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Gold nanocrystal labels provide a sequence-to-3D structure map in SAXS reconstructions.

Zettl T, Mathew RS, Shi X, Doniach S, Herschlag D, Harbury PAB, Lipfert J.

Sci Adv. 2018 May 25;4(5):eaar4418. doi: 10.1126/sciadv.aar4418. eCollection 2018 May.


A stochastic model of active zone material mediated synaptic vesicle docking and priming at resting active zones.

Jung JH, Doniach S.

Sci Rep. 2017 Mar 21;7(1):278. doi: 10.1038/s41598-017-00360-z.


Angular correlations of photons from solution diffraction at a free-electron laser encode molecular structure.

Mendez D, Watkins H, Qiao S, Raines KS, Lane TJ, Schenk G, Nelson G, Subramanian G, Tono K, Joti Y, Yabashi M, Ratner D, Doniach S.

IUCrJ. 2016 Sep 26;3(Pt 6):420-429. eCollection 2016 Nov 1.


The birth of the DS lineshape.

Doniach S.

J Phys Condens Matter. 2016 Oct 26;28(42):421005. doi: 10.1088/0953-8984/28/42/421005. Epub 2016 Aug 26. No abstract available.


Absolute Intramolecular Distance Measurements with Angstrom-Resolution Using Anomalous Small-Angle X-ray Scattering.

Zettl T, Mathew RS, Seifert S, Doniach S, Harbury PA, Lipfert J.

Nano Lett. 2016 Sep 14;16(9):5353-7. doi: 10.1021/acs.nanolett.6b01160. Epub 2016 Jun 22.


Potential for measurement of the distribution of DNA folds in complex environments using Correlated X-ray Scattering.

Schenk G, Krajina B, Spakowitz A, Doniach S.

Mod Phys Lett B. 2016 Mar 30;30(8). pii: 1650117. Epub 2015 Dec 29.


The linac coherent light source single particle imaging road map.

Aquila A, Barty A, Bostedt C, Boutet S, Carini G, dePonte D, Drell P, Doniach S, Downing KH, Earnest T, Elmlund H, Elser V, Gühr M, Hajdu J, Hastings J, Hau-Riege SP, Huang Z, Lattman EE, Maia FR, Marchesini S, Ourmazd A, Pellegrini C, Santra R, Schlichting I, Schroer C, Spence JC, Vartanyants IA, Wakatsuki S, Weis WI, Williams GJ.

Struct Dyn. 2015 Apr 21;2(4):041701. doi: 10.1063/1.4918726. eCollection 2015 Jul.


Tuning micelle dimensions and properties with binary surfactant mixtures.

Oliver RC, Lipfert J, Fox DA, Lo RH, Kim JJ, Doniach S, Columbus L.

Langmuir. 2014 Nov 11;30(44):13353-61. doi: 10.1021/la503458n. Epub 2014 Oct 28.


Observation of correlated X-ray scattering at atomic resolution.

Mendez D, Lane TJ, Sung J, Sellberg J, Levard C, Watkins H, Cohen AE, Soltis M, Sutton S, Spudich J, Pande V, Ratner D, Doniach S.

Philos Trans R Soc Lond B Biol Sci. 2014 Jul 17;369(1647):20130315. doi: 10.1098/rstb.2013.0315.


Understanding nucleic acid-ion interactions.

Lipfert J, Doniach S, Das R, Herschlag D.

Annu Rev Biochem. 2014;83:813-41. doi: 10.1146/annurev-biochem-060409-092720. Epub 2014 Mar 5. Review.


Dependence of micelle size and shape on detergent alkyl chain length and head group.

Oliver RC, Lipfert J, Fox DA, Lo RH, Doniach S, Columbus L.

PLoS One. 2013 May 8;8(5):e62488. doi: 10.1371/journal.pone.0062488. Print 2013.


Caulobacter chromosome in vivo configuration matches model predictions for a supercoiled polymer in a cell-like confinement.

Hong SH, Toro E, Mortensen KI, de la Rosa MA, Doniach S, Shapiro L, Spakowitz AJ, McAdams HH.

Proc Natl Acad Sci U S A. 2013 Jan 29;110(5):1674-9. doi: 10.1073/pnas.1220824110. Epub 2013 Jan 14.


Salt dependence of the radius of gyration and flexibility of single-stranded DNA in solution probed by small-angle x-ray scattering.

Sim AY, Lipfert J, Herschlag D, Doniach S.

Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Aug;86(2 Pt 1):021901. Epub 2012 Aug 1.


Electrostatics of nucleic acid folding under conformational constraint.

Anthony PC, Sim AY, Chu VB, Doniach S, Block SM, Herschlag D.

J Am Chem Soc. 2012 Mar 14;134(10):4607-14. doi: 10.1021/ja208466h. Epub 2012 Feb 27.


AquaSAXS: a web server for computation and fitting of SAXS profiles with non-uniformally hydrated atomic models.

Poitevin F, Orland H, Doniach S, Koehl P, Delarue M.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W184-9. doi: 10.1093/nar/gkr430. Epub 2011 Jun 10.


ATP-independent reversal of a membrane protein aggregate by a chloroplast SRP subunit.

Jaru-Ampornpan P, Shen K, Lam VQ, Ali M, Doniach S, Jia TZ, Shan SO.

Nat Struct Mol Biol. 2010 Jun;17(6):696-702. doi: 10.1038/nsmb.1836. Epub 2010 Apr 27.


Dissecting electrostatic screening, specific ion binding, and ligand binding in an energetic model for glycine riboswitch folding.

Lipfert J, Sim AY, Herschlag D, Doniach S.

RNA. 2010 Apr;16(4):708-19. doi: 10.1261/rna.1985110. Epub 2010 Mar 1.


Combining single-molecule optical trapping and small-angle x-ray scattering measurements to compute the persistence length of a protein ER/K alpha-helix.

Sivaramakrishnan S, Sung J, Ali M, Doniach S, Flyvbjerg H, Spudich JA.

Biophys J. 2009 Dec 2;97(11):2993-9. doi: 10.1016/j.bpj.2009.09.009.


The ligand-free state of the TPP riboswitch: a partially folded RNA structure.

Ali M, Lipfert J, Seifert S, Herschlag D, Doniach S.

J Mol Biol. 2010 Feb 12;396(1):153-65. doi: 10.1016/j.jmb.2009.11.030. Epub 2009 Nov 17.


Do conformational biases of simple helical junctions influence RNA folding stability and specificity?

Chu VB, Lipfert J, Bai Y, Pande VS, Doniach S, Herschlag D.

RNA. 2009 Dec;15(12):2195-205. doi: 10.1261/rna.1747509. Epub 2009 Oct 22.


Mixing and matching detergents for membrane protein NMR structure determination.

Columbus L, Lipfert J, Jambunathan K, Fox DA, Sim AY, Doniach S, Lesley SA.

J Am Chem Soc. 2009 Jun 3;131(21):7320-6. doi: 10.1021/ja808776j.


Riboswitch conformations revealed by small-angle X-ray scattering.

Lipfert J, Herschlag D, Doniach S.

Methods Mol Biol. 2009;540:141-59. doi: 10.1007/978-1-59745-558-9_11.


Redistribution of terbium ions across acetylcholine receptor-enriched membranes induced by agonist desensitization.

Lee TE, Chuang AR, Marek MS, Doniach S, Fairclough RH.

Biophys J. 2009 Apr 8;96(7):2637-47. doi: 10.1016/j.bpj.2008.08.006.


Time-resolved X-ray scattering and RNA folding.

Pollack L, Doniach S.

Methods Enzymol. 2009;469:253-68. doi: 10.1016/S0076-6879(09)69012-1. Epub 2009 Nov 17.


Use of small angle X-ray scattering (SAXS) to characterize conformational states of functional RNAs.

Doniach S, Lipfert J.

Methods Enzymol. 2009;469:237-51. doi: 10.1016/S0076-6879(09)69011-X. Epub 2009 Nov 17.


A repulsive field: advances in the electrostatics of the ion atmosphere.

Chu VB, Bai Y, Lipfert J, Herschlag D, Doniach S.

Curr Opin Chem Biol. 2008 Dec;12(6):619-25. doi: 10.1016/j.cbpa.2008.10.010. Epub 2008 Dec 8. Review.


The complete VS ribozyme in solution studied by small-angle X-ray scattering.

Lipfert J, Ouellet J, Norman DG, Doniach S, Lilley DM.

Structure. 2008 Sep 10;16(9):1357-67. doi: 10.1016/j.str.2008.07.007.


Dynamic charge interactions create surprising rigidity in the ER/K alpha-helical protein motif.

Sivaramakrishnan S, Spink BJ, Sim AY, Doniach S, Spudich JA.

Proc Natl Acad Sci U S A. 2008 Sep 9;105(36):13356-61. doi: 10.1073/pnas.0806256105. Epub 2008 Sep 3.


Critical assessment of nucleic acid electrostatics via experimental and computational investigation of an unfolded state ensemble.

Bai Y, Chu VB, Lipfert J, Pande VS, Herschlag D, Doniach S.

J Am Chem Soc. 2008 Sep 17;130(37):12334-41. doi: 10.1021/ja800854u. Epub 2008 Aug 23.


Long single alpha-helical tail domains bridge the gap between structure and function of myosin VI.

Spink BJ, Sivaramakrishnan S, Lipfert J, Doniach S, Spudich JA.

Nat Struct Mol Biol. 2008 Jun;15(6):591-7. doi: 10.1038/nsmb.1429. Epub 2008 May 30.


Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids.

Bai Y, Greenfeld M, Travers KJ, Chu VB, Lipfert J, Doniach S, Herschlag D.

J Am Chem Soc. 2007 Dec 5;129(48):14981-8. Epub 2007 Nov 9.


Size and shape of detergent micelles determined by small-angle X-ray scattering.

Lipfert J, Columbus L, Chu VB, Lesley SA, Doniach S.

J Phys Chem B. 2007 Nov 1;111(43):12427-38. Epub 2007 Oct 9.


Evaluation of ion binding to DNA duplexes using a size-modified Poisson-Boltzmann theory.

Chu VB, Bai Y, Lipfert J, Herschlag D, Doniach S.

Biophys J. 2007 Nov 1;93(9):3202-9. Epub 2007 Jun 29.


MinActionPath: maximum likelihood trajectory for large-scale structural transitions in a coarse-grained locally harmonic energy landscape.

Franklin J, Koehl P, Doniach S, Delarue M.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W477-82. Epub 2007 Jun 1.


Small-angle X-ray scattering from RNA, proteins, and protein complexes.

Lipfert J, Doniach S.

Annu Rev Biophys Biomol Struct. 2007;36:307-27.


Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae.

Lipfert J, Das R, Chu VB, Kudaravalli M, Boyd N, Herschlag D, Doniach S.

J Mol Biol. 2007 Feb 2;365(5):1393-406. Epub 2006 Oct 13.


Mis-translation of a computationally designed protein yields an exceptionally stable homodimer: implications for protein engineering and evolution.

Dantas G, Watters AL, Lunde BM, Eletr ZM, Isern NG, Roseman T, Lipfert J, Doniach S, Tompa M, Kuhlman B, Stoddard BL, Varani G, Baker D.

J Mol Biol. 2006 Oct 6;362(5):1004-24. Epub 2006 Aug 4.


Early work with synchrotron radiation at stanford.

Doniach S, Hodgson K, Lindau I, Pianetta P, Winick H.

J Synchrotron Radiat. 1997 Nov 1;4(Pt 6):380-95.


Dynamic bond constraints in protein Langevin dynamics.

Franklin J, Doniach S.

J Chem Phys. 2006 Apr 21;124(15):154901.


Fourth-generation X-ray sources: some possible applications to biology.

Doniach S.

J Synchrotron Radiat. 2000 May 1;7(Pt 3):116-20. Epub 2000 May 1.


Expression, purification, and characterization of Thermotoga maritima membrane proteins for structure determination.

Columbus L, Lipfert J, Klock H, Millett I, Doniach S, Lesley SA.

Protein Sci. 2006 May;15(5):961-75. Epub 2006 Apr 5.


Adaptive time stepping in biomolecular dynamics.

Franklin J, Doniach S.

J Chem Phys. 2005 Sep 22;123(12):124909.


How large is an alpha-helix? Studies of the radii of gyration of helical peptides by small-angle X-ray scattering and molecular dynamics.

Zagrovic B, Jayachandran G, Millett IS, Doniach S, Pande VS.

J Mol Biol. 2005 Oct 21;353(2):232-41.


Unusual compactness of a polyproline type II structure.

Zagrovic B, Lipfert J, Sorin EJ, Millett IS, van Gunsteren WF, Doniach S, Pande VS.

Proc Natl Acad Sci U S A. 2005 Aug 16;102(33):11698-703. Epub 2005 Aug 5.


Protein misfolding and amyloid formation for the peptide GNNQQNY from yeast prion protein Sup35: simulation by reaction path annealing.

Lipfert J, Franklin J, Wu F, Doniach S.

J Mol Biol. 2005 Jun 10;349(3):648-58. Epub 2005 Apr 13.


Fold recognition aided by constraints from small angle X-ray scattering data.

Zheng W, Doniach S.

Protein Eng Des Sel. 2005 May;18(5):209-19. Epub 2005 Apr 21.


Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved.

Zheng W, Brooks BR, Doniach S, Thirumalai D.

Structure. 2005 Apr;13(4):565-77.


Effects of nitration on the structure and aggregation of alpha-synuclein.

Uversky VN, Yamin G, Munishkina LA, Karymov MA, Millett IS, Doniach S, Lyubchenko YL, Fink AL.

Brain Res Mol Brain Res. 2005 Mar 24;134(1):84-102.


Probing counterion modulated repulsion and attraction between nucleic acid duplexes in solution.

Bai Y, Das R, Millett IS, Herschlag D, Doniach S.

Proc Natl Acad Sci U S A. 2005 Jan 25;102(4):1035-40. Epub 2005 Jan 12.

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