IBBR Publications

Guo M, Zheng Y, Terell JL, Ad M, Opoku-Temeng C, Bentley WE, Sintim HO. Geminal dihalogen isosteric replacement in hydrated AI-2 affords potent quorum sensing modulators. Chem Commun (Camb). 2015 ;51(13):2617-20.

Agarwal R, Zakharov S, S Hasan S, Ryan CM, Whitelegge JP, Cramer WA. Structure-function of cyanobacterial outer-membrane protein, Slr1270: homolog of Escherichia coli drug export/colicin import protein, TolC. FEBS Lett. 2014 ;588(21):3793-801.

Ha J-H, Eo Y, Grishaev A, Guo M, Smith JAI, Sintim HO, Kim E-H, Cheong H-K, Bentley WE, Ryu K-S. Crystal structures of the LsrR proteins complexed with phospho-AI-2 and two signal-interrupting analogues reveal distinct mechanisms for ligand recognition. J Am Chem Soc. 2013 ;135(41):15526-35.

S Hasan S, Baniulis D, Yamashita E, Zhalnina MV, Zakharov SD, Stofleth JT, Cramer WA. Methods for studying interactions of detergents and lipids with α-helical and β-barrel integral membrane proteins. Curr Protoc Protein Sci. 2013 ;74:29.7.1-29.7.30.

Jain V, Hilton B, Lin B, Jain A, Mackerell AD, Zou Y, Cho BP. Structural and thermodynamic insight into Escherichia coli UvrABC-mediated incision of cluster diacetylaminofluorene adducts on the NarI sequence. Chem Res Toxicol. 2013 ;26(8):1251-62.

Jain V, Hilton B, Lin B, Patnaik S, Liang F, Darian E, Zou Y, Mackerell AD, Cho BP. Unusual sequence effects on nucleotide excision repair of arylamine lesions: DNA bending/distortion as a primary recognition factor. Nucleic Acids Res. 2013 ;41(2):869-80.

Gamby S, Roy V, Guo M, Smith JAI, Wang J, Stewart JE, Wang X, Bentley WE, Sintim HO. Altering the communication networks of multispecies microbial systems using a diverse toolbox of AI-2 analogues. ACS Chem Biol. 2012 ;7(6):1023-30.

Maiti A, Noon MS, Mackerell AD, Pozharski E, Drohat AC. Lesion processing by a repair enzyme is severely curtailed by residues needed to prevent aberrant activity on undamaged DNA. Proc Natl Acad Sci U S A. 2012 ;109(21):8091-6.

Bera AK, Atanasova V, Dhanda A, Ladner JE, Parsons JF. Structure of aminodeoxychorismate synthase from Stenotrophomonas maltophilia. Biochemistry. 2012 ;51(51):10208-17.

Hooshangi S, Bentley WE. LsrR quorum sensing "switch" is revealed by a bottom-up approach. PLoS Comput Biol. 2011 ;7(9):e1002172.

Tsao C-Y, Wang L, Hashimoto Y, Yi H, March JC, DeLisa MP, Wood TK, Valdes JJ, Bentley WE. LuxS coexpression enhances yields of recombinant proteins in Escherichia coli in part through posttranscriptional control of GroEL. Appl Environ Microbiol. 2011 ;77(6):2141-52.

Cramer WA, Zakharov SD, S Hasan S, Zhang H, Baniulis D, Zhalnina MV, Soriano GM, Sharma O, Rochet JC, Ryan C, et al. Membrane proteins in four acts: function precedes structure determination. Methods. 2011 ;55(4):415-20.

Stagno JR, Altieri AS, Bubunenko M, Tarasov SG, Li J, Court DL, R Byrd A, Ji X. Structural basis for RNA recognition by NusB and NusE in the initiation of transcription antitermination. Nucleic Acids Res. 2011 ;39(17):7803-15.

Stourman NV, Branch MC, Schaab MR, Harp JM, Ladner JE, Armstrong RN. Structure and function of YghU, a nu-class glutathione transferase related to YfcG from Escherichia coli. Biochemistry. 2011 ;50(7):1274-81.

Roy V, Fernandes R, Tsao C-Y, Bentley WE. Cross species quorum quenching using a native AI-2 processing enzyme. ACS Chem Biol. 2010 ;5(2):223-32.

Wadington MC, Ladner JE, Stourman NV, Harp JM, Armstrong RN. Analysis of the structure and function of YfcG from Escherichia coli reveals an efficient and unique disulfide bond reductase. Biochemistry. 2009 ;48(28):6559-61.

D Gallagher T, Smith N, Kim S-K, Robinson H, Reddy PT. Profound asymmetry in the structure of the cAMP-free cAMP Receptor Protein (CRP) from Mycobacterium tuberculosis. J Biol Chem. 2009 ;284(13):8228-32.

Byrd CM, Bentley WE. Quieting cross talk--the quorum sensing regulator LsrR as a possible target for fighting bacterial infections. Cell Res. 2009 ;19(11):1229-30.

Ramprakash J, Doseeva V, Galkin A, Krajewski W, Muthukumar L, Pullalarevu S, Demirkan E, Herzberg O, Moult J, Schwarz FP. Comparison of the chemical and thermal denaturation of proteins by a two-state transition model. Anal Biochem. 2008 ;374(1):221-30.

Chao KL, Lim K, Lehmann C, Doseeva V, Howard AJ, Schwarz FP, Herzberg O. The Escherichia coli YdcF binds S-adenosyl-L-methionine and adopts an alpha/beta-fold characteristic of nucleotide-utilizing enzymes. Proteins. 2008 ;72(1):506-9.

Lee J, Zhang X-S, Hegde M, Bentley WE, Jayaraman A, Wood TK. Indole cell signaling occurs primarily at low temperatures in Escherichia coli. ISME J. 2008 ;2(10):1007-23.

Fang X, Bentley WE, Zafiriou E. Stochastic modeling of gene positive autoregulation networks involving signal molecules. Biophys J. 2008 ;95(7):3137-45.

Das R, Loss S, Li J, Waugh DS, Tarasov S, Wingfield PT, R Byrd A, Altieri AS. Structural biophysics of the NusB:NusE antitermination complex. J Mol Biol. 2008 ;376(3):705-20.

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.

McFeeters RL, Altieri AS, Cherry S, Tropea JE, Waugh DS, R Byrd A. The high-precision solution structure of Yersinia modulating protein YmoA provides insight into interaction with H-NS. Biochemistry. 2007 ;46(49):13975-82.