Literature DB >> 18502978

Kinetic barriers and the role of topology in protein and RNA folding.

Tobin R Sosnick1.   

Abstract

This review compares the folding behavior of proteins and RNAs. Topics covered include the role of topology in the determination of folding rates, major folding events including collapse, properties of denatured states, pathway heterogeneity, and the influence of the mode of initiation on the folding pathway.

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Year:  2008        PMID： 18502978      PMCID： PMC2492822          DOI： 10.1110/ps.036319.108

Source DB:  PubMed          Journal:  Protein Sci        ISSN： 0961-8368            Impact factor:   6.725


  113 in total

1.  Chain collapse can occur concomitantly with the rate-limiting step in protein folding.

Authors:  K W Plaxco; I S Millett; D J Segel; S Doniach; D Baker
Journal:  Nat Struct Biol       Date:  1999-06

Review 2.  Beyond kinetic traps in RNA folding.

Authors:  D K Treiber; J R Williamson
Journal:  Curr Opin Struct Biol       Date:  2001-06       Impact factor: 6.809

3.  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

4.  Random-coil behavior and the dimensions of chemically unfolded proteins.

Authors:  Jonathan E Kohn; Ian S Millett; Jaby Jacob; Bojan Zagrovic; Thomas M Dillon; Nikolina Cingel; Robin S Dothager; Soenke Seifert; P Thiyagarajan; Tobin R Sosnick; M Zahid Hasan; Vijay S Pande; Ingo Ruczinski; Sebastian Doniach; Kevin W Plaxco
Journal:  Proc Natl Acad Sci U S A       Date:  2004-08-16       Impact factor: 11.205

Review 5.  RNA and protein folding: common themes and variations.

Authors:  D Thirumalai; Changbong Hyeon
Journal:  Biochemistry       Date:  2005-04-05       Impact factor: 3.162

6.  Surprisingly high correlation between early and late stages in non-two-state protein folding.

Authors:  Kiyoto Kamagata; Kunihiro Kuwajima
Journal:  J Mol Biol       Date:  2006-02-03       Impact factor: 5.469

7.  Effect of point mutations on the folding of globular proteins.

Authors:  C R Matthews
Journal:  Methods Enzymol       Date:  1987       Impact factor: 1.600

8.  Is burst hydrophobic collapse necessary for protein folding?

Authors:  A M Gutin; V I Abkevich; E I Shakhnovich
Journal:  Biochemistry       Date:  1995-03-07       Impact factor: 3.162

9.  Identification of a collapsed intermediate with non-native long-range interactions on the folding pathway of a pair of Fyn SH3 domain mutants by NMR relaxation dispersion spectroscopy.

Authors:  Philipp Neudecker; Arash Zarrine-Afsar; Wing-Yiu Choy; D Ranjith Muhandiram; Alan R Davidson; Lewis E Kay
Journal:  J Mol Biol       Date:  2006-08-22       Impact factor: 5.469

10.  Structural basis for altering the stability of homologous RNAs from a mesophilic and a thermophilic bacterium.

Authors:  Nathan J Baird; Narayanan Srividya; Andrey S Krasilnikov; Alfonso Mondragón; Tobin R Sosnick; Tao Pan
Journal:  RNA       Date:  2006-04       Impact factor: 4.942
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  25 in total

1.  Modeling large regions in proteins: applications to loops, termini, and folding.

Authors:  Aashish N Adhikari; Jian Peng; Michael Wilde; Jinbo Xu; Karl F Freed; Tobin R Sosnick
Journal:  Protein Sci       Date:  2011-12-05       Impact factor: 6.725

2.  A "Link-Psi" strategy using crosslinking indicates that the folding transition state of ubiquitin is not very malleable.

Authors:  Ali T Shandiz; Michael C Baxa; Tobin R Sosnick
Journal:  Protein Sci       Date:  2012-04-23       Impact factor: 6.725

Review 3.  Taming free energy landscapes with RNA chaperones.

Authors:  Sarah A Woodson
Journal:  RNA Biol       Date:  2010-11-01       Impact factor: 4.652

4.  DEAD-box protein facilitated RNA folding in vivo.

Authors:  Andreas Liebeg; Oliver Mayer; Christina Waldsich
Journal:  RNA Biol       Date:  2010-11-01       Impact factor: 4.652

5.  Effects of Preferential Counterion Interactions on the Specificity of RNA Folding.

Authors:  Joon Ho Roh; Duncan Kilburn; Reza Behrouzi; Wokyung Sung; R M Briber; Sarah A Woodson
Journal:  J Phys Chem Lett       Date:  2018-09-18       Impact factor: 6.475

6.  RNA molecules with conserved catalytic cores but variable peripheries fold along unique energetically optimized pathways.

Authors:  Somdeb Mitra; Alain Laederach; Barbara L Golden; Russ B Altman; Michael Brenowitz
Journal:  RNA       Date:  2011-06-28       Impact factor: 4.942

Review 7.  Understanding the contribution of synonymous mutations to human disease.

Authors:  Zuben E Sauna; Chava Kimchi-Sarfaty
Journal:  Nat Rev Genet       Date:  2011-08-31       Impact factor: 53.242

8.  Protein unfolding rates correlate as strongly as folding rates with native structure.

Authors:  Aron Broom; Shachi Gosavi; Elizabeth M Meiering
Journal:  Protein Sci       Date:  2014-12-26       Impact factor: 6.725

9.  Atomic-level description of ubiquitin folding.

Authors:  Stefano Piana; Kresten Lindorff-Larsen; David E Shaw
Journal:  Proc Natl Acad Sci U S A       Date:  2013-03-15       Impact factor: 11.205

10.  Analysis of the RNA Binding Specificity Landscape of C5 Protein Reveals Structure and Sequence Preferences that Direct RNase P Specificity.

Authors:  Hsuan-Chun Lin; Jing Zhao; Courtney N Niland; Brandon Tran; Eckhard Jankowsky; Michael E Harris
Journal:  Cell Chem Biol       Date:  2016-09-29       Impact factor: 8.116
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