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Title: Predicting X-ray solution scattering from flexible macromolecules: WAXS from Flexible Macromolecules

Authors:
 [1];  [2];  [2];  [3]
  1. Department of Electrical and Computer Engineering, Northeastern University, Boston Massachusetts
  2. Department of Chemistry and Chemical Biology, Northeastern University, Boston Massachusetts
  3. Department of Bioengineering, Northeastern University, Boston Massachusetts
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
NSFNIH
OSTI Identifier:
1483071
Resource Type:
Journal Article
Journal Name:
Protein Science
Additional Journal Information:
Journal Volume: 27; Journal Issue: 12; Journal ID: ISSN 0961-8368
Publisher:
The Protein Society
Country of Publication:
United States
Language:
ENGLISH

Citation Formats

Zhou, Hao, Guterres, Hugo, Mattos, Carla, and Makowski, Lee. Predicting X-ray solution scattering from flexible macromolecules: WAXS from Flexible Macromolecules. United States: N. p., 2018. Web. doi:10.1002/pro.3508.
Zhou, Hao, Guterres, Hugo, Mattos, Carla, & Makowski, Lee. Predicting X-ray solution scattering from flexible macromolecules: WAXS from Flexible Macromolecules. United States. doi:10.1002/pro.3508.
Zhou, Hao, Guterres, Hugo, Mattos, Carla, and Makowski, Lee. Tue . "Predicting X-ray solution scattering from flexible macromolecules: WAXS from Flexible Macromolecules". United States. doi:10.1002/pro.3508.
@article{osti_1483071,
title = {Predicting X-ray solution scattering from flexible macromolecules: WAXS from Flexible Macromolecules},
author = {Zhou, Hao and Guterres, Hugo and Mattos, Carla and Makowski, Lee},
abstractNote = {},
doi = {10.1002/pro.3508},
journal = {Protein Science},
issn = {0961-8368},
number = 12,
volume = 27,
place = {United States},
year = {2018},
month = {10}
}

Works referenced in this record:

An improved method for calculating the contribution of solvent to the X-ray diffraction pattern of biological molecules
journal, December 1978

  • Fraser, R. D. B.; MacRae, T. P.; Suzuki, E.
  • Journal of Applied Crystallography, Vol. 11, Issue 6
  • DOI: 10.1107/S0021889878014296

Structural Dynamics in Ras and Related Proteins upon Nucleotide Switching
journal, November 2016

  • Harrison, Rane A.; Lu, Jia; Carrasco, Martin
  • Journal of Molecular Biology, Vol. 428, Issue 23
  • DOI: 10.1016/j.jmb.2016.10.017

Molecular Crowding Inhibits Intramolecular Breathing Motions in Proteins
journal, January 2008

  • Makowski, Lee; Rodi, Diane J.; Mandava, Suneeta
  • Journal of Molecular Biology, Vol. 375, Issue 2
  • DOI: 10.1016/j.jmb.2007.07.075

Recent Developments in Solution X-Ray Scattering
journal, June 1980


Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules
journal, June 2004

  • Hamelberg, Donald; Mongan, John; McCammon, J. Andrew
  • The Journal of Chemical Physics, Vol. 120, Issue 24
  • DOI: 10.1063/1.1755656

Scalable molecular dynamics with NAMD
journal, January 2005

  • Phillips, James C.; Braun, Rosemary; Wang, Wei
  • Journal of Computational Chemistry, Vol. 26, Issue 16, p. 1781-1802
  • DOI: 10.1002/jcc.20289

CRYSOL – a Program to Evaluate X-ray Solution Scattering of Biological Macromolecules from Atomic Coordinates
journal, December 1995

  • Svergun, D.; Barberato, C.; Koch, M. H. J.
  • Journal of Applied Crystallography, Vol. 28, Issue 6
  • DOI: 10.1107/S0021889895007047

Simulated x-ray scattering of protein solutions using explicit-solvent models
journal, April 2009

  • Park, Sanghyun; Bardhan, Jaydeep P.; Roux, Benoît
  • The Journal of Chemical Physics, Vol. 130, Issue 13
  • DOI: 10.1063/1.3099611

Determination of the regularization parameter in indirect-transform methods using perceptual criteria
journal, August 1992


The Amber biomolecular simulation programs
journal, January 2005

  • Case, David A.; Cheatham, Thomas E.; Darden, Tom
  • Journal of Computational Chemistry, Vol. 26, Issue 16
  • DOI: 10.1002/jcc.20290

Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation
journal, May 2014

  • Miao, Yinglong; Sinko, William; Pierce, Levi
  • Journal of Chemical Theory and Computation, Vol. 10, Issue 7
  • DOI: 10.1021/ct500090q

Modulation of HIV protease flexibility by the T80N mutation: HIV Protease Flexibility
journal, September 2015

  • Zhou, Hao; Li, Shangyang; Badger, John
  • Proteins: Structure, Function, and Bioinformatics, Vol. 83, Issue 11
  • DOI: 10.1002/prot.24737

Visualizing global properties of a molecular dynamics trajectory: Visualizing Global Properties
journal, November 2015

  • Zhou, Hao; Li, Shangyang; Makowski, Lee
  • Proteins: Structure, Function, and Bioinformatics, Vol. 84, Issue 1
  • DOI: 10.1002/prot.24957

Decomposing the Energetic Impact of Drug Resistant Mutations in HIV-1 Protease on Binding DRV
journal, March 2010

  • Cai, Yufeng; Schiffer, Celia A.
  • Journal of Chemical Theory and Computation, Vol. 6, Issue 4
  • DOI: 10.1021/ct9004678

Rapid calculation of the solution scattering profile from a macromolecule of known structure
journal, January 1989

  • Lattman, Eaton Edward
  • Proteins: Structure, Function, and Genetics, Vol. 5, Issue 2
  • DOI: 10.1002/prot.340050209

Conformational States of Human Rat Sarcoma (Ras) Protein Complexed with Its Natural Ligand GTP and Their Role for Effector Interaction and GTP Hydrolysis
journal, October 2010

  • Spoerner, Michael; Hozsa, Constantin; Poetzl, Johann A.
  • Journal of Biological Chemistry, Vol. 285, Issue 51
  • DOI: 10.1074/jbc.M110.145235

The Effects of Thermal Disorder on the Solution-Scattering Profiles of Macromolecules
journal, April 2014


Effects of Catalytic Action and Ligand Binding on Conformational Ensembles of Adenylate Kinase
journal, August 2017


How does a symmetric dimer recognize an asymmetric substrate? a substrate complex of HIV-1 protease
journal, September 2000

  • Prabu-Jeyabalan, Moses; Nalivaika, Ellen; Schiffer, Celia A.
  • Journal of Molecular Biology, Vol. 301, Issue 5
  • DOI: 10.1006/jmbi.2000.4018

On the interpretation and prediction of X-ray scattering profiles of biomolecules in solution
journal, April 1982


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

Direct Attack on RAS: Intramolecular Communication and Mutation-Specific Effects
journal, April 2015


X-ray solution scattering studies of the structural diversity intrinsic to protein ensembles
journal, April 2011

  • Makowski, Lee; Gore, David; Mandava, Suneeta
  • Biopolymers, Vol. 95, Issue 8
  • DOI: 10.1002/bip.21631

SoftWAXS : a computational tool for modeling wide-angle X-ray solution scattering from biomolecules
journal, September 2009

  • Bardhan, Jaydeep; Park, Sanghyun; Makowski, Lee
  • Journal of Applied Crystallography, Vol. 42, Issue 5
  • DOI: 10.1107/S0021889809032919

Protein hydration in solution: Experimental observation by x-ray and neutron scattering
journal, March 1998

  • Svergun, D. I.; Richard, S.; Koch, M. H. J.
  • Proceedings of the National Academy of Sciences, Vol. 95, Issue 5
  • DOI: 10.1073/pnas.95.5.2267

X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution
journal, August 2007

  • Putnam, Christopher D.; Hammel, Michal; Hura, Greg L.
  • Quarterly Reviews of Biophysics, Vol. 40, Issue 3
  • DOI: 10.1017/S0033583507004635

All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
journal, April 1998

  • MacKerell, A. D.; Bashford, D.; Bellott, M.
  • The Journal of Physical Chemistry B, Vol. 102, Issue 18
  • DOI: 10.1021/jp973084f

Upgrade of MacCHESS facility for X-ray scattering of biological macromolecules in solution
journal, January 2015

  • Acerbo, Alvin Samuel; Cook, Michael J.; Gillilan, Richard Edward
  • Journal of Synchrotron Radiation, Vol. 22, Issue 1
  • DOI: 10.1107/S1600577514020360

Role of Invariant Thr80 in Human Immunodeficiency Virus Type 1 Protease Structure, Function, and Viral Infectivity
journal, June 2006

  • Foulkes, J. E.; Prabu-Jeyabalan, M.; Cooper, D.
  • Journal of Virology, Vol. 80, Issue 14
  • DOI: 10.1128/JVI.01900-05

Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
journal, October 1992

  • Miyamoto, Shuichi; Kollman, Peter A.
  • Journal of Computational Chemistry, Vol. 13, Issue 8
  • DOI: 10.1002/jcc.540130805

Expression, purification, crystallization and X-ray data collection for RAS and its mutants
journal, March 2016


A Comprehensive Survey of Ras Mutations in Cancer
journal, May 2012


BioXTAS RAW , a software program for high-throughput automated small-angle X-ray scattering data reduction and preliminary analysis
journal, August 2009

  • Nielsen, S. S.; Toft, K. Noergaard; Snakenborg, D.
  • Journal of Applied Crystallography, Vol. 42, Issue 5
  • DOI: 10.1107/S0021889809023863

Allosteric Effects of the Oncogenic RasQ61L Mutant on Raf-RBD
journal, March 2015


The BioCAT undulator beamline 18ID: a facility for biological non-crystalline diffraction and X-ray absorption spectroscopy at the Advanced Photon Source
journal, August 2004

  • Fischetti, R.; Stepanov, S.; Rosenbaum, G.
  • Journal of Synchrotron Radiation, Vol. 11, Issue 5
  • DOI: 10.1107/S0909049504016760

Mapping the Nucleotide and Isoform-Dependent Structural and Dynamical Features of Ras Proteins
journal, June 2008


Hydrophobic Core Flexibility Modulates Enzyme Activity in HIV-1 Protease
journal, February 2012

  • Mittal, Seema; Cai, Yufeng; Nalam, Madhavi N. L.
  • Journal of the American Chemical Society, Vol. 134, Issue 9
  • DOI: 10.1021/ja2095766

The small GTPases K-Ras, N-Ras, and H-Ras have distinct biochemical properties determined by allosteric effects
journal, June 2017

  • Johnson, Christian W.; Reid, Derion; Parker, Jillian A.
  • Journal of Biological Chemistry, Vol. 292, Issue 31
  • DOI: 10.1074/jbc.M117.778886

Three-dimensional triple-resonance NMR Spectroscopy of isotopically enriched proteins
journal, December 2011

  • Kay, Lewis E.; Ikura, Mitsuhiko; Tschudin, Rolf
  • Journal of Magnetic Resonance, Vol. 213, Issue 2
  • DOI: 10.1016/j.jmr.2011.09.004

The GTPase superfamily: conserved structure and molecular mechanism
journal, January 1991

  • Bourne, Henry R.; Sanders, David A.; McCormick, Frank
  • Nature, Vol. 349, Issue 6305
  • DOI: 10.1038/349117a0

Allosteric modulation of Ras positions Q61 for a direct role in catalysis
journal, March 2010

  • Buhrman, G.; Holzapfel, G.; Fetics, S.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 11
  • DOI: 10.1073/pnas.0912226107

VMD: Visual molecular dynamics
journal, February 1996


Intrinsic motions along an enzymatic reaction trajectory
journal, November 2007

  • Henzler-Wildman, Katherine A.; Thai, Vu; Lei, Ming
  • Nature, Vol. 450, Issue 7171
  • DOI: 10.1038/nature06410