Publications

Publications at Rockefeller

(2021)

Leicher R, , , Chua GNL, Watters JW, Christodoulou-Rubalcava S, , ,

Mickolajczyk KJ, Shelton PM, Grasso M, Cao X, Warrington SE, Aher A, Liu S, Kapoor TM. Force-dependent stimulation of RNA unwinding by SARS-CoV-2 nsp13 helicase. Biophys J (2021) 120:1020-1030.

- Biophysical Society Newsroom: "A tool encoded in coronaviruses provides a potential target for COVID-19 and future coronavirus outbreaks"

- Academic Times: "Coronavirus replication protein could be future treatment target"

(2020)

Leicher R, Ge EJ, Lin X, Reynolds MJ, Xie W, Walz T, Zhang B, Muir TW, Liu S. Single-molecule and in silico dissection of the interaction between Polycomb repressive complex 2 and chromatin. Proc Natl Acad Sci USA (2020) 117:30465-30475.

- LUMICKS News: "Distal bridging between nucleosomes by Polycomb complex PRC2 identified with the C-Trap"

Mei L, Espinosa de Los Reyes S, Reynolds MJ, Leicher R, Liu S, Alushin GM. Molecular mechanism for direct actin force-sensing by α-catenin. eLife (2020) 9:e62514.

- RU News: "How cells use mechanical tension sensors to interact with their environment"

Wang L, Johnson ZL, Wasserman MR, Levring J, Chen J, Liu S. Characterization of the kinetic cycle of an ABC transporter by single-molecule and cryo-EM analyses. eLife (2020) 9:e56451.

(2019)

Li S, Zheng EB, Zhao L, Liu S. Nonreciprocal and conditional cooperativity directs the pioneer activity of pluripotency transcription factors. Cell Rep (2019) 28:2689-2703.

Wasserman MR, Schauer GD, O'Donnell ME, Liu S. Replication fork activation is enabled by a single-stranded DNA gate in CMG helicase. Cell (2019) 178:600-611.

F1000Prime Recommendation

- RU News: "With tiny technological tweezers, researchers uncover new aspects of cell division"

Ju X, Li D, Liu S. Full-length RNA profiling reveals pervasive bidirectional transcription terminator in bacteria. Nat Microbiol (2019) 4:1907-1918.

- Behind the paper: "Bacterial transcription machines stop their operation by colliding into each other"

Wasserman MR, Liu S. A tour de force on the double helix: Exploiting DNA mechanics to study DNA-based molecular machines. Biochemistry (2019) 58:4667-4676. Review.

Zheng Q, Omans ND, Leicher R, Osunsade A, Agustinus AS, Finkin-Groner E, D’Ambrosio H, Liu B, Chandariapaty S, Liu S, David Y. Reversible histone glycation is associated with disease-related changes in chromatin architecture. Nat Commun (2019) 10:1289.

- SKI News: "Cellular 'garbage collectors' are key to cancer's growth"

Wang L, Mo CY, Wasserman MR, Rostol JT, Marraffini LA, Liu S. Dynamics of Cas10 govern discrimination between self and non-self in type III CRISPR-Cas immunity. Mol Cell (2019) 73:278-290.

- RU News: "Shape-shifting protein protects bacteria from invaders"

LSX's prior publications

Tafoya S, Large SJ, Liu S, Bustamante C, Sivak DA. Using a system’s equilibrium behavior to reduce its energy dissipation in nonequilibrium processes. Proc Natl Acad Sci USA (2019) 116:5920-5924.

Tafoya S, Liu S, Castillo JP, Atz R, Morais MC, Grimes S, Jardine PJ, Bustamante C. Molecular switch-like regulation enables global subunit coordination in a viral ring ATPase. Proc Natl Acad Sci USA (2018) 115:7961-7966.

Liu S, Tafoya S, Bustamante C. Deciphering the molecular mechanism of the bacteriophage φ29 DNA packaging motor. Methods Mol Biol (2017) 1486:343-355. Protocol.

Cheng B, Wu S, Liu S, Rodriguez-Aliaga P, Yu J, Cui S. Protein denaturation at a single-molecule level: the effect of nonpolar environments and its implications on the unfolding mechanism by proteases. Nanoscale (2015) 7:2970-2977.

Liu S, Chistol G, Bustamante C. Mechanical operation and intersubunit coordination of ring-shaped molecular motors: insights from single-molecule studies. Biophys J (2014) 106:1844-1858. Review.

Liu S, Chistol G, Hetherington CL, Tafoya S, Aathavan K, Schnitzbauer J, Grimes S, Jardine PJ, Bustamante C. A viral packaging motor varies its DNA rotation and step size to preserve subunit coordination as the capsid fills. Cell (2014) 157:702-713.
- LBNL News: "All in the rotation"

Dangkulwanich M, Ishibashi T, Liu S, Kireeva ML, Lubkowska L, Kashlev M, Bustamante C. Complete dissection of transcription elongation reveals slow translocation of RNA polymerase II in a linear ratchet mechanism. eLife (2013) 2:e00971.
- eLife Insight: "Transcription: on the move"

Chistol G, Liu S, Hetherington CL, Moffitt JR, Grimes S, Jardine PJ, Bustamante C. High degree of coordination and division of labor among subunits in a homomeric ring ATPase. Cell (2012) 151:1017-1028.
- F1000Prime Recommendation

Liu S, Harada BT, Miller JT, Le Grice SF, Zhuang X. Initiation complex dynamics direct the transitions between distinct phases of early HIV reverse transcription. Nat Struct Mol Biol (2010) 17:1453-1460.

Chung S, Wendeler M, Rausch JW, Beilhartz G, Gotte M, O’Keefe BR, Bermingham A, Beutler JA, Liu S, Zhuang X, Le Grice SF. Structure-activity analysis of vinylogous urea inhibitors of human immunodeficiency virus-encoded ribonuclease H. Antimicrob Agents Chemother (2010) 54:3913-3921.

Rausch JW, Abbondanzieri EA, Liu S, Zhuang X, Le Grice SF. Retrovirus replication: new perspectives on enzyme and substrate dynamics. In Recent Advances in Human Retroviruses: Principles of Replication and Pathogenesis eds. Lever A, Jeang KT, Berkhout B. World Scientific (2010) pp. 307-343. Book Chapter.

Liu S, Abbondanzieri EA, Rausch JW, Le Grice SF, Zhuang X. Slide into action: dynamic shuttling of HIV reverse transcriptase on nucleic acid substrates. Science (2008) 322:1092-1097.
- Science Perspective: "RT slides home…"
- HHMI News: "An HIV enzyme with a flair for the acrobatic"
- C&EN News: "Acrobatic HIV enzyme caught in action"

Liu S, Bokinsky G, Walter NG, Zhuang X. Dissecting the multistep reaction pathway of an RNA enzyme by single-molecule kinetic “fingerprinting”. Proc Natl Acad Sci USA (2007) 104:12634-12639.

Bokinsky G, Nivón LG, Liu S, Chai G, Hong M, Weeks KM, Zhuang X. Two distinct binding modes of a protein cofactor with its target RNA. J Mol Biol (2006) 361:771-784.

Song Z, Liu S, He H, Hoti N, Wang Y, Feng S, Wu M. A single amino acid change (Asp53→Ala53) converts Survivin from anti-apoptotic to pro-apoptotic. Mol Biol Cell (2004) 15:1287-1296.