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Literature DB >> 8346235

Engineering of stable and fast-folding sequences of model proteins.

Abstract

The statistical mechanics of protein folding implies that the best-folding proteins are those that have the native conformation as a pronounced energy minimum. We show that this can be obtained by proper selection of protein sequences and suggest a simple practical way to find these sequences. The statistical mechanics of these proteins with optimized native structure is discussed. These concepts are tested with a simple lattice model of a protein with full enumeration of compact conformations. Selected sequences are shown to have a native state that is very stable and kinetically accessible.

Mesh：

Substances：
Proteins

Year: 1993 PMID： 8346235 PMCID： PMC47103 DOI： 10.1073/pnas.90.15.7195

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

11 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. Protein folding funnels: a kinetic approach to the sequence-structure relationship.

Authors: P E Leopold; M Montal; J N Onuchic
Journal: Proc Natl Acad Sci U S A Date: 1992-09-15 Impact factor: 11.205

3. Protein folding bottlenecks: A lattice Monte Carlo simulation.

Authors:
Journal: Phys Rev Lett Date: 1991-09-16 Impact factor: 9.161

4. The nature of folded states of globular proteins.

Authors: J D Honeycutt; D Thirumalai
Journal: Biopolymers Date: 1992-06 Impact factor: 2.505

5. Modeling the effects of mutations on the denatured states of proteins.

Authors: D Shortle; H S Chan; K A Dill
Journal: Protein Sci Date: 1992-02 Impact factor: 6.725

6. 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

7. Simulations of the folding of a globular protein.

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

8. Statistical distribution of hydrophobic residues along the length of protein chains. Implications for protein folding and evolution.

Authors: S H White; R E Jacobs
Journal: Biophys J Date: 1990-04 Impact factor: 4.033

9. Formation of unique structure in polypeptide chains. Theoretical investigation with the aid of a replica approach.

Authors: E I Shakhnovich; A M Gutin
Journal: Biophys Chem Date: 1989-11 Impact factor: 2.352

10. Spin glasses and the statistical mechanics of protein folding.

Authors: J D Bryngelson; P G Wolynes
Journal: Proc Natl Acad Sci U S A Date: 1987-11 Impact factor: 11.205

96 in total

1. A polar, solvent-exposed residue can be essential for native protein structure.

Authors: R B Hill; W F DeGrado
Journal: Structure Date: 2000-05-15 Impact factor: 5.006

2. Investigation of routes and funnels in protein folding by free energy functional methods.

Authors: S S Plotkin; J N Onuchic
Journal: Proc Natl Acad Sci U S A Date: 2000-06-06 Impact factor: 11.205

3. Folding protein models with a simple hydrophobic energy function: the fundamental importance of monomer inside/outside segregation.

Authors: A F Pereira De Araújo
Journal: Proc Natl Acad Sci U S A Date: 1999-10-26 Impact factor: 11.205

Engineering of stable and fast-folding sequences of model proteins.

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.

2. Protein folding funnels: a kinetic approach to the sequence-structure relationship.

3. Protein folding bottlenecks: A lattice Monte Carlo simulation.

4. The nature of folded states of globular proteins.

5. Modeling the effects of mutations on the denatured states of proteins.

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

7. Simulations of the folding of a globular protein.

8. Statistical distribution of hydrophobic residues along the length of protein chains. Implications for protein folding and evolution.

9. Formation of unique structure in polypeptide chains. Theoretical investigation with the aid of a replica approach.

10. Spin glasses and the statistical mechanics of protein folding.

1. A polar, solvent-exposed residue can be essential for native protein structure.

2. Investigation of routes and funnels in protein folding by free energy functional methods.

3. Folding protein models with a simple hydrophobic energy function: the fundamental importance of monomer inside/outside segregation.

4. Structure-based conformational preferences of amino acids.

5. Statistical mechanics of protein-like heteropolymers.

6. Quench-flow experiments combined with mass spectrometry show apomyoglobin folds through and obligatory intermediate.

7. Improved recognition of native-like protein structures using a family of designed sequences.

8. Protein topology and stability define the space of allowed sequences.

9. A minimalist model protein with multiple folding funnels.

10. Statistical significance of protein structure prediction by threading.