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Publications (155):

  1. Abbott JA, Guth E, Kim C, Regan C, Siu VM, Rupar CA, Demeler B, Francklyn CS, Robey-Bond SM.The Usher Syndrome Type IIIB Histidyl-tRNA Synthetase Mutation Confers Temperature Sensitivity. Biochemistry. 2017 Jul 18;56(28):3619-3631. doi: 10.1021/acs.biochem.7b00114. Epub 2017 Jul 7.
  2. Fan Y, Guo YR, Yuan W, Zhou Y, Holt MV, Wang T, Demeler B, Young NL, Zhong W, Tao YJ. Structure of a pentameric virion-associated fiber with a potential role in Orsay virus entry to host cells. PLoS Pathog. 2017 Feb 27;13(2):e1006231. doi: 10.1371/journal.ppat.1006231. [Epub ahead of print]
  3. Kim SK, Barron L, Hinck CS, Petrunak EM, Cano KE, Thangirala A, Iskra B, Brothers M, Vonberg M, Leal B, Richter B, Kodali R, Taylor AB, Du S, Barnes CO, Sulea T, Calero G, Hart PJ, Hart MJ, Demeler B, Hinck AP. An Engineered TGF-β Monomer that Functions as a Dominant Negative to Block TGF-β Signaling. J Biol Chem. 2017 Feb 22
  4. Zhang J, Pearson JZ, Gorbet GE, Cölfen H, Germann MW, Brinton MA, Demeler B. Spectral and Hydrodynamic Analysis of West Nile Virus RNA-Protein Interactions by Multiwavelength Sedimentation Velocity in the Analytical Ultracentrifuge. Anal Chem. 2017 Jan 3;89(1):862-870. PMID: 27977168
  5. Walter J, GE Gorbet, T Akdas, D Segets, B Demeler, W. Peukert. 2D analysis of polydisperse core-shell nanoparticles using analytical ultracentrifugation Analyst, 2016, 142(1):206-217. PMID: 27934989
  6. Gray F, Cho HJ, Shukla S, He S, Harris A, Boytsov B, Jaremko ?, Jaremko M, Demeler B, Lawlor ER, Grembecka J, Cierpicki T. BMI1 regulates PRC1 architecture and activity through homo- and hetero-oligomerization. Nat Commun. 2016 Nov 9;7:13343. PMID: 27827373
  7. Smirnova E, Kwan JJ, Siu R, Gao X, Zoidl G, Demeler B, Saridakis V, Donaldson LW. A new mode of SAM domain mediated oligomerization observed in the CASKIN2 neuronal scaffolding protein. Cell Commun Signal. 2016 Aug 22;14(1):17. doi: 10.1186/s12964-016-0140-3.
  8. Karabudak E, Brookes E, Lesnyak V, Gaponik N, Eychmüller A, Walter J, Segets D, Peukert W, Wohlleben W, Demeler B, H Cölfen. Simultaneous Identification of Spectral Properties and Sizes of multiple Particles in Solution with sub-nm Size Resolution. Angewandte Chemie 2016 Sep 19;55(39):11770-4. PMID: 27461742
  9. Wong SJ, Gearhart MD, Taylor AB, Nanyes DR, Ha DJ, Robinson AK, Artigas JA, Lee OJ, Demeler B, Hart PJ, Bardwell VJ, and CA Kim. KDM2B recruitment of the Polycomb group complex, PRC1.1, requires cooperation between PCGF1 and BCORL1. Structure, 2016 Aug 23. pii: S0969-2126(16)30222-2. doi: 10.1016/j.str.2016.07.011.
  10. Bhattacharya A, Wang Z, White T, Buffone C, Nguyen L, Shepard C, Kim B, Demeler B, Diaz-Griffero F, and D Ivanov. Effects of T592 phosphomimetic mutations on tetramer stability and dNTPase activity of SAMHD1 can not explain the retroviral restriction defect. Sci Rep. 2016 Aug 11;6:31353. doi: 10.1038/srep31353.
  11. Alvarez MM, Chen J, Plascencia-Villa G, Black DM, Griffith WP, Garzon IL, José-Yacamán M, Demeler B, Whetten RL. Hidden Components in Aqueous Gold-144 Fractionated by PAGE: High-Resolution Orbitrap ESI-MS Identifies the Gold-102 and Higher All-Aromatic Au-pMBA Cluster Compounds. J Phys Chem B. 2016 Jun 8. PMID: 27275518
  12. G Plascencia-Villa, B Demeler, RL Whetten, WP Griffith, M Alvarez, DM Black, and M José-Yacamán. Analytical Characterization of Size-Dependent Properties of Larger Aqueous Gold Nanoclusters J. Phys. Chem. C, DOI: 10.1021/acs.jpcc.6b00448
  13. Ballandras-Colas A, Brown M, Cook NJ, Dewdney TG, Demeler B, Cherepanov P, Lyumkis D, Engelman AN. Cryo-EM reveals a novel octameric integrase structure for betaretroviral intasome function. Nature. 2016 Feb 18;530(7590):358-61. doi: 10.1038/nature16955.
  14. Rubio-Marrero EN, Vincelli G, Jeffries CM, Shaikh TR, Pakos I, Ranaivoson FM, von Daake S, Demeler B, De Jaco A, Perkins G, Ellisman MH, Trewhella J, Comoletti D. Structural characterization of the extracellular domain of CASPR2 and insights into its association with the novel ligand Contactin1. J Biol Chem. 2015 Dec 31. pii: jbc.M115.705681.
  15. Villarreal OD, LY Chen, RL Whetten, B. Demeler. Aspheric Solute Ions Modulate Gold Nanoparticle Interactions in an Aqueous Solution: An Optimal Way to Reversibly Concentrate Functionalized Nanoparticles. J. Phys. Chem. B 11/2015; DOI:10.1021/acs.jpcb.5b09864
  16. Pearson JZ, Krause F, Haffke D, Demeler B, Schilling K, and H. Cölfen. Next-Generation AUC Adds a Spectral Dimension: Development of Multiwavelength Detectors for the Analytical Ultracentrifuge Methods in Enzymology, Aug. 2015, doi:10.1016/bs.mie.2015.06.033
  17. Gorbet GE, Pearson JZ, Demeler AK, Cölfen H, and B. Demeler. Next-Generation AUC: Analysis of Multiwavelength Analytical Ultracentrifugation Data Methods in Enzymology, Aug 2015. doi:10.1016/bs.mie.2015.04.013
  18. Kim H, Brookes EH, Demeler B. A Performance Predictor for UltraScan Supercomputer Calculations. Proceeding XSEDE '15 Proceedings of the 2015 XSEDE Conference: Scientific Advancements Enabled by Enhanced Cyberinfrastructure Article No. 42 ACM New York, NY, USA 2015. doi:10.1145/2792745.2792787
  19. Ranaivoson FM, Liu Q, Martini F, Bergami F, von Daake S, Li S, Lee D, Demeler B, Hendrickson WA, Comoletti D. Structural and Mechanistic Insights into the Latrophilin3-FLRT3 Complex that Mediates Glutamatergic Synapse Development.Structure. 2015 Jul 28. pii: S0969-2126(15)00275-0. doi: 10.1016/j.str.2015.06.022.
  20. Yudina Z, Roa A, Johnson R, Biris N, de Souza Aranha Vieira DA, Tsiperson V, Reszka N, Taylor AB, Hart PJ, Demeler B, Diaz-Griffero F, Ivanov DN. RING Dimerization Links Higher-Order Assembly of TRIM5? to Synthesis of K63-Linked Polyubiquitin. Cell Rep. 2015 Aug 4;12(5):788-97. doi: 10.1016/j.celrep.2015.06.072. Epub 2015 Jul 23.
  21. Tsutsui Y, Johnson JM, Demeler B, Kinter MT, Hays FA. Conformation-Dependent Human p52Shc Phosphorylation by Human c-Src. Biochemistry. 2015 Jun 9;54(22):3469-82. doi: 10.1021/acs.biochem.5b00122. Epub 2015 May 26.
  22. Pierce, M., S. Marru, B. Demeler, R. Singh, and G. Gorbet. (2014) The Apache Airavata Application Programming Interface: Overview and Evaluation with the UltraScan Science Gateway. In Proceedings of the 9th Gateway Computing Environments Workshop (GCE '14). IEEE Press, Piscataway, NJ, USA, 25-29. DOI=10.1109/GCE.2014.15
  23. Bhattacharya A, Alam SL, Fricke T, Zadrozny K, Sedzicki J, Taylor AB, Demeler B, Pornillos O, Ganser-Pornillos BK, Diaz-Griffero F, Ivanov DN, Yeager M. Structural basis of HIV-1 capsid recognition by PF74 and CPSF6. Proc Natl Acad Sci U S A. 2014 Dec 30;111(52):18625-30, doi: 10.1073/pnas.1419945112.
  24. Cockburn DW, Orlovsky NI, Foley MH, Kwiatkowski KJ, Bahr CM, Maynard M, Demeler B, Koropatkin NM. Molecular details of a starch utilization pathway in the human gut symbiont Eubacterium rectale. Mol Microbiol. 2014 Nov 11. doi: 10.1111/mmi.12859.
  25. Swygert SG, Manning BJ, Senapati S, Kaur P, Lindsay S, Demeler B, Peterson CL. Solution-state conformation and stoichiometry of yeast Sir3 heterochromatin fibres. Nat Commun. 2014 Aug 28;5:4751.
  26. Demeler B., Nguyen TL, Gorbet GE, Schirf V, Brookes EH, Mulvaney P, El-Ballouli AO, Pan J, Bakr OM, Demeler AK, Hernandez Uribe BI, Bhattarai N, and RL Whetten. Characterization of Size, Anisotropy, and Density Heterogeneity of Nanoparticles by Sedimentation Velocity. Anal Chem. 2014 Aug 5;86(15):7688-95.
  27. Memon S., M. Riedel, F. Janetzko, B. Demeler, G. Gorbet, S. Marru, A. Grimshaw, L. Gunathilake, Raminder Singh, N. Attig and T. Lippert. Advancements of the UltraScan scientific gateway for open standards-based cyberinfrastructures. Concurrency Computat.: Pract. Exper. (2014) Wiley. DOI: 10.1002/cpe.3251
  28. Gorbet G., T. Devlin, B. Hernandez Uribe, A. K. Demeler, Z. Lindsey, S. Ganji, S. Breton, L. Weise-Cross, E.M. Lafer, E.H. Brookes, B. Demeler. A parametrically constrained optimization method for fitting sedimentation velocity experiments. Biophys. J. (2014) Vol 106(8), pp1741-1750 dx.doi.org/10.1016/j.bpj.2014.02.022
  29. Pham JD, Demeler B, Nowick JS. Polymorphism of Oligomers of a Peptide from β-Amyloid.. J Am Chem Soc. 2014 Mar 26. PMID: 24669785
  30. Brandariz-Nuñez A, Valle-Casuso JC, White TE, Nguyen L, Bhattacharya A, Wang Z, Demeler B, Amie S, Knowlton C, Kim B, Ivanov DN, Diaz-Griffero F. Contribution of oligomerization to the anti-HIV-1 properties of SAMHD1. Retrovirology. 2013 Nov 12;10(1):131. doi: 10.1186/1742-4690-10-131. PMID: 24219908
  31. Zhang N, Jiang Y, Mao Q, Demeler B, Tao YJ, Pati D. Characterization of the Interaction between the Cohesin Subunits Rad21 and SA1/2. PLoS One. 2013 Jul 12;8(7):e69458. doi: 10.1371/journal.pone.0069458. PMID: 23874961
  32. Takacs M, Petoukhov MV, Atkinson RA, Roblin P, Ogi FX, Demeler B, Potier N, Chebaro Y, Dejaegere A, Svergun DI, Moras D, Billas IML. The Asymmetric Binding of PGC-1α to the ERRα and ERRγ Nuclear Receptor Homodimers Involves a Similar Recognition Mechanism. PloS One, July 16, 2013, doi: 10.137/0067810. PMID: 23874451
  33. Anzini P, Xu C, Hughes SA, Magnotti E, Jiang T, Hemmingsen L, Demeler B, Conticello VP. Controlling Self-assembly of a Peptide-Based Material via Metal-Ion Induced Registry Shift. J Am Chem Soc. 2013 Jul 17;135(28):10278-81. doi: 10.1021/ja404677c. PMID: 23815081
  34. Xue J, Hoorelbeke B, Kagiampakis I, Demeler B, Balzarini J, Liwang PJ. The griffithsin dimer is required for high potency inhibition of HIV-1: Evidence for manipulation of the structure of gp120 as part of the griffithsin dimer mechanism. Antimicrob Agents Chemother. 2013 Aug;57(8):3976-89. doi: 10.1128/AAC.00332-13. PMID: 23752505
  35. Brookes E, Singh R, Pierce M, Marru S, Demeler B, Rocco M. US-SOMO Cluster Methods: Year One Perspective. XSEDE '13 Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery Article No. 65 ACM New York, NY, USA 2013 ISBN: 978-1-4503-2170-9 doi:10.1145/2484762.2484815
  36. Memon S, Riedel S, Janetzko F, Attig N, Lippert T, Demeler B, Gorbet G, Marru S, Singh R, Gunathilake L, Grimshaw A. Improvements of the UltraScan Scientific Gateway to Enable Computational Jobs on Large-scale and Open-standards based Cyberinfrastructures. XSEDE '13 Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery Article No. 39 ACM New York, NY, USA 2013 ISBN: 978-1-4503-2170-9 doi:10.1145/2484762.2484800
  37. Jalan AA, Demeler B, Hartgerink JD. Hydroxyproline-Free Single Composition ABC Collagen Heterotrimer. J Am Chem Soc. 2013 Apr 24;135(16):6014-7. doi: 10.1021/ja402187t. Epub 2013 Apr 15. PMID: 23574286
  38. Ruff Y, Moyer T, Newcomb CJ, Demeler B, Stupp SI. Precision Templating with DNA of a Virus-like Particle with Peptide Nanostructures. J Am Chem Soc. 2013 Apr 24;135(16):6211-9. doi: 10.1021/ja4008003. Epub 2013 Apr 10. PMID: 23574404
  39. Junco SE, Wang R, Gaipa JC, Taylor AB, Schirf V, Gearhart MD, Bardwell VJ, Demeler B, Hart PJ, Kim CA. Structure of the Polycomb Group Protein PCGF1 in Complex with BCOR Reveals Basis for Binding Selectivity of PCGF Homologs. Structure. 2013 Apr 2;21(4):665-71. doi: 10.1016/j.str.2013.02.013. Epub 2013 Mar 21.
  40. Panda SP, Polusani SR, Kellogg DL 3rd, Venkatakrishnan P, Roman MG, Demeler B, Masters BS, Roman LJ. Intra- and inter-molecular effects of a conserved arginine residue of neuronal and inducible nitric oxide synthases on FMN and calmodulin binding. Arch Biochem Biophys. 2013 Mar 15. doi:pii: S0003-9861(13)00085-4. 10.1016/j.abb.2013.03.004. [Epub ahead of print]
  41. Zheng J, Fage CD, Demeler B, Hoffman DW, Keatinge-Clay AT. The Missing Linker: A Dimerization Motif Located within Polyketide Synthase Modules. ACS Chem Biol. 2013 Mar 25. [Epub ahead of print] PMID: 23489133
  42. Fisher OS, Zhang R, Li X, Murphy JW, Demeler B, Boggon TJ. Structural studies of cerebral cavernous malformations 2 (CCM2) reveal a folded helical domain at its C-terminus. FEBS Lett. 2013 Jan 31;587(3):272-7. doi:pii: S0014-5793(12)00930-1. 10.1016/j.febslet.2012.12.011.

  43. Xue J, Gao Y, Hoorelbeke B, Kagiampakis I, Zhao B, Demeler B, Balzarini J, Liwang PJ. The Role of Individual Carbohydrate-Binding Sites in the Function of the Potent Anti-HIV Lectin Griffithsin. Mol Pharm. 2012 Sep 4;9(9):2613-25. Epub 2012 Aug 21.

  44. Robinson AK, Leal BZ, Nanyes DR, Kaur Y, Ilangovan U, Schirf V, Hinck AP, Demeler B, Kim CA. Human Polyhomeotic Homolog 3 (PHC3) Sterile Alpha Motif (SAM) Linker Allows Open-Ended Polymerization of PHC3 SAM. 2012 Jul 10;51(27):5379-86. Epub 2012 Jun 28.

  45. Zheng J, Gay DC, Demeler B, White MA, Keatinge-Clay AT.Divergence of multimodular polyketide synthases revealed by a didomain structure. Nat Chem Biol. 2012 May 27. doi: 10.1038/nchembio.964. PMID: 22634636

  46. Harkness KM, Tang Y, Dass A, Pan J, Kothalawala N, Reddy VJ, Cliffel DE, Demeler B, Stellacci F, Bakr OM, McLean JA. Ag(44)(SR)(30)(4-): a silver-thiolate superatom complex.Nanoscale. 2012 Jun 15.

  47. Brookes E, Singh R, Pierce M, Marru S, Demeler B, Rocco M. Ultrascan solution modeler: integrated hydrodynamic parameter and small angle scattering computation and fitting tools. XSEDE '12 Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment: Bridging from the eXtreme to the campus and beyond . ACM doi:10.1145/2335755.2335839
  48. Robinson AK, Leal BZ, Chadwell LV, Wang R, Ilangovan U, Kaur Y, Junco SE, Schirf V, Osmulski PA, Gaczynska M, Hinck AP, Demeler B, McEwen DG, Kim CA. The growth-suppressive function of the Polycomb group protein Polyhomeotic is mediated by polymerization of its sterile alpha motif (SAM) domain. J Biol Chem. 2012 Mar 16;287(12):8702-13. Epub 2012 Jan 24.

  49. 19. EM Lafer, Y Zhuo, U Ilangovan, V Schirf, B Demeler, R Sousa, AP Hinck. Role of Disorder in Clathrin Lattice Assembly. Biophysical Journal 102 (3), 2a (2012)

  50. Childers BM, Cao X, Weber GG, Demeler B, Hart PJ, Klose KE. N-terminal Residues of the Vibrio cholerae Virulence Regulatory Protein ToxT Involved in Dimerization and Modulation by Fatty Acids. J Biol Chem. 2011 Aug 12;286(32):28644-55. Epub 2011 Jun 14.

  51. Demeler, B., Singh, R., Pierce, M., Brookes, E. H., Marru, S., and Dubbs, B. 2011. UltraScan gateway enhancements. In Proceedings of the 2011 Teragrid Conference: Extreme Digital Discovery (Salt Lake City, Utah, July 18 - 21, 2011). TG '11. ACM, New York, NY, 1-8. DOI= http://doi.acm.org/10.1145/2016741.2016778
  52. Laue T, Demeler B. A postreductionist framework for protein biochemistry. Nat Chem Biol. 2011 Jun;7(6):331-4. PMID: 21587250

  53. Lee S, Xue Y, Hu J, Wang Y, Liu X, Demeler B, Ha Y. The E2 domains of APP and APLP1 share a conserved mode of dimerization. Biochemistry. 2011 Jun 21;50(24):5453-64. Epub 2011 May 26. PMID: 21574595

  54. Lin AP, Demeler B, Minard KI, Anderson SL, Schirf V, Galaleldeen A, McAlister-Henn L. Construction and Analysis of Tetrameric Forms of Yeast NAD+-Specific Isocitrate Dehydrogenase. Biochemistry. 2010 Dec 21. [Epub ahead of print] PMID: 21133413
  55. Zhuo Y, Ilangovan U, Schirf V, Demeler B, Sousa R, Hinck AP, Lafer EM. Dynamic Interactions between Clathrin and Locally Structured Elements in a Disordered Protein Mediate Clathrin Lattice Assembly. J Mol Biol. 2010 Nov 26;404(2):274-90. Epub 2010 Sep 25. PMID: 20875424
  56. Zaytsev DV, Xie F, Mukherjee M, Bludin A, Demeler B, Breece RM, Tierney DL, Ogawa MY. Nanometer to Millimeter Scale Peptide-Porphyrin Materials. Biomacromolecules. 2010 Oct 11;11(10):2602-9.
  57. Comoletti D, Miller M, Jeffries CM, Wilson J, Demeler B, Taylor P, Trewhella J, Nakagawa T. The Macromolecular Architecture of Extracellular Domain of aNRXN1: Domain Organization, Flexibility, and Insights into Trans-Synaptic Disposition. Structure. (2010) 18(8):1044-53.

  58. Seetharaman S, Winkler D, Taylor A, Cao, X, Whitson L, Doucette P, Valentine J, Schirf V, Demeler B, Carroll M, Culotta V, Hart P. Disrupted Zinc-Binding Sites in Structures of Pathogenic SOD1 Variants D124V and H80R Biochemistry (2010) 49(27):5714-25.

  59. Wang R, Taylor AB, Leal BZ, Chadwell LV, Ilangovan U, Robinson AK, Schirf V, Hart PJ, Lafer EM, Demeler B, Hinck AP, McEwen DG, Kim CA. Polycomb Group targeting through different binding partners of RING1B C-terminal domain. Structure (2010) 18(8):966-75.

  60. Brookes, E. H. and Demeler, B. Performance optimization of large non-negatively constrained least squares problems with an application in biophysics. In Proceedings of the 2010 Teragrid Conference TG '10. ACM, New York, NY, 1-9. DOI= http://doi.acm.org/10.1145/1838574.1838579
  61. Demeler, B Methods for the Design and Analysis of Sedimentation Velocity and Sedimentation Equilibrium Experiments with Proteins. Cur. Protoc. Prot. Sci. (2010) Chapter 7:Unit 7.13.

  62. Brookes E, Demeler B, Rocco M. Developments in the US-SOMO Bead Modeling Suite: New Features in the Direct Residue-to-Bead Method, Improved Grid Routines, and Influence of Accessible Surface Area Screening Macromol. Biosci. 10.1002/mabi.200900474 (2010) 10(7):746-53. (Associated Materials/Views story)

  63. Demeler B, Brookes E, Wang R, Schirf V, Kim CA. Characterization of Reversible Associations by Sedimentation Velocity with UltraScan. Macromol. Biosci. Macromol Biosci. 2010 Jul 7;10(7):775-82.PMID: 20486142

  64. Xiao F, Demeler B, Guo P. Assembly mechanism of the sixty-subunit nanoparticles via interaction of RNA with the reengineered protein connector of phi29 DNA-packaging motor.ACS Nano. 2010 Jun 22;4(6):3293-301. doi: 10.1021/nn100158k.

  65. Lee YS, Lee S, Demeler B, Molineux IJ, Johnson KA, Yin YW. Each monomer of the dimeric accessory protein for human mitochondrial DNA polymerase has a distinct role in conferring processivity. J Biol Chem. 2010 Jan 8;285(2):1490-9. Epub 2009 Oct 26.

  66. Hoopes JT, Liu X, Xu X, Demeler B, Folta-Stogniew E, Li C, Ha Y. Structural characterization of the E2 domain of APL-1, a Caenorhabditis elegans homolog of human amyloid precursor protein, and its heparin binding site. J Biol Chem. 2010 Jan 15;285(3):2165-73. Epub 2009 Nov 10.

  67. Whidby J, Mateu G, Scarborough H, Demeler B, Grakoui A, Marcotrigiano J. Blocking hepatitis C virus infection with recombinant form of envelope protein 2 ectodomain. J Virol. 2009 Nov;83(21):11078-89. Epub 2009 Aug 26.

  68. 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 3(8):2163-70.

  69. 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. (2010) 39(3):347-59

  70. 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. (2010) 39(3):405-14.

  71. 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. (2010) 39(3):415-22.

  72. 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. (2010) 39(3):423-35.

  73. 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.

  74. 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.

  75. 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.

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

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

  78. 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.

  79. Schuermann JP, Jiang J, Cuellar J, Llorca O, Wang L, Gimenez LE, Jin S, Taylor AB, Demeler B, Morano KA, Hart PJ, Valpuesta JM, Lafer EM, Sousa R. Structure of the Hsp110:Hsc70 nucleotide exchange machine. Mol Cell. 2008 31(2):232-43.

  80. 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.

  81. 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

  82. 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.

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

  84. 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

  85. 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.

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

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

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

  89. 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

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

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

  92. 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.

  93. 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

  94. Khakshoor O, Demeler B, Nowick JS. Design of a thiolate rich metal binding site in a peptidic framework. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 233, 719-719 (2007)

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

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

  97. Comoletti D, Flynn RE, Boucard AA, Jennings LL, Demeler B, Schirf V, Newlin HR, Shi J, Südhof TC, Taylor P. Gene Selection, Alternative Splicing, and Post-translational Processing Regulate Neuroligin Selectivity for beta-Neurexins. Biochemistry (2006) 45(42):12816-27

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

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

  100. 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.

  101. Hays FA, Schirf V, Ho PS, Demeler B. Formation of Holliday Junctions in Inverted-Repeat DNA Sequences in Solution. Biochemistry. (2006) 45(8):2467-71.

  102. 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

  103. 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.

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

  105. 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.

  106. Kharenko OA, Kennedy DC, Demeler B, Maroney MJ, Ogawa MY. Cu(I) Luminescence from the Tetranuclear Cu4S4 Cofactor of a Synthetic 4-Helix Bundle. Journal of American Chemical Society (2005) 127(21):7678-9.

  107. Koblinski, J.E., M. Wu, Demeler B, 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

  108. 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.

  109. Mikula I, Demeler B, Martasek P. Study of the oligomeric status of Coproporphyrinogen Oxidase (CPO) using Analytical Ultracentrifugation (AU). FASEB JOURNAL 19 (4), A265-A265

  110. Lee DS, Flachsova E, Bodnarova M, Prochazkova J, Nioche P, Demeler B, Martasek P, Raman CS. Molecular Basis of Hereditary Coproporphyria. J Inherited Metabolic Disease. (28) 258 (2005)

  111. Flachsov E, Bodnarova M, Demeler B, Raman CS, Martasek P. Structural basis of hereditary coproporphyria. PNAS (40) 14232-14237 (2005)

  112. Doucette, P.A., L.J. Whitson, X. Cao, V. Schirf, Demeler B, 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

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

  114. 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.

  115. 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

  116. Martasek P, Demeler B, Jachymova M , Roman LJ, Shea TM, Masters BS. Oligomerization status of NOS reductase domains: analytical ultracentrifugation study. Nitric Oxide Biology and Chemistry 11 (1), 85 (2004)

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

  118. Russell, T.R., Demeler B, 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

  119. Mikula I, Bodnarova M, Lee DS, Flachsova E, Demeler B, Raman CS, Martasek P. Structure-function relationships studies of human coproporphyrinogen oxidase (CPO), biochemical characterization of wild-type and mutant forms FASEB JOURNAL 18 (8), 240 (2004)

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

  121. Rashid R., M. Aittaleb, Q. Chen, K. Spiegel Demeler B, 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.

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

  123. Mikula I, Flachsova E, Rosipal R, Demeler B, Camadro JM, Zeman J, Deybach JC, Raman CS, P Martasek P. Human coproporphyrinogen oxidase (CPO): Biochemical characterization of wild-type enzyme and its naturally occurring mutant forms. Amer. J. Human Genetics 73(5) 460. (2003)

  124. Andrew F. Mehl, Luke D. Heskett, Sumesh S. Jain, and Demeler B 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.

  125. 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

  126. Srikumar M. Raja, Baikun Wang, Mandakini Dantuluri, Umesh R. Desai, Demeler B , 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

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

  128. Li-Jung Tai, Sally M. McFall, Kai Huang, Demeler B, 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)

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

  130. 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)

  131. Leslie T. Hall, Raylene J. Sanchez, Stephen P. Holloway, Haining Zhu, Jennifer E. Stine, Thomas J. Lyons, Demeler B, 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)

  132. Andrej Musatov, Jaime Ortega-Lopez, Demeler B, 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)

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

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

  135. 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)

  136. 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)

  137. Demeler B 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)

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

  139. Demeler B, Saber H, and Hansen JC. Identification and Interpretation of Complexity in Sedimentation Velocity Boundaries. Biophysical Journal 72, 397-407 (1997)

  140. Pavel Martasek, Jean-Michel Camadro, C.S. Raman, Marie Christine Lecomte, Jean Pierre Le Caer, Demeler B, 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)

  141. 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)

  142. Behal RH, DeBuysere MS, Demeler B, Hansen JC, Olson MS. Pyruvate Dehydrogenase Multienzyme Complex - Characterization of Assembly Intermediates by Sedimentation Velocity Analysis. Journal of Biological Chemistry 269, No. 50, 31372-31377 (1994)

  143. Georgel P, Demeler B, Terpening C, Paule MR, van Holde KE. 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)

  144. Demeler B 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., and G. Gorbet. Analytical Ultracentrifugation Data Analysis with UltraScan-III. Ch. 8, In Analytical Ultracentrifugation: Instrumentation, Software, and Applications. Eds: Uchiyama S., Stafford W. F. and T. Laue. Springer, 119-143 (2016)
  2. Nagel-Steger L, Demeler B, Willbold D. 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, Brookes E. 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 Demeler B. 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. Demeler B. 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. Demeler B, 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, Demeler B, 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. Hansen JC. Kreider I, Demeler B, 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. Hansen JC, Lebowitz J, and Demeler B. Analytical Ultracentrifugation of Complex Macromolecular Systems. Biochemistry 33, No. 45, 13155-13163, (1994)