IBBR Publications

Found 243 results
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2008
Xu Y, Colletier J-P, Weik M, Jiang H, Moult J, Silman I, Sussman JL. Flexibility of aromatic residues in the active-site gorge of acetylcholinesterase: X-ray versus molecular dynamics. Biophys J. 2008 ;95(5):2500-11.
Zhong S, Chen X, Zhu X, Dziegielewska B, Bachman KE, Ellenberger T, Ballin JD, Wilson GM, Tomkinson AE, Mackerell AD. Identification and validation of human DNA ligase inhibitors using computer-aided drug design. J Med Chem. 2008 ;51(15):4553-62.
Yu W-M, Guvench O, Mackerell AD, Qu C-K. Identification of small molecular weight inhibitors of Src homology 2 domain-containing tyrosine phosphatase 2 (SHP-2) via in silico database screening combined with experimental assay. J Med Chem. 2008 ;51(23):7396-404.
Deng L, Cho S, Malchiodi EL, Kerzic MC, Dam J, Mariuzza RA. Molecular architecture of the major histocompatibility complex class I-binding site of Ly49 natural killer cell receptors. J Biol Chem. 2008 ;283(24):16840-9.
Struble EB, Ladner JE, Brabazon DM. New crystal structures of ColE1 Rom and variants resulting from mutation of a surface exposed residue: Implications for RNA-recognition. Proteins. 2008 ;72(2):761-8.
Grishaev A, Tugarinov V, Kay LE, Trewhella J, Bax A. Refined solution structure of the 82-kDa enzyme malate synthase G from joint NMR and synchrotron SAXS restraints. J Biomol NMR. 2008 ;40(2):95-106.
Narayanan BC, Niu W, Han Y, Zou J, Mariano PS, Dunaway-Mariano D, Herzberg O. Structure and function of PA4872 from Pseudomonas aeruginosa, a novel class of oxaloacetate decarboxylase from the PEP mutase/isocitrate lyase superfamily. Biochemistry. 2008 ;47(1):167-82.
Malashkevich VN, Varney KM, Garrett SC, Wilder PT, Knight D, Charpentier TH, Ramagopal UA, Almo SC, Weber DJ, Bresnick AR. Structure of Ca2+-bound S100A4 and its interaction with peptides derived from nonmuscle myosin-IIA. Biochemistry. 2008 ;47(18):5111-26.
Parsons JF, Shi KM, Ladner JE. Structure of isochorismate synthase in complex with magnesium. Acta Crystallogr D Biol Crystallogr. 2008 ;64(Pt 5):607-10.
Willis MA, Zhuang Z, Song F, Howard A, Dunaway-Mariano D, Herzberg O. Structure of YciA from Haemophilus influenzae (HI0827), a hexameric broad specificity acyl-coenzyme A thioesterase. Biochemistry. 2008 ;47(9):2797-805.
2007
Galkin A, Kulakova L, Melamud E, Li L, Wu C, Mariano P, Dunaway-Mariano D, Nash TE, Herzberg O. Characterization, kinetics, and crystal structures of fructose-1,6-bisphosphate aldolase from the human parasite, Giardia lamblia. J Biol Chem. 2007 ;282(7):4859-67.
Toth EA. Molecular replacement. Methods Mol Biol. 2007 ;364:121-48.
Günther S, Varma AK, Moza B, Kasper KJ, Wyatt AW, Zhu P, Rahman AKMNur-ur, Li Y, Mariuzza RA, McCormick JK, et al. A novel loop domain in superantigens extends their T cell receptor recognition site. J Mol Biol. 2007 ;371(1):210-21.
Wiehe K, Pierce BG, Tong WWei, Hwang H, Mintseris J, Weng Z. The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI. Proteins. 2007 ;69(4):719-25.
Parsons JF, Greenhagen BT, Shi K, Calabrese K, Robinson H, Ladner JE. Structural and functional analysis of the pyocyanin biosynthetic protein PhzM from Pseudomonas aeruginosa. Biochemistry. 2007 ;46(7):1821-8.
Deng L, Langley RJ, Brown PH, Xu G, Teng L, Wang Q, Gonzales MI, Callender GG, Nishimura MI, Topalian SL, et al. Structural basis for the recognition of mutant self by a tumor-specific, MHC class II-restricted T cell receptor. Nat Immunol. 2007 ;8(4):398-408.
Cho S, Wang Q, Swaminathan CP, Hesek D, Lee M, Boons G-J, Mobashery S, Mariuzza RA. Structural insights into the bactericidal mechanism of human peptidoglycan recognition proteins. Proc Natl Acad Sci U S A. 2007 ;104(21):8761-6.
Chao KL, Muthukumar L, Herzberg O. Structure of human hyaluronidase-1, a hyaluronan hydrolyzing enzyme involved in tumor growth and angiogenesis. Biochemistry. 2007 ;46(23):6911-20.
Velikovsky CA, Deng L, Chlewicki LK, Fernández MM, Kumar V, Mariuzza RA. Structure of natural killer receptor 2B4 bound to CD48 reveals basis for heterophilic recognition in signaling lymphocyte activation molecule family. Immunity. 2007 ;27(4):572-84.
Fernández MM, Bhattacharya S, De Marzi MC, Brown PH, Kerzic M, Schuck P, Mariuzza RA, Malchiodi EL. Superantigen natural affinity maturation revealed by the crystal structure of staphylococcal enterotoxin G and its binding to T-cell receptor Vbeta8.2. Proteins. 2007 ;68(1):389-402.
Lim K, Read RJ, Chen CCH, Tempczyk A, Wei M, Ye D, Wu C, Dunaway-Mariano D, Herzberg O. Swiveling domain mechanism in pyruvate phosphate dikinase. Biochemistry. 2007 ;46(51):14845-53.
Guvench O, Qu C-K, Mackerell AD. Tyr66 acts as a conformational switch in the closed-to-open transition of the SHP-2 N-SH2-domain phosphotyrosine-peptide binding cleft. BMC Struct Biol. 2007 ;7:14.