Up ] [ references ] troubleshooting and questions ] Concepts for Getting Started ] sedphat help ] download ] Search ]


References describing specific models and capabilities of SEDPHAT are


J.C.D. Houtman, P.H. Brown, B. Bowden, H. Yamagushi, E. Appella, L.E. Samelson, P. Schuck.  (2007) Studying multi-site binary and ternary protein interactions by global analysis of isothermal titration calorimetry data in SEDPHAT: Application to adaptor protein complexes in cell signaling. Protein Science 16:30-42

J. Dam, C.A. Velikovsky, R.A. Mariuzza, C. Urbanke, P. Schuck (2005) Sedimenetation velocity analysis of heterogeneous protein-protein interactions: Lamm equation modeling and sedimentation coefficient distributions c(s).  Biophysical Journal 89:619-634 [properties of c(s) when applied to for reacting systems]

J. Dam, P. Schuck (2005) Sedimentation velocity analysis of heterogeneous protein-protein interactions: Sedimentation coefficient distributions c(s) and asymptotic boundary profiles from Gilbert-Jenkins theory.    Biophysical Journal 89:651-666 [properties of c(s) when applied to for reacting systems]

A. Balbo, K.H. Minor, C.A. Velikovsky, R.A. Mariuzza, C.B. Peterson, P. Schuck (2005) Studying multi-protein complexes by multi-signal sedimentation velocity analytical ultracentrifugation.  Proceedings of the National Academy of Sciences 102:81-86

P. Schuck. (2005) Diffusion-deconvoluted sedimentation coefficient distributions for the analysis of interacting and non-interacting protein mixtures. In: Modern Analytical Ultracentrifugation: Techniques and Methods (D.J. Scott, S.E. Harding, A.J. Rowe, Editors) The Royal Society of Chemistry, Cambridge (in press) (preprint)

J. Vistica, J. Dam, A. Balbo, E. Yikilmaz, R.A. Mariuzza, T.A. Rouault, P. Schuck (2004) Sedimentation equilibrium analysis of protein interactions with global implicit mass conservation constraints and systematic noise decomposition.  Analytical Biochemistry 326:234-256  (preprint)

P. Schuck (2003) On the analysis of protein self-association by sedimentation velocity analytical ultracentrifugation.  Analytical Biochemistry 320:104-124 (preprint)

Solovyova, A., P. Schuck, L. Costenaro, C. Ebel (2001) Non-ideality by sedimentation velocity of halophilic malate dehydrogenase in complex solvents.  Biophysical Journal 81:1868-1880



Papers with applications of Sedphat include:


Mutation of Glu-166 blocks the substrate-induced dimerization of SARS coronavirus main protease; Shu-Chun Cheng, Gu-Gang Chang, Chi-Yuan Chou 7 April 2010 Biophys. J. 98(7) pp. 1327-1336


Eichner T, Radford SE A Generic Mechanism of beta(2)-Microglobulin Amyloid Assembly at Neutral pH Involving a Specific Proline Switch , JOURNAL OF MOLECULAR BIOLOGY   Volume: 386   Issue: 5   Pages: 1312-1326   Published: MAR 13 2009

Rufer AC, Rumpf J, von Holleben M, et al., Isoform-Selective Interaction of the Adaptor Protein Tks5/FISH with Sos1 and Dynamins  JOURNAL OF MOLECULAR BIOLOGY   Volume: 390   Issue: 5   Pages: 939-950   Published: JUL 31 2009

Patel A, Dharmarajan V, Vought VE, et al. On the Mechanism of Multiple Lysine Methylation by the Human Mixed Lineage Leukemia Protein-1 (MLL1) Core Complex  JOURNAL OF BIOLOGICAL CHEMISTRY   Volume: 284   Issue: 36   Pages: 24242-24256   Published: SEP 4 2009

Markham AP, Jaafar ZA, Kemege KE, et al., Biophysical Characterization of Chlamydia trachomatis CT584 Supports Its Potential Role as a Type III Secretion Needle Tip Protein  BIOCHEMISTRY   Volume: 48   Issue: 43   Pages: 10353-10361   Published: NOV 3 2009

Reyda MR, Fugate CJ, Jarrett JT  A Complex between Biotin Synthase and the Iron-Sulfur Cluster Assembly Chaperone HscA That Enhances in Vivo Cluster Assembly  BIOCHEMISTRY   Volume: 48   Issue: 45   Pages: 10782-10792   Published: NOV 17 2009

Iwig JS, Chivers PT DNA Recognition and Wrapping by Escherichia coli RcnR JOURNAL OF MOLECULAR BIOLOGY   Volume: 393   Issue: 2   Pages: 514-526   Published: OCT 23 2009

Jones RPO, Wang MC, Jowitt TA, et al.Fibulin 5 Forms a Compact Dimer in Physiological Solutions  JOURNAL OF BIOLOGICAL CHEMISTRY   Volume: 284   Issue: 38   Pages: 25938-25943   Published: SEP 18 2009

Mahler HC, Friess W, Grauschopf U, et al. Protein Aggregation: Pathways, Induction Factors and Analysis JOURNAL OF PHARMACEUTICAL SCIENCES   Volume: 98   Issue: 9   Pages: 2909-2934   Published: SEP 2009

Pesiridis GS, Diamond E, Van Duyne GD  Role of pICLn in Methylation of Sm Proteins by PRMT5  JOURNAL OF BIOLOGICAL CHEMISTRY   Volume: 284   Issue: 32   Pages: 21347-21359   Published: AUG 7 2009

Chaudhry C, Plested AJR, Schuck P, et al. Energetics of glutamate receptor ligand binding domain dimer assembly are modulated by allosteric ions  PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA   Volume: 106   Issue: 30   Pages: 12329-12334   Published: JUL 28 2009

Gupta YK, Lee TH, Edwards TA, et al. Co-occupancy of two Pumilio molecules on a single hunchback NRE RNA-A PUBLICATION OF THE RNA SOCIETY   Volume: 15   Issue: 6   Pages: 1029-1035   Published: JUN 2009

Kumar J, Schuck P, Jin RS, et al. The N-terminal domain of GluR6-subtype glutamate receptor ion channels NATURE STRUCTURAL & MOLECULAR BIOLOGY   Volume: 16   Issue: 6   Pages: 631-U58   Published: JUN 2009

Mack TR, Gao R, Stock AM  Probing the Roles of the Two Different Dimers Mediated by the Receiver Domain of the Response Regulator PhoB  JOURNAL OF MOLECULAR BIOLOGY   Volume: 389   Issue: 2   Pages: 349-364   Published: JUN 5 2009

Berry R, Jowitt TA, Ferrand J, et al. Role of dimerization and substrate exclusion in the regulation of bone morphogenetic protein-1 and mammalian tolloid  PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA   Volume: 106   Issue: 21   Pages: 8561-8566   Published: MAY 26 2009

Gondeau C, Corradin G, Heitz F, et al. The C-terminal domain of Plasmodium falciparum merozoite surface protein 3 self-assembles into alpha-helical coiled coil tetramer  MOLECULAR AND BIOCHEMICAL PARASITOLOGY   Volume: 165   Issue: 2   Pages: 153-161   Published: JUN 2009

Hao XT, Ryan T, Bailey MF, et al. Molar Mass Determination of Water-Soluble Light-Emitting Conjugated Polymers by Fluorescence-Based Analytical Ultracentrifugation  MACROMOLECULES   Volume: 42   Issue: 7   Pages: 2737-2740   Published: APR 14 2009

Mortuza GB, Goldstone DC, Pashley C, et al. Structure of the Capsid Amino-Terminal Domain from the Betaretrovirus, Jaagsiekte Sheep Retrovirus  JOURNAL OF MOLECULAR BIOLOGY   Volume: 386   Issue: 4   Pages: 1179-1192   Published: MAR 6 2009

Kami K, Chidgey M, Dafforn T, et al. The Desmoglein-Specific Cytoplasmic Region Is Intrinsically Disordered in Solution and Interacts with Multiple Desmosomal Protein Partners   JOURNAL OF MOLECULAR BIOLOGY   Volume: 386   Issue: 2   Pages: 531-543   Published: FEB 20 2009

Brombacher E, Urwyler S, Ragaz C, et al. Rab1 Guanine Nucleotide Exchange Factor SidM Is a Major Phosphatidylinositol 4-Phosphate-binding Effector Protein of Legionella pneumophila JOURNAL OF BIOLOGICAL CHEMISTRY   Volume: 284   Issue: 8   Pages: 4846-4856   Published: FEB 20 2009

Bansal PK, Nourse A, Abdulle R, et al. Sgt1 Dimerization Is Required for Yeast Kinetochore Assembly JOURNAL OF BIOLOGICAL CHEMISTRY   Volume: 284   Issue: 6   Pages: 3586-3592   Published: FEB 6 2009

Erik Martinez-Hackert, Wayne A. Hendrickson  Promiscuous Substrate Recognition in Folding and Assembly Activities of the Trigger Factor Chaperone  September 2009 Cell 138(5) pp. 923 - 934

Diego Alvarado, Daryl E. Klein, Mark A. Lemmon  ErbB2 resembles an autoinhibited invertebrate epidermal growth factor receptor  Nature 461, 287-291 (30 August 2009) doi:10.1038/nature08297 Letter

Charu Chaudhry, Matthew C Weston, Peter Schuck, Christian Rosenmund, Mark L Mayer  Stability of ligand-binding domain dimer assembly controls kainate receptor desensitization  The EMBO Journal 28, 1518-1530 (2 April 2009) doi:10.1038/emboj.2009.86 Article

Xinwang Cao, Ünal Coskun, Manfred Rössle, Sabine B. Buschhorn, Michal Grzybek, Timothy R. Dafforn, Marc Lenoir, Michael Overduin, Kai Simons, Golgi protein FAPP2 tubulates membranesPNAS 2009 106:21121-21125; published online before print November 25, 2009, doi:10.1073/pnas.0911789106


horizontal rule

Solution Structure of the Complex Formed between Human Complement C3d and Full-length Complement Receptor Type 2
Journal of Molecular Biology, Volume 384, Issue 1, 5 December 2008, Pages 137-150
Keying Li, Azubuike I. Okemefuna, Jayesh Gor, Jonathan P. Hannan, Rengasamy Asokan, V. Michael Holers, Stephen J. Perkins

Role of tryptophan-208 residue in cytochrome c oxidation by ascorbate peroxidase from Leishmania major-kinetic studies on Trp208Phe mutant and wild type enzyme
Biochimica et Biophysica Acta (BBA) - Proteins & Proteomics, Volume 1784, Issue 5, May 2008, Pages 863-871
Rajesh K. Yadav, Subhankar Dolai, Swati Pal, Subrata Adak

The dimeric assembly of Photobacterium leiognathi and Salmonella typhimurium SodC1 Cu,Zn superoxide dismutases is affected differently by active site demetallation and pH: An analytical ultracentrifuge study
Archives of Biochemistry and Biophysics, Volume 471, Issue 1, 1 March 2008, Pages 77-84
B. Catacchio, M. D’Orazio, A. Battistoni, E. Chiancone

tRNA-dependent asparagine formation in prokaryotes: Characterization, isolation and structural and functional analysis of a ribonucleoprotein particle generating Asn-tRNAAsn
Methods, Volume 44, Issue 2, February 2008, Pages 146-163
Marc Bailly, Mickaël Blaise, Hervé Roy, Marzanna Deniziak, Bernard Lorber, Catherine Birck, Hubert D. Becker, Daniel Kern

Characterization and Further Stabilization of Designed Ankyrin Repeat Proteins by Combining Molecular Dynamics Simulations and Experiments
Journal of Molecular Biology, Volume 375, Issue 3, 18 January 2008, Pages 837-854
Gianluca Interlandi, Svava K. Wetzel, Giovanni Settanni, Andreas Plückthun, Amedeo Caflisch

On the quaternary structure of a C-type lectin from Bothrops jararacussu venom – BJ-32 (BjcuL)
Toxicon, Volume 52, Issue 8, 15 December 2008, Pages 944-953
F.P. Silva Jr., G.M.C. Alexandre, C.H.I. Ramos, S.G. De-Simone

Correlation between dissociation and catalysis of SARS-CoV main protease
Archives of Biochemistry and Biophysics, Volume 472, Issue 1, 1 April 2008, Pages 34-42
Pei-Ying Lin, Chi-Yuan Chou, Hui-Chuan Chang, Wen-Chi Hsu, Gu-Gang Chang

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
Journal of Molecular Biology, Volume 375, Issue 1, 4 January 2008, Pages 80-101
Azubuike I. Okemefuna, Hannah E. Gilbert, Kim M. Griggs, Rebecca J. Ormsby, David L. Gordon, Stephen J. Perkins

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
Journal of Molecular Biology, Volume 375, Issue 1, 4 January 2008, Pages 102-118
Patricia B. Furtado, Chen Y. Huang, Demvihin Ihyembe, Russell A. Hammond, Henry C. Marsh, Stephen J. Perkins

Assembly of the Mitochondrial Tim9–Tim10 Complex: A Multi-step Reaction with Novel Intermediates
Journal of Molecular Biology, Volume 375, Issue 1, 4 January 2008, Pages 229-239
Ekaterina Ivanova, Thomas A. Jowitt, Hui Lu

Jason S. McLellan, Xiaoyan Zheng, Glenn Hauk, Rodolfo Ghirlando, Philip A. Beachy, Daniel J. Leahy. The mode of Hedgehog binding to Ihog homologues is not conserved across different phyla Nature (14 Sep 2008), doi: 10.1038/nature07358, Abstract |

Marcin Nowotny, Susana M Cerritelli, Rodolfo Ghirlando, Sergei A Gaidamakov, Robert J Crouch, Wei Yang Specific recognition of RNA/DNA hybrid and enhancement of human RNase H1 activity by HBD  The EMBO Journal 27, 1172 - 1181 (09 Apr 2008), doi: 10.1038/emboj.2008.44, Full Text

Kuan-Ming Chen, Elena Harjes, Phillip J. Gross, Amr Fahmy, Yongjian Lu, Keisuke Shindo, Reuben S. Harris, Hiroshi Matsuo Structure of the DNA deaminase domain of the HIV-1 restriction factor APOBEC3G, Nature 452, 116 - 119 (20 Feb 2008), doi: 10.1038/nature06638

Peng Yuan, Kushol Gupta, Gregory D. Van Duyne Tetrameric Structure of a Serine Integrase Catalytic Domain 6 August 2008 Structure 16(8) pp. 1275 - 1286, Summary | Full Text

Yann Gohon, Tassadite Dahmane, Rob W.H. Ruigrok, Peter Schuck, Delphine Charvolin, Fabrice Rappaport, Peter Timmins, Donald M. Engelman, Christophe Tribet, Jean-Luc Popot et al. Bacteriorhodopsin/Amphipol Complexes: Structural and Functional Properties 1 May 2008 Biophysical Journal 94(9) pp. 3523 - 3537 Abstract | Full Text | PDF (1826 kb)

Patrick Koenig, Mislav Oreb, Anja Höfle, Sabine Kaltofen, Karsten Rippe, Irmgard Sinning, Enrico Schleiff, Ivo Tews The GTPase Cycle of the Chloroplast Import Receptors Toc33/Toc34: Implications from Monomeric and Dimeric Structures 8 April 2008 Structure 16(4) pp. 585 - 596 Summary | Full Text | PDF (2005 kb)

Doan N, Gettins PGW: alpha-macroglobulins are present in some Gram-negative bacteria - Characterization of the alpha(2)-macroglobulin from Escherichia coli JOURNAL OF BIOLOGICAL CHEMISTRY   Volume: 283   Issue: 42   Pages: 28747-28756   Published: OCT 17 2008

Moncrieffe MC, Grossmann JG, Gay NJ: Assembly of Oligomeric Death Domain Complexes during Toll Receptor Signaling JOURNAL OF BIOLOGICAL CHEMISTRY   Volume: 283   Issue: 48  Pages: 33447-33454   Published: NOV 28 2008

Klosi E, Saro D, Spaller MR: Bivalent peptides as PDZ domain ligands BIOORGANIC & MEDICINAL CHEMISTRY LETTERS   Volume: 17   Issue: 22   Pages: 6147-6150   Published: NOV 15 2007

Machius M, Brautigam CA, Tomchick DR, et al.: Structural and biochemical basis for polyamine binding to the tp0655 lipoprotein of Treponema pallidum: Putative role for tp0655 (TpPotD) as a polyamine receptor JOURNAL OF MOLECULAR BIOLOGY   Volume: 373   Issue: 3   Pages: 681-694   Published: OCT 26 2007

Ryan TM, Howlett GJ, Bailey MF: Fluorescence Detection of a Lipid-induced Tetrameric Intermediate in Amyloid Fibril Formation by Apolipoprotein C-II  JOURNAL OF BIOLOGICAL CHEMISTRY   Volume: 283   Issue: 50  Pages: 35118-35128   Published: DEC 12 2008

Zamorano LS, Pina DG, Arellano JB, et al.: Thermodynamic characterization of the palm tree Roystonea regia peroxidase stability BIOCHIMIE   Volume: 90   Issue: 11-12   Pages: 1737-1749   Published: NOV-DEC 2008

Hakobyan S, Harris CL, van den Berg CW, et al.: Complement Factor H Binds to Denatured Rather than to Native Pentameric C-reactive Protein JOURNAL OF BIOLOGICAL CHEMISTRY   Volume: 283   Issue: 45   Pages: 30451-30460   Published: NOV 7 2008

Demene H, Ducat T, De Guillen K, et al.: Structural Mechanism of Signal Transduction between the RNA-binding Domain and the Phosphotransferase System Regulation Domain of the LicT Antiterminator  JOURNAL OF BIOLOGICAL CHEMISTRY   Volume: 283   Issue: 45   Pages: 30838-30849   Published: NOV 7 2008

Pearce FG, Dobson RCJ, Weber A, et al.: Mutating the Tight-Dimer Interface of Dihydrodipicolinate Synthase Disrupts the Enzyme Quaternary Structure: Toward a Monomeric Enzyme BIOCHEMISTRY   Volume: 47   Issue: 46   Pages: 12108-12117   Published: NOV 18 2008 

Burgess BR, Dobson RCJ, Bailey MF, et al.: Structure and evolution of a novel dimeric enzyme from a clinically important bacterial pathogenJOURNAL OF BIOLOGICAL CHEMISTRY   Volume: 283   Issue: 41   Pages: 27598-27603   Published: OCT 10 2008

Koti JS, Morais MC, Rajagopal R, et al.: DNA packaging motor assembly intermediate of bacteriophage phi 29  JOURNAL OF MOLECULAR BIOLOGY   Volume: 381   Issue: 5   Pages: 1114-1132   Published: SEP 19 2008

Babon JJ, Sabo JK, Soetopo A, et al.: The SOCS box domain of SOCS3: Structure and interaction with the elonginBC-cullin5 ubiquitin ligase JOURNAL OF MOLECULAR BIOLOGY   Volume: 381   Issue: 4   Pages: 928-940   Published: SEP 12 2008 

Llorente MT, Taylor IA, Lopez-Vinas E, et al.: Structural properties of the human respiratory syncytial virus P protein: Evidence for an elongated homotetrameric molecule that is the smallest orthologue within the family of paramyxovirus polymerase cofactors.  PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS   Volume: 72   Issue: 3   Pages: 946-958   Published: AUG 15 2008

Iwig JS, Leitch S, Herbst RW, et al.: Ni(II) and Co(II) sensing by Escherichia coli RcnR. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY   Volume: 130   Issue: 24   Pages: 7592-7606   Published: JUN 18 2008

Zhang XC, Perugini MA, Yao S, et al.: Solution conformation, backbone dynamics and lipid interactions of the intrinsically unstructured malaria surface protein MSP2.  JOURNAL OF MOLECULAR BIOLOGY   Volume: 379   Issue: 1   Pages: 105-121   Published: MAY 23 2008

Baden EM, Owen BAL, Peterson FC, et al.: Altered dimer interface decreases stability in an amyloidogenic protein JOURNAL OF BIOLOGICAL CHEMISTRY   Volume: 283   Issue: 23   Pages: 15853-15860   Published: JUN 6 2008

Reyda MR, Dippold R, Dotson ME, et al.: Loss of iron-sulfur clusters from biotin synthase as a result of catalysis promotes unfolding and degradation ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS   Volume: 471   Issue: 1   Pages: 32-41   Published: MAR 1 2008

Galea CA, Nourse A, Wang Y, et al.Source: Role of intrinsic flexibility in signal transduction mediated by the cell cycle regulator, p27(Kip1) JOURNAL OF MOLECULAR BIOLOGY   Volume: 376   Issue: 3   Pages: 827-838   Published: FEB 22 2008

Renata Grzela, Ewa Szolajska, Christine Ebel, Dominique Madern, Adrien Favier, Izabela Wojtal, Wlodzimierz Zagorski, and Jadwiga Chroboczek
Virulence Factor of Potato Virus Y, Genome-attached Terminal Protein VPg, Is a Highly Disordered Protein
J. Biol. Chem., Jan 2008; 283: 213 - 221.

Stefano Franceschini, Andrea Ilari, Daniela Verzili, Carlotta Zamparelli, Anaid Antaramian, Angélica Rueda, Hector H. Valdivia, Emilia Chiancone, and Gianni Colotti (2008) Molecular basis for the impaired function of the natural F112L sorcin mutant: X-ray crystal structure, calcium affinity, and interaction with annexin VII and the ryanodine receptor.  FASEB J, Jan 2008; 22: 295 - 306.

Jørgensen CM, Fields CJ, Chander P, Watt D, Burgner JW 2nd, Smith JL, Switzer RL. (2008) pyr RNA binding to the Bacillus caldolyticus PyrR attenuation protein - characterization and regulation by uridine and guanosine nucleotides. FEBS J. 2008 Jan 8; [Epub ahead of print]

Johnston JW, Coussens NP, Allen S, Houtman JC, Turner KH, Zaleski A, Ramaswamy S, Gibson BW, Apicella MA (2008) Characterization of the N-Acetyl-5-neuraminic Acid-binding Site of the Extracytoplasmic Solute Receptor (SiaP) of Nontypeable Haemophilus influenzae Strain 2019. J Biol Chem. 2008 Jan 11;283(2):855-65. Epub 2007 Oct 18.

J.S. Lengyel, K.M. Stott, X. Wu, B.R. Brooks, A. Balbo, P. Schuck, R.N. Perham, S. Subramaniam, J.L.S. Milne (2008) Extended polypeptide linkers establish the spatial architecture of a pyruvate dehydrogenase.  Structure 16:93-103

Leonard JN, Ghirlando R, Askins J, Bell JK, Margulies DH, Davies DR, Segal DM. (2008) The TLR3 signaling complex forms by cooperative receptor dimerization. Proc Natl Acad Sci U S A. 2008 Jan 8;105(1):258-63. Epub 2008 Jan 2.

Nikola Wenta, Holger Strauss, Stefanie Meyer, Uwe Vinkemeier. Tyrosine phosphorylation regulates the partitioning of STAT1 between different dimer conformationsPNAS 2008 105:9238-9243; doi:10.1073/pnas.0802130105

Timothy Bowles, Audrey H. Metz, Jami O'Quin, Zdzislaw Wawrzak, and Brandt F. Eichman.Structure and DNA binding of alkylation response protein AidBPNAS 2008 105:15299-15304; doi:10.1073/pnas.0806521105

horizontal rule

Lengsfeld BM, Rattray AJ, Bhaskara V, Ghirlando R, Paull TT. (2007) Sae2 is an endonuclease that processes hairpin DNA cooperatively with the Mre11/Rad50/Xrs2 complex. Mol Cell. 2007 Nov 30;28(4):638-51.

Modesti M, Budzowska M, Baldeyron C, Demmers JA, Ghirlando R, Kanaar R. (2007) RAD51AP1 is a structure-specific DNA binding protein that stimulates joint molecule formation during RAD51-mediated homologous recombination. Mol Cell. 2007 Nov 9;28(3):468-81.

Nowotny M, Gaidamakov SA, Ghirlando R, Cerritelli SM, Crouch RJ, Yang W. (2007) Structure of human RNase H1 complexed with an RNA/DNA hybrid: insight into HIV reverse transcription. Mol Cell. 2007 Oct 26;28(2):264-76.

Prag G, Watson H, Kim YC, Beach BM, Ghirlando R, Hummer G, Bonifacino JS, Hurley JH. (2007) The Vps27/Hse1 complex is a GAT domain-based scaffold for ubiquitin-dependent sorting. Dev Cell. 2007 Jun;12(6):973-86

Iwanczyk J, Damjanovic D, Kooistra J, Leong V, Jomaa A, Ghirlando R, Ortega J. (2007) Role of the PDZ domains in Escherichia coli DegP protein. J Bacteriol. 2007 Apr;189(8):3176-86. Epub 2007 Feb 2.

Bai Y, Auperin TC, Chou CY, Chang GG, Manley JL, Tong L.
Crystal structure of murine CstF-77: dimeric association and implications for polyadenylation of mRNA precursors.
Mol Cell. 2007 Mar 23;25(6):863-75.

Sudarshan Rajagopal and Stephen B.H. Kent
Total chemical synthesis and biophysical characterization of the minimal isoform of the KChIP2 potassium channel regulatory subunit
Protein Science (2007), 16:2056-2064

Horng Der Ou, 2, Frank Löhr, Vitali Vogel, Werner Mäntele and Volker Dötsch
Structural evolution of C-terminal domains in the p53 family
The EMBO Journal (2007) 26, 3463–3473, doi:10.1038/sj.emboj.7601764

Kostelansky MS, Schluter C, Tam YY, Lee S, Ghirlando R, Beach B, Conibear E, Hurley JH.
Molecular architecture and functional model of the complete yeast ESCRT-I heterotetramer.
Cell. 2007 May 4;129(3):485-98. Epub 2007 Apr 19

Franceschini S, Ilari A, Verzili D, Zamparelli C, Antaramian A, Rueda A, Valdivia HH, Chiancone E, Colotti G.
Molecular basis for the impaired function of the natural F112L sorcin mutant: X-ray crystal structure, calcium affinity, and interaction with annexin VII and the ryanodine receptor.
FASEB J. 2008 Jan;22(1):295-306. Epub 2007 Aug 15.

Kuo-Hsiang Tang, Marc Niebuhr, Ann Aulabaugh and Ming-Daw Tsai,
Solution structures of 2 : 1 and 1 : 1 DNA polymerase–DNA complexes probed by ultracentrifugation and small-angle X-ray scattering
Nucleic Acids Research, doi:10.1093/nar/gkm1101

Yan Q, Malashkevich VN, Fedorov A, Fedorov E, Cao E, Lary JW, Cole JL, Nathenson SG, Almo SC.
Structure of CD84 provides insight into SLAM family function.
Proc Natl Acad Sci U S A. 2007 Jun 19;104(25):10583-8. Epub 2007 Jun 11.

Susan K Buchanan, Petra Lukacik, Sylvestre Grizot, 4, Rodolfo Ghirlando, Maruf M U Ali, 5, Travis J Barnard, Karen S Jakes, Paul K Kienker and Lothar Esser
Structure of colicin I receptor bound to the R-domain of colicin Ia: implications for protein import
The EMBO Journal (2007) 26, 2594–2604, doi:10.1038/sj.emboj.7601693

Deng L, Langley RJ, Brown PH, Xu G, Teng L, Wang Q, Gonzales MI, Callender GG, Nishimura MI, Topalian SL, Mariuzza RA.
Structural basis for the recognition of mutant self by a tumor-specific, MHC class II-restricted T cell receptor.
Nat Immunol. 2007 Apr;8(4):398-408. Epub 2007 Mar 4.

Nicholas P. Morrisa, Carmen Petersa, Ryan Montlera, Hong-Ming Hua, Brendan D. Curtia, Walter J. Urbaa and Andrew D. Weinberg
Development and characterization of recombinant human Fc:OX40L fusion protein linked via a coiled-coil trimerization domain
Molecular Immunology, Volume 44, Issue 12, May 2007, Pages 3112-3121

Gloyd M, Ghirlando R, Matthews LA, Guarné A.
MukE and MukF form two distinct high affinity complexes.
J Biol Chem. 2007 May 11;282(19):14373-8. Epub 2007 Mar 12.

Tracy L. Putoczki, Filomena Pettolino, Michael D. W. Griffin, Ralf Möller, Juliet A. Gerrard, Antony Bacic and Sandra L. Jackson
Characterization of the structure, expression and function of Pinus radiata D. Don arabinogalactan-proteins
Planta An International Journal of Plant Biology 10.1007/s00425-007-0559-2

Yang Kang, Xiang Chen, Jeffrey W. Lary, James L. Cole and Kylie J. Walters
Defining how Ubiquitin Receptors hHR23a and S5a Bind Polyubiquitin
Journal of Molecular Biology, Volume 369, Issue 1, 25 May 2007, Pages 168-176

Ahmad Jomaa, Daniela Damjanovic, Vivian Leong, Rodolfo Ghirlando, Jack Iwanczyk, and Joaquin Ortega
The Inner Cavity of Escherichia coli DegP Protein Is Not Essential for Molecular Chaperone and Proteolytic Activity.
J Bacteriol. 2007 February; 189(3): 706–716.

Patrick D. Robertson, Eric M. Warren, Haijiang Zhang, David B. Friedman, Jeffrey W. Lary, James L. Cole, Antonin V. Tutter, Johannes C. Walter, Ellen Fanning, and Brandt F. Eichman
Domain architecture and biochemical characterization of vertebrate MCM10
J. Biol. Chem., Dec 2007; doi:10.1074/jbc.M706267200

U. Mirian Obiozo, T. Harma C. Brondijk, Andrew J. White, Gijs van Boxel, Tim R. Dafforn, Scott A. White, and J. Baz Jackson
Substitution of Tyrosine 146 in the dI Component of Proton-translocating Transhydrogenase Leads to Reversible Dissociation of the Active Dimer into Inactive Monomers
J. Biol. Chem., Dec 2007; 282: 36434 - 36443.

Sudarshan Rajagopal and Stephen B.H. Kent
Total chemical synthesis and biophysical characterization of the minimal isoform of the KChIP2 potassium channel regulatory subunit
Protein Sci., Sep 2007; 16: 2056 - 2064.

Mengli Cai, Ying Huang, Jeong-Yong Suh, John M. Louis, Rodolfo Ghirlando, Robert Craigie, and G. Marius Clore
Solution NMR Structure of the Barrier-to-Autointegration Factor-Emerin Complex
J. Biol. Chem., May 2007; 282: 14525 - 14535.

Machius M, Brautigam CA, Tomchick DR, et al.
Structural and biochemical basis for polyamine binding to the tp0655 lipoprotein of Treponema pallidum: Putative role for tp0655 (TpPotD) as a polyamine receptor 
JOURNAL OF MOLECULAR BIOLOGY 373 (3): 681-694 OCT 26 2007

H. Schmeisser, I. Gorshkova, P.H. Brown, P. Kontsek, P. Schuck, K. Zoon.  (2007) Two interferons alpha influence each other during their interaction with the extracellular domain of human type I interferon receptor subunit 2 Biochemistry 46:14638-14649

Putoczki TL, Pettolino F, Griffin MDW, et al.
Characterization of the structure, expression and function of Pinus radiata D. Don arabinogalactan-proteins 
PLANTA 226 (5): 1131-1142 OCT 2007

Ghosh K, Guo F, Van Duyne GD
Synapsis of loxP sites by cre recombinase 
JOURNAL OF BIOLOGICAL CHEMISTRY 282 (33): 24004-24016 AUG 17 2007

Jorissen HJMM, Ulery PG, Henry L, et al.
Dimerization and DNA-binding properties of the transcription factor Delta FosB 
BIOCHEMISTRY 46 (28): 8360-8372 JUL 17 2007

Fernandez MM, Bhattacharya S, De Marzi MC, et al.
Superantigen natural affinity maturation revealed by the crystal structure of staphylococcal enterotoxin g and its binding to T-cell receptor v beta 8.2 

Krell T, Teran W, Mayorga OL, et al.
Optimization of the palindromic order of the TtgR operator enhances binding cooperativity 
JOURNAL OF MOLECULAR BIOLOGY 369 (5): 1188-1199 JUN 22 2007

Yun MK, Nourse A, White SW, et al.
Crystal structure and allosteric regulation of the cytoplasmic Escherichia coli L-asparaginase I 
JOURNAL OF MOLECULAR BIOLOGY 369 (3): 794-811 JUN 8 2007

Romier C, James N, Birck C, et al.
Crystal structure, biochemical and genetic characterization of yeast and E-cuniculi TAF(II)5 N-terminal domain: Implications for TRID assembly 
JOURNAL OF MOLECULAR BIOLOGY 368 (5): 1292-1306 MAY 18 2007

Tarasev M, Kaddis CS, Yin S, et al.
Similar enzymes, different structures: Phthalate dioxygenase is an alpha(3)alpha(3) stacked hexamer, not an alpha(3)beta(3) trimer like "normal" Rieske oxygenases 

Tae Hyeon Yoo, A. James Link, and David A. Tirrell
Evolution of a fluorinated green fluorescent protein
PNAS, Aug 2007; 104: 13887 - 13890.

Kristina L. Carroll, Rodolfo Ghirlando, Jessica M. Ames, and Jeffry L. Corden
Interaction of yeast RNA-binding proteins Nrd1 and Nab3 with RNA polymerase II terminator elements
RNA, Mar 2007; 13: 361 - 373.

Hongmin Li, Yiwei Zhao, Yi Guo, Zhong Li, Leslie Eisele, and Walid Mourad
Zinc Induces Dimerization of the Class II Major Histocompatibility Complex Molecule That Leads to Cooperative Binding to a Superantigen
J. Biol. Chem., Mar 2007; 282: 5991 - 6000.

Li HM, Zhao YW, Guo Y, VanVranken SJ, Li Z, Eisele L, Mourad W (2007) Mutagenesis, biochemical, and biophysical characterization of Mycoplasma arthritidis-derived mitogen. MOLECULAR IMMUNOLOGY 44 (5): 763-773

Datta SA, Zhao Z, Clark PK, Tarasov S, Alexandratos JN, Campbell SJ, Kvaratskhelia M, Lebowitz J, Rein A. (2007) Interactions between HIV-1 Gag Molecules in Solution: An Inositol Phosphate-mediated Switch. J Mol Biol. 2007 Jan 19;365(3):799-811

Ranjit K. Deka, Chad A. Brautigam, Farol L. Tomson, Sarah B. Lumpkins, Diana R. Tomchick, Mischa Machius, and Michael V. Norgard
Crystal Structure of the Tp34 (TP0971) Lipoprotein of Treponema pallidum: IMPLICATIONS OF ITS METAL-BOUND STATE AND AFFINITY FOR HUMAN LACTOFERRIN
J. Biol. Chem., Feb 2007; 282: 5944 - 5958.

horizontal rule

Masato Kato, R Max Wynn, Jacinta L Chuang, Chad A Brautigam, Myra Custorio, David T Chuang (2006) A synchronized substrate-gating mechanism revealed by cubic-core structure of the bovine branched-chain α-ketoacid dehydrogenase complex. The EMBO Journal 25, 5983 - 5994 (13 Dec 2006)

Jason S. McLellan, Shenqin Yao, Xiaoyan Zheng, Brian V. Geisbrecht, Rodolfo Ghirlando, Philip A. Beachy, and Daniel J. Leahy (2006) From the Cover: Structure of a heparin-dependent complex of Hedgehog and Ihog.  PNAS, Nov 2006; 103: 17208 - 17213.

Kate N. Bishop, Gulnahar B. Mortuza, Steven Howell, Melvyn W. Yap, Jonathan P. Stoye, and Ian A. Taylor (2006)
Characterization of an Amino-Terminal Dimerization Domain from Retroviral Restriction Factor Fv1. J. Virol., Aug 2006; 80: 8225 - 8235.

Hiromasa Y, Hu L, Roche TE. (2006) Ligand-induced effects on pyruvate dehydrogenase kinase isoform 2. J Biol Chem. 2006 May 5;281(18):12568-79. Epub 2006 Mar 3.

Liu YZ, Cheney MD, Gaudet JJ, Chruszcz M, Lukasik SM, Sugiyama D, Lary J, Cole J, Dauter Z, Minor W, Speck NA, Bushweller JH (2006) The tetramer structure of the Nervy homology two domain, NHR2, is critical for AM1/ETO's activity. CANCER CELL 9 (4): 249-260 APR 2006

Carneiro MJVM, Zhang WK, Ioannou C, Scott DJ, Allen S, Roberts CJ, Soultanas P (2006) The DNA-remodelling activity of DnaD is the sum of oligomerization and DNA-binding activities on separate domains. MOLECULAR MICROBIOLOGY 60 (4): 917-924 MAY 2006

Rousselot M, Jaenicke E, Lamkemeyer T, Harris JR, Pirow R (2006) Native and subunit molecular mass and quarternary structure of the hemoglobin from the primitive branchiopod crustacean Triops cancriformis. FEBS JOURNAL 273 (17): 4055-4071 SEP 2006

Grainge I, Gaudier M, Schuwirth BS, Westcott SL, Sandall J, Atanassova N, Wigley DB (2006) Biochemical analysis of a DNA replication origin in the archaeon Aeropyrum pernix. JOURNAL OF MOLECULAR BIOLOGY 363 (2): 355-369 OCT 20 2006

Yang M, Horii K, Herr AB, Kirley TL (2006) 'Calcium-dependent dimerization of human soluble calcium activated nucleotidase: Characterization of the dimer interface.' J Biol Chem 2006 Jul [Epub ahead of print]

Olieric N, Bey G, Nierengarten H, Wang ED, Moras D, Eriani G, Cavarelli J (2006) Expression, purification, and characterization of a new heterotetramer structure of leucyl-tRNA synthetase from Aquifex aeolicus in Escherichia coli. PROTEIN EXPRESSION AND PURIFICATION 47 (1): 1-9 MAY 2006  

Lee HJ, Chen YS, Chou CY, Chien CH, Lin CH, Chang GG, Chen X. (2006) Investigation of the Dimer Interface and Substrate Specificity of Prolyl Dipeptidase DPP8. J Biol Chem. 2006 Dec 15;281(50):38653-62.

Gillian E. Begg, Lyle Carrington, Philippa H. Stokes, Jacqueline M. Matthews, Merridee A. Wouters, Ahsan Husain, Laszlo Lorand, Siiri E. Iismaa, and Robert M. Graham. (2006) Mechanism of allosteric regulation of transglutaminase 2 by GTP. PNAS 103(52):19683-19688

Shimp RL Jr, Martin LB, Zhang Y, Henderson BS, Duggan P, MacDonald NJ, Lebowitz J, Saul A, Narum DL. (2006) Abstract Production and characterization of clinical grade Escherichia coli derived Plasmodium falciparum 42 kDa merozoite surface protein 1 (MSP1(42)) in the absence of an affinity tag. Protein Expr Purif. 2006 Nov;50(1):58-67. Epub 2006 Jun 27.

Leslie E. Eisele, Karen J. Chave, Andrew C. Lehning and Thomas J. Ryan (2006) Characterization of Human-glutamyl hydrolase in solution demonstrates that the enzyme is a non-dissociating homodimer. Biochim Biophys Acta. 2006 Sep;1764(9):1479-86.

Cao E, Ramagopal UA, Fedorov A, Fedorov E, Yan Q, Lary JW, Cole JL, Nathenson SG, Almo SC. (2006) NTB-A receptor crystal structure: insights into homophilic interactions in the signaling lymphocytic activation molecule receptor family. Immunity. 2006 Oct;25(4):559-70.

M.C. Weston, C. Rosenmund, P. Schuck, A. Ghosal, M.L. Mayer.  Rational design of non-desensitizing glutamate receptor ion channels.  Nature Structural and Molecular Biology 13:1120-1127

Connaghan-Jones KD, Heneghan AF, Miura MT, Bain DL. (2006) Hydrodynamic Analysis of the Human Progesterone Receptor A-Isoform Reveals that Self-Association Occurs in the Micromolar Range.  Biochemistry. 45(39):12090-9.

David Wildes, L. Meadow Anderson, Alex Sabogal and Susan Marqusee (2006) Native state energetics of the Src SH2 domain: Evidence for a partially structured state in the denatured ensemble.  Protein Science 15:1769-1779

Lebaupain F, Salvay AG, Olivier B, Durand G, Fabiano AS, Michel N, Popot JL, Ebel C, Breyton C, and Pucci B. (2006) Lactobionamide Surfactants with Hydrogenated, Perfluorinated or Hemifluorinated Tails: Physical-Chemical and Biochemical
Langmuir 22(21):8881-8890

M. Rousselot, E. Jaenicke, T. Lamkemeyer, J.R. Harris, and R. Pirow (2006) Native and subunit molecular mass and quarternary structure of the hemoglobin from the primitive branchiopod crustacean Triops cancriformis. FEBS Journal 273:4055-4071

J.C.D. Houtman, H. Yamaguchi, M. Barda-Saad, A. Graiman, B. Bowden, E. Appella, P. Schuck, L.E. Samelson (2006) Oligomerization of signaling complexes by the multipoint binding of Grb2 to both LAT and Sos1. Nature Structural and Molecular Biology 13:798-805

A.C.K. Chan, B. Lelj-Garolla, F.I. Rosell, K.A. Pedersen, A.G. Mauk, and M.E.P. Murphy (2006) Cofacial heme binding is linked to dimerization by a bacterial heme transport protein. Journal of Molecular Biology 362:1108-1119

J. Dam, J. Barber, A. Grishaev, E.L. Malchiodi, P. Schuck, A. Bax, R.A. Mariuzza (2006) Variable dimerization of the Ly49A natural killer cell receptor results in differential engagement of its MHC class I ligand.  Journal of Molecular Biology 362:102-113

Patel HV, Vyas KA, Savtchenko R, Roseman S (2006) The monomer/dimer transition of enzyme I of the Escherichia coli phosphotransferase system. JOURNAL OF BIOLOGICAL CHEMISTRY 281 (26): 17570-17578 JUN 30 2006

Patel HV, Vyas KA, Mattoo RL, Southworth M, Perler FB, Comb D, Roseman S (2006) Properties of the C-terminal domain of enzyme I of the Escherichia coli phosphotransferase system. JOURNAL OF BIOLOGICAL CHEMISTRY 281 (26): 17579-17587 JUN 30 2006

Maria J. V. M. Carneiro1, Wenke Zhang, Charikleia Ioannou, David J. Scott, Stephanie Allen, Clive J. Roberts and Panos Soultanas (2006) The DNA-remodelling activity of DnaD is the sum of oligomerization and DNA-binding activities on separate domains. Molecular Microbiology Volume 60 Page 917 - May 2006 doi:10.1111/j.1365-2958.2006.05152.x Volume 60 Issue 4

F.G. Pearce, M.A. Perugini, H.J. McKerchar, J.A. Gerrard (2006) Dihydrodipicolinate synthase from Thermotoga maritima. Biochemical Journal Epub ahead of print.

Y. Shen, C.Y. Chou, G.G. Chang, L. Tong. (2006) Is dimerization required for the catalytic activity of bacterial biotin carboxylase? MOLECULAR CELL 22:807-818

Olieric N, Bey G, Nierengarten H, Wang ED, Moras D, Eriani G, Cavarelli J (2006) Expression, purification, and characterization of a new heterotetramer structure of leucyl-tRNA synthetase from Aquifex aeolicus in Escherichia coli.  PROTEIN EXPRESSION AND PURIFICATION 47 (1): 1-9 MAY 2006

Hiromasa Y, Hu LY, Roche TE (2006) Ligand-induced effects on pyruvate dehydrogenase kinase isoform 2.  JOURNAL OF BIOLOGICAL CHEMISTRY 281 (18): 12568-12579 MAY 5 2006

Chou CY, Jen WP, Hsieh YH, Shiao MS, Chang GG. (2006) Structural and functional variations in human apolipoprotein E3 and E4.  J Biol Chem. 2006 May 12;281(19):13333-44. Epub 2006 Mar 14

Pullan L, Mullapudi S, Huang Z, Baldwin PR, Chin C, Sun W, Tsujimoto S, Kolodziej SJ, Stoops JK, Lee JC, Waxham MN, Bean AJ, Penczek PA (2006) The endosome-associated protein Hrs is hexameric and controls cargo sorting as a "master molecule". STRUCTURE 14 (4): 661-671 APR 2006

Garcia AD, Otero J, Lebowitz J, Schuck P, Moss B (2006) Quaternary structure and cleavage specificity of a poxvirus Holliday junction resolvase. JOURNAL OF BIOLOGICAL CHEMISTRY 281 (17): 11618-11626 APR 28 2006

Lelj-Garolla B., Mauk A.G. (2006) Self-association and chaperone activity of Hsp27 are thermally activated.  Journal of Biological Chemistry 281:8169-8174

Fairlie WD, Perugini MA, Kvansakul M, Chen L, Huang DCS, Colman PM (2006) CED-4 forms a 2 : 2 heterotetrameric complex with CED-9 until specifically displaced by EGL-1 or CED-13 CELL DEATH AND DIFFERENTIATION 13 (3): 426-434 MAR 2006

Wei P, Fan KQ, Chen H, Ma L, Huang CK, Tan L, Xi D, Li CM, Liu Y, Cao AN, Lai LH (2006) The N-terminal octapeptide acts as a dimerization inhibitor of SARS coronavirus 3C-like proteinase. BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 339 (3): 865-872 JAN 20 2006

Meyer S, Dutzler R. (2006) Crystal structure of the cytoplasmic domain of the chloride channel ClC-0. Structure. 2006 Feb;14(2):299-307

horizontal rule

Mythili Nadella, Mario A. Bianchet, Sandra B. Gabelli, Jennifer Barrila, and L. Mario Amzel (2005) Structure and activity of the axon guidance protein MICAL. Proc Natl Acad Sci U S A. 2005 November 15; 102(46): 16830–16835.

Lee JY, Chang J, Joseph N, Ghirlando R, Rao DN, Yang W (2005) MutH complexed with hemi- and unmethylated DNAs: Coupling base recognition and DNA cleavage, MOLECULAR CELL 20 (1): 155-166 OCT 7 2005

Hickman AB, Perez ZN, Zhou LQ, Musingarimi P, Ghirlando R, Hinshaw JE, Craig NL, Dyda F (2005) Molecular architecture of a eukaryotic DNA transposase. NATURE STRUCTURAL & MOLECULAR BIOLOGY, 12 (8): 715-721 AUG 2005

Weber ANR, Moncrieffe MC, Gangloff M, Imler JL, Gay NJ (2005) Ligand-receptor and receptor-receptor interactions act in concert to activate signaling in the Drosophila toll pathway. JOURNAL OF BIOLOGICAL CHEMISTRY 280 (24): 22793-22799 JUN 17 2005

Li HM, Van Vranken S, Zhao Y, Li Z, Guo Y, Eisele L, Li YX (2005) Crystal structures of T cell receptor beta chains related to rheumatoid arthritis PROTEIN SCIENCE 14 (12): 3025-3038 DEC 2005

Taylor CM, Keating AE (2005) Orientation and oligomerization specificity of the Bcr coiled-coil oligomerization domain. BIOCHEMISTRY 44 (49): 16246-16256 DEC 13 2005

Thevenin D, Roberts MF, Lazarova T, Robinson CR (2005) Identifying interactions between transmembrane helices from the adenosine A(2A) receptor. BIOCHEMISTRY 44 (49): 16239-16245 DEC 13 2005

Pancera M, Lebowitz J, Schon A, Zhu P, Freire E, Kwong PD, Roux KH, Sodroski J, Wyatt R (2005) Soluble mimetics of human immunodeficiency virus type 1 viral spikes produced by replacement of the native trimerization domain with a heterologous trimerization motif: Characterization and ligand binding analysis. JOURNAL OF VIROLOGY 79 (15): 9954-9969 AUG 2005

Aurikko JP, Ruotolo BT, Grossmann JG, Moncrieffe MC, Stephens E, Leppanen VM, Robinson CV, Saarma M, Bradshaw RA, Blundell TL (2005) Characterization of symmetric complexes of nerve growth factor and the ectodomain of the pan-neurotrophin receptor, p75(NTR) JOURNAL OF BIOLOGICAL CHEMISTRY 280 (39): 33453-33460 SEP 30 2005

Aldaz-Carroll L, Whitbeck JC, de Leon MP, Lou H, Pannell LK, Lebowitz J, Fogg C, White CL, Moss B, Cohen GH, Eisenberg RJ (2005) Physical and immunological characterization of a recombinant secreted form of the membrane protein encoded by the vaccinia virus L1R gene. VIROLOGY 341 (1): 59-71 OCT 10 2005

Foss TR, Wiseman RL, Kelly JW (2005) The pathway by which the tetrameric protein transthyretin dissociates. BIOCHEMISTRY 44 (47): 15525-15533 NOV 29 2005

Zhu JH, Burgner JW, Harms E, Belitsky BR, Smith JL (2005) A new arrangement of (beta/alpha)(8) barrels in the synthase subunit of PLP synthase. JOURNAL OF BIOLOGICAL CHEMISTRY 280 (30): 27914-27923 JUL 29 2005

Chou CY, Lin YL, Huang YC, Sheu SY, Lin TH, Tsay HJ, Chang GG, Shiao MS (2005) Structural variation in human apolipoprotein E3 and E4: Secondary structure, tertiary structure, and size distribution. BIOPHYSICAL JOURNAL 88 (1): 455-466 JAN 2005

Nollmann M, Byron O, Stark WM (2005) Behavior of Tn3 resolvase in solution and its interaction with res. BIOPHYSICAL JOURNAL 89 (3): 1920-1931 SEP 2005

B.R. Burgess, P. Schuck, D.N. Garboczi (2005) Dissection of a merozoite surface protein 3, a representative of a family of plasmodium falciparum surface proteins, reveals an oligomeric and highly elongated molecule.  Journal of Biological Chemistry 280:37236-37245

J.F. Kepert, J. Mazurkiewicz, G.L. Heuvelman, K.F. Toth, K. Rippe (2005) NAP1 modulates binding of linker histone H1 to chromatin and induces an extended chromatin fiber conformation.  Journal of Biological Chemistry 280:34063-34072

J.P. Auriko, B.T. Ruotolo, J.G. Grossmann, M.C. Moncrieffe, E. Stephens, V.M. Leppanen, C.V. Robinson, M. Saarma, r.A. Bradshaw, T.L. Blundell. (2005) Characterization of symmetric complexes of nerve growth factor and the ectodomain of the pan-neurotrophin receptor, p75NTR. Journal of Biological Chemistry 280:33453-33460

S.J. Greive, A.F. Lins, P.H. von Hippel. (2005) Assembly of an RNA-protein complex: Binding of NusB and NusE (S10) proteins to boxA RNA nucleates the formation of the antitermination complex involved in controlling rRNA transcription in E. coli.  Journal of Biological Chemistry [Epub ahead of print]

S. Boulant, C. Vanbelle, C. Ebel, F. Penin, J.P. Lavergne. (2005) Hepatitis C virus core protein is a dimeric alpha-helical protein exhibiting membrane protein features.  Journal of Virology 27:11353-11365

D. Noy, B.M. Discher, I.V. Rubtsov, R.M. Hochstrasser, and P.L. Dutton (2005).  Design of amphiphilic protein maquettes: Enhancing maquette functionality through binding of extremely hydrophobic cofactors to lipophilic domains.  Biochemistry 44:12344-12354

J.A. Kornblatt and P. Schuck. (2005) The influence of temperature on the conformation of canine plasminogen: an analytical ultracentrifugation and dynamic light scattering study.  Biochemistry 44:13122-13131

M. Pancera, J. Lebowitz, A. Schon, P. Zhu, E. Freire, P.D. Kwong, K.H. Roux, J. Sodroski, R. Wyatt. (2005) Soluble mimetics of human immunodeficiency virus type 1 viral spikes produced by replacement of the native trimerization domain with a heterologous trimerization motif: characterization and ligand binding analysis.  Journal of Virology 79:9954-9969

P.G. Wilmann, J. Petersen, A. Pettikiriarachchi, B.M. Buckle, S.C. Smith, S. Olsen, M.A. Perugini, R.J. Devenish, M. Prescott, J. Rossjohn. (2005) The 2.1A crystal structure of the far-red fluorescent protein HcRed: inherent conformational flexibility of the chromophore.  Journal of Molecular Biology 349-233-237

M.A. Perugini, M.D.W. Griffin, B.J. Smith, L.E. Webb, A.J. Davis, E. Handman, J.A. Gerrard. (2005) Insight into the self-association of key enzymes from pathogenic species.  European Biophysics Journal 34:469-476

W.C. Hsu, H.C. Chang, C.Y. Chou, P.J. Tsai, P.I. Lin, G.G. Chang. (2005) Critical assessment of important regions in the subunit association and catalytic action of the severe acute respiratory syndrome coronavirus main protease.  Journal of Biological Chemistry 280:22741-22748

K.H. Minor, C.R. Schar, G.E. Blouse, J.D. Shore, D.A. Lawrence, P. Schuck, C.B. Peterson. (2005) A mechanism for assembly of complexes of vitronectin and plasminogen activator inhibitor-1 from sedimentation velocity analysis.  Journal of Biological Chemistry.  Epub ahead of print

J.M. Mancheno, H. Tateno, I.J. Goldstein, M. Martinez-Ripoll, J.A. Hermoso. (2005) Structural analysis of the Laetiporus sulphureus hemolytic pore-forming lectin in complex with sugars. Journal of Biological Chemistry 280:17251-17259

K. F. Toth, J. Mazurkiewicz, K. Rippe (2005) Association States of nucleosome assembly protein 1 and its complexes with histones. Journal of Biological Chemistry 280:15890-15899

I.M. Yu, C.L. Gustafson, J. Diao, J.W. Burgner II, Z. Li, J. Zhang, J. Chen. (2005) Recombinant SARS coronavirus nucleocapsid protein forms a dimer through its C-terminal domain. Journal of Biological Chemistry [Epub ahead of print].

S.S. Doun, J.W. Burgner II, S.D. Briggs, V.W. Rodwell. (2005) Enterococcus faecalis phosphomevalonate kinase. Protein Science 14:1134-1139

E. Yikilmaz, T.A. Rouault, P. Schuck (2005) Self-association and ligand-induced conformational changes of iron-regulatory proteins 1 and 2. Biochemistry 44:8470-8478

S.A. Gaidamakov, I.I. Gorshkova, P. Schuck, M. Haruki, H. Yamada, S.M. Cerritelli, R.J. Crouch. (2005) Eukaryotic RNases H1 act processively by interactions through the duplex RNA-binding domain.  Nucleic Acids Research 33:2166-2175

G.A. Snyder, P. Torabi-Parizi, J.M. Ford, J.A. Arthos, P. Schuck, M. Colonna, P.D. Sun. (2005) The DC-SIGN and DC-SIGNR repeat oligomerizes the receptor and increases gp120 binding affinity.  Journal of Virology 79:4589-4598.

V. Vogel, D. Lochmann, J. Weyermann, G. Mayer, C. Tziatzios, J.A. van den Broek, W. Haase, D. Wouters, U.S. Schubert, J. Kreuter, A. Zimmer, D. Schubert.  (2005) Oligonucleotide-protamine-albumin nanoparticles: preparation, physical properties, and intracellular distribution.  J. Control Release 103:99-111

M.H. Ali, C.M. Taylor, G. Grigoryan, K.N. Allen, B. Imperiali, A.E. Keating (2005) Design of a heterospecific, tetrameric, 21-residue miniprotein with mixed alpha/beta structure.  Structure 13:225-234

B. Lelj-Garolla, A.G. Mauk (2005) Self-association of a small heat shock protein. Journal of Molecular Biology 345:631-642

horizontal rule

Beddoe T, Bushell SR, Perugini MA, Lithgow T, Mulhern TD, Bottomley SP, Rossjohn J (2004) A biophysical analysis of the tetratricopeptide repeat-rich mitochondrial import receptor, Tom70, reveals an elongated monomer that is inherently flexible, unstable, and unfolds via a multistate pathway. JOURNAL OF BIOLOGICAL CHEMISTRY 279 (45): 46448-46454 NOV 5 2004

Chou CY, Chang HC, Hsu WC, Lin TZ, Lin CH, Chang GG (2004) Quaternary structure of the severe acute respiratory syndrome (SARS) coronavirus main protease. BIOCHEMISTRY 43 (47): 14958-14970 NOV 30 2004

H. Boukari, R. Nossal, D.L. Sackett, P. Schuck. (2004) Hydrodynamics of nanoscopic tubulin rings in dilute solution. Physical Review Letters 93:098106.

A. Turkan, Y. Hiromasa, T.E. Roche. (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 PD1c as a monomer.  Biochemistry 43:15073-15085

K. Galesa, R.M. Thomas, M. Kidric, R.H. Pain (2004) Clitocypin, a new cystein proteinase inhibitor, is monomeric: impact on the mechanism of folding. Biochemical and Biophysical Research Communications 324:576-578

S.R. Collins, A. Douglass, R.D. Vale, J.S. Weissman. (2004) Mechanism of prion propagation: Amyloid growth occurs by monomer addition.  PLosS Biology 2(10):e321

V. Gupta, C.B. Peterson, L.T. Dice, T. Uchiki, J. Racca, J.T. Guo, Y. Xu, R. Hettrich, X.L. Zhao, R. Rothstein, C.G. Dealwis. (2004) Sm11p is a dimer in solution: Characterization of denaturation and of recombinant Sm11p.  Biochemistry 43:8568-8578

R. Guan, E.L. Malchiodi, Q. Wang, P. Schuck, R.A. Mariuzza. (2004) Cyrstal structur of the C-terminal peptidoglycan-binding domain of humnan peptidoglycan recognition protein Ia reveals sodium-mediated receptor dimerization.  Journal of Biological Chemistry 279:31873-31882

A.J. Davis, M.A. Perugini, B.J. Smith, J.D. Stewart, T. Ilg, A.N. Holder, E. Handman. (2004) Properties of GDP-mannose pyrophosphorylase, a critical enzyme and drug target in Leishmania mexicana.  Journal of Biological Chemistry 279:12462-12468

J.C.D. Houtman, Y. Higashimoto, N. Dimasi, S. Cho, H. Yamaguchi, B. Bowden, C. Regan, E.L. Malichiodi, R. Mariuzza, P. Schuck, E. Appella, L.E. Samelson (2004) Binding specificity of multi-protein signaling complexes is determined by both cooperative interactions and affinity preferences.  Biochemistry 43:4170-2178

horizontal rule


J. Dam, R. Guan, K. Natarajan, N. Dimasi, L.K. Chlewicki, D.M. Kranz, P. Schuck, D.H. Margulies, R.A. Mariuzza. (2003) Variable MHC class I engagement by Ly49 NK cell receptors revealed by the crystal structure of Ly49C bound to H-2Kb Nature Immunology 4:1213-1222

S.A. Ali, N. Iwabuchi, T. Matsui, K. Hirota, S. Kidokoro, M. Arai, K. Kuwajima, P. Schuck, F. Arisaka.  (2003) Reversible and fast association equilibrium of a molecular chaperone, gp57a, of bacteriophage T4.  Biophysical Journal 85:2606-2618

M.J. Rosovitz, P. Schuck, M. Varughese, A.P. Chopra, Y. Singh, L.M. McGinnis, and S.H. Leppla. (2003) Alanine scanning mutations in anthrax toxin protective antigen domain 4 reveal residues important for binding to the cellular receptor and to a neutralizing monoclonal antibody.  Journal of Biological Chemistry 278:30936-30944

horizontal rule

J. Arthos, C. Cicala, T.D. Steenbeke, T.-W. Chun, C. Dela Cruz, D.B. Hanback, P. Khazanie, D. Nam, P. Schuck, S.M. Selig, D. VanRyk, M. Chaikin, A.S. Fauci.  (2002) Efficient inhibition of HIV-1 viral replication by a novel modification of sCD4. Journal of Biological Chemistry 277:11456-11464.

F. Taraporewala, P. Schuck, R.F. Ramig, J.T. Patton. (2002) Analysis of rotavirus temperature-sensitive mutant indicates that NSP2 octamers are the functional form of the protein.  Journal of Virology 76:7082-7093

horizontal rule

Y. Li, H. Li, N. Dimasi, J.K. McCormick, R. Martin, P. Schuck, P.M. Schlievert, R.A. Mariuzza (2001) Crystal structure of a superantigen bound to the high-affinity, zinc-dependent site on MHC class II. Immunity 14:93-104




References for the mathematical approaches developed for Sedfit which are also used in Sedphat are:

* P. Schuck (2003) On the analysis of protein self-association by sedimentation velocity analytical ultracentrifugation.  Analytical Biochemistry 320:104-124

* J. Dam, P. Schuck (2003) Calculating sedimentation coefficient distributions by direct modeling of sedimentation velocity concentration profiles.  Methods in Enzymology (in press) [comprehensive review of the concepts and numerical methods]

* P. Schuck (2003) A model for sedimentation in inhomogeneous media. I. Dynamic density gradients from sedimenting co-solutes. Biophysical Chemistry 108:187-200

* P. Schuck (2003) A model for sedimentation in inhomogeneous media. II. Compressibility of aqueous and organic solvents. Biophysical Chemistry 108:201-214

* P. Schuck, M.S. Perugini, N.R. Gonzales, G.J. Howlett, and D. Schubert. (2002) Size-distribution analysis of proteins by analytical ultracentrifugation: strategies and application to model systems.  Biophysical Journal 82:1096-1111 (get preprint) [non-linear regression of c(s) and comparison with other methods, extrapolation of ls-g*(s) to infinite time]

* Solovyova, A., P. Schuck, L. Costenaro, C. Ebel (2001) Non-ideality by sedimentation velocity of halophilic malate dehydrogenase in complex solvents.  Biophysical Journal 81:1868-1880 [concentration-dependent sedimentation] 

* P. Schuck and P. Rossmanith (2000) Determination of the sedimentation coefficient distribution g*(s) by least-squares boundary modeling. Biopolymers 54:328-341.  [analysis of g*(s) and introduction of the ls-g*(s) method without Dt-broadening]

* P. Schuck (2000) Size distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and Lamm equation modeling. Biophysical Journal 78:1606-1619.  [continuous size-distribution analysis c(s) and c(M) with Tikhonov-Phillips and maximum entropy regularization]

* P. Schuck and B. Demeler (1999) Direct sedimentation analysis of interference-optical data in analytical ultracentrifugation. Biophysical Journal 76:2288-2296.  [introduces algebraic noise decomposition allowing systematic noise and jitter to be directly modeled]

* P. Schuck (1998) Sedimentation analysis of non-interacting and self-associating solutes using numerical solutions to the Lamm equation. Biophysical Journal 75:1503-1512.  [introduction of new moving grid finite element method, extension to self-associating systems by using predictor-corrector scheme]

* P. Schuck, C.E. McPhee, and G.J. Howlett. (1998) Determination of sedimentation coefficients for small peptides. Biophysical Journal 74:466-474.  [use of finite difference and Claverie's finite element method in Crank-Nicholson scheme for fast direct boundary modeling]