Literature DB >> 18077415

Consequences of localized frustration for the folding mechanism of the IM7 protein.

Ludovico Sutto1, Joachim Lätzer, Joseph A Hegler, Diego U Ferreiro, Peter G Wolynes.   

Abstract

In the laboratory, IM7 has been found to have an unusual folding mechanism in which an "on-pathway" intermediate with nonnative interactions is formed. We show that this intermediate is a consequence of an unusual cluster of highly frustrated interactions in the native structure. This cluster is involved in the binding of IM7 to its target, Colicin E7. Redesign of residues in this cluster to eliminate frustration is predicted by simulations to lead to faster folding without the population of an intermediate ensemble.

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Year:  2007        PMID： 18077415      PMCID： PMC2148258          DOI： 10.1073/pnas.0709922104

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


  13 in total

1.  Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins.

Authors:  C Clementi; H Nymeyer; J N Onuchic
Journal:  J Mol Biol       Date:  2000-05-19       Impact factor: 5.469

2.  Im7 folding mechanism: misfolding on a path to the native state.

Authors:  Andrew P Capaldi; Colin Kleanthous; Sheena E Radford
Journal:  Nat Struct Biol       Date:  2002-03

3.  Structural analysis of the rate-limiting transition states in the folding of Im7 and Im9: similarities and differences in the folding of homologous proteins.

Authors:  Claire T Friel; Andrew P Capaldi; Sheena E Radford
Journal:  J Mol Biol       Date:  2003-02-07       Impact factor: 5.469

4.  The effects of nonnative interactions on protein folding rates: theory and simulation.

Authors:  Cecilia Clementi; Steven S Plotkin
Journal:  Protein Sci       Date:  2004-07       Impact factor: 6.725

Review 5.  Theory of protein folding.

Authors:  José Nelson Onuchic; Peter G Wolynes
Journal:  Curr Opin Struct Biol       Date:  2004-02       Impact factor: 6.809

Review 6.  Energy landscapes and solved protein-folding problems.

Authors:  Peter G Wolynes
Journal:  Philos Trans A Math Phys Eng Sci       Date:  2005-02-15       Impact factor: 4.226

7.  Localizing frustration in native proteins and protein assemblies.

Authors:  Diego U Ferreiro; Joseph A Hegler; Elizabeth A Komives; Peter G Wolynes
Journal:  Proc Natl Acad Sci U S A       Date:  2007-12-05       Impact factor: 11.205

8.  Funnels, pathways, and the energy landscape of protein folding: a synthesis.

Authors:  J D Bryngelson; J N Onuchic; N D Socci; P G Wolynes
Journal:  Proteins       Date:  1995-03

9.  Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading.

Authors:  S Miyazawa; R L Jernigan
Journal:  J Mol Biol       Date:  1996-03-01       Impact factor: 5.469

10.  Water in protein structure prediction.

Authors:  Garegin A Papoian; Johan Ulander; Michael P Eastwood; Zaida Luthey-Schulten; Peter G Wolynes
Journal:  Proc Natl Acad Sci U S A       Date:  2004-02-26       Impact factor: 11.205
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  44 in total

1.  The structural and energetic basis for high selectivity in a high-affinity protein-protein interaction.

Authors:  Nicola A G Meenan; Amit Sharma; Sarel J Fleishman; Colin J Macdonald; Bertrand Morel; Ruth Boetzel; Geoffrey R Moore; David Baker; Colin Kleanthous
Journal:  Proc Natl Acad Sci U S A       Date:  2010-05-17       Impact factor: 11.205

2.  Structural characterization of a misfolded intermediate populated during the folding process of a PDZ domain.

Authors:  Stefano Gianni; Ylva Ivarsson; Alfonso De Simone; Carlo Travaglini-Allocatelli; Maurizio Brunori; Michele Vendruscolo
Journal:  Nat Struct Mol Biol       Date:  2010-11-14       Impact factor: 15.369

3.  On the reliability of peptide nonplanarity seen in ultra-high resolution crystal structures.

Authors:  Andrew E Brereton; P Andrew Karplus
Journal:  Protein Sci       Date:  2016-02-08       Impact factor: 6.725

4.  Localizing frustration in native proteins and protein assemblies.

Authors:  Diego U Ferreiro; Joseph A Hegler; Elizabeth A Komives; Peter G Wolynes
Journal:  Proc Natl Acad Sci U S A       Date:  2007-12-05       Impact factor: 11.205

5.  The spectrum of biomolecular states and motions.

Authors:  Joseph A Hegler; Patrick Weinkam; Peter G Wolynes
Journal:  HFSP J       Date:  2008-11-14

6.  Quantitative criteria for native energetic heterogeneity influences in the prediction of protein folding kinetics.

Authors:  Samuel S Cho; Yaakov Levy; Peter G Wolynes
Journal:  Proc Natl Acad Sci U S A       Date:  2008-12-15       Impact factor: 11.205

7.  The ruggedness of protein-protein energy landscape and the cutoff for 1/r(n) potentials.

Authors:  Anatoly M Ruvinsky; Ilya A Vakser
Journal:  Bioinformatics       Date:  2009-02-23       Impact factor: 6.937

8.  Folding energy landscape of cytochrome cb562.

Authors:  Tetsunari Kimura; Jennifer C Lee; Harry B Gray; Jay R Winkler
Journal:  Proc Natl Acad Sci U S A       Date:  2009-04-28       Impact factor: 11.205

9.  Theoretical and experimental demonstration of the importance of specific nonnative interactions in protein folding.

Authors:  Arash Zarrine-Afsar; Stefan Wallin; A Mirela Neculai; Philipp Neudecker; P Lynne Howell; Alan R Davidson; Hue Sun Chan
Journal:  Proc Natl Acad Sci U S A       Date:  2008-07-14       Impact factor: 11.205

10.  Conformational dynamics is more important than helical propensity for the folding of the all α-helical protein Im7.

Authors:  Angelo Miguel Figueiredo; Sara B-M Whittaker; Stuart E Knowling; Sheena E Radford; Geoffrey R Moore
Journal:  Protein Sci       Date:  2013-10-19       Impact factor: 6.725
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