Intramolecular Structural Vibrations of Triose Phosphate Isomerase

It has long been contended that protein conformational access is through thermally populated intramolecular structural vibrations (ISV). The possible optimization of the ISV is particularly intriguing for the ubiquitous “perfect enzyme” triose phosphate isomerase (TIM). TIM is found in the two domains of life: archaea and bacteria . Beyond this, TIM’s structural motif, named the TIM-barrel fold, is present in ~10% of known protein catalyst structures. Raising the question, do the structural dynamics of the TIM-barrel fold provide biochemical advantages? In particular the possible long range dynamical coupling between the dimer interface and the substrate access gating by loop 6. the structural dynamics can be examined by Stationary Sample Anisotropic Terahertz Microspectroscopy (SSATM). TIM SSATM measurements were done on large crystals made using a batch microseeding method. This uses smaller crystals harvested, crushed, and diluted into a crystal slurry. Then a whisker tool picks up microcrystals from the slurry to drop some in the wells to stimulate growth of larger crystals. Crystals are used so the orientation of the molecules is known from the unit cell by having a known crystal facet on the aperture. The unit cell and crystal facets are characterized using X-ray crystallography and face indexing. Modeling can then be used to assign collective displacements to the ISV SSATM spectra. Our early measurements have shown reproducibility of an anisotropic band around 26cm^-1 that may be loop 6 motions.