We will communicate applications and development of SASSIE that have been carried out by our group and others using the software.

We have used the system to study various protein, protein complexes, and protein-nucleic acid assemblies, both in solution and on membrane surfaces.  We are looking for new systems to apply our experimental and analysis methods, including both biological and non-biological systems (polymers).

Monte Carlo simulation algorithm for B-DNA

S. C. Howell, X. Qiu, J. E. Curtis

J. Comput. Chem., (in press: 2016).

Defining the intrinsically disordered c-terminal domain of ssb reveals DNA-mediated compaction

M. Green, L. Hatter, E. Brookes, P. Soultanas, D. J. Scott

J. Mol. Biol., 428, 357-364 (2016).

Linkage via k27 bestows ubiquitin chains with unique properties among polyubiquitins

C. A. Castaneda, E. Dixon, O. Walker, A. Chaturvedi, M. A. Nakasone, J. E. Curtis, M. R. Reed, S. Krueger, T. A. Cropp, D. Fushman

Structure, 24, 424-436 (2016).

Linkage-specific conformational ensembles of non-canonical polyubiquitin chains

C. A. Castaneda, J. E. Curtis,  S. Krueger, D. Fushman

Phys. Chem. Chem. Phys., 18, 5771-5788 (2016).

Deuterium labeling together with contrast variation small-angle neutron scattering suggests how skp captures and releases unfolded outer membrane proteins

N. R. Zaccai, C. W. Sandlin, J. T. Hoopes, J. E. Curtis,  P. J. Fleming, K. G. Fleming, S. Krueger

Meth. Enzymol., 566, 159-210 (2016).

The solution structures of native and patient monomeric human igga1 reveal asymmetric extended structures: implications for function and igan disease

G. K. Hui, D. W. Wright, O. L. Vennard, L. E. Rayner, M. Pang, S. C. Yeo, J. Gor, K. Molyneux, J. Barratt, S. J. Perkins

Biochem. J. 471, 167-185 (2015).

The leucine-rich amelogenin protein (LRAP) is primarily monomeric and unstructured in physiological solution

B. J. Tarasevich, J. S. Philo, N. K. Mauf, S. Krueger, G. W. Buchko, G. Lin, W. J. Shaw

J. Struct. Biol. 190, 81-91 (2015).

Structural Model of an mRNA in complex with the bacterial chaperone hfq

Y. Peng, J. E. Curtis, X. Fang, S. Woodson

Proc. Natl. Acad. Sci. USA 111, 17134-17139 (2014).

The GenApp framework integrated with airavata for managed compute resource submissions

E. H. Brookes, N. Anjum, J. E. Curtis, R. Marru, M. Pierce

Concurr. Comput. DOI: 10.1002/cpe.3519 (2014).

SLDMOL: A tool for the structural characterization of thermally disordered membrane proteins

J. E. Curtis, H. Zhang, H. Nanda

Comp. Phys. Comm. 185, 3010-3015 (2014).

Atomistic structure of bottlebrush polymers: simulations and neutron scattering studies

Z. Zhang, J-M. Y. Carrillo, S, Ahn, B. Wu, K. Hong, G. S. Smith, C. Do

Macromolecules 47, 5808-5814 (2014).

The solution structure of full-length dodecameric MCM by SANS and molecular modeling

S. Krueger, J. H. Shin, J. E. Curtis, K. A. Rubinson, Z. Kelman

Proteins: Structure, Function, and Bioinformatics 82, 2364-2374 (2014).

Probing the average local structure of biomolecules using small-angle scattering and scaling laws

1000. M.C. Watson and J. E. Curtis
      

Biophys. J. 106 (11), 2474-2482 (2014).

Structures of TraI in solution

N. J. Clark, M. Raththagala, N. T. Wright, E. A. Buenger, J. F. Schildbach, S. Krueger, J. E. Curtis

J. Mol. Model. 20, 2308 (2014).

Observation of small cluster formation in concentrated monoclonal antibody solutions and its implications to solution viscosity

E. J. Yearly, P. D. Godfrin, T. Perevozchikova, H. Zhang, P. Falus, L. Porcar, M. Nagao, J. E. Curtis, P. Gawande, R. Taing, I. E. Zarraga, N. J. Wagner, Y. Liu

Biophys. J. 106, 1763-1770 (2014).

Small-angle neutron scattering study of a monoclonal antibody using free-energy constraints

N. J. Clark, H. Zhang, S. Krueger, H. J. Lee, R. R. Ketchem, B. A. Kerwin, S. R. Kanapuram, M. J. Treuheit, A. McAuley, J. E. Curtis

J. Phys. Chem. B 117, 14029-14038 (2013).

Small-angle scattering contrast calculator for protein and nucleic acid complexes in solution

11. K.L. Sarachan, J. E. Curtis, S. Krueger
    

J. Appl. Cryst. 46 1889-1893 (2013).

Role of water and ions on the dynamical transition of RNA

H. Zhang, S. Khodadadi, S. L. Fiedler, J. E. Curtis

J. Phys. Chem. Letters 4, 3325-3329 (2013).

Rapid and accurate calculation of small-angle scattering profiles using the golden ratio

1000. M.C. Watson and J. E. Curtis
      

J. Appl. Cryst. 46, 1171-1177 (2013).

Solution conformations of prototype foamy virus integrase and its stable synaptic complex with u5 virial DNA

K. Gupta, J. E. Curtis, S. Krueger, Y. Hwang, P. Cherepanov, F. Bushman, G. D. V. Duyne

Structure 20, 1-11 (2012).

Solution structure and small angle scattering analysis of TraI (381-569)

14. N.T. Wright, M. Raththagala, C. W. Hemmis, S. Edwards, J. E. Curtis, S. Krueger, J. Schildbach
    

Proteins: Structure, Function, and Bioinformatics 80, 2250-2261 (2012).

SASSIE: A program to study intrinsically disordered biological molecules and macromolecular ensembles using experimental scattering restraints

J. E. Curtis, S. Raghunandan, H. Nanda, S. Krueger

Comp. Phys. Comm. 183, 382-389 (2012).

Atomistic ensemble modeling and SANS of intrinsically disordered protein complexes: applied to MCM helicase

S. Krueger, J. E. Curtis, S. Raghunandan, Z. Kelman

Biophys. J. 101, 2999-3007 (2011).

HIV-1 gag extension: conformational changes require simultaneous interaction with membrane and nucleic acid

S. A. K. Datta, F. Heinrich, S. Raghunandan, S. Krueger, J. E. Curtis, A. Rein, H. Nanda

10. J.Mol. Biol. 406, 205-214   (2011).
    

Electrostatic interactions and binding orientation of HIV-1 matrix, studied by neutron reflectivity

H. Nanda, S. A. K. Datta, F. Heinrich, A. Rein, S. Krueger,  J. E. Curtis

Biophys. J. 99, 2516-2524  (2010).

Neutron reflectivity study of the conformation of HIV Nef bound to lipid membranes

M. S. Kent,  J. K. Murton, S. Satija, B. Akgun, H. Nanda, J. E. Curtis, J. Majewski, J. R. Engen, C. R. Morgan

Biophys. J. 99, 1940-1948  (2010).

Conformation of the HIV-1 Gag protein in solution

S. A. K. Datta, J. E. Curtis, W. Ratcliff, P. K. Clark, R. M. Crist, J. Lebowitz, S. Krueger, A. Rein

10. J.Mol. Biol. 365, 812-824  (2007).
    

RAP uses a histidine switch to regulate its interaction with LRP in the ER and golgi

D. Lee, J. D. Walsh, I. Mikhallenko,  P. Yu, M. Migliorini, Y. Wu, S. Krueger, J. E. Curtis, B. Harris, S. Lockett, S. C. Blacklow, D. K. Strickland, Y. Wang

Mol. Cell  22, 423-430  (2006).