Protein energy landscapes determined by five-dimensional crystallography

Acta Crystallogr D Biol Crystallogr. 2013 Dec;69(Pt 12):2534-42. doi: 10.1107/S0907444913025997. Epub 2013 Nov 19.

Abstract

Free-energy landscapes decisively determine the progress of enzymatically catalyzed reactions [Cornish-Bowden (2012), Fundamentals of Enzyme Kinetics, 4th ed.]. Time-resolved macromolecular crystallography unifies transient-state kinetics with structure determination [Moffat (2001), Chem. Rev. 101, 1569-1581; Schmidt et al. (2005), Methods Mol. Biol. 305, 115-154; Schmidt (2008), Ultrashort Laser Pulses in Medicine and Biology] because both can be determined from the same set of X-ray data. Here, it is demonstrated how barriers of activation can be determined solely from five-dimensional crystallography, where in addition to space and time, temperature is a variable as well [Schmidt et al. (2010), Acta Cryst. A66, 198-206]. Directly linking molecular structures with barriers of activation between them allows insight into the structural nature of the barrier to be gained. Comprehensive time series of crystallographic data at 14 different temperature settings were analyzed and the entropy and enthalpy contributions to the barriers of activation were determined. One hundred years after the discovery of X-ray scattering, these results advance X-ray structure determination to a new frontier: the determination of energy landscapes.

Keywords: chemical kinetics; five-dimensional crystallography; photoactive yellow protein; time-resolved crystallography; time-resolved microspectrophotometry.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Bacteria / chemistry
  • Bacterial Proteins / chemistry*
  • Crystallography, X-Ray / methods
  • Kinetics
  • Photoreceptors, Microbial / chemistry*
  • Protein Conformation
  • Thermodynamics*

Substances

  • Bacterial Proteins
  • Photoreceptors, Microbial
  • photoactive yellow protein, Bacteria