Publications

2020

56. Hewitt CS, Krabill AD, Das C, Flaherty DP. (2020) Development of Ubiquitin Variants with Selectivity for Ubiquitin C-Terminal Hydrolase Deubiquitinases. Biochemistry 59(37), 3447-3462.

55. Puvar K, Iyer S, Fu J, Kenny S, Negrón Terón KI, Luo ZQ, Brzovic PS, Klevit RE, Das C. (2020) Legionella effector MavC targets the Ube2N~Ub conjugate for noncanonical ubiquitination. Nat Commun. 11(1), 2365.

54. Hausman JM, Kenny S, Iyer S, Babar A, Qiu J, Fu J, Luo ZQ, Das C. (2020) The Two Deubiquitinating Enzymes from Chlamydia trachomatis Have Distinct Ubiquitin Recognition Properties. Biochemistry 59(16), 1604-1617.

53. Puvar K, Saleh AM, Curtis RW, Zhou Y, R Nyalapatla P, Fu J, Rovira AR, Tor Y, Luo ZQ, Ghosh AK, Wirth MJ, Chmielewski J, Kinzer-Ursem TL, Das C. (2020) Fluorescent Probes for Monitoring Serine Ubiquitination. Biochemistry 59(13), 1309-1313.

52. Krabill AD, Chen H, Hussain S, Feng C, Abdullah A, Das C, Aryal UK, Post CB, Wendt MK, Galardy PJ, Flaherty DP. (2020) Ubiquitin C-Terminal Hydrolase L1: Biochemical and Cellular Characterization of a Covalent Cyanopyrrolidine-Based Inhibitor. Chembiochem 21(5), 712-722.

51. Gan N, Guan H, Huang Y, Yu T, Fu J, Nakayasu ES, Puvar K, Das C, Wang D, Ouyang S, Luo ZQ. (2020) Legionella pneumophila regulates the activity of UBE2N by deamidase-mediated deubiquitination. EMBO J. 39(4), e102806.

2019

50.Gan N, Zhen X, Liu Y, Xu X, He C, Qiu J, Liu Y, Fujimoto GM, Nakayasu ES, Zhou B, Zhao L, Puvar K, Das C, Ouyang S, Luo ZQ. (2019) Regulation of phosphoribosyl ubiquitination by a calmodulin-dependent glutamylase. Nature. 572(7769), 387-391.

49. Puvar K, Iyer S, Sheedlo MJ, Das C. (2019) Purification and functional characterization of the DUB domain of SdeA. Methods Enzymol. 618, 343-355.

2018

48. Puvar K, Luo Z-Q, Das C. (2018) Uncovering the Structural Basis of a New Twist in Protein Ubiquitination. Trends Biochem Sci. 44(5), 467-477.

47. Ha L, Colquhoun J, Noinaj N, Das C, Dunman PM, Flaherty DP. (2018) Crystal structure of the ribonuclease-P-protein subunit from Staphylococcus aureus. Acta Crystallogr. F. Struct. Biol. Commun. F74, 632-637.

2017

46. Puvar K, Zhou Y, Qiu J, Luo Z.-Q, Wirth MJ, Das C. (2017) Ubiquitin Chains Modified by the Bacterial Ligase SdeA Are Protected from Deubiquitinase Hydrolysis. Biochemistry. 56(36),4762-4766.

45. Qiu J, Yu K, Fei X, Liu Y, Nakayasu ES, Piehowski PD, Shaw JB, Puvar K, Das C, Liu X, Luo ZQ. (2017) A unique deubiquitinase that deconjugates phosphoribosyl-linked protein ubiquitination. Cell Research. 27(7), 865-881.

44. Scarborough NM, Godaliyadda GM, Ye DH, Kissick DJ, Zhang S, Newman JA, Sheedlo MJ, Chowdhury AU, Fischetti RF, Das C, Buzzard GT, Bouman CA, Simpson GJ. (2017) Dynamic X-ray diffraction sampling for protein crystal positioning. J Synchrotron Radiat. 24(Pt 1), 188-195.

2016

43. Nepal M, Sheedlo MJ, Das C, Chmielewski J. (2016) Accessing Three-Dimensional Crystals with Incorporated Guests through Metal-Directed Coiled-Coil Peptide Assembly. J. Am. Chem. Soc. 138(34) 11051-7.

42. Newman JA, Zhang S, Sullivan SZ, Dow XY, Becker M, Sheedlo MJ, Stepanov S, Carlsen MS, Everly RM, Das C, Fischetti RF, Simpson GJ. (2016) Guiding synchrotron X-ray diffraction by multimodal video-rate protein crystal imaging. J Synchrotron Radiat. 23(Pt 4):959-65.

41. Qiu, J. Sheedlo, MJ. Yu, K. Tan, Y. Nakayasu, ES. Das, C. Liu, X. Luo, Z-Q. (2016) Ubiquitination Independent of E1 and E2 Enzymes by Bacterial Effectors. Nature, 533(7601):120-4.

2015

40. Sheedlo, MJ. Qiu, J. Tan, Y. Paul, LN. Luo, Z-Q, Das, C(2015) Structural Basis of Substrate Recognition by a Bacterial Deubiquitinase Important for Dynamics of Phagosome Ubiquitination. Proc. Natl. Acad. Sci. U.S.A., 112 (49), 15090–15095.

39. Bueno, AN, Shrestha, RK, Ronau, JA, Babar, A, Sheedlo, MJ, Fuchs, JE, Paul, LN, Das, C(2015) Dynamics of an Active-Site Flap Contributes to Catalysis in a JAMM Family Metallo Deubiquitinase. Biochemistry, 54 (39), 6038–6051.

38. Newman, J. A. Scarborough, N. M. Pogranichniy, N. R. Shrestha, R. K. Closser, R. G. Das, C. Simpson, G. J. (2015) Intercalating Dyes for Enhanced Contrast in Second-Harmonic Generation Imaging of Protein Crystals. Acta Crystallogr. D Biol. Crystallogr., 71 (Pt 7), 1471–1477.

37. Shrestha, RK, Ronau, JA, Das, C(2015) Understanding the Molecular Basis of MIC-CAP Syndrome through Structural and Functional Studies of the Deubiquitinase AMSH. FASEB J, 29, 883.7.

2014

36. Ronau, JA, Paul, LN, Fuchs, JE, Liedl, KR, Abu-Omar, MM, Das, C(2014) A Conserved Acidic Residue in Phenylalanine Hydroxylase Contributes to Cofactor Affinity and Catalysis. Biochemistry, 53 (43), 6834–6848.

35. Shrestha, RK, Ronau, JA, Davies, CW, Guenette, RG, Strieter, ER, Paul, LN, Das, C(2014) Insights into the Mechanism of Deubiquitination by JAMM Deubiquitinases from Cocrystal Structures of the Enzyme with the Substrate and Product. Biochemistry, 53 (19), 3199–3217.

34. Morrow, ME, Kim, M, Paul, LN, Ronau, JA, Das, C(2014) Structural and Biophysical Analysis of UCH37: Ubiquitin Recognition and Binding to ADRM1 (952.3). FASEB J, 28, 952.3.

2013

33. Davies, CW, Paul, LN, Das, C(2013) Mechanism of Recruitment and Activation of the Endosome-Associated Deubiquitinase AMSH. Biochemistry, 52 (44), 7818–7829.

32. Ronau, JA, Paul, LN, Fuchs, JE, Corn, IR, Wagner, KT, Liedl, KR, Abu-Omar, MM, Das, C(2013) An Additional Substrate Binding Site in a Bacterial Phenylalanine Hydroxylase. Eur Biophys J, 42 (9), 691–708.

31. Madden, JT, Toth, SJ, Dettmar, CM, Newman, JA, Oglesbee, RA, Hedderich, HG, Everly, RM, Becker, M, Ronau, JA, Buchanan, SK, Cherezov, V, Morrow, ME, Xu, S, Ferguson, D, Makarov, O, Das, C, Fischetti, R, Simpson, GJ. (2013) Integrated Nonlinear Optical Imaging Microscope for on-Axis Crystal Detection and Centering at a Synchrotron Beamline. Journal of Synchrotron Radiation 2013, 20 (4), 531–540.

30. Morrow, ME, Kim, M, Ronau, JA, Sheedlo, MJ, White, RR, Chaney, J, Paul, LN, Lill, MA, Artavanis-Tsakonas, K, Das, C. (2013) Stabilization of an Unusual Salt Bridge in Ubiquitin by the Extra C-Terminal Domain of the Proteasome-Associated Deubiquitinase UCH37 as a Mechanism of Its Exo Specificity. Biochemistry 52 (20), 3564–3578.

29. DeWalt, EL, Begue, VJ, Ronau, JA, Sullivan, SZ, Das, C, Simpson, GJ. (2013) Polarization-Resolved Second-Harmonic Generation Microscopy as a Method to Visualize Protein-Crystal Domains. Acta Crystallographica Section D Biological Crystallography 69 (1), 74–81.

2012

28. Tsou, WL, Sheedlo, MJ, Morrow, ME, Blount, JR, McGregor, KM, Das, C, Todi, SV. (2012) Systematic Analysis of the Physiological Importance of Deubiquitinating Enzymes. PLoS ONE 7 (8), e43112.

27. Davies, CW, Chaney, J, Korbel, G, Ringe, D, Petsko, GA, Ploegh, H, Das, C. (2012) The Co-Crystal Structure of Ubiquitin Carboxy-Terminal Hydrolase L1 (UCHL1) with a Tripeptide Fluoromethyl Ketone (Z-VAE(OMe)-FMK). Bioorganic & Medicinal Chemistry Letters 22 (12), 3900–3904.

26. Todi, SV, Das, C. (2012) Should Deubiquitinating Enzymes Be Targeted for Therapy? Clinical Pharmacology & Biopharmaceutics 1 (3), 1000e108.

25. Boudreaux D, Chaney J, Maiti T and Das C.* (2012) Contribution of active-site glutamine to rate enhancement in ubiquitin carboxy terminal hydrolases. FEBS Journal. doi: 10.1111/j.1742-4658.2012.08507.x.

2011

24. Maiti TK, Permaul M, Boudreaux D, Mahanic C, Mauney S, Das C* (2011) Crystal structure of the catalytic domain of UCHL5, a proteasome-associated human deubiquitinating enzyme, reveals an unproductive form of the enzyme. FEBS Journal 278 4917-4926.

23. Davies C, Paul L, Kim M, and Das C* (2011) Structural and Thermodynamic Comparison of the Catalytic Domain of AMSH and AMSH-LP: Nearly Identical Fold but Different Stability. Journal of Molecular Biology 413 416-42.

22. Andersson FI, McMorran L, Werrell EF, Crone WJ, Das C, Hsu SD, Jackson SE (2011). The Effect of Parkinson’s Disease Associated Mutations on the Stability, Structure and Dynamics of the Deubiquitinating Enzyme UCH-L1. Journal of Molecular Biology 407 261-271.

2010

21. Boudreaux, D, Maiti, T, Davies, C, Das C* (2010) Ubiquitin vinyl methyl ester binding orients the misaligned active site of the ubiquitin hydrolase UCHL1 into productive conformation. Proceedings of the National Academy of Sciences USA 107 9117-9122.

Pre-Purdue

20. Das C, Hoang, QQ, Kreinbring CA, Luchansky SJ, Meray RK, Ray SS, Lansbury PT, Ringe D, Petsko, GA (2006) Structural basis of conformational plasticity of the Parkinson’s disease- associated ubiquitin hydrolase UCH-L1. Proceedings of the National Academy of Sciences USA 103 4675-4680.

19. Kornilova AY, Bihel F, Das C, Wolfe MS (2005) The initial substrate-binding site of gamma-secretase is located on presenilin near the active site. Proceedings of the National Academy of Sciences USA 102 3230-3235.

18. Bihel F, Das C, Bowman MJ, Wolfe MS (2004) Discovery of a Subnanomolar helical D-tridecapeptide inhibitor of gamma-secretase. Journal of Medicinal Chemistry 47 3931-3933.

17. Esler WP, Das C, Wolfe MS (2004) Probing pockets S2-S4' of the gamma-secretase active site with (hydroxyethyl)urea peptidomimetics. Bioorganic and Medicinal Chemistry Letters 14 1935-1938.

16. Aravinda S, Harini VV, Shamala N, Das C, Balaram P (2004) Structure and assembly of designed beta-hairpin peptides in crystals as models for beta-sheet aggregation. Biochemistry 43 1832-1846.

15. Das C, Berezovska O, Diehl TS, Genet C, Buldyrev I, Tsai JY, Hyman BT, Wolfe MS (2003) Designed helical peptides inhibit an intramembrane protease. Journal of the American Chemical Society 125 11794-11795.

14. Aravinda S, Shamala N, Das C, Sriranjani A, Karle IL, Balaram P (2003) Aromatic-aromatic interactions in crystal structures of helical peptide scaffolds containing projecting phenylalanine residues. Journal of the American Chemical Society 125 5308-5315.

13. Kornilova AY, Das C, Wolfe MS (2003) Differential effects of inhibitors on the gamma-secretase complex. Mechanistic implications. Journal of Biological Chemistry 278 16470-16473.

12. Wolfe MS, Esler WP, Das C (2002) Continuing strategies for inhibiting Alzheimer's gamma-secretase. Journal of Molecular Neuroscience 19 83-87.

11. Aravinda S, Shamala N, Das C, Balaram P (2002) Structural analysis of peptide helices containing centrally positioned lactic acid residues. Biopolymers 64 255-267.

10. Esler WP, Das C, Campbell WA, Kimberly WT, Kornilova AY, Diehl, TS, Ye W, Ostaszewski BL, Xia W, Selkoe DJ, Wolfe MS (2002) Amyloid-lowering isocoumarins are not direct inhibitors of gamma-secretase. Nature Cell Biology 4 E110-111.

9. Karle IL, Das C, Balaram P (2001) Effects of hydrogen-bond deletion on peptide helices: structural characterization of depsipeptides containing lactic acid. Biopolymers 59 276-289.

8. Das C, Shankaramma SC, Balaram P (2001) Molecular carpentry: piecing together helices and hairpins in designed peptides. Chemistry- A European Journal 7 840-847.

7. Das C, Naganagowda GA, Karle IL, Balaram P (2001) Designed beta-hairpin peptides with defined tight turn stereochemistry. Biopolymers 58 335-346.

6. Das C, Nayak V, Raghothama S, Balaram P (2000) Synthetic protein design: construction of a four-stranded beta-sheet structure and evaluation of its integrity in methanol-water systems. The Journal of Peptide Research 56 307-317.

5. Karle IL, Das C, Balaram P (2000) De novo protein design: crystallographic characterization of a synthetic peptide containing independent helical and hairpin domains. Proceedings of the National Academy of Sciences USA 97 3034-3037.

4. Zhao C, Polavarapu PL, Das C, Balaram P (2000) Vibrational circular dichroism of β-hairpin peptides. Journal of the American Chemical Society 122 8228-8231.

3. Aravinda S, Shamala N, Pramanik A, Das C, Balaram P (2000) An unusual C-H...O hydrogen bond mediated reversal of polypeptide chain direction in a synthetic peptide helix. Biochemical and Biophysical research Communications 273 933-936.

2. Das C, Raghothama S, Balaram P (1999) A four stranded β-sheet structure in a designed, synthetic polypeptide. Chemical Communications 967-968.

1. Das C, Raghothama S, Balaram P (1998) A designed three stranded β-sheet peptide as a multiple β-hairpin model. Journal of the American Chemical Society 120 5812-5813.