Publications

Selected Publications from the Woodside Lab

2020

“Anti-frameshifting ligand active against SARS coronavirus-2 is resistant to natural mutations of the frameshift-stimulatory pseudoknot.” K. Neupane, S. Munshi, M. Zhao, D.B. Ritchie, S.M. Ileperuma, M.T. Woodside. J. Mol. Biol. in press (2020). Link to manuscript

“Structural and functional conservation of the programmed −1 ribosomal frameshift signal of SARS coronavirus 2 (SARS-CoV-2).” J.A. Kelly, A.N. Olson, K. Neupane, S. Munshi, J. San Emeterio, L. Pollack, M.T. Woodside, J.D. Dinman. J. Biol. Chem. 295:10741–10748 (2020). Link to manuscript. (preprint)

2019

“Memory effects in single-molecule force spectroscopy measurements of biomolecular folding.” A.G.T. Pyo, M.T. Woodside. Phys. Chem. Chem. Phys., 21:24527-24534 (2019).  Link to manuscript.

“Molecular free energy profiles from force spectroscopy experiments by inversion of observed committors.” R. Covino, M.T. Woodside, G. Hummer, A. Szabo, P. Cossino. J. Chem. Phys., 151:154115 (2019). Link to manuscript, highlighted as “Featured Article”.

“Probing the basis of α-synuclein aggregation by comparing simulations to single-molecule experiments.” C.D.M. Churchill, M.A. Healey, J. Preto, J.A. Tuszynski, M.T. Woodside. Biophys. J., 117(6):1125-1135 (2019). Link to manuscript.

“Probing microscopic conformational dynamics in folding reactions by measuring transition paths.” N.Q. Hoffer, M.T. Woodside. Curr. Opin. Chem. Biol., 53:68–74 (2019). Link to manuscript.

“Complex dynamics under tension in a high-efficiency frameshift stimulatory structure.” M.T.J. Halma, D.B. Ritchie, T.R. Cappellano, K. Neupane, M.T. Woodside. Proc. Natl. Acad. Sci. USA, 116(39):19500-19505 (2019). Link to manuscript, and highlight in Commentary in PNAS .

“Characterizing the inhibition of α-synuclein oligomerisation by a pharmacological chaperone that prevents prion formation by the protein PrP.” C. Dong, C.R. Garen, P. Mercier, N.O. Petersen, M.T. Woodside. Prot. Sci., 28:1690–1702 (2019). Link to manuscript.

“Measuring the average shape of transition paths during the folding of a single biological molecule.” N.Q. Hoffer, K. Neupane, A.G.T. Pyo, M.T. Woodside. Proc. Natl. Acad. Sci. USA, 116(17):8125-8130 (2019). Link to manuscript.

“Early stages of aggregation of engineered α-synuclein monomers and oligomers in solution.” X. Li, C. Dong, M. Hoffmann, C. Garen, M. Wang, M.T. Woodside, N.O. Petersen. Sci. Rep., 9:1734 (2019). Link to manuscript.

2018

“High-precision single-molecule characterization of the folding of an HIV RNA hairpin by atomic force microscopy.” R. Walder, W.J. Van Patten, D.B. Ritchie, R.K. Montange, T.W. Miller, M.T. Woodside, T.T. Perkins. Nano Lett., 18:6318 (2018). Link to manuscript.

“Transition-path properties for folding reactions in the limit of small barriers.” A.G.T. Pyo, N.Q. Hoffer, K. Neupane, M.T. Woodside. J. Chem. Phys., 149:115101 (2018). Link to manuscript.

“Testing kinetic identities involving transition-path properties using single-molecule folding trajectories.” K. Neupane, N.Q. Hoffer, M.T. Woodside. J. Phys. Chem. B, 122:11095-11099 (2018). Link to manuscript.

“Measuring the velocity along transition paths during the folding of single biological molecules.” K. Neupane, N.Q. Hoffer, M.T. Woodside. Phys. Rev. Lett., 121:018102 (2018). Link to manuscript.

“Structural characteristics and membrane interactions of tandem α-synuclein oligomers.” C. Dong, M. Hoffmann, X. Li, M. Wang, N.O. Petersen, M.T. Woodside. Sci. Rep., 8:6755 (2018). Link to manuscript.

“Probing position-dependent diffusion in folding reactions using single-molecule force spectroscopy.” D.A.N. Foster, R. Petrosyan, A.G.T. Pyo, A. Hoffmann, F. Wang, M.T. Woodside. Biophys. J., 114:1657-1666 (2018). Link to manuscript.

2017

“Partially native intermediates mediate misfolding of SOD1 in single-molecule folding trajectories.” S. Sen Mojumdar, Z.N. Scholl, D.R. Dee, L. Rouleau, U. Anand, C. Garen, M.T. Woodside. Nature Communications. 8:1881 (2017). Link to manuscript.

“Conformational dynamics of the frameshift stimulatory structure in HIV-1.” D.B. Ritchie, T. Cappellano, C. Tittle, N. Rezajooei, L. Rouleau, W.K.A. Sikkema, M.T. Woodside. RNA, 23:1379-1384s (2017). Link to manuscript.

“Direct measurement of sequence-dependent transition path times and conformational diffusion in DNA duplex formation.” K. Neupane, F. Wang, M.T. Woodside. Proc. Natl. Acad. Sci. USA, 114:1329-1334 (2017). Link to manuscript.

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). Link to manuscript.

“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.

2008 – 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). Link to manuscript

“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). Link to manuscript

Postdoctoral Publications

“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). Link to manuscript.

“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). Link to manuscript.

“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). Link to manuscript. 

“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). Link to manuscript