Borries Demeler, PhD

Research

1. Hydrodynamic and thermodynamic modeling: Using tools such as analytical ultracentrifugation and dynamic light scattering my research group focuses on the elucidation of structure and function of macromolecules, assemblies, nanoparticles and synthetic polymers. To this end, we have developed several numerical methods and computational approaches, including parallel distributed computing, for the analysis of experimental data from these hydrodynamic techniques. This long-time effort has resulted in the creation of the UltraScan software suite. By creating this software our goal is to implement novel technology in a user-friendly data analysis environment so that the methods can be applied by any investigator, even those without extensive expertise in computing, mathematics or biophysics.

A major emphasis in developing these new methods is placed on the global approach, which takes advantage of the added information content of multiple datasets from different experimental methods and experimental conditions. The global approach presents new challenges with respect to optimization algorithms and requires new paradigms to deal with the large amounts of data from combined experiments (such as multi-speed, multi-wavelength, and multi-concentration sedimentation velocity and equilibrium experiments).

Our current efforts focus on the development of novel adaptive space-time finite element solutions to partial differential equations describing sedimentation velocity experiments at a very detailed level, which extends beyond non-interacting, ideal systems to multi-component reactions, concentration dependent non-ideality, slow kinetics and reaction equilibria determinations, co-sedimenting solutes, and methods for the spectral decomposition of dissimilar absorbing components such as nucleic acids, proteins and molecules containing unique chromophores. the tcnovel analysis methods utilizing the latest advances in technology and instrumentation. Among them are parallel computational approaches using Linux Beowulf systems. Such tools are required to model the large and computationally demanding systems of experimental data in a global approach.

2. Rigid Body Bead Modeling In collaboration with Dr. Mattia Rocco we are developing the SOlution MOdeler (SOMO) software which uses atomic level resolution models to derive bead replacement models to calculate hydrodynamic properties as well as modeling of small angle X-ray scattering profiles. Small groups of atoms (for example, in proteins, the backbone may be represented with one bead for each amino acid, while the sidechain is replaced with one or more beads, depending on size.

The beads have the same average mass, center of gravity and approximate radius as the the atoms they replace. By preventing overlaps of these spherical beads by applying certain rules, an assembly of non-overlapping spherical beads can be used to predict hydrodynamic properties such as radius of gyration, sedimentation coefficient, translational diffusion coefficient and intrinsic viscosity on a macromolecule, which can then be compared to the observed hydrodynamic information from an AUC experiment. The SOMO software is integrated in UltraScan releases greater than version 9.9.

3. Software Development Our development team includes extensive expertise in software development. We employ modern open source tools to create a high-performance data analysis package for the management of research data from biophysical experiments. The software can be used to simulate and design experiments, analyze equilibrium and velocity sedimentation experiments, and includes a Laboratory Information Management System (LIMS) with a MySQL database back-end.

Our expertise includes programming in C, C++, MPI, PERL, SQL, FORTRAN, PHP, HTML, Java, Python and other languages. Developments include portals and web interfaces to supercomputing applications, queuing systems, remote execution calls, XML procedures, and parallel file system storage technology. We follow standard programming procedures and employ open source tools such as Linx, gcc, and QT, QWT and QWT3D for our GUI frameworks.

4. Experimental Design and Analysis: Our laboratory engages in a wide range of research projects involving proteins, protein assemblies, DNA, DNA binding protein complexes, nano particles, nano- and carbon tubes, colloids, interfaces, membrane proteins and other macromolecular systems. We design and conduct experiments to test scientific hypotheses and to research macromolecular structure and function, to characterize shape, and size distributions. To this end we engage in frequent collaborations with investigators at our institution and institutions across the US, Canada, Asia and Europe.

Publications

1. Stoutjesdyk M, Brookes E, Henrickson A, Demeler B. Measuring compressibility in the optima AUC™ analytical ultracentrifuge. Eur Biophys J. 2020 Dec;49(8):711-718. doi: 10.1007/s00249-020-01482-5. Epub 2020 Nov 24. PMID: 33236172
2. Horne CR, Henrickson A, Demeler B, Dobson RCJ. Multi-wavelength analytical ultracentrifugation as a tool to characterise protein-DNA interactions in solution Eur Biophys J. 2020 Nov 21. doi: 10.1007/s00249-020-01481-6. Online ahead of print. PMID: 33219833
3. Koebke KJ, Kühl T, Lojou E, Demeler B, Schoepp-Cothenet B, Iranzo O, Pecoraro VL, Ivancich A. The pH-Induced Selectivity Between Cysteine or Histidine Coordinated Heme in an Artificial α-Helical Metalloprotein Angew Chem Int Ed Engl. 2020 Nov 20. doi: 10.1002/anie.202012673. Online ahead of print. PMID: 33215801
4. Savelyev A, Gorbet GE, Henrickson A, Demeler B. Moving analytical ultracentrifugation software to a good manufacturing practices (GMP) environment. PLoS Comput Biol. 2020 Jun 19;16(6):e1007942. doi: 10.1371/journal.pcbi.1007942. PMID: 32559250
5. Obi O, Lubula MY, Cornilescu G, Henrickson A, Evans CM, McGuire K, Phillips M, Demeler B, Markley JL, Glass KC The BRPF1 bromodomain is a molecular reader of di-acetyllysineCur. Res. Struct. Biol. Vol 2, 2020, 104-115. doi.org/10.1016/j.crstbi.2020.05.001
6. Mullen P, Abbott JA, Wellman T, Aktar M, Fjeld C, Demeler B, Ebert AM, Francklyn CS. Neuropathy-associated histidyl-tRNA synthetase variants attenuate protein synthesis in vitro and disrupt axon outgrowth in developing zebrafish. FEBS J. 2020 Jun 15. doi: 10.1111/febs.15449. Online ahead of print. PMID: 32543048
7. Stoutjesdyk M, Henrickson A, Minors G, Demeler B. A calibration disk for the correction of radial errors from chromatic aberration and rotor stretch in the Optima AUC™ analytical ultracentrifuge. Eur Biophys J. 2020 May 9. doi: 10.1007/s00249-020-01434-z. Online ahead of print. PMID: 32388675
8. Mrozowich T, Henrickson A, Demeler B, Patel TR. Nanoscale Structure Determination of Murray Valley Encephalitis and Powassan Virus Non-Coding RNAs. Viruses. 2020 Feb 8;12(2). pii: E190. doi: 10.3390/v12020190. PMID: 32046304
9. Adusei-Danso F, Khaja FT, DeSantis M, Jeffrey PD, Dubnau E, Demeler B, Neiditch MB, Dubnau D. Structure-Function Studies of the Bacillus subtilis Ric Proteins Identify the Fe-S Cluster-Ligating Residues and Their Roles in Development and RNA Processing. MBio. 2019 Sep 17;10(5). pii: e01841-19. doi: 10.1128/mBio.01841-19.
10. Demeler, B. Measuring molecular interactions in solution using multi-wavelength analytical ultracentrifugation: combining spectral analysis with hydrodynamics. Biophysics – using physics to explore biological systems The Biochemist 41(2). 2019. 14-18.
11. Hu J, Soraiz EH, Johnson CN, Demeler B, Brancaleon L. Novel combinations of experimental and computational analysis tested on the binding of metalloprotoporphyrins to albumin. Int J Biol Macromol. 2019 May 9. pii: S0141-8130(19)31864-1. doi: 10.1016/j.ijbiomac.2019.05.060.
12. Ranaivoson FM, Turk LS, Ozgul S, Kakehi S, von Daake S, Lopez N, Trobiani L, De Jaco A, Denissova N, Demeler B, Özkan E, Montelione GT, Comoletti D.A Proteomic Screen of Neuronal Cell-Surface Molecules Reveals IgLONs as Structurally Conserved Interaction Modules at the Synapse. Structure. 2019 Mar 23. pii: S0969-2126(19)30082-6. doi: 10.1016/j.str.2019.03.004.
13. Bansal A, Karanth NM, Demeler B, Schindelin H, Sarma SP.Crystallographic Structures of IlvN·Val/Ile Complexes: Conformational Selectivity for Feedback Inhibition of Aceto Hydroxy Acid Synthases. Biochemistry. 2019 Apr 16;58(15):1992-2008. doi: 10.1021/acs.biochem.9b00050.
14. Wang Z, Bhattacharya A, White T, Buffone C, McCabe A, Nguyen LA, Shepard CN, Pardo S, Kim B, Weintraub ST, Demeler B, Diaz-Griffero F, Ivanov DN. Functionality of Redox-Active Cysteines Is Required for Restriction of Retroviral Replication by SAMHD1. Cell Rep. 2018 Jul 24;24(4):815-823. doi: 10.1016/j.celrep.2018.06.090. PMID: 30044979
15. Salveson PJ, Haerianardakani S, Thuy-Boun A, Yoo S, Kreutzer AG, Demeler B, Nowick JS. Repurposing Triphenylmethane Dyes to Bind to Trimers Derived from Aβ. J Am Chem Soc. 2018 Sep 19;140(37):11745-11754. doi: 10.1021/jacs.8b06568. Epub 2018 Sep 6. Erratum in: J Am Chem Soc. 2018 Nov 14;140(45):15546. PMID: 30125493
16. Salveson PJ, Haerianardakani S, Thuy-Boun A, Yoo S, Kreutzer AG, Demeler B, Nowick JS. Correction to “Repurposing Triphenylmethane Dyes To Bind to Trimers Derived from Aβ”. J Am Chem Soc. 2018 Nov 14;140(45):15546. doi: 10.1021/jacs.8b11195. Epub 2018 Nov 5. PMID: 30394740
17. Sterritt OW, Lang EJM, Kessans SA, Ryan TM, Demeler B, Jameson GB, Parker EJ. Structural and functional characterisation of the entry point to pyocyanin biosynthesis in Pseudomonas aeruginosa defines a new 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase subclass. Biosci Rep. 2018 Oct 17;38(5). pii: BSR20181605. doi: 10.1042/BSR20181605. Print 2018 Oct 31. PMID: 30242059
18. English LR, Tischer A, Demeler AK, Demeler B, Whitten ST. Sequence Reversal Prevents Chain Collapse and Yields Heat-Sensitive Intrinsic Disorder. Biophys J. 2018 Jul 17;115(2):328-340. doi: 10.1016/j.bpj.2018.06.006. PMID: 30021108
19. Kim H, Brookes E, Cao W, Demeler B. Two-dimensional grid optimization for sedimentation velocity analysis in the analytical ultracentrifuge. Eur Biophys J. 2018 Oct;47(7):837-844. doi: 10.1007/s00249-018-1309-z. PMID: 29777290
20. Williams TL, Gorbet GE, Demeler B. Multi-speed sedimentation velocity simulations with UltraScan-III. Eur Biophys J. 2018 Oct;47(7):815-823. doi: 10.1007/s00249-018-1308-0. PMID: 29748855
21. Johnson CN, Gorbet GE, Ramsower H, Urquidi J, Brancaleon L, Demeler B. Multi-wavelength analytical ultracentrifugation of human serum albumin complexed with porphyrin. Eur Biophys J. 2018 Jul 17;115(2):328-340. doi: 10.1007/s00249-018-1301-7.
22. Lopez P, Lara HH, Mullins SM, Black DM, Ramsower HH, Alvarez MM, Williams TL, Lopez-Lozano X, Weissker HC, García AP, Garzón IL, Demeler B, Lopez-Ribot JL, Yacamán MJ, and Whetten RL. Tetrahedral (T) Closed-Shell Cluster of 29 Silver Atoms & 12 Lipoate Ligands, [Ag29(R-α-LA)12](3-): Antibacterial and Antifungal Activity. ACS Appl. Nano Mater., 2018, 1 (4), pp 1595-1602
23. Gorbet GE, Mohapatra S, Demeler B. Multi-speed sedimentation velocity implementation in UltraScan-III. Eur Biophys J. 2018 Oct;47(7):825-835. doi: 10.1007/s00249-018-1297-z.
24. Serwer P, Wright ET, Demeler B, Jiang W. States of phage T3/T7 capsids: buoyant density centrifugation and cryo-EM. Biophys Rev. 2018 Apr;10(2):583-596. doi: 10.1007/s12551-017-0372-5. Epub 2017 Dec 14. Review. PMID: 29243090
25. Abbott JA, Meyer-Schuman R, Lupo V, Feely S, Mademan I, Oprescu SN, Griffin LB, Alberti MA, Casasnovas C, Aharoni S, Basel-Vanagaite L, Züchner S, De Jonghe P, Baets J, Shy ME, Espinós C, Demeler B, Antonellis A, Francklyn C.Substrate interaction defects in histidyl-tRNA synthetase linked to dominant axonal peripheral neuropathy. Hum Mutat. 2018 Mar;39(3):415-432. doi: 10.1002/humu.23380. Epub 2017 Dec 26. PMID: 29235198
26. Wagner JM, Christensen DE, Bhattacharya A, Dawidziak DM, Roganowicz MD, Wan Y, Pumroy RA, Demeler B, Ivanov DN, Ganser-Pornillos BK, Sundquist WI, Pornillos O. A general model for retroviral capsid pattern recognition by TRIM5 proteins. J Virol. 2018 Jan 30;92(4). pii: e01563-17. doi: 10.1128/JVI.01563-17. Print 2018 Feb 15. PMID: 29187540
27. Tian S, Yu G, He H, Zhao Y, Liu P, Marshall AG, Demeler B, Stagg SM, Li H. Pih1p-Tah1p Puts a Lid on Hexameric AAA+ ATPases Rvb1/2p. Structure. 2017 Oct 3;25(10):1519-1529.e4. doi: 10.1016/j.str.2017.08.002. Epub 2017 Sep 14. PMID: 28919439
28. 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. PMID: 28632987
29. 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. eCollection 2017 Feb. PMID: 28241071
30. 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 Apr 28;292(17):7173-7188. doi: 10.1074/jbc.M116.768754. Epub 2017 Feb 22. PMID: 28228478
31. 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
32. 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
33. 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. doi: 10.1038/ncomms13343. PMID: 27827373
34. 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.
35. 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
36. 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.
37. 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.
38. 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 Jul 7;120(26):6430-8. doi: 10.1021/acs.jpcb.6b04525. PMID: 27275518
39. 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, (2016) 120(16):8950-8958
40. 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.
41. 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.
42. 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
43. 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 526(1); 1-26 (2015)
44. 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;562:27-47. doi:10.1016/bs.mie.2015.04.013
45. 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
46. 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.
47. 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.
48. 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.
49. 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
50. 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.
51. 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.
52. 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.
53. 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.
54. 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
55. 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
56. Pham JD, Demeler B, Nowick JS. Polymorphism of Oligomers of a Peptide from β-Amyloid.. J Am Chem Soc. 2014 Mar 26. PMID: 24669785
57. 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
58. 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
59. 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
60. 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
61. 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
62. 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
63. 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
64. 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
65. 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
66. 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.
67. 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]
68. 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
69. 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.
70. 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.
71. 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.
72. 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
73. 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.
74. 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
75. 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.
76. 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)
77. 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.
78. 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
79. Laue T, Demeler B. A postreductionist framework for protein biochemistry. Nat Chem Biol. 2011 Jun;7(6):331-4. PMID: 21587250
80. 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
81. 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
82. 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
83. 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.
84. 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.
85. 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.
86. 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.
87. 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
88. 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.
89. 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)
90. 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
91. 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.
92. 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.
93. 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.
94. 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.
95. 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.
96. 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
97. 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.
98. 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.
99. 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.
100. 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.
101. 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.
102. 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.
103. 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.
104. Serwer P, Hayes SJ, Thomas JA, Demeler B, Hardies SC. Isolation of novel large and aggregating bacteriophages. Methods Mol Biol. 2009;501:55-66.
105. 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.
106. 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.
107. 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.
108. 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
109. 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.
110. 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
111. 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
112. 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.
113. 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)
114. Demeler B and E. Brookes. Monte Carlo analysis of sedimentation experiments. Colloid Polym Sci (2008) 286(2) 129-137
115. Brookes E, Demeler B. Parallel computational techniques for the analysis of sedimentation velocity experiments in UltraScan. Colloid Polym Sci (2008) 286(2) 138-148
116. 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
117. 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.
118. Brookes E, Demeler B. Parsimonious Regularization using Genetic Algorithms Applied to the Analysis of Analytical Ultracentrifugation Experiments. GECCO ’07: Proceedings of the 9th annual conference on Genetic and evolutionary computation, July 2007, 361–368, https://doi.org/10.1145/1276958.1277035, ACM 978-1-59593-697-4/07/0007 (2007)
119. 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.
120. 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
121. 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)
122. 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.
123. 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
124. 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
125. Belogrudov GI, Schirf V, Demeler B. Reversible Self-Association of Recombinant Bovine Factor B. Biochim Biophys Acta. (2006) 1764(11):1741-9
126. 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.
127. 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.
128. 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.
129. 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
130. 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.
131. 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.
132. 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.
133. 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.
134. 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
135. 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.
136. 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
137. 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)
138. Flachsov E, Bodnarova M, Demeler B, Raman CS, Martasek P. Structural basis of hereditary coproporphyria. PNAS (40) 14232-14237 (2005)
139. 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
140. Demeler B and K.E. van Holde. Sedimentation velocity analysis of highly heterogeneous systems. (2004). Anal. Biochem. Vol 335(2):279-288
141. 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.
142. 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
143. 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)
144. 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
145. 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
146. 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)
147. 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
148. 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.
149. 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.
150. 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)
151. 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.
152. 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
153. 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
154. 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)
155. 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)
156. 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)
157. 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)
158. 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)
159. 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)
160. 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)
161. Schuck P, Demeler B. Direct Sedimentation Boundary Analysis of Interference Optical Data in Analytical Ultracentrifugation. Biophysical Journal, 76:2288-2296 (1999)
162. 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)
163. 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)
164. 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)
165. 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)
166. Demeler B, Saber H, and Hansen JC. Identification and Interpretation of Complexity in Sedimentation Velocity Boundaries. Biophysical Journal 72, 397-407 (1997)
167. 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)
168. 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)
169. 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)
170. 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)
171. 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)
BOOK CHAPTERS:
172. Demeler B. Measuring molecular interactions in solution using multi-wavelength analytical ultracentrifugation: combining spectral analysis with hydrodynamics. The Biochemist. Chapter 3. Editor: Chris Willmott, Portland Press, April 2019.
173. Mitra S, Demeler B. Probing RNA-Protein Interactions and RNA Compaction by Sedimentation Velocity Analytical Ultracentrifugation. Methods Mol Biol. 2020;2113:281-317.
174. Demeler B. and Gorbet, GE (2016). Analytical Ultracentrifugation Data Analysis with UltraScan-III. In Analytical Ultracentrifugation: Instrumentation, Software, and Applications. Chapter 8. Eds: Uchiyama S., Stafford W. F. and T. Laue. Springer. (in press)
175. 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
176. 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
177. 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)
178. 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
179. 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
180. 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.
181. 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
182. 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
183. 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.
184. Hansen JC, Lebowitz J, and Demeler B. Analytical Ultracentrifugation of Complex Macromolecular Systems. Biochemistry 33, No. 45, 13155-13163, (1994)