Publications:

Refereed Journal Articles:

  1. Xiao F, Cai Y, Wang JC, Green D, Cheng RH, Demeler B, Guo P. Adjustable Ellipsoid Nanoparticles Assembled from Re-engineered Connectors of the Bacteriophage Phi29 DNA Packaging Motor. ACS Nano. 2009 Jul 17. [Epub ahead of print]

  2. Cölfen H, Laue TM, Wohlleben W, Schilling K, Karabudak E, Langhorst BW, Brookes E, Dubbs B, Zollars D, Rocco M, Demeler B. The Open AUC Project. Eur Biophys J. 2009 Mar 19. [Epub ahead of print]

  3. Brookes E, Cao W, Demeler B. A two-dimensional spectrum analysis for sedimentation velocity experiments of mixtures with heterogeneity in molecular weight and shape. Eur Biophys J. 2009 Feb 27. [Epub ahead of print]

  4. Nagel-Steger L, Demeler B, Meyer-Zaika W, Hochdörffer K, Schrader T, Willbold D. Modulation of aggregate size- and shape-distributions of the amyloid-beta peptide by a designed beta-sheet breaker. Eur Biophys J. 2009 Feb 24. [Epub ahead of print]

  5. Brookes E, Demeler B, Rosano C, Rocco M. The implementation of SOMO (SOlution MOdeller) in the UltraScan analytical ultracentrifugation data analysis suite: enhanced capabilities allow the reliable hydrodynamic modeling of virtually any kind of biomacromolecule. Eur Biophys J. 2009 Feb 21. [Epub ahead of print]

  6. Demeler B, Brookes E, Nagel-Steger L. Analysis of heterogeneity in molecular weight and shape by analytical ultracentrifugation using parallel distributed computing. Methods Enzymol. 2009. 454:87-113.

  7. Luczkowski M, Stachura M, Schirf V, Demeler B, Hemmingsen L, Pecoraro VL. Design of Thiolate Rich Metal Binding Sites within a Peptidic Framework. Inorg Chem. 2008 47(23):10875-88.

  8. Kuo S, Demeler B, Haldenwang WG. The growth-promoting and stress response activities of the Bacillus subtilis GTP binding protein Obg are separable by mutation. J Bacteriol. 2008 190(20):6625-35.

  9. Çeliç, A., Petri, E. T., Demeler, B., Ehrlich, B. E., Boggon, T. J. Domain mapping of the polycystein-2 C-terminal tail using de novo molecular modeling and biophysical analysis. J Biol Chem. 2008 283(42):28305-12.

  10. Serwer P, Hayes SJ, Thomas JA, Demeler B, Hardies SC. Isolation of novel large and aggregating bacteriophages. Methods Mol Biol. 2009;501:55-66.

  11. Yuan P, Leser GP, Demeler B, Lamb RA, Jardetzky TS. Domain architecture and oligomerization properties of the paramyxovirus PIV 5 hemagglutinin-neuraminidase (HN) protein. Virology. 2008 378(2):282-91.

  12. Schuermann J. P., Jiang J., Cuellar J., Llorca O., Wang L., Gimenez L. E., Jin S., Taylor A. B., Demeler B., Morano K. A., Hart P. J., Valpuesta J. M., Lafer E. M., Sousa R. Structure of the Hsp110:Hsc70 nucleotide exchange machine. Mol Cell. 2008 31(2):232-43.

  13. Wang R, Ilangovan U, Robinson AK, Schirf V, Schwarz PM, Lafer EM, Demeler B, Hinck AP, Kim CA. Structural transitions of the RING1B C-terminal region upon binding the polycomb cbox domain. Biochemistry. 2008 47(31):8007-15.

  14. Chinnaswamy S, Yarbrough I, Palaninathan S, Kumar CT, Vijayaraghavan V, Demeler B, Lemon SM, Sacchettini JC, Kao CC. A locking mechanism regulates RNA synthesis and host protein interaction by the hepatitis C virus polymerase. J Biol Chem. 2008 283(29):20535-46

  15. Takata T, Oxford JT, Demeler B, Lampi KJ. Deamidation destabilizes and triggers aggregation of a lens protein, β-A3-crystallin. Protein Sci. 2008 17(9):1565-75.

  16. Cao, W and B. Demeler. Modeling Analytical Ultracentrifugation Experiments with an Adaptive Space-Time Finite Element Solution for Multi-Component Reacting Systems. Biophys. J. (2008) 95(1):54-65

  17. Taylor AB, Meyer B, Leal BZ, Kötter P, Schirf V, Demeler B, Hart PJ, Entian KD, Wöhnert J The crystal structure of Nep1 reveals an extended SPOUT-class methyltransferase fold and a pre-organized SAM-binding site. Nucleic Acids Res. (2008) 36(5):1542-54

  18. Lounes, K., Demeler, B., Anderson, D., Gomes, A., Potter, J., Nassar, R., Anderson, P. Cardiac Troponin T Forms a Tetramer In Vitro. Biochemistry. (2008) 47(7):1970-6.

  19. Korotkova, N., Y. Yang, I. Le Trong, E. Cota, B. Demeler, J. Marchant, W.E. Thomas, R.E. Stenkamp, S. L. Moseley and S. Matthews. Binding of Dr adhesins of Escherichia coli to carcinoembryonic antigen triggers receptor dissociation. Mol. Microbiology 67 (2), 420-434 (2008)

  20. Demeler, B. and E. Brookes. Monte Carlo analysis of sedimentation experiments. Colloid Polym Sci (2008) 286(2) 129-137

  21. Brookes, E. and B. Demeler. Parallel computational techniques for the analysis of sedimentation velocity experiments in UltraScan. Colloid Polym Sci (2008) 286(2) 138-148

  22. Tan X, Kagiampakis I, Surovtsev IV, Demeler B, Lindahl PA. Nickel-Dependent Oligomerization of the Alpha Subunit of Acetyl-Coenzyme A Synthase/Carbon Monoxide Dehydrogenase. Biochemistry. 2007 46(41):11606-13

  23. Blain, K.Y., W. Kwiatkowski, Q. Zhao, D. La Fleur, C. Naik, T.W. Chun, T. Tsareva, P. Kanakaraj, M.W. Laird, R. Shah, L. George, I. Sanyal, P.A. Moore, B. Demeler, and S. Choe. Structural and Functional Characterization of CC Chemokine CCL14. Biochemistry (2007) 46(35):10008-15.

  24. Brookes, E and B. Demeler. Parsimonious Regularization using Genetic Algorithms Applied to the Analysis of Analytical Ultracentrifugation Experiments. GECCO Proceedings ACM 978-1-59593-697-4/07/0007 (2007)

  25. Gai H, Griess GA, Demeler B, Weintraub ST, Serwer P. Abstract Routine fluorescence microscopy of single untethered protein molecules confined to a planar zone. J Microsc. (2007) 226(Pt 3):256-62.

  26. Khakshoor O, Demeler B, Nowick JS. Macrocyclic beta-sheet peptides that mimic protein quaternary structure through intermolecular beta-sheet interactions. J Am Chem Soc. (2007) 129(17):5558-69

  27. Mehl, A.F., Demeler B. and A. Zraikat. A Water Mediated Electrostatic Interaction Gives Thermal Stability to the Tail Region. Protein J. (2007) 26(4):239-45.

  28. Brookes, E., Boppana, R.V., and B. Demeler. (2006) Computing Large Sparse Multivariate Optimization Problems with an Application in Biophysics. Supercomputing '06 ACM 0-7695-2700-0/06

  29. Comoletti, D., R.E. Flynn, A.A. Boucard, L.L. Jennings, B. Demeler, V. Schirf, H.R. Newlin, J. Shi, T.C. Südhof, and P. Taylor. Gene Selection, Alternative Splicing, and Post-translational Processing Regulate Neuroligin Selectivity for beta-Neurexins. Biochemistry (2006) 45(42):12816-27

  30. Belogrudov, G.I., Schirf, V., and B. Demeler. Reversible Self-Association of Recombinant Bovine Factor B. Biochim Biophys Acta. (2006) 1764(11):1741-9

  31. Zhang, Y. Z. Zhang, B. Demeler and I. Radhakrishnan. Coupled Unfolding and Dimerization by the PAH2 Domain of the Mammalian Sin3A Corepressor. J Mol Biol. (2006) 360(1):7-14.

  32. Yan N, Huh JR, Schirf V, Demeler B, Hay BA, Shi Y. Structure and activation mechanism of the Drosophila initiator caspase Dronc. J Biol Chem. (2006) 281(13):8667-74.

  33. Hays, F.A., V. Schirf, P.S. Ho, and B. Demeler. Formation of Holliday Junctions in Inverted-Repeat DNA Sequences in Solution. Biochemistry. (2006) 45(8):2467-71.

  34. Lee DS, Flachsova E, Bodnarova M, Demeler B, Martasek P, Raman CS. Structural basis of hereditary coproporphyria. Proc Natl Acad Sci U S A. (2005) 102(40):14232-7

  35. Ghosh D, Lee KH, Demeler B, Pecoraro VL. Linear free-energy analysis of mercury(II) and cadmium(II) binding to three-stranded coiled coils. Biochemistry. (2005) 44(31):10732-40.

  36. Cao W. and B. Demeler. Modeling analytical ultracentrifugation experiments with an adaptive space-time finite element solution of the Lamm equation. (2005) Biophys J. 89(3):1589-602.

  37. Ilangovan U, Ding W, Zhong Y, Wilson CL, Groppe JC, Trbovich JT, Zuniga J, Demeler B, Tang Q, Gao G, Mulder KM, Hinck AP. Structure and Dynamics of the Homodimeric Dynein Light Chain km23. J Mol Biol. (2005) 352(2):338-54.

  38. Kharenko O.A., D.C. Kennedy, B. Demeler, M.J. Maroney, and M.Y. Ogawa Cu(I) Luminescence from the Tetranuclear Cu4S4 Cofactor of a Synthetic 4-Helix Bundle. Journal of American Chemical Society (2005) 127(21):7678-9.

  39. Koblinski, J.E., M. Wu, B. Demeler, H.P. Erickson, K. Jacob, and H.K. Kleinman. Matrix cell adhesion activation by non-adhesion proteins. Journal of Cell Science 2005 Jul 1;118(Pt 13):2965-74

  40. Mao X, Ren Z, Parker GN, Sondermann H, Pastorello MA, Wang W, McMurray JS, Demeler B, Darnell JE Jr, Chen X. Structural Bases of Unphosphorylated STAT1 Association and Receptor Binding. (2005) Mol Cell. 17(6):761-71.

  41. Doucette, P.A., L.J. Whitson, X. Cao, V. Schirf, B. Demeler, J.S. Valentine, J.C. Hansen, and P.J. Hart.Dissociation of Human Copper-Zinc Superoxide Dismutase Dimers Using Chaotrope and Reductant: Insights into the Molecular Basis for Dimer Stability (2004) J. Biol. Chem. Vol 279(52):54558-66

  42. Demeler, B. and K.E. van Holde. Sedimentation velocity analysis of highly heterogeneous systems. (2004). Anal. Biochem. Vol 335(2):279-288

  43. Benjamin JM, Torke SJ, Demeler B, McGarry TJ. Abstract Geminin Has Dimerization, Cdt1-binding, and Destruction Domains That Are Required for Biological Activity. J Biol Chem. 2004 279(44):45957-68.

  44. Lambert LJ, Wei Y, Schirf V, Demeler B, Werner MH. T4 AsiA blocks DNA recognition by remodeling sigma(70) region 4. (2004) Eur J Biochem. 23(15):2952-62

  45. Li Y, Karnak D, Demeler B, Margolis B, Lavie A. Structural basis for L27 domain-mediated assembly of signaling and cell polarity complexes. (2004) Eur J Biochem. 23(14):2723-33

  46. Russell, T.R., B. Demeler, and S.C. Tu. Kinetic Mechanism and Quaternary Structure of Aminobacter aminoVorans NADH:Flavin Oxidoreductase: An Unusual Flavin Reductase with Bound Flavin (2004). Biochemistry, 43(6):1580-90

  47. Basha, E., G.J. Lee, B. Demeler and E. Vierling. Chaperone Activity of Cytosolic Small Heat Shock Proteins from Wheat (2004) Eur J Biochem. 271(8):1426-36

  48. Rashid R., M. Aittaleb, Q. Chen, K. Spiegel B. Demeler, and H. Li. Functional requirement for symmetric assembly of archaeal box C/D small ribonucleoprotein particles. Journal of Molecular Biology. 333(2):295-306, 2003.

  49. Lambert, L.J., V. Schirf, B. Demeler, and M.H. Werner. Molecular analysis of activator engagement with RNA polymerase. Methods in Enzymology. 370:505-21, 2003.

  50. Andrew F. Mehl, Luke D. Heskett, Sumesh S. Jain, and B. Demeler Insights into dimerization and four-helix bundle formation found by dissection of the dimer interface of the GrpE protein from Escherichia coli Protein Sci 2003 12: 1205-1215.

  51. Amy K. Wernimont, David L. Huffman, Lydia A. Finney, B. Demeler, Thomas V. O Halloran, and Amy C. Rosenzweig. Crystal structure and dimerization equilibria of PcoC, a methionine rich copper resistance protein from Escherichia coli. Journal of Biological Inorganic Chemistry 8(1-2):185-94, 2003

  52. Srikumar M. Raja, Baikun Wang, Mandakini Dantuluri, Umesh R. Desai, B. Demeler , Katharina Spiegel, Sunil S. Metkar, and Christopher J. Froelich. Cytotoxic Cell Granule-Mediated Apoptosis: Characterization of the Macromolecular Complex of Granzyme B with Serglycin. Journal of Biological Chemistry 277(51):49523-30, 2002

  53. Michael L. Bovee, Karen S. Champagne, B. Demeler, and Christopher S. Francklyn. Quaternary Structure of the HisZ-HisG N-1-(5'-Phosphoribosyl)-ATP Transferase from Lactococcus lactis Biochemistry, 41, 11838-11846 (2002)

  54. Li-Jung Tai, Sally M. McFall, Kai Huang, B. Demeler, Sue G. Fox, Kurt Brubaker, Ishwar Radhakrishnan, and Richard I. Morimoto. Structure-function analysis of the heat shock factor binding protein reveals a protein composed solely of a highly conserved and dynamic coiled-coil trimerization domain. JBC 277(1), 735-745 (2002)

  55. Lester J. Lambert, Virgil Schirf, B. Demeler, Martine Cademe and Milton H. Werner. Flipping a genetic switch by subunit exchange. EMBO J. 20(24), 7149-7159 (2001)

  56. Keyhani NO, Rodgers M, Demeler B, Hansen JC, Roseman S. Characterization of the IIAChb and IIBChb Proteins of the Escherichia coli N,N'-Diacetylchitobiose Phosphotransferase System by Analytical Sedimentation: Formation of a Model Phosphotransfer Transition State Complex. J Biol Chem., 275(42):33110-33115 (2000)

  57. Leslie T. Hall, Raylene J. Sanchez, Stephen P. Holloway, Haining Zhu, Jennifer E. Stine, Thomas J. Lyons, B. Demeler, Virgil Schirf, Jeffrey C. Hansen, Aram M. Nersissian, Joan Selverstone Valentine and P. John Hart. X-ray crystallographic and analytical ultracentrifugation analysis of truncated and full-length yeast copper caperones for SOD (LYS7): A dimer-dimer model of LYS7-SOD Association and Copper Delivery. Biochemistry, 39:3611-3623 (2000)

  58. Andrej Musatov, Jaime Ortega-Lopez, B. Demeler, Jeffrey P. Osborne, Robert B. Gennis, and Neal C. Robinson. Detergent-solubilized Escherichia coli cytochrome bo3 ubiquinol oxidase: a monomeric, not a dimeric complex. FEBS Letters, 457:153-156 (1999)

  59. James M. Bullard, Cai, Yin Chun, B. Demeler and Linda L. Spremulli. Expression and Characterization of a Human Mitochondrial Phenylalanyl-tRNA Synthetase. J. Mol. Biol. 288.4:567-577 (1999)

  60. Peter Schuck and B. Demeler. Direct Sedimentation Boundary Analysis of Interference Optical Data in Analytical Ultracentrifugation. Biophysical Journal, 76:2288-2296 (1999)

  61. Anant, J. S., Desnoyers, L., Machius, M., Demeler, B., Hansen, J. C., Westover, K. D., Deisenhofer, J., Seabra, M. C., Mechanism of Rab Geranylgeranylation: Formation of the Catalytic Ternary Complex. Biochemistry 37(36) 12559-12568 (1998)

  62. Rich RL., Demeler B., Ashby K., Deivanayagam CC., Petrich JW., Patti JM., Narayana SV., Hook M. Domain structure of the Staphylococcus aureus collagen adhesin. Biochemistry. 37(44):15423-33 (1998)

  63. B. Demeler and Hashim Saber. Determination of Molecular Parameters by Fitting Sedimentation Data to Finite Element Solutions of the Lamm Equation. Biophysical Journal. 74, 444-454 (1998)

  64. Jeffrey W. Seale, John M. Chirgwin, B. Demeler, and Paul M. Horowitz. Preformed GroES oligomers are not required as functional cochaperonins. Journal of Protein Chemistry 16:661-668. (1997)

  65. B. Demeler, Hashim Saber and Jeffrey C. Hansen. Identification and Interpretation of Complexity in Sedimentation Velocity Boundaries. Biophysical Journal 72, 397-407 (1997)

  66. Pavel Martasek, Jean-Michel Camadro, C.S. Raman, Marie Christine Lecomte, Jean Pierre Le Caer, B. Demeler, Bernard Grandchamp, Pierre Labbe. Human Coproporphyrinogen Oxidase. Biochemical Characterization of Recombinant Normal and R231W Mutated Enzymes Expressed in E. Coli as Soluble, Catalytically Active Homodimers. Cellular and Molecular Biology 43, 47-58 (1997)

  67. Mendoza, Jose A., Demeler, B. and Paul M. Horowitz. Alterations of the quarternary Structure of CPN 60 modulates Chaperonin assisted folding; Implications for the Mechanism of Chaperonin Action. Journal of Biological Chemistry 269, No. 4, 2447-2451 (1994)

  68. Robert H. Behal, Michael S. DeBuysere, B. Demeler, Jeffrey C. Hansen, and Merle S. Olson. Pyruvate Dehydrogenase Multienzyme Complex - Characterization of Assembly Intermediates by Sedimentation Velocity Analysis. Journal of Biological Chemistry 269, No. 50, 31372-31377 (1994)

  69. Philippe Georgel, B. Demeler, C. Terpening, Marvin R. Paule and Kensal E. van Holde. Binding of the RNA polymerase I transcription complex to its promoter can modify positioning of downstream nucleosomes assembled in vitro. Journal of Biological Chemistry 268, No. 3 Jan 25 1947-1954 (1993)

  70. B. Demeler and Guangwen Zhou. Neural network optimization for E. coli Promoter Prediction. Nucleic Acids Research, 19-7 1593-1599 (1991) (also selected as high-level article by the editorial board of the International Medical Informatics Association for publication in the 1992 IMIA Yearbook of Medical Informatics)

Submitted Articles:

Invited Articles and Book Chapters:

  1. Demeler, B., Brookes, E. and Nagel-Steger, L. Analysis of heterogeneity in molecular weight and shape by analytical ultracentrifugation using parallel distributed computing. Computer Applications in Biology. Methods in Enzymology Ludwig Brand and Michael L. Johnson, eds. (in press)

  2. Nagel-Steger, L., B. Demeler, K. Hochdörfer, Th. Schrader, D. Willbold. Modulation of Aggregate Size and Shape Distributions of Amyloid-β Peptide Solutions by a Designed β-Sheet Breaker. NIC Series Volume 40: From Computational Biophysics to Systems Biology. U.H.E. Hansmann, J.H. Meinke, S. Mohanty, W. Nadler, O. Zimmermann (Editors). 2008. ISBN: 978-3-9810843-6-8, 333-336

  3. Demeler, B., E. Brookes. Modeling Conformational and Molecular Weight Heterogeneity with Analytical Ultracentrifugation Experiments. in: NIC Series Volume 40: From Computational Biophysics to Systems Biology. U.H.E. Hansmann, J.H. Meinke, S. Mohanty, W. Nadler, O. Zimmermann (Editors). 2008. ISBN: 978-3-9810843-6-8, 77-80

  4. Brookes, E. and B. Demeler. Genetic Algorithm Optimization for obtaining accurate Molecular Weight Distributions from Sedimentation Velocity Experiments. Analytical Ultracentrifugation VIII, Progr. Colloid Polym. Sci. 131:78-82. C. Wandrey and H. Cölfen, Eds. Springer (2006)

  5. B. Demeler. Hydrodynamic Methods. Bioinformatics Basics: Applications in Biological Science and Medicine. 2nd Edition. H. Rashidi and L. Buehler, Eds. CRC Press LLC. (2005) 226-255

  6. Demeler, B.. UltraScan A Comprehensive Data Analysis Software Package for Analytical Ultracentrifugation Experiments. Modern Analytical Ultracentrifugation: Techniques and Methods. D. J. Scott, S.E. Harding and A.J. Rowe. Eds. Royal Society of Chemistry (UK) (2005) 210-229

  7. Lambert, Lester. J.; Schirf, Virgil; Demeler, B.; Werner, Milton H. Molecular analysis of activator engagement with RNA polymerase. Methods in Enzymology. 370:505-21, 2003.

  8. B. Demeler, Joachim Behlke, and Otto Ristau. Determination of molecular parameters from sedimentation velocity experiments: Whole boundary fitting using approximate and numerical solutions of the lamm equation. Methods in Enzymology, Numerical Computer Methods, Part C M. L. Johnson and Ludwig Brand, Eds. (2000) 321:38-66

  9. Lenny M. Carruthers, Virgil R. Schirf, B. Demeler, and Jeffrey C. Hansen. Sedimentation velocity analysis of macromolecular assemblies Methods in Enzymology, Numerical Computer Methods, Part C M. L. Johnson and Ludwig Brand, Eds. (2000) 321:66-80

  10. Jeffrey C. Hansen, J. Isabelle Kreider, B. Demeler, and Terace Fletcher. (1997) Analytical Ultracentrifugation and Agarose Gel Electrophoresis as Tools for Studying Chromatin Folding in Solution: A Companion to Methods in Enzymology, 12:62-72.

  11. Jeffrey C. Hansen, Jacob Lebowitz, and B. Demeler. Analytical Ultracentrifugation of Complex Macromolecular Systems. Biochemistry 33, No. 45, 13155-13163, (1994)