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)

Bassett, E.A., J. DeNizio, M.C. Barnhart-Dailey, T. Panchenko, N. Sekulic, D.J. Rogers, D.R. Foltz, B.E. 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

Castro, Carlos, Fabian Kilcherr, Do-Nyun Kim, Enrique Lin Shiao, Tobias Wauer, Philipp Wortmann, Mark Bathe, Hendrik 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, Alexandra M., Sofia A. Santos, Yinghua Guan, J. Adam Hendricks, Balaram Ghosh, D. Miklos Szantai-Kis, Surya A. Reis, Jagesh V. Shah, Ralph Mazitschek (2014) Monoalkoxy BODIPYs—A Fluorophore Class for Bioimaging, Bioconjugate Chem. 25(6):1043-51.

DeNizio, J.E., S.J. Elsässer SJ, 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]

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

Dodevski I, Nucci NV, Valentine KG, Sidhu GK, O'Brien ES, Pardi A, Wand A. (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

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 Disulfide Isomerase A6 Controls the Decay of IRE1 Signaling via Disulfide-Dependent Association. Mol Cell. 53(4): 562-76.

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, Dutton PL. (2013) Elementary tetrahelical protein design for diverse oxidoreductase functions. Nat Chem Biol. 9(12):826-33.

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

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

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.

Ikotun OF, Higbee EM, Ouellette W, 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, 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 K.R., J.E. DeNizio, B.E. Black, and B.A. Garcia. (2013) Identification and interrogation of combinatorial histone modifications. Front. Genet. 4:264.

Kasinath V, Valentine KG and Wand AJ (2013).A 13C labeling strategy reveals a range of aromatic side chain motion in calmodulin. J Am Chem Soc. 135(26):9560-3.

Kasinath V, Sharp KA, Wand AJ. (2013) Microscopic insights into the NMR relaxation-based protein conformational entropy meter. J Am Chem Soc. Oct 9;135(40):15092-100.

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.

Lichtenstein, Bruce R., Tammer A. Farid, Goutham Kodali, Lee A. Solomon, J.L. Ross Anderson, Molly M. Sheehan, Nathan M. Ennist, Bryan A. Fry, Sarah E. Chobot, Christopher Bialas, Joshua A. Mancini, Craig T. Armstrong, Zhenyu Zhao, Tatiana V. Esipova, David Snell, Sergei A. Vinogradov, Bohdana M. Discher, Christopher C. Moser and P. Leslie 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.

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

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, N.M., Pan, Q., Cole, B.S., Yarosh, C.A., Babcock, G.A., Heyd, F., Ajith, S., Zhu, W., Blencowe, B.J., and K.W. 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

Mendrola JM, Shi F, Park JH, Lemmon MA. Receptor tyrosine kinases with intracellular pseudokinase domains. Biochem Soc Trans. 2013 Aug;41(4):1029-36.

Metcalf DG, Moore DT, Wu Y, Kielec JM, Molnar K, Valentine KG, Wand AJ, Bennett JS, DeGrado WF.(2010 )NMR analysis of the alphaIIb beta3 cytoplasmic interaction suggests a mechanism for integrin regulation. Proc Natl Acad Sci U S A. 107(52):22481-6.

Moronetti Mazzeo LE, Dersh D, Boccitto M, Kalb RG and Lamitina T. (2012) Stress and aging induce distinct polyQ protein aggregation states. Proc Natl Acad Sci. 109(26):10587-92.

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.

Park JH, Lemmon MA. Occupy EGFR. Cancer Discov. 2012 May;2(5):398-400.

Park JH, Liu Y, Lemmon MA, Radhakrishnan R. Erlotinib binds both inactive and active conformations of the EGFR tyrosine kinase domain. Biochem J. 2012 Dec 15;448(3):417-23.

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., & 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, Kasinath V and Wand AJ. (2014) Banding of NMR-derived methyl order parameters: Implications for protein dynamics. Proteins. Mar 26. doi: 10.1002/prot.24566. [Epub ahead of print]

Stalker TJ, Welsh JD, Tomaiuolo M, et al. (2014) A systems approach to hemostasis: 3. Thrombus consolidation regulates intrathrombus solute transport and local thrombin activity. Blood. DOI: http://dx.doi.org/10.1182/blood-2014-01-550319

Tomaiuolo M, Stalker TJ, Welsh JD, Diamond SL, Sinno T, Brass LF .(2014) A systems approach to hemostasis: 2. Computational analysis of molecular transport in the thrombus microenvironment. Blood.
DOI: http://dx.doi.org/10.1182/blood-2014-01-550343

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

Waegele MM, Culik RM, Gai F. (2011) Site-Specific Spectroscopic Reporters of the Local Electric Field, Hydration, Structure, and Dynamics of Biomolecules. J Phys Chem Lett. 2:2598-2609.

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.

Welsh JD, Stalker TJ, Voronov R, et al (2014) A systems approach to hemostasis: 1 The interdependence of thrombus architecture and agonist movements in the gaps between platelets. Blood. DOI: http://dx.doi.org/10.1182/blood-2014-01-550335

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

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

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.

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, Toli?-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(1):76-87.

DeSantis ME, Shorter J. (2012) Hsp104 drives "protein-only" positive selection of Sup35 prion strains encoding strong [PSI(+)]. Chem Biol. 19(11):1400-10.

DeSantis ME, Dersh D. (2010) Preventing Parkinson's pathology. Dis Model Mech. 3(7-8): 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(2):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(11):2321-30

Donald JE, Kulp DW, DeGrado WF. (2011) Salt bridges: geometrically specific, designable interactions. Proteins. 79(3):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.

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.

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

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.

Jackrel ME, DeSantis ME, Martinez BA, Castellano LM, Stewart RM, Caldwell KA, Caldwell GA, Shorter J. (2014) Potentiated Hsp104 variants antagonize diverse proteotoxic misfolding events.
Cell. 156(1-2):170-82.

Janmey PA, Slochower DR, Wang YH, Wen Q, Cebers A. (2014) Polyelectrolyte properties of filamentous biopolymers and their consequences in biological fluids. Soft Matter 10(10):1439-49.

Jian C, Xiao J, Gong L, Skipwith CG, Jin SY, Kwaan HC, Zheng XL.(2012) Gain-of-function ADAMTS13 variants that are resistant to autoantibodies against ADAMTS13 in patients with acquired thrombotic thrombocytopenic purpura. Blood. 119(16):3836-43

Jin SY, Skipwith CG, Shang D, Zheng XL. (2009) von Willebrand factor cleaved from endothelial cells by ADAMTS13 remains ultralarge in size.J Thromb Haemost. 7(10):1749-52.

Jin SY, Skipwith CG, Zheng XL. (2010) Amino acid residues Arg(659), Arg(660), and Tyr(661) in the spacer domain of ADAMTS13 are critical for cleavage of von Willebrand factor. Blood. 115(11):2300-10.

Jo, H*.; Meinhardt, N*.; Wu, Y.; Kulkarni, S.; Hu, X.; Low, K. E.; Davies, P.L.; DeGrado, W. F., Greenbaum, D. C (2012) .Development of α-Helical Calpain Probes by Mimicking a Natural Protein-Protein Interaction. J. Am. Chem. Soc. 134(42), 17704-17713
(*Co-first author)

Jo, H, Culik RM, Korendovych IV, DeGrado WF, Gai F. (2010) Selective incorporation of nitrile-based infrared probes into proteins via cysteine alkylation. Biochemistry. 49(49):10354-6.

Joudeh J, Allen JE, Das A, Prabhu V, Farbaniec M, Adler J, El-Deiry WS. (2013)Novel antineoplastics targeting genetic changes in colorectal cancer. Adv Exp Med Biol. 779:1-34

Kan ZY, Walters BT, Mayne L, Englander SW. (2013) Protein hydrogen exchange at residue resolution by proteolytic fragmentation mass spectrometry analysis. Proc Natl Acad Sci U S A. 110(41):16438-43

Korendovych IV, Kulp DW, Wu Y, Cheng H, Roder H, DeGrado WF.(2011)Design of a switchable eliminase. Proc Natl Acad Sci U S A. 108(17):6823-7.

Lichtenstein BR, Cerda JF, Koder RL, Dutton PL. (2009) Reversible proton coupled electron transfer in a peptide-incorporated naphthoquinone amino acid. Chem Commun (Camb). (2):168-70.

Lichtenstein BR, Moorman VR, Cerda JF, Wand AJ, Dutton PL.(2012) Electrochemical and structural coupling of the naphthoquinone amino acid. Chem Commun (Camb). 48(14):1997-9.

Lin CW, Culik RM, Gai F. (2013) Using VIPT-jump to distinguish between different folding mechanisms: application to BBL and a Trpzip. J Am Chem Soc. 135(20):7668-73.

Lin CC, Huoh YS, Schmitz KR, Jensen LE, Ferguson KM. (2008) Pellino proteins contain a cryptic FHA domain that mediates interaction with phosphorylated IRAK1. Structure. 16(12):1806-16.

Ma C, Polishchuk AL, Ohigashi Y, Stouffer AL, Schön A, Magavern E, Jing X, Lear JD, Freire E, Lamb RA, DeGrado WF, Pinto LH. (2009) Identification of the functional core of the influenza A virus A/M2 proton-selective ion channel. Proc Natl Acad Sci U S A. 106(30):12283-8.

Mani, Tomoyasu, Ana Christina L. Opina, Piyu Zhao, Mary Evbuomwan, Nate Milburn, Gyula Tircso, Cemile Kumas, and A. Dean Sherr (2014) . The stereochemistry of amide side-chains containing carboxyl groups influences water exchange rates in EuDOTA-tetraamide complexes, Journal of Biological Inorganic Chemistry 19:161-171.

Mani, Tomoyasu, Dariusz M. Niedzwiedzik, and Sergei A. Vinogradov (2012) Generation of phosphorescent triplet states via photoinduced electron transfer: energy and electron transfer dynamics in Pt porphyrin-Rhodamine B dyads. Journal of Physical Chemistry A, 116:3598–3610

Mani, Tomoyasu, Mana Tanabe, Seigo Yamauchi, Nikolai V. Tkachenko, Sergei A. Vinogrado (2012), Modulation of Visible Room Temperature Phosphorescence by Weak Magnetic Fields, Journal of Physical Chemistry Letters, 3:3115-3119.

Mani, Tomoyasu,, Gyula Tircso, Piyu Zhao, A. Dean Sherry, and Mark Woods (2009. The Effect of the Regiochemistry of Butyl Amide Substituents on the Solution-State Structures of Lanthanide(III) DOTA-tetraamide complexes, Inorganic Chemistry, 48:10338-10345.

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