Literature DB >> 16624879

Common attributes of native-state structures of proteins, disordered proteins, and amyloid.

Trinh X Hoang1, Luca Marsella, Antonio Trovato, Flavio Seno, Jayanth R Banavar, Amos Maritan.   

Abstract

We show that a framework derived from the common character of globular proteins can be used to understand the design of protein sequences, the behavior of intrinsically unstructured proteins, and the formation of amyloid fibrils in a unified manner. Our studies provide compelling support for the idea that protein native-state structures, the structures adopted by intrinsically unstructured proteins on binding as well as those of amyloid aggregates, all reside in a physical state of matter in which the free energy landscape is sculpted not by the specific sequence of amino acids, but rather by considerations of geometry and symmetry. We elucidate the key role played by sequence design in selecting the structure of choice from the predetermined menu of putative native-state structures.

Entities:  

Mesh:

Substances:

Year:  2006        PMID: 16624879      PMCID: PMC1458988          DOI: 10.1073/pnas.0601824103

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


  40 in total

1.  Nature disfavors sequences of alternating polar and non-polar amino acids: implications for amyloidogenesis.

Authors:  B M Broome; M H Hecht
Journal:  J Mol Biol       Date:  2000-03-03       Impact factor: 5.469

Review 2.  What does it mean to be natively unfolded?

Authors:  Vladimir N Uversky
Journal:  Eur J Biochem       Date:  2002-01

3.  The protein trinity--linking function and disorder.

Authors:  A K Dunker; Z Obradovic
Journal:  Nat Biotechnol       Date:  2001-09       Impact factor: 54.908

4.  Rationally designed mutations convert de novo amyloid-like fibrils into monomeric beta-sheet proteins.

Authors:  Weixun Wang; Michael H Hecht
Journal:  Proc Natl Acad Sci U S A       Date:  2002-03-05       Impact factor: 11.205

Review 5.  Coupling of folding and binding for unstructured proteins.

Authors:  H Jane Dyson; Peter E Wright
Journal:  Curr Opin Struct Biol       Date:  2002-02       Impact factor: 6.809

6.  Proteins. One thousand families for the molecular biologist.

Authors:  C Chothia
Journal:  Nature       Date:  1992-06-18       Impact factor: 49.962

7.  Protein design by binary patterning of polar and nonpolar amino acids.

Authors:  S Kamtekar; J M Schiffer; H Xiong; J M Babik; M H Hecht
Journal:  Science       Date:  1993-12-10       Impact factor: 47.728

8.  Origins of structure in globular proteins.

Authors:  H S Chan; K A Dill
Journal:  Proc Natl Acad Sci U S A       Date:  1990-08       Impact factor: 11.205

Review 9.  Structured disorder and conformational selection.

Authors:  C J Tsai; B Ma; Y Y Sham; S Kumar; R Nussinov
Journal:  Proteins       Date:  2001-09-01

10.  Inherent toxicity of aggregates implies a common mechanism for protein misfolding diseases.

Authors:  Monica Bucciantini; Elisa Giannoni; Fabrizio Chiti; Fabiana Baroni; Lucia Formigli; Jesús Zurdo; Niccolò Taddei; Giampietro Ramponi; Christopher M Dobson; Massimo Stefani
Journal:  Nature       Date:  2002-04-04       Impact factor: 49.962

View more
  13 in total

1.  The role of secondary structure in protein structure selection.

Authors:  Yong-Yun Ji; You-Quan Li
Journal:  Eur Phys J E Soft Matter       Date:  2010-05-25       Impact factor: 1.890

2.  Amyloidogenic potential of transthyretin variants: insights from structural and computational analyses.

Authors:  Laura Cendron; Antonio Trovato; Flavio Seno; Claudia Folli; Beatrice Alfieri; Giuseppe Zanotti; Rodolfo Berni
Journal:  J Biol Chem       Date:  2009-07-14       Impact factor: 5.157

Review 3.  Regulation of protein phosphatase 1 by intrinsically disordered proteins.

Authors:  Meng S Choy; Rebecca Page; Wolfgang Peti
Journal:  Biochem Soc Trans       Date:  2012-10       Impact factor: 5.407

4.  Folding of Intrinsically Disordered Protein Phosphatase 1 Regulatory Proteins.

Authors:  Wolfgang Peti; Angus C Nairn; Rebecca Page
Journal:  Curr Phys Chem       Date:  2012-01

5.  Exploring the universe of protein structures beyond the Protein Data Bank.

Authors:  Pilar Cossio; Antonio Trovato; Fabio Pietrucci; Flavio Seno; Amos Maritan; Alessandro Laio
Journal:  PLoS Comput Biol       Date:  2010-11-04       Impact factor: 4.475

6.  A coarse-grained approach to protein design: learning from design to understand folding.

Authors:  Ivan Coluzza
Journal:  PLoS One       Date:  2011-07-01       Impact factor: 3.240

7.  Insight into the structure of amyloid fibrils from the analysis of globular proteins.

Authors:  Antonio Trovato; Fabrizio Chiti; Amos Maritan; Flavio Seno
Journal:  PLoS Comput Biol       Date:  2006-10-30       Impact factor: 4.475

8.  A condensation-ordering mechanism in nanoparticle-catalyzed peptide aggregation.

Authors:  Stefan Auer; Antonio Trovato; Michele Vendruscolo
Journal:  PLoS Comput Biol       Date:  2009-08-14       Impact factor: 4.475

9.  A generic mechanism of emergence of amyloid protofilaments from disordered oligomeric aggregates.

Authors:  Stefan Auer; Filip Meersman; Christopher M Dobson; Michele Vendruscolo
Journal:  PLoS Comput Biol       Date:  2008-11-14       Impact factor: 4.475

10.  Structural reorganisation and potential toxicity of oligomeric species formed during the assembly of amyloid fibrils.

Authors:  Mookyung Cheon; Iksoo Chang; Sandipan Mohanty; Leila M Luheshi; Christopher M Dobson; Michele Vendruscolo; Giorgio Favrin
Journal:  PLoS Comput Biol       Date:  2007-09       Impact factor: 4.475

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.