Sebastian Doniach

Sebastian Doniach

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Sebastian Doniach

Publications by authors named "Sebastian Doniach"

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

Sci Adv 2018 05 25;4(5):eaar4418. Epub 2018 May 25.

Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich, Munich, Germany.

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http://advances.sciencemag.org/lookup/doi/10.1126/sciadv.aar
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http://dx.doi.org/10.1126/sciadv.aar4418DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5969820PMC
May 2018

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

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

Department of Applied Physics, Stanford University, Stanford, CA 94305, USA; SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA.

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http://dx.doi.org/10.1107/S2052252516013956DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5094444PMC
November 2016

The birth of the DS lineshape.

J Phys Condens Matter 2016 10 26;28(42):421005. Epub 2016 Aug 26.

Department of Applied Physics, Stanford University, Stanford, CA 94305-4045, USA.

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http://dx.doi.org/10.1088/0953-8984/28/42/421005DOI Listing
October 2016

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

Nano Lett 2016 09 22;16(9):5353-7. Epub 2016 Jun 22.

Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich , Amalienstrasse 54, 80799 Munich, Germany.

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http://dx.doi.org/10.1021/acs.nanolett.6b01160DOI Listing
September 2016

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

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

Geballe Lab for Advanced Materials, Stanford University, Stanford CA, USA.

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http://dx.doi.org/10.1142/S0217984916501177DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4846288PMC
March 2016

Understanding nucleic acid-ion interactions.

Annu Rev Biochem 2014 5;83:813-41. Epub 2014 Mar 5.

Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2628 CJ Delft, Netherlands; email:

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4384882PMC
http://dx.doi.org/10.1146/annurev-biochem-060409-092720DOI Listing
January 2015

Tuning micelle dimensions and properties with binary surfactant mixtures.

Langmuir 2014 Nov 28;30(44):13353-61. Epub 2014 Oct 28.

Department of Chemistry, University of Virginia , Charlottesville, Virginia 22904, United States.

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http://dx.doi.org/10.1021/la503458nDOI Listing
November 2014

Observation of correlated X-ray scattering at atomic resolution.

Philos Trans R Soc Lond B Biol Sci 2014 Jul;369(1647):20130315

Department of Applied Physics, Menlo Park, CA 94025, USA SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA

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http://dx.doi.org/10.1098/rstb.2013.0315DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4052857PMC
July 2014

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

PLoS One 2013 8;8(5):e62488. Epub 2013 May 8.

Department of Chemistry, University of Virginia, Charlottesville, Virginia, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0062488PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3648574PMC
December 2013

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

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

Applied Physics Department, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1103/PhysRevE.86.021901DOI Listing
August 2012

Electrostatics of nucleic acid folding under conformational constraint.

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

Biophysics Program, Stanford University, Stanford, California 94305, United States.

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http://dx.doi.org/10.1021/ja208466hDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303965PMC
March 2012

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

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

Institut Pasteur, Unit of Structural Dynamics of Macromolecules, CNRS, URA 2185, 91191 Gif/Yvette Cedex, France.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkr430DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125794PMC
July 2011

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

Methods Enzymol 2009 17;469:237-51. Epub 2009 Nov 17.

Department of Applied Physics, Stanford University, Stanford, California, USA.

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http://dx.doi.org/10.1016/S0076-6879(09)69011-XDOI Listing
January 2011

Time-resolved X-ray scattering and RNA folding.

Methods Enzymol 2009 17;469:253-68. Epub 2009 Nov 17.

School of Applied and Engineering Physics, Cornell University, Ithaca, New York, USA.

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http://dx.doi.org/10.1016/S0076-6879(09)69012-1DOI Listing
January 2011

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

Nat Struct Mol Biol 2010 Jun 27;17(6):696-702. Epub 2010 Apr 27.

Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA.

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http://dx.doi.org/10.1038/nsmb.1836DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2917185PMC
June 2010

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

RNA 2010 Apr 1;16(4):708-19. Epub 2010 Mar 1.

Department of Physics, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1261/rna.1985110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2844619PMC
April 2010

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

J Mol Biol 2010 Feb 17;396(1):153-65. Epub 2009 Nov 17.

Department of Applied Physics, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1016/j.jmb.2009.11.030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2944767PMC
February 2010

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

RNA 2009 Dec 22;15(12):2195-205. Epub 2009 Oct 22.

Department of Applied Physics, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1261/rna.1747509DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779674PMC
December 2009

Mixing and matching detergents for membrane protein NMR structure determination.

J Am Chem Soc 2009 Jun;131(21):7320-6

Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA.

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http://dx.doi.org/10.1021/ja808776jDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2751809PMC
June 2009

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

Methods Mol Biol 2009 ;540:141-59

Department of Physics, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1007/978-1-59745-558-9_11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393248PMC
May 2009

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

Curr Opin Chem Biol 2008 Dec 8;12(6):619-25. Epub 2008 Dec 8.

Department of Applied Physics, Stanford University, GLAM, McCullough 318, 476 Lomita Mall, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1016/j.cbpa.2008.10.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2976615PMC
December 2008

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

J Am Chem Soc 2008 Sep 23;130(37):12334-41. Epub 2008 Aug 23.

Department of Biochemistry, Stanford University, California 94305, USA.

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http://dx.doi.org/10.1021/ja800854uDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3167486PMC
September 2008

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

Proc Natl Acad Sci U S A 2008 Sep 3;105(36):13356-61. Epub 2008 Sep 3.

Departments of Biochemistry, Applied Physics, and Physics, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1073/pnas.0806256105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2533194PMC
September 2008

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

Structure 2008 Sep;16(9):1357-67

Department of Physics, Geballe Laboratory of Advanced Materials, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1016/j.str.2008.07.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4390040PMC
September 2008

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

Nat Struct Mol Biol 2008 Jun 30;15(6):591-7. Epub 2008 May 30.

Department of Biochemistry, Stanford University, 279 Campus Drive, Stanford, California 94305, USA.

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http://dx.doi.org/10.1038/nsmb.1429DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2441774PMC
June 2008

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

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

Biophysics Program, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1021/ja075020gDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3167487PMC
December 2007

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

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

Department of Applied Physics, Stanford University, California, USA.

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http://dx.doi.org/10.1529/biophysj.106.099168DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2025650PMC
November 2007

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

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

Departments of Physics and Applied Physics, Biophysics Program, and Stanford Synchrotron Radiation Laboratory, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1021/jp073016lDOI Listing
November 2007

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

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

Department of Physics, Biophysics Program, Stanford University, Stanford, California 94305, USA.

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http://www.annualreviews.org/doi/10.1146/annurev.biophys.36.
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http://dx.doi.org/10.1146/annurev.biophys.36.040306.132655DOI Listing
August 2007

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

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

Department of Physics, Reed College, Portland, OR 97202, USA.

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http://dx.doi.org/10.1093/nar/gkm342DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933200PMC
July 2007

Toward the mechanism of dynamical couplings and translocation in hepatitis C virus NS3 helicase using elastic network model.

Proteins 2007 Jun;67(4):886-96

Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.

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http://dx.doi.org/10.1002/prot.21326DOI Listing
June 2007

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

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

Department of Physics, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1016/j.jmb.2006.10.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1941672PMC
February 2007

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

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

The Joint Center for Structural Genomics and The Scripps Research Institute, Department of Molecular Biology, La Jolla, California 92037, USA.

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http://dx.doi.org/10.1110/ps.051874706DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2242514PMC
May 2006

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

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

Department of Chemistry and Applied Biosciences, Laboratory of Physical Chemistry, ETH Hönggerberg, Zürich 8093, Switzerland.

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http://dx.doi.org/10.1016/j.jmb.2005.08.053DOI Listing
October 2005

Unusual compactness of a polyproline type II structure.

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

Department of Chemistry, Laboratory of Physical Chemistry, Eidgenössische Technische Hochschule Zürich, Hönggerberg, 8093 Zürich, Switzerland.

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http://dx.doi.org/10.1073/pnas.0409693102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1187952PMC
August 2005

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

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

Department of Physics, Stanford University, Stanford CA 94305, USA.

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http://dx.doi.org/10.1016/j.jmb.2005.03.083DOI Listing
June 2005

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

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

Department of Physics, Stanford University, CA 94305, USA.

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http://dx.doi.org/10.1093/protein/gzi026DOI Listing
May 2005

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

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

Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.

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http://dx.doi.org/10.1016/j.str.2005.01.017DOI Listing
April 2005

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

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

Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1016/j.molbrainres.2004.11.014DOI Listing
March 2005

Principles of RNA compaction: insights from the equilibrium folding pathway of the P4-P6 RNA domain in monovalent cations.

J Mol Biol 2004 Nov;343(5):1195-206

Department of Physiology and Biophysics, Albert Einstein College of Medicine of Yeshiva University, New York, NY 10461, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S002228360401080
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http://dx.doi.org/10.1016/j.jmb.2004.08.080DOI Listing
November 2004

Random-coil behavior and the dimensions of chemically unfolded proteins.

Proc Natl Acad Sci U S A 2004 Aug 16;101(34):12491-6. Epub 2004 Aug 16.

Interdepartmental Program in Biomolecular Science and Engineering, University of California-Santa Barbara, Santa Barbara, CA 93106, USA.

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http://dx.doi.org/10.1073/pnas.0403643101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC515087PMC
August 2004

Stimulation of insulin fibrillation by urea-induced intermediates.

J Biol Chem 2004 Apr 20;279(15):14999-5013. Epub 2004 Jan 20.

Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA.

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http://dx.doi.org/10.1074/jbc.M313134200DOI Listing
April 2004

Toward a taxonomy of the denatured state: small angle scattering studies of unfolded proteins.

Adv Protein Chem 2002 ;62:241-62

Department of Applied Physics, Stanford University, Stanford, California 92343, USA.

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http://dx.doi.org/10.1016/s0065-3233(02)62009-1DOI Listing
February 2004

Natively unfolded C-terminal domain of caldesmon remains substantially unstructured after the effective binding to calmodulin.

Proteins 2003 Dec;53(4):855-62

Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.

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http://dx.doi.org/10.1002/prot.10481DOI Listing
December 2003

A comparative study of motor-protein motions by using a simple elastic-network model.

Proc Natl Acad Sci U S A 2003 Nov 29;100(23):13253-8. Epub 2003 Oct 29.

Department of Physics and Applied Physics, Stanford University, Stanford CA 94305, USA.

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http://dx.doi.org/10.1073/pnas.2235686100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC263771PMC
November 2003

Partially folded intermediates in insulin fibrillation.

Biochemistry 2003 Oct;42(39):11404-16

Department of Chemistry and Biochemistry, University of California, Santa Cruz 95064, USA.

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http://dx.doi.org/10.1021/bi034868oDOI Listing
October 2003

Nuclear localization of alpha-synuclein and its interaction with histones.

Biochemistry 2003 Jul;42(28):8465-71

Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA.

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http://dx.doi.org/10.1021/bi0341152DOI Listing
July 2003

Closing the folding chamber of the eukaryotic chaperonin requires the transition state of ATP hydrolysis.

Cell 2003 May;113(3):369-81

Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1016/s0092-8674(03)00307-6DOI Listing
May 2003

Prediction of the association state of insulin using spectral parameters.

J Pharm Sci 2003 Apr;92(4):847-58

Institute for Biological Instrumentation, Russian Academy of Sciences, 142292 Pushchino, Moscow Region, Russia.

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http://linkinghub.elsevier.com/retrieve/pii/S002235491631216
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http://dx.doi.org/10.1002/jps.10355DOI Listing
April 2003

Biophysical properties of the synucleins and their propensities to fibrillate: inhibition of alpha-synuclein assembly by beta- and gamma-synucleins.

J Biol Chem 2002 Apr 25;277(14):11970-8. Epub 2002 Jan 25.

Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA.

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http://dx.doi.org/10.1074/jbc.M109541200DOI Listing
April 2002

Elucidation of the molecular mechanism during the early events in immunoglobulin light chain amyloid fibrillation. Evidence for an off-pathway oligomer at acidic pH.

J Biol Chem 2002 Apr 28;277(15):12666-79. Epub 2002 Jan 28.

Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1074/jbc.M109229200DOI Listing
April 2002

Effect of association state and conformational stability on the kinetics of immunoglobulin light chain amyloid fibril formation at physiological pH.

J Biol Chem 2002 Apr 28;277(15):12657-65. Epub 2002 Jan 28.

Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1074/jbc.M109230200DOI Listing
April 2002

Rapid compaction during RNA folding.

Proc Natl Acad Sci U S A 2002 Apr;99(7):4266-71

Department of Biochemistry, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1073/pnas.072589599DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC123637PMC
April 2002

Distribution of molecular size within an unfolded state ensemble using small-angle X-ray scattering and pulse field gradient NMR techniques.

J Mol Biol 2002 Feb;316(1):101-12

Protein Engineering Network Centers of Excellence and Department of Medical Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.

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http://dx.doi.org/10.1006/jmbi.2001.5328DOI Listing
February 2002

Protein structure prediction constrained by solution X-ray scattering data and structural homology identification.

J Mol Biol 2002 Feb;316(1):173-87

Departments of Physics, Stanford University, CA 94305, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S002228360195324
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http://dx.doi.org/10.1006/jmbi.2001.5324DOI Listing
February 2002

Exploring the folding landscape of a structured RNA.

Proc Natl Acad Sci U S A 2002 Jan 26;99(1):155-60. Epub 2001 Dec 26.

Department of Biochemistry, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1073/pnas.221593598DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC117531PMC
January 2002

Equilibrium collapse and the kinetic 'foldability' of proteins.

Biochemistry 2002 Jan;41(1):321-5

Department of Applied Physics, Stanford University, Stanford, California 92343, USA.

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http://dx.doi.org/10.1021/bi015695aDOI Listing
January 2002