Wenwei Zheng

Wiggers F, Wohl S, Dubovetskyi A, Rosenblum G, Zheng W, and Hofmann H. Diffusion of a Disordered Protein on its Folded Ligand.  Proc. Natl. Acad. Sci. USA 118:e2106690118 (2021) https://www.pnas.org/content/118/37/e2106690118.short

Ramaraju B, Nelson SL, Zheng W, Ghirlando R, and Deshmukh L. Quantitative NMR Study of Insulin-Degrading Enzyme Using Amyloid-β and HIV-1 p6 Elucidates Its Chaperone Activity.  Biochemistry 60:2519 (2021) https://pubs.acs.org/doi/abs/10.1021/acs.biochem.1c00342

Wohl S, Jakubowski M, and Zheng W. Salt-Dependent Conformational Changes of Intrinsically Disordered Proteins.  J. Phys. Chem. Lett. 12:6684 (2021) https://pubs.acs.org/doi/full/10.1021/acs.jpclett.1c01607

Regy RM, Zheng W, and Mittal J. Using a sequence-specific coarse-grained model for studying protein liquid–liquid phase separation.  Methods Enzymol. 646:1 (2021) https://www.sciencedirect.com/science/article/pii/S0076687920302846

Zheng W*, Dignon GL*, Jovic N, Xu X, Regy RM, Fawzi NL, Kim YC, Best RB, and Mittal J. Molecular Details of Protein Condensates Probed by Microsecond Long Atomistic Simulations.  J. Phys. Chem. B 124:11671 (2020) https://pubs.acs.org/doi/abs/10.1021/acs.jpcb.0c10489

Regy RM, Dignon GL, Zheng W, Kim YC, and Mittal J. Sequence dependent phase separation of protein-polynucleotide mixtures elucidated using molecular simulations.  Nucleic Acids Res. 48:12593 (2020) https://academic.oup.com/nar/article/48/22/12593/6017354

Zheng W, Dignon G, Brown M, Kim YC, and Mittal J. Hydropathy Patterning Complements Charge Patterning to Describe Conformational Preferences of Disordered Proteins.  J. Phys. Chem. Lett. 11:3408 (2020) https://pubs.acs.org/doi/abs/10.1021/acs.jpclett.0c00288

Vancraenenbroeck R, Harel YS, Zheng W, and Hofmann H. Polymer effects modulate binding affinities in disordered proteins.  Proc. Natl. Acad. Sci. USA 116:19506 (2019) https://doi.org/10.1073/pnas.1904997116

Zheng W, Chung HS. Single-molecule fluorescence studies of IDPs and IDRs. Intrinsically Disordered Proteins: Dynamics, Binding, and Function 93:136 (2019) https://www.sciencedirect.com/science/article/pii/B9780128163481000041

Dignon G*, Zheng W*, Kim YC, and Mittal J. Temperature-Controlled Liquid–Liquid Phase Separation of Disordered Proteins. ACS Cent. Sci. 5:821 (2019) https://pubs.acs.org/doi/abs/10.1021/acscentsci.9b00102

Zerze GH, Zheng W, Best RB, and Mittal J. Evolution of All-atom Protein Force Fields to Improve Local and Global Properties. J. Phys. Chem. Lett. 10:2227 (2019) https://pubs.acs.org/doi/abs/10.1021/acs.jpclett.9b00850

Dignon G, Zheng W, and Mittal J. Simulation methods for liquid–liquid phase separation of disordered proteins. Curr. Opin. Chem. Eng. 23:92 (2019) https://www.sciencedirect.com/science/article/pii/S2211339818300807

Peng Y, Cao S, Kiselar J, Xiao X, Du Z, Hsieh A, Ko S, Chen Y, Agrawal P, Zheng W, Shi W, Jiang W, Yang L, Chance M, Surewicz W, Buck M and Yang S. A metastable contact and structural disorder in the estrogen receptor transactivation domain. Structure 27:229 (2019) https://www.sciencedirect.com/science/article/pii/S0969212618303873

Holmstrom ED, Holla A, Zheng W, Nettels D, Best RB and Schuler B. Accurate Transfer Efficiencies, Distance Distributions, and Ensembles of Unfolded and Intrinsically Disordered Proteins From Single-Molecule FRET. Methods in Enzymology-Intrinsically Disordered Proteins 611:287-325 (2018) https://www.sciencedirect.com/bookseries/methods-in-enzymology/vol/611/suppl/C

Zheng W, Hofmann H, Schuler B, and Best RB. Origin of internal friction in disordered proteins depends on solvent quality. J. Phys. Chem. B 122:11478 (2018) https://pubs.acs.org/doi/abs/10.1021/acs.jpcb.8b07425

Dignon G*, Zheng W*, Kim YC, Best RB, and Mittal J. Relation between Single-molecule Properties and Phase Behavior of Intrinsically Disordered Proteins. Proc. Natl. Acad. Sci. USA 115:9929 (2018) http://www.pnas.org/content/115/40/9929

Best RB, Zheng W, Borgia A, Buholzer K, Borgia MB, Hofmann H, Soranno A, Nettels D, Gast K, Grishaev A and Schuler B. Comment on “Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water”.  Science 361:eaar7101 (2018) http://science.sciencemag.org/content/361/6405/eaar7101

Zheng W, and Best RB. An Extended Guinier Analysis for Intrinsically Disordered Proteins. J. Mol. Biol. 16:2540 (2018) https://www.sciencedirect.com/science/article/pii/S0022283618301359

Zheng W, Zerze G, Borgia A, Mittal J, Schuler B and Best RB. Inferring properties of disordered chains from FRET transfer efficiencies. J. Chem. Phys. 148:123329 (2018) JCP 2018 Editors’ Choice http://aip.scitation.org/doi/full/10.1063/1.5025418

Dignon G*, Zheng W*, Kim YC, Best RB, and Mittal J. Sequence determinants of protein phase behavior from a coarse-grained model. PLOS Comput. Biol. 14:e1005941 (2018) https://doi.org/10.1371/journal.pcbi.1005941.

Monahan Z, Ryan VH, Janke AM, Burke KA, Zerze GH, O’Meally R, Dignon GL, Conicella AE, Zheng W, Best RB, Cole RN, Mittal J, and Shewmaker F.  Phosphorylation of the FUS low-complexity domain disrupts phase separation, aggregation, and toxicity.  EMBO J. e201696394 (2017)

Borgia A*, Zheng W*, Buholzer K, Borgia M, Schuler A, Hofmann H, Soranno A, Nettels D, Gast K, Grishaev A, Best RB and Schuler B. Consistent View of Polypeptide Chain Expansion in Chemical Denaturants from Multiple Experimental Methods.  J. Am. Chem. Soc. 138:11714 (2016)

Zheng W, Borgia A, Buholzer K, Grishaev A, Schuler B and Best RB.  Probing the Action of Chemical Denaturant on an Intrinsically Disordered Protein by Simulation and Experiment.  J. Am. Chem. Soc. 138:11702 (2016)

Zheng W, De Sancho D, and Best RB.  Modulation of folding internal friction by local and global barrier heights.  J. Phys. Chem. Lett. 6:1028 (2016)

Zheng W and Best RB.  Reduction of all-atom folding dynamics to one-dimensional diffusion. J. Phys. Chem. B, 119:15247 (2015)

Zheng W, Borgia A, Borgia MB, Schuler B and Best RB.  Empirical optimization of interactions between proteins and chemical denaturants in molecular simulations.  J. Chem. Theory Comput. 11:5543 (2015)

Zheng W, De Sancho D, Hoppe T and Best RB. Dependence of internal friction on folding mechanism.  J. Am. Chem. Soc. 137:3283 (2015)

Cazade PA, Zheng W, Prada-Gracia D, Berezovska G, Rao F, Clementi C and Meuwly M.  A comparative analysis of clustering algorithms: O2 migration in truncated hemoglobin I from transition networks.  J. Chem. Phys. 142:025103 (2015)

Best RB, Zheng W and Mittal J.  Balanced protein-water interactions improve properties of disordered proteins and non-specific protein association.  J. Chem. Theory Comput. 10:5113 (2014)

Rohrdanz MA, Zheng W, Lambeth B and Clementi C. Mutliscale approach to the determination of the photoactive yellow protein signaling state ensemble.  PLOS Comput. Biol. 10:e1003797 (2014)

Sambasivan R, Zheng W, Burya J, Popp BV, Turro C, Clementi C and Ball Z.  A tripodal peptide ligand for asymmetric Rh(II) catalysis highlights unique features of on-bead catalyst development.  Chem. Sci. 5: 1401-1407 (2014)

Zheng W, Vargiu A, Rohrdanz MA, Carloni P and Clementi C.  Molecular recognition of DNA by ligands: Roughness and complexity of the free energy profile.  J. Chem. Phys. 139:145102 (2013)

Zheng W, Rohrdanz MA and Clementi C.  Rapid exploration of configuration space with Diffusion Map-directed Molecular Dynamics.  J. Phys. Chem. B 117:12769-12776 (2013)

Rohrdanz MA, Zheng W and Clementi C.  Discovering mountain passes via torchlight: methods for the definition of reaction coordinates and pathways in complex macromolecular reactions.  Annu. Rev. Phys. Chem. 64: 295-316 (2013)

Zheng W, Qi B, Rohrdanz MA, Caflisch A, Dinner AR and Clementi C.  Delineation of folding pathways of a β-sheet miniprotein. J. Phys. Chem. B 115:13065–13074 (2011)

Zheng W, Rohrdanz MA, Maggioni M and Clementi C.  Polymer reversal rate calculated via locally scaled diffusion map. J. Chem. Phys. 134:144109 (2011)

Rohrdanz MA, Zheng W, Maggioni M, Clementi C.  Determination of reaction coordinates via locally scaled diffusion map. J. Chem. Phys. 134:124116 (2011)

Zheng W, Fan D, Feng M and Wang Z.  The intrinsic load-resisting capacity of kinesin. Phys. Biol. 6:036002 (2009)

Fan D*, Zheng W*, Hou R, Li F and Wang Z.  Modeling motility of the kinesin dimer from molecular properties of individual monomers. Biochemistry 47:4733–4742 (2008)

Li D, Fan D, Zheng W, Le Y and Wang Z.  From molecular shuttles to directed procession of nanorings. Chem. Phys. 352:235–240 (2008)

Li D, Zheng W and Wang Z.  Periodic thermodynamics of laser-driven molecular motor. Chinese Phys. B 17:1916–1924 (2008)

Wang Z, Feng M, Zheng W, Fan D.  Kinesin is an evolutionarily fine-tuned molecular ratchet-and-pawl device of decisively locked direction. Biophys. J. 93:3363–3372 (2007)