Structural evolution of proteinlike heteropolymers

Erik D. Nelson, Nick V. Grishin

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

The biological function of a protein often depends on the formation of an ordered structure in order to support a smaller, chemically active configuration of amino acids against thermal fluctuations. Here we explore the development of proteins evolving to satisfy this requirement using an off-lattice polymer model in which monomers interact as low resolution amino acids. To evolve the model, we construct a Markov process in which sequences are subjected to random replacements, insertions, and deletions and are selected to recover a predefined minimum number of solid-ordered monomers using the Lindemann melting criterion. We show that polymers generated by this process consistently fold into soluble, ordered globules of similar length and complexity to small protein motifs. To compare the evolution of the globules with proteins, we analyze the statistics of amino acid replacements, the dependence of site mutation rates on solvent exposure, and the dependence of structural distance on sequence distance for homologous alignments. Despite the simplicity of the model, the results display a surprisingly close correspondence with protein data.

Original languageEnglish (US)
Article number062715
JournalPhysical Review E - Statistical, Nonlinear, and Soft Matter Physics
Volume90
Issue number6
DOIs
StatePublished - Dec 23 2014

Fingerprint

proteins
Protein
amino acids
Amino Acids
globules
Replacement
Polymers
monomers
deletion
Markov processes
polymers
mutations
Melting
Markov Process
Deletion
Insertion
insertion
Simplicity
Mutation
Alignment

ASJC Scopus subject areas

  • Condensed Matter Physics
  • Statistical and Nonlinear Physics
  • Statistics and Probability

Cite this

Structural evolution of proteinlike heteropolymers. / Nelson, Erik D.; Grishin, Nick V.

In: Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, Vol. 90, No. 6, 062715, 23.12.2014.

Research output: Contribution to journalArticle

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