Research Highlights


Kudlacek, S. T.; Premkumar, L.; Metz, S. W.; Tripathy, A.; Bobkov, A. A.; Payne, A. M.; Graham, S.; Brackbill, J. A.; Miley, M. J.; de Silva, A. M.; Kuhlman, B. Physiological Temperatures Reduce Dimerization of Dengue and Zika Virus Recombinant Envelope Proteins. J Biol Chem 2018, jbc.RA118.002658.

Little, M.S., Pellock, S.J., Walton, W.G., Tripathy, A. and Redinbo. M.R. Structural Basis for the Regulation of b-Glucuronidase Expression by Human Gut Enterobacteriaceae. Proceedings of the National Academy of Sciences USA115, E152-E161. (2018). PMID: 29269393

Yumerefendi, H.; Wang, H.; Dickinson, D. J.; Lerner, A. M.; Malkus, P.; Goldstein, B.; Hahn, K.; Kuhlman, B. Light-Dependent Cytoplasmic Recruitment Enhances the Dynamic Range of a Nuclear Import Photoswitch. Chembiochem 201842, 443.

An ordered pattern of Ana2 phosphorylation by Plk4 is required for centriole assembly. McLamarrah TA, Buster DW, Galletta BJ, Boese CJ, Ryniawec JM, Hollingsworth NA, Byrnes AE, Brownlee CW, Slep KC, Rusan NM, Rogers GC. J Cell Biol. 2018 Apr 2;217(4):1217-1231. doi: 10.1083/jcb.201605106. Epub 2018 Mar 1. PMID: 29496738 

Stu2 uses a 15-nm parallel coiled coil for kinetochore localization and concomitant regulation of the mitotic spindle. Haase KP, Fox JC, Byrnes AE, Adikes RC, Speed SK, Haase J, Friedman B, Cook DM, Bloom K, Rusan NM, Slep KC. Mol Biol Cell. 2018 Feb 1;29(3):285-294. doi: 10.1091/mbc.E17-01-0057. Epub 2017 Nov 29. PMID:29187574

M. M. So, N. A. Mansukhani, E. B. Peters, M. S. Albaghdadi, Z. Wang, C. M. Rubert Pérez, M. R. Kibbe, S. I. Stupp, Adv. Biosys. 2018, 2, 1700123.

Suh J. L.; Watts, B.; Stuckey, J. I.; Norris-Drouin, J. L.; Cholensky, S. H.; Dickson, B. M.; An, Y.; Mathea, S.; Salah, E.; Knapp, S.; Khan, A.; Adams, A. T.; Strahl, B. D.; Sagum, C. A.; Bedford, M. T.; James, L. I.; Kireev, D. B.*; Frye, S. V.* “Quantitative characterization of bivalent probes for a dual bromodomain protein, Transcription Initiation Factor TFIID subunit 1, TAF1.” Biochemistry2018, Just Accepted.

A.J. Guseman, S.L. Speer, G.M. Perez Goncalves and G.J. Pielak, Surface Charge Modulates Protein-Protein Interactions in Physiologically Relevant Environments. Biochemistry 57, 1681-1684 (2018). PMID: 29473738

Lauren E. St Louis, Tayliz M. RodriguezMarcey L. Waters*, “A study of 2-component i, i+3 peptide stapling using thioethers”Bioorg. Med. Chem. 201826, 1203-5, DOI: 10.1016/j.bmc.2017.10.037


Pollet, R.M., D’Agostino, E.H., Walton, W.G., Xu, Y., Little, M.S., Biernat, K.B., Pellock, S.J., Patterson, L.M., Creekmore, B.C., Isenberg, H.N., Bahethi, R.R., Bhatt, A.P., Liu, J., Gharaibeh, R.Z., and Redinbo, M.R. An Atlas of b-Glucuronidases in the Human Intestinal Microbiome. Structure25, 967-977.  (2017).  PMCID:  PMC5533298

Structure of the ACF7 EF-Hand-GAR Module and Delineation of Microtubule Binding Determinants. Lane TR, Fuchs E, Slep KC. Structure. 2017 Jul 5;25(7):1130-1138.e6. doi: 10.1016/j.str.2017.05.006. Epub 2017 Jun 8. PMID: 28602822

TOG-tubulin binding specificity promotes microtubule dynamics and mitotic spindle formation. Byrnes AE, Slep KC. J Cell Biol. 2017 Jun 5;216(6):1641-1657. doi: 10.1083/jcb.201610090. Epub 2017 May 16. PMID: 28512144

Nishimura, MT, RG Anderson, KA Cherkis, TF Law, Q Liu, M Machius, Z Nimchuk, L Yang, E-H Chung, F El-Kasmi, M Hyunh, EO Nishimura, J Sondek and JL Dangl (2017) The TIR-only protein RBA1 recognizes a pathogen effector to regulate cell death inArabidopsisProc. Natl. Acad. Sci., USA. 114, E2053–E2062.doi: 10.1073/pnas.1620973114. Published online January 30, 2017 PR PMID 28137883.

Barnash, K. D.; The, J.; Norris-Drouin, J. L.; Cholensky, S. H.; Worley, B. M.; Li, F.; Stuckey, J. I.; Brown, P. J.; Vedadi, M.; Arrowsmith, C. H.; Frye, S. V.*; James, L. I.* “Discovery of peptidomimetic ligands of EED as allosteric inhibitors of PRC2.”ACS Comb. Sci201719, 161-172.

Li, B, Urano, D, Mowrey, DD, Dokholyan, NV,  Torres, MP, Jones, AM (2017) Tyrosine  phosphorylation switching of a G protein substrate.  J. Biol Chem. Jan 30. pii: jbc.RA117.000163. doi: 10.1074/jbc.RA117.000163. [Epub ahead of print]

L.C. Acosta, G.M. Perez Goncalves, G.J. Pielak and A.H. Gorensek-Benitez, Large cosolutes, small cosolutes and dihydrofolate reductase activity.Protein Sci. 26, 2417–2425 (2017). PMID: 

A.H. Gorensek-Benitez, A.E. Smith, S.S. Stadmiller, G.M. Perez Goncalves and G.J. Pielak, Cosolutes, Crowding and Protein Folding Kinetics. J. Phys. Chem. B 121, 6527-6537 (2017). PMID: 28605189

A.J. Guseman and G.J. Pielak, Cosolute and Crowding Effects on a Side-By-Side Protein Dimer. Biochemistry 56, 971–976 (2017). PMID: 28102665

Stefanie A. Baril, Amber L. Koenig, Mackenzie W. Krone, Katherine I. Albanese, Qixin Cyndi He, Ga Young Lee, Kendall N. Houk, Marcey L. Waters*, Eric M. Brustad*, “Investigation of Trimethyllysine Binding by the HP1 Chromodomain via Unnatural Amino Acid Mutagenesis”, J. Am. Chem. Soc.2017139, 17253–6, DOI: 10.1021/jacs.7b09223

Kaiulani M. Houston, Adam T. Melvin, Gregery S. Woss, Effrat L. Fayer, Marcey L. Waters*, and Nancy L. Allbritton*, “Development of beta-Hairpin Peptides for the Measurement of SCF-Family E3 Ligase Activity in Vitro via Ornithine Ubiquitination”, ACS Omega20172, 1198-1206.

Isaiah N. Gober, Marcey L. Waters*, “Optimization of a synthetic receptor for dimethyllysine using a biphenyl-2, 6-dicarboxylic acid scaffold: insights into selective recognition of hydrophilic guests in water”, Org. Biomol. Chem2017, 15, 7789-7795, DOI: 10.1039/C7OB01921A

Sperlazza MJ, Bilinovich SM, Sinanan LM, Javier FR,Williams DC Jr. Structural basis of MeCP2 distribution on non‑CpG methylated and hydroxymethylated DNA. J. Mol. Biol., 2017 May 19; 429(10):1581-1594

Cramer JM, Pohlmann D, Gomez F, Mark L, Kornegay B, Hall C, Siraliev-Perez E, Walavalkar NM, Sperlazza MJ, Bilinovich S, Prokop JW, Hill AL, Williams DC Jr.Methylation specific targeting of a chromatin remodeling complex from sponges to humans. Sci. Rep. 2017 Jan 17; 7:40674


Sapienza PJ and Lee AL, Widespread perturbation of function, structure, and dynamics by a conservative single atom substitution in thymidylate synthase, Biochemistry(2016), 55, 5702-5713.

Falk BT, Sapienza PJ, and Lee AL, Chemical shift imprint of intersubunit communication in a symmetric homodimer, Proc. Natl. Acad. Sci. U.S.A. (2016), 113, 9533-9538.  (Commentary in same issue, pp. 9407-9409)

Walton, W.G. Ahmad, S., Little, M.R., Kim, C., Tyrrell, J., Lin, Q., Di, Y.-P., Tarran, R., and Redinbo, M.R. Structural Features Essential to the Antimicrobial Functions of Human SPLUNC1. Biochemistry55, 2979-2991. (2016).  PMICD: PMC4887393.  doi:10.1021/acs.biochem.6b00090

Washington, EJ, MS Mukhtar, OM Finkel, L Wan, MJ Banfield, JJ Kieber and JL Dangl (2016) The P. syringae type III effector HopAF1 suppresses plant immunity by targeting methionine recycling to block ethylene induction. Proc. Natl. Acad. Sci., USA. 113,E3577-3586. doi: 10.1073/pnas.1606322113. published online June 6, 2016 PR PMID 27274076.

Stuckey, J. I.; Simpson, C.; Norris-Drouin, J. L.; Cholensky, S. H.; Lee, J.; Pasca, R.; Cheng, N.; Dickson, B. M.; Pearce, K. H.; Frye, S. V.*; James, L. I.* “Structure-activity relationships and kinetic studies of peptidic antagonists of CBX chromodomains.” J. Med. Chem201659, 8913-8923.

Barnash, K. D.; Lamb, K. N.; Stuckey, J. I.; Norris, J. L.; Cholensky, S. H.; Kireev, D. B.; Frye, S. V.*; James, L. I.* “Chromodomain ligand optimization via target-class directed combinatorial repurposing.” ACS Chem. Biol201611, 2475-2483.

Stuckey, J. I.; Dickson, B. M.; Cheng, N.;  Liu, Y.; Norris, J. L.; Cholensky, S. H.; Tempel, W.; Qin, S.; Huber, K. G.; Sagum, C.; Black, K.; Li, F.; Huang, X-P; Roth, B. L.; Baughman, B. M.;  Senisterra, G.; Pattenden, S. G.;  Vedadi, M.; Brown, P. J.; Bedford, M. T.; Min, J.; Arrowsmith, C. H.; James, L. I.*; Frye, S. V.* “A cellular chemical probe targeting the chromodomains of Polycomb Repressive Complex 1.” Nat. Chem. Biol. 201612, 180-187

Li, B, Makino,S, Beebe, ET, Urano, D,  Aceti, DJ, Misenheimer, TM, Peters, J, Fox, BG, Jones, AM (2016) Cell-free translation and purification ofArabidopsis thaliana regulator of G  protein signaling 1. Protein Expression and Purification  126: 33-41 doi: 10.1016/j.pep.2016.04.016

Jaiswal, DK, Werth, EG, McConnel, EW, Hicks, LM, Jones, AM 2016 Time-dependent,glucose-regulated Arabidopsis Regulator of G-protein Signaling 1 network. Curr. Plant Biol. (on-line 23Dec2015)

Isaiah N. Gober and Marcey L. Waters*, “Supramolecular Affinity Labeling of Histone Peptides Containing Trimethyllysine and Its Application to Histone Deacetylase Assays”, J. Am. Chem. Soc.,2016138, 9452-9;

Andrews, F. H.*, Shinsky, A. S.*, Shanle, E. K., Bridgers, J. B., Gest, A., Tsun, I. K., Krajewski, K., Shi, X., Strahl, B. D.* & Kutateladze, T. G.* (2016) The Taf14 YEATS domain is a reader of histone crotonylation.Nat Chem Biol 12:396-398.

Jacobs, T. M.; Williams, B.; Williams, T.; Xu, X.; Eletsky, A.; Federizon, J. F.; Szyperski, T.; Kuhlman, B. Design of Structurally Distinct Proteins Using Strategies Inspired by Evolution. Science 2016352 (6286), 687–690.

Harrison, J. S.; Cornett, E. M.; Goldfarb, D.; DaRosa, P. A.; Li, Z. M.; Yan, F.; Dickson, B. M.; Guo, A. H.; Cantu, D. V.; Kaustov, L.; Brown, P. J.; Arrowsmith, C. H.; Erie, D. A.; Major, M. B.; Klevit, R. E.; Krajewski, K.; Kuhlman, B.; Strahl, B. D.; Rothbart, S. B. Hemi-Methylated DNA Regulates DNA Methylation Inheritance Through Allosteric Activation of H3 Ubiquitylation by UHRF1. eLife 20165, 818.

Zimmerman, S. P.; Hallett, R. A.; Bourke, A. M.; Bear, J. E.; Kennedy, M. J.; Kuhlman, B. Tuning the Binding Affinities and Reversion Kinetics of a Light Inducible Dimer Allows Control of Transmembrane Protein Localization. Biochemistry 2016,55 (37), 5264–5271.

Wang, H.; Vilela, M.; Winkler, A.; Tarnawski, M.; Schlichting, I.; Yumerefendi, H.; Kuhlman, B.; Liu, R.; Danuser, G.; Hahn, K. M. LOVTRAP: an Optogenetic System for Photoinduced Protein Dissociation. Nat Methods 201613 (9), 755–758.

Guffy, S. L.; Der, B. S.; Kuhlman, B. Probing the Minimal Determinants of Zinc Binding with Computational Protein Design. Protein Eng Des Sel 201629 (8), 327–338.

Hallett, R. A.; Zimmerman, S. P.; Yumerefendi, H.; Bear, J. E.; Kuhlman, B. Correlating in Vitro and in Vivo Activities of Light-Inducible Dimers: a Cellular Optogenetics Guide. ACS Synth Biol 20165 (1), 53–64.

Guntas, G.; Lewis, S. M.; Mulvaney, K. M.; Cloer, E. W.; Tripathy, A.; Lane, T. R.; Major, M. B.; Kuhlman, B. Engineering a Genetically Encoded Competitive Inhibitor of the KEAP1-NRF2 Interaction via Structure-Based Design and Phage Display. Protein Eng Des Sel 201629 (1), 1–9


Rajarshi Choudhury, Sreerupa Ghose Roy, Yihsuan S. Tsai, Ashutosh Tripathy, Lee M. Graves and Zefeng Wang. 2014. The splicing activator DAZAP1 integrates splicing control into MEK/Erk-regulated cell proliferation and migration. Nature Communications.  5:3078 | DOI: 10.1038/ncomms4078.


Garland, A.L., Walton, W.G., Coakley, R.D., Tan, C.D., Gilmore, R.C., Hobbs, C.A., Tripathy, A., Clunes, L.A., Bencharit, S., Stutts, M.J., Betts, L., Redinbo, M.R., and Tarran, R. 2013. Molecular Basis for pH-Dependent Mucosal Dehydration in Cystic Fibrosis Airways. Proceedings of the National Academy of Sciences USA 110 (40) 15973-15978.

Thomas C Freeman, Justin L Black, Holly G Bray, Onur Dagliyan, Yi I. Wu, Ashutosh Tripathy, Nikolay V. Dokholyan, Tina M Leisner, and Leslie V. Parise. (2013). Identification of novel integrin binding partners for CIB1: structural and thermodynamic basis of CIB1 promiscuity. Biochemistry, 52 (40) 7082-7090 Publication Date (Web): September 6, 2013 (Article). DOI: 10.1021/bi400678y.

Bradford,W., Buckholz,   A., Morton, J., Price, C., Jones, AM, Urano D. (2013). Ancestral regulation of eukaryotic G protein signaling. Science Signaling,  in press.

James, L. I.; Barsyte-Lovejoy, D.; Zhong, N.; Krichevsky, L.; Korboukh, V. K.; Herold, J. M.; MacNevin, C. J.; Norris, J. L.; Sagum, C. A.; Tempel, W.; Marcon, E.; Guo, H.; Gao, C.; Huang, X.-P.; Duan, S.; Emili, A.; Greenblatt, J.; Kireev, D. B.; Jin, J.; Janzen, William P.; Brown, P. J.; Bedford, M. T.; Arrowsmith, C. H.; Frye, S. V. (2013) “Discovery of a Chemical Probe for a Methyl-Lysine Reader Domain: L3MBTL3.” Nature Chemical Biology 9, 184-191. (cover story)

Chopra, S., Palencia, A., Virus, C., Tripathy, A., Temple, B.R., Velazquez-Campoy, A., Cusack, S., and Reader, J. S. (2013). Plant tumour biocontrol agent employs a tRNA-dependent mechanism to inhibit leucyl-tRNA synthetase . Nature Communications 4: 1417. doi: 10.1038/ncomms2421.

Rao L, Romes EM, Nicholas MP, Brenner S, Tripathy A, Gennerich A, Slep KC. (2013). The Yeast Dynein Dyn2-Pac11 Complex is a Dynein Dimerization/Processivity Factor: Structural and Single Molecule Characterization. Mol Biol Cell 2013 Jun 12. [Epub ahead of print]
PMID: 23761070 [PubMed - as supplied by publisher].

Leano JB, Rogers SL, Slep KC. (2013). A Cryptic TOG Domain with a Distinct Architecture Underlies CLASP-Dependent Bipolar Spindle Formation. Structure 2013 May 29. doi:pii: S0969-2126(13)00130-5. 10.1016/j.str.2013.04.018. [Epub ahead of print]
PMID: 23727231 [PubMed - as supplied by publisher].

Tarafdar, P.K., Chakraborty, H., Dennison, S. Moses and Lentz, B.R. (2013). Phosphatidylserine Inhibits and Calcium Promotes Model Membrane Fusion. Biophysical Journal 103, 1880-89.

Lihong Huang and Susan T. Lord (2013), Thrombosis Research 131, e258-e263.

Cai L, Rothbart SB, Lu R, Xu B, Chen WY, Tripathy A, Rockowitz S, Zheng D, Patel DJ, Allis CD, Strahl BD, Song J, Wang GG. (2013). An H3K36 methylation-engaging Tudor motif of polycomb-like proteins mediates PRC2 complex targeting. Mol Cell. 49(3):571-82. doi: 10.1016/j.molcel.2012.11.026. Epub 2012 Dec 27. PubMed PMID: 23273982; PubMed Central PMCID: PMC3570589.


Herold, J. M.; James, L. I.; Korboukh, V. K.; Gao, C.; Coil, K. E.; Bua, D. J.; Norris, J. L.; Kireev, D. B.; Brown, P. J.; Jin, J.; Janzen, W. P.; Gozani, O.; Frye, S. V. (2012) “Structure-activity relationships of methyl-lysine reader antagonists.” Med Chem Comm 3, 45-51.

Slevin LK, Nye J, Pinkerton DC, Buster DW, Rogers GC, Slep KC. (2012). The structure of the plk4 cryptic polo box reveals two tandem polo boxes required for centriole duplication. Structure. 20(11):1905-17. doi: 10.1016/j.str.2012.08.025. Epub 2012 Sep 20.
PMID: 23000383 [PubMed - indexed for MEDLINE]

Romes EM, Tripathy A, Slep KC. (2012). The Structure of a yeast Dyn2-Nup159 complex and the molecular basis for the dynein light chain - nuclear pore interaction. J Biol Chem. 287: 15862-15873. Mar 12, 2012 [Epub ahead of print]

Kim D, Yan Y, Valencia CA, Liu R. (2012). Heptameric targeting ligands against EGFR and HER2 with high stability and avidity. PLoS One. 7(8):e43077. doi: 10.1371/journal.pone.0043077. Epub 2012 Aug 9.

Perry JL; Reuter KG; Kai MP; Herlihy KP; Jones SW; Luft C; Napier M; Bear JE; DeSimone, JM. (2012). PEGylated PRINT Nanoparticles: The Impact of PEG Density on Protein Binding, Macrophage Association, Biodistribution, and Pharmacokinetics”. Nanoletters 12(10), 5304-10. 

Carroll MJ, Mauldin RV, Gromova AV, Singleton SF, Collins EJ, and Lee AL. (2012). Evidence for dynamics in proteins as a mechanism for ligand dissociation. Nat. Chem. Biol. 8, 246-252.

Hung CW, Aoh QL, Joglekar AP, Payne GS, Duncan MC. (2012). Adaptor autoregulation promotes coordinated binding within clathrin coats. J Biol Chem. 287(21):17398-407. doi: 10.1074/jbc.M112.349035. Epub 2012 Mar 28. PMID: 22457357

Miller KR, Koide A, Leung B, Fitzsimmons J, Yoder B, Yuan H, Jay M, Sidhu SS, Koide S,Collins EJ. (2012). T cell receptor-like recognition of tumor in vivo by synthetic antibody fragment. PLoS One. 7(8):e43746. doi: 10.1371/journal.pone.0043746. Epub 2012 Aug 20.

Urano,  D., Phan, N.,  Jones, JC, Yang, J.,  Huang, J., Grigston, J., Taylor,  JP., Jones, AM .(2012).  Endocytosis of seven-transmembrane RGS protein activates G-coupled signaling in Arabidopsis.   Nature Cell Biology 14: 1079-1088.

Urano, D., Jones, JC, Wang, H., Matthews, M., Bradford, W., Bennetzen, JL, Jones AM (2012). G protein activation without a GEF in the plant kingdom.  PLoS Genetics 8:e1002756.

Jones, JC, Jones, AM, Temple, BRS, Dohlman, HG (2012). Differences in intradomain and interdomain motion confer distinct activation properties to structurally similar Gα proteins. PNAS  109:7275-9.

Chakraborty, H and Lentz, BR (2012). A simple method for correction of circular dichroism spectra obtained from membrane-containing samples. Biochemistry 51, 1005-8.

Chakraborty, H, Tarafdar, PK, Bruno, MJ, Sengupta, T and Lentz, BR (2012). Activation Thermodynamics of PEG-Mediated Model Membrane Fusion Support Mechanistic Models of Stalk and Pore Formation. Biophysical Journal 102, 2751-2760.


Zhang J, Petit CM, King DS, and Lee AL (2011). Phosphorylation of a PDZ domain extension modulates binding affinity and interdomain interactions in PSD-95, J. Biol. Chem. 286, 41776-41785.

Redler, R. L., Wilcox, K. C., Proctor, E. A., Fee, L., Caplow, M., and Dokholyan, N. V. (2011) "Glutathionylation at cys 111 triggers dissociation of wild type and fals mutant SOD1 dimers",Biochemistry, 50:7057-7066.

Stranges PB, Machius M, Miley MJ, Tripathy A, Kuhlman B. (2011). Computational design of a symmetric homodimer using β-strand assembly.  PNAS USA, 108 (51) 20562-20567

Vedadi M, Barsyte-Lovejoy D, Liu F, Rival-Gervier S, Allali-Hassani A, Labrie V, Wigle TJ, Dimaggio PA, Wasney GA, Siarheyeva A, Dong A, Tempel W, Wang SC, Chen X, Chau I, Mangano TJ, Huang XP, Simpson CD, Pattenden SG, Norris JL, Kireev DB, Tripathy A, Edwards A, Roth BL, Janzen WP, Garcia BA, Petronis A, Ellis J, Brown PJ, Frye SV, Arrowsmith CH, Jin J.  (2011). A chemical probe selectively inhibits G9a and GLP methyltransferase activity in cells. Nature Chemical Biology 7(8) 566-574 DOI: 10.1038/nchembio.599. [Epub ahead of print].

J. Martin Herold, Tim J. Wigle, Jacqueline L. Norris, Robert Lam, Victoria K. Korboukh, Cen Gao, Lindsey A. Ingerman, Dmitri B. Kireev, Guillermo Senisterra, Masoud Vedadi, Ashutosh Tripathy, Peter J. Brown, Cheryl H. Arrowsmith, Jian Jin, William P. Janzen, and Stephen V. Frye. (2011). Small-Molecule Ligands of Methyl-Lysine Binding Proteins. Journal of Medicinal Chemistry 54 (7), pp 2504–2511. DOI: 10.1021/jm200045v.

Carroll, Mary; Gromova, Anna; Miller, Keith; Tang, Hao; Wang, Xiang; Tripathy, Ashutosh; Singleton, Scott; Collins, Edward; Lee, Andrew. (2011). Direct detection of structurally resolved dynamics in a multi-conformation receptor-ligand complex. Journal of American Chemical Society 133(16):6422-8. Epub 2011 Apr 6.

Joseph V. Lomino,  Ashutosh Tripathy, and Matthew R. Redinbo. (2011). Triggered Mycobacterium tuberculosis Heparin-Binding Hemagglutinin Adhesin Folding and Dimerization. Journal of Bacteriology 193: 2089–2096. doi:10.1128/JB.01231-10.

Jones, JC, Duffy, JW, Machius, M,  Temple,  BRS,  Dohlman, HG  and Jones  AM (2011). The crystal structure of a self-activating G protein reveals a new mechanism of G protein activation.  Science Signaling Vol. 4, Issue 159, p. ra8 (cover feature).

Jones, JC, Temple, BRS, Jones, AM  and Dohlman HG .(2011). Functional reconstitution of an  atypical G protein heterotrimer and RGS protein from Arabidopsis thaliana. J Biol. Chem286: 13143-13150.

Haque, MdE, Chakraborty, H, Koklic, T, Komatsu, H, Axelsen, PH, and Lentz, BR (2011). Hemagglutinin Fusion Peptide Mutants in Model Membranes: Structural Properties; Membrane Physical Properties and PEG-Mediated Fusion. Biophysical Journal, 101, 1095-1104.


Haque,  M., Elmore, K.B., Tripathy, A., Koc, H., Koc, E.C., and Spremulli, L. 2010. Properties of the C-terminal tail of human mitochondrial inner membrane protein Oxa1L and its interactions with mammalian mitochondrial ribosomes.  Journal of Biological Chemistry 285: 28353-28362. First Published on July 2, 2010, doi:10.1074/jbc.M110.148262.


Chattopadhyay, R, Iacob, R, Majumder, R, Sen, S, Tomer, K, and Lentz, BR. 2009. Functional and Structural Characterization of Factor Xa Dimer in Solution, Biophysical Journal, in press.

Guogas, L.M., Kennedy, S.A., Lee, J.-H., and Redinbo, M.R. (2009). A novel fold in the TraI relaxase-helicase C-terminal domain is essential for conjugative DNA transfer. Journal of Molecular Biolog, 386: 554-568.

Riemen, A. J., Waters, M. L. 2009. Design of Highly Stabilized b-Hairpin Peptides through Cation-p Interactions of Lysine and N-Methyllysine with an Aromatic Pocket. Biochemistry, 48:1525-31.

Stewart, A. L., Waters, M. L. 2009. Structural Effects on DNA Recognition by a Designed beta-Hairpin. ChemBiochem 10: 539-544.

Meissner, G., Pasek, D.A., Yamaguchi, N., Ramachandran, S., Dokholyan, N.V., and Tripathy, A. 2009. Thermodynamics of calmodulin binding to cardiac and skeletal muscle ryanodine receptor ion channels. Proteins: Structure, Function, and Bioinformatics.74: 207-211.

Palmer SM, Playford MP, Craig SW, Schaller MD, Campbell SL. 2009. Lipid Binding to the Tail Domain of Vinculin: SPECIFICITY AND THE ROLE OF THE N AND C TERMINI. J Biol Chem. 284: 7223-31.


Riemen, A. J., Waters, M. L. 2008. Stabilization of the N-Terminal β-Hairpin of Ubiquitin by a Terminal Hydrophobic Cluster. Peptide Science, 90: 394-398 (for the Merrifield Memorial Issue).

Serohijos AW, Hegedus T, Aleksandrov AA, He L, Cui L, Dokholyan NV, Riordan JR. 2008. Phenylalanine-508 mediates a cytoplasmic-membrane domain contact in the CFTR 3D structure crucial to assembly and channel function. Proc Natl Acad Sci USA. 105(9):3256-61. Epub 2008 Feb 27.

Boyer, J.A. and Lee, A.L. 2008. Monitoring aromatic ps-ns dynamics in proteins via 13C relaxation:  Expanding perturbation mapping of the rigidifying core mutation, V54A, in eglin c.  Biochemistry, 47: 4876-4886.

Md. Emdadul Haque, Domenick Grasso and Linda L. Spremulli. 2008. The interaction of mammalian mitochondrial translational initiation factor 3 with ribosomes: evolution of terminal extensions in IF3mt. Nucleic Acids Research, 36: 589-597.

Md. Emdadul Haque and Linda L. Spremull. 2008. Roles of the N- and C-domains of mammalian mitochondrial initiation factor 3 in protein biosynthesis J. Mol. Biol. 384: 929-940.

Johnston CA, Afshar K, Snyder JT, Tall GG, Gonczy P, Siderovski DP, Willard FS. 2008. Structural determinants underlying the temperature-sensitive nature of a Galpha mutant in asymmetric cell division of Caenorhabditis elegans. J Biol Chem. 283(31): 21550-8.

Majumder, R, Quinn-Allen, MA, Kane, WH and Lentz, BR. 2008. A Phosphatidylserine Binding Site in Factor Va C1 Domain Regulates both Assembly and Activity of the Prothrombinase Complex. Blood, 112: 2795-802.

Charlton LM, Barnes CO, Li C, Orans J, Young GB, Pielak GJ. 2008. Residue-level interrogation of macromolecular crowding effects on protein stability. Journal of the American Chemical Society 130: 6826-6830.

Hyunmin Kang, Md. Rowshon Alam, Vidula Dixit, Michael Fisher, and Rudy L. Juliano. 2008. Cellular Delivery and Biological Activity of Antisense Oligonucleotides Conjugated to a Targeted Protein Carrier. Bioconjugate Chem. 19(11): 2182-2188.

Palmer SM, Schaller MD, Campbell SL. 2008. Vinculin tail conformation and self-association is independent of pH and H906 protonation. Biochemistry 47:12467-75.

Dixon RD, Arneman DK, Rachlin AS, Sundaresan NR, Costello MJ, Campbell SL, Otey CA. 2008. Palladin is an actin cross-linking protein that uses immunoglobulin-like domains to bind filamentous actin. J Biol Chem. 283: 6222-31. Epub 2008 Jan 7. Erratum in: J Biol Chem. 2008 Oct 3; 283(40):27344.


Retailleau, P., Weinreb, V., Hu, M., & Carter, C. W., Jr. 2007. Crystal Structure of Tryptophanyl-tRNA Synthetase Complexed with Adenosine-5- Tetraphosphate: Evidence for Distributed Use of Catalytic Binding Energy in Amino Acid Activation by Class I Aminoacyl-tRNA Synthetases. J. Mol. Biol., 369: 108-128.

Kapustina, M., Weinreb, V., and Carter, C.W., Jr. 2007. A Conformational Transition State Accompanies Amino Acid Activation by B. stearothermphilus Tryptophanyl-tRNA Synthetase. Structure 15:1272-1284.

DeRose, E.F., Clarkson M.W., Gilmore S.A., Galban C.J., Tripathy A., Havener J.M., Mueller, G.A., Ramsden D.A., London R.E., and Lee A.L. 2007. Solution structure of polymerase μ-s BRCT domain reveals an element essential for its role in nonhomologous end joining. Biochemistry 46: 12100-12110.

Eletr, Z.M., & Kuhlman, B. (2007) Sequence determinants of E2-E6AP binding affinity and specificity. J. Mol. Biol., 369, 419-428.

Sammond, D.W., Eletr, Z.M., Purbeck, C., Kimple, RJ, Siderovski, D.P., & Kuhlman, B. (2007) Structure-based protocol for identifying mutations that enhance protein-protein binding affinities. J. Mol. Biol., 371, 1392-1404.

Geer, C. B., Tripathy, A., Schoenfisch, M. H., Lord, S. T., and Gorkun, O. V. 2007. Role of B-b knob-hole interactions in fibrin binding to adsorbed fibrinogen. Journal of Thrombosis and Haemostasis, 5: 2344-2351.

Derewenda, U., Tarricone, C., Choi, W. C., Cooper, D. R., Lukasik, S., Perrina, F., Tripathy, A., Kim, M. H., Cafiso, D. S., Musacchio, A., and Derewenda, Z. 2007. The structure of the coiled coil domain of Ndel1 and the basis of its interaction with Lis1, the causal protein of Miller-Dieker lissencephaly. Structure 5: 1467-1481.

Pielak GJ, Patel CN, Winzor DJ. 2007. Reconsideration of sedimentation equilibrium distributions reflecting the effects of small inert cosolutes on the dimerization of alpha-chymotrypsin. Biophysical Chemistry 130: 89-92.

Tian, S., Maile,R., Collins, E.J., and Frelinger , J.A . 2007. T cell cytotoxicity is governed by TCR-pMHC affinity, not dissociation rate. J. Immunol 179: 2952-2960.

Miller, PJ Pazy, Y., Conti, B. Riddle, D, Biddison, WE, Appella, E and Collins, EJ. 2007. Single MHC Mutation Eliminates Enthalpy Associated with T Cell Receptor Binding. J. Mol Biol 373: 315-327.

Ambroggio, X.I., & Kuhlman, B. (2006) Computational design of a single amino acid sequence that can switch between two distinct protein folds. JACS, 128, 1154-1161.


Noble, S.N., Carnahan, V.E., Moore, L.B., Luntz, T., Wang. H., Ittoop, O.R., Stimmel, J.B., Davis-Searles, P.R., Watkins, R.E., Wisely, G.B., LeCluyse, E.L., Tripathy, A., McDonnell, D.P., and Redinbo, M.R. 2006. Human PXR forms a tryptophan zipper-mediated homodimer. Biochemistry, 45, 8579-8589.

McCall, S J, Nassar, R, Malouf, NN, Saunders, AJ, Oakeley, AE, Henderson, PM, Solaro, RJ, Pielak, GJ, Alexander, KA, and Anderson, PAW. 2006. Development and cardiac contractility: cardiac troponin T isoforms and cytosolic calcium. Pediatric Research, 60: 276-281.

McNulty, BC, Young, GB, Pielak, GJ. 2006. Macromolecular crowding in the Escherichia coli periplasm maintains α-synuclein disorder. Journal of Molecular Biology, 355: 893-897.

McNulty, B. C., Tripathy, A., Young, G. B., Orans, J., Charlton, L. M. and Pielak, G. J. (2006) Temperature- Induced Reversible Conformational Change in the First 100 Residues of Alpha-Synuclein. Protein Science 15:602-608.

Lentz, BR. 2006. Seeing is Believing: the Stalk Intermediate. Biophysical Journal, 91, 2747-8, 2006 (mini-review to highlight a recent BJ paper).


Kevin A. Wilkinson, Edward J. Merino, and Kevin M. Weeks. 2005. RNA SHAPE Chemistry Reveals Nonhierarchical Interactions Dominate Equilibrium Structural Transitions in tRNA Asp Transcripts. J. Am. Chem. Soc. 127:4659-4667.

Ortlund, EA, Lee, Y, Solomon, IH, Hager, JM, Safi, R, Choi, Y, Guan, Z, Tripathy, A, Raetz, CR, McDonnell, DP, Moore, DD, Redinbo, MR. 2005. Modulation of human nuclear receptor LRH-1 activity by phospholipids and SHP. Nat Struct Mol Biol 12:357-363.

Barrett, DG, Minder, CM, Mian, MU, Whittington, SJ, Cooper, J, Fuchs, KM, Tripathy, A, Waters, ML, Creamer, TP, Pielak, GJ. 2005. Pressure perturbation calorimetry of helical peptides. Proteins: Structure Function and Bioinformatics, 63: 322-326.

Solomon, I.H., Hager, J.M., Safi, R., McDonnell, D.P., Redinbo, M.R., and Ortlund, E.A. 2005. Crystal structure of the human LRH-1 DBD DNA complex reveals Ftz-F1 domain positioning is required for receptor activity. Journal of Molecular Biology, 354, 1091-1102.

Majumder, R, Quinn-Allen, MA, Kane, WH and Lentz, BR. 2005. The Phosphatidylserine Binding Site of the Factor Va C2 Domain Accounts for Membrane Binding but Does Not Contribute to the Assembly or Activity of a Human Factor Xa-Factor Va Complex. Biochemistry, 44, 711-718.

Haque, Md E, Koppaka, V, Axelsen, PH, and Lentz, BR. 2005. Properties and Structures of the Influenza and HIV Fusion Peptides on Lipid Membranes: Implications for a Role in Fusion. Biophysical Journal, 89, 3183-3194.

Heo J, Thapar R, Campbell SL. 2005. Recognition and activation of Rho GTPases by Vav1 and Vav2 guanine nucleotide exchange factors. Biochemistry 44(17): 6573-85.


Batchelor, JD, Olteanu, A, Tripathy, A, Pielak, GJ. 2004. Impact of protein denaturants and stabilizers on water structure. Journal of the American Chemical Society 126: 1958-1961.

Hostetter, D, Rice, S, Dean, S, Altman, D, McMahon, PM, Sutton, S, Tripathy, A, Spudich, JA. 2004. Dictyostelium Myosin Bipolar Thick Filament Formation: Importance of Charge and Specific Domains of the Myosin Rod. PLoS Biol. 2(11):e356 [Epub ahead of print].

Feeney, B, Pop, C, Tripathy, A, Clark, AC. 2004. Ionic interactions near loop L4 are important for maintaining the active site environment and the dimer stability of (pro)caspase-3. Biochem J. 384, 515-525.

Thapar R, Williams JG, Campbell SL. 2004. NMR characterization of full-length farnesylated and non-farnesylated H-Ras and its implications for Raf activation. J Mol Biol. 343(5): 1391-1408.

Gao G, Prutzman KC, King ML, Scheswohl DM, DeRose EF, London RE, Schaller MD, Campbell SL. 2004. NMR solution structure of the focal adhesion targeting domain of focal adhesion kinase in complex with a paxillin LD peptide: evidence for a two-site binding model. J Biol Chem. 279(9): 8441-51.

Thapar, R., Marzluff, W., Redinbo, M. 2004. Electrostatic contribution of protein phosphorylation to the Drosophila SLBP-histone mRNA complex. Biochemistry 43: 9401-9412

Thapar, R., Mueller, G., Marzluff, W. 2004. The N-terminal domain of the Drosophila histone mRNA binding protein, SLBP, is intrinsically unfolded with nascent helical structure. Biochemistry 43: 9390-9400

Prutzman, K., Gao, G., King, M., Iyer, V., Mueller, G., Schaller, M., Campbell, S. 2004. The focal adhesion targeting domain of focal adhesion kinase contains a hinge region that modulates tyrosine 926 phosphorylation. Structure ( Cambridge) 12: 881-891

John, D., Merino, E., Weeks, K. 2004. Mechanics of DNA flexibility by selective 2'-amine acylation at nucleotide bulges. Journal of Molecular Biology 337: 611-619

Haque, M., Lentz, B. 2004. Role of Curvature and hydrophobic interstice energy in fusion: studies of lipid perturbant effects. Biochemistry 43: 3507-3517

Edavettal, S., Lee, K., Negishi, M., Linhardt, R., Liu, J., Pedersen, L. 2004. Crystal structure and mutational analysis of heparin sulfate 3-O-sulfotransferase isoform 1. Journal of Biological Chemistry 279: 25789-25797

Edavettal, S., Carrick, K., Shah, R., Pedersen, L., Alexander, A., Pope, R., Liu, J. 2004. A conformational change in heparin sulfate 3-O-sulfotransferase-1 is induced by binding to heparin sulfate. Biochemistry 43: 4680-4688

Dominick, P., Jarstfer, M. 2004. A conformationally constrained nucleotide analogue controls the folding topology of a DNA G-quadruplex. Journal of the American Chemical Society 126: 5050-5051

Daughdrill, G., Pielak, G., Uversky, V., Cortese, M., Dunker, A. 2004. Natively disordered proteins. In Handbook of Protein Folding (Buchner, J. & Kiefhaber, T., eds.). Wiley-VCH, Weinheim, in press

Batchelor, J., Olteanu, A., Tripathy, A., Pielak, G. 2004. Impact of protein denaturants and stabilizers on water structure. Journal of the American Chemical Society 126: 1958-1961


Watkins, R., Davis-Searles, P., Lambert, M., Redinbo, M. 2003. Coactivator binding promotes the specific interaction between ligand and the pregnane X receptor. Journal of Molecular Biology 331: 815-821

Majumdar, R., Wang, F.-F., Lentz, B. 2003. Effects of water soluble phosphatidylserine on bovine factor Xa:  functional and structural changes plus dimerization. Biophysical Journal 84: 1238-1251

Kim, S.-J., Beard, W., Harvey, J., Shock, D., Knutson, J., Wilson, S. 2003. Rapid segmental and subdomain motions of DNA polymerase. Journal of Biological Chemistry 278: 5072-5081

He, B., Wilson, E. 2003. Electrostatic modulation in steroid receptor recruitment of LXXLL and FXXLF motifs. Molecular and Cellular Biology 23: 2135-2150

Carrick, K., Topal, M. 2003. Amino acid substitutions at position 43 of NaeI endonuclease - evidence for changes in NaeI structure. Journal of Biological Chemistry 278: 9733-9739

Buslepp, J., Elliott, S., Frelinger, J., Appella, E., Collins, E. 2003. High affinity xenoreactive TCR:MHC interaction recruits CD8 in absence of binding to MHC. Journal of Immunology 170: 373-383

Brogan, A., Widger, W., Kohn, H. 2003. Bicyclomycin fluorescent probes: synthesis and biochemical, biophysical, and biological properties. Journal of Organic Chemistry 68: 5575-5587


Zhai, X., Srivastava, A., Drummond, D., Daleke, D., Lentz, B. 2002. Phosphatidylserine binding alters the conformation and specifically enhances the cofactor activity of bovine factor Va. Biochemistry 41: 5675-5684

Singer, A., Waldo, G., Harden, T., Sondek, J. 2002. A unique fold of phospholipase C-b mediates dimerization and interaction with Gaq. Nature Structural Biology 9: 32-36

Patel, C., Noble, S., Weatherly, G., Tripathy, A., Winzor, D., Pielak, G. 2002. Effects of molecular crowding by saccharides on a-chymotrypsin dimerization. Protein Science 11: 997-1003

Morar, A., Pielak, G. 2002. Crowding by trisaccharides and the 2:1 cytochrome c / cytochrome c peroxidase complex. Biochemistry 41: 547-551

Dedmon, M., Patel, C., Young, G., Pielak, G. 2002. FlgM gains structure in living cells. Proceedings of the National Academy of Sciences of the United States of America 99: 12681-12684

Caplow, M., Lee, F. 2002. Dissociation of the tubulin dimer is extremely slow, thermodynamically very unfavorable, and reversible in the absence of an energy source. Molecular Biology of the Cell 13: 2120-2131

Bencharit, S., Morton, C., Howard-Williams, E., Danks, M., Potter, P., Redinbo, M. 2002. Structural insights into CPT-11 activation by mammalian carboxylesterases. Nature Structural Biology 9: 337-342

Beasley, J., Doyle, D., Chen, L., Cohen, D., Fine, B., Pielak, G. 2002. Searching for quantitative entropy-enthalpy compensation among protein variants. Proteins: Structure Function and Genetics 49: 398-402

Bassi, G., de Oliviera, D., White, M., Weeks, K. 2002. Recruitment of intron encoded and co-opted proteins in splicing of the bI3 group I intron RNA. Proceedings of the National Academy of Sciences of the United States of America 99: 128-133

Barry, W., Boudignon-Proudhon, C., Shock, D., McFadden, A., Weiss, J., Sondek, J., Parise, L. 2002. Molecular basis of CIB binding to the integrin aIIb cytoplasmic domain. Journal of Biological Chemistry 277: 28877-28883


Weatherly, G., Pielak, G. 2001. Second virial coefficients as a measure of protein-osmolyte interactions. Protein Science 10: 12-16

Srivastava, A., Quinn-Allen, M., Kim, S., Kane, W., Lentz, B. 2001. Soluble phosphatidylserine (C6PS) binds to a single identified site in the C2-domain of human factor Va. Biochemistry 40: 8246-8255

Snyder, J., Rossman, K., Baumeister, M., Pruitt, W., Siderovski, D., Der, C., Lemmon, M., Sondek, J. 2001. Quantitative analysis of the effect of phosphoinositide interactions on the function of Dbl family proteins. Journal of Biological Chemistry 276: 45868-45875

Rabenau, K., Sohrabi, A., Tripathy, A., Reitter, C., Ajioka, J., Tomley, F., Carruthers, V. 2001. TgM2AP participates in Toxoplasma gondii invasion of host cells and is tightly associated with the adhesive protein TgMIC2. Molecular Microbiology 41: 537-547

Presnell, S., Tripathy, A., Lentz, B., Jin, D.-Y., Stafford, D. 2001. A novel fluorescence assay to study propeptide interaction with γ-glutamly carboxylase. Biochemistry 40: 11723-11733

Prasad, R., Lavrik, O., Kim, S.-J., Kedar, P., Yang, X.-P., Vande Berg, B., Wilson, S. 2001. DNA polymerase-mediated long patch base excision repair: poly(ADP-ribose) polymerase-1 stimulates strand dispacement DNA synthesis. Journal of Biological Chemistry 276: 32411-32414

Pop, C., Chen, Y.-R., Smith, B., Bose, K., Bobay, B., Tripathy, A., Franzen, S., Clark, A. 2001. Removal of the pro-domain does not affect the conformation of the procaspase-3 dimer. Biochemistry 40: 14224-14235

Pielak, G., Wang, X. 2001. Interactions between yeast iso-1-cytochrome c and its peroxidase. Biochemistry 40: 422-428

Patel, C., Lind, M., Pielak, G. 2001. Characterization of horse cytochrome c expressed in Escherichia coli. Protein Expression and Purification 22: 220-224

Morar, A., Olteanu, A., Young, G., Pielak, G. 2001. Solvent-induced collapse of a-synuclein and acid denatured cytochrome c. Protein Science 10: 2195-2199

Morar, A., Wang, X., Pielak, G. 2001. Effects of crowding by mono-, di-, and tetrasaccharides on cytochrome c / cytochrome c peroxidase binding: comparing theory to experiment. Biochemistry 40: 281-285

Davis-Searles, P., Saunders, A., Erie, D., Winzor, D. 2001. Interpreting the effects of small uncharged solutes on protein-folding equilibria. Annual Review of Biophysics and Biomolecular Structure 30: 271-306


Saunders, A., Davis-Searles, P., Allen, D., Pielak, G., Erie, D. 2000. Osmolyte-induced changes in protein conformational equilibria. Biopolymers 53: 293-307


Wang, X., Pielak, G. 1999. Equilibrium thermodynamics of a physiologically-relevant heme-protein complex. Biochemistry 38: 16876-16881

Waldner, J., Lahr, S., Edgell, M., Pielak, G. 1999. Nonideality and protein thermal denaturation. Biopolymers 49: 471-479

Shock, D., Naik, U., Brittain, J., Alahari, S., Sondek, J., Parise, L. 1999. Calcium-dependent properties of CIB binding to the integrin aIIb cytoplasmic domain and translocation to the platelet cytoskeleton. Biochemical Journal 342: 729-735

Mechanic, L., Hall, M., Mattson, S. 1999. Escherichia coli DNA helicase II is active as a monomer. Journal of Biological Chemistry 274: 12488-12498

Hostetter, D., Weatherly, G., Beasley, J., Bortone, K., Cohen, D., Finger, S., Hardwidge, P., Kakouras, D., Saunders, A., Trojak, S., Waldner, J., Pielak, G. 1999. Partially formed native tertiary interactions in the A-state of cytochrome c. Journal of Molecular Biology 289: 639-644

Chen, L., Pielak, G., Thompson, N. 1999. The cytoplasmic  region of Fc(g)RIIb1, but not Fc(g)RIIb2, binds phospholipids membranes. Biochemistry 38: 2102-2109


Waldner, J., Lahr, S., Edgell, M., Pielak, G. 1998. Effects of a polyhistidine terminal extension on eglin c stability. Analytical Biochemistry 263: 116-118

Marmorino, J., Lehti, M., Pielak, G. 1998. Native tertiary structure in an A-state. Journal of Molecular Biology 275: 379-388

Davis-Searles, P., Morar, A., Saunders, A., Erie, D., Pielak, G. 1998. Sugar-induced molten-globule model. Biochemistry 37: 17048-17053

Allen, D., Pielak, G. 1998. Baseline length and automated fitting of denaturation data. Protein Science 7: 1262-1263

Chen, L., Thompson, N., Pielak, G. 1997. Design, synthesis, and characterization of the genes for mouse FcgRIIb1 and FcgRIIb2 cytoplasmic regions. Protein Science 6: 1038-1046

Rajarshi Choudhury, Sreerupa Ghose Roy, Yihsuan S. Tsai, Ashutosh Tripathy, Lee M. Graves and Zefeng Wang. 2014. The splicing activator DAZAP1 integrates splicing

control into MEK/Erk-regulated cell proliferation and migration. Nature Communications.  5:3078 | DOI: 10.1038/ncomms4078.