Literature DB >> 7568102

Lattice model for rapidly folding protein-like heteropolymers.

I Shrivastava1, S Vishveshwara, M Cieplak, A Maritan, J R Banavar.   

Abstract

Protein folding is a relatively fast process considering the astronomical number of conformations in which a protein could find itself. Within the framework of a lattice model, we show that one can design rapidly folding sequences by assigning the strongest attractive couplings to the contacts present in a target native state. Our protein design can be extended to situations with both attractive and repulsive contacts. Frustration is minimized by ensuring that all the native contacts are again strongly attractive. Strikingly, this ensures the inevitability of folding and accelerates the folding process by an order of magnitude. The evolutionary implications of our findings are discussed.

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Year:  1995        PMID: 7568102      PMCID: PMC40953          DOI: 10.1073/pnas.92.20.9206

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


  24 in total

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Journal:  Annu Rev Phys Chem       Date:  1989       Impact factor: 12.703

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Journal:  Annu Rev Biochem       Date:  1990       Impact factor: 23.643

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Journal:  J Mol Biol       Date:  1987-02-20       Impact factor: 5.469

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Authors:  A Sali; E Shakhnovich; M Karplus
Journal:  Nature       Date:  1994-05-19       Impact factor: 49.962

6.  Finding the lowest free energy conformation of a protein is an NP-hard problem: proof and implications.

Authors:  R Unger; J Moult
Journal:  Bull Math Biol       Date:  1993-11       Impact factor: 1.758

7.  Kinetics of protein folding.

Authors:  H S Chan
Journal:  Nature       Date:  1995-02-23       Impact factor: 49.962

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Authors:  A A Rabow; H A Scheraga
Journal:  J Mol Biol       Date:  1993-08-20       Impact factor: 5.469

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

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

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  7 in total

1.  A method for parameter optimization in computational biology.

Authors:  J B Rosen; A T Phillips; S Y Oh; K A Dill
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2.  How optimization of potential functions affects protein folding.

Authors:  M H Hao; H A Scheraga
Journal:  Proc Natl Acad Sci U S A       Date:  1996-05-14       Impact factor: 11.205

3.  Folding funnels and frustration in off-lattice minimalist protein landscapes.

Authors:  H Nymeyer; A E García; J N Onuchic
Journal:  Proc Natl Acad Sci U S A       Date:  1998-05-26       Impact factor: 11.205

4.  Computational Cellular Dynamics Based on the Chemical Master Equation: A Challenge for Understanding Complexity.

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Journal:  J Comput Sci Technol       Date:  2010-01       Impact factor: 1.571

5.  Statistical geometry of lattice chain polymers with voids of defined shapes: sampling with strong constraints.

Authors:  Ming Lin; Rong Chen; Jie Liang
Journal:  J Chem Phys       Date:  2008-02-28       Impact factor: 3.488

6.  Biomolecular dynamics: order-disorder transitions and energy landscapes.

Authors:  Paul C Whitford; Karissa Y Sanbonmatsu; José N Onuchic
Journal:  Rep Prog Phys       Date:  2012-06-28

7.  Pseudo-Improper-Dihedral Model for Intrinsically Disordered Proteins.

Authors:  Łukasz Mioduszewski; Bartosz Różycki; Marek Cieplak
Journal:  J Chem Theory Comput       Date:  2020-06-12       Impact factor: 6.006

  7 in total

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