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Complete list of publications on Pubmed and  Google Scholar

2021

Keskin O, Miller Y, Liu J, Lu S. Tribute to Ruth Nussinov. J Phys Chem B. 2021 Jul 1;125(25):6733-6734. doi: 10.1021/acs.jpcb.1c04721. PubMed PMID: 34192874.
Hayatshahi HS, Luedtke RR, Taylor M, Chen PJ, Blass BE, Liu J. Factors Governing Selectivity of Dopamine Receptor Binding Compounds for D2R and D3R Subtypes. J Chem Inf Model. 2021 Jun 28;61(6):2829-2843. doi: 10.1021/acs.jcim.1c00036. Epub 2021 May 14. PubMed PMID: 33988991.
Yang KS, Ma XR, Ma Y, Alugubelli YR, Scott DA, Vatansever EC, Drelich AK, Sankaran B, Geng ZZ, Blankenship LR, Ward HE, Sheng YJ, Hsu JC, Kratch KC, Zhao B, Hayatshahi HS, Liu J, Li P, Fierke CA, Tseng CK, Xu S, Liu WR. A Quick Route to Multiple Highly Potent SARS-CoV-2 Main Protease Inhibitors*. ChemMedChem. 2021 Mar 18;16(6):942-948. doi: 10.1002/cmdc.202000924. Epub 2020 Dec 10. PubMed PMID: 33283984; PubMed Central PMCID: PMC7979488.

2020

Hayatshahi HS, Liu J. Filtering out Low-Affinity Bitropic Ligands for Dopamine Receptors Based on Ligand Conformation. ACS Chem Neurosci. 2020 Aug 18;. doi: 10.1021/acschemneuro.0c00263. [Epub ahead of print] PubMed PMID: 32786308.
Collias, D, Slotkowski, RA, Collins SP, Liu J, Beisel L. A positive, growth-based PAM screen identifies noncanonical motifs recognized by the S. pyogenes Cas9. Science Advances  15 Jul 2020:Vol. 6, no. 29, eabb4054 DOI: 10.1126/sciadv.abb4054
Zuo Z, Liu J. Allosteric regulation of CRISPR-Cas9 for DNA-targeting and cleavage. Curr Opin Struct Biol. 2020 Jun;62:166-174. doi: 10.1016/j.sbi.2020.01.013. Epub 2020 Feb 18. Review. PubMed PMID: 32070859; PubMed Central PMCID: PMC7308215.
Liu J, Lai L. Editorial overview: Allosteric assemblies. Curr Opin Struct Biol. 2020 Jun;62:vi-vii. doi: 10.1016/j.sbi.2020.03.009. Epub 2020 Apr 30. PubMed PMID: 32362348.

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 Engl. 2019 Oct 28;58(44):15904-15909. doi: 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 Model. 2019 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. Elife. 2019 Jul 30;8. doi: 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 Lett. 2019 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 Model. 2019 Jan 28;59(1):399-408. doi: 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 Neurosci. 2018 Dec 19;9(12):2972-2983. doi: 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 Cancer. 2018 Dec;119(12):1538-1551. doi: 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 Commun. 2018 May 25;9(1):2082. doi: 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 Rep. 2017 Dec 8;7(1):17271. doi: 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 A. 2017 Jul 18;114(29):7480-7482. doi: 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 J. 2017 Feb 20;474(5):781-795. doi: 10.1042/BCJ20160748. PubMed PMID: 28082425.

2016

Zuo Z, Liu J. Cas9-catalyzed DNA Cleavage Generates Staggered Ends: Evidence from Molecular Dynamics Simulations. Sci Rep. 2016 Nov 22;5:37584. doi: 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 Biol. 2016 Jun;12(6):e1004966. doi: 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 Biol. 2016 Apr;12(4):e1004893. doi: 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 Biol. 2015 Jul;22(7):555-64. doi: 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 A. 2015 Mar 5;119(9):1689-700. doi: 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 Soc. 2014 Dec 24;136(51):17692-701. doi: 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 One. 2013;8(12):e81980. doi: 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 Biol. 2013 Mar-Apr;48(2):89-97. doi: 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 Biol. 2012;8(8):e1002665. doi: 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 Model. 2012 Jun 25;52(6):1698-712. doi: 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 Chem. 2011 Nov 25;286(47):40934-42. doi: 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 J. 2010 Aug 4;99(3):736-44. doi: 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 Biol. 2010 Mar 12;396(5):1508-23. doi: 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 Biol. 2009 Oct;5(10):e1000527. doi: 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 A. 2008 Jan 22;105(3):901-6. doi: 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 Sci. 2007 Mar 1;307(1):124-34. doi: 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. Structure. 2006 Dec;14(12):1811-21. doi: 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 A. 2005 Mar 31;109(12):2816-21. doi: 10.1021/jp045254b. PubMed PMID: 16833595.
Liu J, Hadad CM, Platz MS. The reaction of triplet nitrenes with oxygen: a computational study. Org Lett. 2005 Feb 17;7(4):549-52. doi: 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 Chem. 2004 Dec 10;69(25):8583-93. doi: 10.1021/jo048433y. PubMed PMID: 15575733.

This page was last modified on August 10, 2021