Hydrophobic collapse

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Schematic representation of the hydrophobic collapse during protein folding with polar areas (blue) and non-polar hydrophobic areas (red) in an aqueous environment.

The hydrophobic collapse is a hypothesis about the folding of protein structures due to the hydrophobic effect .

properties

The hydrophobic collapse describes the development of the native conformation of a protein in polar solvents. This mostly affects aqueous solvents as they occur within a cell or in the extracellular space . Correct folding is necessary for protein-protein interactions and, in the case of enzymes, for enzyme activity . The hydrophobic collapse can be represented by a folding funnel.

The kinetics of protein folding via hydrophobic collapse has been demonstrated for myoglobin , barstar and a nuclease from Staphylococcus . The hydrophobic collapse can be simulated in silico by molecular dynamics , Monte Carlo simulation and Φ analysis .

Individual evidence

  1. ↑ M. Arai, K. Kuwajima: Rapid formation of a molten globule intermediate in refolding of alpha-lactalbumin. In: Folding & design. Volume 1, Number 4, 1996, pp. 275-287, PMID 9079390 .
  2. ^ VR Agashe, MC Shastry, JB Udgaonkar: Initial hydrophobic collapse in the folding of barstar. In: Nature . Volume 377, Number 6551, October 1995, pp. 754-757, doi : 10.1038 / 377754a0 , PMID 7477269 .
  3. ↑ GJ Vidugiris, JL Markley, CA Royer: Evidence for a molten globule-like transition state in protein folding from determination of activation volumes. In: Biochemistry. Volume 34, Number 15, April 1995, pp. 4909-4912, PMID 7711012 .
  4. ↑ NJ Marianayagam, SE Jackson: The folding pathway of ubiquitin from all-atom molecular dynamics simulations. In: Biophysical chemistry. Volume 111, Number 2, October 2004, pp. 159-171, doi : 10.1016 / j.bpc.2004.05.009 , PMID 15381313 .
  5. ↑ M. Brylinski, L. Konieczny, I. Roterman: Hydrophobic collapse in (in silico) protein folding. In: Computational Biology and Chemistry. Volume 30, Number 4, August 2006, pp. 255-267, doi : 10.1016 / j.compbiolchem . 2006.04.007 , PMID 16798094 .
  6. ↑ E. Paci, CT Friel, K. Lindorff-Larsen, SE Radford, M. Karplus, M. Vendruscolo: Comparison of the transition state ensembles for folding of Im7 and Im9 determined using all-atom molecular dynamics simulations with phi value restraints. In: Proteins. Volume 54, Number 3, February 2004, pp. 513-525, doi : 10.1002 / prot.10595 , PMID 14747999 .