Literature DB >> 15136744

Scattered Hammond plots reveal second level of site-specific information in protein folding: phi' (beta++).

Linda Hedberg1, Mikael Oliveberg.   

Abstract

Site-specific information about structural heterogeneities of the protein-folding transition-state ensemble is commonly derived from the scatter of the Brønsted plot through the individual values of = Delta logk(f)/Delta logK(D-N). Here, we provide a second level of site-specific detail in the transition-state analysis by demonstrating that the scatter of the Hammond plot is related to heterogeneities in the -value growth. That is, the extent of transition-state movement (Delta beta(++)) is proportional to the free-energy gradient of the mutational perturbation across the top of the activation barrier, '(beta(++)) proportional, variant Delta logK(D-N). The analysis is applied to the two-state protein L23 where the site-specific free-energy gradients are used to identify the interactions that show the highest degree of consolidation after crossing the barrier top. These interactions are distributed as a shell around the high- initiation point and denote the side-chain contacts that add criticality to the folding nucleus.

Entities:  

Mesh:

Year:  2004        PMID: 15136744      PMCID: PMC419653          DOI: 10.1073/pnas.0308497101

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  46 in total

1.  A theoretical search for folding/unfolding nuclei in three-dimensional protein structures.

Authors:  O V Galzitskaya; A V Finkelstein
Journal:  Proc Natl Acad Sci U S A       Date:  1999-09-28       Impact factor: 11.205

2.  Computer-based redesign of a protein folding pathway.

Authors:  S Nauli; B Kuhlman; D Baker
Journal:  Nat Struct Biol       Date:  2001-07

Review 3.  Matching theory and experiment in protein folding.

Authors:  E Alm; D Baker
Journal:  Curr Opin Struct Biol       Date:  1999-04       Impact factor: 6.809

4.  Complete change of the protein folding transition state upon circular permutation.

Authors:  Magnus Lindberg; Jeanette Tångrot; Mikael Oliveberg
Journal:  Nat Struct Biol       Date:  2002-11

5.  Unifying features in protein-folding mechanisms.

Authors:  Stefano Gianni; Nicholas R Guydosh; Faaizah Khan; Teresa D Caldas; Ugo Mayor; George W N White; Mari L DeMarco; Valerie Daggett; Alan R Fersht
Journal:  Proc Natl Acad Sci U S A       Date:  2003-10-31       Impact factor: 11.205

6.  Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition.

Authors:  S E Jackson; A R Fersht
Journal:  Biochemistry       Date:  1991-10-29       Impact factor: 3.162

7.  High-energy channeling in protein folding.

Authors:  M Silow; M Oliveberg
Journal:  Biochemistry       Date:  1997-06-24       Impact factor: 3.162

8.  Protein folding transition states: elicitation of Hammond effects by 2,2,2-trifluoroethanol.

Authors:  C P Yiu; M G Mateu; A R Fersht
Journal:  Chembiochem       Date:  2000-07-03       Impact factor: 3.164

Review 9.  Protein denaturation. C. Theoretical models for the mechanism of denaturation.

Authors:  C Tanford
Journal:  Adv Protein Chem       Date:  1970

10.  The order of secondary structure elements does not determine the structure of a protein but does affect its folding kinetics.

Authors:  A R Viguera; F J Blanco; L Serrano
Journal:  J Mol Biol       Date:  1995-04-07       Impact factor: 5.469

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  19 in total

1.  Relationship of Leffler (Bronsted) alpha values and protein folding Phi values to position of transition-state structures on reaction coordinates.

Authors:  Alan R Fersht
Journal:  Proc Natl Acad Sci U S A       Date:  2004-09-21       Impact factor: 11.205

2.  Insights into protein folding mechanisms from large scale analysis of mutational effects.

Authors:  Athi N Naganathan; Victor Muñoz
Journal:  Proc Natl Acad Sci U S A       Date:  2010-04-23       Impact factor: 11.205

3.  Phi value versus psi analysis.

Authors:  Alan R Fersht
Journal:  Proc Natl Acad Sci U S A       Date:  2004-12-06       Impact factor: 11.205

4.  Protein folding: defining a "standard" set of experimental conditions and a preliminary kinetic data set of two-state proteins.

Authors:  Karen L Maxwell; David Wildes; Arash Zarrine-Afsar; Miguel A De Los Rios; Andrew G Brown; Claire T Friel; Linda Hedberg; Jia-Cherng Horng; Diane Bona; Erik J Miller; Alexis Vallée-Bélisle; Ewan R G Main; Francesco Bemporad; Linlin Qiu; Kaare Teilum; Ngoc-Diep Vu; Aled M Edwards; Ingo Ruczinski; Flemming M Poulsen; Birthe B Kragelund; Stephen W Michnick; Fabrizio Chiti; Yawen Bai; Stephen J Hagen; Luis Serrano; Mikael Oliveberg; Daniel P Raleigh; Pernilla Wittung-Stafshede; Sheena E Radford; Sophie E Jackson; Tobin R Sosnick; Susan Marqusee; Alan R Davidson; Kevin W Plaxco
Journal:  Protein Sci       Date:  2005-02-02       Impact factor: 6.725

5.  Identification of the minimal protein-folding nucleus through loop-entropy perturbations.

Authors:  Magnus O Lindberg; Ellinor Haglund; Isaac A Hubner; Eugene I Shakhnovich; Mikael Oliveberg
Journal:  Proc Natl Acad Sci U S A       Date:  2006-02-27       Impact factor: 11.205

6.  Structural comparison of the two alternative transition states for folding of TI I27.

Authors:  Christian D Geierhaas; Robert B Best; Emanuele Paci; Michele Vendruscolo; Jane Clarke
Journal:  Biophys J       Date:  2006-04-07       Impact factor: 4.033

7.  Folding of Cu/Zn superoxide dismutase suggests structural hotspots for gain of neurotoxic function in ALS: parallels to precursors in amyloid disease.

Authors:  Anna Nordlund; Mikael Oliveberg
Journal:  Proc Natl Acad Sci U S A       Date:  2006-06-23       Impact factor: 11.205

8.  Protein folding kinetics: barrier effects in chemical and thermal denaturation experiments.

Authors:  Athi N Naganathan; Urmi Doshi; Victor Muñoz
Journal:  J Am Chem Soc       Date:  2007-04-10       Impact factor: 15.419

9.  Constrained proper sampling of conformations of transition state ensemble of protein folding.

Authors:  Ming Lin; Jian Zhang; Hsiao-Mei Lu; Rong Chen; Jie Liang
Journal:  J Chem Phys       Date:  2011-02-21       Impact factor: 3.488

10.  Structural investigation of disordered stress proteins. Comparison of full-length dehydrins with isolated peptides of their conserved segments.

Authors:  Jean-Marie Mouillon; Petter Gustafsson; Pia Harryson
Journal:  Plant Physiol       Date:  2006-03-24       Impact factor: 8.340

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