Selected Publications

Zhang S^#, Zou S^#, Yin D, Zhao L, Finley D, Wu Z, Mao Y*. USP14-regulated allostery of the human proteasome by time-resolved cryo-EM. Nature 2022; 605: 567-574. https://doi.org/10.1038/s41586-022-04671-8

Zhang S^#, Wang K^#, Wang WL^#, Nguyen HT, Chen S, Lu M, Go EP, Ding H, Steinbock RT, Desaire H, Kappes JC, Sodroski J*, Mao Y*. Asymmetric structures and conformational plasticity of the uncleaved full-length human immunodeficiency virus (HIV-1) envelope glycoprotein trimer. J. Virol. 2021; 95: e00529-21. https://doi.org/10.1128/JVI.00529-21

Dong Y, Zhang S, Wu Z, Li X, Wang WL, Zhu Y, Stoilova-McPhie S, Lu Y, Finley D, Mao Y*. Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome. Nature 565, 49-55 (2019). doi: 10.1038/s41586-018-0736-4.

2018_Nature-s41586-018-0736-4.pdf

Sharif H, Wang L, Wang WL, Magupalli VG, Andreeva L, Qiao Q, Hauenstein AV, Wu Z, Nunez G, Mao Y*, Wu H*. Structural mechanism for NEK7-licensed NLRP3 inflammasome activation. Nature 570, 338–343 (2019). doi: 10.1038/s41586-019-1295-z.

2019_Nature-s41586-019-1295-z.pdf

Zhu Y, Wang WL, Yu D, Ouyang Q, Lu Y*, Mao Y*. Structural mechanism for nucleotide-driven remodeling of the AAA-ATPase unfoldase in the activated human 26S proteasome. Nat. Commun. 9, 1360 (2018). doi: 10.1038/s41467-018-03785-w.

Dong Y, Chen S, Zhang S, Sodroski J, Yang Z, Liu D, Mao Y*. Folding DNA into a lipid-conjugated nanobarrel for controlled reconstitution of membrane proteins. Angew. Chem. Int. Ed. 57, 2072-2076 (2018). doi:10.1002/anie.201710147.

2018_Angewandte_Chemie_International_Edition-Dong.pdf

Lu Y, Wu J, Dong Y, Chen S, Sun S, Ma YB, Ouyang Q, Finley D, Kirschner MW*, Mao Y*. Conformational landscape of the p28-bound human proteasome regulatory particle. Mol. Cell 67, 322-333.e6 (2017). doi: 10.1016/j.molcel.2017.06.007.

2017_Mol_Cell_Lu_Wu.pdf

Zhu Y, Ouyang Q, Mao Y*. A deep convolutional neural network approach to single-particle recognition in cryo-electron microscopy. BMC Bioinformatics 18, 348 (2017). doi: 10.1186/s12859-017-1757-y.

Wu J, Ma Y, Congdon C, Brett B, Chen S, Ouyang Q, Mao Y*. Massively parallel unsupervised single-particle cryo-EM data clustering via statistical manifold learning. PLoS ONE 12, e0182130 (2017). doi: 10.1371/journal.pone.0182130.

Chen S, Wu J, Lu Y, Ma YB, Lee BH, Yu Z, Ouyang Q, Finley D, Kirschner MW*, Mao Y*. Structural basis for dynamic regulation of the human 26S proteasome. Proc. Natl. Acad. Sci. USA 113, 12991-12996 (2016). doi: 10.1073/pnas.1614614113.

2016_PNAS_Chen.pdf

Zhang L, Chen S, Ruan J, Wu J, Tong AB, Yin Q, Li Y, David L, Lu A, Wang WL, Marks C, Ouyang Q, Zhang X, Mao Y*, Wu H*. Cryo-EM structure of the activated NAIP2-NLRC4 inflammasome reveals nucleated polymerization. Science 350, 404-409 (2015). doi: 10.1126/science.aac5789.

2015_Science_Zhang.pdf

Mao Y*, Wang L, Gu C, Herschhorn A, Xiang SH, Haim H, Yang X, Sodroski J*. Subunit organization of the membrane-bound HIV-1 envelope glycoprotein trimer. Nat. Struct. Mol. Biol. 19, 893-899 (2012). doi: 10.1038/nsmb.2351.

2012_NSMB_Mao.pdf

Mao Y*, Zhang J. Understanding thermodynamic competitivity between biopolymer folding and misfolding under large-scale intermolecular interactions. J. Am. Chem. Soc. 134, 631-639 (2012). doi: 10.1021/ja209534c.

2012_JACS_Mao.pdf

Mao Y, Chang S, Yang S, Ouyang Q*, Jiang L*. Tunable non-equilibrium gating of flexible DNA nanochannels in response to transport flux. Nat. Nanotechnol. 2, 366-371 (2007). doi: 10.1038/nnano.2007.

2007_Nature_Nano_Mao.pdf

2022

Zhang S^#, Zou S^#, Yin D, Zhao L, Finley D, Wu Z, Mao Y*. USP14-regulated allostery of the human proteasome by time-resolved cryo-EM. Nature 2022; 605: 567-574. https://doi.org/10.1038/s41586-022-04671-8

Mao Y, Zhang S. Control of human protein-degradation machinery revealed. Nature 2022; https://doi.org/10.1038/d41586-022-01144-w

2021

Zhang S^#, Wang K^#, Wang WL^#, Nguyen HT, Chen S, Lu M, Go EP, Ding H, Steinbock RT, Desaire H, Kappes JC, Sodroski J*, Mao Y*. Asymmetric structures and conformational plasticity of the uncleaved full-length human immunodeficiency virus (HIV-1) envelope glycoprotein trimer. J. Virol. 2021; 95: e00529-21. 

https://doi.org/10.1128/JVI.00529-21

Mao Y. Structure, dynamics and function of the 26S proteasome. In: Harris J.R., Marles-Wright J. (eds) Macromolecular Protein Complexes III: Structure and Function. Subcell. Biochem. 2021; 96: 1-151. https://doi.org/10.1007/978-3-030-58971-4_1

2020

Zhang S, Mao Y*. AAA+ ATPases in protein degradation: structures, functions and mechanisms. Biomolecules 2020; 10: 629. https://doi.org/10.3390/biom10040629

2019

Sharif H, Wang L, Wang WL, Magupalli VG, Andreeva L, Qiao Q, Hauenstein AV, Wu Z, Nunez G, Mao Y*, Wu H*. Structural mechanism for NEK7-licensed NLRP3 inflammasome activation. Nature 570, 338–343 (2019). doi: 10.1038/s41586-019-1295-z.

Dong Y, Mao Y. DNA origami as scaffolds for self-assembly of lipids and proteins. ChemBioChem (2019). doi: 10.1002/cbic.201900073.

Wang WL, Yu Z, Castillo-Menendez LR, Sodroski J, Mao Y*. Robustness of signal detection in cryo-electron microscopy via a bi-objective-function approach. BMC Bioinformatics 20, 169 (2019). doi: 10.1186/s12859-019-2714-8.

Dong Y, Zhang S, Wu Z, Li X, Wang WL, Zhu Y, Stoilova-McPhie S, Lu Y, Finley D, Mao Y*. Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome. Nature 565, 49-55 (2019). doi: 10.1038/s41586-018-0736-4.

2018

Zhu Y, Wang WL, Yu D, Ouyang Q, Lu Y*, Mao Y*. Structural mechanism for nucleotide-driven remodeling of the AAA-ATPase unfoldase in the activated human 26S proteasome. Nat. Commun. 9, 1360 (2018). doi: 10.1038/s41467-018-03785-w.

Dong Y, Chen S, Zhang S, Sodroski J, Yang Z, Liu D, Mao Y*. Folding DNA into a lipid-conjugated nanobarrel for controlled reconstitution of membrane proteins. Angew. Chem. Int. Ed. 57, 2072-2076 (2018). doi:10.1002/anie.201710147.

2017

Lu Y, Wu J, Dong Y, Chen S, Sun S, Ma YB, Ouyang Q, Finley D, Kirschner MW*, Mao Y*. Conformational landscape of the p28-bound human proteasome regulatory particle. Mol. Cell 67, 322-333.e6 (2017). doi: 10.1016/j.molcel.2017.06.007.2017_Mol_Cell_Lu_Wu.pdf

Wu J, Ma Y, Congdon C, Brett B, Chen S, Ouyang Q, Mao Y*. Massively parallel unsupervised single-particle cryo-EM data clustering via statistical manifold learning. PLoS ONE 12, e0182130 (2017). doi: 10.1371/journal.pone.0182130.

Zhu Y, Ouyang Q, Mao Y*. A deep convolutional neural network approach to single-particle recognition in cryo-electron microscopy. BMC Bioinformatics 18, 348 (2017). doi: 10.1186/s12859-017-1757-y.

Sharif H, Yang L, Dong Y, Dong L, Wang WL, Mao Y, Wu H. Cryo-EM structure of the DNA-PK holoenzyme. Proc. Natl. Acad. Sci. USA 114, 7367-7372 (2017). doi: 10.1073/pnas.17073861142017_PNAS_Sharif.pdf

Pacheco B, Alsahafi N, Debbeche O, Prevost J, Ding S, Chapleau JP, Hershhorn A, Madani N, Princiotto A, Melillo B, Gu C, Zeng X, Mao Y, Smith III A, Sodroski J, Finzi A. Residues in the gp41 ectodomain regulate HIV-1 envelope glycoprotein conformational transitions induced by gp120-directed inhibitors. J. Virol. 91, e02219-16 (2017). Download2017_J_Virol_Pacheco.pdf

Nguyen HT, Madani N, Ding H, Elder E, Princiotto A, Gu C, Darby P, Alin J, Herschhorn A, Kappes JC, Mao Y, Sodroski JG. Evaluation of the contribution of the transmembrane region to the ectodomain conformation of the human immunodeficiency virus (HIV-1) envelope glycoprotein. Virol. J. 14, 33 (2017). Download2017_Virol_J_Nguyen.pdf

2016

Chen S, Wu J, Lu Y, Ma YB, Lee BH, Yu Z, Ouyang Q, Finley D, Kirschner MW*, Mao Y*. Structural basis for dynamic regulation of the human 26S proteasome. Proc. Natl. Acad. Sci. USA 113, 12991-12996 (2016). doi: 10.1073/pnas.1614614113.2016_PNAS_Chen.pdf

Xu Y, Wu J, Yin CC*, Mao Y*. Unsupervised cryo-EM data clustering through adaptively constrained K-means algorithm. PLoS ONE 11, e0167765 (2016). doi: 10.1371/journal.pone.0167765.

Lu A, Li Y, Schmidt FI, Yin Q, Chen S, Fu TM, Tong AB, Mao Y, Wu H. Molecular basis of caspase-1 polymerization and its inhibition by a new capping mechanism. Nat. Struct. Mol. Biol. 23, 416-425 (2016). doi: 10.1038/nsmb.31992016_NSMB_Lu.pdf

Mao Y. Chapter 3, Smart materials for protein-based nanoconstructions. Design, Fabrication, Properties and Applications of Smart and Advanced Materials. CRC Press, Taylor & Francis Group, Boca Raton, FL; pp. 53-89 (2016).

2015

Zhang L, Chen S, Ruan J, Wu J, Tong AB, Yin Q, Li Y, David L, Lu A, Wang WL, Marks C, Ouyang Q, Zhang X, Mao Y*, Wu H*. Cryo-EM structure of the activated NAIP2-NLRC4 inflammasome reveals nucleated polymerization. Science 350, 404-409 (2015). doi: 10.1126/science.aac5789.2015_Science_Zhang.pdf

Go EP, Herschhorn A, Gu C, Castillo-Menendez L, Zhang S, Mao Y, Chen H, Ding H, Wakefield JK, Hua D, Liao HX, Kappes JC, Sodroski J, Desaire H. Comparative analysis of the glycosylation profiles of membrane-anchored HIV-1 envelope glycoprotein trimers and soluble gp140. J. Virol. 89, 8245-8257 (2015). Download2015_J_Virol_Go.pdf

2011-2013

Mao Y*, Wang L, Gu C, Herschhorn A, Désormeaux A, Finzi A, Xiang SH, Sodroski JG*. Molecular architecture of the uncleaved HIV-1 envelope glycoprotein trimer. Proc. Natl. Acad. Sci. USA 110, 12438-12443 (2013). Download

2013_PNAS_Mao.pdf

Mao Y, Castillo-Menendez LR, Sodroski J. Validity of the cryo-electron microscopy structures of the HIV-1 envelope glycoprotein complex. Proc. Natl. Acad. Sci. USA 110, E4178-E4182 (2013). Download2013_PNAS_Letter.pdf

Bohl C, Bowder D, Thompson J, Abrahamyan L, Gonzalez-Ramirez S, Mao Y, Sodroski J, Wood C, Xiang SH. A twin-cysteine motif in the V2 region of gp120 is associated with SIV envelope trimer stabilization. PLoS One 8, e69406 (2013). Download

Désormeaux A, Coutu M, Medjahed H, Pacheco B, Herschhorn A, Gu C, Xiang SH, Mao Y, Sodroski J, Finzi A. The highly conserved layer-3 component of the HIV-1 gp120 inner domain is critical for CD4-required conformational transitions. J. Virol. 87, 2549-2562 (2013). Download

Mao Y*, Wang L, Gu C, Herschhorn A, Xiang SH, Haim H, Yang X, Sodroski J*. Subunit organization of the membrane-bound HIV-1 envelope glycoprotein trimer. Nat. Struct. Mol. Biol. 19, 893-899 (2012). Download

2012_NSMB_Mao.pdf

Mao Y*, Zhang J. Understanding thermodynamic competitivity between biopolymer folding and misfolding under large-scale intermolecular interactions. J. Am. Chem. Soc. 134, 631-639 (2012). Download2012_JACS_Mao.pdf

Mao Y*, Wang WL, Wei D, Kaxiras E, Sodroski JG*. Graphene structures at an extreme degree of buckling. ACS Nano 5, 1395-400 (2011). Download2011_ACS_Nano_Mao.pdf

Kar AK, Mao Y, Bird G, Walensky L, Sodroski J. Characterization of a core fragment of the rhesus monkey TRIM5a protein. BMC Biochem. 12, 1 (2011).

2007-2009

Mao Y, Sun Q, Wang X, Ouyang Q, Han L, Jiang L, Han D. In vivo nanomechanical imaging of blood-vessel tissues directly in mammals using atomic force microscopy. Appl. Phys. Lett. 95, 013704 (2009). Download

Betti A, Fiori G, Iannaccone G, Mao Y. Physical insights on graphene nanoribbon mobility through atomistic simulations. IEEE International Electron Devices Meeting (IEDM) doi: 10.1109/IEDM.2009.5424276 (2009).

Xia F, Guo W, Mao Y, Hou X, Xue J, Xia H, Wang L, Song Y, Ji H, Ouyang Q, Wang Y, Jiang L. Gating of single synthetic nanopores by proton-driven DNA molecular motors. J. Am. Chem. Soc. 130, 8345-8350 (2008). Download

2008_JACS_Xia.pdf

Mao Y, Luo C, Ouyang Q. Reversibly switchable DNA nanocompartment on surfaces: experiments, applications, and theory. Front. Phys. China 3, 72-87 (2008).

Mao Y, Chang S, Yang S, Ouyang Q, Jiang L. Tunable non-equilibrium gating of flexible DNA nanochannels in response to transport flux. Nat. Nanotechnol. 2, 366-371 (2007). Download2007_Nature_Nano_Mao.pdf

Mao Y, Liu D, Wang S, Luo S, Wang W, Yang Y, Ouyang Q, Jiang L. Alternating-electric-field-enhanced reversible switching of DNA nanocontainers with pH. Nucleic Acids Res. 35, e33 (2007).

2000-2006

Chang S, Mao Y, Luo C, Ouyang Q. Monte Carlo simulation of melting transition on DNA nanocompartment. J. Phys. Conf. Ser. 29, 18-26 (2006).

Mao Y, Luo C, Deng W, Jin G, Yu X, Zhang Z, Ouyang Q, Chen R, Yu D. Reversibly switchable DNA nanocompartment on surfaces. Nucleic Acids Res. 32, e144 (2004).

Mao Y, Luo C, Ouyang Q. Studies of temperature-dependent electronic transduction on DNA hairpin loop sensor. Nucleic Acids Res. 31, e108 (2003).

Xu J, Liu L, Mao Y, Li B. The realization of a fast and effective optimization method on atomic structure. J. Phys. Soc. Japan 71, 762-766 (2002).

Xu J, Liu L, Mao Y. Using an evolutionary algorithm based on cell-division operation to calculate ground-state energies of double-electron systems in magnetic fields. Chin. Phys. 10, 1118-1123 (2001).

Liu L, Zhao L, Mao Y, Xu D, Xu J, Li Y. Using an evolutionary algorithm to calculate the ground-state energy of double-electron atoms in a uniform magnetic field (B≤109G). Int. J. Mod. Phys. C 11, 183-194 (2000).

Publications in Chinese

Wu Z, Mao Y. Cryo-electron microscopy: A powerful tool to determine high-resolution structures of biological macromolecules. (Invited Review) Chin. Sci. Bulletin (科学通报) doi: 10.1360/N972017-01201 (2017).

Zhu Y, Zhang S, Mao Y. Cryo-electron microscopy revolutionizes molecular biophysics. (Invited Review) Physics （物理） 46, 76-83 (2017).

Luo C, Mao Y, Ouyang Q. DNA duplex membrane effect for the electrochemical detection of single-base DNA mutations. Acta Biophys. Sin. 21, 151-156 (2005).

Xu J, Liu L, Mao Y. Using a cellular evolutionary algorithm to study atomic structure. Chin. J. Atom. Mol. Phys. 18, 67-71 (2001).

Xu J, Liu L, Mao Y. Evolutionary solution of H- and He magnetic field. Chin. J. Comp. Phys. 18, 43-46 (2001).

Xu J, Liu L, Zhao L, Mao Y, Li Y. Using an evolutionary algorithm for calculating the ground-state energy of a double-electron system in a uniform magnetic field below 10+9G. Acta Phys. Sin. 49, 225-229 (2000).

Xu J, Liu L, Mao Y, et al. Magnetic field parameter optimization using an evolutionary algorithm. Chin. J. Atom. Mol. Phys. 17, 343-348 (2000).

Xu J, Liu L, Mao Y, Li Y. Cellular evolutionary algorithm: a new optimization method on ground-state energy of the atomic structure. Wuhan Univ. J. Nat. Sci. 5, 425-430 (2000).