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Literature DB >> 11381526

Evolution of functionality in lattice proteins.

P D Williams¹, D D Pollock, R A Goldstein.

Abstract

We study the evolution of protein functionality using a two-dimensional lattice model. The characteristics particular to evolution, such as population dynamics and early evolutionary trajectories, have a large effect on the distribution of observed structures. Only subtle differences are observed between the distribution of structures evolved for function and those evolved for their ability to form compact structures.

Mesh：

Substances：
Ligands
Proteins

Year: 2001 PMID： 11381526 PMCID： PMC2943963 DOI： 10.1016/s1093-3263(00)00125-x

Source DB: PubMed Journal: J Mol Graph Model ISSN： 1093-3263 Impact factor: 2.518

15 in total

1. The evolutionary landscape of functional model proteins.

Authors: J D Hirst
Journal: Protein Eng Date: 1999-09

2. The distribution of structures in evolving protein populations.

Authors: D M Taverna; R A Goldstein
Journal: Biopolymers Date: 2000-01 Impact factor: 2.505

3. Gradual development of protein-like global structures through functional selection.

Authors: T Yomo; S Saito; M Sasai
Journal: Nat Struct Biol Date: 1999-08

4. Evolution of model proteins on a foldability landscape.

Authors: S Govindarajan; R A Goldstein
Journal: Proteins Date: 1997-12

5. 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

6. Statistical mechanics of simple models of protein folding and design.

Authors: V S Pande; A Y Grosberg; T Tanaka
Journal: Biophys J Date: 1997-12 Impact factor: 4.033

7. Why are some proteins structures so common?

Authors: S Govindarajan; R A Goldstein
Journal: Proc Natl Acad Sci U S A Date: 1996-04-16 Impact factor: 11.205

8. On the thermodynamic hypothesis of protein folding.

Authors: S Govindarajan; R A Goldstein
Journal: Proc Natl Acad Sci U S A Date: 1998-05-12 Impact factor: 11.205

9. Protein design: a perspective from simple tractable models

Authors:
Journal: Fold Des Date: 1998

10. Impact of local and non-local interactions on thermodynamics and kinetics of protein folding.

Authors: V I Abkevich; A M Gutin; E I Shakhnovich
Journal: J Mol Biol Date: 1995-09-29 Impact factor: 5.469

21 in total

Review 1. Natively unfolded proteins: a point where biology waits for physics.

Authors: Vladimir N Uversky
Journal: Protein Sci Date: 2002-04 Impact factor: 6.725

2. Stability and the evolvability of function in a model protein.

Authors: Jesse D Bloom; Claus O Wilke; Frances H Arnold; Christoph Adami
Journal: Biophys J Date: 2004-05 Impact factor: 4.033

3. Funnel-like organization in sequence space determines the distributions of protein stability and folding rate preferred by evolution.

Authors: Yu Xia; Michael Levitt
Journal: Proteins Date: 2004-04-01

4. Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential.

Authors: Michael Slutsky; Leonid A Mirny
Journal: Biophys J Date: 2004-10-01 Impact factor: 4.033

5. Context dependence and coevolution among amino acid residues in proteins.

Authors: Zhengyuan O Wang; David D Pollock
Journal: Methods Enzymol Date: 2005 Impact factor: 1.600

6. 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