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Items: 49

1.

Memory effects in single-molecule force spectroscopy measurements of biomolecular folding.

Pyo AGT, Woodside MT.

Phys Chem Chem Phys. 2019 Nov 13;21(44):24527-24534. doi: 10.1039/c9cp04197d.

PMID:
31663550
2.

Molecular free energy profiles from force spectroscopy experiments by inversion of observed committors.

Covino R, Woodside MT, Hummer G, Szabo A, Cossio P.

J Chem Phys. 2019 Oct 21;151(15):154115. doi: 10.1063/1.5118362.

PMID:
31640370
3.

Probing microscopic conformational dynamics in folding reactions by measuring transition paths.

Hoffer NQ, Woodside MT.

Curr Opin Chem Biol. 2019 Aug 30;53:68-74. doi: 10.1016/j.cbpa.2019.07.006. [Epub ahead of print] Review.

PMID:
31479831
4.

Probing the Basis of α-Synuclein Aggregation by Comparing Simulations to Single-Molecule Experiments.

Churchill CDM, Healey MA, Preto J, Tuszynski JA, Woodside MT.

Biophys J. 2019 Sep 17;117(6):1125-1135. doi: 10.1016/j.bpj.2019.08.013. Epub 2019 Aug 16.

PMID:
31477241
5.

Complex dynamics under tension in a high-efficiency frameshift stimulatory structure.

Halma MTJ, Ritchie DB, Cappellano TR, Neupane K, Woodside MT.

Proc Natl Acad Sci U S A. 2019 Sep 24;116(39):19500-19505. doi: 10.1073/pnas.1905258116. Epub 2019 Aug 13.

PMID:
31409714
6.

Characterizing the inhibition of α-synuclein oligomerization by a pharmacological chaperone that prevents prion formation by the protein PrP.

Dong C, Garen CR, Mercier P, Petersen NO, Woodside MT.

Protein Sci. 2019 Sep;28(9):1690-1702. doi: 10.1002/pro.3684. Epub 2019 Aug 2.

PMID:
31306510
7.

Measuring the average shape of transition paths during the folding of a single biological molecule.

Hoffer NQ, Neupane K, Pyo AGT, Woodside MT.

Proc Natl Acad Sci U S A. 2019 Apr 23;116(17):8125-8130. doi: 10.1073/pnas.1816602116. Epub 2019 Apr 5.

8.

Early stages of aggregation of engineered α-synuclein monomers and oligomers in solution.

Li X, Dong C, Hoffmann M, Garen CR, Cortez LM, Petersen NO, Woodside MT.

Sci Rep. 2019 Feb 11;9(1):1734. doi: 10.1038/s41598-018-37584-6.

9.

Transition-path properties for folding reactions in the limit of small barriers.

Pyo AGT, Hoffer NQ, Neupane K, Woodside MT.

J Chem Phys. 2018 Sep 21;149(11):115101. doi: 10.1063/1.5046692.

PMID:
30243275
10.

High-Precision Single-Molecule Characterization of the Folding of an HIV RNA Hairpin by Atomic Force Microscopy.

Walder R, Van Patten WJ, Ritchie DB, Montange RK, Miller TW, Woodside MT, Perkins TT.

Nano Lett. 2018 Oct 10;18(10):6318-6325. doi: 10.1021/acs.nanolett.8b02597. Epub 2018 Sep 24.

PMID:
30234311
11.

Measuring the Local Velocity along Transition Paths during the Folding of Single Biological Molecules.

Neupane K, Hoffer NQ, Woodside MT.

Phys Rev Lett. 2018 Jul 6;121(1):018102. doi: 10.1103/PhysRevLett.121.018102.

PMID:
30028173
12.

Testing Kinetic Identities Involving Transition-Path Properties Using Single-Molecule Folding Trajectories.

Neupane K, Hoffer NQ, Woodside MT.

J Phys Chem B. 2018 Dec 13;122(49):11095-11099. doi: 10.1021/acs.jpcb.8b05355. Epub 2018 Jul 26.

PMID:
30004229
13.

Structural characteristics and membrane interactions of tandem α-synuclein oligomers.

Dong C, Hoffmann M, Li X, Wang M, Garen CR, Petersen NO, Woodside MT.

Sci Rep. 2018 Apr 30;8(1):6755. doi: 10.1038/s41598-018-25133-0.

14.

Probing Position-Dependent Diffusion in Folding Reactions Using Single-Molecule Force Spectroscopy.

Foster DAN, Petrosyan R, Pyo AGT, Hoffmann A, Wang F, Woodside MT.

Biophys J. 2018 Apr 10;114(7):1657-1666. doi: 10.1016/j.bpj.2018.02.026.

15.

Partially native intermediates mediate misfolding of SOD1 in single-molecule folding trajectories.

Sen Mojumdar S, N Scholl Z, Dee DR, Rouleau L, Anand U, Garen C, Woodside MT.

Nat Commun. 2017 Dec 1;8(1):1881. doi: 10.1038/s41467-017-01996-1.

16.

Conformational dynamics of the frameshift stimulatory structure in HIV-1.

Ritchie DB, Cappellano TR, Tittle C, Rezajooei N, Rouleau L, Sikkema WKA, Woodside MT.

RNA. 2017 Sep;23(9):1376-1384. doi: 10.1261/rna.061655.117. Epub 2017 May 18.

17.

Direct measurement of sequence-dependent transition path times and conformational diffusion in DNA duplex formation.

Neupane K, Wang F, Woodside MT.

Proc Natl Acad Sci U S A. 2017 Feb 7;114(6):1329-1334. doi: 10.1073/pnas.1611602114. Epub 2017 Jan 23.

18.

Quantifying Instrumental Artifacts in Folding Kinetics Measured by Single-Molecule Force Spectroscopy.

Neupane K, Woodside MT.

Biophys J. 2016 Jul 26;111(2):283-286. doi: 10.1016/j.bpj.2016.06.011. Epub 2016 Jun 29.

19.

Pharmacological chaperone reshapes the energy landscape for folding and aggregation of the prion protein.

Gupta AN, Neupane K, Rezajooei N, Cortez LM, Sim VL, Woodside MT.

Nat Commun. 2016 Jun 27;7:12058. doi: 10.1038/ncomms12058.

20.

Comparing the energy landscapes for native folding and aggregation of PrP.

Dee DR, Woodside MT.

Prion. 2016 May 3;10(3):207-20. doi: 10.1080/19336896.2016.1173297.

21.

Direct observation of transition paths during the folding of proteins and nucleic acids.

Neupane K, Foster DA, Dee DR, Yu H, Wang F, Woodside MT.

Science. 2016 Apr 8;352(6282):239-42. doi: 10.1126/science.aad0637.

22.

Phase transitions and structure analysis in wild-type, A30P, E46K, and A53T mutants of α-synuclein.

Healey MA, Woodside MT, Tuszynski JA.

Eur Biophys J. 2016 May;45(4):355-64. doi: 10.1007/s00249-015-1103-0. Epub 2015 Dec 22.

PMID:
26695014
23.

Transition-Path Probability as a Test of Reaction-Coordinate Quality Reveals DNA Hairpin Folding Is a One-Dimensional Diffusive Process.

Neupane K, Manuel AP, Lambert J, Woodside MT.

J Phys Chem Lett. 2015 Mar 19;6(6):1005-10. doi: 10.1021/acs.jpclett.5b00176. Epub 2015 Mar 5.

PMID:
26262860
24.

α-Synuclein dimer structures found from computational simulations.

Sahu KK, Woodside MT, Tuszynski JA.

Biochimie. 2015 Sep;116:133-40. doi: 10.1016/j.biochi.2015.07.011. Epub 2015 Jul 18.

PMID:
26193124
25.

Probing the structural dynamics of proteins and nucleic acids with optical tweezers.

Ritchie DB, Woodside MT.

Curr Opin Struct Biol. 2015 Oct;34:43-51. doi: 10.1016/j.sbi.2015.06.006. Epub 2015 Jul 17. Review.

PMID:
26189090
26.

Protein misfolding occurs by slow diffusion across multiple barriers in a rough energy landscape.

Yu H, Dee DR, Liu X, Brigley AM, Sosova I, Woodside MT.

Proc Natl Acad Sci U S A. 2015 Jul 7;112(27):8308-13. doi: 10.1073/pnas.1419197112. Epub 2015 Jun 24.

27.

Reconstructing folding energy landscapes from splitting probability analysis of single-molecule trajectories.

Manuel AP, Lambert J, Woodside MT.

Proc Natl Acad Sci U S A. 2015 Jun 9;112(23):7183-8. doi: 10.1073/pnas.1419490112. Epub 2015 May 26.

28.

Reconstructing folding energy landscape profiles from nonequilibrium pulling curves with an inverse Weierstrass integral transform.

Engel MC, Ritchie DB, Foster DA, Beach KS, Woodside MT.

Phys Rev Lett. 2014 Dec 5;113(23):238104. Epub 2014 Dec 3.

PMID:
25526163
29.

Determining intrachain diffusion coefficients for biopolymer dynamics from single-molecule force spectroscopy measurements.

Woodside MT, Lambert J, Beach KS.

Biophys J. 2014 Oct 7;107(7):1647-53. doi: 10.1016/j.bpj.2014.08.007.

30.

Reconstructing folding energy landscapes by single-molecule force spectroscopy.

Woodside MT, Block SM.

Annu Rev Biophys. 2014;43:19-39. doi: 10.1146/annurev-biophys-051013-022754. Review.

31.

Single-molecule force spectroscopy of rapidly fluctuating, marginally stable structures in the intrinsically disordered protein α-synuclein.

Solanki A, Neupane K, Woodside MT.

Phys Rev Lett. 2014 Apr 18;112(15):158103. Epub 2014 Apr 16.

PMID:
24785077
32.

Diverse metastable structures formed by small oligomers of α-synuclein probed by force spectroscopy.

Neupane K, Solanki A, Sosova I, Belov M, Woodside MT.

PLoS One. 2014 Jan 24;9(1):e86495. doi: 10.1371/journal.pone.0086495. eCollection 2014.

33.

Anti-frameshifting ligand reduces the conformational plasticity of the SARS virus pseudoknot.

Ritchie DB, Soong J, Sikkema WK, Woodside MT.

J Am Chem Soc. 2014 Feb 12;136(6):2196-9. doi: 10.1021/ja410344b. Epub 2014 Jan 28.

PMID:
24446874
34.

Single-molecule assays for investigating protein misfolding and aggregation.

Hoffmann A, Neupane K, Woodside MT.

Phys Chem Chem Phys. 2013 Jun 7;15(21):7934-48. doi: 10.1039/c3cp44564j. Epub 2013 Apr 23.

PMID:
23612887
35.

Single-molecule approaches to prion protein misfolding.

Yu H, Dee DR, Woodside MT.

Prion. 2013 Mar-Apr;7(2):140-6. doi: 10.4161/pri.23303. Epub 2013 Jan 28.

36.

Transition path times for nucleic Acid folding determined from energy-landscape analysis of single-molecule trajectories.

Neupane K, Ritchie DB, Yu H, Foster DA, Wang F, Woodside MT.

Phys Rev Lett. 2012 Aug 10;109(6):068102. Epub 2012 Aug 6.

PMID:
23006308
37.

Programmed -1 frameshifting efficiency correlates with RNA pseudoknot conformational plasticity, not resistance to mechanical unfolding.

Ritchie DB, Foster DA, Woodside MT.

Proc Natl Acad Sci U S A. 2012 Oct 2;109(40):16167-72. doi: 10.1073/pnas.1204114109. Epub 2012 Sep 17.

38.

Energy landscape analysis of native folding of the prion protein yields the diffusion constant, transition path time, and rates.

Yu H, Gupta AN, Liu X, Neupane K, Brigley AM, Sosova I, Woodside MT.

Proc Natl Acad Sci U S A. 2012 Sep 4;109(36):14452-7. doi: 10.1073/pnas.1206190109. Epub 2012 Aug 20.

39.

Phthalocyanine tetrasulfonates bind to multiple sites on natively-folded prion protein.

Dee DR, Gupta AN, Anikovskiy M, Sosova I, Grandi E, Rivera L, Vincent A, Brigley AM, Petersen NO, Woodside MT.

Biochim Biophys Acta. 2012 Jun;1824(6):826-32. doi: 10.1016/j.bbapap.2012.03.011. Epub 2012 Mar 28.

PMID:
22480824
40.

Direct observation of multiple misfolding pathways in a single prion protein molecule.

Yu H, Liu X, Neupane K, Gupta AN, Brigley AM, Solanki A, Sosova I, Woodside MT.

Proc Natl Acad Sci U S A. 2012 Apr 3;109(14):5283-8. doi: 10.1073/pnas.1107736109. Epub 2012 Mar 15.

41.

Signal-pair correlation analysis of single-molecule trajectories.

Hoffmann A, Woodside MT.

Angew Chem Int Ed Engl. 2011 Dec 23;50(52):12643-6. doi: 10.1002/anie.201104033. Epub 2011 Nov 4.

PMID:
22057589
42.

Single-molecule force spectroscopy of the add adenine riboswitch relates folding to regulatory mechanism.

Neupane K, Yu H, Foster DA, Wang F, Woodside MT.

Nucleic Acids Res. 2011 Sep 1;39(17):7677-87. doi: 10.1093/nar/gkr305. Epub 2011 Jun 8.

43.

Folding and unfolding single RNA molecules under tension.

Woodside MT, García-García C, Block SM.

Curr Opin Chem Biol. 2008 Dec;12(6):640-6. doi: 10.1016/j.cbpa.2008.08.011. Epub 2008 Sep 9. Review.

44.

Direct observation of hierarchical folding in single riboswitch aptamers.

Greenleaf WJ, Frieda KL, Foster DA, Woodside MT, Block SM.

Science. 2008 Feb 1;319(5863):630-3. doi: 10.1126/science.1151298. Epub 2008 Jan 3.

45.

High-resolution, single-molecule measurements of biomolecular motion.

Greenleaf WJ, Woodside MT, Block SM.

Annu Rev Biophys Biomol Struct. 2007;36:171-90. Review.

46.

Direct measurement of the full, sequence-dependent folding landscape of a nucleic acid.

Woodside MT, Anthony PC, Behnke-Parks WM, Larizadeh K, Herschlag D, Block SM.

Science. 2006 Nov 10;314(5801):1001-4. Erratum in: Science. 2007 Feb 9;315(5813):766.

47.

Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins.

Woodside MT, Behnke-Parks WM, Larizadeh K, Travers K, Herschlag D, Block SM.

Proc Natl Acad Sci U S A. 2006 Apr 18;103(16):6190-5. Epub 2006 Apr 10.

48.

Passive all-optical force clamp for high-resolution laser trapping.

Greenleaf WJ, Woodside MT, Abbondanzieri EA, Block SM.

Phys Rev Lett. 2005 Nov 11;95(20):208102. Epub 2005 Nov 8.

49.

Scanned probe imaging of single-electron charge states in nanotube quantum dots.

Woodside MT, McEuen PL.

Science. 2002 May 10;296(5570):1098-101.

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