Literature DB >> 19580767

Slowing down downhill folding: a three-probe study.

Seung Joong Kim1, Yoshitaka Matsumura, Charles Dumont, Hiroshi Kihara, Martin Gruebele.   

Abstract

The mutant Tyr22Trp/Glu33Tyr/Gly46Ala/Gly48Ala of lambda repressor fragment lambda(6-85) was previously assigned as an incipient downhill folder. We slow down its folding in a cryogenic water-ethylene-glycol solvent (-18 to -28 degrees C). The refolding kinetics are probed by small-angle x-ray scattering, circular dichroism, and fluorescence to measure the radius of gyration, the average secondary structure content, and the native packing around the single tryptophan residue. The main resolved kinetic phase of the mutant is probe independent and faster than the main phase observed for the pseudo-wild-type. Excess helical structure formed early on by the mutant may reduce the formation of turns and prevent the formation of compact misfolded states, speeding up the overall folding process. Extrapolation of our main cryogenic folding phase and previous T-jump measurements to 37 degrees C yields nearly the same refolding rate as extrapolated by Oas and co-workers from NMR line-shape data. Taken together, all the data consistently indicate a folding speed limit of approximately 4.5 micros for this fast folder.

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Year:  2009        PMID: 19580767      PMCID: PMC2711359          DOI: 10.1016/j.bpj.2009.04.041

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  47 in total

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Authors:  S J Hagen; W A Eaton
Journal:  J Mol Biol       Date:  2000-03-31       Impact factor: 5.469

2.  Structural and kinetic characterization of early folding events in beta-lactoglobulin.

Authors:  K Kuwata; R Shastry; H Cheng; M Hoshino; C A Batt; Y Goto; H Roder
Journal:  Nat Struct Biol       Date:  2001-02

3.  Refolding of beta-lactoglobulin studied by stopped-flow circular dichroism at subzero temperatures.

Authors:  Z Qin; D Hu; L Shimada; T Nakagawa; M Arai; J M Zhou; H Kihara
Journal:  FEBS Lett       Date:  2001-11-02       Impact factor: 4.124

4.  Preorganized secondary structure as an important determinant of fast protein folding.

Authors:  J K Myers; T G Oas
Journal:  Nat Struct Biol       Date:  2001-06

5.  Experimental identification of downhill protein folding.

Authors:  Maria M Garcia-Mira; Mourad Sadqi; Niels Fischer; Jose M Sanchez-Ruiz; Victor Muñoz
Journal:  Science       Date:  2002-12-13       Impact factor: 47.728

6.  On the extended beta-conformation propensity of polypeptides at high temperature.

Authors:  Wei Yuan Yang; Edgar Larios; Martin Gruebele
Journal:  J Am Chem Soc       Date:  2003-12-31       Impact factor: 15.419

7.  Folding at the speed limit.

Authors:  Wei Yuan Yang; Martin Gruebele
Journal:  Nature       Date:  2003-05-08       Impact factor: 49.962

8.  How fast is protein hydrophobic collapse?

Authors:  Mourad Sadqi; Lisa J Lapidus; Victor Muñoz
Journal:  Proc Natl Acad Sci U S A       Date:  2003-10-06       Impact factor: 11.205

Review 9.  The protein folding 'speed limit'.

Authors:  Jan Kubelka; James Hofrichter; William A Eaton
Journal:  Curr Opin Struct Biol       Date:  2004-02       Impact factor: 6.809

10.  Spin glasses and the statistical mechanics of protein folding.

Authors:  J D Bryngelson; P G Wolynes
Journal:  Proc Natl Acad Sci U S A       Date:  1987-11       Impact factor: 11.205

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  13 in total

1.  Multiscaled exploration of coupled folding and binding of an intrinsically disordered molecular recognition element in measles virus nucleoprotein.

Authors:  Yong Wang; Xiakun Chu; Sonia Longhi; Philippe Roche; Wei Han; Erkang Wang; Jin Wang
Journal:  Proc Natl Acad Sci U S A       Date:  2013-09-16       Impact factor: 11.205

2.  How to mark off paths on the protein energy landscape.

Authors:  Martin Gruebele
Journal:  Proc Natl Acad Sci U S A       Date:  2009-11-04       Impact factor: 11.205

3.  CARPe diem.

Authors:  Martin Gruebele
Journal:  Biophys J       Date:  2014-07-01       Impact factor: 4.033

4.  Cooperative folding near the downhill limit determined with amino acid resolution by hydrogen exchange.

Authors:  Wookyung Yu; Michael C Baxa; Isabelle Gagnon; Karl F Freed; Tobin R Sosnick
Journal:  Proc Natl Acad Sci U S A       Date:  2016-04-13       Impact factor: 11.205

5.  A survey of lambda repressor fragments from two-state to downhill folding.

Authors:  Feng Liu; Yi Gui Gao; Martin Gruebele
Journal:  J Mol Biol       Date:  2010-02-06       Impact factor: 5.469

6.  Transient helical structure during PI3K and Fyn SH3 domain folding.

Authors:  Yoshitaka Matsumura; Masaji Shinjo; Seung Joong Kim; Nobuyuki Okishio; Martin Gruebele; Hiroshi Kihara
Journal:  J Phys Chem B       Date:  2013-04-18       Impact factor: 2.991

7.  Structural study of hNck2 SH3 domain protein in solution by circular dichroism and X-ray solution scattering.

Authors:  Yoshitaka Matsumura; Masaji Shinjo; Tsutomu Matsui; Kaoru Ichimura; Jianxing Song; Hiroshi Kihara
Journal:  Biophys Chem       Date:  2013-02-26       Impact factor: 2.352

8.  Microsecond folding experiments and simulations: a match is made.

Authors:  M B Prigozhin; M Gruebele
Journal:  Phys Chem Chem Phys       Date:  2013-01-29       Impact factor: 3.676

Review 9.  Fast protein folding kinetics.

Authors:  Hannah Gelman; Martin Gruebele
Journal:  Q Rev Biophys       Date:  2014-03-18       Impact factor: 5.318

Review 10.  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
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