Michael T Woodside

Summary

Affiliation: National Research Council
Country: Canada

Publications

  1. 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
  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. pmc Single-molecule approaches to prion protein misfolding
    Hao Yu
    Department of Physics, University of Alberta, Edmonton, AB Canada
    Prion 7:140-6. 2013
  7. 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
  8. 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
  9. 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
  10. 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

Collaborators

  • Feng Wang
  • Daniel Herschlag
  • Krishna Neupane
  • Hao Yu
  • Dustin B Ritchie
  • William J Greenleaf
  • Allison Solanki
  • Iveta Sosova
  • Armin Hoffmann
  • Daniel A N Foster
  • Derek R Dee
  • Amar Nath Gupta
  • Angela M Brigley
  • Steven M Block
  • Xia Liu
  • Jingchyuan Soong
  • William K A Sikkema
  • Miro Belov
  • Abhilash Vincent
  • Max Anikovskiy
  • Elena Grandi
  • Nils O Petersen
  • Laura Rivera
  • Kirsten L Frieda
  • Elio A Abbondanzieri

Detail Information

Publications19

  1. 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...
  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. 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...
  7. 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
    ....
  8. 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
    ....
  9. 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...
  10. 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
    ....
  11. 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. ..
  12. 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...
  13. 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...
  14. ncbi request reprint 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. ..
  15. 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
    ....
  16. 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. ..
  17. 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...
  18. 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...
  19. 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...