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James Briggs

TitleProfessor
InstitutionUniversity of Houston
DepartmentBiology
Address4800 Calhoun Rd
Houston TX 77004
Phone713-743-8366
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    Collapse Research 
    Collapse research activities and funding
    R01GM063789     (MARTINIS, SUSAN A)Sep 1, 2001 - Apr 30, 2015
    NIH/NIGMS
    tRNA Synthetase Fidelity Mechanisms
    Role: Co-Principal Investigator
    R21AI055883     (BRIGGS, JAMES M.)Aug 15, 2003 - Jul 31, 2006
    NIH/NIAID
    Dynamic Drug Design Targeting Botulinum Neurotoxins
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Cherubin P, Garcia MC, Curtis D, Britt CB, Craft JW, Burress H, Berndt C, Reddy S, Guyette J, Zheng T, Huo Q, Quiñones B, Briggs JM, Teter K. Inhibition of Cholera Toxin and Other AB Toxins by Polyphenolic Compounds. PLoS One. 2016; 11(11):e0166477. PMID: 27829022.
      View in: PubMed
    2. Smith IN, Briggs JM. Structural mutation analysis of PTEN and its genotype-phenotype correlations in endometriosis and cancer. Proteins. 2016 Nov; 84(11):1625-1643. PMID: 27481051.
      View in: PubMed
    3. Singh K, Briggs JM. Functional Implications of the spectrum of BCL2 mutations in Lymphoma. Mutat Res Rev Mutat Res. 2016 Jul-Sep; 769:1-18. PMID: 27543313.
      View in: PubMed
    4. Craft JW, Shen TW, Brier LM, Briggs JM. Biophysical characteristics of cholera toxin and Escherichia coli heat-labile enterotoxin structure and chemistry lead to differential toxicity. J Phys Chem B. 2015 Jan 22; 119(3):1048-61. PMID: 25322200.
      View in: PubMed
    5. Craft JW, Zhang H, Charendoff MN, Mindrebo JT, Schwartz RJ, Briggs JM. Associations between the Rho kinase-1 catalytic and PH domain regulatory unit. J Mol Graph Model. 2013 Nov; 46:74-82. PMID: 24149321.
      View in: PubMed
    6. Charendoff MN, Shah HP, Briggs JM. New insights into the binding and catalytic mechanisms of Bacillus thuringiensis lactonase: insights into B. thuringiensis AiiA mechanism. PLoS One. 2013; 8(9):e75395. PMID: 24058683; PMCID: PMC3776789.
      View in: PubMed, PubMed Central
    7. Oliveira GS, Leite FL, Amarante AM, Franca EF, Cunha RA, Briggs JM, Freitas LC. Molecular modeling of enzyme attachment on AFM probes. J Mol Graph Model. 2013 Sep; 45:128-36. PMID: 24029365.
      View in: PubMed
    8. Mallipeddi PL, Pedersen SE, Briggs JM. Interactions of acetylcholine binding site residues contributing to nicotinic acetylcholine receptor gating: role of residues Y93, Y190, K145 and D200. J Mol Graph Model. 2013 Jul; 44:145-54. PMID: 23831994.
      View in: PubMed
    9. Anastasio NC, Gilbertson SR, Bubar MJ, Agarkov A, Stutz SJ, Jeng Y, Bremer NM, Smith TD, Fox RG, Swinford SE, Seitz PK, Charendoff MN, Craft JW, Laezza FM, Watson CS, Briggs JM, Cunningham KA. Peptide inhibitors disrupt the serotonin 5-HT2C receptor interaction with phosphatase and tensin homolog to allosterically modulate cellular signaling and behavior. J Neurosci. 2013 Jan 23; 33(4):1615-30. PMID: 23345234; PMCID: PMC3711763.
      View in: PubMed, PubMed Central
    10. Mallipeddi PL, Joshi M, Briggs JM. Pharmacophore-based virtual screening to aid in the identification of unknown protein function. Chem Biol Drug Des. 2012 Dec; 80(6):828-42. PMID: 22568756.
      View in: PubMed
    11. Zhu H, Briggs JM. Mechanistic role of NS4A and substrate in the activation of HCV NS3 protease. Proteins. 2011 Aug; 79(8):2428-43. PMID: 21633972.
      View in: PubMed
    12. Xie F, Briggs JM, Dupureur CM. Nucleophile activation in PD...(D/E)xK metallonucleases: an experimental and computational pK(a) study. J Inorg Biochem. 2010 Jun; 104(6):665-72. PMID: 20347155; PMCID: PMC2913505.
      View in: PubMed, PubMed Central
    13. Joshi M, Ebalunode JO, Briggs JM. Computational insights into the interaction of the anthrax lethal factor with the N-terminal region of its substrates. Proteins. 2009 May 01; 75(2):323-35. PMID: 18831046.
      View in: PubMed
    14. Mandal PK, Limbrick D, Coleman DR, Dyer GA, Ren Z, Birtwistle JS, Xiong C, Chen X, Briggs JM, McMurray JS. Conformationally constrained peptidomimetic inhibitors of signal transducer and activator of transcription. 3: Evaluation and molecular modeling. J Med Chem. 2009 Apr 23; 52(8):2429-42. PMID: 19334714; PMCID: PMC2735258.
      View in: PubMed, PubMed Central
    15. Singh N, Briggs JM. Molecular dynamics simulations of Factor Xa: insight into conformational transition of its binding subsites. Biopolymers. 2008 Dec; 89(12):1104-13. PMID: 18680100.
      View in: PubMed
    16. Huang HC, Jupiter D, Qiu M, Briggs JM, Vanburen V. Cluster analysis of hydration waters around the active sites of bacterial alanine racemase using a 2-ns MD simulation. Biopolymers. 2008 Mar; 89(3):210-9. PMID: 18023020.
      View in: PubMed
    17. Jawanda N, Ebalunode J, Gribenko A, Briggs J, Lee JC, Tu SC. A single-residue mutation destabilizes Vibrio harveyi flavin reductase FRP dimer. Arch Biochem Biophys. 2008 Apr 01; 472(1):51-7. PMID: 18294448.
      View in: PubMed
    18. Nunthaboot N, Pianwanit S, Parasuk V, Ebalunode JO, Briggs JM, Kokpol S. Hybrid quantum mechanical/molecular mechanical molecular dynamics simulations of HIV-1 integrase/inhibitor complexes. Biophys J. 2007 Nov 15; 93(10):3613-26. PMID: 17693479; PMCID: PMC2072063.
      View in: PubMed, PubMed Central
    19. Fu W, Shen J, Luo X, Zhu W, Cheng J, Yu K, Briggs JM, Jin G, Chen K, Jiang H. Dopamine D1 receptor agonist and D2 receptor antagonist effects of the natural product (-)-stepholidine: molecular modeling and dynamics simulations. Biophys J. 2007 Sep 01; 93(5):1431-41. PMID: 17468175; PMCID: PMC1948031.
      View in: PubMed, PubMed Central
    20. Zhai Y, Nawaz MH, Lee KW, Kirkbride E, Briggs JM, Martinis SA. Modulation of substrate specificity within the amino acid editing site of leucyl-tRNA synthetase. Biochemistry. 2007 Mar 20; 46(11):3331-7. PMID: 17311409.
      View in: PubMed
    21. Meltzer RH, Vila-Carriles W, Ebalunode JO, Briggs JM, Pedersen SE. Computed pore potentials of the nicotinic acetylcholine receptor. Biophys J. 2006 Aug 15; 91(4):1325-35. PMID: 16751248; PMCID: PMC1518625.
      View in: PubMed, PubMed Central
    22. Meltzer RH, Thompson E, Soman KV, Song XZ, Ebalunode JO, Wensel TG, Briggs JM, Pedersen SE. Electrostatic steering at acetylcholine binding sites. Biophys J. 2006 Aug 15; 91(4):1302-14. PMID: 16751247; PMCID: PMC1518644.
      View in: PubMed, PubMed Central
    23. Deng J, Sanchez T, Neamati N, Briggs JM. Dynamic pharmacophore model optimization: identification of novel HIV-1 integrase inhibitors. J Med Chem. 2006 Mar 09; 49(5):1684-92. PMID: 16509584.
      View in: PubMed
    24. Mulder BA, Anaya S, Yu P, Lee KW, Nguyen A, Murphy J, Willson R, Briggs JM, Gao X, Hardin SH. Nucleotide modification at the gamma-phosphate leads to the improved fidelity of HIV-1 reverse transcriptase. Nucleic Acids Res. 2005; 33(15):4865-73. PMID: 16141194; PMCID: PMC1197130.
      View in: PubMed, PubMed Central
    25. Brigo A, Lee KW, Fogolari F, Mustata GI, Briggs JM. Comparative molecular dynamics simulations of HIV-1 integrase and the T66I/M154I mutant: binding modes and drug resistance to a diketo acid inhibitor. Proteins. 2005 Jun 01; 59(4):723-41. PMID: 15815973.
      View in: PubMed
    26. Brigo A, Mustata GI, Briggs JM, Moro S. Discovery of HIV-1 integrase inhibitors through a novel combination of ligand and structure-based drug design. Med Chem. 2005 May; 1(3):263-75. PMID: 16787322.
      View in: PubMed
    27. Brigo A, Lee KW, Iurcu Mustata G, Briggs JM. Comparison of multiple molecular dynamics trajectories calculated for the drug-resistant HIV-1 integrase T66I/M154I catalytic domain. Biophys J. 2005 May; 88(5):3072-82. PMID: 15764656; PMCID: PMC1305459.
      View in: PubMed, PubMed Central
    28. Deng J, Lee KW, Sanchez T, Cui M, Neamati N, Briggs JM. Dynamic receptor-based pharmacophore model development and its application in designing novel HIV-1 integrase inhibitors. J Med Chem. 2005 Mar 10; 48(5):1496-505. PMID: 15743192.
      View in: PubMed
    29. Lee MC, Deng J, Briggs JM, Duan Y. Large-scale conformational dynamics of the HIV-1 integrase core domain and its catalytic loop mutants. Biophys J. 2005 May; 88(5):3133-46. PMID: 15731379; PMCID: PMC1305464.
      View in: PubMed, PubMed Central
    30. LeMagueres P, Im H, Ebalunode J, Strych U, Benedik MJ, Briggs JM, Kohn H, Krause KL. The 1.9 A crystal structure of alanine racemase from Mycobacterium tuberculosis contains a conserved entryway into the active site. Biochemistry. 2005 Feb 08; 44(5):1471-81. PMID: 15683232.
      View in: PubMed
    31. Barreca ML, Rao A, De Luca L, Zappalà M, Gurnari C, Monforte P, De Clercq E, Van Maele B, Debyser Z, Witvrouw M, Briggs JM, Chimirri A. Efficient 3D database screening for novel HIV-1 IN inhibitors. J Chem Inf Comput Sci. 2004 Jul-Aug; 44(4):1450-5. PMID: 15272853.
      View in: PubMed
    32. Mustata G, Briggs JM. Cluster analysis of water molecules in alanine racemase and their putative structural role. Protein Eng Des Sel. 2004 Mar; 17(3):223-34. PMID: 15115851.
      View in: PubMed
    33. Mustata GI, Brigo A, Briggs JM. HIV-1 integrase pharmacophore model derived from diverse classes of inhibitors. Bioorg Med Chem Lett. 2004 Mar 22; 14(6):1447-54. PMID: 15006380.
      View in: PubMed
    34. Lee KW, Briggs JM. Molecular modeling study of the editing active site of Escherichia coli leucyl-tRNA synthetase: two amino acid binding sites in the editing domain. Proteins. 2004 Mar 01; 54(4):693-704. PMID: 14997565.
      View in: PubMed
    35. Adesokan AA, Roberts VA, Lee KW, Lins RD, Briggs JM. Prediction of HIV-1 integrase/viral DNA interactions in the catalytic domain by fast molecular docking. J Med Chem. 2004 Feb 12; 47(4):821-8. PMID: 14761184.
      View in: PubMed
    36. Mursinna RS, Lee KW, Briggs JM, Martinis SA. Molecular dissection of a critical specificity determinant within the amino acid editing domain of leucyl-tRNA synthetase. Biochemistry. 2004 Jan 13; 43(1):155-65. PMID: 14705941.
      View in: PubMed
    37. Mustata GI, Soares TA, Briggs JM. Molecular dynamics studies of alanine racemase: a structural model for drug design. Biopolymers. 2003 Oct; 70(2):186-200. PMID: 14517907.
      View in: PubMed
    38. Barreca ML, Lee KW, Chimirri A, Briggs JM. Molecular dynamics studies of the wild-type and double mutant HIV-1 integrase complexed with the 5CITEP inhibitor: mechanism for inhibition and drug resistance. Biophys J. 2003 Mar; 84(3):1450-63. PMID: 12609852; PMCID: PMC1302719.
      View in: PubMed, PubMed Central
    39. Laurents DV, Huyghues-Despointes BM, Bruix M, Thurlkill RL, Schell D, Newsom S, Grimsley GR, Shaw KL, Treviño S, Rico M, Briggs JM, Antosiewicz JM, Scholtz JM, Pace CN. Charge-charge interactions are key determinants of the pK values of ionizable groups in ribonuclease Sa (pI=3.5) and a basic variant (pI=10.2). J Mol Biol. 2003 Jan 31; 325(5):1077-92. PMID: 12527309.
      View in: PubMed
    40. Huyghues-Despointes BM, Thurlkill RL, Daily MD, Schell D, Briggs JM, Antosiewicz JM, Pace CN, Scholtz JM. pK values of histidine residues in ribonuclease Sa: effect of salt and net charge. J Mol Biol. 2003 Jan 31; 325(5):1093-105. PMID: 12527310.
      View in: PubMed
    41. Pace CN, Huyghues-Despointes BM, Briggs JM, Grimsley GR, Scholtz JM. Charge-charge interactions are the primary determinants of the pK values of the ionizable groups in Ribonuclease T1. Biophys Chem. 2002 Dec 10; 101-102:211-9. PMID: 12488002.
      View in: PubMed
    42. Mustata GI, Briggs JM. A structure-based design approach for the identification of novel inhibitors: application to an alanine racemase. J Comput Aided Mol Des. 2002 Dec; 16(12):935-53. PMID: 12825624.
      View in: PubMed
    43. Cui M, Huang X, Luo X, Briggs JM, Ji R, Chen K, Shen J, Jiang H. Molecular docking and 3D-QSAR studies on gag peptide analogue inhibitors interacting with human cyclophilin A. J Med Chem. 2002 Nov 21; 45(24):5249-59. PMID: 12431052.
      View in: PubMed
    44. Soares TA, Lins RD, Straatsma TP, Briggs JM. Internal dynamics and ionization states of the macrophage migration inhibitory factor: comparison between wild-type and mutant forms. Biopolymers. 2002 Nov 15; 65(4):313-23. PMID: 12382291.
      View in: PubMed
    45. Fu W, Cui M, Briggs JM, Huang X, Xiong B, Zhang Y, Luo X, Shen J, Ji R, Jiang H, Chen K. Brownian dynamics simulations of the recognition of the scorpion toxin maurotoxin with the voltage-gated potassium ion channels. Biophys J. 2002 Nov; 83(5):2370-85. PMID: 12414674; PMCID: PMC1302326.
      View in: PubMed, PubMed Central
    46. Cui M, Shen J, Briggs JM, Fu W, Wu J, Zhang Y, Luo X, Chi Z, Ji R, Jiang H, Chen K. Brownian dynamics simulations of the recognition of the scorpion toxin P05 with the small-conductance calcium-activated potassium channels. J Mol Biol. 2002 Apr 26; 318(2):417-28. PMID: 12051848.
      View in: PubMed
    47. Huang HC, Briggs JM. The association between a negatively charged ligand and the electronegative binding pocket of its receptor. Biopolymers. 2002 Apr 05; 63(4):247-60. PMID: 11807752.
      View in: PubMed
    48. Cui M, Shen J, Briggs JM, Luo X, Tan X, Jiang H, Chen K, Ji R. Brownian dynamics simulations of interaction between scorpion toxin Lq2 and potassium ion channel. Biophys J. 2001 Apr; 80(4):1659-69. PMID: 11259281; PMCID: PMC1301357.
      View in: PubMed, PubMed Central
    49. Ondrechen MJ, Briggs JM, McCammon JA. A model for enzyme-substrate interaction in alanine racemase. J Am Chem Soc. 2001 Mar 28; 123(12):2830-4. PMID: 11456969.
      View in: PubMed
    50. Lee KW, Briggs JM. Comparative molecular field analysis (coMFA) study of epothilones-tubulin depolymerization inhibitors: pharmacophore development using 3D QSAR methods. J Comput Aided Mol Des. 2001 Jan; 15(1):41-55. PMID: 11217918.
      View in: PubMed
    51. Liu N, Samartzidou H, Lee KW, Briggs JM, Delcour AH. Effects of pore mutations and permeant ion concentration on the spontaneous gating activity of OmpC porin. Protein Eng. 2000 Jul; 13(7):491-500. PMID: 10906344.
      View in: PubMed
    52. Carlson HA, Masukawa KM, Rubins K, Bushman FD, Jorgensen WL, Lins RD, Briggs JM, McCammon JA. Developing a dynamic pharmacophore model for HIV-1 integrase. J Med Chem. 2000 Jun 01; 43(11):2100-14. PMID: 10841789.
      View in: PubMed
    53. Soares T, Goodsell D, Ferreira R, Olson AJ, Briggs JM. Ionization state and molecular docking studies for the macrophage migration inhibitory factor: the role of lysine 32 in the catalytic mechanism. J Mol Recognit. 2000 May-Jun; 13(3):146-56. PMID: 10867710.
      View in: PubMed
    54. Lins RD, Straatsma TP, Briggs JM. Similarities in the HIV-1 and ASV integrase active sites upon metal cofactor binding. Biopolymers. 2000 Apr 05; 53(4):308-15. PMID: 10685051.
      View in: PubMed
    55. Lins RD, Adesokan A, Soares TA, Briggs JM. Investigations on human immunodeficiency virus type 1 integrase/DNA binding interactions via molecular dynamics and electrostatics calculations. Pharmacol Ther. 2000 Mar; 85(3):123-31. PMID: 10739867.
      View in: PubMed
    56. Soares TA, Goodsell DS, Briggs JM, Ferreira R, Olson AJ. Docking of 4-oxalocrotonate tautomerase substrates: implications for the catalytic mechanism. Biopolymers. 1999 Sep; 50(3):319-28. PMID: 10397792.
      View in: PubMed
    57. Lins RD, Briggs JM, Straatsma TP, Carlson HA, Greenwald J, Choe S, McCammon JA. Molecular dynamics studies on the HIV-1 integrase catalytic domain. Biophys J. 1999 Jun; 76(6):2999-3011. PMID: 10354426; PMCID: PMC1300270.
      View in: PubMed, PubMed Central
    58. Carlson HA, Briggs JM, McCammon JA. Calculation of the pKa values for the ligands and side chains of Escherichia coli D-alanine:D-alanine ligase. J Med Chem. 1999 Jan 14; 42(1):109-17. PMID: 9888837.
      View in: PubMed
    59. Blachut-Okrasinska E, Lesyng B, Briggs JM, McCammon JA, Antosiewicz JM. Poisson-Boltzmann model studies of molecular electrostatic properties of the cAMP-dependent protein kinase. Eur Biophys J. 1999; 28(6):457-67. PMID: 10460339.
      View in: PubMed
    60. Tara S, Elcock AH, Kirchhoff PD, Briggs JM, Radic Z, Taylor P, McCammon JA. Rapid binding of a cationic active site inhibitor to wild type and mutant mouse acetylcholinesterase: Brownian dynamics simulation including diffusion in the active site gorge. Biopolymers. 1998 Dec; 46(7):465-74. PMID: 9838872.
      View in: PubMed
    61. Weber W, Demirdjian H, Lins RD, Briggs JM, Ferreira R, McCammon JA. Brownian and essential dynamics studies of the HIV-1 integrase catalytic domain. J Biomol Struct Dyn. 1998 Dec; 16(3):733-45. PMID: 10052629.
      View in: PubMed
    62. Zhou HX, Briggs JM, Tara S, McCammon JA. Correlation between rate of enzyme-substrate diffusional encounter and average Boltzmann factor around active site. Biopolymers. 1998 Apr; 45(5):355-60. PMID: 9530014.
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    63. Baginski M, Fogolari F, Briggs JM. Electrostatic and non-electrostatic contributions to the binding free energies of anthracycline antibiotics to DNA. J Mol Biol. 1997 Nov 28; 274(2):253-67. PMID: 9398531.
      View in: PubMed
    64. Briggs JM. Protein-protein diffusional encounter. Biophys J. 1997 May; 72(5):1915-6. PMID: 9129796; PMCID: PMC1184388.
      View in: PubMed, PubMed Central
    65. Fogolari F, Elcock AH, Esposito G, Viglino P, Briggs JM, McCammon JA. Electrostatic effects in homeodomain-DNA interactions. J Mol Biol. 1997 Mar 28; 267(2):368-81. PMID: 9096232.
      View in: PubMed
    66. Marrone TJ, Briggs JM, McCammon JA. Structure-based drug design: computational advances. Annu Rev Pharmacol Toxicol. 1997; 37:71-90. PMID: 9131247.
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    67. Marrone TJ, Straatsma TP, Briggs JM, Wilson DK, Quiocho FA, McCammon JA. Theoretical study of inhibition of adenosine deaminase by (8R)-coformycin and (8R)-deoxycoformycin. J Med Chem. 1996 Jan 05; 39(1):277-84. PMID: 8568817.
      View in: PubMed
    68. Wlodek ST, Antosiewicz J, McCammon JA, Straatsma TP, Gilson MK, Briggs JM, Humblet C, Sussman JL. Binding of tacrine and 6-chlorotacrine by acetylcholinesterase. Biopolymers. 1996 Jan; 38(1):109-17. PMID: 8679940.
      View in: PubMed
    69. Antosiewicz J, Briggs JM, McCammon JA. Orientational steering in enzyme-substrate association: ionic strength dependence of hydrodynamic torque effects. Eur Biophys J. 1996; 24(3):137-41. PMID: 8852560.
      View in: PubMed
    70. Cannon WR, Briggs JM, Shen J, McCammon JA, Quiocho FA. Conservative and nonconservative mutations in proteins: anomalous mutations in a transport receptor analyzed by free energy and quantum chemical calculations. Protein Sci. 1995 Mar; 4(3):387-93. PMID: 7795522; PMCID: PMC2143071.
      View in: PubMed, PubMed Central
    71. Wade RC, Luty BA, Demchuk E, Madura JD, Davis ME, Briggs JM, McCammon JA. Simulation of enzyme-substrate encounter with gated active sites. Nat Struct Biol. 1994 Jan; 1(1):65-9. PMID: 7656010.
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