Biochemistry and Molecular Biophysics Graduate Group

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Student Publications


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Publications of Current Students
Publications of Former Students


PUBLICATIONS OF CURRENT STUDENTS (Names of students are in bold)

Anderson JL, Armstrong CT, Kodali G, Lichtenstein BR, Watkins DW, Mancini JA, Boyle AL, Farid TA, Crump MP, Moser CC, Dutton PL (2014) Constructing a man-made c-type cytochrome maquette in vivo: electron transfer, oxygen transport and conversion to a photoactive light harvesting maquette. Chem Sci. 5(2):507-514.

Baud M.G.J., Lin-Shiao E., Zengerle M., Tallant C. and Ciulli A. (2015) New Synthetic Routes to Triazolo-Benzodiazepine Analogues: Expanding the Scope of the Bump-and-Hole Approach for Selective BET Bromodomain Inhibition. Journal of Medicinal Chemistry Sep 14. [Epub ahead of print]

Bassett, EA., J. DeNizio, MC. Barnhart-Dailey, T. Panchenko, N. Sekulic, DJ. Rogers, DR. Foltz, BE. Black (2012) HJURP uses distinct CENP-A surfaces to recognize and to stabilize CENP-A/histone H4 for centromere assembly. Dev. Cell. 22(4):749-62.

Bassett EA, Wood S, Salimian KJ, Ajith S, Foltz DR, Black BE (2010) Epigenetic centromere specification directs aurora B accumulation but is insufficient to efficiently correct mitotic errors. J Cell Biol. 190(2):177-85

Baud MGJ*, Lin-Shiao E*, Cardote T*, Tallant C, Pschibul A, Chan KH, Zengerle M, Garcia JR, Kwan TTL, Ferguson FM and Ciulli A (2014) ‘A Bump-and-Hole Approach to Engineer Controlled Selectivity of BET Bromodomain Chemical Probes. Science, 16 October 2014 (10.1126/science.1249830).
* These authors contributed equally to this work

Bessman, N.J., Bagchi, A., Ferguson, K.M. and Lemmon, M.A. (2014) Complex relationship between ligand binding and dimerization in the Epidermal Growth Factor Receptor. Cell Reports. 9:1-12.

Castro, C, F Kilcherr, Do-Nyun Kim, E Lin Shiao, T Wauer, P Wortmann, M Bathe and K Dietz (2011) A primer to scaffolded DNA origami. Nature Methods; 8(3):221-9.

Choi DW, Semrau JD, Antholine WE, Hartsel SC, Anderson RC, Carey JN, Dreis AM, Kenseth EM, Renstrom JM, Scardino LL, Van Gorden GS, Volkert AA, Wingad AD, Yanzer PJ, McEllistrem MT, de la Mora AM, and DiSpirito AA (2008) Oxidase, superoxide dismutase, and hydrogen peroxide reductase activities of methanobactin from types I and II methanotrophs. J Inorg Biochem 102:1571-1580

Courtis, A ., SA Santos, Y Guan, JA Hendricks,B Ghos M Szantai-Kis, S A. Reis, J V. Shah and R Mazitschek (2014) Monoalkoxy BODIPYs—A Fluorophore Class for Bioimaging, Bioconjugate Chem. 25(6):1043-51.

DeNizio, J.E., S.J. Elsässer SJ and B.E. Black (2014) DAXX co-folds with H3.3/H4 using high local stability conferred by the H3.3 variant recognition residues. Nucl. Acids Res. Feb 3. [Epub ahead of print]

Dodevski I, Nucci NV, Valentine KG, Sidhu GK, O'Brien ES, Pardi A and AJ Wand. (2014) Optimized reverse micelle surfactant system for high-resolution NMR spectroscopy of encapsulated proteins and nucleic acids dissolved in low viscosity fluids. J Am Chem Soc 136(9), 3465-74

Falk SJ*, Guo LY*, Sekulic N*, Smoak EM*, Mani T, Logsdon GA, Gupta K, Jansen LE, Van Duyne GD, Vinogradov SA, Lampson MA, Black BE (2015). CENP-C reshapes and stabilizes CENP-A nucleosomes at the centromere. Science. 2015 May 8 (10.1126/science.1259308).
* These authors contributed equally to this work

Farid TA, Kodali G, Solomon LA, Lichtenstein BR, Sheehan MM, Fry BA, Bialas C, Ennist NM, Siedlecki JA, Zhao Z, Stetz MA, Valentine KG, Anderson JL, Wand AJ, Discher BM, Moser CC and Dutton PL. (2013) Elementary tetrahelical protein design for diverse oxidoreductase functions. Nat Chem Biol. 9(12):826-33.

Fields, PA., Cox, .M. and Karch, KR. (2012) Latitudinal variation in protein expression after heat stress in the salt marsh mussel Geukensia demissa. Integr. Comp. Biol. 52, 636–647.

Ganetzky R, Finn E, Bagchi A, Zollo O, Conlin L, Deardorff M, Harr M, Simpson MA, McGrath JA, Zackai E, Lemmon MA, Sondheimer N. EGFR mutations cause a lethal syndrome of epithelial dysfunction with progeroid features. Mol Genet Genomic Med. 2015 Sep;3(5):452-8. doi: 10.1002/mgg3.156. Epub 2015 Jun 4.

Guo, LY, Alekseev O, Li Y, Song Y, Dunaief JL (2014). Iron increases APP translation and amyloid-beta production in the retina (2014). Exp Eye Res. 2014 Dec;129:31-7.

Harpole KW, O'Brien ES, Clark MA, McKnight CJ, Vugmeyster L, Wand AJ. The unusual internal motion of the villin headpiece subdomain. Protein Sci. 2016 Feb;25(2):423-32. doi: 10.1002/pro.2831

Ikotun OF, Higbee EM, Ouellette W and Doyle RP. Pyrophosphate-bridged complexes with picomolar toxicity. J Inorg Biochem. 2009, 103, 1254-1264.

Ikotun OF, Higbee EM, Ouellette W, Lloret F, Julve M, and Doyle R (2008). Synthesis, Structural, Magnetic and Thermal Characterization of {[Cu(bipy)]2(μ-HP2O7)(μ-Cl)}·H2O. Eur J Inorg Chem. 2008:5281-5286.

Karch KR., JE. DeNizio, BE. Black and BA. Garcia. (2013) Identification and interrogation of combinatorial histone modifications. Front. Genet. 4:264.

Karch, KR., Zee, BM. and Garcia, BA. (2014). High resolution is not a strict requirement for characterization and quantification of histone post-translational modifications. J. Proteome Res. 13, 6152-6259.

Ko GJ, Linfert D, Jang HR, Higbee E, Watkins T, Cheadle C, Liu M, Racusen L, Grigoryev and Rabb H. (2012) Transcriptional analysis of infiltrating T cells in kidney ischemia/reperfusion injury reveals a pathophysiologic role for CCR5. Am J Physiol Renal Physiol. 302, F762-73.

Ko GJ, Jang HR, Huang Y, Womer KL, Liu M, Higbee E, Xiao Z, Yagita H, Racusen L, Hamad AR and Rabb H .(2011) Blocking Fas ligand on leukocytes attenuates kidney ischemia-reperfusion injury. J Am Soc Nephrol. 22:732-42.

Kramer, M.C., D. Liang, D.C. Tatomer, B. Gold, Z.M. March, S. Cherry, and J.E. Wilusz. (2015). Combinatorial control of Drosophila circular RNA expression by intronic repeats, hnRNPs, and SR proteins. Genes and Dev. dos: 10.1101/gad.270421.115

Lichtenstein, BR., TA. Farid, G Kodali, L A. Solomon, J.L. Anderson, MM. Sheehan, N M. Ennist, B A. Fry, S E. Chobot, C Bialas, JA. Mancini, T. Armstrong, Z Zhao, Tatiana V. Esipova, D Snell, SA. Vinogradov, B M. Discher, C C. Moser and P. L Dutton (2012) Engineering oxidoreductases: maquette proteins designed from scratch. Biochemical Society Transactions. 40 (2):561-566.

Liu M, Reddy N, Higbee E, Potetti H, Racusen L, Kensler T, Sporn M, Reddy and Rabb H.(2014) Nrf2 activator triterpenoid CDDO-imidazolide protects kidneys from ischemia reperfusion injury in mice. Kidney Int. 85:134-41.

Logsdon, GA, Barrey, EJ., Bassett, EA., DeNizio, JE., Guo, LY., Panchenko, T., Dawicki-McKenna, JM., Heun, P., and Black, BE. (2015). Both tails and the centromere targeting domain of CENP-A are required for centromere establishment. J Cell Biol jcb.201412011.

Mack KL, Shorter J. (2016). Engineering and evolution of molecular chaperones and protein disaggregases with enhanced activity. Front. Mol. Biosci. 3:8.

Mack KL, Moroz OV, Moroz YS, Olsen AB, McLaughlin J ,and Korendovych IV (2013) Reprogramming EF-hands for design of catalytically amplified lanthanide sensors. J. Biol. Inorg. Chem. 4:411-8.

Mallory MJ, Allon SJ, Qiu J, Gazzara MR, Tapescu I, Martinez NM, Fu XD, Lynch KW. Induced transcription and stability of CELF2 mRNA drives widespread alternative splicing during T-cell signaling. Proc Natl Acad Sci U S A. 2015 Apr 28;112(17):E2139-48. doi: 10.1073/pnas.1423695112. Epub 2015 Apr 13.

Marques, Bryan S.; Nucci, Nathaniel V.; Dodevski, Igor; Wang, Kristina W. C.; Athanasoula, Evangelia A.; Jorge, Christine; Wan and A. Joshua (2014) Measurement and control of pH in the aqueous interior of reverse micelles. J. Phys. Chem. B. 118: 2020-31.

Martinez NM, Agosto L, Qiu J, Mallory MJ, Gazzara MR, Barash Y, Fu XD, Lynch KW Widespread JNK-dependent alternative splicing induces a positive feedback loop through CELF2-mediated regulation of MKK7 during T-cell activation.
.Genes Dev. 2015 Oct 1;29(19):2054-66. doi: 10.1101/gad.267245.115.

Martinez NM, Lynch KW. Control of alternative splicing in immune responses: many regulators, many predictions, much still to learn. Immunol Rev. 2013 May;253(1):216-36

Martinez, NM., Pan, Q., Cole, BS., Yarosh, CA., Babcock, GA., Heyd, F., Ajith, S., Zhu, W., Blencowe, BJ., and KW. Lynch (2012) Alternative splicing networks regulated by signaling in human T cells. RNA 18: 1029-1040.

Mayne L, Kan ZY, Chetty PS, Ricciuti A, Walters BT, Englander SW. (2011) Many overlapping peptides for protein hydrogen exchange experiments by the fragment separation-mass spectrometry method. J Am Soc Mass Spectrom.22(11):1898-905

Moroz YS, Dunston TT, Makhlynets OV, Moroz OV, Wu Y, Yoon JH, Olsen AB, McLaughlin JM, Mack KL, Gosavi PM, van Nuland NA, Korendovych IV (2015) New Tricks for Old Proteins: Single Mutations in a Nonenzymatic Protein Give Rise to Various Enzymatic Activities. J. Am. Chem. Soc. 137:14905-11.

Moroz OV, Moroz YS, Wu Y, Olsen AB, Cheng H, Mack KL, McLaughlin JM, Raymond EA, Zhezherya K, Roder H, Korendovych IV. (2013) A single mutation in a regulatory protein produces evolvable allosterically regulated catalyst of nonnatural reaction. Angew. Chem. Int. Ed. Engl. 24:6246-9.

Morozova, O.A., Z.M. March, A.S. Robinson and D.W. Colby (2013) (2013). Conformational features of tau fibrils from Alzheimer's disease brain are faithfully propagated by unmodified recombinant protein. Biochemistry. 52(40): 6960-6967

Mutter; A C., J A Norman; M T Tiederrmna Singh; Sha Sha; Sara Morsi; Ismail Ahmed; Martin J Stillman; Ronald L Koder (2014) Rational Design of a Zinc Phthalocyanine Binding Protein. Journal of Structural Biology, 185:178-185.

O'Brien ES, Nucci NV, Fuglestad B, Tommos C, Wand AJ. Defining the Apoptotic Trigger: The Interaction of Cytochrome c and Cardiolipin. J Biol Chem. 2015 Dec 25;290(52):30879-87. doi: 10.1074/jbc.M115.689406

Raymond EA, Mack KL, Yoon JH, Moroz OV, Moroz YS, Korendovych IV (2014). Design of an allosterically regulated retroaldolase. Protein Sci. Dec 16. [Epub ahead of print]

Rogers JM, Lippert LG, Gai F. (2010) Non-natural amino acid fluorophores for one- and two-step fluorescence resonance energy transfer applications. Anal Biochem. 399(2):182-9.

Salimian, K.J., Ballister, E.R., Smoak, E.M., Wood, S., Panchenko, T., Lampson, M.A, and Black, B.E. (2011) Feedback control in sensing chromosome biorientation by the aurora B kinase. Current Biology, 21(13), 1158–65. doi:10.1016/j.cub.2011.06.015

Schmitz, K.R., Bagchi, A., Roovers, R.C., van Bergen en Henegouwen, P.M.P. and Ferguson, K.M. (2013) Structural evaluation of EGFR inhibition mechanisms for nanobodies/VHH domains. Structure 21: 1214-1224.

Shah PP, Zheng X, Epshtein A, Carey JN, Bishop DK and Klein HL (2010) Swi2/Snf2-related translocases prevent accumulation of toxic Rad51 complexes during mitotic growth. Mol Cell 39:862-872

Sharp KA, O'Brien E, Kasinath V, Wand AJ.On the relationship between NMR-derived amide order parameters and protein backbone entropy changes. Proteins. 2015 May;83(5):922-30. doi: 10.1002/prot.24789

Sidoli, S., Lin, S., Xiong, L., Bhanu, N.V., Karch, K.R., Johansen, E., Hunter, C., Mollah, S., and Garcia, B.A. (2015). SWATH analysis for characterization and quantification of histone post-translational modifications. Mol. Cell. Proteomics mcp.O114.046102.

Sidoli, S., Yuan, Z.-F., Lin, S., Karch, K., Wang, X., Bhanu, N., Arnaudo, A.M., Britton, L.-M., Cao, X.-J., Gonzales-Cope, M., Han, Y., Liu, S., Molden, R.C., Wein, S., Afjehi-Sadat, L., Garcia, B.A. (2015). Drawbacks in the use of unconventional hydrophobic anhydrides for histone derivatization in bottom-up proteomics PTM analysis. Proteomics. 10.1002/pmic.201400483

Sidoli, S., Lin, S., Karch, KR., Garcia, BA (2015). Bottom-up and middle-down proteomics have comparable accuracies in defining histone PTM relative abundance and stoichiometry. Anal. Chem. ac-2015-00072w.R1

Soufi, A., M. Fernandez Garcia, A. Jaroszewicz, N. Osman, M. Pellegrini and K. Zaret (2015) Pioneer transcription factors target partial DNA motifs on nucleosomesto initiate reprogramming. Cell 161: 1–14

Turegun B, Kast D, Dominguez R (2013) Subunit Rtt102 controls the conformation of the Arp7/9 heterodimer and its interactions with nucleotide and the catalytic subunit of SWI/SNF remodelers. J Biol Chem 288:35758-35768

Walters BT, Ricciuti A, Mayne L, Englander SW. (2012) Minimizing back exchange in the hydrogen exchange-mass spectrometry experiment. J Am Soc Mass Spectrom. 23(12):2132-9

Wand AJ, Moorman VR, Harpole KW. (2013) A surprising role for conformational entropy in protein function. Top Curr Chem. 2013;337:69-94.

Yarosh, C. A., Iacona, J. R., Lutz, C. S. & Lynch, K. W. (2015) PSF: nuclear busy-body or nuclear facilitator? Wiley Interdisciplinary Reviews: RNA 6, 351-367.

Yarosh, C. A., Tapescu, I., Thompson, M. G., Qiu, J., Mallory, M. J., Fu, X. & Lynch, K. W. (2015). TRAP150 interacts with the RNA-binding domain of PSF and antagonizes splicing of numerous PSF-target genes in T cells. Nucleic Acids Res. 43 (18), 9006–9016.

Yoon S, Carey JN, and Semrau JD (2009) Feasibility of atmospheric methane removal using methanotrophic biotrickling filters. Appl Microbiol Biot 83:949-956

Zhang, L, Anderson, J L; Ahmed, I; Norman, J; Negron, C; Mutter, A; Dutton PL; Koder R (2011), Manipulating cofactor binding thermodynamics in an artificial oxygen transport protein. Biochemistry 5:10254-61.

PUBLICATIONS OF FORMER STUDENTS (past 5 years) (Names of former students are in bold)

Artim SC, Mendrola JM, Lemmon MA. (2012) Assessing the range of kinase autoinhibition mechanisms in the insulin receptor family. Biochem J. 448(2):213-20.

Abdulghani J, Allen JE, Dicker DT, Liu YY, Goldenberg D, Smith CD, Humphreys R, El-Deiry WS (2013) Sorafenib sensitizes solid tumors to Apo2L/TRAIL and Apo2L/TRAIL receptor agonist antibodies by the Jak2-Stat3-Mcl1 axis. PLoS One. 8(9):e75414

Acharya R, Carnevale V, Fiorin G, Levine BG, Polishchuk AL, Balannik V, Samish I, Lamb RA, Pinto LH, DeGrado WF, Klein ML.(2010) Structure and mechanism of proton transport through the transmembrane tetrameric M2 protein bundle of the influenza A viru. Proc Natl Acad Sci U S A. 107(34):15075-80.

Allen JE, El-Deiry WS. (2011) Oxaliplatin uses JNK to restore TRAIL sensitivity in cancer cells through Bcl-xL inactivation. Gastroenterology. 141(2):430-4.

Allen JE, Ferrini R, Dicker DT, Batzer G, Chen E, Oltean DI, Lin B, Renshaw MW, Kretz-Rommel A, El-Deiry WS. (2012) Targeting TRAIL death receptor 4 with trivalent DR4 Atrimer complexes. Mol Cancer Ther. (10):2087-95

Allen JE, Gallant JN, Dicker DT, Amin S, Irby RB, Sharma AK, El-Deiry WS.(2013)Correction: The Akt Inhibitor ISC-4 Synergizes with Cetuximab in 5-FU-Resistant Colon Cancer. PLoS One. 8(11).

Allen JE, El-Deiry WS. (2013) Calcein-effluxing human colon cancer cells are enriched for self-renewal capacity and depend on β-catenin. Oncotarget. 4(2):184-91

Allen, Joshua E, Gabriel Krigsfeld, Patrick A. Mayes, Luv Patel, David T. Dicker, Akshal S. Patel, Nathan G. Dolloff,, Evangelos Messaris, Kimberly A. Scata, Wenge Wang, Jun-Ying Zhou, Gen Sheng W6 and Wafik S. El-Deiry (2013) Dual inactivation of Akt and ERK by TIC10 signals Foxo3a nuclear translocation, TRAIL gene induction, and potent antitumor effects. Transl Med 5: p. 171ra17

Allen JE, El-Deiry WS. (2012) Regulation of the human TRAIL gene. Cancer Biol Ther 13(12):1143-51

Allen JE, Gallant JN, Dicker DT, Amin S, Irby RB, Sharma AK, El-Deiry WS. (2013 )The Akt inhibitor ISC-4 synergizes with cetuximab in 5-FU-resistant colon cancer. PLoS One. 8(3):e59380.

Allen JE, Krigsfeld G, Mayes PA, Patel L, Dicker DT, Patel AS, Dolloff NG, Messaris E, Scata KA, Wang W, Zhou JY, Wu GS, El-Deiry WS. (2013) Dual inactivation of Akt and ERK by TIC10 signals Foxo3a nuclear translocation, TRAIL gene induction, and potent antitumor effects. Sci Transl Med. 5(171):171ra17.

Allen JE, El-Deiry WS. (2010) Circulating Tumor Cells and Colorectal Cancer. Curr Colorectal Cancer Rep. 6(4):212-220.

Allen JE, Hart LS, Dicker DT, Wang W, El-Deiry WS. (2009) Visualization and enrichment of live putative cancer stem cell populations following p53 inactivation or Bax deletion using non-toxic fluorescent dyes. Cancer Biol Ther. 8(22):2194-205

Allen JE, Patel A, Prabhu VV, Dicker DT, Sheehan JM, Glantz M, El-Deiry WS. COX-2 drives metastatic breast cells from brain lesions into the cerebrospinal fluid and systemic circulation. Cancer Res. 2014 Mar 10. [Epub ahead of print

Allen JE, Saroya BS, Kunkel M, Dicker DT, Das A, Peters KL, Joudeh J, Zhu J, El-Deiry WS. Apoptotic circulating tumor cells (CTCs) in the peripheral blood of metastatic colorectal cancer patients are associated with liver metastasis but not CTCs. Oncotarget. 2013 Oct 17. [Epub ahead of print]

Alvarado D, Klein DE, Lemmon MA. Structural basis for negative cooperativity in growth factor binding to an EGF receptor. Cell. 2010 Aug 20;142(4):568-79

Alvarado D, Klein DE, Lemmon MA. ErbB2 resembles an autoinhibited invertebrate epidermal growth factor receptor. Nature. 2009 Sep 10;461(7261):287-91

Barnhart MC, Kuich PH, Stellfox ME, Ward JA, Bassett EA, Black BE, Foltz DR. (2011) HJURP is a CENP-A chromatin assembly factor sufficient to form a functional de novo kinetochore. J Cell Biol. 194(2):229-43.

Ballister ER, Riegman M, Lampson MA (2014) Recruitment of Mad1 to metaphase kinetochores is sufficient to reactivate the mitotic checkpoint. J Cell Biol. 204(6):901-908.

Berger BW, Kulp DW, Span LM, DeGrado JL, Billings PC, Senes A, Bennett JS, DeGrado WF. (2010) Consensus motif for integrin transmembrane helix association. Proc Natl Acad Sci U S A. 107(2):703-8.

Bessman NJ, Lemmon MA. Finding the missing links in EGFR. Nat Struct Mol Biol. 2012 Jan 5;19(1):1-3.

Bethoney KA, King MC, Hinshaw JE, Ostap EM, Lemmon MA. A possible effector role for the pleckstrin homology (PH) domain of dynamin. Proc Natl Acad Sci U SA. 2009 Aug 11:106(32):13359-64

Bresler SC, Wood AC, Haglund EA, Courtright J, Belcastro LT, Plegaria JS, Cole K, Toporovskaya Y, Zhao H, Carpenter EL, Christensen JG, Maris JM, Lemmon MA, Mossé YP .(2011) Differential inhibitor sensitivity of anaplastic lymphoma kinase variants found in neuroblastoma. Sci Transl Med. 3(108):108ra114.

Carpenter EL, Haglund EA, Mace EM, Deng D, Martinez D, Wood AC, Chow AK, Weiser DA, Belcastro LT, Winter C, Bresler SC, Vigny M, Mazot P, Asgharzadeh S, Seeger RC, Zhao H, Guo R, Christensen JG, Orange JS, Pawel BR, Lemmon MA, Mossé YP. (2012) Antibody targeting of anaplastic lymphoma kinase induces cytotoxicity of human neuroblastoma.Oncogene. 31(46):4859-67.

Cheng H, Hong B, Zhou L, Allen JE, Tai G, Humphreys R, Dicker DT, Liu YY, El-Deiry WS. (2012) Mitomycin C potentiates TRAIL-induced apoptosis through p53-independent upregulation of death receptors: evidence for the role of c-Jun N-terminal kinase activation. Cell Cycle.11(17):3312-23.

Coelho M, Dereli A, Haese A, Kühn S, Malinovska L, DeSantis ME, Shorter J, Alberti S, Gross T, Toicl-Nørrelykke IM (2013) Fission yeast does not age under favorable conditions, but does so after stress. Curr Biol. 23(19):1844-52.

Culik RM, Annavarapu S, Nanda V, Gai F. (2013) Using D-amino acids to delineate the mechanism of protein folding: application to Trp-cage.Chem Phys. 422:131-134

Culik RM, Jo H, DeGrado WF, Gai F. (2012) Using thioamides to site-specifically interrogate the dynamics of hydrogen bond formation in β-sheet folding. J Am Chem Soc. 134(19):8026-9.

Culik RM, Serrano AL, Bunagan MR, Gai F (2011) Achieving secondary structural resolution in kinetic measurements of protein folding: a case study of the folding mechanism of Trp-cage. Angew Chem Int Ed Engl. 50(46):10884-7.

Daber R, Sochor MA, Lewis M. (2011) Thermodynamic analysis of mutant lac repressors. J Mol Biol. 409:76-87.

Dersh D, Jones SM, Eletto D, Christianson JC, Argon Y. (2014) OS-9 facilitates turnover of nonnative GRP94 marked by hyperglycosylation. Mol Biol Cell. 25(15):2220-34

DeSantis ME, Shorter J. (2012) Hsp104 drives "protein-only" positive selection of Sup35 prion strains encoding strong [PSI(+)]. Chem Biol. 19:1400-10.

DeSantis ME, Dersh D. (2010) Preventing Parkinson's pathology. Dis Model Mech. 3: 399-400.

DeSantis, M.E., Leung, E.H., Sweeny, E.A., Jackrel, M., Cushman-Nick, M., Neuhaus-Follini, A., Vashist, S., Sochor, M.A, Knight, M.N, and Shorter, J. (2012) Operational Plasticity Enables Hsp104 to Disaggregate Diverse Amyloid and Nonamyloid Clients. Cell 151:778-793.

DeSantis, M.E., Sweeny, E.A., Snead, D., Leung, E.H., Go, M.S., Gupta, K, Wendler, P., and Shorter, J. (2013) Conserved distal loop residues in the Hsp104 and ClpB middle domain contact nucleotide-binding domain 2 and enable Hsp70-dependent protein disaggregation. J. Biol. Chem. 289:848-67.

Dolloff NG, Allen JE, Dicker DT, Aqui N, Vogl D, Malysz J, Talamo G, El-Deiry WS (2012) Sangivamycin-like molecule 6 exhibits potent anti-multiple myeloma activity through inhibition of cyclin-dependent kinase-9. Mol Cancer Ther. 11:2321-30

Donald JE, Kulp DW, DeGrado WF. (2011) Salt bridges: geometrically specific, designable interactions. Proteins. 79:898-915.

Doulias PT, Tenopoulou M, Greene JL, Raju K, Ischiropoulos H. (2013) Nitric oxide regulates mitochondrial fatty acid metabolism through reversible protein S-nitrosylation. Sci Signal. 2013 6(256):rs1.

Doulias PT, Raju K, Greene JL, Tenopoulou M, Ischiropoulos H. (2013) Mass spectrometry-based identification of S-nitrosocysteine in vivo using organic mercury assisted enrichment. Methods. 62(2):165-70.

Doulias PT, Greene JL, Greco TM, Tenopoulou M, Seeholzer SH, Dunbrack RL, Ischiropoulos H. (2010)Structural profiling of endogenous S-nitrosocysteine residues reveals unique features that accommodate diverse mechanisms for protein S-nitrosylation. Proc Natl Acad Sci U S A.107(39):16958-63.

Eletto D, Dersh D, Argon Y. (2010) GRP94 in ER quality control and stress responses. Semin Cell Dev Biol. 21(5):479-85

Eletto D, Maganty A, Eletto D, Dersh D, Makarewich C, Biswas C, Paton JC, Paton AW, Doroudgar S, Glembotski CC, Argon Y. (2012) Limitation of individual folding resources in the ER leads to outcomes distinct from the unfolded protein response. J Cell Sci. 125(Pt 20): 4865-75.

Eletto D, Eletto D, Dersh D, Gidalevitz T, Argon Y. (2014) Protein disulfideiIsomerase A6 controls the decay of IRE1 signaling via disulfide-dependen-association. Mol Cell. 53(4): 562-76.

Faltas B, Zeidan A, Peters K, Das A, Joudeh J, Navaraj A, Dolloff NG, Harvey HA, Jiang Y, Allen JE, Dicker DT, El Deiry WS.(2011) Identifying circulating tumor stem cells that matter: the key to prognostication and therapeutic targeting. J Clin Oncol. 29(21):2946-7

Foltz DR, Jansen LE, Bailey AO, Yates JR 3rd, Bassett EA, Wood S, Black BE, Cleveland DW (2009 .Centromere-specific assembly of CENP-a nucleosomes is mediated by HJURP. Cell. 137(3):472-84.

Fu Y, Kasinath V, Moorman VR, Nucci NV, Hilser VJ and Wand AJ (2012) Coupled motion in proteins revealed by pressure perturbation. J Am Chem Soc. 134(20):8543-50

Gallant JN, Allen JE, Smith CD, Dicker DT, Wang W, Dolloff NG, Navaraj A, El-Deiry WS.(2011) Quinacrine synergizes with 5-fluorouracil and other therapies in colorectal cancer.
Cancer Biol Ther. 12(3):239-51.

Gibb B, Gupta K, Ghosh K, Sharp R, Chen J, Van Duyne GD. (2010) Requirements for catalysis in the Cre recombinase active site. Nucleic Acids Res. 38(17):5817-32.

Gledhill JM Jr, Walters BT, Wand AJ (2009) AMORE-HX: a multidimensional optimization of radial enhanced NMR-sampled hydrogen exchange. J Biomol NMR. 45(1-2):233-9

Gledhill JM Jr, Kasinath V and Wand AJ. (2011) Optimized linear prediction for radial sampled multidimensional NMR experiments. J Magn Reson. Sep;212(1):240-4. doi: 10.1016/j.jmr.2011.06.019. Epub 2011 Jun 28.

Goldberg, J.M.; Chen, X., Meinhardt, N.; Greenbaum, D.C.; Petersson, E.J. (2014) Thioamide-Based Fluorescent Protease Sensors. J. Am. Chem. Soc. 136(5), 2086-2093.

Gonzalez, Gabriel, Brett Hannigan and William F. DeGrado (2014) A Real-Time All-Atom Structural Search Engine for Protein. PLOS Computational Biology DOI: 10.1371/journal.pcbi.1003750

Grigoryan G, Moore DT, DeGrado WF (2011) Transmembrane communication: general principles and lessons from the structure and function of the M2 proton channel, K? channels, and integrin receptors. Annu Rev Biochem. 80:211-37.

Hasson D, Panchenko T, Salimian KJ, Salman MU, Sekulic N, Alonso A, Warburton PE, Black BE .(2013) The octamer is the major form of CENP-A nucleosomes at human centromeres. Nat Struct Mol Biol. 20(6):687-95

Hernandez, Dulce Alonso, Wei Liu, Gabriel Rosenblum, Tomoyasu Mani, Yale Goldman, Barry Cooperman (2013) Tb3+-tRNA for LRET studies of Protein Synthesis, Bioconjugate Chemistry, 24, 1186-1190.

Hu W, Walters BT, Kan ZY, Mayne L, Rosen LE, Marqusee S, Englander SW (2013)Stepwise protein folding at near amino acid resolution by hydrogen exchange and mass spectrometry.
Proc Natl Acad Sci U S A. 110(19):7684-9.

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