Literature DB >> 21442608

Minireview: structural insights into early folding events using continuous-flow time-resolved small-angle X-ray scattering.

Sagar V Kathuria1, Liang Guo, Rita Graceffa, Raul Barrea, R Paul Nobrega, C Robert Matthews, Thomas C Irving, Osman Bilsel.   

Abstract

Small-angle X-ray scattering (SAXS) is a powerful method for obtaining quantitative structural information on the size and shape of proteins, and it is increasingly used in kinetic studies of folding and association reactions. In this minireview, we discuss recent developments in using SAXS to obtain structural information on the unfolded ensemble and early folding intermediates of proteins using continuous-flow mixing devices. Interfacing of these micromachined devices to SAXS beamlines has allowed access to the microsecond time regime. The experimental constraints in implementation of turbulence and laminar flow-based mixers with SAXS detection and a comparison of the two approaches are presented. Current improvements and future prospects of microsecond time-resolved SAXS and the synergy with ab initio structure prediction and molecular dynamics simulations are discussed.
Copyright © 2011 Wiley Periodicals, Inc.

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Year:  2011        PMID: 21442608      PMCID: PMC3278217          DOI: 10.1002/bip.21628

Source DB:  PubMed          Journal:  Biopolymers        ISSN: 0006-3525            Impact factor:   2.505


  57 in total

1.  Microsecond hydrophobic collapse in the folding of Escherichia coli dihydrofolate reductase, an alpha/beta-type protein.

Authors:  Munehito Arai; Elena Kondrashkina; Can Kayatekin; C Robert Matthews; Masahiro Iwakura; Osman Bilsel
Journal:  J Mol Biol       Date:  2007-02-07       Impact factor: 5.469

2.  Ultrafast dynamics of protein collapse from single-molecule photon statistics.

Authors:  Daniel Nettels; Irina V Gopich; Armin Hoffmann; Benjamin Schuler
Journal:  Proc Natl Acad Sci U S A       Date:  2007-02-14       Impact factor: 11.205

3.  Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39).

Authors:  Vincent A Voelz; Gregory R Bowman; Kyle Beauchamp; Vijay S Pande
Journal:  J Am Chem Soc       Date:  2010-02-10       Impact factor: 15.419

4.  Protein denaturation: a small-angle X-ray scattering study of the ensemble of unfolded states of cytochrome c.

Authors:  D J Segel; A L Fink; K O Hodgson; S Doniach
Journal:  Biochemistry       Date:  1998-09-08       Impact factor: 3.162

5.  A continuous-flow capillary mixing method to monitor reactions on the microsecond time scale.

Authors:  M C Shastry; S D Luck; H Roder
Journal:  Biophys J       Date:  1998-05       Impact factor: 4.033

6.  Submillisecond protein folding kinetics studied by ultrarapid mixing.

Authors:  C K Chan; Y Hu; S Takahashi; D L Rousseau; W A Eaton; J Hofrichter
Journal:  Proc Natl Acad Sci U S A       Date:  1997-03-04       Impact factor: 11.205

7.  Mapping the folding free energy surface for metal-free human Cu,Zn superoxide dismutase.

Authors:  Anna-Karin E Svensson; Osman Bilsel; Elena Kondrashkina; Jill A Zitzewitz; C Robert Matthews
Journal:  J Mol Biol       Date:  2006-09-07       Impact factor: 5.469

8.  Mapping protein collapse with single-molecule fluorescence and kinetic synchrotron radiation circular dichroism spectroscopy.

Authors:  Armin Hoffmann; Avinash Kane; Daniel Nettels; David E Hertzog; Peter Baumgärtel; Jan Lengefeld; Gerd Reichardt; David A Horsley; Robert Seckler; Olgica Bakajin; Benjamin Schuler
Journal:  Proc Natl Acad Sci U S A       Date:  2006-12-21       Impact factor: 11.205

9.  Effects of denaturants and osmolytes on proteins are accurately predicted by the molecular transfer model.

Authors:  Edward P O'Brien; Guy Ziv; Gilad Haran; Bernard R Brooks; D Thirumalai
Journal:  Proc Natl Acad Sci U S A       Date:  2008-08-29       Impact factor: 11.205

10.  A helical structural nucleus is the primary elongating unit of insulin amyloid fibrils.

Authors:  Bente Vestergaard; Minna Groenning; Manfred Roessle; Jette S Kastrup; Marco van de Weert; James M Flink; Sven Frokjaer; Michael Gajhede; Dmitri I Svergun
Journal:  PLoS Biol       Date:  2007-05       Impact factor: 8.029

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  23 in total

1.  X-ray scattering experiments with high-flux X-ray source coupled rapid mixing microchannel device and their potential for high-flux neutron scattering investigations.

Authors:  R Jain; M Petri; S Kirschbaum; H Feindt; S Steltenkamp; S Sonnenkalb; S Becker; C Griesinger; A Menzel; T P Burg; S Techert
Journal:  Eur Phys J E Soft Matter       Date:  2013-09-27       Impact factor: 1.890

Review 2.  Emerging applications of small angle solution scattering in structural biology.

Authors:  Barnali N Chaudhuri
Journal:  Protein Sci       Date:  2015-02-12       Impact factor: 6.725

3.  Complex Folding Landscape of Apomyoglobin at Acidic pH Revealed by Ultrafast Kinetic Analysis of Core Mutants.

Authors:  Takuya Mizukami; Ming Xu; Ruzaliya Fazlieva; Valentina E Bychkova; Heinrich Roder
Journal:  J Phys Chem B       Date:  2018-08-31       Impact factor: 2.991

Review 4.  How, when and why proteins collapse: the relation to folding.

Authors:  Gilad Haran
Journal:  Curr Opin Struct Biol       Date:  2011-11-19       Impact factor: 6.809

5.  Combined probes of X-ray scattering and optical spectroscopy reveal how global conformational change is temporally and spatially linked to local structural perturbation in photoactive yellow protein.

Authors:  Tae Wu Kim; Cheolhee Yang; Youngmin Kim; Jong Goo Kim; Jeongho Kim; Yang Ouk Jung; Sunhong Jun; Sang Jin Lee; Sungjun Park; Irina Kosheleva; Robert Henning; Jasper J van Thor; Hyotcherl Ihee
Journal:  Phys Chem Chem Phys       Date:  2016-04-07       Impact factor: 3.676

6.  Measurement of Submillisecond Protein Folding Using Trp Fluorescence and Photochemical Oxidation.

Authors:  David Witalka; Lisa J Lapidus
Journal:  Methods Mol Biol       Date:  2022

7.  Aging can transform single-component protein condensates into multiphase architectures.

Authors:  Adiran Garaizar; Jorge R Espinosa; Jerelle A Joseph; Georg Krainer; Yi Shen; Tuomas P J Knowles; Rosana Collepardo-Guevara
Journal:  Proc Natl Acad Sci U S A       Date:  2022-06-21       Impact factor: 12.779

8.  Advances in turbulent mixing techniques to study microsecond protein folding reactions.

Authors:  Sagar V Kathuria; Alexander Chan; Rita Graceffa; R Paul Nobrega; C Robert Matthews; Thomas C Irving; Blair Perot; Osman Bilsel
Journal:  Biopolymers       Date:  2013-11       Impact factor: 2.505

Review 9.  Integrative structural modeling with small angle X-ray scattering profiles.

Authors:  Dina Schneidman-Duhovny; Seung Joong Kim; Andrej Sali
Journal:  BMC Struct Biol       Date:  2012-07-16

10.  Direct observation of cooperative protein structural dynamics of homodimeric hemoglobin from 100 ps to 10 ms with pump-probe X-ray solution scattering.

Authors:  Kyung Hwan Kim; Srinivasan Muniyappan; Key Young Oang; Jong Goo Kim; Shunsuke Nozawa; Tokushi Sato; Shin-ya Koshihara; Robert Henning; Irina Kosheleva; Hosung Ki; Youngmin Kim; Tae Wu Kim; Jeongho Kim; Shin-ichi Adachi; Hyotcherl Ihee
Journal:  J Am Chem Soc       Date:  2012-04-12       Impact factor: 15.419

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