Osman Bilsel

Biophysics, protein science, spectroscopy, data analysis and instrumentation

Publications

Peer-reviewed publications

  1. Bilsel, J. Rodriguez and D. Holten. Picosecond Relaxation of Strongly-Coupled Porphyrin Dimers. J. Phys. Chem. 94: 3508-3512 (1990).
  2. Bilsel, J. Rodriguez, D. Holten, G.S. Girolami, S.N. Milam and K.S. Suslick. Observation of a New Low-Energy 1(1,1*) Excited State in Strongly-Coupled Porphyrin Dimers. J. Am. Chem. Soc. 112: 4075-4077 (1990).
  3. Bilsel, J.W. Buchler, P. Hammershmitt, J. Rodriguez and D. Holten. Electronic States and (1,1*) Absorption and Emission Characteristics of Strongly-Coupled Porphyrins: Sandwich Complexes of HfIVand ZrIV Chem. Phys. Lett. 182: 415-421 (1991).
  4. Bilsel, J. Rodriguez, S.N. Milam, P.A. Gorlin, G.S. Girolami, K.S. Suslick and D. Holten. Electronic States and Optical Properties of Porphyrins in Van der Waals Contact: ThIV Sandwich Complexes. J. Am. Chem. Soc. 114: 6528-6538 (1992).
  5. Bilsel, J. Rodriguez, D. Holten, G.S. Girolami, S.N. Milam and K.S. Suslick. Ultrafast Deactivation and Vibrational Dynamics of Photoexcited UIVPorphyrin Sandwich Complexes. J. Phys. Chem. 97: 7216-7221 (1993)
  6. A. Zitzewitz, O. Bilsel, J. Luo, B.E. Jones and C.R. Matthews. Probing the Folding Mechanism of a Leucine Zipper Peptide by Stopped-Flow Circular Dichroism. Biochemistry 34: 12812-12819 (1995).
  7. Bilsel, J. A. Zitzewitz, K.E. Bowers and C.R. Matthews. The Folding Mechanism of the a/b Barrel Protein, a-Tryptophan Synthase: Global Analysis Highlights the Interconversion of Multiple Native, Intermediate and Unfolded Forms Through Parallel Channels. Biochemistry 33: 1018-1029 (1999).
  8. Bilsel, L. Yang, J. A. Zitzewitz, J.M. Beechem and C. R. Matthews. Time-Resolved Anisotropy During Refolding of the -subunit of Tryptophan Synthase Reveals a Non-monotonic Behavior of the Rotational Correlation Time. Biochemistry 38: 4177-4187 (1999).
  9. J. Gualfetti, O. Bilsel and C.R. Matthews. The Progressive Development of Structure and Stability During the Folding of the a-subunit of Tryptophan Synthase from E. coli. Protein Science 8: 1623-1635 (1999).
  10. J. Gualfetti, M. Iwakura, J.C. Lee, H. Kihara, O. Bilsel, J.A. Zitzewitz and C. R. Matthews. Apparent Radii of the Native, Stable Intermediates and Unfolded Conformers of the a Subunit of Tryptophan Synthase from E. coli, a TIM Barrel Protein. Biochemistry 38: 13367-13378 (1999).
  11. Bilsel and C.R. Matthews. Barriers in Protein Folding Reactions. Advances in Protein Chemistry 53: 153-207 (2000).
  12. M. Doyle, O. Bilsel, C.M. Teschke. SecA folding kinetics: a large dimeric protein rapidly forms multiple native states. J Mol Biol. 34: 199-214 (2004).
  13. Bilsel*, C. Kayatekin, L.A. Wallace and C.R. Matthews. A microchannel solution mixer for studying microsecond protein folding reactions. Rev. Sci. Inst. 76: 14302-14308 (2005). *denotes corresponding author
  14. Bilsel* and C.R. Matthews. Molecular dimensions and their distributions in early folding intermediates. Curr. Opin. Struct. Biol. 16: 86-93 (2006). *denotes corresponding author
  15. -K. Svensson, O. Bilsel, E. Kondrashkina, J.A. Zitzewitz and C.R. Matthews, “Mapping the folding free energy surface for metal-free human Cu,Zn superoxide dismutase”, J. Mol. Biol. 364: 1084-1102 (2006).
  16. Arai*, E. Kondrashkina, C. Kayatekin, C.R. Matthews, M. Iwakura and O. Bilsel*. Microsecond hydrophobic collapse in the folding of Escherichia coli dihydrofolate reductase, an alpha/beta-type protein. J. Mol. Biol. 368: 219-229 (2007). *denotes co-corresponding authors
  17. Venkatraman, TT Nguyen, M. Sainlos, O. Bilsel, S. Chitta, B. Imperiali and L.J. Stern. Fluorogenic probes for monitoring peptide binding to class II MHC proteins in living cells. Nat. Chem. Biol., 3: 222-228 (2007).
  18. R. Forsyth, O. Bilsel, Z. Gu and C.R. Matthews. Topology and sequence in the folding of a TIM barrel protein: Global analysis highlights partitioning between transient off-pathway and stable on-pathway folding intermediates in the complex folding mechanism of a (ba)8 barrel of unknown function from B. subtilis. J. Mol. Biol. 372: 236-253 (2007).
  19. Bilsel*, Y. Wu, C. Kayatekin and C.R. Matthews. Merging microsecond mixing and time-correlated single-photon counting: using time-resolved FRET and time-resolved anisotropy to probe early events in protein folding. Proc. SPIE, 6771, 677103 (2007). *denotes corresponding author
  20. Wu, E. Kondrashkina, C. Kayatekin, C.R. Matthews and O. Bilsel*. Microsecond acquisition of heterogeneous structure in the folding of a TIM barrel protein. Proc. Natl. Acad. Sci., U.S.A. 105: 13367-13372 (2008). *denotes corresponding author
  21. F. Noel, O. Bilsel, A. Kundu, Y. Wu, J.A. Zitzewitz and C.R. Matthews. The folding free-energy surface of HIV-1 protease: Insights into the thermodynamic basis for resistance to inhibitors. J. Mol. Biol., 387: 1002-1016 (2009).
  22. Tiwari, A. Liba, S.H. Sohn, S.V. Seetharaman, O. Bilsel, C.R. Matthews, P.J. Hart, J.S. Valentine and L.J. Hayward. Metal deficiency increases aberrant hydrophobicity of mutant superoxide dismutases that cause amyotrophic lateral sclerosis. J. Biol. Chem. 284: 27746-27758 (2009).
  23. -K.E. Svensson, O. Bilsel, C. Kayatekin, J.A. Adefusika, J.A. Zitzewitz and C.R. Matthews. Metal-free ALS variants of human Cu,Zn-superoxide dismutase have enhanced populations of monomeric species. PLoS ONE 5: e10064 (2010).
  24. V. Kathuria, L. Guo, R. Graceffa, R. Barrea, R.P. Nobrega, C.R. Matthews, T.C. Irving and O. Bilsel*. Minireview: structural insights into early foldig events using continuous-flow time-resolved small-angle X-ray scattering. Biopolymers 95: 550-558 (2011). *denotes corresponding author
  25. Arai*, M. Iwakura, C.R. Matthews and O. Bilsel*. Microsecond subdomain folding in dihydrofolate reductase. J. Mol. Biol. 410: 329-242 (2011). *denotes corresponding authors
  26. L. Serrano, O. Bilsel* and F. Gai*. Native state conformational heterogeneity of HP35 revealed by time-resolved FRET. J. Phys. Chem. B. 116: 10631-10638 (2012). *denotes corresponding authors
  27. V. Kathuria, A. Chan, R. Graceffa, R.P. Nobrega, C.R. Matthews, T.C. Irving, B. Perot and O. Bilsel*. Advances in turbulent mixing techniques to study microsecond protein folding reactions. Biopolymers 99: 888-896 (2013). *denotes corresponding author
  28. Graceffa, R.P. Nobrega, R.A. Barrea, S.V. Kathuria, S. Chakravarthy, O. Bilsel and T. C. Irving. Sub-millisecond time-resolved SAXS using a continuous-flow mixer and X-ray microbeam. J. Synchrotron Radiat. 20: 820-825 (2013).
  29. X. Zhou and O. Bilsel. SAXS/SANS probe of intermolecular interactions in concentrated protein solutions. Biophys. J. 106: 771-773 (2014).
  30. V. Kathuria, C. Kayatekin, R. Barrea, E. Kondrashkina, R. Graceffa, L. Guo, R.P. Nobrega, S. Chakravarthy, C.R. Matthews, T.C. Irving and O. Bilsel*. Microsecond barrier-limited chain collapse observed by time-resolved FRET and SAXS. J. Mol. Biol. 426: 1980-1994 (2014). *denotes corresponding author
  31. P. Nobrega, K. Arora, S.V. Kathuria, R. Graceffa, R.A. Barrea, L. Guo, S. Chakravarthy, O. Bilsel, T.C. Irving, C.L. Brooks, III and C.R. Matthews. Modulation of frustration in folding by sequence permutation. Proc. Natl. Acad. Sci., U.S.A. 426: 10562-10567 (2014).
  32. E. Rosen, S.V. Kathuria, C.R. Matthews, O. Bilsel* and S. Marqusee*. Non-native structure appears in microseconds during the folding of E. coli RNase H. J. Mol. Biol. 427: 443-452 (2015). *denotes corresponding authors
  33. W. Malaby, S. Chakravarthy, T.C. Irving, S.V. Kathuria, O. Bilsel and D.G. Lambright. Methods for analysis of size-exclusion chromatography-small-angle X-ray scattering and reconstruction of protein scattering. J. Appl. Crystallogr. 48: 1102-1113 (2015).
  34. Wu, H. Lee, O. Bilsel, Y. Zhang, Z. Li, T. Chen, Y. Liu, C. Duan, J. Shen, A. Punjabi and G. Han. Tailoring dye-sensitized upconversion nanoparticle excitation bands towards excitation wavelengths selective imaging. Nanoscale 7: 18424-18428 (2015).
  35. Orevi, G. Rahamin, D. Amir, S. Kathuria, O. Bilsel, C.R. Matthews and E. Haas. Sequential closure of loop structures forms the folding nucleus during the refolding transition of the Escherichia coli adenylate kinase molecule. Biochemistry 55: 79-91 (2016).
  36. Peran, M.D. Watson, O. Bilsel and D.P. Raleigh. Selenomethionine p-cyanophenylalanine pairs provide a convenient, sensitive, non-perturbing fluorescent probe of local helical structure. Chem. Commun. (Camb.) 52: 2055-2058 (2016).
  37. Wu, Y. Zhang, K. Takle, O. Bilsel, Z. Li, H. Lee, Z. Zhang, D. Li, W. Fan, C. Duan, E.M. Chan, C. Lois, Y. Xiang and G. Han. Dye-sensitized core/active shell upconversion nanoparticles for optogenetics and bioimaging applications. ACS Nano. 10: 1060-1068 (2016).
  38. D. Watson, I. Peran, J. Zou, O. Bilsel and D.P. Raleigh. Selenomethionine quenching of tryptophan fluorescence provides a simple probe of protein structure. Biochemistry 56: 1085-1094 (2017).
  39. Shi, R.P. Nobrega, C. Schwantes, S.V. Kathuria, O. Bilsel, C.R. Matthews, T.J. Lane and V.S. Pande. Atomistic structural ensemble refinement reveals non-native structure stabilizes a sub-millisecond folding intermediate of CheY. Sci. Rep. 7: 44116 (2017).
  40. W. Malaby, S. Das, S. Chakravarthy, T.C. Irving, O. Bilsel and D.G. Lambright. Structural dynamics control allosteric activation of cytohesin family arf GTPase exchange factor. Structure 26: 106-117 (2018).
  41. Peran, A.S. Holehouse, S.V. Kathuria, R.V. Pappu, I.S. Carrico, O. Bilsel* and D.P. Raleigh.* Direct observation of a protein collapse transition: A high efficiency bioorthogonal labeling strategy facilitates studies of protein unfolded states. J. Am. Chem. Soc., revised version under review (2018). *denotes corresponding authors
  42. Inguva, S.V. Kathuria, O. Bilsel and B.J. Perot. Computer design of microfluidic mixers for protein/RNA folding studies. PLoS ONE 13(6): e0198534. https://doi.org/10.1371/journal.pone.0198534 (2018).
  43. K. Singh, S. Watanabe, O. Bilsel, C. L. Peterson. Transient kinetic analysis of SWR1C-catalyzed H2A.Z deposition unravels the impact of nucleosome dynamics and the asymmetry of stepwise histone exchange. BioRXiv doi: https://doi.org/10.1101/304998 (2018).
  44. Kalkowski, C. Liu, P. Leon-Plata, M. Szymusiak, P. Zhang, T. Irving, W. Shang, S. Kathuria, O. Bilsel, Y. Liu. In-situ Measurements of Polymer Micellization Kinetics with Millisecond Temporal Resolution, Nature Communication, under review (2018).
  45. Inguva, J. P. Rothstein, O. Bilsel, B. J. Perot. High-speed velocimetry in microfluidic protein mixers using confocal fluorescence decay microscopy. Experiments in Fluids, in press (2018).
  46. I. Peran, A. S. Holehouse, I. S. Carrico, R. V. Pappu*, O. Bilsel*, D. P. Raleigh*. Unfolded states under folding conditions accommodate sequence-specific conformational preferences alongside ensemble-averaged features of random coils, Nature Structural and Molecular Biology, under review.
  47. Inguva,  R. Graceffa,  J. Schulz,  O. Bilsel,  B. J. Perot. Creating  round  focused  micro-jets  from  rectangular  nozzles, Manuscript in preparation (2018).
  48. T. Halloran, Y. Wang, K. Arora, S. Charkravarthy, T.C. Irving, O. Bilsel, C. Brooks III, C. Robert Matthews. Topological frustration in a TIM barrel. Manuscript in preparation.
  49. C. Mackness, N. Johli, C.O. McCollum, M.T. Tran, C.R. Matthews, C.R., J.A. Zitzewitz* and O. Bilsel*. A Time-resolved FRET assay and small molecule screen targeting stabilizing of the SOD1 native state dimer. Manuscript in preparation.  *denotes corresponding authors

Books & Chapters

  1. V. Kathuria and O. Bilsel*. Probing microsecond reactions with microfluidic mixers and TPSCS. in Advanced Time-correlated Single Photon Counting Applications (W. Becker, Ed.) 357-384. Springer Series in Chemical Physics, Vol. 111, Springer, Cham (2015). *denotes corresponding author
This work was supported by the NSF, NIH and the ALS Therapy Alliance.
2024 Osman Bilsel