Home SVEDBERG DCDT+ Download Useful Links Installation Help

Return to DCDT+ description | List of users

Below is a partial list of publications in which DCDT+ has been used (243 known), in reverse order by year. If you know of others, please send the citation to John Philo.

2014

Khalil, S., Jaworski, I., and Pawelek, P. D. (2014). Identification of a surface glutamine residue (Q64) of Escherichia coli EntA required for interaction with EntE. Biochem. Biophys. Res. Commun. [Epub ahead of print]

Reilly, S. M., Lyons, D. F., Wingate, S. E., Wright, R. T., Correia, J. J., Jameson, D. M., and Wadkins, R. M. (2014). Folding and Hydrodynamics of a DNA i-Motif from the c-MYC Promoter Determined by Fluorescent Cytidine Analogs. Biophys. J 107, 1703-1711. [Abstract]

Holley, A., Parsons, K., Wan, W., Lyons, D., Bishop, R., Correia, J., Huang, F., and McCormick, C. (2014) Block ionomer complexes consisting of siRNA and aRAFT-synthesized hydrophilic-block-cationic copolymers: The influence of cationic block length on gene suppression. Polymer Chem., epub ahead of print [Abstract]

Higgins, C. D., Malashkevich, V. N., Almo, S. C., and Lai, J. R. (2014). Influence of a heptad repeat stutter on the pH-dependent conformational behavior of the central coiled-coil from influenza hemagglutinin HA2. Proteins, April 21 2014, epub ahead of print [Abstract]

Lyons, D. F., Le, V., Kramer, W. H., Bidwell, G. L., III, Lewis, E. A., Raucher, D., and Correia, J. J. (2014). Effect of basic cell-penetrating peptides on the structural, thermodynamic, and hydrodynamic properties of a novel drug delivery vector, ELP[V5G3A2-150]. Biochemistry 53, 1081-1091. [Abstract]

Padlan, C. S., Malashkevich, V. N., Almo, S. C., Levy, M., Brenowitz, M., and Girvin, M. E. (2014). An RNA aptamer possessing a novel monovalent cation-mediated fold inhibits lysozyme catalysis by inhibiting the binding of long natural substrates. RNA 20, 447-461.  [Free PDF]

Driggers, C. M., Dayal, P. V., Ellis, H. R., and Karplus, P. A. (2014). Crystal structure of Escherichia coli SsuE: Defining a General Catalytic Cycle for FMN reductases of the Flavodoxin-like Superfamily. Biochemistry, epub before print DOI: 10.1021/bi500314f [Free PDF]

Mitra, S. (2014). Detecting RNA Tertiary Folding by Sedimentation Velocity Analytical Ultracentrifugation. In: RNA folding. (Methods in Molecular Biology vol. 1086). C.Waldsich, ed. Humana Press, pp. 265-288. [Abstract]

2013

Ramagopal, U. A., Dulyaninova, N. G., Varney, K. M., Wilder, P. T., Nallamsetty, S., Brenowitz, M., Weber, D. J., Almo, S. C., and Bresnick, A. R. (2013). Structure of the S100A4/myosin-IIA complex. BMC Struct. Biol. 13, 31. [Free full text]

Winnen, B., Anderson, E., Cole, J. L., King, G. F., and Rowland, S. L. (2013). Role of the PAS sensor domains in the Bacillus subtilis sporulation kinase KinA. J. Bacteriol. 195, 2349-2358. [Free PDF]

Zhao, C., Bachu, R., Popovic, M., Devany, M., Brenowitz, M., Schlatterer, J. C., and Greenbaum, N. L. (2013). Conformational heterogeneity of the protein-free human spliceosomal U2-U6 snRNA complex. RNA 19, 561-573. [Abstract]

Connaghan, K. D., Miura, M. T., Maluf, N. K., Lambert, J. R., and Bain, D. L. (2013). Analysis of a glucocorticoid-estrogen receptor chimera reveals that dimerization energetics are under ionic control. Biophys. Chem. 172, 8-17. [Abstract]

Acar, S., Carlson, D. B., Budamagunta, M. S., Yarov-Yarovoy, V., Correia, J. J., Ninonuevo, M. R., Jia, W., Tao, L., Leary, J. A., Voss, J. C., Evans, J. E., and Scholey, J. M. (2013). The bipolar assembly domain of the mitotic motor kinesin-5. Nat. Commun. 4, 1343. [free full text]

Chen, C., Mitra, S., Jonikas, M., Martin, J., Brenowitz, M., and Laederach, A. (2013). Understanding the Role of Three-Dimensional Topology in Determining the Folding Intermediates of Group I Introns. Biophys. J 104, 1326-1337. [Abstract]

Ho, M. C., Wilczek, C., Bonanno, J. B., Xing, L., Seznec, J., Matsui, T., Carter, L. G., Onikubo, T., Kumar, P. R., Chan, M. K., Brenowitz, M., Cheng, R. H., Reimer, U., Almo, S. C., and Shechter, D. (2013). Structure of the Arginine Methyltransferase PRMT5-MEP50 Reveals a Mechanism for Substrate Specificity. PLoS ONE 8, e57008. [free full text]

2012

Samara, N. L., Ringel, A. E., and Wolberger, C. (2012). A role for intersubunit interactions in maintaining SAGA deubiquitinating module structure and activity. Structure 20, 1414-1424.  [free full text]

Kumar, A., Paslay, L. C., Lyons, D., Morgan, S. E., Correia, J. J., and Rangachari, V. (2012). Specific soluble oligomers of amyloid-beta peptide undergo replication and form non-fibrillar aggregates in interfacial environments. J. Biol Chem. 287, 21253-21264. [free PDF]

Husain, B., Mukerji, I., and Cole, J. L. (2012). Analysis of high-affinity binding of protein kinase R to double-stranded RNA. Biochemistry 51, 8764-8770. [Abstract]

Wostenberg, C., Lary, J. W., Sahu, D., Acevedo, R., Quarles, K. A., Cole, J. L., and Showalter, S. A. (2012). The role of human Dicer-dsRBD in processing small regulatory RNAs. PLoS One 7, e51829 [free full text]

Robblee, J. P., Miura, M. T., and Bain, D. L. (2012). Glucocorticoid receptor-promoter interactions: energetic dissection suggests a framework for the specificity of steroid receptor-mediated gene regulation. Biochemistry 51, 4463-4472. [Abstract]

Vinther, T. N., Norrman, M., Strauss, H. M., Huus, K., Schlein, M., Pedersen, T. A., Kjeldsen, T., Jensen, K. J., and Hubalek, F. (2012). Novel covalently linked insulin dimer engineered to investigate the function of insulin dimerization. PLoS One 7, e30882. [free PDF]

Neumann, H. and Chin, J. (2012). Acetyl lysine incorporation with tRNA synthetase. US Patent Application # 20120190825. [free PDF]

O'Neill, M. J., Bhakta, M. N., Fleming, K. N., and Wilks, A. (2012). Induced fit on heme binding to the Pseudomonas aeruginosa cytoplasmic protein (PhuS) drives interaction with heme oxygenase (HemO). Proc. Natl. Acad. Sci. USA, epub ahead of print [free PDF]

Gokarn, Y. R., McLean, M., and Laue, T. M. (2012). Effect of PEGylation on protein hydrodynamics. Mol Pharm., epub ahead of print [Abstract]

2011

Anderson, E., Pierre-Louis, W. S., Wong, C. J., Lary, J. W., and Cole, J. L. (2011). Heparin activates PKR by inducing dimerization. J. Mol. Biol. 413, 973-984. [Abstract]

Dignam, J. D., Guo, J., Griffith, W. P., Garbett, N. C., Holloway, A., and Mueser, T. (2011). Allosteric interaction of nucleotides and tRNA(ala) with E. coli alanyl-tRNA synthetase. Biochemistry 50, 9886-9900. [Abstract]

Krementsova, E. B., Hodges, A. R., Bookwalter, C. S., Sladewski, T. E., Travaglia, M., Sweeney, H. L., and Trybus, K. M. (2011). Two single-headed myosin V motors bound to a tetrameric adapter protein form a processive complex. J. Cell Biol. 195, 631-641. [Abstract]

Ando, N., Brignole, E. J., Zimanyi, C. M., Funk, M. A., Yokoyama, K., Asturias, F. J., Stubbe, J., and Drennan, C. L. (2011). Structural interconversions modulate activity of Escherichia coli ribonucleotide reductase. Proc. Natl. Acad. Sci. USA 108, 21046-21051. [Abstract]

Danoff, E. J. and Fleming, K. G. (2011). The soluble, periplasmic domain of OmpA folds as an independent unit and displays chaperone activity by reducing the self-association propensity of the unfolded OmpA transmembrane beta-barrel. Biophys. Chem. 159, 194-204. [Abstract]

Mitra, S., Laederach, A., Golden, B. L., Altman, R. B., and Brenowitz, M. (2011). RNA molecules with conserved catalytic cores but variable peripheries fold along unique energetically optimized pathways. RNA 17, 1589-1603. [Abstract]

Wong, C. J., Launer-Felty, K., and Cole, J. L. (2011). Analysis of PKR-RNA interactions by sedimentation velocity. Methods Enzymol. 488, 59-79. [PDF]

Firer-Sherwood, M. A., Ando, N., Drennan, C. L., and Elliott, S. J. (2011) Solution-based Structural Analysis of the Decaheme Cytochrome, MtrA, by Small Angle X-Ray Scattering and Analytical Ultracentrifugation. J. Phys. Chem. B. 115, 11208-11214. [Abstract]

Philo, J. S. (2011). Limiting the sedimentation coefficient for sedimentation velocity data analysis: Partial boundary modeling and g(s*) approaches revisited. Anal. Biochem. 412, 189-202. [PDF]

2010

Stahl, S. J., Watts, N. R., Rader, C., DiMattia, M. A., Mage, R. G., Palmer, I., Kaufman, J. D., Grimes, J. M., Stuart, D. I., Steven, A. C., and Wingfield, P. T. (2010). Generation and characterization of a chimeric rabbit/human Fab for co-crystallization of HIV-1 Rev J. Mol. Biol. 397, 697-708. [Full text]

Galloway, C. A., Kumar, A., Krucinska, J., and Smith, H. C. (2010). APOBEC-1 complementation factor (ACF) forms RNA-dependent multimers. Biochem. Biophys. Res. Commun. 398, 38-43. [Abstract]

Saluja, A., Fesinmeyer, R. M., Hogan, S., Brems, D. N., and Gokarn, Y. R. (2010). Diffusion and sedimentation interaction parameters for measuring the second virial coefficient and their utility as predictors of protein aggregation. Biophys. J 99, 2657-2665. [Full text]

Dailey, M. M., Miller, M. C., Bates, P. J., Lane, A. N., and Trent, J. O. (2010). Resolution and characterization of the structural polymorphism of a single quadruplex-forming sequence. Nucleic Acids Res. 38, 4877-4888. [Full text]

Updegrove, T. B., Correia, J. J., Chen, Y., Terry, C., and Wartell, R. M. (2011). The stoichiometry of the Escherichia coli Hfq protein bound to RNA. RNA 17, 489-500. [Abstract]

Garbett, N. C., Mekmaysy, C. S., and Chaires, J. B. (2010). Sedimentation velocity ultracentrifugation analysis for hydrodynamic characterization of G-quadruplex structures. Methods Mol. Biol. 608, 97-120. [PDF]

Rass, U., Compton, S. A., Matos, J., Singleton, M. R., Ip, S. C., Blanco, M. G., Griffith, J. D., and West, S. C. (2010). Mechanism of Holliday junction resolution by the human GEN1 protein. Genes Dev. 24, 1559-1569. [Abstract]

Launer-Felty, K., Wong, C. J., Wahid, A. M., Conn, G. L., and Cole, J. L. (2010). Magnesium-dependent interaction of PKR with adenovirus VAI. J Mol Biol 402, 638-644. [Abstract]

Updegrove, T. B., Correia, J. J., Galletto, R., Bujalowski, W., and Wartell, R. M. (2010). E. coli DNA associated with isolated Hfq interacts with Hfq's distal surface and C-terminal domain. Biochim. Biophys. Acta 1799, 588-596. [Abstract]

Ebie Tan, A., Burgess, N. K., DeAndrade, D. S., Marold, J. D., and Fleming, K. G. (2010). Self-association of unfolded outer membrane proteins. Macromol. Biosci. 10, 763-767. [Abstract]

May, C. A., Grady, J. K., Laue, T. M., Poli, M., Arosio, P., and Chasteen, N. D. (2010). The sedimentation properties of ferritins. New insights and analysis of methods of nanoparticle preparation. Biochim. Biophys. Acta 1800, 858-870. [Abstract]

Paul, D., O'Leary, S. E., Rajashankar, K., Bu, W., Toms, A., Settembre, E. C., Sanders, J. M., Begley, T. P., and Ealick, S. E. (2010). Glycal formation in crystals of uridine phosphorylase. Biochemistry 49, 3499-3509. [Abstract]

Anderson, E., Quartararo, C., Brown, R. S., Shi, Y., Yao, X., and Cole, J. L. (2010). Analysis of monomeric and dimeric phosphorylated forms of protein kinase R. Biochemistry 49, 1217-1225. [Abstract]

Edwards, A. A., Tipton, J. D., Brenowitz, M. D., Emmett, M. R., Marshall, A. G., Evans, G. B., Tyler, P. C., and Schramm, V. L. (2010). Conformational states of human purine nucleoside phosphorylase at rest, at work, and with transition state analogues. Biochemistry 49, 2058-2067. [Abstract]

Kapinos, L. E., Schumacher, J., Mucke, N., Machaidze, G., Burkhard, P., Aebi, U., Strelkov, S. V., and Herrmann, H. (2010). Characterization of the head-to-tail overlap complexes formed by human lamin A, B1 and B2 ''half-minilamin'' dimers. J. Mol. Biol. 396, 719-731. [Abstract]

2009

Rosenfeld, S. S., van, D. M., Behnke-Parks, W. M., Beadle, C., Corrreia, J., and Xing, J. (2009). The ATPase cycle of the mitotic motor CENP-E. J Biol Chem. 284, 32858-32868. [Abstract]

Heinz, D. and Niemann, H. (2009). Inhibitor of the met-receptor and its use. EU patent patent application # EP2019116A1.

McCulloch, K. M., Mukherjee, T., Begley, T. P., and Ealick, S. E. (2009). Structure of the PLP degradative enzyme 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase from Mesorhizobium loti MAFF303099 and its mechanistic implications. Biochemistry 48, 4139-4149. [Abstract]

Alday, P. H. and Correia, J. J. (2009). Macromolecular interaction of halichondrin B analogues eribulin (E7389) and ER-076349 with tubulin by analytical ultracentrifugation. Biochemistry 48, 7927-7938. [Abstract]

Heinicke, L. A., Wong, C. J., Lary, J., Nallagatla, S. R., egelman-Parente, A., Zheng, X., Cole, J. L., and Bevilacqua, P. C. (2009). RNA dimerization promotes PKR dimerization and activation. J. Mol. Biol. 390, 319-338. [Abstract]

Root, B. C., Pellegrino, L. D., Crawford, E. D., Kokona, B., and Fairman, R. (2009). Design of a heterotetrameric coiled coil. Protein Sci. 18, 329-336. [Abstract]

Correia, J. J. and Stafford, W. F. (2009). Extracting equilibrium constants from kinetically limited reacting systems. Methods Enzymol. 455, 419-446. [PDF]

Turner, G. J., Chittiboyina, S., Pohren, L., Hines, K. G., Correia, J. J., and Mitchell, D. C. (2009). The bacteriorhodopsin carboxyl-terminus contributes to proton recruitment and protein stability. Biochemistry 48, 1112-1122. [PDF]

de Carvalho, L. P., Frantom, P. A., Argyrou, A., and Blanchard, J. S. (2009). Kinetic evidence for interdomain communication in the allosteric regulation of alpha-isopropylmalate synthase from Mycobacterium tuberculosis. Biochemistry 48, 1996-2004. [Abstract]

Pimentel, T. A., Yan, Z., Jeffers, S. A., Holmes, K. V., Hodges, R. S., and Burkhard, P. (2009). Peptide nanoparticles as novel immunogens: design and analysis of a prototypic severe acute respiratory syndrome vaccine. Chem. Biol. Drug Des. 73, 53-61. [Abstract]

Bonner, A., Almogren, A., Furtado, P. B., Kerr, M. A., and Perkins, S. J. (2009). The nonplanar secretory IgA2 and near-planar secretory IgA1 solution structures rationalize their different mucosal immune responses. J. Biol. Chem. 284, 5077-5087. [Abstract]

Kroe, R. R. and Laue, T. M. (2009). NUTS and BOLTS: Applications of fluorescence-detected sedimentation. Anal. Biochem. 390, 1-13.

2008

Robertson, P. D., Warren, E. M., Zhang, H., Friedman, D. B., Lary, J. W., Cole, J. L., Tutter, A. V., Walter, J. C., Fanning, E., and Eichman, B. F. (2008). Domain architecture and biochemical characterization of vertebrate Mcm10. J. Biol. Chem. 283, 3338-3348. [PDF]

Lu, Y., Harding, S. E., Rowe, A. J., Davis, K. G., Fish, B., Varley, P., Gee, C., and Mulot, S. (2008). The effect of a point mutation on the stability of IgG4 as monitored by analytical ultracentrifugation. J. Pharm. Sci. 97, 960-969. [Abstract]

Chen, W., Lam, S. S., Srinath, H., Jiang, Z., Correia, J. J., Schiffer, C. A., Fitzgerald, K. A., Lin, K., and Royer, W. E., Jr. (2008). Insights into interferon regulatory factor activation from the crystal structure of dimeric IRF5. Nat. Struct. Mol. Biol. 15, 1213-1220. [Abstract]

Hiromasa, Y., Yan, X., and Roche, T. E. (2008). Specific ion influences on self-association of pyruvate dehydrogenase kinase isoform 2 (PDHK2), binding of PDHK2 to the L2 lipoyl domain, and effects of the lipoyl group-binding site inhibitor, Nov3r. Biochemistry 47, 2312-2324. [Abstract]

Hodges, A. R., Krementsova, E. B., and Trybus, K. M. (2008). She3p binds to the rod of yeast myosin V and prevents it from dimerizing, forming a single-headed motor complex. J. Biol. Chem. 283, 6906-6914. [PDF]

Kingsbury, J. S., Laue, T. M., Klimtchuk, E. S., Theberge, R., Costello, C. E., and Connors, L. H. (2008). The modulation of transthyretin tetramer stability by cysteine 10 adducts and the drug diflunisal. Direct analysis by fluorescence-detected analytical ultracentrifugation. J. Biol. Chem. 283, 11887-11896. [PDF]

Shen, K., Sergeant, S., Hantgan, R. R., McPhail, L. C., and Horita, D. A. (2008). Mutations in the PX-SH3(A) linker of p47(Phox) decouple PI(3,4)P-2 binding from NADPH oxidase activation. Biochemistry 47, 8855-8865. [Abstract]

Egea, P. F., Tsuruta, H., de Leon, G. P., Napetschnig, J., Walter, P., and Stroud, R. M. (2008). Structures of the signal recognition particle receptor from the Archaeon Pyrococcus furiosus: Implications for the targeting step at the membrane. PLoS ONE 3, e3619 [PDF]

Info, S., Thoresen, T., and Gelles, J. (2008). Processive movement by a kinesin heterodimer with an inactivating mutation in one head. Biochemistry 47, 9514-9521. [Abstract]

Lemaire, P. A., Anderson, E., Lary, J., and Cole, J. L. (2008). Mechanism of PKR Activation by dsRNA. J Mol Biol 381, 351-360. [Abstract]

Houmeida, A., Baron, A., Keen, J., Khan, G. N., Knight, P. J., Stafford, W. F., Thirumurugan, K., Thompson, B., Tskhovrebova, L., and Trinick, J. (2008). Evidence for the oligomeric state of 'elastic' titin in muscle sarcomeres. J. Mol. Biol. 384, 299-312. [Abstract]

Robinson, P. J. J., An, W., Routh, A., Martino, F., Chapman, L., Roeder, R. G., and Rhodes, D. (2008). 30 nm chromatin fibre decompaction requires both H4-K16 acetylation and linker histone eviction. J. Mol. Biol. 381, 816-825. [Abstract]

Wu, X., Oppermann, M., Berndt, K. D., Bergman, T., Jörnvall, H., Knapp, S., and Oppermann, U. (2008). Thermal unfolding of the archaeal DNA and RNA binding protein Ssh10. Biochem. Biophys. Res. Commun. 373, 482-487. [Abstract]

Kokona, B., Rigotti, D. J., Wasson, A. S., Lawrence, S. H., Jaffe, E. K., and Fairman, R. (2008). Probing the oligomeric assemblies of pea porphobilinogen synthase by analytical ultracentrifugation. Biochemistry 47, 10649-10656. [Abstract]

Routh, A., Sandin, S., and Rhodes, D. (2008). Nucleosome repeat length and linker histone stoichiometry determine chromatin fiber structure. Proc Natl Acad Sci USA 105, 8872-8877. [full text]

Azarov, I., He, X., Jeffers, A., Basu, S., Ucer, B., Hantgan, R. R., Levy, A., and Kim-Shapiro, D. B. (2008). Rate of nitric oxide scavenging by hemoglobin bound to haptoglobin. Nitric Oxide - Biology and Chemistry 18, 296-302. [Abstract]

Malashkevich, V. N., Varney, K. M., Garrett, S. C., Wilder, P. T., Knight, D., Charpentier, T. H., Ramagopal, U. A., Almo, S. C., Weber, D. J., and Bresnick, A. R. (2008). Structure of Ca2+-bound S100A4 and its interaction with peptides derived from nonmuscle myosin-IIA. Biochemistry 47, 5111-5126. [Abstract]

Anderson, E. and Cole, J. L. (2008). Domain stabilities in protein kinase R (PKR): evidence for weak interdomain interactions. Biochemistry 47, 4887-4897. [Abstract]

Das, R., Loss, S., Li, J., Waugh, D. S., Tarasov, S., Wingfield, P. T., Byrd, R. A., and Altieri, A. S. (2008). Structural biophysics of the NusB:NusE antitermination complex. J. Mol. Biol. 376, 705-720. [Abstract]

Chen, K. M., Harjes, E., Gross, P. J., Fahmy, A., Lu, Y., Shindo, K., Harris, R. S., and Matsuo, H. (2008). Structure of the DNA deaminase domain of the HIV-1 restriction factor APOBEC3G. Nature 452, 116-119. [Abstract]

Cole, J. L., Lary, J. W., Moody, P., and Laue, T. M. (2008). Analytical ultracentrifugation: sedimentation velocity and sedimentation equilibrium. Methods Cell Biol. 84, 143-179. [Abstract]

Kitamura, A., Jardine, P. J., Anderson, D. L., Grimes, S., and Matsuo, H. (2008). Analysis of intermolecular base pair formation of prohead RNA of the phage phi29 DNA packaging motor using NMR spectroscopy. Nucleic Acids Res. 36, 839-848. [Abstract]

Furtado, P. B., Huang, C. Y., Ihyembe, D., Hammond, R. A., Marsh, H. C., and Perkins, S. J. (2008). The partly folded back solution structure arrangement of the 30 SCR domains in human complement receptor type 1 (CR1) permits access to its C3b and C4b ligands. J. Mol. Biol. 375, 102-118. [Abstract]

Okemefuna, A. I., Gilbert, H. E., Griggs, K. M., Ormsby, R. J., Gordon, D. L., and Perkins, S. J. (2008). The regulatory SCR-1/5 and cell surface-binding SCR-16/20 fragments of factor H reveal partially folded-back solution structures and different self-associative properties. J. Mol. Biol. 375, 80-101. [Abstract]

back to top

2007

Burton, R. A., Tsurupa, G., Hantgan, R. R., Tjandra, N., and Medved, L. (2007). NMR solution structure, stability, and interaction of the recombinant bovine fibrinogen alphaC-domain fragment. Biochemistry 46, 8550-8560. [Abstract]

Niemann, H. H., Jager, V., Butler, P. J., van den, H. J., Schmidt, S., Ferraris, D., Gherardi, E., and Heinz, D. W. (2007). Structure of the human receptor tyrosine kinase met in complex with the Listeria invasion protein InlB. Cell 130, 235-246. [Abstract]

Spano, A. J., Chen, F. S., Goodman, B. E., Sabat, A. E., Simon, M. N., Wall, J. S., Correia, J. J., McIvor, W., Newcomb, W. W., Brown, J. C., Schnur, J. M., and Lebedev, N. (2007). In vitro assembly of a prohead-like structure of the Rhodobacter capsulatus gene transfer agent. Virology 364, 95-102. [Abstract]

Bosch, M., Le, K. H., Bugyi, B., Correia, J. J., Renault, L., and Carlier, M. F. (2007). Analysis of the function of Spire in actin assembly and its synergy with formin and profilin. Molecular Cell 28, 555-568. [Abstract]

Bonner, A., Perrier, C., Corthesy, B., and Perkins, S. J. (2007). Solution structure of human secretory component and implications for biological function. J. Biol. Chem. 282, 16969-16980. [abstract]

Cao, E., Zang, X., Ramagopal, U. A., Mukhopadhaya, A., Fedorov, A., Fedorov, E., Zencheck, W. D., Lary, J. W., Cole, J. L., Deng, H., Xiao, H., Dilorenzo, T. P., Allison, J. P., Nathenson, S. G., and Almo, S. C. (2007). T cell immunoglobulin mucin-3 crystal structure reveals a galectin-9-independent ligand-binding surface. Immunity. 26, 311-321. [full text]

Holmes, O., Pillozzi, S., Deakin, J. A., Carafoli, F., Kemp, L., Butler, P. J., Lyon, M., and Gherardi, E. (2007). Insights into the structure/function of hepatocyte growth factor/scatter factor from studies with individual domains. J. Mol. Biol. 367, 395-408. [Abstract]

Ramsey, J. E., Daugherty, M. A., and Kelm, R. J., Jr. (2007). Hydrodynamic studies on the quaternary structure of recombinant mouse Purβ. J. Biol. Chem. 282, 1552-1560. [Full text]

Morris, N. P., Peters, C., Montler, R., Hu, H. M., Curti, B. D., Urba, W. J., and Weinberg, A. D. (2007). Development and characterization of recombinant human Fc:OX40L fusion protein linked via a coiled-coil trimerization domain. Mol. Immunol. 44, 3112-3121. [Abstract]

Ross, N. T., Mace, C. R., and Miller, B. L. (2007). Biophysical analysis of the EPEC translocated intimin receptor-binding domain. Biochem. Biophys. Res. Commun. 362, 1073-1078. [Abstract]

Kang, Y., Chen, X., Lary, J. W., Cole, J. L., and Walters, K. J. (2007). Defining how ubiquitin receptors hHR23a and S5a bind polyubiquitin. J. Mol. Biol. 369, 168-176. [Abstract]

Daumke, O., Lundmark, R., Vallis, Y., Martens, S., Butler, P. J., and McMahon, H. T. (2007). Architectural and mechanistic insights into an EHD ATPase involved in membrane remodelling. Nature 449, 923-927. [Abstract]

Yan, Q., Malashkevich, V. N., Fedorov, A., Fedorov, E., Cao, E., Lary, J. W., Cole, J. L., Nathenson, S. G., and Almo, S. C. (2007). Structure of CD84 provides insight into SLAM family function. Proc. Natl. Acad. Sci. U. S. A 104, 10583-10588. [PDF]

Schwarz-Romond, T., Fiedler, M., Shibata, N., Butler, P. J., Kikuchi, A., Higuchi, Y., and Bienz, M. (2007). The DIX domain of Dishevelled confers Wnt signaling by dynamic polymerization. Nat. Struct. Mol. Biol. 14, 484-492. [Abstract]

White, S. R., Evans, K. J., Lary, J., Cole, J. L., and Lauring, B. (2007). Recognition of C-terminal amino acids in tubulin by pore loops in Spastin is important for microtubule severing. J. Cell Biol. 176, 995-1005. [Abstract]

Fernando, A. N., Furtado, P. B., Clark, S. J., Gilbert, H. E., Day, A. J., Sim, R. B., and Perkins, S. J. (2007). Associative and structural properties of the region of complement factor H encompassing the Tyr402His disease- related polymorphism and its interactions with heparin. J. Mol. Biol. 368, 564-581. [Abstract]

back to top

2006

Hepler, R. W., Grimm, K. M., Nahas, D. D., Breese, R., Dodson, E. C., Acton, P., Keller, P. M., Yeager, M., Wang, H., Shughrue, P., Kinney, G., and Joyce, J. G. (2006). Solution state characterization of amyloid beta-derived diffusible ligands. Biochemistry 45, 15157-15167. [Abstract]

Maluf, N. K., Gaussier, H., Bogner, E., Feiss, M., and Catalano, C. E. (2006). Assembly of bacteriophage lambda terminase into a viral DNA maturation and packaging machine. Biochemistry 45, 15259-15268. [Abstract]

Salvay, A. G. and Ebel, C. (2006). Analytical ultracentrifuge for the characterization of detergent in solution. Prog. Colloid. Polymer. Sci. 131, 73 [Abstract]

Correia, J. J., Sontag, C. A., Stafford, W. F., III, and Sherwood, P. J. (2006). Models for direct boundary fitting of indefinite ligand-linked self-association. In: Analytical ultracentrifugation: techniques and methods. D. J. Scott, S. E. Harding, and S. M. Rowe, eds. Royal Society of Chemistry, London, pp. 51-63.

Kauth, C. W., Woehlbier, U., Kern, M., Mekonnen, Z., Lutz, R., Mucke, N., Langowski, J., and Bujard, H. (2006). Interactions between merozoite surface proteins 1, 6, and 7 of the malaria parasite Plasmodium falciparum. J. Biol. Chem. 281, 31517-31527. [Full text]

Mok, Y. F. and Howlett, G. J. (2006). Sedimentation velocity analysis of amyloid oligomers and fibrils. Methods Enzymol. 413, 199-217. [Abstract]

Bär, H., Mücke, N., Ringler, P., Müller, S. A., Kreplak, L., Katus, H. A., Aebi, U., and Herrmann, H. (2006). Impact of disease mutations on the desmin filament assembly process. J. Mol. Biol. 360, 1031-1042. [Abstract]

Hantgan, R. R., Stahle, M. C., Connor, J. H., Horita, D. A., Rocco, M., McLane, M. A., Yakovlev, S., and Medved, L. (2006). Integrin αII3:ligand interactions are linked to binding-site remodeling. Protein Sci. 15, 1893-1906. [Abstract]

Cao, E., Ramagopal, U. A., Fedorov, A., Fedorov, E., Yan, Q., Lary, J. W., Cole, J. L., Nathenson, S. G., and Almo, S. C. (2006). NTB-A receptor crystal structure: insights into homophilic interactions in the signaling lymphocytic activation molecule receptor family. Immunity. 25, 559-570. [Abstract]

Eisele, L. E., Chave, K. J., Lehning, A. C., and Ryan, T. J. (2006). Characterization of human gamma-glutamyl hydrolase in solution demonstrates that the enzyme is a non-dissociating homodimer. Biochim. Biophys. Acta 1764, 1479-1486. [Abstract]

Massey, T. H., Mercogliano, C. P., Yates, J., Sherratt, D. J., and Lowe, J. (2006). Double-stranded DNA translocation: structure and mechanism of hexameric FtsK. Mol. Cell 23, 457-469. [Abstract]

Foeger, N., Wiesel, N., Lotsch, D., Mucke, N., Kreplak, L., Aebi, U., Gruenbaum, Y., and Herrmann, H. (2006). Solubility properties and specific assembly pathways of the B-type lamin from Caenorhabditis elegans. J. Struct. Biol. 155, 340-350. [Abstract]

Han, S., Forman, M. D., Loulakis, P., Rosner, M. H., Xie, Z., Wang, H., Danley, D. E., Yuan, W., Schafer, J., and Xu, Z. (2006). Crystal structure of nicotinic acid mononucleotide adenylyltransferase from Staphyloccocus aureus: structural basis for NaAD interaction in functional dimer. J. Mol. Biol. 360, 814-825. [Abstract]

Philo, J. S. (2006). Improved methods for fitting sedimentation coefficient distributions derived by time-derivative techniques. Anal. Biochem. 354, 238-246. [Abstract] [PDF]

Naseem, R., Sturdy, A., Finch, D., Jowitt, T., and Webb, M. (2006). Mapping and conformational characterization of the DNA-binding region of the breast cancer susceptibility protein BRCA1. Biochem. J. 395, 529-535. [Abstract]

Laguri, C., Stenzel, R. A., Donohue, T. J., Phillips-Jones, M. K., and Williamson, M. P. (2006). Activation of the global gene regulator PrrA (RegA) from Rhodobacter sphaeroides. Biochemistry 45, 7872-7881. [Abstract]

Hiromasa, Y., Hu, L., and Roche, T. E. (2006). Ligand-induced effects on pyruvate dehydrogenase kinase isoform 2. J. Biol. Chem. 281, 12568-12579. [Abstract] [PDF]

Rovner, A. S., Fagnant, P. M., and Trybus, K. M. (2006). Phosphorylation of a single head of smooth muscle myosin activates the whole molecule. Biochemistry 45, 5280-5289. [Abstract]

Gilbert, H. E., Aslam, M., Guthridge, J. M., Holers, V. M., and Perkins, S. J. (2006). Extended flexible linker structures in the complement chimaeric conjugate CR2-Ig by scattering, analytical ultracentrifugation and constrained modelling: implications for function and therapy. J. Mol. Biol. 356, 397-412. [Abstract]

Almogren, A., Furtado, P. B., Sun, Z., Perkins, S. J., and Kerr, M. A. (2006). Purification, properties and extended solution structure of the complex formed between human immunoglobulin A1 and human serum albumin by scattering and ultracentrifugation. J. Mol. Biol. 356, 413-431. [Abstract]

Barbier, A., Clement-Collin, V., Dergunov, A. D., Visvikis, A., Siest, G., and Aggerbeck, L. P. (2006). The structure of human apolipoprotein E2, E3 and E4 in solution 1. Tertiary and quaternary structure. Biophys. Chem. 119, 158-169. [Abstract]

Schietke, R., Brohl, D., Wedig, T., Mucke, N., Herrmann, H., and Magin, T. M. (2006). Mutations in vimentin disrupt the cytoskeleton in fibroblasts and delay execution of apoptosis. Eur. J. Cell Biol. 85, 1-10. [Abstract]

back to top

2005

Ikebe, M., Li, X. D., Mabuchi, K., and Ikebe, R. (2005). Conformational change and regulation of myosin molecules. Adv. Exp. Med. Biol. 565, 61-72. [Abstract]

Masters, E. I., Pratt, G., Forster, A., and Hill, C. P. (2005). Purification and analysis of recombinant 11S activators of the 20S proteasome: Trypanosoma brucei PA26 and human PA28 alpha, PA28 beta, and PA28 gamma. Methods Enzymol. 398, 306-321. [Abstract]

Cristiani, C., Rusconi, L., Perego, R., Schiering, N., Kalisz, H. M., Knapp, S., and Isacchi, A. (2005). Regulation of the wild-type and Y1235D mutant Met kinase activation. Biochemistry 44, 14110-14119. [Abstract]

English, C. M., Maluf, N. K., Tripet, B., Churchill, M. E., and Tyler, J. K. (2005). ASF1 binds to a heterodimer of histones H3 and H4: a two-step mechanism for the assembly of the H3-H4 heterotetramer on DNA. Biochemistry 44, 13673-13682. [Abstract]

Bär, H., Mucke, N., Kostareva, A., Sjoberg, G., Aebi, U., and Herrmann, H. (2005). Severe muscle disease-causing desmin mutations interfere with in vitro filament assembly at distinct stages. Proc. Natl. Acad. Sci. U. S. A. 102, 15099-15104. [PDF]

Sun, Z., Almogren, A., Furtado, P. B., Chowdhury, B., Kerr, M. A., and Perkins, S. J. (2005). Semi-extended solution structure of human myeloma immunoglobulin D determined by constrained X-ray scattering. J. Mol. Biol. 353, 155-173. [Abstract]

Heneghan, A. F., Berton, N., Miura, M. T., and Bain, D. L. (2005). Self-association energetics of an intact, full-length nuclear receptor: The B-isoform of human progesterone receptor dimerizes in the micromolar range. Biochemistry 44, 9528-9537. [Abstract]

Ignjatovic, T., Yang, J. C., Butler, J., Neuhaus, D., and Nagai, K. (2005). Structural basis of the interaction between P-element somatic inhibitor and U1-70k essential for the alternative splicing of P-element transposase. J. Mol. Biol. 351, 52-65. [Abstract]

Forster, A., Masters, E. I., Whitby, F. G., Robinson, H., and Hill, C. P. (2005). The 1.9 A structure of a proteasome-11S activator complex and implications for proteasome-PAN/PA700 interactions. Mol. Cell 18, 589-599. [Abstract]

Harding, S. E. (2005). Challenges for the modern analytical ultracentrifuge analysis of polysaccharides. Carbohydr. Res. 340, 811-826. [Abstract]

Foss, T. R., Kelker, M. S., Wiseman, R. L., Wilson, I. A., and Kelly, J. W. (2005). Kinetic stabilization of the native state by protein engineering: implications for inhibition of transthyretin amyloidogenesis. J. Mol. Biol. 347, 841-854. [Abstract]

Hunter, D. J., Roberts, G. A., Ost, T. W., White, J. H., Muller, S., Turner, N. J., Flitsch, S. L., and Chapman, S. K. (2005). Analysis of the domain properties of the novel cytochrome P450 RhF. FEBS Lett. 579, 2215-2220. [Abstract]

Hu, Y. L., Sun, Z., Eaton, J. T., Bouloux, P. M. G., and Perkins, S. J. (2005). Extended and flexible domain solution structure of the extracellular matrix protein Anosmin-1 by X-ray scattering, analytical ultracentrifugation and constrained modelling. J. Mol. Biol. 350, 553-570. [Abstract]

Schneeweis, L. A., Willard, D., and Milla, M. E. (2005). Functional dissection of osteoprotegerin and its interaction with receptor activator of NF-kappaB ligand. J. Biol. Chem. 280, 41155-41164. [PDF]

Dennis, C. A., Baron, A. J., Grossmann, J. G., Mazaleyrat, S., Harris, M., and Jaeger, J. (2005). Co-translational myristoylation alters the quaternary structure of HIV-1 Nef in solution. Proteins 60, 658-669. [Abstract]

Philo, J.S. (2005). Analytical ultracentrifugation. In: Methods for Structural Analysis of Protein Pharmaceuticals. W. Jiskoot and D. Crommelin, eds. AAPS Press, pp. 379-412.

Kepert, J. F., Mazurkiewicz, J., Heuvelman, G. L., Toth, K. F., and Rippe, K. (2005). NAP1 modulates binding of linker histone H1 to chromatin and induces an extended chromatin fiber conformation. J. Biol. Chem. 280, 34063-34072. [PDF]

Carmelo, E., Barilla, D., Golovanov, A. P., Lian, L. Y., Derome, A., and Hayes, F. (2005). The unstructured N-terminal tail of ParG modulates assembly of a quaternary nucleoprotein complex in transcription repression. J. Biol. Chem. 280, 28683-28691. [PDF]

Ivancic, M., Spuches, A. M., Guth, E. C., Daugherty, M. A., Wilcox, D. E., and Lyons, B. A. (2005). Backbone nuclear relaxation characteristics and calorimetric investigation of the human Grb7-SH2/erbB2 peptide complex. Protein Sci. 14, 1556-1569. [PDF]

Liou, G. G., Tanny, J. C., Kruger, R. G., Walz, T., and Moazed, D. (2005). Assembly of the SIR complex and its regulation by O-acetyl-ADP-ribose, a product of NAD-dependent histone deacetylation. Cell 121, 515-527. [PDF]

Fothergill, T. J., Barilla, D., and Hayes, F. (2005). Protein diversity confers specificity in plasmid segregation. J. Bacteriol. 187, 2651-2661. [PDF]

Leonard, T. A., Butler, P. J., and Lowe, J. (2005). Bacterial chromosome segregation: structure and DNA binding of the Soj dimer--a conserved biological switch. EMBO J. 24, 270-282. [Abstract] [free full text]

Maluf, N. K., Yang, Q., and Catalano, C. E. (2005). Self-association properties of the bacteriophage lambda terminase holoenzyme: Implications for the DNA packaging motor. J. Mol. Biol. 347, 523-542. [Abstract]

Wickert, U., Mucke, N., Wedig, T., Muller, S. A., Aebi, U., and Herrmann, H. (2005). Characterization of the in vitro co-assembly process of the intermediate filament proteins vimentin and desmin: mixed polymers at all stages of assembly. Eur. J. Cell Biol. 84, 379-391. [Abstract]

Dam, J. and Schuck, P. (2005). Sedimentation velocity analysis of heterogeneous protein-protein interactions: sedimentation coefficient distributions c(s) and asymptotic boundary profiles from Gilbert-Jenkins theory. Biophys. J. 89, 651-666. [Abstract]

Gilbert, H. E., Eaton, J. T., Hannan, J. P., Holers, V. M., and Perkins, S. J. (2005). Solution structure of the complex between CR2 SCR 1-2 and C3d of human complement: an X-ray scattering and sedimentation modelling study. J. Mol. Biol. 346, 859-873. [Abstract]

Platt, G. W., McParland, V. J., Kalverda, A. P., Homans, S. W., and Radford, S. E. (2005). Dynamics in the unfolded state of beta2-microglobulin studied by NMR. J. Mol. Biol. 346, 279-294. [Abstract]

back to top

2004

Tarricone, C., Perrina, F., Monzani, S., Massimiliano, L., Kim, M. H., Derewenda, Z. S., Knapp, S., Tsai, L. H., and Musacchio, A. (2004). Coupling PAF signaling to dynein regulation: structure of LIS1 in complex with PAF-acetylhydrolase. Neuron 44, 809-821. [Abstract]

Malmqvist, U. P., Aronshtam, A., and Lowey, S. (2004). Cardiac myosin isoforms from different species have unique enzymatic and mechanical properties. Biochemistry 43, 15058-15065. [Abstract]

Madern, D., Camacho, M., Rodriguez-Arnedo, A., Bonete, M. J., and Zaccai, G. (2004). Salt-dependent studies of NADP-dependent isocitrate dehydrogenase from the halophilic archaeon Haloferax volcanii. Extremophiles. 8, 377-384. [Abstract]

Brill, L. M., Dechongkit, S., DeLaBarre, B., Stroebel, J., Beachy, R. N., and Yeager, M. (2004). Dimerization of recombinant tobacco mosaic virus movement protein. J. Virol. 78, 3372-3377. [PDF]

Li, X. D., Mabuchi, K., Ikebe, R., and Ikebe, M. (2004). Ca2+-induced activation of ATPase activity of myosin Va is accompanied with a large conformational change. Biochem. Biophys. Res. Commun. 315, 538-545. [Abstract]

Brautigam, C. A., Chelliah, Y., and Deisenhofer, J. (2004). Tetramerization and ATP binding by a protein comprising the A, B, and C domains of rat synapsin I. J. Biol. Chem. 279, 11948-11956. [PDF]

Devred, F., Barbier, P., Douillard, S., Monasterio, O., Andreu, J. M., and Peyrot, V. (2004). Tau induces ring and microtubule formation from alphabeta-tubulin dimers under nonassembly conditions. Biochemistry 43, 10520-10531. [Abstract] [PDF]

Pauleta, S. R., Cooper, A., Nutley, M., Errington, N., Harding, S., Guerlesquin, F., Goodhew, C. F., Moura, I., Moura, J. J., and Pettigrew, G. W. (2004). A copper protein and a cytochrome bind at the same site on bacterial cytochrome c peroxidase. Biochemistry 43, 14566-14576. [Abstract]

Jobstl, E., O'Connell, J., Fairclough, J. P., and Williamson, M. P. (2004). Molecular model for astringency produced by polyphenol/protein interactions. Biomacromolecules. 5, 942-949. [Abstract] [PDF]

Spence, G. R., Capaldi, A. P., and Radford, S. E. (2004). Trapping the on-pathway folding intermediate of Im7 at equilibrium. J. Mol. Biol. 341, 215-226. [Abstract] [PDF]

Irimia, A., Madern, D., Zaccai, G., and Vellieux, F. M. (2004). Methanoarchaeal sulfolactate dehydrogenase: prototype of a new family of NADH-dependent enzymes. EMBO J. 23, 1234-1244. [PDF]

Caryl, J. A., Smith, M. C., and Thomas, C. D. (2004). Reconstitution of a staphylococcal plasmid-protein relaxation complex in vitro. J. Bacteriol. 186, 3374-3383. [PDF]

Sontag, C. A., Stafford, W. F., and Correia, J. J. (2004). A comparison of weight average and direct boundary fitting of sedimentation velocity data for indefinite polymerizing systems. Biophys. Chem. 108, 215-230. [Abstract]

Sturdy, A., Naseem, R., and Webb, M. (2004). Purification and characterisation of a soluble N-terminal fragment of the breast cancer susceptibility protein BRCA1. J. Mol. Biol. 340, 469-475. [Abstract]

Turkan, A., Hiromasa, Y., and Roche, T. E. (2004). Formation of a complex of the catalytic subunit of pyruvate dehydrogenase phosphatase isoform 1 (PDP1c) and the L2 domain forms a Ca2+ binding site and captures PDP1c as a monomer. Biochemistry 43, 15073-15085. [Abstract]

Bao, H., Kasten, S. A., Yan, X., Hiromasa, Y., and Roche, T. E. (2004). Pyruvate dehydrogenase kinase isoform 2 activity stimulated by speeding up the rate of dissociation of ADP. Biochemistry 43, 13442-13451. [Abstract]

Zhang, R. and Somasundaran, P. (2004). Abnormal micellar growth in sugar-based and ethoxylated nonionic surfactants and their mixtures in dilute regimes using analytical ultracentrifugation. Langmuir 20, 8552-8558. [Abstract]

Joel, P. B., Fagnant, P. M., and Trybus, K. M. (2004). Expression of a nonpolymerizable actin mutant in Sf9 cells. Biochemistry 43, 11554-11559. [Abstract]

Herrmann, H. and Aebi, U. (2004). Intermediate filaments: molecular structure, assembly mechanism, and integration into functionally distinct intracellular Scaffolds. Annu. Rev. Biochem. 73, 749-789. [Abstract]

Cochran, J. C., Sontag, C. A., Maliga, Z., Kapoor, T. M., Correia, J. J., and Gilbert, S. P. (2004). Mechanistic analysis of the mitotic kinesin Eg5. J. Biol. Chem. 279, 38861-38870. [PDF]

Hiromasa, Y., Fujisawa, T., Aso, Y., and Roche, T. E. (2004). Organization of the cores of the mammalian pyruvate dehydrogenase complex formed by E2 and E2 plus the E3-binding protein and their capacities to bind the E1 and E3 components. J. Biol. Chem. 279, 6921-6933. [PDF]

Krementsov, D. N., Krementsova, E. B., and Trybus, K. M. (2004). Myosin V: regulation by calcium, calmodulin, and the tail domain. J. Cell Biol. 164, 877-886. [PDF]

Sun, Z., Reid, K. B., and Perkins, S. J. (2004). The dimeric and trimeric solution structures of the multidomain complement protein properdin by X-ray scattering, analytical ultracentrifugation and constrained modelling. J. Mol. Biol. 343, 1327-1343. [Abstract]

Leonard, T. A., Butler, P. J., and Lowe, J. (2004). Structural analysis of the chromosome segregation protein Spo0J from Thermus thermophilus. Mol. Microbiol. 53, 419-432. [Abstract]

Doran, J. D., Liu, X., Taslimi, P., Saadat, A., and Fox, T. (2004) New insights into structure-function relationships of Rho-kinase. A thermodynamic and hydrodynamic study of the dimer to monomer transition and its kinetic implications. Biochem. J. 384, 255-262. [Abstract]

Butler, P.J.G., Ubarretxena-Belandia, I., Warne, T. & Tate, C.G. (2004) The Escherichia coli multidrug transporter EmrE is a dimer in the detergent solubilised state. J. Mol. Biol. 340, 797-808. [Abstract]

Furtado, P. B., Whitty, P. W., Robertson, A., Eaton, J. T., Almogren, A., Kerr, M. A., Woof, J. M., and Perkins, S. J. (2004). Solution structure determination of monomeric human IgA2 by X-ray and neutron scattering, analytical ultracentrifugation and constrained modelling: A comparison with monomeric human IgA1. J. Mol. Biol. 338, 921-941. [Abstract]

Akoev, V., Gogol, E. P., Barnett, M. E., and Zolkiewski, M. (2004). Nucleotide-induced switch in oligomerization of the AAA+ ATPase ClpB. Protein Sci. 13, 567-574. [Abstract]

Mucke, N., Wedig, T., Burer, A., Marekov, L. N., Steinert, P. M., Langowski, J., Aebi, U., and Herrmann, H. (2004). Molecular and biophysical characterization of assembly-starter units of human vimentin. J. Mol. Biol. 340, 97-114. [Abstract] [PDF]

Upadhyay, A., Williams, C., Gill, A. C., Philippe, D. L., Davis, K., Taylor, L. A., Stevens, M. P., Galyov, E. E., and Bagby, S. (2004). Biophysical characterization of the catalytic domain of guanine nucleotide exchange factor BopE from Burkholderia pseudomallei. Biochim. Biophys. Acta 1698, 111-119. [Abstract]

Jiang, S., Jacobs, A., Laue, T. M., and Caffrey, M. (2004). Solution structure of the coxsackievirus and adenovirus receptor domain 1. Biochemistry 43, 1847-1853. [Abstract]

Kunkel, M. and Watowich, S. J. (2004). Biophysical characterization of hepatitis C virus core protein: implications for interactions within the virus and host. FEBS Lett. 557, 174-180. [Abstract]

back to top

2003

Mayor, U., Grossmann, J. G., Foster, N. W., Freund, S. M., and Fersht, A. R. (2003). The denatured state of Engrailed Homeodomain under denaturing and native conditions. J. Mol. Biol. 333, 977-991. [Abstract]

Pettigrew, G. W., Pauleta, S. R., Goodhew, C. F., Cooper, A., Nutley, M., Jumel, K., Harding, S. E., Costa, C., Krippahl, L., Moura, I., and Moura, J. (2003). Electron transfer complexes of cytochrome c peroxidase from Paracoccus denitrificans containing more than one cytochrome. Biochemistry 42, 11968-11981. [Abstract]

Hammarstrom, P., Sekijima, Y., White, J. T., Wiseman, R. L., Lim, A., Costello, C. E., Altland, K., Garzuly, F., Budka, H., and Kelly, J. W. (2003). D18G transthyretin is monomeric, aggregation prone, and not detectable in plasma and cerebrospinal fluid: a prescription for central nervous system amyloidosis? Biochemistry 42, 6656-6663. [Abstract]

Majzoobi, M., Rowe, A. J., Connock, M., Hill, S. E., and Harding, S. E. (2003). Partial fractionation of wheat starch amylose and amylopectin using zonal ultracentrifugation. Carbohydrate Polymers 52, 269-274. [Abstract]

Hokputsa, S., Jumel, K., Alexander, C., and Harding, S. E. (2003). Hydrodynamic characterisation of chemically degraded hyaluronic acid. Carbohydrate Polymers 52, 111-117. [Abstract]

Borges-Walmsley, M. I., Beauchamp, J., Kelly, S. M., Jumel, K., Candlish, D., Harding, S. E., Price, N. C., and Walmsley, A. R. (2003). Identification of oligomerization and drug-binding domains of the membrane fusion protein EmrA. J. Biol. Chem. 278, 12903-12912. [Abstract]

De Marco, V., De Marco, A., Goldie, K. N., Correia, J. J., and Hoenger, A. (2003). Dimerization properties of a Xenopus laevis kinesin-II carboxy-terminal stalk fragment. EMBO Rep. 4, 717-722. [Abstract]

Bailey, S., Sedelnikova, S. E., Mesa, P., Ayora, S., Waltho, J. P., Ashcroft, A. E., Baron, A. J., Alonso, J. C., and Rafferty, J. B. (2003). Structural analysis of Bacillus subtilis SPP1 phage helicase loader protein G39P. J. Biol. Chem. 278, 15304-15312. [PDF]

Timoteo, C. G., Tavares, P., Goodhew, C. F., Duarte, L. C., Jumel, K., Girio, F. M., Harding, S., Pettigrew, G. W., and Moura, I. (2003). Ca2+ and the bacterial peroxidases: the cytochrome c peroxidase from Pseudomonas stutzeri. J. Biol. Inorg. Chem. 8, 29-37. [Abstract]

Miller, D. L. and Schildbach, J. F. (2003). Evidence for a monomeric intermediate in the reversible unfolding of F factor TraM. J. Biol. Chem. 278, 10400-10407. [PDF]

Harding, S. E., Longman, E., Carrasco, B., Ortega, A., and Garcia de la Torre, J. (2003). Studying antibody conformations by ultracentrifugation and hydrodynamic modelling. Methods in Molecular Biology 248, 93-113. [PDF]

Kepert, J. F., Toth, K. F., Caudron, M., Mucke, N., Langowski, J., and Rippe, K. (2003). Conformation of reconstituted mononucleosomes and effect of linker histone H1 binding studied by scanning force microscopy. Biophys. J. 85, 4012-4022. [PDF]

Errington, N. and Rowe, A. J. (2003). Probing conformation and conformational change in proteins is optimally undertaken in relative mode. Eur. Biophys. J. 32, 511-517. [Abstract]

Hiromasa, Y. and Roche, T. E. (2003). Facilitated interaction between the pyruvate dehydrogenase kinase isoform 2 and the dihydrolipoyl acetyltransferase. J. Biol. Chem. 278, 33681-33693. [PDF]

Doyle, S. M., Anderson, E., Zhu, D., Braswell, E. H., and Teschke, C. M. (2003). Rapid unfolding of a domain populates an aggregation-prone intermediate that can be recognized by GroEL. J. Mol. Biol. 332, 937-951. [abstract]

Hokputsa, S., Hu, C., Paulsen, B. S., and Harding, S. E. (2003). A physico-chemical comparative study on extracellular carbohydrate polymers from five desert algae. Carbohydrate Polymers 54, 27-32. [Abstract] [PDF]

Zou, P., Gautel, M., Geerlof, A., Wilmanns, M., Koch, M. H., and Svergun, D. I. (2003). Solution scattering suggests cross-linking function of telethonin in the complex with titin. J. Biol. Chem. 278, 2636-2644. [PDF]

Fee, M., Errington, N., Jumel, K., Illum, L., Smith, A., and Harding, S. E. (2003). Correlation of SEC/MALLS with ultracentrifuge and viscometric data for chitosans. Eur. Biophys. J. 32, 457-464. [Abstract]

Marks, P., McGeehan, J., Wilson, G., Errington, N., and Kneale, G. (2003). Purification and characterisation of a novel DNA methyltransferase, M.AhdI. Nucleic Acids Res. 31, 2803-2810. [PDF]

Idowu, S. M., Gautel, M., Perkins, S. J., and Pfuhl, M. (2003). Structure, stability and dynamics of the central domain of cardiac myosin binding protein C (MyBP-C): Implications for multidomain assembly and causes for cardiomyopathy. J. Mol. Biol. 329, 745-761. [abstract]

Barilla, D. and Hayes, F. (2003). Architecture of the ParF*ParG protein complex involved in prokaryotic DNA segregation. Mol. Microbiol. 49, 487-499. [abstact]

Gherardi, E., Youles, M. E., Miguel, R. N., Blundell, T. L., Iamele, L., Gough, J., Bandyopadhyay, A., Hartmann, G., and Butler, P. J. (2003). Functional map and domain structure of MET, the product of the c-met protooncogene and receptor for hepatocyte growth factor/scatter factor. Proc. Natl. Acad. Sci. U. S. A. 100, 12039-12044. [PDF]

Anderson, E. and Teschke, C. M. (2003). Folding of phage P22 coat protein monomers: kinetic and thermodynamic properties. Virology 313, 184-197. [Abstract]

Perraud, A. L., Shen, B., Dunn, C. A., Rippe, K., Smith, M. K., Bessman, M. J., Stoddard, B. L., and Scharenberg, A. M. (2003). NUDT9, a member of the Nudix hydrolase family, is an evolutionarily conserved mitochondrial ADP-ribose pyrophosphatase. J. Biol. Chem. 278, 1794-1801. [PDF]

Myszka, D. G., Abdiche, Y. N., Arisaka, F., Byron, O., Eisenstein, E., Hensley, P., Thomson, J. A., Lombardo, C. R., Schwarz, F., Stafford, W., and Doyle, M. L. (2003). The ABRF-MIRG'02 study: assembly state, thermodynamic, and kinetic analysis of an enzyme/inhibitor interaction. J. Biomol. Tech. 14, 247-269. [Abstract] [Full Text]

Aslam, M., Guthridge, J. M., Hack, B. K., Quigg, R. J., Holers, V. M., and Perkins, S. J. (2003). The extended multidomain solution structures of the complement protein Crry and its chimeric conjugate Crry-Ig by scattering, analytical ultracentrifugation and constrained modelling: Implications for function and therapy. J. Mol. Biol. 329, 525-550. [Abstract]

Epand, R. M., Braswell, E. H., Yip, C. M., Epand, R. F., and Maekawa, S. (2003). Quaternary structure of the neuronal protein NAP-22 in aqueous solution. Biochim. Biophys. Acta 1650, 50-58. [Abstract]

Irimia, A., Ebel, C., Madern, D., Richard, S. B., Cosenza, L. W., Zaccaï, G., and Vellieux, F. M. D. (2003). The oligomeric states of Haloarcula marismortui malate dehydrogenase are modulated by solvent components as shown by crystallographic and biochemical studies. J. Mol. Biol. 326, 859-873. [Abstract]

Hantgan, R. R., Lyles, D. S., Mallett, T. C., Rocco, M., Nagaswami, C., and Weisel, J. W. (2003). Ligand binding promotes the entropy-driven oligomerization of integrin αIIbβ3. J. Biol. Chem. 278, 3417-3426. [Abstract] [PDF]

back to top

2002

Hofmann, I., Winter, H., Mucke, N., Langowski, J., and Schweizer, J. (2002). The in vitro assembly of hair follicle keratins: comparison of cortex and companion layer keratins. Biol. Chem. 383, 1373-1381. [Abstract]

Morris, G. A., Hromadkova, Z., Ebringerova, A., Malovikova, A., Alfoldi, J., and Harding, S. E. (2002). Modification of pectin with UV-absorbing substitutents and its effect on the structural and hydrodynamic properties of the water-soluble derivatives. Carbohydrate Polymers 48, 351-359. [PDF]

McParland, V. J., Kalverda, A. P., Homans, S. W., and Radford, S. E. (2002). Structural properties of an amyloid precursor of beta(2)-microglobulin. Nat. Struct. Biol. 9, 326-331. [Abstract]

Errington, N., Mistry, P., and Rowe, A. J. (2002). Protein hydration varies with protein crowding and with applied pressure: a sedimentation velocity study. Progr. Colloid Polym. Sci. 119, 58-63. [Abstract]

Lee, H., Deo, N., and Somasunduran, P. (2002). Ultracentrifugal study of liposome solubilization by sodium dodecylsulfate. Journal of Dispersion Science and Technology 23, 483-490. [Abstract]

Kumar, V., Carlson, J. E., Ohgi, K. A., Edwards, T. A., Rose, D. W., Escalante, C. R., Rosenfeld, M. G., and Aggarwal, A. K. (2002). Transcription corepressor CtBP is an NAD(+)-regulated dehydrogenase. Mol. Cell 10, 857-869. [Abstract] [PDF]

Wood, Z. A., Poole, L. B., Hantgan, R. R., and Karplus, P. A. (2002). Dimers to doughnuts: redox-sensitive oligomerization of 2-cysteine peroxiredoxins. Biochemistry 41, 5493-5504. [Abstract]

Qin, B. Y., Lam, S. S., Correia, J. J., and Lin, K. (2002). Smad3 allostery links TGF-beta receptor kinase activation to transcriptional control. Genes Dev. 16, 1950-1963. [PDF]

Perkins, S. J., Gilbert, H. E., Aslam, M., Hannan, J., Holers, V. M., and Goodship, T. H. J. (2002). Solution structures of complement components by X-ray and neutron scattering and analytical ultracentrifugation. Biochemical Society Transactions 30, 996-1001. [Abstract]

Lee, Y. C., Boehm, M. K., Chester, K. A., Begent, R. H. J., and Perkins, S. J. (2002). Reversible dimer formation and stability of the anti-tumour single-chain Fv antibody MFE-23 by neutron scattering, analytical ultracentrifugation, and NMR and FT-IR spectroscopy. J. Mol. Biol. 320, 107-127. [Abstract]

Schuck, P., Perugini, M. A., Gonzales, N. R., Howlett, G. J., and Schubert, D. (2002). Size-distribution analysis of proteins by analytical ultracentrifugation: Strategies and application to model systems. Biophys. J. 82, 1096-1111. [Abstract] [Full Text]

Walters, C., Errington, N., Rowe, A. J., and Harding, S. E. (2002). Hydrolysable ATP is a requirement for the correct interaction of molecular chaperonins cpn60 and cpn10. Biochem. J. 364, 849-855. [Abstract]

Cadieux, E., Vrajmasu, V., Achim, C., Powlowski, J., and Munck, E. (2002). Biochemical, Mossbauer, and EPR studies of the diiron cluster of phenol hydroxylase from Pseudomonas sp. strain CF 600. Biochemistry 41, 10680-10691. [Abstract]

Patel, V. B. and Cunningham, C. C. (2002). Altered hepatic mitochondrial ribosome structure following chronic ethanol consumption. Arch. Biochem. Biophys. 398, 41-50. [Abstract]

back to top

2001

Guthridge, J. M., Rakstang, J. K., Young, K. A., Hinshelwood, J., Aslam, M., Robertson, A., Gipson, M. G., Sarrias, M. R., Moore, W. T., Meagher, M., Karp, D., Lambris, J. D., Perkins, S. J., and Holers, V. M. (2001). Structural studies in solution of the recombinant N-terminal pair of short consensus/complement repeat domains of complement receptor type 2 (CR2/CD21) and interactions with its ligand C3dg. Biochemistry 40, 5931-5941. [abstract]

Laue, T. (2001). Biophysical studies by ultracentrifugation. Curr. Opin. Struct. Biol. 11, 579-583. [PDF]

Patel, V. B., Cunningham, C. C., and Hantgan, R. R. (2001). Physiochemical properties of rat liver mitochondrial ribosomes. J. Biol. Chem. 276, 6739-6746. [PDF]

Steen, I. H., Madern, D., Karlstrom, M., Lien, T., Ladenstein, R., and Birkeland, N. K. (2001). Comparison of isocitrate dehydrogenase from three hyperthermophiles reveals differences in thermostability, cofactor specificity, oligomeric state, and phylogenetic affiliation. J. Biol. Chem. 276, 43924-43931. [PDF]

White, J. T. and Kelly, J. W. (2001). Support for the multigenic hypothesis of amyloidosis: the binding stoichiometry of retinol-binding protein, vitamin A, and thyroid hormone influences transthyretin amyloidogenicity in vitro. Proc. Natl. Acad. Sci. U. S. A 98, 13019-13024. [PDF]

Correia, J. J., Chacko, B. M., Lam, S. S., and Lin, K. (2001). Sedimentation studies reveal a direct role of phosphorylation in Smad3:Smad4 homo- and hetero-trimerization. Biochemistry 40: 1473-1482. [PDF]

Jiang, X., Smith, C. S., Petrassi, H. M., Hammarstrom, P., White, J. T., Sacchettini, J. C., and Kelly, J. W. (2001). An engineered transthyretin monomer that is nonamyloidogenic, unless it is partially denatured. Biochemistry 40, 11442-11452. [Abstract]

Kad, N. M., Thomson, N. H., Smith, D. P., Smith, D. A., and Radford, S. E. (2001). Beta(2)-microglobulin and its deamidated variant, N17D form amyloid fibrils with a range of morphologies in vitro. J. Mol. Biol. 313, 559-571. [Abstract]

White, P. W., Pelletier, A., Brault, K., Titolo, S., Welchner, E., Thauvette, L., Fazekas, M., Cordingley, M. G., and Archambault, J. (2001). Characterization of recombinant HPV6 and 11 E1 helicases: effect of ATP on the interaction of E1 with E2 and mapping of a minimal helicase domain. J. Biol. Chem. 276, 22426-22438. [Abstract] [Full Text]  

Carrasco, B., de la Torre, J. G., Davis, K. G., Jones, S., Athwal, D., Walters, C., Burton, D. R., and Harding, S. E. (2001). Crystallohydrodynamics for solving the hydration problem for multi-domain proteins: open physiological conformations for human IgG. Biophys. Chem. 93, 181-196. [Abstract]

Aslam, M. and Perkins, S. J. (2001). Folded-back solution structure of monomeric factor H of human complement by synchrotron X-ray and neutron scattering, analytical ultracentrifugation and constrained molecular modeling. J. Mol. Biol. 309, 1117-1138. [Abstract]

Correia, J. J., Chacko, B. M., Lam, S. S., and Lin, K. (2001). Sedimentation studies reveal a direct role of phosphorylation in Smad3:Smad4 homo- and hetero-trimerization. Biochemistry 40, 1473-1482. [Abstract]

Hantgan, R. R., Rocco, M., Nagaswami, C., and Weisel, J. W. (2001). Binding of a fibrinogen mimetic stabilizes integrin aIIbb3's open conformation. Protein Sci. 10, 1614-1626. [Abstract]

Tokunaga, M., Shiraishi, Y., Odachi, M., Mizukami, M., Tokunaga, H., Philo, J. S., Arakawa, T., Ishibashi, M., Tanaka, R., and Takagi, H. (2001). Molecular cloning of groESL locus, and purification and characterization of chaperonins, GroEL and GroES, from Bacillus brevis. Biosci. Biotechnol. Biochem. 65, 1379-1387. [Abstract]

Toonkool, P., Regan, D. G., Kuchel, P. W., Morris, M. B., and Weiss, A. S. (2001). Thermodynamic and hydrodynamic properties of human tropoelastin - Analytical ultracentrifuge and pulsed field-gradient spin-echo NMR studies. J. Biol. Chem. 276, 28042-28050. [Abstract] [Full Text]

Patel, V. B., Cunningham, C. C., and Hantgan, R. R. (2001). Physiochemical properties of rat liver mitochondrial ribosomes. J. Biol. Chem. 276, 6739-6746. [Abstract]

Madern, D., Ebel, C., Dale, H. A., Lien, T., Steen, I. H., Birkeland, N. K., and Zaccai, G. (2001). Differences in the oligomeric states of the LDH-like L-MalDH from the hyperthermophilic archaea Methanococcus jannaschii and Archaeoglobus fulgidus. Biochemistry 40, 10310-10316. [Abstract]

Rudyak, S. G., Brenowitz, M., and Shrader, T. E. (2001). Mg2+-linked oligomerization modulates the catalytic activity of the Lon (La) protease from Mycobacterium smegmatis. Biochemistry 40, 9317-9323. [Abstract]

Schuck, P. and Rossmanith, P. (2000). Determination of the sedimentation coefficient distribution by least-squares boundary modeling. Biopolymers 54, 328-341. [Abstract]

back to top

2000

Buchberger, A., Howard, M. J., Freund, S. M., Proctor, M., Butler, P. J., Fersht, A. R., and Bycroft, M. (2000). Biophysical characterization of elongin C from Saccharomyces cerevisiae. Biochemistry 39, 11137-11146. [abstract] [PDF]

Cabezon, E., Arechaga, I., Jonathan, P., Butler, G., and Walker, J. E. (2000). Dimerization of bovine F1-ATPase by binding the inhibitor protein, IF1. J. Biol. Chem. 275, 28353-28355. [PDF]

Brendza, K. M., Sontag, C. A., Saxton, W. M., and Gilbert, S. P. (2000). A kinesin mutation that uncouples motor domains and desensitizes the gamma-phosphate sensor. J. Biol. Chem. 275, 22187-22195. [Abstract] [Full Text]

Schuck, P. (2000). Size-distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and Lamm equation modeling. Biophys J 78, 1606-1619. [Abstract] [Full Text]

Philo, J. S. (2000). A method for directly fitting the time derivative of sedimentation velocity data and an alternative algorithm for calculating sedimentation coefficient distribution functions. Anal. Biochem. 279, 151-163. [Abstract]

back to top