Braun Group Recent Publications


Negi, S.S., and Braun, W., Cross-React: a new structural bioinformatics method for predicting allergen cross-reactivity,
Bioinformatics, Jan 5, 2017
Abstract      Full Paper

Fongang, B., Kong, F., Negi, S.S., Braun, W. Kudlicki, A., A Conserved Structural Signature of the Homeobox Coding DNA in HOX genes,
Scientific Reports 6, Article number: 35415 (2016)
Abstract      Full Paper

Chen, X., Negi SS, Liao S, Gao V, Braun W, Dreskin SC. Conformational IgE epitopes of peanut allergens Ara h 2 and Ara h 6
Clin Exp Allergy. 2016 May 30. doi: 10.1111/cea.12764. [Epub ahead of print]
Abstract      Full Paper

Bergren, N.A., Auguste, A.J., Forrester, N.L., Negi, S.S., Braun, W. and Weaver, S.C. Western Equine encephalitis virus: evolutionary analysis of a declining alphavirus based on complete genome sequences
J. Virol.,  4, JVI.01463-14, 2014.
Abstract      Full Paper

Marceau, C.D., Negi, S.S., Hernandez, H., Callison, J., Marzi, A., Borisevich, V., Braun, W., Berry, Jody., Feldmann, H. and Rockx, B. Novel neutralizing monoclonal antibodies protect rodents against lethal filovirus challenges
Trials in Vaccinology,  3, 89-94, 2014.
Abstract      Full Paper

Rana, T., Hasan, R.J., Nowicki, S., Venkatarajan, M.S., Singh, R., Urvil, P.T., Popov, V., Braun, W., Popik, W., Goodwin, J.S. and Nowicki, B.J.  Complement Protective Epitopes and CD55-Microtubule Complexes Facilitate the Invasion and Intracellular Persistence of Uropathogenic Escherichia coli.
J. Infec. Dis., 209(7) 1066-1076, 2014 (Epub Nov 20, 2013).
Abstract      Full Paper

Braun, W. and Schein, C.H.  Membrane Interaction and Functional Plasticity of Inositol Polyphosphate 5-Phosphatases
Structure, 22(5), 664-666, 2014.
Abstract      Full Paper

Power, T.D, Ivanciuc, O., Schein, C.H. and Braun, W.  Assessment of 3D models for allergen research.
PROTEINS: Struct. Funct. and Bioinf., 81(4), 545-554, 2013.
Abstract      Full Paper

Navaratnarajah, C.K., Negi, S.S., Braun, W. and Cattaneo, R. Membrane fusion triggering: three modules with different structure and function in the upper half of the measles virus attachment protein stalk.
J. Biol. Chem., 287(46), 38543-38551, 2012.
Abstract      Full Paper

Apte-Sengupta, S., Negi, S.S., Leonard, V.H.J., Oezguen, N., Navaratnarajah, C.K., W. Braun, W. and Cattaneo, R.  Base of the measles virus fusion trimer head receives the signal that triggers membrane fusion.
J. Biol. Chem., 287(39), 33026-33035, 2012.
Abstract      Full Paper

Oezguen, N., Power, T.D., Urvil, P., Feng, H., Pothoulakis, C., Stamler, J.S., Braun, W. and Savidge, T.C.  Clostridial toxins: Sensing a target in a hostile gut environment.
Gut Microbes, 3(1), 35-41, 2012.
Abstract      Full Paper

Lu, W., Negi, S.S., Oberhauser, A.F. and Braun, W.  Engineering proteins with enhanced mechanical stability by force-specific sequence motifs.
Proteins, 80(5), 1308-1315, 2012.
Abstract      Full Paper

Tiwari, R., Negi, S.S., Braun, B., Braun, W., Pomes, A., Chapman, M.D., Goldblum, R.M. and Midoro-Horiuti, T.  Validation of a Phage Display and Computational Algorithm by Mapping a Conformational Epitope of Bla g 2.
Int. Arch. Allergy Immunol., 157(4), 323-330, 2012.
Abstract      Full Paper

Oezguen, N., Mantha, A.K., Izumi, T., Schein, C.H., Mitra, S. and Braun, W.  MD simulation and experimental evidence for Mg2+ binding at the b site in human AP endonuclease 1.
Bioinformation, 7(4), 184-198, 2011.
Abstract      Full Paper

Savidge, T.C., Urvil, P., Oezguen, N., Ali, K., Choudhury, A., Acharya, V., Pinchuk, I., Torres, A.G., English, R.D., Wiktorowicz, J.E., Loeffelholz, M., Kumar, R., Shi, L., Nie, W., Braun, W., Herman, B., Hausladen, A., Feng, H., Stamler, J.S. and Pothoulakis, C.  Host S-nitrosylation inhibits clostridial small molecule-activated glucosylating toxins.
Nat. Med., 17(9), 1136-1142, 2011.
Abstract      Full Paper

Ivanciuc, O., Gendel, S.M., Power, T.D., Schein, C.H. and Braun, W.  AllerML: Markup language for allergens.
Regul. Toxicol. Pharmacol., 60(1), 151-160, 2011.
Abstract      Full Paper

Navaratnarajah, C.K., Oezguen, N., Rupp, L., Kay, L., Leonard, V.H.J., Braun, W. and Cattaneo, R.  The heads of the measles virus attachment protein move to transmit the fusion-triggering signal.
Nat. Struct. Mol. Biol., 18(2), 128-134, 2011.
Abstract      Full Paper

Schein, C.H., Ivanciuc, O., Midoro-Horiuti, T., Goldblum, R.M. and Braun, W.  An allergen portrait gallery: representative structures and an overview of IgE binding surfaces.
Bioinform. Biol. Insights, 4, 113-125, 2010.
Abstract      Full Paper

Schein, C.H., Oezguen, N., van der Heden van Noort, G.J., Filippov, D.V., Paul, A., Kumar, E. and Braun, W.  NMR solution structure of poliovirus uridylyated peptide linked to the genome (VPgpU).
Peptides, 31(8), 1441-1448, 2010.
Abstract      Full Paper

Negi, S.S. and Braun, W.  Automated Detection of Conformational Epitopes using Phage Display Peptide Sequences.
Bioinform. Biol. Insights,  3, 71-81, 2009.
Abstract      Full Paper

Ivanciuc, O., Schein, C.H., Garcia, T.I., Oezguen, N., Negi, S.S. and Braun, W.  Structural analysis of linear and conformational epitopes of allergens.
Regul. Toxicol. Pharmacol., 54(3 Suppl), S11-S19, 2009.
Abstract      Full Paper 

Garcia, T.I., Oberhauser, A.F. and Braun, W.  Mechanical stability and differentially conserved physical-chemical properties of Titin Ig-domains.
PROTEINS: Struct. Funct. and Bioinf., 75(3), 706-718, 2009.
Abstract      Full Paper

Ivanciuc, O., Midoro-Horiuti, T., Schein, C.H., Xie, L., Hillman, G.R., Goldblum, R.M. and Braun, W.  The property index PD predicts peptides that cross-react with IgE antibodies.
Mol. Immunol., 46(5), 873-883, 2009.
Abstract      Full Paper

Ivanciuc, O., Garcia, T.I., Torres, M., Schein, C.H. and Braun, W.  Characteristic motifs for families of allergenic proteins.
Mol. Immunol., 46(4), 559-568, 2009.
Abstract      Full Paper

Oezguen, N., Zhou, B., Negi, S.S., Ivanciuc, O., Schein, C.H., Labesse, G. and Braun, W.  Comprehensive 3D-modeling of allergenic proteins and amino acid composition of potential conformational IgE epitopes.
Mol. Immunol., 45(14), 3740-3747, 2008.
Abstract      Full Paper

Oezguen, N., Kumar, S., Hindupur, A., Braun, W., Muralidhara, B.K. and Halpert, J.R.  Identification and analysis of conserved motifs in cytochrome P450 family 2: Functional and structural role of a Motif 187RFDYKD192 in CYP2B enzymes.
J. Biol. Chem., 283(31), 21808-21816, 2008.
Abstract      Full Paper

Leonard, V.H.J., Sinn, P.L., Hodge, G., Miest, T., Devaux, P., Oezguen, N., Braun, W., McCray, P.B. Jr., McChesney, M.B. and Cattaneo, R.  Measles virus blind to its epithelial cell receptor remains virulent in rhesus monkeys but cannot cross the airway epithelium and is not shed.
J. Clin. Invest., 118(7), 2448-2458, 2008.
Abstract      Full Paper

Mantha, A.K., Oezguen, N., Bhakat, K.K., Izumi, T., Braun, W. and Mitra, S.  Unusual Role of a Cysteine Residue in Substrate Binding and Activity of Human AP-Endonuclease 1.
J. Mol. Biol., 379(1), 28-37, 2008.
Abstract      Full Paper

Navaratnarajah, C.K., Vongpunsawad, S., Oezguen, N., Stehle, T., Braun, W., Hashiguchi, T., Maenaka, K., Yanagi, Y. and Cattaneo, R.  Dynamic interaction of the measles virus hemagglutinin with its receptor SLAM.
J. Biol. Chem., 283(17), 11763-11771, 2008.
Abstract      Full Paper

Negi, S.S., Carol, A., Pandya, S., Braun, W. and Anderson, L.  Co-Localization of Glyceraldehyde-3-Phosphate Dehydrogenase with Ferredoxin-NADP Reductase in Pea Leaf Chloroplasts.
J. Struct. Biol., 161(1), 18-30, 2008.
Abstract      Full Paper

Ivanciuc, O. and Braun, W.  Robust quantitative modeling of peptide binding affinities for MHC molecules using physical-chemical descriptors.
Protein Pept. Lett., 14(9), 903-916, 2007.
Abstract      Full Paper

Negi, S., Schein, C.H., Oezguen, N., Power, T.D. and Braun, W.  InterProSurf: a web server for predicting interacting sites on protein surfaces.
Bioinformatics,  23(24), 3397-3399, 2007.
Abstract      Full Paper

Negi, S. and Braun, W. Statistical analysis of physical-chemical properties and prediction of protein-protein interfaces.
J. Mol. Model., 13(11), 1157-1167, 2007.
Abstract      Full Paper

Oezguen, N., Schein, C.H., Peddi, S.R.,  Power, T.D., Izumi, T. and Braun, W.  A "moving metal mechanism" for substrate cleavage by DNA repair endonuclease APE-1.
, 68(1), 313-323, 2007.
Abstract      Full Paper

Chen, D, Menche, G, Power, T.D., Peterson, J.W. and Schein, C.H . Accounting for ligand-bound metal ions in docking small molecules on adenylyl cyclase toxins.
, 67(3), 593-605, 2007.
Abstract      Full Paper

Schein, C.H. Ivanciuc O. and Braun, W.  Bioinformatics approaches to classifying allergens and predicting cross-reactivity.
Immunol. Allergy Clin. North Am., 27(1):1-27 2007.
Abstract      Full Paper

Schein, C.H., Ivanciuc, O. and Braun, W.  Structural Database of Allergenic Proteins (SDAP).
Food Allergy
, Edited by S.J. Maleki, 2006 ASM Press, Washington D.C. 257-283.
Book Chapter

Negi, S.S., Kolokoltsov, A.A., Schein, C.H., Davey, R.A. and Braun, W.  Determining functionally important amino acid residues of the E1 protein of Venezuelan equine encephalitis virus.
J. Mol. Model. (Online)
, 12(6):921-929, 2006.
Abstract      Full Paper

Schein, C.H., Oezguen, N., Volk, D.E., Garimella, R., Paul, A. and Braun, W. NMR structure of the viral peptide linked to the genome (VPg) of poliovirus.
,  27(7):1676-1684 2006.
Abstract      Full Paper

Muralidhara, B.K., Negi., S., Chin, C.C., Braun, W. and Halpert. J.R. Conformational flexibility of mammalian cytochrome P450 2B4 in binding imidazole inhibitors with different ring chemistry and side chains.
J. Biol. Chem.
  281(12):8051-8061, 2006.
Abstract      Full Paper

Midoro-Horiuti, T., Schein, C.H., Mathura, V., Braun, W., Czerwinski, E.W., Togawa, A., Kondo, Y., Oka, T., Watanabe, M. and Goldblum, R.M. Structural basis for epitope sharing between group 1 allergens of cedar pollen.
Mol. Immunol
.  43(6):509-518, 2006.
Abstract      Full Paper

Schein, C.H., Ivanciuc, O. and Braun, W. Common physical-chemical properties correlate with similar structure of the IgE epitopes of peanut allergens.
J. Agric. Food Chem.
53(22):8752-8759, 2005.
Abstract      Full Paper

Schein, C.H., Zhou, B. and Braun, W. Stereophysicochemical variability plots highlight conserved antigenic areas in Flaviviruses.
Virol. J.
  2(1):40, 2005.
Abstract      Full Paper

von Messling, V., Oezguen, N., Zheng, Q., Vongpunsawad, S., Braun, W. and Cattaneo, R. Nearby clusters of hemagglutinin residues sustain SLAM-dependent canine distemper virus entry in peripheral blood mononuclear cells.
J. Virol.  79(9):5857-5862, 2005.
Abstract      Full Paper

Cummins, S.F., Schein, C.H., Xu, Y., Braun, W. and Nagle, G.T. Molluscan attractins, a family of water-borne protein pheromones with interspecific attractiveness.
  26(1):121-129, 2005.
Abstract      Full Paper

Schein, C.H., Zhou, B., Oezguen, N., Mathura, V.S., and Braun, W. Molego-based definition of the architecture and specificity of metal binding sites.
Proteins  58
(1):200-210, 2005.
Abstract      Full Paper

Painter, S.D., Cummins, S.F., Nichols, A.E., Akalal, D.B.G., Schein, C.H., Braun, W., Smith, J.S., Susswein, A.J., Levy, M., de Boer, P.A.C.M., ter Maat, A., Miller, M.W., Scanlan, C., Milberg, R.M., Sweedler, J.V. and  Nagle, G.T. Structural and functional analysis of Aplysa attractins, a family of water-borne protein phermones with interspecific attractiveness.
Proc. Natl. Acad. Sci. USA
  101(18):6929-6933, 2004.
Abstract      Full Paper

Ivanciuc, O., Oezguen, N., Mathura, V.S., Schein, C.H., Xu, Y. and Braun, W.  Using property based sequence motifs and 3D modeling to determine structure and functional regions of proteins. 
Curr. Med. Chem.
  11:583-593, 2004.
Abstract      Full Paper

Izumi, T., Schein, C.H., Oezguen, N., Feng, Y. and Braun, W.  Effects of backbone contacts 3' to the abasic site on the cleavage and the product binding by human apurinic/apyrimidinic endonuclease (APE1). 
   43(3):684-689, 2004.
Abstract      Full Paper

Vongpunsawad, S., Oezgun, N., Braun, W. and Cattaneo R.  Selectively receptor-blind measles viruses:  identification of residues necessary for SLAM- or CD46-induced fusion and their localization on a new hemagglutinin structural model. 
J. Virol.  78(1):302-313, 2004.
Abstract      Full Paper

Midoro-Horiuti, T., Mathura, V., Schein, C.H., Braun, W., Yu, S., Watanabe, M., Lee, J.C., Brooks, E.G. and Goldblum, R.  Major linear IgE epitopes of mountain cedar pollen allergen Jun a 1 map to the pectate lyase catalytic site. 
Mol. Immunol.
  40(8):555-562, 2003.
Abstract      Full Paper

Braun, W.  Developing computational tools for NMR:  the early days of protein NMR.
 Magn. Res. Chem.  41(S1):S51-S55, 2003.
Abstract      Full Paper

Ivanciuc, O., Mathura, V., Midoro-Horiuti, T., Braun, W., Goldblum, R. and Schein, C.H.  Detecting potential IgE-reactive sites on food proteins using a sequence and structure database, SDAP-Food. 
J. Agr. Food Chem.
  51(16):4830-4837, 2003.
Abstract      Full Paper

Garimella, R., Xu, Y., Schein, C.H., Rajarathnam, K., Painter, S.D., Nagle, G.T. and Braun, W.  NMR solution structure of attractin, a water-borne protein pheromone from the mollusk Aplysia californica
  42(33):9970-9979, 2003.
Abstract       Full Paper

Mathura, V.S., Soman, K.V., Varma, T.K. and Braun, W.  A multimeric model for murine anti-apoptotic protein Bcl-2 and structural insights for its regulation by post-translational modification. 
J. Mol. Model.
  9(5):298-303, 2003.
Abstract       Full Paper

Ivanciuc, O., Schein, C.H. and Braun, W.  SDAP:  database and computational tools for allergenic proteins. 
Nucleic Acids Res
.  31(1):359-362, 2003.
Abstract       Full Paper

Mathura, M.S., Schein, C.H. and Braun, W.  Identifying property based sequence motifs in protein families and superfamilies:  application to DNase-1 related endonucleases. 
  19(11):1381-1390, 2003.
Abstract       Full Paper

Schein, C.H., Ozgun, N., Izumi, T. and Braun, W.  Total sequence decomposition distinguishes functional modules, "molegos" in apurinic/apyrimidinic endonucleases. 
BMC Bioinformatics  3(1):37, 2002.
Abstract       Full Paper

Ivanciuc, O.I., Schein, C.H. and Braun, W.  Data mining of sequences and 3D structures of allergenic proteins. 
  18(10):1358-1364, 2002.
Abstract       Full Paper

Murtazina, D., Puchkaev, A.V., Schein, C.H., Oezguen, N., Braun, W., Nanavati, A. and Pikuleva, I.A.  Membrane-protein interactions contribute to efficient 27-hydroxylation of cholesterol by mitochondrial cytochrome P450 27A1. 
J. Biol. Chem
.  277(40):37582-37589, 2002.
Abstract       Full Paper

Hasan, R.J., Pawelczek, E., Urvil, P.T., Venkatarajan, M.S., Goluszko, P., Kur, J., Selvarangan, R., Nowicki, S., Braun, W. and Nowicki, B.J.  Structure-function analysis of decay-accelerating factor:  identification of residues important for binding of the escherichia coli Dr adhesin and complement regulation. 
Infect. Immun
.  70(8):4485-4493, 2002.
Abstract       Full Paper

Oezguen, N., Adamian, L., Xu, Y., Rajarathnam, K. and Braun, W.  Automated assignment and 3D structure calculations using combinations of 2D homonuclear and 3D heteronuclear NOESY spectra. 
J. Biomol. NMR
  22(3):249-263, 2002.
Abstract       Full Paper

Venkatarajan, M.S. and Braun, W.  New quantitative descriptors of amino acids based on multidimensional scaling of a large number of physical-chemical properties. 
J. Mol. Model
.  7(12):445-453, 2001.
Abstract       Full Paper

Soman ,K.V. and Braun, W.   Determining the 3D-fold of a protein from approximate constraints:  a simulation study. 
Cell. Biochem. Biophys
.  34(3):283-304, 2001.
Abstract       Full Paper Not Available Humana Press, INC.

Schein, C.H., Nagle, G.T., Page, J., Sweedler, J.V., Xu, Y., Painter, S.D. and Braun, W.  Aplysia attractin:  biophysical characterization and modeling of a water-borne pheromone. 
Biophys. J.
  81(1):463-472, 2001.
Abstract       Full Paper

Williams, R.M., Obradovi. Z., Mathura, V., Braun, W., Garner, E.C., Young, J., Takayama, S., Brown, C.J., Dunker, A.K.  The protein non-folding problem: amino acid determinants of intrinsic order and disorder. 
Pac. Symp. Biocomput.
  89-100, 2001.
Abstract       Full Paper

Soman , K.V., Schein, C.H., Zhu, H. and Braun, W.   Homology modeling and simulations of nuclease structures. 
Methods Mol. Biol. 
160:263-286, 2001.
Abstract       Full Paper Not Available Online

Xu, Y., Jablonsky, M., Jackson, P.L., Braun, W. and Krishna, N.R.   Automated assignment of NOESY cross peaks and determination of the protein structure of a new world scorpion neurotoxin using NOAH/DIAMOD. 
J. Mag. Res.
  148(1):35-46, 2001.
Abstract       Full Paper

Zhu, H., Schein, C.H. and Braun, W.  MASIA:  recognition of common patterns and properties in multiple aligned protein sequences.  Bioinformatics  16(10):950-951, 2000.
Abstract       Full Paper

Soman, K.V., Midoro-Horiuti, T., Chu, J.Y., Goldblum, R.M., Brooks, E.G., Braun, W. and Schein, C.H.   Automated Homology modeling and characterization of IgE binding epitopes of mountain cedar allergen Jun a 3. 
Biophys. J.  79(3):1601-1609, 2000.
Abstract       Full Paper