Publications

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A Partial Nudged Elastic Band Implementation for Use with Large or Explicitly Solvated Systems.
Bergonzo C, Campbell AJ, Walker RC, Simmerling C. 2009. A Partial Nudged Elastic Band Implementation for Use with Large or Explicitly Solvated Systems. International journal of quantum chemistry 109(15): 3781.
Structural basis for the mechanism and substrate specificity of glycocyamine kinase, a phosphagen kinase family member.
Lim K, Pullalarevu S, Surabian KT, Howard A, Suzuki T, Moult J, Herzberg O. 2010. Structural basis for the mechanism and substrate specificity of glycocyamine kinase, a phosphagen kinase family member. Biochemistry 49(9): 2031-41. DOI: 10.1021/bi9020988
Contributions of the histidine side chain and the N-terminal alpha-amino group to the binding thermodynamics of oligopeptides to nucleic acids as a function of pH.
Ballin JD, Prevas JP, Ross CR, Toth EA, Wilson GM, Record MT. 2010. Contributions of the histidine side chain and the N-terminal alpha-amino group to the binding thermodynamics of oligopeptides to nucleic acids as a function of pH. Biochemistry 49(9): 2018-30. DOI: 10.1021/bi902027z
New biotechnological and nanomedicine strategies for treatment of lysosomal storage disorders.
Muro S. 2022. New biotechnological and nanomedicine strategies for treatment of lysosomal storage disorders. Wiley interdisciplinary reviews. Nanomedicine and nanobiotechnology 2(2): 189-204. DOI: 10.1002/wnan.73
Engineered biological nanofactories trigger quorum sensing response in targeted bacteria.
Fernandes R, Roy V, Wu HC, Bentley WE. 2010. Engineered biological nanofactories trigger quorum sensing response in targeted bacteria. Nature nanotechnology 5(3): 213-7. DOI: 10.1038/nnano.2009.457
The multiple mechanisms of T cell receptor cross-reactivity.
Yin Y, Mariuzza RA. 2009. The multiple mechanisms of T cell receptor cross-reactivity. Immunity 31(6): 849-51. DOI: 10.1016/j.immuni.2009.12.002
Autonomous induction of recombinant proteins by minimally rewiring native quorum sensing regulon of E. coli.
Tsao CY, Hooshangi S, Wu HC, Valdes JJ, Bentley WE. 2010. Autonomous induction of recombinant proteins by minimally rewiring native quorum sensing regulon of E. coli. Metabolic engineering 12(3): 291-7. DOI: 10.1016/j.ymben.2010.01.002
The effects of CapZ peptide (TRTK-12) binding to S100B-Ca2+ as examined by NMR and X-ray crystallography.
Charpentier TH, Thompson LE, Liriano MA, Varney KM, Wilder PT, Pozharski E, Toth EA, Weber DJ. 2010. The effects of CapZ peptide (TRTK-12) binding to S100B-Ca2+ as examined by NMR and X-ray crystallography. Journal of molecular biology 396(5): 1227-43. DOI: 10.1016/j.jmb.2009.12.057
A practical implementation of cross-spectrum in protein backbone resonance assignment.
Chen K, Delaglio F, Tjandra N. 2010. A practical implementation of cross-spectrum in protein backbone resonance assignment. Journal of magnetic resonance (San Diego, Calif. : 1997) 203(2): 208-12. DOI: 10.1016/j.jmr.2009.12.018
Biofabrication methods for the patterned assembly and synthesis of viral nanotemplates.
Gerasopoulos K, McCarthy M, Banerjee P, Fan X, Culver JN, Ghodssi R. 2010. Biofabrication methods for the patterned assembly and synthesis of viral nanotemplates. Nanotechnology 21(5): 055304. DOI: 10.1088/0957-4484/21/5/055304
Comprehensive density functional theory study on the mechanism of activation of the nonapeptide hormone oxytocin by metal ions.
Xu X, Yu W, Huang Z, Lin Z. 2010. Comprehensive density functional theory study on the mechanism of activation of the nonapeptide hormone oxytocin by metal ions. The journal of physical chemistry. B 114(3): 1417-23. DOI: 10.1021/jp907436p
In-plane homogeneity and lipid dynamics in tethered bilayer lipid membranes (tBLMs).
Shenoy S, Moldovan R, Fitzpatrick J, Vanderah DJ, Deserno M, Lösche M. 2010. In-plane homogeneity and lipid dynamics in tethered bilayer lipid membranes (tBLMs). Soft matter 2010(6): 1263-1274.
Relationship between antibody 2F5 neutralization of HIV-1 and hydrophobicity of its heavy chain third complementarity-determining region.
Ofek G, McKee K, Yang Y, Yang ZY, Skinner J, Guenaga FJ, Wyatt R, Zwick MB, Nabel GJ, Mascola JR, et al. 2010. Relationship between antibody 2F5 neutralization of HIV-1 and hydrophobicity of its heavy chain third complementarity-determining region. Journal of virology 84(6): 2955-62. DOI: 10.1128/JVI.02257-09
Stabilization of native and non-native structures by salt bridges in a lattice model of the GCN4 leucine dimer.
Liu Y, Chapagain PP, Gerstman BS. 2010. Stabilization of native and non-native structures by salt bridges in a lattice model of the GCN4 leucine dimer. The journal of physical chemistry. B 114(2): 796-803. DOI: 10.1021/jp909872a
Cross species quorum quenching using a native AI-2 processing enzyme.
Roy V, Fernandes R, Tsao CY, Bentley WE. 2010. Cross species quorum quenching using a native AI-2 processing enzyme. ACS chemical biology 5(2): 223-32. DOI: 10.1021/cb9002738