Exploring biomolecular energy landscapes

Jerelle A. Joseph, Konstantin Röder, Debayan Chakraborty, Rosemary G. Mantell, David J. Wales

Research output: Contribution to journalReview articlepeer-review

69 Scopus citations

Abstract

The potential energy landscape perspective provides both a conceptual and a computational framework for predicting, understanding and designing molecular properties. In this Feature Article, we highlight some recent advances that greatly facilitate structure prediction and analysis of global thermodynamics and kinetics in proteins and nucleic acids. The geometry optimisation procedures, on which these calculations are based, can be accelerated significantly using local rigidification of selected degrees of freedom, and through implementations on graphics processing units. Results of progressive local rigidification are first summarised for trpzip1, including a systematic analysis of the heat capacity and rearrangement rates. Benchmarks for all the essential optimisation procedures are then provided for a variety of proteins. Applications are then illustrated from a study of how mutation affects the energy landscape for a coiled-coil protein, and for transitions in helix morphology for a DNA duplex. Both systems exhibit an intrinsically multifunnel landscape, with the potential to act as biomolecular switches.

Original languageEnglish (US)
Pages (from-to)6974-6988
Number of pages15
JournalChemical Communications
Volume53
Issue number52
DOIs
StatePublished - 2017
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Electronic, Optical and Magnetic Materials
  • General Chemistry
  • Ceramics and Composites
  • Metals and Alloys
  • Materials Chemistry
  • Surfaces, Coatings and Films
  • Catalysis

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