Literature DB >> 8570645

How the first biopolymers could have evolved.

V I Abkevich1, A M Gutin, E I Shakhnovich.   

Abstract

In this work, we discuss a possible origin of the first biopolymers with stable unique structures. We suggest that at the prebiotic stage of evolution, long organic polymers had to be compact to avoid hydrolysis and had to be soluble and thus must not be exceedingly hydrophobic. We present an algorithm that generates such sequences for model proteins. The evolved sequences turn out to have a stable unique structure, into which they quickly fold. This result illustrates the idea that the unique three-dimensional native structures of first biopolymers could have evolved as a side effect of nonspecific physicochemical factors acting at the prebiotic stage of evolution.

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Year:  1996        PMID: 8570645      PMCID: PMC40144          DOI: 10.1073/pnas.93.2.839

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


  16 in total

1.  Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effect of specific amino acid sequence represented by specific inter-unit interactions.

Authors:  H Taketomi; Y Ueda; N Gō
Journal:  Int J Pept Protein Res       Date:  1975

2.  Proteins with selected sequences fold into unique native conformation.

Authors: 
Journal:  Phys Rev Lett       Date:  1994-06-13       Impact factor: 9.161

3.  Implications of thermodynamics of protein folding for evolution of primary sequences.

Authors:  E I Shakhnovich; A M Gutin
Journal:  Nature       Date:  1990-08-23       Impact factor: 49.962

4.  Simulations of the folding of a globular protein.

Authors:  J Skolnick; A Kolinski
Journal:  Science       Date:  1990-11-23       Impact factor: 47.728

5.  RNA evolution and the origins of life.

Authors:  G F Joyce
Journal:  Nature       Date:  1989-03-16       Impact factor: 49.962

Review 6.  Why are the same protein folds used to perform different functions?

Authors:  A V Finkelstein; A M Gutun
Journal:  FEBS Lett       Date:  1993-06-28       Impact factor: 4.124

7.  A new approach to the design of stable proteins.

Authors:  E I Shakhnovich; A M Gutin
Journal:  Protein Eng       Date:  1993-11

8.  Evolution-like selection of fast-folding model proteins.

Authors:  A M Gutin; V I Abkevich; E I Shakhnovich
Journal:  Proc Natl Acad Sci U S A       Date:  1995-02-28       Impact factor: 11.205

9.  Kinetics of protein folding. A lattice model study of the requirements for folding to the native state.

Authors:  A Sali; E Shakhnovich; M Karplus
Journal:  J Mol Biol       Date:  1994-02-04       Impact factor: 5.469

10.  Specific nucleus as the transition state for protein folding: evidence from the lattice model.

Authors:  V I Abkevich; A M Gutin; E I Shakhnovich
Journal:  Biochemistry       Date:  1994-08-23       Impact factor: 3.162

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  12 in total

1.  Evolvability and single-genotype fluctuation in phenotypic properties: a simple heteropolymer model.

Authors:  Tao Chen; David Vernazobres; Tetsuya Yomo; Erich Bornberg-Bauer; Hue Sun Chan
Journal:  Biophys J       Date:  2010-06-02       Impact factor: 4.033

2.  Comparing folding codes in simple heteropolymer models of protein evolutionary landscape: robustness of the superfunnel paradigm.

Authors:  Richard Wroe; Erich Bornberg-Bauer; Hue Sun Chan
Journal:  Biophys J       Date:  2004-10-22       Impact factor: 4.033

3.  Getting specificity from simplicity in putative proteins from the prebiotic earth.

Authors:  Jaime López de la Osa; David A Bateman; Sylvia Ho; Carlos González; Avijit Chakrabartty; Douglas V Laurents
Journal:  Proc Natl Acad Sci U S A       Date:  2007-09-12       Impact factor: 11.205

4.  Evolution of the folding ability of proteins through functional selection.

Authors:  S Saito; M Sasai; T Yomo
Journal:  Proc Natl Acad Sci U S A       Date:  1997-10-14       Impact factor: 11.205

5.  How are model protein structures distributed in sequence space?

Authors:  E Bornberg-Bauer
Journal:  Biophys J       Date:  1997-11       Impact factor: 4.033

6.  RNA folding kinetics using Monte Carlo and Gillespie algorithms.

Authors:  Peter Clote; Amir H Bayegan
Journal:  J Math Biol       Date:  2017-08-05       Impact factor: 2.259

7.  Foldamer hypothesis for the growth and sequence differentiation of prebiotic polymers.

Authors:  Elizaveta Guseva; Ronald N Zuckermann; Ken A Dill
Journal:  Proc Natl Acad Sci U S A       Date:  2017-08-22       Impact factor: 11.205

8.  Conformation-dependent sequence design: evolutionary approach.

Authors:  A V Chertovich; E N Govorun; V A Ivanov; P G Khalatur; A R Khokhlov
Journal:  Eur Phys J E Soft Matter       Date:  2004-01       Impact factor: 1.890

9.  Origination of the Protein Fold Repertoire from Oily Pluripotent Peptides.

Authors:  Ranjan V Mannige
Journal:  Proteomes       Date:  2014-03-25

Review 10.  Dynamic New World: Refining Our View of Protein Structure, Function and Evolution.

Authors:  Ranjan V Mannige
Journal:  Proteomes       Date:  2014-03-07
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