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Yanxin Liu

Macromolecular Structure Group

Mission Bay, Genentech Hall, Room S414

University of California, San Francisco

600 16th Street

San Francisco, CA 94143

Home Department: Dept of Biochemistry and Biophysics, School of Medicine

Email Address: yanxin@msg.ucsf.edu

Education

• Ph.D. in Physics, University of Illinois at Urbana-Champaign, 2013
• M.S. in Physics, Florida International University, 2007
• B.S. in Applied Physics, Xi'an Jiaotong University, 2004

Research Interests

Protein Folding Highlights I, II, III		Motor Protein Highlights I, II		Virus Highlight

Publications

• Cryo-EM analysis of human mitochondrial Hsp90 in multiple tetrameric states.

Yanxin Liu, Ming Sun, Daniel Elnatan, Adam G. Larson, David A. Agard. BioRxiv, 2021.


• Cryo-EM reveals the dynamic interplay between mitochondrial Hsp90 and SdhB folding intermediates.

Yanxin Liu, Daniel Elnatan, Ming Sun, Alexander G. Myasnikov, David A. Agard. BioRxiv, 2021.


• Cryo-EM structures reveal a multistep mechanism of Hsp90 activation by co-chaperone Aha1.

Yanxin Liu, Ming Sun, Alexander G. Myasnikov, Daniel Elnatan, Nicolas Delaeter, Michael Nguyenquang, David A. Agard. BioRxiv, 2021.


• General and robust covalently linked graphene oxide affinity grids for high-resolution cryo-EM.

Feng Wang, Yanxin Liu, Zanlin Yu, Sam Li, Shengjie Feng, Yifan Cheng, and David A. Agard. Proceedings of the National Academy of Sciences, 117:24269-24273, 2020.


• The mitochondrial HSP90 paralog TRAP1 forms an OXPHOS-regulated tetramer and is involved in mitochondrial metabolic homeostasis.

Abhinav Joshi, Li Dai, Yanxin Liu, Jungsoon Lee, Nastaran Mohammadi Ghahhari, Gregory Segala, Kristin Beebe, Lisa M. Jenkins, Gaelyn C. Lyons, Lilia Bernasconi, Francis T. F. Tsai, David A. Agard, Len Neckers, Didier Picard. BMC Biology, 18:10, 2020.


• An ultrapotent synthetic nanobody neutralizes SARS-CoV-2 by stabilizing inactive Spike.

Michael Schoof, Bryan Faust, Reuben A. Saunders, Smriti Sangwan, Veronica Rezelj, Nick Hoppe, Morgane Boone, Christian B. Billesbølle, Cristina Puchades, Caleigh M. Azumaya, Huong T. Kratochvil, Marcell Zimanyi, Ishan Deshpande, Jiahao Liang, Sasha Dickinson, Henry C. Nguyen, Cynthia M. Chio, Gregory E. Merz, Michael C. Thompson, Devan Diwanji, Kaitlin Schaefer, Aditya A. Anand, Niv Dobzinski, Beth Shoshana Zha, Camille R. Simoneau, Kristoffer Leon, Kris M. White, Un Seng Chio, Meghna Gupta, Mingliang Jin, Fei Li, Yanxin Liu, Kaihua Zhang, David Bulkley, Ming Sun, Amber M. Smith, Alexandrea N. Rizo, Frank Moss, Axel F. Brilot, Sergei Pourmal, Raphael Trenker, Thomas Pospiech, Sayan Gupta, Benjamin Barsi-Rhyne, Vladislav Belyy, Andrew W. Barile-Hill, Silke Nock, Yuwei Liu, Nevan J. Krogan, Corie Y. Ralston, Danielle L. Swaney, Adolfo García-Sastre, Melanie Ott, Marco Vignuzzi, QCRG Structural Biology Consortium, Peter Walter, Aashish Mangli. Science, 370:1473-1479, 2020.


• Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms.

David E. Gordon, Joseph Hiatt, Mehdi Bouhaddou, Veronica V. Rezelj, Svenja Ulferts, Hannes Braberg, Alexander S. Jureka, Kirsten Obernier, Jeffrey Z. Guo, Jyoti Batra, Robyn M. Kaake, Andrew R. Weckstein, Tristan W. Owens, Meghna Gupta, Sergei Pourmal, Erron W. Titus, Merve Cakir, Margaret Soucheray, Michael McGregor, Zeynep Cakir, Gwendolyn Jang, Matthew J. O′Meara, Tia A. Tummino, Ziyang Zhang, Helene Foussard, Ajda Rojc, Yuan Zhou, Dmitry Kuchenov, Ruth Hüttenhain, Jiewei Xu, Manon Eckhardt, Danielle L. Swaney, Jacqueline M. Fabius, Manisha Ummadi, Beril Tutuncuoglu, Ujjwal Rathore, Maya Modak, Paige Haas, Kelsey M. Haas, Zun Zar Chi Naing, Ernst H. Pulido, Ying Shi, Inigo Barrio-Hernandez, Danish Memon, Eirini Petsalaki, Alistair Dunham, Miguel Correa Marrero, David Burke, Cassandra Koh, Thomas Vallet, Jesus A. Silvas, Caleigh M. Azumaya, Christian Billesbølle, Axel F. Brilot, Melody G. Campbell, Amy Diallo, Miles Sasha Dickinson, Devan Diwanji, Nadia Herrera, Nick Hoppe, Huong T. Kratochvil, Yanxin Liu, Gregory E. Merz, Michelle Moritz, Henry C. Nguyen, Carlos Nowotny, Cristina Puchades, Alexandrea N. Rizo, Ursula Schulze-Gahmen, Amber M. Smith, Ming Sun, Iris D. Young, Jianhua Zhao, Daniel Asarnow, Justin Biel, Alisa Bowen, Julian R. Braxton, Jen Chen, Cynthia M. Chio, Un Seng Chio, Ishan Deshpande, Loan Doan, Bryan Faust, Sebastian Flores, Mingliang Jin, Kate Kim, Victor L. Lam, Fei Li, Junrui Li, Yen-Li Li, Yang Li, Xi Liu, Megan Lo, Kyle E. Lopez, Arthur A. Melo, Frank R. Moss III, Phuong Nguyen, Joana Paulino, Komal Ishwar Pawar, Jessica K. Peters, Thomas H. Pospiech Jr., Maliheh Safari, Smriti Sangwan, Kaitlin Schaefer, Paul V. Thomas, Aye C. Thwin, Raphael Trenker, Eric Tse, Tsz Kin Martin Tsui, Feng Wang, Natalie Whitis, Zanlin Yu, Kaihua Zhang, Yang Zhang, Fengbo Zhou, Daniel Saltzberg, QCRG Structural Biology Consortium, Anthony J. Hodder, Amber S. Shun-Shion, Daniel M. Williams, Kris M. White, Romel Rosales, Thomas Kehrer, Lisa Miorin, Elena Moreno, Arvind H. Patel, Suzannah Rihn, Mir M. Khalid, Albert Vallejo-Gracia, Parinaz Fozouni, Camille R. Simoneau,Theodore L. Roth, David Wu, Mohd Anisul Karim, Maya Ghoussaini, Ian Dunham, Francesco Berardi, Sebastian Weigang, Maxime Chazal, Jisoo Park, James Logue, Marisa McGrath, Stuart Weston, Robert Haupt, C. James Hastie, Matthew Elliott, Fiona Brown, Kerry A. Burness, Elaine Reid, Mark Dorward, Clare Johnson, Stuart G. Wilkinson, Anna Geyer, Daniel M. Giesel, Carla Baillie, Samantha Raggett, Hannah Leech, Rachel Toth, Nicola Goodman, Kathleen C. Keough, Abigail L. Lind, Zoonomia Consortium, Reyna J. Klesh, Kafi R. Hemphill, Jared Carlson-Stevermer, Jennifer Oki, Kevin Holden, Travis Maures, Katherine S. Pollard, Andrej Sali, David A. Agard, Yifan Cheng, James S. Fraser, Adam Frost, Natalia Jura, Tanja Kortemme, Aashish Manglik, Daniel R. Southworth, Robert M. Stroud, Dario R. Alessi, Paul Davies, Matthew B. Frieman, Trey Ideker, Carmen Abate, Nolwenn Jouvenet, Georg Kochs, Brian Shoichet, Melanie Ott, Massimo Palmarini, Kevan M. Shokat, Adolfo García-Sastre, Jeremy A. Rassen, Robert Grosse, Oren S. Rosenberg, Kliment A. Verba, Christopher F. Basler, Marco Vignuzzi, Andrew A. Peden, Pedro Beltrao, Nevan J. Krogan. Science, 370:abe9403, 2020.


• Design of peptides that assemble into cross-&alpha amyloid-like structures.

Shao-Qing Zhang, Hai Huang, Junjiao Yang, Huong T. Kratochvil, Marco Lolicato, Yanxin Liu, Xiaokun Shu, Lijun Liu, William F. DeGrado. Nature Chemical Biology, 14:870-875, 2018.
Highlighted in News & Views.

• Symmetry broken and rebroken during the ATP hydrolysis cycle of the mitochondrial Hsp90 TRAP1.

Daniel Elnatan, Miguel Betegon, Yanxin Liu, Theresa Ramelot, Michael A. Kennedy, David A. Agard. eLife, 6:e25235, 2017.


• Atomic structure of Hsp90-Cdc37-Cdk4 reveals that Hsp90 traps and stabilizes an unfolded kinase.

Kliment A. Verba, Ray Yu-Ruei Wang, Akihiko Arakawa, Yanxin Liu, Mikako Shirouzu, Shigeyuki Yokoyama, David A. Agard. Science, 352:1542-1547, 2016.


• Comparing fast pressure jump and temperature jump protein folding experiments and simulations.

Anna Jean Wirth*, Yanxin Liu*, Maxim B. Prigozhin, Klaus Schulten, and Martin Gruebele. Journal of the American Chemical Society, 137:7152-7159, 2015.


• Stable small quantum dots for synaptic receptor tracking on live neurons.

En Cai, Pinghua Ge, Sang Hak Lee, Okunola Jeyifous, Yong Wang, Yanxin Liu, Katie M. Wilson, Sung Jun Lim, Michele A. Baird, John E. Stone, Kwan Young Lee, David G. Fernig, Michael W. Davidson, Hee Jung Chung, Klaus Schulten, Andrew M. Smith, William N. Green, Paul R. Selvin. Angewandte Chemie International Edition, 53:12484-12488, 2014.
Highlighted by the Senior Editer in Laser Focus World.

• Molecular insights into the membrane-associated phosphatidylinositol 4-kinase IIα

Qiangjun Zhou, Jiangmei Li, Hang Yu, Yujia Zhai, Zhen Gao, Yanxin Liu, Xiaoyun Pang, Lunfeng Zhang, Klaus Schulten, Fei Sun, and Chang Chen, Nature Communications, 5:3552, 2014.
Recommended by F1000Prime.


• Observation of complete pressure-jump protein refolding in molecular dynamics simulation and experiment.

Yanxin Liu, Maxim B. Prigozhin, Klaus Schulten, and Martin Gruebele. Journal of the American Chemical Society, 136:4265-4272, 2014.
Cover article and highlighted by the Editers in JACS Spotlights.

• Single molecule FRET reveals pore size and opening mechanism of a mechano-sensitive ion channel.

Yong Wang, Yanxin Liu, Hannah A. DeBerg, Takeshi Nomura, Melinda T. Hoffman, Paul R. Rohde, Klaus Schulten, Boris Martinac, and Paul R. Selvin. eLife, 3:e01834, 2014.
Highlighted in news stories at the UIUC Physics Department and at the NSF Center for the Physics of Living Cells.

• Flexible interwoven termini determine the thermal stability of thermosomes.

Kai Zhang, Li Wang, Yanxin Liu, Kwok-Yan Chan, Xiaoyun Pang, Klaus Schulten, Zhiyang Dong, and Fei Sun. Protein & Cell, 4:432-444, 2013.
Cover article

• Misplaced helix slows down ultrafast pressure-jump protein folding.

Maxim B. Prigozhin, Yanxin Liu, Anna Jean Wirth, Shobhna Kapoor, Roland Winter, Klaus Schulten, and Martin Gruebele. Proceedings of the National Academy of Sciences, 110:8087-8092, 2013.


• Fusion pore formation and expansion induced by Ca²⁺ and synaptotagmin 1.

Ying Lai, Jiajie Diao, Yanxin Liu, Yuji Ishitsuka, Zengliu Su, Klaus Schulten, Taekjip Ha, and Yeon-Kyun Shin. Proceedings of the National Academy of Sciences, 110:1333-1338, 2013.


• Atomic model of rabbit hemorrhagic disease virus by cryo-electron microscopy and crystallography.

Xue Wang, Fengting Xu, Jiasen Liu, Bingquan Gao, Yanxin Liu, Yujia Zhai, Jun Ma, Kai Zhang, Timothy Baker, Klaus Schulten, Dong Zheng, Hai Pang, and Fei Sun. PLOS Pathogens, 9:e1003132, 2013.
Highlighted in news stories at the National Science Foundation (NSF) and at the National Center for Supercomputing Applications (NCSA).

• Structural characterization of λ-repressor folding from all-atom molecular dynamics simulations.

Yanxin Liu, Johan Strümpfer, Peter L Freddolino, Martin Gruebele, and Klaus Schulten. Journal of Physical Chemistry Letters, 3:1117-1123, 2012.
Highlighted in Projects in Scientific Computing at the Pittsburgh Supercomputing Center in both 2011 and 2012.


• Extension of a three-helix bundle domain of myosin VI and key role of calmodulins.

Yanxin Liu*, Jen Hsin*, HyeongJun Kim, Paul R. Selvin, and Klaus Schulten. Biophysical Journal, 100:2964-2973, 2011.
Cover article

• Formation of salt bridges mediates internal dimerization of myosin VI medial tail domain.

HyeongJun Kim*, Jen Hsin*, Yanxin Liu*, Paul R. Selvin, and Klaus Schulten. Structure, 18:1443-1449, 2010.
Preview by D. Thirumalai and Z. Zhang.

• Challenges in protein-folding simulations.

Peter L. Freddolino, Christopher B. Harrison, Yanxin Liu, and Klaus Schulten. Nature Physics, 6:751-758, 2010.


• Flow-induced β-hairpin folding of the Glycoprotein Ib_α β-switch.

Xueqing Zou, Yanxin Liu, Zhongzhou Chen, Gloria Ines Cárdenas-Jirón, and Klaus Schulten. Biophysical Journal, 99:1182-1191, 2010.

• Stabilization of native and non-native structures by salt bridges in a lattice model of the GCN4 leucine dimer.

Yanxin Liu, Prem P. Chapagain, and Bernard S. Gerstman. Journal of Physical Chemistry B, 114:796-803, 2010.

• The trigger sequence in the GCN4 Leucine zipper: alpha-helical propensity and multistate dynamics of folding and dimerization.

Prem P. Chapagain, Yanxin Liu, and Bernard S. Gerstman. Journal of Chemical Physics, 129:175103, 2008.


• Lattice model simulation of interchain protein interactions and the folding dynamics and dimerization of the GCN4 Leucine zipper.

Yanxin Liu, Prem P. Chapagain, Jose L. Parra, and Bernard S. Gerstman. Journal of Chemical Physics, 128:045106, 2008.


• Sampling of states for estimating the folding funnel entropy and energy landscape of a model alpha-helical hairpin peptide.

Prem P. Chapagain, Jose L. Parra, Bernard S. Gerstman, and Yanxin Liu. Journal of Chemical Physics, 127:075103, 2007.


• The study of I-V characteristics of single electron triple-barrier tunnel-junction.

Yanxin Liu, Yongchang Wang, and Shaoyi Du. Acta Physica Sinica, 53:2734-2740, 2004.

Awards

• UCSF/CCSF Inclusive Mentoring Fellow, University of California, San Francisco and City College of San Francisco, 2021
• Independent Postdoctoral Fellow Research Award, UCSF Program for Breakthrough Biomedical Research, 2019-2020
• American Heart Association Postdoctoral Fellowship, American Heart Association, 2018-2020
• Helen Hay Whitney Postdoctoral Fellowship, Helen Hay Whitney Foundation, 2015-2018
• Outstanding Reviewer, Computers in Biology and Medicine, 2015
• Baxter Young Investigator Award (2nd Tier), Baxter International Inc., 2014
• CBSB13 Outstanding Young Researcher Award, From Computational Biophysics to Systems Biology, 2013
• Chemical Computing Group Excellence Award, 245th American Chemical Society National Meeting, 2013
• Student Research Achievement Award, Biophysical Society 56th Annual Meeting, 2012
• Young Scientist Travel Award, 17th International Biophysics Congress (IUPAB), 2011
• Student Travel Award, Division of Chemical Physics, American Physical Society March Meeting, 2007
• Outstanding Bachelor Thesis Award, Xi'an Jiaotong University, China, 2004

Professional Services

• Reviewer for Journals: Journal of the American Chemical Society, Nature Communications, Proceedings of the National Academy of Sciences, PLOS Computational Biology, Current Opinion in Virology, Physical Chemistry Chemical Physics, Journal of Physical Chemistry B, Nanoscale, Journal of Chemical Information and Modeling, Journal of Molecular Modeling, Current Drug Targets, RSC Advances, Physical Biology, International Journal of Biological Macromolecules, PLOS One, Computers in Biology and Medicine