Tuesday, August 18, 2009

Finding the protons in proteins

X-ray crystallography has proven to be an extremely powerful tool to determine the structure of proteins. However, it does have several limitations:
  • real biology happens in water not in a crystal (How do we know the protein structure is the same in a crystal as in the native state in water?)
  • one can't see the location of protons (many important biochemical processes involve proton transfer and so knowing where the protons are is extremely important)
An alternative probe is neutron scattering. It does not have as high as resolution as X-ray scattering but one can see deuterium (which can be substituted for protons). It can also see water molecules.
A recent PNAS paper, Low-barrier hydrogen bond in photoactive yellow protein, illustrates the power and importance of the technique. Using nuetron scattering they were able to identify the positions of 819 H atoms out of 942 . More importantly, they showed that the hydrogen bond between the chromophore and the carboxylic acid group of the Glu46 residue was particularly short. The authors propose that in the excited state the fast relaxation of this bond into a normal hydrogen bond is the trigger for the photo-signal.

[I stumbled across this paper while looking at the Protein Data Bank as part of the PHYS3170 course]

I am curious as to how this relates to an earlier JACS by Gerrit Groenhof et al, which uses an extensive Quantum-Classical Molecular Dynamics study to argue that the Arg52 residue controls the photo-isomerisation process.

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