Literature DB >> 23345791

Correlation between the conformation space and the sequence space of Peptide chain.

T N Sasaki1, M Sasai.   

Abstract

Effects of point mutations are investigated in a computer model ofsequence selection. In the model, sequences are selected according totheir functional ability defined by the configuration at the active site.Through such functional selection on the local configuration, sequenceswhich fold globally into a unique conformation can be selected from randomsequences. The selected sequence accepts many point mutations as neutralmutations. More structurally fluctuating sites in the chain accept alarger variety of point mutations, which shows correlation between theconformational fluctuation and the sequence fluctuation.

Keywords:  functional selection; knowledge-based potential; mutational robustness; neutral evolution; off-lattice model; sequence space; super-funnel

Year:  2002        PMID: 23345791      PMCID: PMC3456737          DOI: 10.1023/A:1020301714197

Source DB:  PubMed          Journal:  J Biol Phys        ISSN: 0092-0606            Impact factor:   1.365


  21 in total

1.  Analysis of a local fitness landscape with a model of the rough Mt. Fuji-type landscape: application to prolyl endopeptidase and thermolysin.

Authors:  T Aita; H Uchiyama; T Inaoka; M Nakajima; T Kokubo; Y Husimi
Journal:  Biopolymers       Date:  2000-07       Impact factor: 2.505

2.  Experiment and theory highlight role of native state topology in SH3 folding.

Authors:  D S Riddle; V P Grantcharova; J V Santiago; E Alm; I Ruczinski; D Baker
Journal:  Nat Struct Biol       Date:  1999-11

3.  Anatomy of protein structures: visualizing how a one-dimensional protein chain folds into a three-dimensional shape.

Authors:  C J Tsai; J V Maizel; R Nussinov
Journal:  Proc Natl Acad Sci U S A       Date:  2000-10-24       Impact factor: 11.205

4.  Crystal structure of an engrailed homeodomain-DNA complex at 2.8 A resolution: a framework for understanding homeodomain-DNA interactions.

Authors:  C R Kissinger; B S Liu; E Martin-Blanco; T B Kornberg; C O Pabo
Journal:  Cell       Date:  1990-11-02       Impact factor: 41.582

5.  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

6.  Emergence of preferred structures in a simple model of protein folding.

Authors:  H Li; R Helling; C Tang; N Wingreen
Journal:  Science       Date:  1996-08-02       Impact factor: 47.728

7.  Functional rapidly folding proteins from simplified amino acid sequences.

Authors:  D S Riddle; J V Santiago; S T Bray-Hall; N Doshi; V P Grantcharova; Q Yi; D Baker
Journal:  Nat Struct Biol       Date:  1997-10

8.  Step-wise mutation of barnase to binase. A procedure for engineering increased stability of proteins and an experimental analysis of the evolution of protein stability.

Authors:  L Serrano; A G Day; A R Fersht
Journal:  J Mol Biol       Date:  1993-09-20       Impact factor: 5.469

9.  Conformation, energy, and folding ability of selected amino acid sequences.

Authors:  M Sasai
Journal:  Proc Natl Acad Sci U S A       Date:  1995-08-29       Impact factor: 11.205

Review 10.  Theoretical studies of protein folding.

Authors:  N Go
Journal:  Annu Rev Biophys Bioeng       Date:  1983
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  2 in total

1.  Correlation between evolutionary structural development and protein folding.

Authors:  Chioko Nagao; Tomoki P Terada; Tetsuya Yomo; Masaki Sasai
Journal:  Proc Natl Acad Sci U S A       Date:  2005-12-19       Impact factor: 11.205

Review 2.  Biophysical Models of Protein Evolution: Understanding the Patterns of Evolutionary Sequence Divergence.

Authors:  Julian Echave; Claus O Wilke
Journal:  Annu Rev Biophys       Date:  2017-03-15       Impact factor: 12.981

  2 in total

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