Literature DB >> 19529835

Reconstructing three-dimensional shape envelopes from time-resolved small-angle X-ray scattering data.

Jessica Lamb1, Lisa Kwok, Xiangyun Qiu, Kurt Andresen, Hye Yoon Park, Lois Pollack.   

Abstract

Modern computing power has made it possible to reconstruct low-resolution, three-dimensional shapes from solution small-angle X-ray scattering (SAXS) data on biomolecules without a priori knowledge of the structure. In conjunction with rapid mixing techniques, SAXS has been applied to time resolve conformational changes accompanying important biological processes, such as biomolecular folding. In response to the widespread interest in SAXS reconstructions, their value in conjunction with such time-resolved data has been examined. The group I intron from Tetrahymena thermophila and its P4-P6 subdomain are ideal model systems for investigation owing to extensive previous studies, including crystal structures. The goal of this paper is to assay the quality of reconstructions from time-resolved data given the sacrifice in signal-to-noise required to obtain sharp time resolution.

Entities:  

Year:  2008        PMID: 19529835      PMCID: PMC2648657          DOI: 10.1107/S0021889808028264

Source DB:  PubMed          Journal:  J Appl Crystallogr        ISSN: 0021-8898            Impact factor:   3.304


  21 in total

1.  Compactness of the denatured state of a fast-folding protein measured by submillisecond small-angle x-ray scattering.

Authors:  L Pollack; M W Tate; N C Darnton; J B Knight; S M Gruner; W A Eaton; R H Austin
Journal:  Proc Natl Acad Sci U S A       Date:  1999-08-31       Impact factor: 11.205

2.  An optimal Mg(2+) concentration for kinetic folding of the tetrahymena ribozyme.

Authors:  M S Rook; D K Treiber; J R Williamson
Journal:  Proc Natl Acad Sci U S A       Date:  1999-10-26       Impact factor: 11.205

3.  Reconstruction of protein form with X-ray solution scattering and a genetic algorithm.

Authors:  P Chacón; J F Díaz; F Morán; J M Andreu
Journal:  J Mol Biol       Date:  2000-06-23       Impact factor: 5.469

4.  Rapid compaction during RNA folding.

Authors:  Rick Russell; Ian S Millett; Mark W Tate; Lisa W Kwok; Bradley Nakatani; Sol M Gruner; Simon G J Mochrie; Vijay Pande; Sebastian Doniach; Daniel Herschlag; Lois Pollack
Journal:  Proc Natl Acad Sci U S A       Date:  2002-04-02       Impact factor: 11.205

5.  Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing.

Authors:  D I Svergun
Journal:  Biophys J       Date:  1999-06       Impact factor: 4.033

6.  The solution structure of a cardiac troponin C-troponin I-troponin T complex shows a somewhat compact troponin C interacting with an extended troponin I-troponin T component.

Authors:  William T Heller; Ekram Abusamhadneh; Natosha Finley; Paul R Rosevear; Jill Trewhella
Journal:  Biochemistry       Date:  2002-12-31       Impact factor: 3.162

7.  Structure of the Tetrahymena ribozyme: base triple sandwich and metal ion at the active site.

Authors:  Feng Guo; Anne R Gooding; Thomas R Cech
Journal:  Mol Cell       Date:  2004-11-05       Impact factor: 17.970

8.  Concordant exploration of the kinetics of RNA folding from global and local perspectives.

Authors:  Lisa W Kwok; Inna Shcherbakova; Jessica S Lamb; Hye Yoon Park; Kurt Andresen; Heather Smith; Michael Brenowitz; Lois Pollack
Journal:  J Mol Biol       Date:  2005-11-10       Impact factor: 5.469

9.  Crystal structure of a group I ribozyme domain: principles of RNA packing.

Authors:  J H Cate; A R Gooding; E Podell; K Zhou; B L Golden; C E Kundrot; T R Cech; J A Doudna
Journal:  Science       Date:  1996-09-20       Impact factor: 47.728

10.  Conformational landscape of cytochrome c folding studied by microsecond-resolved small-angle x-ray scattering.

Authors:  Shuji Akiyama; Satoshi Takahashi; Tetsunari Kimura; Koichiro Ishimori; Isao Morishima; Yukihiro Nishikawa; Tetsuro Fujisawa
Journal:  Proc Natl Acad Sci U S A       Date:  2002-01-02       Impact factor: 11.205

View more
  9 in total

1.  Visualizing large RNA molecules in solution.

Authors:  Ajaykumar Gopal; Z Hong Zhou; Charles M Knobler; William M Gelbart
Journal:  RNA       Date:  2011-12-21       Impact factor: 4.942

2.  Small-angle solution scattering using the mixed-mode pixel array detector.

Authors:  Lucas J Koerner; Richard E Gillilan; Katherine S Green; Suntao Wang; Sol M Gruner
Journal:  J Synchrotron Radiat       Date:  2010-12-08       Impact factor: 2.616

3.  Kinetic and thermodynamic framework for P4-P6 RNA reveals tertiary motif modularity and modulation of the folding preferred pathway.

Authors:  Namita Bisaria; Max Greenfeld; Charles Limouse; Dmitri S Pavlichin; Hideo Mabuchi; Daniel Herschlag
Journal:  Proc Natl Acad Sci U S A       Date:  2016-08-04       Impact factor: 11.205

4.  How the Conformations of an Internal Junction Contribute to Fold an RNA Domain.

Authors:  Yen-Lin Chen; Julie L Sutton; Lois Pollack
Journal:  J Phys Chem B       Date:  2018-10-17       Impact factor: 2.991

5.  Time-resolved structural studies of protein reaction dynamics: a smorgasbord of X-ray approaches.

Authors:  Sebastian Westenhoff; Elena Nazarenko; Erik Malmerberg; Jan Davidsson; Gergely Katona; Richard Neutze
Journal:  Acta Crystallogr A       Date:  2010-02-18       Impact factor: 2.290

6.  Methods for SAXS-based structure determination of biomolecular complexes.

Authors:  Sichun Yang
Journal:  Adv Mater       Date:  2014-05-30       Impact factor: 30.849

7.  Millisecond timescale reactions observed via X-ray spectroscopy in a 3D microfabricated fused silica mixer.

Authors:  Diego A Huyke; Ashwin Ramachandran; Oscar Ramirez-Neri; Jose A Guerrero-Cruz; Leland B Gee; Augustin Braun; Dimosthenis Sokaras; Brenda Garcia-Estrada; Edward I Solomon; Britt Hedman; Mario U Delgado-Jaime; Daniel P DePonte; Thomas Kroll; Juan G Santiago
Journal:  J Synchrotron Radiat       Date:  2021-05-19       Impact factor: 2.557

8.  Viral RNAs are unusually compact.

Authors:  Ajaykumar Gopal; Defne E Egecioglu; Aron M Yoffe; Avinoam Ben-Shaul; Ayala L N Rao; Charles M Knobler; William M Gelbart
Journal:  PLoS One       Date:  2014-09-04       Impact factor: 3.240

9.  Combined small angle X-ray solution scattering with atomic force microscopy for characterizing radiation damage on biological macromolecules.

Authors:  Luca Costa; Alexander Andriatis; Martha Brennich; Jean-Marie Teulon; Shu-Wen W Chen; Jean-Luc Pellequer; Adam Round
Journal:  BMC Struct Biol       Date:  2016-10-27
  9 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.