate. ..
  26. doi request reprint Signal-pair correlation analysis of single-molecule trajectories
    Armin Hoffmann
    Department of Physics, University of Alberta, and National Institute of Nanotechnology, NRC, Edmonton AB T6G 2M9, Canada
    Angew Chem Int Ed Engl 50:12643-6. 2011
    ....
  27. doi request reprint Anti-frameshifting ligand reduces the conformational plasticity of the SARS virus pseudoknot
    Dustin B Ritchie
    Department of Physics, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
    J Am Chem Soc 136:2196-9. 2014
    ..This result extends the connection between -1 PRF and conformational dynamics and, moreover, suggests that targeting the conformational dynamics of pseudoknots may be an effective strategy for anti-viral drug design. ..
  28. pmc Direct observation of hierarchical folding in single riboswitch aptamers
    William J Greenleaf
    Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
    Science 319:630-3. 2008
    ..These results provide an integrated view of hierarchical folding in an aptamer, demonstrating how complex folding can be resolved into constituent parts, and supply further insights into tertiary structure formation...
  29. pmc High-resolution, single-molecule measurements of biomolecular motion
    William J Greenleaf
    Department of Applied Physics, Stanford University, Stanford, California 94305 5030, USA
    Annu Rev Biophys Biomol Struct 36:171-90. 2007
    ..Extensions to these methods are also discussed, with an eye toward future application to outstanding biological problems...
  30. pmc Passive all-optical force clamp for high-resolution laser trapping
    William J Greenleaf
    Department of Applied Physics, Stanford University, Stanford, California 94305 5020, USA
    Phys Rev Lett 95:208102. 2005
    ..We demonstrate the utility of such a force clamp by measuring the unfolding of DNA hairpins and the effect of trap stiffness on opening distance and transition rates...