Publications

Complete list of publications on Pubmed

2019

Wang XS, Chen PC, Hampton JT, Tharp JM, Reed CA, Das SK, Wang DS, Hayatshahi HS, Shen Y, Liu J, Liu WR. A Genetically Encoded, Phage-Displayed Cyclic-Peptide Library. Angew Chem Int Ed Engl2019 Oct 28;58(44):15904-15909doi: 10.1002/anie.201908713. Epub 2019 Sep 9. Review. PubMed PMID: 31398275; PubMed Central PMCID: PMC6803038.
Hayatshahi HS, Ahuactzin E, Tao P, Wang S, Liu J. Probing Protein Allostery as a Residue-Specific Concept via Residue Response Maps. J Chem Inf Model2019 Oct 21;doi: 10.1021/acs.jcim.9b00447. [Epub ahead of print] PubMed PMID: 31589429.
Zuo Z, Zolekar A, Babu K, Lin VJ, Hayatshahi HS, Rajan R, Wang YC, Liu J. Structural and functional insights into the bona fidecatalytic state of Streptococcus pyogenes Cas9 HNH nuclease domain. Elife2019 Jul 30;8doi: 10.7554/eLife.46500. PubMed PMID: 31361218; PubMed Central PMCID: PMC6706240.
Chen PJ, Taylor M, Griffin SA, Amani A, Hayatshahi H, Korzekwa K, Ye M, Mach RH, Liu J, Luedtke RR, Gordon JC, Blass BE.Design, synthesis, and evaluation of N-(4-(4-phenyl piperazin-1-yl)butyl)-4-(thiophen-3-yl)benzamides as selective dopamine D3 receptor ligands. Bioorg Med Chem Lett2019 Jul 11;doi: 10.1016/j.bmcl.2019.07.020. [Epub ahead of print] PubMed PMID: 31387791.
Zuo Z, Liu J. Assessing the Performance of the Nonbonded Mg2+ Models in a Two-Metal-Dependent Ribonuclease. J Chem Inf Model2019 Jan 28;59(1):399-408doi: 10.1021/acs.jcim.8b00627. Epub 2018 Dec 19. PubMed PMID: 30521334.

2018

Hayatshahi HS, Xu K, Griffin SA, Taylor M, Mach RH, Liu J, Luedtke RR. Analogues of ArylamidePhenylpiperazine Ligands To Investigate the Factors Influencing D3 Dopamine Receptor Bitropic Binding and Receptor Subtype Selectivity. ACS Chem Neurosci2018 Dec 19;9(12):2972-2983doi: 10.1021/acschemneuro.8b00142. Epub 2018 Jul 30. PubMed PMID: 30010318.
Zolekar A, Lin VJT, Mishra NM, Ho YY, Hayatshahi HS, Parab A, Sampat R, Liao X, Hoffmann P, Liu J, Emmitte KA, Wang YC.Stress and interferon signalling-mediated apoptosis contributes to pleiotropic anticancer responses induced by targeting NGLY1. Br J Cancer2018 Dec;119(12):1538-1551doi: 10.1038/s41416-018-0265-9. Epub 2018 Nov 2. PubMed PMID: 30385822; PubMed Central PMCID: PMC6288164.
Zuo Z, Smith RN, Chen Z, Agharkar AS, Snell HD, Huang R, Liu J, Gonzales EB. Identification of a unique Ca2+-binding site in rat acid-sensing ion channel 3. Nat Commun2018 May 25;9(1):2082doi: 10.1038/s41467-018-04424-0. PubMed PMID: 29802295; PubMed Central PMCID: PMC5970173.

2017

Zuo Z, Liu J. Structure and Dynamics of Cas9 HNH Domain Catalytic State. Sci Rep2017 Dec 8;7(1):17271doi: 10.1038/s41598-017-17578-6. PubMed PMID: 29222528; PubMed Central PMCID: PMC5722908.
Liu J, Nussinov R. Energetic redistribution in allostery to execute protein function. Proc Natl Acad Sci U S A2017 Jul 18;114(29):7480-7482doi: 10.1073/pnas.1709071114. Epub 2017 Jul 10. PubMed PMID: 28696318; PubMed Central PMCID: PMC5530713.
Onel M, Sumbul F, Liu J, Nussinov R, Haliloglu T. Cullin neddylation may allosterically tune polyubiquitin chain length and topology. Biochem J2017 Feb 20;474(5):781-795doi: 10.1042/BCJ20160748. PubMed PMID: 28082425.

2016

Zuo Z, Liu J. Cas9-catalyzed DNA Cleavage Generates Staggered Ends: Evidence from Molecular Dynamics Simulations. Sci Rep2016 Nov 22;5:37584doi: 10.1038/srep37584. PubMed PMID: 27874072; PubMed Central PMCID: PMC5118739.
Liu J, Nussinov R. Allostery: An Overview of Its History, Concepts, Methods, and Applications. PLoS Comput Biol2016 Jun;12(6):e1004966doi: 10.1371/journal.pcbi.1004966. eCollection 2016 Jun. PubMed PMID: 27253437; PubMed Central PMCID: PMC4890769.
Kalescky R, Zhou H, Liu J, Tao P. Rigid Residue Scan Simulations Systematically Reveal Residue Entropic Roles in Protein Allostery. PLoS Comput Biol2016 Apr;12(4):e1004893doi: 10.1371/journal.pcbi.1004893. eCollection 2016 Apr. PubMed PMID: 27115535; PubMed Central PMCID: PMC4846164.

2015

Brewer KD, Bacaj T, Cavalli A, Camilloni C, Swarbrick JD, Liu J, Zhou A, Zhou P, Barlow N, Xu J, Seven AB, Prinslow EA, Voleti R, Häussinger D, Bonvin AM, Tomchick DR, Vendruscolo M, Graham B, Südhof TC, Rizo J. Dynamic binding mode of a Synaptotagmin-1-SNARE complex in solution. Nat Struct Mol Biol2015 Jul;22(7):555-64doi: 10.1038/nsmb.3035. Epub 2015 Jun 1. PubMed PMID: 26030874; PubMed Central PMCID: PMC4496268.

Before joining UNTHSC in 2015

Kalescky R, Liu J, Tao P. Identifying key residues for protein allostery through rigid residue scan. J Phys Chem A2015 Mar 5;119(9):1689-700doi: 10.1021/jp5083455. Epub2014 Dec 11. PubMed PMID: 25437403.
Nussinov R, Tsai CJ, Liu J. Principles of allosteric interactions in cell signaling. J Am Chem Soc2014 Dec 24;136(51):17692-701doi: 10.1021/ja510028c. Epub 2014 Dec 15. Review. PubMed PMID: 25474128; PubMed Central PMCID: PMC4291754.
Liu J, Tawa GJ, Wallqvist A. Identifying cytochrome p450 functional networks and their allosteric regulatory elements. PLoS One2013;8(12):e81980doi: 10.1371/journal.pone.0081980. eCollection 2013. PubMed PMID: 24312617; PubMed Central PMCID: PMC3849357.
Liu J, Nussinov R. The role of allostery in the ubiquitin-proteasome system. Crit Rev Biochem Mol Biol2013 Mar-Apr;48(2):89-97doi: 10.3109/10409238.2012.742856. Epub 2012 Dec 13. Review. PubMed PMID: 23234564; PubMed Central PMCID: PMC3609921.
Ripoll DR, Khavrutskii IV, Chaudhury S, Liu J, Kuschner RA, Wallqvist A, Reifman J. Quantitative predictions of binding free energy changes in drug-resistant influenza neuraminidase. PLoS Comput Biol2012;8(8):e1002665doi: 10.1371/journal.pcbi.1002665. Epub 2012 Aug 30. PubMed PMID: 22956900; PubMed Central PMCID: PMC3431292.
Liu R, Liu J, Tawa G, Wallqvist A. 2D SMARTCyp reactivity-based site of metabolism prediction for major drug-metabolizing cytochrome P450 enzymes. J Chem Inf Model2012 Jun 25;52(6):1698-712doi: 10.1021/ci3001524. Epub 2012 Jun 4. PubMed PMID: 22631565.
Liu J, Nussinov R. Flexible cullins in cullin-RING E3 ligases allosterically regulate ubiquitination. J Biol Chem2011 Nov 25;286(47):40934-42doi: 10.1074/jbc.M111.277236. Epub 2011 Sep 20. PubMed PMID: 21937436; PubMed Central PMCID: PMC3220518.
Liu J, Nussinov R. Rbx1 flexible linker facilitates cullin-RING ligase function before neddylation and after deneddylation.Biophys J2010 Aug 4;99(3):736-44doi: 10.1016/j.bpj.2010.05.021. PubMed PMID: 20682250; PubMed Central PMCID: PMC2913186.
Liu J, Nussinov R. Molecular dynamics reveal the essential role of linker motions in the function of cullin-RING E3 ligases. J Mol Biol2010 Mar 12;396(5):1508-23doi: 10.1016/j.jmb.2010.01.022. Epub 2010 Jan 18. PubMed PMID: 20083119; PubMed Central PMCID: PMC2824043.
Liu J, Nussinov R. The mechanism of ubiquitination in the cullin-RING E3 ligase machinery: conformational control of substrate orientation. PLoS Comput Biol2009 Oct;5(10):e1000527doi: 10.1371/journal.pcbi.1000527. Epub 2009 Oct 2. PubMed PMID: 19798438; PubMed Central PMCID: PMC2741574.
Liu J, Nussinov R. Allosteric effects in the marginally stable von Hippel-Lindau tumor suppressor protein and allostery-based rescue mutant design. Proc Natl Acad Sci U S A2008 Jan 22;105(3):901-6doi: 10.1073/pnas.0707401105. Epub 2008 Jan 14. PubMed PMID: 18195360; PubMed Central PMCID: PMC2242715.
Hwang YS, Liu J, Lenhart JJ, Hadad CM. Surface complexes of phthalic acid at the hematite/water interface. J Colloid Interface Sci2007 Mar 1;307(1):124-34doi: 10.1016/j.jcis.2006.11.020. Epub 2006 Dec 22. PubMed PMID: 17188289.
Liu J, Pan Y, Ma B, Nussinov R. “Similarity trap” in protein-protein interactions could be carcinogenic: simulations of p53 core domain complexed with 53BP1 and BRCA1 BRCT domains. Structure2006 Dec;14(12):1811-21doi: 10.1016/j.str.2006.10.009. PubMed PMID: 17161371; PubMed Central PMCID: PMC2429992.
Mandel S, Liu J, Hadad CM, Platz MS. Study of singlet and triplet 2,6-difluorophenylnitrene by time-resolved infrared spectroscopy. J Phys Chem A2005 Mar 31;109(12):2816-21doi: 10.1021/jp045254b. PubMed PMID: 16833595.
Liu J, Hadad CM, Platz MS. The reaction of triplet nitrenes with oxygen: a computational study. Org Lett2005 Feb 17;7(4):549-52doi: 10.1021/ol047782b. PubMed PMID: 15704891.
Liu J, Mandel S, Hadad CM, Platz MS. A comparison of acetyl- and methoxycarbonylnitrenes by computational methods and a laser flash photolysis study of benzoylnitrene. J Org Chem2004 Dec 10;69(25):8583-93doi: 10.1021/jo048433y. PubMed PMID: 15575733.

This page was last modified on November 1, 2019