Publications

Upcoming Publications

Ren, Y., Yang, J., Jin, H., Zhang, Y.L. & Berro, J. Force redistribution during clathrin-mediated endocytosis revealed by new phase-separating force sensors. biorxiv preprint, https://www.biorxiv.org/content/10.1101/2021.06.29.450294v2 (2023). Science Advances, in revision.

M. Meijer, M. Ottl, J. Yang, A. Subkhangulova, Avinash Kumar, A. J. Groffen, J. van Weering, Y. L. Zhang*, & M. Verhage*. Tomosyns attenuate SNARE assembly and synaptic depression by binding to VAMP2-containing template complexes. Neuron, under review (2023).

PubMed.gov Citation Links

Cross-regulations of two connected domains form a mechanical circuit for steady force transmission during clathrin-mediated endocytosis.Ren Y, Yang J, Fujita B, Zhang Y, Berro J. Cell Rep. 2024 Sep 24; 2024 Sep 13. PMID: 39276354.
Nonlinear compliance of NompC gating spring and its implication in mechanotransduction.Wang Y, Jin P, Kumar A, Jan L, Cheng Y, Jan YN, Zhang Y. bioRxiv. 2024 Jun 24; 2024 Jun 24. PMID: 38979198.
Lipid osmosis, membrane tension, and other mechanochemical driving forces of lipid flow.Zhang Y, Lin C. Curr Opin Cell Biol. 2024 Jun; 2024 May 31. PMID: 38823338.
Lipid osmosis, membrane tension, and other mechanochemical driving forces of lipid flow.Zhang Y, Lin C. bioRxiv. 2024 Apr 28; 2024 Apr 28. PMID: 38260424.
Tomosyns attenuate SNARE assembly and synaptic depression by binding to VAMP2-containing template complexes.Meijer M, Öttl M, Yang J, Subkhangulova A, Kumar A, Feng Z, van Voorst TW, Groffen AJ, van Weering JRT, Zhang Y, Verhage M. Nat Commun. 2024 Mar 26; 2024 Mar 26. PMID: 38531902.
Force redistribution in clathrin-mediated endocytosis revealed by coiled-coil force sensors.Ren Y, Yang J, Fujita B, Jin H, Zhang Y, Berro J. Sci Adv. 2023 Oct 13; 2023 Oct 13. PMID: 37831774.
A dynamic template complex mediates Munc18-chaperoned SNARE assembly.Yang J, Jin H, Liu Y, Guo Y, Zhang Y. Proc Natl Acad Sci U S A. 2022 Dec 6; 2022 Dec 1. PMID: 36454760.
Energetics, kinetics, and pathways of SNARE assembly in membrane fusion.Zhang Y, Ma L, Bao H. Crit Rev Biochem Mol Biol. 2022 Aug; 2022 Sep 24. PMID: 36151854.
Polybasic Patches in Both C2 Domains of Synaptotagmin-1 Are Required for Evoked Neurotransmitter Release.Wu Z, Ma L, Courtney NA, Zhu J, Landajuela A, Zhang Y, Chapman ER, Karatekin E. J Neurosci. 2022 Jul 27; 2022 Jun 14. PMID: 35701163.
Stepwise membrane binding of extended synaptotagmins revealed by optical tweezers.Ge J, Bian X, Ma L, Cai Y, Li Y, Yang J, Karatekin E, De Camilli P, Zhang Y. Nat Chem Biol. 2022 Mar; 2021 Dec 16. PMID: 34916620.
Quantitative Models of Lipid Transfer and Membrane Contact Formation.Zhang Y, Ge J, Bian X, Kumar A. Contact (Thousand Oaks). 2022; 2022 May 4. PMID: 36120532.
Single-Molecule Manipulation Study of Chaperoned SNARE Folding and Assembly with Optical Tweezers.Jin H, Ge J, Yang J, Zhang Y. Methods Mol Biol. 2022. PMID: 36063331.
Single-Molecule Optical Tweezers Study of Protein-Membrane Interactions.Ma L, Ge J, Bian X, Zhang Y. Methods Mol Biol. 2022. PMID: 35819776.
Single-molecule manipulation of macromolecules on GUV or SUV membranes using optical tweezers.Wang Y, Kumar A, Jin H, Zhang Y. Biophys J. 2021 Dec 21; 2021 Nov 20. PMID: 34813728.
Chaperoning SNARE Folding and Assembly.Zhang Y, Hughson FM. Annu Rev Biochem. 2021 Jun 20; 2021 Apr 6. PMID: 33823650.
Munc13 binds and recruits SNAP25 to chaperone SNARE complex assembly.Kalyana Sundaram RV, Jin H, Li F, Shu T, Coleman J, Yang J, Pincet F, Zhang Y, Rothman JE, Krishnakumar SS. FEBS Lett. 2021 Feb; 2020 Dec 5. PMID: 33222163.
Securing SNAREs for assembly.Zhang Y, Yang J. J Biol Chem. 2020 Jul 24; 2020 Jul 24. PMID: 32709759.
Munc13-1 MUN domain and Munc18-1 cooperatively chaperone SNARE assembly through a tetrameric complex.Shu T, Jin H, Rothman JE, Zhang Y. Proc Natl Acad Sci U S A. 2020 Jan 14; 2019 Dec 30. PMID: 31888993.
Synaptic vesicle fusion: today and beyond.Brose N, Brunger A, Cafiso D, Chapman ER, Diao J, Hughson FM, Jackson MB, Jahn R, Lindau M, Ma C, Rizo J, Shin YK, Söllner TH, Tamm L, Yoon TY, Zhang Y. Nat Struct Mol Biol. 2019 Aug. PMID: 31384060.
Single-Molecule Optical Tweezers Study of Regulated SNARE Assembly.Ma L, Jiao J, Zhang Y. Methods Mol Biol. 2019. PMID: 30317500.
Munc18-1 catalyzes neuronal SNARE assembly by templating SNARE association.Jiao J, He M, Port SA, Baker RW, Xu Y, Qu H, Xiong Y, Wang Y, Jin H, Eisemann TJ, Hughson FM, Zhang Y. Elife. 2018 Dec 12; 2018 Dec 12. PMID: 30540253.
Editorial Overview: Single-Molecule Approaches up to Difficult Challenges in Folding and Dynamics.Zhang Y, Ha T, Marqusee S. J Mol Biol. 2018 Feb 16; 2017 Dec 27. PMID: 29288633.
Two Disease-Causing SNAP-25B Mutations Selectively Impair SNARE C-terminal Assembly.Rebane AA, Wang B, Ma L, Qu H, Coleman J, Krishnakumar S, Rothman JE, Zhang Y. J Mol Biol. 2018 Feb 16; 2017 Oct 19. PMID: 29056461.
Single-molecule force spectroscopy of protein-membrane interactions.Ma L, Cai Y, Li Y, Jiao J, Wu Z, O'Shaughnessy B, De Camilli P, Karatekin E, Zhang Y. Elife. 2017 Oct 30; 2017 Oct 30. PMID: 29083305.
Energetics, kinetics, and pathway of SNARE folding and assembly revealed by optical tweezers.Zhang Y. Protein Sci. 2017 Jul; 2017 Mar 8. PMID: 28097727.
Single-Molecule Protein Folding Experiments Using High-Precision Optical Tweezers.Jiao J, Rebane AA, Ma L, Zhang Y. Methods Mol Biol. 2017. PMID: 27844436.
Stability, folding dynamics, and long-range conformational transition of the synaptic t-SNARE complex.Zhang X, Rebane AA, Ma L, Li F, Jiao J, Qu H, Pincet F, Rothman JE, Zhang Y. Proc Natl Acad Sci U S A. 2016 Dec 13; 2016 Nov 28. PMID: 27911771.
Hidden Markov Modeling with Detailed Balance and Its Application to Single Protein Folding.Zhang Y, Jiao J, Rebane AA. Biophys J. 2016 Nov 15. PMID: 27851936.
Regulation of DNA Translocation Efficiency within the Chromatin Remodeler RSC/Sth1 Potentiates Nucleosome Sliding and Ejection.Clapier CR, Kasten MM, Parnell TJ, Viswanathan R, Szerlong H, Sirinakis G, Zhang Y, Cairns BR. Mol Cell. 2016 May 5. PMID: 27153540.
α-SNAP Enhances SNARE Zippering by Stabilizing the SNARE Four-Helix Bundle.Ma L, Kang Y, Jiao J, Rebane AA, Cha HK, Xi Z, Qu H, Zhang Y. Cell Rep. 2016 Apr 19; 2016 Apr 7. PMID: 27068468.
Structure-Based Derivation of Protein Folding Intermediates and Energies from Optical Tweezers.Rebane AA, Ma L, Zhang Y. Biophys J. 2016 Jan 19. PMID: 26789767.
Munc18-1-regulated stage-wise SNARE assembly underlying synaptic exocytosis.Ma L, Rebane AA, Yang G, Xi Z, Kang Y, Gao Y, Zhang Y. Elife. 2015 Dec 23; 2015 Dec 23. PMID: 26701912.
Kinetically coupled folding of a single HIV-1 glycoprotein 41 complex in viral membrane fusion and inhibition.Jiao J, Rebane AA, Ma L, Gao Y, Zhang Y. Proc Natl Acad Sci U S A. 2015 Jun 2; 2015 May 18. PMID: 26038562.
Quantifying and optimizing single-molecule switching nanoscopy at high speeds.Lin Y, Long JJ, Huang F, Duim WC, Kirschbaum S, Zhang Y, Schroeder LK, Rebane AA, Velasco MG, Virrueta A, Moonan DW, Jiao J, Hernandez SY, Zhang Y, Bewersdorf J. PLoS One. 2015; 2015 May 26. PMID: 26011109.
Common intermediates and kinetics, but different energetics, in the assembly of SNARE proteins.Zorman S, Rebane AA, Ma L, Yang G, Molski MA, Coleman J, Pincet F, Rothman JE, Zhang Y. Elife. 2014 Sep 1; 2014 Sep 1. PMID: 25180101.
High-resolution optical tweezers for single-molecule manipulation.Zhang X, Ma L, Zhang Y. Yale J Biol Med. 2013 Sep; 2013 Sep 20. PMID: 24058311.
Single reconstituted neuronal SNARE complexes zipper in three distinct stages.Gao Y, Zorman S, Gundersen G, Xi Z, Ma L, Sirinakis G, Rothman JE, Zhang Y. Science. 2012 Sep 14; 2012 Aug 16. PMID: 22903523.
Combined versatile high-resolution optical tweezers and single-molecule fluorescence microscopy.Sirinakis G, Ren Y, Gao Y, Xi Z, Zhang Y. Rev Sci Instrum. 2012 Sep. PMID: 23020384.
Single-molecule observation of helix staggering, sliding, and coiled coil misfolding.Xi Z, Gao Y, Sirinakis G, Guo H, Zhang Y. Proc Natl Acad Sci U S A. 2012 Apr 10; 2012 Mar 26. PMID: 22451899.
DNA translocation of ATP-dependent chromatin remodeling factors revealed by high-resolution optical tweezers.Zhang Y, Sirinakis G, Gundersen G, Xi Z, Gao Y. Methods Enzymol. 2012. PMID: 22929763.
Highly anisotropic stability and folding kinetics of a single coiled coil protein under mechanical tension.Gao Y, Sirinakis G, Zhang Y. J Am Chem Soc. 2011 Aug 17; 2011 Jul 22. PMID: 21707065.
The RSC chromatin remodelling ATPase translocates DNA with high force and small step size.Sirinakis G, Clapier CR, Gao Y, Viswanathan R, Cairns BR, Zhang Y. EMBO J. 2011 May 6; 2011 May 6. PMID: 21552204.
Anomalous DNA binding by E2 regulatory protein driven by spacer sequence TATA.Xi Z, Zhang Y, Hegde RS, Shakked Z, Crothers DM. Nucleic Acids Res. 2010 Jun; 2010 Feb 25. PMID: 20185566.
Conformational flexibility in the chromatin remodeler RSC observed by electron microscopy and the orthogonal tilt reconstruction method.Leschziner AE, Saha A, Wittmeyer J, Zhang Y, Bustamante C, Cairns BR, Nogales E. Proc Natl Acad Sci U S A. 2007 Mar 20; 2007 Mar 13. PMID: 17360331.
Analysis of in-vivo LacR-mediated gene repression based on the mechanics of DNA looping.Zhang Y, McEwen AE, Crothers DM, Levene SD. PLoS One. 2006 Dec 27; 2006 Dec 27. PMID: 17205140.
DNA translocation and loop formation mechanism of chromatin remodeling by SWI/SNF and RSC.Zhang Y, Smith CL, Saha A, Grill SW, Mihardja S, Smith SB, Cairns BR, Peterson CL, Bustamante C. Mol Cell. 2006 Nov 17. PMID: 17188033.
Effect of force on mononucleosomal dynamics.Mihardja S, Spakowitz AJ, Zhang Y, Bustamante C. Proc Natl Acad Sci U S A. 2006 Oct 24; 2006 Oct 16. PMID: 17043216.
Statistical-mechanical theory of DNA looping.Zhang Y, McEwen AE, Crothers DM, Levene SD. Biophys J. 2006 Mar 15; 2005 Dec 16. PMID: 16361335.
Predicting indirect readout effects in protein-DNA interactions.Zhang Y, Xi Z, Hegde RS, Shakked Z, Crothers DM. Proc Natl Acad Sci U S A. 2004 Jun 1; 2004 May 17. PMID: 15148366.
High-throughput approach for detection of DNA bending and flexibility based on cyclization.Zhang Y, Crothers DM. Proc Natl Acad Sci U S A. 2003 Mar 18; 2003 Mar 10. PMID: 12629220.
Statistical mechanics of sequence-dependent circular DNA and its application for DNA cyclization.Zhang Y, Crothers DM. Biophys J. 2003 Jan. PMID: 12524271.

Past Publications

2010 & Older

Levene, S. D. and Zhang, Y. L. . (2009). Closing the loop on protein-DNA interactions: Interplay between shape and flexibility in nucleoprotein assemblies having implications for biological regulation. Book chapter in Mathematics of DNA Structure, Function, and Interactions , (IMA Volumes in Mathematics and its Applications), 195-212.

Metzler, R., Ambjornsson, T., Hanker, A., Zhang, Y. L., and Levene, S. (2007). Single DNA conformations and biological function. Computational and Theoretical Nanoscience , 4, 1–49.

Zhang, Y. L. & Zheng, W. M. (1997). Self-consistent phonon approaches for the hydrogen bond chain. Phys. Rev. E 55, 4531-4535.

Zhang, Y. L. , Zheng, W. M., Liu, J. X., & Chen, Y. Z. (1997). Theory of DNA melting based on Peyrard-Bishop model. Phys. Rev. E. 56, 7100-7115.

Chen, Y. Z. & Zhang, Y. L. , & Prohofsky, E. W. (1997). Binding stability of a cross-linked drug: Calculation of an anticancer drug cisplatin-DNA complex. Phys. Rev. E. 55, 5843-5848.

Chen, Y. Z. & Zhang, Y. L. (1997). Calculation of binding affinity of anticancer drug daunomycin to DNA by a statistical mechanics approach. Phys. Rev. E 55, 7390-7395.