Publications

Services Provided by the Biophysics Resource Contributed to at Least 70 Publications (44 from Yale)

(Publications sorted by technology and listed in chronological order)

[SEC/LS] and Dynamic LS

E. Folta-Stogniew and K.R. Williams (1999) “Determination of molecular masses of protein: implementation of a size exclusion chromatography/laser light scattering service in a core laboratory” J. Biomol. Tech.  10: 51-63 .
P. D. Zamore, D. P. Bartel, R. Lehmann and J. R. Williamson (1999) “The PUMILIO-RNA Interaction: A Single RNA-Binding Domain Monomer Recognizes a Bipartite Target Sequence” Biochemistry 38 : 596-604
K. J. Lampi,  J. T. Oxford, H. Bachinger, T. R. Shearer, L. L. David and D. M. Kapfer (2002)  “Deamidation of Human bB1 Alters the Elongated Structure of the Dimer” Exp. Eye Res . 72 : 279-288
S. A. Robson, K. A. Michie, J. P. Mackay, E. Harry and G. F. King (2002)  ”The Bacillus subtilis cell division proteins FtsL and DivIC are intrinsically unstable and do not interact with one another in the absence of other septasomal components” Mol. Microbiol. 44 : 663–674
M. L. Bovee, K. S. Champagne, B. Demeler and C. S. Francklyn (2002) “ The Quaternary Structure of the HisZ-HisG N-1-(5’-Phosphoribosyl)-ATP Transferase from Lactococcus lactis” Biochemistry41:11838-11846
T. Makagiansar, P. D. Nguyen, A. Ikesue, K. Kuczera, W. Dentler, J. L. Urbauer, N. Galeva, M. Alterman and T. J. Siahaan (2002) “Disulfide Bond Formation Promotes the cis- and trans-Dimerization of the E-cadherin-derived First Repeat” J. Biol. Chem. 277:  16002–16010
G. P. Bertenshaw,  M. T. Norcum and J. S. Bond (2003) “Structure of homo- and hetero-oligomeric meprin metalloproteases. Dimers, tetramers, and high molecular mass multimers”  J. Biol. Chem .  278:  2522–2532
Fraser, G. M.; Gonzalez-Pedrajo, B.; Tame, J.R.H.; Macnab, R. M. (2003) “Interactions of FliJ with the Salmonella Type III Flagellar Export Apparatus” J. Bacteriol . 185: 5546-5554
C. Keeler, P. S. Dannies and M. E. Hodsdon (2003) “The Tertiary Structure and Backbone Dynamics of Human Prolactin” J. Mol. Biol . 328: 1105–1121
Mitic, L. L.; Unger, V. M.; Anderson, J. M. (2003) “Expression, solubilization, and biochemical characterization of the tight junction transmembrane protein claudin-4” Protein Sci.  12: 218-227
D. Yernool, O. Boudker, E. Folta-Stogniew and E. Gouaux (2003) " Trimeric Subunit Stoichiometry of the Glutamate Transporters from Bacillus caldotenax and Bacillus stearothermophilus" Biochemistry  42: 12981-12988
T. H. Scheuermann, E. Lolis and M. E. Hodsdon (2003) “Tertiary Structure of Thiopurine Methyltransferase from Pseudomonas syringae, a Bacterial Orthologue of a Polymorphic, Drug-metabolizing Enzyme”  J. Mol. Biol . 333: 573–585
Bruderer, R. M.; Brasseur, C.; Meyer, H. H.(2004)  “The AAA ATPase p97/VCP Interacts with Its Alternative Co-factors, Ufd1-Npl4 and p47, through a Common Bipartite Binding Mechanism” J. Biol. Chem. 279 : 49609-49616
Minamino, T.; Saijo-Hamano, Y.; Furukawa, Y.; Gonzalez-Pedrajo, B.; Macnab, R. M.; Namba, K. (2004) “Domain Organization and Function of Salmonella FliK, a Flagellar Hook-length Control Protein” J. Mol. Biol.  341: 491-502
Wang, Y. and Ha, Y. (2004) “The X-Ray Structure of an Antiparallel Dimer of the Human Amyloid Precursor Protein E2 Domain” Mol. Cell  15: 343-353
M. E. Hahn and Muir T.W. (2004) “Photocontrol of Smad2, a multiphosphorylated cell-signaling protein, through caging of activating phosphoserines”  Angew Chem. Int. Ed. Engl . 43 : 5800-5803
Thorne, M.E.; McQuade, K.L. (2004) “Heat-induced oligomerization of gp96 occurs via a site distinct from substrate binding and is regulated by ATP” Biochem. Biophys. Res. Commun .  323 : 1163-1171
Chang, J.; Chen, J.; Zhou, D. (2005) “Delineation and characterization of the actin nucleation and effector translocation activities of Salmonella SipC” Mol. Microbiol .  55:  1379-1389
Yu I.M., Gustafson, C.L., Diao J., Burgner J.W. 2nd, Li Z., Zhang J., and Chen J. (2005) "Recombinant Severe Acute Respiratory Syndrome (SARS) Coronavirus Nucleocapsid Protein Forms a Dimer through Its C-terminal Domain"  J. Biol. Chem. 280 : 23280-23286
Folta-Stogniew, E. (2006) “Oligomeric States of Proteins Determined by Size-Exclusion Chromatography Coupled with Light Scattering, Absorbance and Refractive Index Detectors” Humana Press,  Methods in Molecular Biology, Nedelkov and Randall editors , 328: 97-112
Bunce, J.; Achila, D.; Hetrick, E.; Lesley, L.; Huffman, D.L. (2006) “Copper Transfer Studies between the N-terminal Copper Binding Domains One and Four of Human Wilson Protein” Biochim. Biophys. Acta . 1760 : 907-912
Robles Lopez SM, Hortua Triana MA and Barbara H. Zimmermann (2006) “Cloning and preliminary characterization of the dihydroorotase from Toxoplasma gondii”  Mol. Biochem. Parasitol .  148 : 93-98
Stavropoulos, P., Blobel, G., Hoelz, A. (2006) “Crystal structure and mechanism of the human lysine-specific demethylase-1”  Nat. Struct. Mol. Biol. 13 : 626-632
Nelson, D., Schuch, R., Chahales, P. Zhu, S., Fischetti, V.A. (2006) “PlyC: the First Multimeric Bacteriophage Lysin” Proc. Natl. Acad. Sci. U.S.A. 103 : 10765-10770
Albright, R.A., Vazquez Ibar, J.-L., Kim, C. U., Gruner, S.M., Morais Cabral, J.H.  (2006) "The RCK domain from a KtrAB K+ transporter: 

Multiple conformations of the octameric ring” Cell 126: 1147-1159

Ramsey, J.E., Daugherty, M. A., Kelm, R. J. (2007) “Hydrodynamic Studies on the Quaternary Structure of Recombinant Mouse Purb”  J. Biol .Chem. 282 : 1552-1560
Li X., Pal U., Ramamoorthi N., Liu X., Desrosiers D.C., Eggers C., Anderson J.F., Radolf J.D., and Fikrig E. (2007) "The Lyme disease agent Borrelia burgdorferi requires BB0690, a Dps homologue, to persist within ticks" Mol. Microbiol. 63: 694-710
Fogel A I, Akins M. R., Krupp A. J., Stagi M., Stein V., and Biederer T. (2007) "SynCAMs Organize Synapses through Heterophilic Adhesion" J. Neurosci. 27: 12516-12530
Albright R.A., Joh K., and Morais-Cabral J.H. (2007) "Probing the Structure of the Dimeric KtrB Membrane Protein" J. Biol. Chem. 282: 35046-35055
Chang J., Myeni S.K., Lin T.L., Wu C.C., Staiger C.J., and Zhou D. (2007) "SipC multimerization promotes actin nucleation and contributes to Salmonella-induced inflammation" Mol. Microbiol. 66 : 1548-1556
Crichlow, G.V., Zhou, H., Hsiao, H-h., Frederick, K.B., Debrosse, M., Yuande Yang, Y., Folta-Stogniew, E.J.,  Chung, H-J., Chengpeng Fan, C., De La Cruz, E., Levens, D., Lolis, E., and Braddock, D. (2008) “Dimerization of FIR upon FUSE binding suggests a mechanism of c-myc inhibition”  EMBO J. 27: 277-289
Petersson E.J. and Schepartz A. (2008) "Toward beta-Amino Acid Proteins: Design, Synthesis, and Characterization of a Fifteen Kilodalton beta;-Peptide Tetramer" J. Am. Chem. Soc. 130: 821-823  
Das S, Stivison E, Folta-Stogniew E, Oliver D. (2008) “Re-examination of the Role of the Amino-Terminus of SecA in Promoting Its Dimerization and Functional State”  J. Bacteriol.190 : 7302-7307
Hilvo M, Baranauskiene L, Salzano AM, Scaloni A, Matulis D, Innocenti A, Scozzafava A, Monti SM, Di Fiore A, De Simone G, Lindfors M, Jänis J, Valjakka J, Pastoreková S, Pastorek J, Kulomaa MS, Nordlund HR, Supuran CT, Parkkila S. (2008)  “Biochemical characterization of CA IX, one of the most active carbonic anhydrase isozymes” J. Biol. Chem. 283:  27799-27809
Huang R.H., Wang Y., Roth R., Yu X., Purvis A.R., Heuser J.E., Egelman E.H., and Sadler J.E. (2008) "Assembly of Weibel-Palade body-like tubules from N-terminal domains of von Willebrand factor" Proc. Natl. Acad. Sci. U.S.A. 105 : 482-487
Ebersbach G., Briegel A., Jensen G.J., and Jacobs-Wagner C. (2008) "A Self-Associating Protein Critical for Chromosome Attachment, Division, and Polar Organization in Caulobacter" Cell 134: 956-968
Apetri A.C. and Horwich A.L. (2008) "Chaperonin chamber accelerates protein folding through passive action of preventing aggregation" Proc. Natl. Acad. Sci. U.S.A. 105: 17351-17355
Lauren, J., D.A.Gimbel, H.B., Nygaard, Gilbert, J.W., Strittmatter, S.M. (2009) "Cellular prion protein mediates impairment of synaptic plasticity by amyloid-[bgr] oligomers" Nature 457: 1128-1132
Folta-Stogniew, Ewa J. (2009) “Light Scattering”. In: ENCYCLOPEDIA OF LIFE SCIENCES. John Wiley & Sons, Ltd: Chichester http://www.els.net/ [DOI: 10.1002/9780470015902.a0003143]
Hoopes,  J.T., Liu, X., Xu, X., Demeler, B., Folta-Stogniew, E., Li, C., and Ha, Y. (2010) “Structural Characterization of the E2 Domain Of APL-1, A Caenorhabditis elegans Homolog of Human Amyloid Precursor Protein, and its Heparin Binding Site”  J. Biol. Chem.  28: 2165-2173
Green J.M., Hollandsworth R., Pitstick L., and Carter E.L. (2010) "Purification and Characterization of the Folate Catabolic Enzyme p-Aminobenzoyl-Glutamate Hydrolase from Escherichia coli" J. Bacteriol. 192 ; 2407-2413
Hsiao H., Nath A., Lin C.-Y., Folta-Stogniew E., Rhoades E., Braddock D. (2010) “Quantitative Characterization of the Interactions between c-myc Transcriptional Regulators FUSE, FBP and FIR"  Biochemistry 49: 4620-4634
Kapoor N., Gupta R., Menon S.T., Folta-Stogniew E., Raleigh D.P., and Sakmar T.P. (2010) "Nucleobindin 1 is a calcium-regulated guanine nucleotide dissociation inhibitor of G{alpha}i1"  J. Biol. Chem. 285 : 31647-31660
Molland K.L., Narayanan A., Burgner J.W., and Yernool D.A. (2010) "Identification of the structural motif responsible for trimeric assembly of the C-terminal regulatory domains of polycystin channels PKD2L1 and PKD2" Biochem. J. 429 : 171-183
Shuart N.G., Haitin Y., Camp S.S., Black K.D., and Zagotta W.N. (2011) "Molecular mechanism for 3:1 subunit stoichiometry of rod cyclic nucleotide-gated ion channels" Nat. Commun. 2 : 457
Merten J.A., Schultz K.M., and Klug C.S. (2012) "Concentration-dependent oligomerization and oligomeric arrangement of LptA" Protein Sci. 21 : 211-218
Gupta R., Kapoor N., Raleigh D. P., and Sakmar T. P. (2012) "Nucleobindin 1 Caps Human Islet Amyloid Polypeptide Protofibrils to Prevent Amyloid Fibril Formation" J. Mol. Biol.421 : 378-389
Rangarajan E.S. and Izard T. (2012) "The cytoskeletal protein +¦-catenin unfurls upon binding to vinculin" J. Biol. Chem.287 : 18492-18499
Gupta R, Kapoor N., Raleigh D.P., and Sakmar T.P. (2012) "Nucleobindin 1 Caps Human Islet Amyloid Polypeptide Protofibrils to Prevent Amyloid Fibril Formation" J. Mol. Bio. 421 : 378-389
Ducas V.C. and Rhoades E. (2012) "Quantifying Interactions of beta-Synuclein and gamma-Synuclein with Model Membranes" J. Mol. Bio. 423 : 528-539

Stopped Flow

Marlovits TC, Haase W, Herrmann C, Aller SG, Unger VM. (2002) "The membrane protein FeoB contains an intramolecular G protein essential for Fe(II) uptake in bacteria" Proc. Natl. Acad. Sci. U.S.A.  99: 16243-16248
Purohit V, Grindley ND, Joyce CM (2003) “Use of 2-Aminopurine Fluorescence To Examine Conformational Changes during Nucleotide Incorporation by DNA Polymerase I (Klenow Fragment)” Biochemistry  42: 10200-10211
E. Folta-Stogniew, S. O’Malley, R. Gupta, K.S. Anderson and C.M. Radding (2004) “Exchange of DNA Base Pairs that Coincides with Recognition of Homology Promoted by E. coli RecA Protein” Mol. Cell  15: 965-975
Eng ET, Jalilian AR, Spasov KA, Unger VM. (2008) “Characterization of a novel prokaryotic GDP dissociation inhibitor domain from the G protein coupled membrane protein FeoB”  J. Mol. Biol.  375: 1086-1097
Hung K.W., Chang Y.W., Eng E.T., Chen J.H., Chen Y.C., Sun Y.J., Hsiao C.D., Dong G., Spasov K A., Unger V.M., and Huang T.H. (2010) "Structural fold, conservation and Fe(II) binding of the intracellular domain of prokaryote FeoB" J. Struct. Biol. 170: 501-512

SLM8000-Fluorometer

Bazemore LR, Takahashi M, Radding CM. (1997) “Kinetic analysis of pairing and strand exchange catalyzed by RecA. Detection by fluorescence energy transfer” J. Biol. Chem . 272: 14672-14682
Bazemore LR, Folta-Stogniew E, Takahashi M, Radding CM. (1997) “RecA tests homology at both pairing and strand exchange” Proc. Natl. Acad. Sci. U.S.A . 94: 11863-11868
Gupta RC, Golub EI, Wold MS, Radding CM. (1998) “Polarity of DNA strand exchange promoted by recombination proteins of the RecA family” Proc. Natl. Acad. Sci. U.S.A . 95: 9843-9848
Gupta RC, Folta-Stogniew E, Radding CM. (1999) “Human Rad51 protein can form homologous joints in the absence of net strand exchange”  J. Biol. Chem. 274: 1248-56
Gupta RC, Folta-Stogniew E, O'Malley S, Takahashi M, Radding CM  (1999) "Rapid exchange of A:T base pairs is essential for recognition of DNA homology by human Rad51 recombination protein"  Mol. Cell  4: 705-714

ITC or SPR or both

Morgan JR, Di Paolo G, Werner H, Schedrina VA, Pypaert M, Pieribone V, and De Camilli P.  (2004) "A role for talin in presynaptic function"  J. Cell Biol.  167: 43-50
Lee SY, Voronov S, Letinic K, Nairn AC, Di Paolo G, and De Camilli P. (2005) "Regulation of the interaction between PIPKI(gamma) and talin by proline-directed protein kinases"  J. Cell Biol.  168: 789-799
Benach, J., Swaminathan, S.J., Tamayo, R., Handelman, S., Folta Stogniew, E., Ramos, J.E., Forouhar, F., Neely, H., Seetharaman, J., Camilli, A., and Hunt, J.F. (2007) “The structural basis of cyclic diguanylate signal transduction by PilZ domains”  EMBO J .  26 : 5153-5166
Erdmann K.S., Mao Y., McCrea H.J., Zoncu R., Lee S., Paradise S., Modregger J., Biemesderfer D., Toomre D., and De Camilli P. (2007) "A Role of the Lowe Syndrome Protein OCRL in Early Steps of the Endocytic Pathway" Dev. Cell 13: 377-390
Celic A., Petri E.T., Demeler B., Ehrlich B.E., and Boggon T.J. (2008) "Domain Mapping of the Polycystin-2 C-terminal Tail Using de Novo Molecular Modeling and Biophysical Analysis" J. Biol. Chem. 283: 28305-28312
Piermarini, P.M., Kim, E.Y., Boron, W.F. (2007) “Evidence Against a Direct Interaction Between Intracellular Carbonic Anhydrase II and Pure C-terminal Domains of SLC4 Bicarbonate Transporters” J. Biol. Chem. 282, 1409-1421
Bae, J.H., E.D. Lew, S. Yuzawa, F. Tomq, I. Lax, and J. Schlessinger (2009) "The Selectivity of Receptor Tyrosine Kinase Signaling Is Controlled by a Secondary SH2 Domain Binding Site" Cell 138: 514-524
Casuscelli, J., Schmidt, S., DeGray, B.,  Petri, E.T., Celic, A.,  Folta-Stogniew, E., Ehrlich, B.E., and Boggon, T.J. (2009) “Analysis of the cytoplasmic interaction between polycystin-1 and polycystin-2” Am. J. Physiol. Renal Physiol. 297 : 1310-1315
Swan L.E., Tomasini L., Pirruccello M., Lunardi J.l., and De Camilli P. (2010) "Two closely related endocytic proteins that share a common OCRL-binding motif with APPL1" Proc. Natl. Acad. of Sci. U.S.A. 107: 3511-3516
Li, X., Ji, W., Zhang, R., Folta-Stogniew, E., Min, W. and Boggon, T. (2011) "Molecular recognition of leucine-aspartate repeat (LD) motifs by the focal adhesion targeting-homology domain of cerebral cavernous malformation 3 (CCM3)" J. Biol. Chem. 286: 26138-26147
Xue Y., Lee S., and Ha Y. (2011) "Crystal structure of amyloid precursor-like protein 1 and heparin complex suggests a dual role of heparin in E2 dimerization" Proc. Natl. Acad. Sci. U.S.A. 108: 16229-16234
Benbow J.H., DeGray B., and Ehrlich B.E. (2011) "Protection of Neuronal Calcium Sensor 1 Protein in Cells Treated with Paclitaxel" J. Biol. Chem. 288: 34575-34582
Pirruccello M., Swan L. E., Folta-Stogniew E., and De Camilli P. (2011) "Recognition of the F&H motif by the Lowe syndrome protein OCRL" Nat. Struct. Mol. Biol. 18: 789-795 (also light scattering data)
Raycroft M.T., Harvey B.P., Bruck M.J., and Mamula M.J. (2012) "Inhibition of Antigen Trafficking through Scavenger Receptor A"  J. Biol. Chem. 287: 5310-5316

MALDIMS/TOF open access

Mahajan MC, Narlikar GJ, Boyapaty G, Kingston RE, Weissman SM (2005) “Heterogeneous nuclear ribonucleoprotein C1/C2, MeCP1, and SWI/SNF form a chromatin remodeling complex at the beta-globin locus control region” Proc. Natl. Acad. Sci. U.S.A . 102: 15012-15017