(*Corresponding authors, †Authors with equal contributions)

42. “Frustrated microphase separation produces interfacial environment within biological condensates”, bioRxiv, DOI: 10.1101/ 2023. 03.30.534967, submitted.

41. Micropolarity governs the structural organization of biomolecular condensates”, bioRxiv, DOI: 10.1101/2023.03.30.534881, submitted.

40. “Installing excited state hydrogen bonds as a general strategy to control viscosity sensitivity of molecular rotor fluorophores”, in review.

39. “Nuclear bodies protect phase separated proteins from degradation in stressed proteome”, in review.

38. “A high-fidelity, fluorescence-based assay to visualize the cellular maintenance of proteostasis”, in revision.

37. “Protic state-dependent internal conversion governs the anti-solvatochromic behavior of rotationally constrained chalcones”, in revision.

36. “Lipid-binding GRP20 regulates RNA splicing and flower development”, in revision.

35. D. Shen, Q. Zhao, M. Wang, B. Zhong, W. Jin, Y. Huang, H. Jin, B. Jing, W. Wan, X. Zhang, L. Zhang*, Y. Liu*, “Developing an affinity-based chemical proteomics method to in-situ capture amorphous aggregated proteome and profile its heterogeneity in stressed cells”, Anal. Chem., accepted.

34. Z. Zhang, L. Zhu, J. Feng, H. Zhang, X. Zhang, J. Sun, B. Tang*, “In situ monitoring of protein aggregation via clusteroluminescence”, Mat. Chem. Front., 2023, 7, 713-719.

33. Y. Bai, W. Wan, Y. Huang, J. Wu, L. Liu, B. Jing, J. Chen, X. Zhang*, Y. Liu*, “Tailoring the positive and negative solvatochromism for chalcone analogues to detect heterozygous protein co-aggregation”, ChemComm, 2023, 59, 4016 – 4019.

32. H. Feng, Q. Zhao, B. Zhang, H. Hu, M. Liu, K. Wu, X. Li, X. Zhang*, L. Zhang*, Y. Liu*, “Enabling photo-crosslinking and photo-sensitizing properties for synthetic fluorescent protein chromophores”, Angew. Chem. Int. Ed.,2022, 62(2), e202215215.

31. B. Shen, K. H. Jung, S. Ye, C. A. Hoelzel, C. H. Wolstenholme, H. Huang*, Y. Liu*, X. Zhang*, “A dual-functional BODIPY-based molecular rotor probe reveals different viscosity of protein aggregates in live cells”, Aggregate, (2022) e301.

30. L. Liu, Y. Huang, Y. Zhou, Y. Zhao, J. Qia, X. Zhang*, B. Shen*, “Fluorogenic toolbox for visualizing protein aggregation: From designing principles to biological application”, Trends in Anal. Chem., 157 (2022) 116764.

29. L. Wang, C-H Hsiung, X. Liu, S. Wang, A. Loredo, X. Zhang*, H. Xiao*, “Xanthone-based solvatochromic fluorophores for quantifying micropolarity of protein aggregates”, Chem. Sci., 13 (2022) 12540.

28. E. Pinho Melo*, T. Konno, I. Farace, M. Ali Awadelkareem, L. R. Skov, F. Teodoro, T. P. Sancho, A. W. Paton, J. C. Paton, M. Fares, P. M. R. Paulo, X. Zhang, E. Avezov*,Stress-induced protein disaggregation in the Endoplasmic Reticulum catalysed by BiP”, Nat. Comm., 13 (2022), 2501.

27. S. Ye, Y. Tang, X. Zhang*, “Principles, modulation and applications of fluorescent protein chromophores”, Chem Phys Rev, 3 (2022), 011308.

26. S. Ye, C.-H. Hsiung, Y. Tang, X. Zhang*, “Visualize the multi-step process of protein aggregation in live cells”, Acc. Chem. Res., 55 (2022), 381–390.

25. W. Dion, H. Ballance, J. Lee, Y. Pan, S. Irfan, C. Edwards, M. Sun, J. Zhang, X. Zhang, S. Liu, B. Zhu*, Four-dimensional nuclear speckle phase separation dynamics regulate proteostasis", Science Adv., 8 (2022), eabl4150.

24. Y. Jiang, C. Chen, L. N. Randolph, S. Ye, X. Zhang, X. Bao*, X. Lian*, “Generation of pancreatic progenitors from human pluripotent stem cells by small molecules”, Stem Cell Rep., 16(2021), 2395-2409.

23 S. Tang*, W. Wang and X. Zhang*, “Direct visualization and profiling of protein misfolding and aggregation in live cells”, Curr. Opin. Chem. Biol., 64 (2021), 116-123.

22. G. C. Carter, C. Hsiung, L. W. Simpson, H. Yang and X. Zhang*, “N-terminal domain of TDP43 enhances liquid-liquid phase separation of globular proteins“, J. Mol. Biol., 433 (2021), 166948.        

21. S. Tang, S. Ye and X. Zhang*, “When aggregation-induced emission meets protein aggregates”, Nat. Sci. Rev., Volume 8, Issue 6, 2021, nwab013.

20. S. Ye, H. Zhang, J. Fei, C. Wolstenholme and X. Zhang*, “A general strategy to control viscosity sensitivity of molecular rotor-based fluorophores”, Angew. Chem. Int. Ed., 60 (2021), 1339-1346.                

19. C.H. Wolstenholme, H. Hu, S. Ye, B.E. Funk, D. Jain, C. -H. Hsiung, G. Ning, Y. Liu*, X. Li* and X. Zhang*, “AggFluor: Fluorogenic toolbox enables direct visualization of the multi-step protein aggregation process in live cells”, J. Am. Chem. Soc., 142 (2020), 17515–17523.(highlighted by JACS Spotlights, Protein Aggregation: It’s a Process)                  

18. C.A. Hoelzel and X. Zhang*, “Visualizing and manipulating biological processes using HaloTag and SNAP-Tag technologies“, ChemBioChem, 21 (2020), 1935-1946.                            

17. K.H. Jung and X. Zhang*, “Fluorogenic detection of protein aggregates in live cells using the AggTag method“, Methods Enzymol., 639 (2020), 1-22.                            

16. C.A. Hoelzel, H. Hu, C.H. Wolstenholme, B.A. Karim, K.T. Munson, K.H. Jung, H. Zhang, Y. Liu, H.P. Yennawar, J.B. Asbury, X. Li*, X. Zhang*,“A general strategy to enhance donor-acceptor molecules using solvent-excluding substituents“, Angew. Chem. Int. Ed., 59 (2020), 4785-4792.                            

15. S.H. Kim, Y. Liu, C. Hoelzel, X. Zhang* and T.-H. Lee*, “Super-resolution optical lithography with DNA“, ACS Nano Letter, 19 (2019), 6035-6042.                           

14. K.H. Jung, S.F. Kim, Y. Liu and X. Zhang*, “A fluorogenic AggTag method based on Halo- and SNAP-tag to simultaneously detect the aggregation of two proteins in live cells“, ChemBioChem, 20 (2019), 1078-1087. 

13. K.H. Jung, M. Fares, L.S. Grainger, C.H. Wolstenholme, A. Hou, Y. Liu and X. Zhang*, “A SNAP-tag fluorogenic probe mimicking the chromophore of the red fluorescent protein Kaede“, Org. Biomol. Chem., 17 (2019), 1906-1915. 

12. Y. Liu, M. Fares and X. Zhang*, “Monitoring proteome stress in live cells using HaloTag-based fluorogenic sensor”, Methods Mol. Biol., 1873 (2019), 171-182.                             

11. M. Fares and X. Zhang*, “Quantification of cellular proteostasis in live cells by fluorogenic assay using the AgHalo sensor, Curr. Protoc. Chem. Biol., 2018:e58.

10. H. Hu, C.H. Wolstenholme, X. Zhang* and X.S. Li*, “Inverted solvatochromic stokes shift in GFP-like chromophores with extended conjugation“, Chin. J. Chem. Phys., 31 (2018), 599-607.                            

9. Y. Liu, K. Miao, Y. Li, M. Fares, S. Chen and X. Zhang* “A HaloTag-based multi-color fluorogenic sensor visualizes and quantifies proteome stress in live cells using solvatochromic and molecular rotor-based fluorophores“, Biochemistry, 57 (2018), 4663-4674. 

8. B.I. Leach, X. Zhang, J.W. Kelly, H.J. Dyson and P.E. Wright*, “NMR measurements reveal the structural basis of transthyretin destabilization by pathogenic mutations“, Biochemistry, 57 (2018), 4421-4430.

7. Y. Liu, C.H. Wolstenholme, G. Carter, H. Liu, H. Hu, L.S. Grainger, K. Miao, M. Fares, C.A. Hoelzel, H. Yennawar, G. Ning, M. Du, L. Bai, X. Li and X. Zhang*, “Modulation of fluorescent protein chromophores to detect protein aggregation with turn-on fluorescence“, J. Am. Chem. Soc., 140 (2018), 7381-7384.                                                           

6. A. Pedley, G. Karras, X. Zhang, S. Lindquist and S. Benkovic*, “Role of HSP90 in the regulation of de novo purine biosynthesis“, Biochemistry, 57 (2018), 3217-3221.

5. X. Li, T. Wang, P. Duan, M. Baldini, H. Huang, B. Chen, S. Juhl, D. Koeplinger, V. Crespi, K. Schmidt-Rohr, R. Hoffmann, N. Alem, M. Guthrie, X. Zhang and J. Badding*, “Carbon nitride nanothread crystals derived from pyridine”, J. Am. Chem. Soc., 140 (2018), 4969-4972.                                                                                                                     

4. Y. Liu and X. Zhang*, “Heat shock protein reports on proteome stress”, Biotechnology J, 13 (2018), 1800039.                            

3. M. Fares, Y. Li, Y. Liu, K. Miao, Z. Gao, Y. Zhai and X. Zhang*, “A molecular rotor-based Halo-tag ligand enables a fluorogenic proteome stress sensor to detect protein misfolding in mildly stressed proteome“, Bioconjutate Chem., 29 (2018), 215-224.             

2. Y. Liu, M. Fares, N. P. Dunham, Z. Gao, K. Miao, X. Jiang, S. S. Bollinger, A. K. Boal and X. Zhang*, “AgHalo: A facile fluorogenic sensor to detect drug induced proteome stress“, Angew. Chem. Int. Ed., 56 (2017), 8672-8676.                                                         

1. Y. Liu, K. Miao, N.P. Dunham, H. Liu, M. Fares, A.B. Boal, X. Li, X. Zhang*,  “The cation-π interaction enables a Halo-Tag fluorogenic probe for fast no-wash live cell imaging and gel-free protein quantification“, Biochemistry, 56 (2017), 1585-1595, (ACS Editor’s Choice). Featured by Viewpoint in Biochemistry.                            

From Scripps and Caltech:

36. Y. Liu, X. Zhang, W.T. Chen, Y.L. Tan, J.W. Kelly*, “Fluorescence turn-on folding sensor to monitor proteome stress in live cells”, J. Am. Chem. Soc., 2015, 137(35), 11303-11311. (co-first authors)

35. Y.H. Cho, X. Zhang, Y. Liu, K. Fayer, D.L. Powers, J.W. Kelly, L. Gierasch*., E.T. Powers*, “Individual and collective contributions of chaperonin and degradation to protein homeostasis in E. coli”, Cell Reports, 2015, 11(2), 321-33.

34. Y. Liu, Y.L. Tan, X. Zhang*, G. Bhabha, D. Ekiert, J.C. Genereux, Y.H. Cho, Y. Kipnis, S. Bjelic, D. Baker, J.W. Kelly*, “Small molecule probes to quantify the functional fraction of a specific protein in a cell with minimal folding equilibrium shifts”, Proc. Natl. Acad. Sci. (USA), 2014,111 (12),  4449-54.

33. X. Zhang, Y. Liu, J.C. Genereux, C. Nolan, M. Singh, J.W. Kelly*, “Heat-shock response transcriptional program enables high-yield and high-quality recombinant protein production in Escherichia coli”, ACS Chem. Biol., 2014, 9, 1945−1949. (ACS Editor’s Choice)

32. Y. Liu, X. Zhang, Y.L. Tan, G. Bhabha, D. Ekiert, Y. Kipnis, S. Bjelic, D. Baker, J.W. Kelly, “De novo designed enzymes as small molecule-regulated fluorescence imaging tags and fluorescent reporters”, J. Am. Chem. Soc., 2014, 136(38), 13102-13105. (co-first authors).

31. X. Zhang and J.W. Kelly*, “Chaperonins resculpt folding free energy landscapes to avoid kinetic traps and accelerate protein folding” J. Mol. Biol., 2014, 426(15), 2736-8.

30. X. Zhang, S. Shan*, “Fidelity of co-translational protein targeting by the signal recognition particle”, Ann. Rev. Biophysics, 2014, 43, 381-408.

29. D. Akopian, K. Shen, X. Zhang, S. Shan*, “Signal recognition particle: An essential targeting machine”, Ann. Rev. Biochemistry, 2013, 82, 693-721. (*co-first authors listed alphabetically)

28. X. Li*, X. Zhang, A.R. Ladiwala, D. Du, J. Yadav, P. Tessier, P. Wright, J.W. Kelly, and J. Buxbaum*, “Mechanism of transthyretin inhibition of β-amyloid aggregation in vitro”, J. Neuroscience, 2013, 33(50), 19423-33.

27. Ottilie von Loeffelholz, K. Knoops, A. Ariosa, X. Zhang, M. Karuppasamy, K. Huard, G. Schoehn, I. Berger, S. Shan*, C. Schaffitzel*, “Structural basis of signal sequence surveillance and selection by the SRP-FtsY complex”, Nat. Struct. Mol. Biol.2013, 20, 604-610.

26. X. Liu, W. Wei, Q. Yuan, X. Zhang, N. Li, Y. Du, G. Ma, C. Yan, D. Ma*, “Apoferritin–CeO2 nano-truffle that has excellent artificial redox enzyme activity”, Chem. Comm., 2012, 48, 3155-3157.

25. X. Zhang, V.Q. Lam, Y. Mou, T. Kimura, J. Chung, S. Chandrasekar, J.R. Winkler, S.L. Mayo, S. Shan*, “Direct visualization reveals dynamics of a transient intermediate during protein assembly”, Proc. Natl. Acad. Sci. (USA), 2011, 108 (16), 6450-55.

24. K. Shen, X. Zhang, S. Shan, “Synergistic actions between the SRP RNA and translating ribosome allow efficient delivery of the correct cargos during co-translational protein targeting”, RNA, 2011, 17(5), 892-902.

23. M.J. Yang, X. Zhang*, “Molecular dynamics simulations reveal structural coordination of Ffh-FtsY heterodimer towards GTPase activation”, Proteins: Struc., Funct., Bioinf., 2011, 79 (6), 1774-85. 

22. M.J. Yang, X.Q. Pang, X. Zhang, K.L. Han*, “Molecular dynamics simulation reveals preorganization of the Chloroplast FtsY towards complex formation induced by GTP-binding”, J. Struct. Biol., 2011, 173(1), 57-66.

21. X. Zhang, R. Rashid, K. Wang, S. Shan*, “Sequential checkpoints govern substrate selection during co-translational protein targeting”, Science, 2010, 328 (5979), 757-60.

20. M.J. Yang, X. Zhang, K.L. Han*, “Molecular dynamics simulation of SRP GTPases: towards an understanding of complex formation from equilibrium fluctuations”, Proteins: Struc., Funct., Bioinf., 2010, 78(10), 2222-37.

19. X. Zhang, C. Schaffitzel, N. Ban, S. Shan*, “Multiple conformational switches in a GTPase complex control co-translational protein targeting”, Proc. Natl. Acad. Sci. (USA),2009, 106 (6), 1754-59.

18. S. Shan*, S. L. Schmid, X. Zhang*, “Signal recognition particle (SRP) and SRP receptor: A new paradigm for multi-state regulatory GTPases”, Biochemistry, 2009, 48(29), 6696–6704.

17. E.L. Wu, K. Wong, X. Zhang, K.L. Han*, J.L. Gao*, “Determination of the structure form of the fourth ligand of zinc in acutolysin a using combined quantum mechanical and molecular mechanical simulation”, J. Phys. Chem. B2009, 113(8), 2477–2485.

16. X. Zhang, S. Kung, S. Shan*, “Demonstration of a multistep mechanism for assembly of the SRP•SRP receptor complex: Implications for the catalytic role of SRP RNA”, J. Mol. Biol., 2008, 381(3), 581-93.

15. X. Zhang and K.L. Han, “High-order symplectic integration in quasi-classical trajectory simulation: Case study for O(1D)+H2, Int. J. Quant. Chem., 2006, 106 (8), 1815-19.

14. T.S. Chu, X. Zhang, L.P. Ju, L. Yao, K.L. Han*, M.L. Wang, J.Z.H. Zhang*, “First principles quantum dynamics study reveals subtle resonance in polyatomic reaction: The case of F+CH4 → HF+CH3 ”, Chem. Phys. Lett., 2006, 424 (4-6), 243-46.

13. X.F. Chen, X. Zhang, K.L. Han*, A.J.C. Varandas*, “ab initio study of the H+ClONO2 reaction, Chem. Phys. Lett., 2006, 421 (4-6), 453-59.

12. L.P. Ju, T.X. Xie, X. Zhang, K.L. Han*, “A modified potential energy surface for the C2H+H2↔ C2H2+H reaction and a theoretical study on its rate constants, Chem. Phys. Lett., 2005, 409 (4-6), 249-54.

11. T.S. Chu, X. Zhang, K.L. Han*, “A quantum wave-packet study of intersystem crossing effects in the O(3P, 1D)+H2 reaction, J. Chem. Phys., 2005, 122 (21), 214301-6.

10. G.H Yang, L. Yao, X. Zhang, Q.T. Meng, K.L. Han*, “Theoretical study of the mechanism for spin-forbidden quenching process O(1D)+CO2 (1Sg+) → O(3P)+CO2 (1Sg+)”, Int. J. Quant. Chem., 2005, 105 (2), 154-159.

9. C.L. Yang*, X. Zhang, K.L. Han, “Theoretical study on analytical potential function and spectroscopic parameters for CaF molecule, J. Mol. Struct-Theochem, 2004, 678 (1-3), 183-88.

8. C.L. Yang*, X. Zhang, K.L. Han, “ab initio geometries, electronic structures of MgB2 molecule, J. Mol. Struct-Theochem, 2004, 677 (1-3), 11-14.

7. C.L. Yang*, X. Zhang, K.L. Han, “Analytical potential energy function and spectroscopic parameters for the ground and excited states of NaH”, J. Mol. Struct-Theochem, 2004, 676 (1-3), 209-13.

6. G.H. Yang*, X. Zhang, Q.T. Meng, K.L. Han, “Theoretical studies on the intermediate complex mechanism of the energy transfer reaction of O(1D)+CO2 (1Sg+) → O(3P)+CO2 (1Sg+)”, Chem. J. Chin. Univ., 2004, 25 (4), 689-92.

5. G.H. Yang, Q.T. Meng, X. Zhang, K.L. Han*, “Theoretical study on the formation mechanism of Iso-CH2l-Cl”, Int. J. Quant. Chem., 2004, 97 (2), 719-24.

4. X. Zhang, G.H. Yang, K.L. Han*, M.L. Wang, J.Z.H. Zhang, “Quantum dynamics study of isotope effect for H + CH4 reaction using the SVRT model, J. Chem. Phys., 2003, 118 (20), 9266-71.

3. C.L. Yang*, Y.J. Huang, X. Zhang, K.L. Han, “MRCI potential curve and analytical potential energy function of the ground state of H2”, J. Mol. Struct-Theochem, 2003, 625 (1-3), 289-93.

2. X. Zhang, K.L. Han, J.Z.H. Zhang, “SVRT calculation for bond-selective reaction H+HOD → H2+OD, HD+OH, J. Chem. Phys., 2002, 116 (23), 10197-200.

1. X. Zhang, T.X. Xie, M.Y. Zhao, K.L. Han*, “Quasiclassical trajectory simulation of the chemical reaction Ba+HF (n, J) → BaF (n‘, J‘)+H”, Chin. J. Chem. Phys., 2002, 15 (3), 169-74.

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