Members of the Woodside Team and the Department of Physics at a workshop-retreat at Black Cat Guest Ranch near Hinton, AB (Feb 2016) Photo credit: Nils Petersen
Selected Publications from the Woodside Lab

2016

“Quantifying instrumental artifacts in folding kinetics measured by single-molecule force spectroscopy.” K. Neupane, M.T. Woodside. Biophys. J. 111(2): 283-286 (2016). Link to manuscript.

“Pharmacological chaperone reshapes the energy landscape for folding and aggregation of the prion protein.” A.N. Gupta, K. Neupane, N. Rezajooei, Leo Cortez, Valerie Sim, M.T. Woodside. Nature Communications, 7: 12058 (2016). Link to manuscript.

“Comparing the energy landscapes for native folding and aggregation of PrP.” D.R. Dee, M.T. Woodside. Prion, 10: 207-220 (2016). Link to manuscript.

"Direct observation of transition paths during the folding of proteins and nucleic acids." K. Neupane, D.A.N. Foster, D.R. Dee, H. Yu, F. Wang, M.T. Woodside. Science, 352: 239-242 (2016).  Link to manuscript and Perspective commentary, as well as link to commentary in Physics Today.            

"Protein folding trajectories can be described quantitively by one-dimensional diffusion over measured energy landscapes." K. Neupane. A.P. Manuel, M.T. Woodside. Nature Physics, 12: 700-703 (2016). Link to manuscript.


2015

“Probing the structural dynamics of proteins and nucleic acids with optical tweezers.” D.B. Ritchie, M.T. Woodside. Curr. Opin. Struct. Biol., 34:43-51 (2015). Link to manuscript.

“Protein misfolding occurs by slow diffusion across multiple barriers in a rough energy landscape.” H. Yu, D.R. Dee, X. Liu, A.M. Brigley, I. Sosova, M.T. Woodside. Proc. Natl. Acad. Sci. USA, 112: 8308-8313 (2015). Link to manuscript.

"Reconstructing folding energy landscapes from splitting probability analysis of single-molecule trajectories.” A.P. Manuel, J. Lambert, M.T. Woodside. Proc. Natl. Acad. Sci. USA, 112:7183-7188 (2015). Link to manuscript

“Transition path probability as a test of reaction-coordinate quality reveals DNA hairpin folding is a one-dimensional diffusive process.” K. Neupane, A.P. Manuel, J. Lambert, M.T. Woodside. J. Phys. Chem. Lett., 6:1005-1010 (2015). Link to manuscript.


2014

“Reconstructing folding energy landscape profiles from non-equilibrium pulling curves with an inverse Weierstrass integral transform.” M.C. Engel, D.B. Ritchie, D.A.N. Foster, K.S.D. Beach, M.T. Woodside. Phys. Rev. Lett., 113:238104 (2014). Featured as an “Editor's Suggestion.” Link to manuscript.

“Determining intra-chain diffusion coefficients for biopolymer dynamics from single-molecule force spectroscopy measurements.” M.T. Woodside, J. Lambert, K.S.D. Beach. Biophys J.,107: 1647-1653 (2014). Link to manuscript

"Reconstructing folding energy landscapes by single-molecule force spectroscopy." M.T. Woodside, S.M. Block, Annu. Rev. Biophys., 43: 19-39 (2014). Link to manuscript.

"Single-molecule force spectroscopy of rapidly-fluctuating, marginally-stable structures in the intrinsically-disordered protein α-synuclein." A. Solanki, K. Neupane, M.T. Woodside, Phys. Rev. Lett., 112: 158103 (2014). Link to manuscript.

"Diverse metastable structures formed by small oligomers of alpha-synuclein probed by force spectroscopy." K. Neupane, A. Solanki, I. Sosova, M. Belov, M.T. Woodside, PLoS One, 9: e86495 (2014). Link to manuscript.

"Anti-frameshifting ligand reduces the conformational plasticity of the SARS virus pseudoknot." D.B. Ritchie, J. Soong, W.K.A. Sikkema, M.T. Woodside, J. Am. Chem. Soc., 136: 2196-2199 (2014). Link to manuscript


2013

"Single-molecule assays for investigating protein misfolding and aggregation." A. Hoffmann, K. Neupane, M.T. Woodside, Phys. Chem. Chem. Phys., 15: 7934-7948 (2013). Link to manuscript.
 
"Single-molecule approaches to prion protein misfolding." H. Yu, D.R. Dee, M.T. Woodside, Prion , 7: 140-146 (2013). Link to manuscript.


2012

"Programmed -1 frameshifting efficiency correlates with RNA pseudoknot conformational plasticity, not resistance to mechanical unfolding." D.B. Ritchie, D.A.N. Foster, M.T. Woodside, Proc. Natl. Acad. Sci. USA, 109: 16167-16172 (2012). Link to manuscript.

"Energy landscape analysis of native folding of the prion protein yields the diffusion constant, transition path time, and rates." H. Yu, A.N. Gupta, X. Liu, K. Neupane, A.M. Brigley, I. Sosova, M.T. Woodside, Proc. Natl. Acad. Sci. USA, 109: 14452-14457 (2012). Link to manuscript.

"Transition path times for nucleic acid folding determined from energy-landscape analysis of single-molecule trajectories." K. Neupane, D.B. Ritchie, H. Yu, D.A.N. Foster, F. Wang, M.T. Woodside, Phys. Rev. Lett., 109: 068102 (2012). Links to manuscript and Viewpoint commentary in Physics.

"Phthalocyanine tetrasulfonates bind to mulitple sites on natively-folded prion protein." D.R. Dee, A.N. Gupta, M. Anikovskiy, I. Sosova, E. Grandi, L. Rivera, A. Vincent, A.M. Brigley, N.O. Petersen, M.T. Woodside, BBA Proteins & Proteomics , 1824: 826-832 (2012). Link to manuscript.

"Direct observation of multiple misfolding pathways in a single prion protein molecule." H. Yu, X. Liu, K. Neupane, A.N. Gupta, A.M. Brigley, A. Solanki, I. Sosova, M.T. Woodside, Proc. Natl. Acad. Sci. USA , 109: 5283-5288 (2012). Link to manuscript.


2011  

"Signal-pair correlation analysis of single-molecule trajectories." A. Hoffman, M.T. Woodside, Agnew Chem. Int. Ed., 50: 12643-12646 (2011). Links to manuscript and Highlight commentary in ChemPhys Chem. 

"Single-molecule force spectroscopy of the add adenine riboswitch relates folding to regulatory mechanism." K. Neupane, H. Yu, D.A.N. Foster, F. Wang, M.T. Woodside, Nucleic Acids Res., 39: 7677-7687 (2011). PDF document.

"Experimental validation of free-energy-landscape reconstruction from non-equilibrium single-molecule force spectroscopy measurements." A.N. Gupta, A. Vincent, K. Neupane, H. Yu, F. Wang, M.T. Woodside, Nature Physics, 7: 631-634 (2011). Links to manuscript and News and Views commentary. 


2005 - 2010

"Folding and unfolding single RNA molecules under tension." M.T. Woodside, C. Garcia-Garcia, S.M. Block, Curr. Opin. Chem. Biol., 12: 640-646 (2008). PDF document.                                                                                    

"Direct observation of hierarchical folding in single riboswitch aptamers." W.J. Greenleaf, K.L. Frieda, D.A.N. Foster, M.T. Woodside, S.M. Block, Science, 319: 630-633 (2008). PDF document.

"High-resolution, single-molecule measurements of biomolecular motion." W.J. Greenleaf, M.T. Woodside, S.M. Block, Annu. Rev. Biophys. Biomol. Struct., 36: 171-190 (2007). PDF document. 

"Direct measurement of the full, sequence-dependent folding landscape of a nucleic acid." M.T. Woodside, P.C. Anthony, K. Larizadeh, W.M. Behnke-Parks, D. Herschlag, S.M. Block, Science , 314: 1001-1004 (2006). PDF document.

"Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins." M.T. Woodside, W.M. Behnke-Parks, K. Larizadeh, K. Travers, D. Herschlag, S.M. Block, Proc. Natl. Acad. Sci. USA, 103: 6190-6195 (2006). PDF document.

"Passive all-optical force clamp for high-precision laser trapping." W.J. Greenleaf, M.T. Woodside, E.A. Abbondanzieri, S.M. Block, Phys. Rev. Lett., 95: 208102 (2005). PDF document.


2000 - 2005

"Imaging inter edge state scattering centers in the quantum Hall regime." M.T. Woodside, C. Vale, P.L. McEuen, C. Kadow, K.D. Maranowski, A.C. Gossard, Phys. Rev. B , 64: 041310 (2001). PDF document.

"Scanned probe imaging of single-electron charge states in nanotube quantum dots." M.T. Woodside, P.L. McEuen, Science , 296: 1098-1101 (2002). PDF document.
 

Members of the Woodside Team and the Department of Physics at a workshop-retreat at Bearberry Guest Ranch near Sundre, AB (Feb 2015) Photo credit: Susanna Lynn
Members of the Woodside Team and the Department of Physics at a workshop-retreat at Black Cat Guest Ranch near Hinton, AB (Feb 2014) Photo credit: Kamlesh Sahu