Publications

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Gene network homology in prokaryotes using a similarity search approach: queries of quorum sensing signal transduction.
Quan DN, Bentley WE. 2012. Gene network homology in prokaryotes using a similarity search approach: queries of quorum sensing signal transduction. PLoS computational biology 8(8): e1002637. DOI: 10.1371/journal.pcbi.1002637
Contrast-matched small-angle X-ray scattering from a heavy-atom-labeled protein in structure determination: application to a lead-substituted calmodulin-peptide complex.
Grishaev A, Anthis NJ, Clore GM. 2012. Contrast-matched small-angle X-ray scattering from a heavy-atom-labeled protein in structure determination: application to a lead-substituted calmodulin-peptide complex. Journal of the American Chemical Society 134(36): 14686-9. DOI: 10.1021/ja306359z
Mass spectrometry quantification of clusterin in the human brain.
Chen J, Wang M, Turko IV. 2012. Mass spectrometry quantification of clusterin in the human brain. Molecular neurodegeneration 7: 41. DOI: 10.1186/1750-1326-7-41
Glucose oxidase-mediated gelation: a simple test to detect glucose in food products.
Liu Y, Javvaji V, Raghavan SR, Bentley WE, Payne GF. 2012. Glucose oxidase-mediated gelation: a simple test to detect glucose in food products. Journal of agricultural and food chemistry 60(36): 8963-7. DOI: 10.1021/jf301376b
Encapsulated fusion protein confers "sense and respond" activity to chitosan-alginate capsules to manipulate bacterial quorum sensing.
Gupta A, Terrell JL, Fernandes R, Dowling MB, Payne GF, Raghavan SR, Bentley WE. 2013. Encapsulated fusion protein confers "sense and respond" activity to chitosan-alginate capsules to manipulate bacterial quorum sensing. Biotechnology and bioengineering 110(2): 552-62. DOI: 10.1002/bit.24711
Some new speculative ideas about the "behavioral homeostasis theory" as to how the simple learned behaviors of habituation and sensitization improve organism survival throughout phylogeny.
Eisenstein EM, Eisenstein DL, Sarma JS, Knapp H, Smith JC. 2012. Some new speculative ideas about the "behavioral homeostasis theory" as to how the simple learned behaviors of habituation and sensitization improve organism survival throughout phylogeny. Communicative & integrative biology 5(3): 233-9. DOI: 10.4161/cib.19480
HIV-1 neutralizing antibodies display dual recognition of the primary and coreceptor binding sites and preferential binding to fully cleaved envelope glycoproteins.
Li Y, O'Dell S, Wilson R, Wu X, Schmidt SD, Hogerkorp CM, Louder MK, Longo NS, Poulsen C, Guenaga J, et al. 2012. HIV-1 neutralizing antibodies display dual recognition of the primary and coreceptor binding sites and preferential binding to fully cleaved envelope glycoproteins. Journal of virology 86(20): 11231-41.
Crystal structure of the Sema-PSI extracellular domain of human RON receptor tyrosine kinase.
Chao KL, Tsai IW, Chen C, Herzberg O. 2012. Crystal structure of the Sema-PSI extracellular domain of human RON receptor tyrosine kinase. PloS one 7(7): e41912. DOI: 10.1371/journal.pone.0041912
Target binding to S100B reduces dynamic properties and increases Ca(2+)-binding affinity for wild type and EF-hand mutant proteins.
Liriano MA, Varney KM, Wright NT, Hoffman CL, Toth EA, Ishima R, Weber DJ. 2012. Target binding to S100B reduces dynamic properties and increases Ca(2+)-binding affinity for wild type and EF-hand mutant proteins. Journal of molecular biology 423(3): 365-85. DOI: 10.1016/j.jmb.2012.07.011
Extension of the CHARMM General Force Field to sulfonyl-containing compounds and its utility in biomolecular simulations.
Yu W, He X, Vanommeslaeghe K, MacKerell AD. 2012. Extension of the CHARMM General Force Field to sulfonyl-containing compounds and its utility in biomolecular simulations. Journal of computational chemistry 33(31): 2451-68. DOI: 10.1002/jcc.23067
The effect of remodelling and contractility of the actin cytoskeleton on the shear resistance of single cells: a computational and experimental investigation.
Dowling EP, Ronan W, Ofek G, Deshpande VS, McMeeking RM, Athanasiou KA, McGarry JP. 2012. The effect of remodelling and contractility of the actin cytoskeleton on the shear resistance of single cells: a computational and experimental investigation. Journal of the Royal Society, Interface 9(77): 3469-79. DOI: 10.1098/rsif.2012.0428
X-ray crystal structure of the streptococcal specific phage lysin PlyC.
McGowan S, Buckle AM, Mitchell MS, Hoopes JT, Gallagher DT, Heselpoth RD, Shen Y, Reboul CF, Law RH, Fischetti VA, et al. 2012. X-ray crystal structure of the streptococcal specific phage lysin PlyC. Proceedings of the National Academy of Sciences of the United States of America 109(31): 12752-7. DOI: 10.1073/pnas.1208424109
Expression and characterization of 15N-labeled human C-reactive protein in Escherichia coli and Pichia pastoris for use in isotope-dilution mass spectrometry.
Kilpatrick EL, Liao WL, Camara JE, Turko IV, Bunk DM. 2012. Expression and characterization of 15N-labeled human C-reactive protein in Escherichia coli and Pichia pastoris for use in isotope-dilution mass spectrometry. Protein expression and purification 85(1): 94-9. DOI: 10.1016/j.pep.2012.06.019
High-resolution definition of vaccine-elicited B cell responses against the HIV primary receptor binding site.
Sundling C, Li Y, Huynh N, Poulsen C, Wilson R, O'Dell S, Feng Y, Mascola JR, Wyatt RT, Karlsson Hedestam GB. 2012. High-resolution definition of vaccine-elicited B cell responses against the HIV primary receptor binding site. Science translational medicine 4(142): 142ra96. DOI: 10.1126/scitranslmed.3003752
Identification of multiple RIG-I-specific pathogen associated molecular patterns within the West Nile virus genome and antigenome.
Shipley JG, Vandergaast R, Deng L, Mariuzza RA, Fredericksen BL. 2012. Identification of multiple RIG-I-specific pathogen associated molecular patterns within the West Nile virus genome and antigenome. Virology 432(1): 232-8. DOI: 10.1016/j.virol.2012.06.009