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Title: Validation of macromolecular flexibility in solution by small-angle X-ray scattering (SAXS)

Abstract

The dynamics of macromolecular conformations are critical to the action of cellular networks. Solution X-ray scattering studies, in combination with macromolecular X-ray crystallography (MX) and nuclear magnetic resonance (NMR), strive to determine complete and accurate states of macromolecules, providing novel insights describing allosteric mechanisms, supramolecular complexes, and dynamic molecular machines. This review addresses theoretical and practical concepts, concerns, and considerations for using these techniques in conjunction with computational methods to productively combine solution-scattering data with high-resolution structures. I discuss the principal means of direct identification of macromolecular flexibility from SAXS data followed by critical concerns about the methods used to calculate theoretical SAXS profiles from high-resolution structures. The SAXS profile is a direct interrogation of the thermodynamic ensemble and techniques such as, for example, minimal ensemble search (MES), enhance interpretation of SAXS experiments by describing the SAXS profiles as population-weighted thermodynamic ensembles. I discuss recent developments in computational techniques used for conformational sampling, and how these techniques provide a basis for assessing the level of the flexibility within a sample. Although these approaches sacrifice atomic detail, the knowledge gained from ensemble analysis is often appropriate for developing hypotheses and guiding biochemical experiments. Examples of the use of SAXS and combinedmore » approaches with X-ray crystallography, NMR, and computational methods to characterize dynamic assemblies are presented.« less

Authors:
 [1]
+ Show Author Affiliations
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Physical Biosciences Division
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1815576
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
European Biophysics Journal
Additional Journal Information:
Journal Volume: 41; Journal Issue: 10; Journal ID: ISSN 0175-7571
Publisher:
Springer Nature
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Small-angle X-ray scattering (SAXS); Macromolecular flexibility; Rigid-body modeling; Ensemble analysis

Citation Formats

Hammel, Michal. Validation of macromolecular flexibility in solution by small-angle X-ray scattering (SAXS). United States: N. p., 2012. Web. doi:10.1007/s00249-012-0820-x.
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Hammel, Michal. Validation of macromolecular flexibility in solution by small-angle X-ray scattering (SAXS). United States. https://doi.org/10.1007/s00249-012-0820-x
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Hammel, Michal. Sat . "Validation of macromolecular flexibility in solution by small-angle X-ray scattering (SAXS)". United States. https://doi.org/10.1007/s00249-012-0820-x. https://www.osti.gov/servlets/purl/1815576.
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@article{osti_1815576,
title = {Validation of macromolecular flexibility in solution by small-angle X-ray scattering (SAXS)},
author = {Hammel, Michal},
abstractNote = {The dynamics of macromolecular conformations are critical to the action of cellular networks. Solution X-ray scattering studies, in combination with macromolecular X-ray crystallography (MX) and nuclear magnetic resonance (NMR), strive to determine complete and accurate states of macromolecules, providing novel insights describing allosteric mechanisms, supramolecular complexes, and dynamic molecular machines. This review addresses theoretical and practical concepts, concerns, and considerations for using these techniques in conjunction with computational methods to productively combine solution-scattering data with high-resolution structures. I discuss the principal means of direct identification of macromolecular flexibility from SAXS data followed by critical concerns about the methods used to calculate theoretical SAXS profiles from high-resolution structures. The SAXS profile is a direct interrogation of the thermodynamic ensemble and techniques such as, for example, minimal ensemble search (MES), enhance interpretation of SAXS experiments by describing the SAXS profiles as population-weighted thermodynamic ensembles. I discuss recent developments in computational techniques used for conformational sampling, and how these techniques provide a basis for assessing the level of the flexibility within a sample. Although these approaches sacrifice atomic detail, the knowledge gained from ensemble analysis is often appropriate for developing hypotheses and guiding biochemical experiments. Examples of the use of SAXS and combined approaches with X-ray crystallography, NMR, and computational methods to characterize dynamic assemblies are presented.},
doi = {10.1007/s00249-012-0820-x},
journal = {European Biophysics Journal},
number = 10,
volume = 41,
place = {United States},
year = {Sat May 26 00:00:00 EDT 2012},
month = {Sat May 26 00:00:00 EDT 2012}
}
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Solution X-ray scattering combined with computational modeling reveals multiple conformations of covalently bound ubiquitin on PCNA
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Nbs1 Flexibly Tethers Ctp1 and Mre11-Rad50 to Coordinate DNA Double-Strand Break Processing and Repair
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The Immunoglobulin-like Domains 1 and 2 of the Protein Tyrosine Phosphatase LAR Adopt an Unusual Horseshoe-like Conformation
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Structural Characterization of Intramolecular Hg2+ Transfer between Flexibly Linked Domains of Mercuric Ion Reductase
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Bridging the solution divide: comprehensive structural analyses of dynamic RNA, DNA, and protein assemblies by small-angle X-ray scattering
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Free State Conformational Sampling of the SAM-I Riboswitch Aptamer Domain
journal, July 2010

XLF Regulates Filament Architecture of the XRCC4·Ligase IV Complex
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SAXS Ensemble Refinement of ESCRT-III CHMP3 Conformational Transitions
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Solution Structure of Human and Bovine β2-Glycoprotein I Revealed by Small-angle X-ray Scattering
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Human DNA Ligase III Recognizes DNA Ends by Dynamic Switching between Two DNA-Bound States
journal, July 2010

  • Cotner-Gohara, Elizabeth; Kim, In-Kwon; Hammel, Michal
  • Biochemistry, Vol. 49, Issue 29
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Refinement of Multidomain Protein Structures by Combination of Solution Small-Angle X-ray Scattering and NMR Data
journal, November 2005

  • Grishaev, Alexander; Wu, Justin; Trewhella, Jill
  • Journal of the American Chemical Society, Vol. 127, Issue 47
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Structural Characterization of Flexible Proteins Using Small-Angle X-ray Scattering
journal, May 2007

  • Bernadó, Pau; Mylonas, Efstratios; Petoukhov, Maxim V.
  • Journal of the American Chemical Society, Vol. 129, Issue 17
  • DOI: 10.1021/ja069124n

Improved Fitting of Solution X-ray Scattering Data to Macromolecular Structures and Structural Ensembles by Explicit Water Modeling
journal, November 2010

  • Grishaev, Alexander; Guo, Liang; Irving, Thomas
  • Journal of the American Chemical Society, Vol. 132, Issue 44
  • DOI: 10.1021/ja106173n

Conformational Space of Flexible Biological Macromolecules from Average Data
journal, September 2010

  • Bertini, Ivano; Giachetti, Andrea; Luchinat, Claudio
  • Journal of the American Chemical Society, Vol. 132, Issue 38
  • DOI: 10.1021/ja1063923

Evidence of Reciprocal Reorientation of the Catalytic and Hemopexin-Like Domains of Full-Length MMP-12
journal, May 2008

  • Bertini, Ivano; Calderone, Vito; Fragai, Marco
  • Journal of the American Chemical Society, Vol. 130, Issue 22
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Human DNA ligase I completely encircles and partially unwinds nicked DNA
journal, November 2004

  • Pascal, John M.; O'Brien, Patrick J.; Tomkinson, Alan E.
  • Nature, Vol. 432, Issue 7016
  • DOI: 10.1038/nature03082

Dynamic personalities of proteins
journal, December 2007

  • Henzler-Wildman, Katherine; Kern, Dorothee
  • Nature, Vol. 450, Issue 7172
  • DOI: 10.1038/nature06522

A structural basis for complement inhibition by Staphylococcus aureus
journal, March 2007

  • Hammel, Michal; Sfyroera, Georgia; Ricklin, Daniel
  • Nature Immunology, Vol. 8, Issue 4
  • DOI: 10.1038/ni1450

Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS)
journal, July 2009

  • Hura, Greg L.; Menon, Angeli L.; Hammel, Michal
  • Nature Methods, Vol. 6, Issue 8
  • DOI: 10.1038/nmeth.1353

ABC ATPase signature helices in Rad50 link nucleotide state to Mre11 interface for DNA repair
journal, March 2011

  • Williams, Gareth J.; Williams, R. Scott; Williams, Jessica S.
  • Nature Structural & Molecular Biology, Vol. 18, Issue 4
  • DOI: 10.1038/nsmb.2038

Common architecture of nuclear receptor heterodimers on DNA direct repeat elements with different spacings
journal, April 2011

  • Rochel, Natacha; Ciesielski, Fabrice; Godet, Julien
  • Nature Structural & Molecular Biology, Vol. 18, Issue 5
  • DOI: 10.1038/nsmb.2054

Hexameric structures of the archaeal secretion ATPase GspE and implications for a universal secretion mechanism
journal, January 2007

Structural analysis of intrinsically disordered proteins by small-angle X-ray scattering
journal, January 2012

  • Bernadó, Pau; Svergun, Dmitri I.
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Self-association and domain rearrangements between complement C3 and C3u provide insight into the activation mechanism of C3
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Structure determinations of human and chimaeric antibodies by solution scattering and constrained molecular modelling
journal, January 2008

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X-ray diffraction "fingerprinting" of DNA structure in solution for quantitative evaluation of molecular dynamics simulation
journal, February 2006

  • Zuo, X.; Cui, G.; Merz, K. M.
  • Proceedings of the National Academy of Sciences, Vol. 103, Issue 10
  • DOI: 10.1073/pnas.0600022103

Multidomain assembled states of Hck tyrosine kinase in solution
journal, August 2010

  • Yang, S.; Blachowicz, L.; Makowski, L.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 36
  • DOI: 10.1073/pnas.1004569107

Solution X-ray scattering combined with computational modeling reveals multiple conformations of covalently bound ubiquitin on PCNA
journal, October 2011

  • Tsutakawa, S. E.; Van Wynsberghe, A. W.; Freudenthal, B. D.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 43
  • DOI: 10.1073/pnas.1110480108

Disorder-to-order transition underlies the structural basis for the assembly of a transcriptionally active PGC-1 /ERR  complex
journal, November 2011

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  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 46
  • DOI: 10.1073/pnas.1113813108

Ku and DNA-dependent Protein Kinase Dynamic Conformations and Assembly Regulate DNA Binding and the Initial Non-homologous End Joining Complex
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  • Hammel, Michal; Yu, Yaping; Mahaney, Brandi L.
  • Journal of Biological Chemistry, Vol. 285, Issue 2
  • DOI: 10.1074/jbc.m109.065615

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  • Hammel, Michal; Rey, Martial; Yu, Yaping
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  • DOI: 10.1074/jbc.m111.272641

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  • Hammel, Michal; Fierobe, Henri-Pierre; Czjzek, Mirjam
  • Journal of Biological Chemistry, Vol. 279, Issue 53
  • DOI: 10.1074/jbc.m408979200

Structural Basis of Cellulosome Efficiency Explored by Small Angle X-ray Scattering
journal, September 2005

  • Hammel, Michal; Fierobe, Henri-Pierre; Czjzek, Mirjam
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  • DOI: 10.1074/jbc.m503168200

The MutSα-Proliferating Cell Nuclear Antigen Interaction in Human DNA Mismatch Repair
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  • Bernstein, N. K.; Hammel, M.; Mani, R. S.
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  • DOI: 10.1093/nar/gkp597

Crystal structure of the Mre11-Rad50-ATP S complex: understanding the interplay between Mre11 and Rad50
journal, April 2011

  • Lim, H. S.; Kim, J. S.; Park, Y. B.
  • Genes & Development, Vol. 25, Issue 10
  • DOI: 10.1101/gad.2037811

Computation of small-angle scattering profiles with three-dimensional Zernike polynomials
journal, February 2012

  • Liu, Haiguang; Morris, Richard J.; Hexemer, Alexander
  • Acta Crystallographica Section A Foundations of Crystallography, Vol. 68, Issue 2
  • DOI: 10.1107/s010876731104788x

The Staphylococcus aureus extracellular adherence protein (Eap) adopts an elongated but structured conformation in solution
journal, December 2007

  • Hammel, Michal; Němeček, Daniel; Keightley, J. Andrew
  • Protein Science, Vol. 16, Issue 12
  • DOI: 10.1110/ps.073170807

Structural Mechanism of Abscisic Acid Binding and Signaling by Dimeric PYR1
journal, October 2009

Improving small-angle X-ray scattering data for structural analyses of the RNA world
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Global Rigid Body Modeling of Macromolecular Complexes against Small-Angle Scattering Data
journal, August 2005

Structure and flexibility within proteins as identified through small angle X-ray scattering
journal, January 2009

  • Pelikan, M.; Hura, G.; Hammel, M.
  • General Physiology and Biophysics, Vol. 28, Issue 2
  • DOI: 10.4149/gpb_2009_02_174
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