There are no substantial holes and almost no water molecules in the protein interior. The interior of protein subunits and domains consists of closely packed atoms. One guiding principle enormously simplifies the analysis of protein structure. Hydrodynamics, in particular sedimentation and gel filtration, can provide this structural information, and it becomes even more powerful when combined with electron microscopy (EM). However, structural information at the nanometer level is frequently invaluable. The ultimate structural understanding of a protein comes from an atomic-level structure obtained by X-ray crystallography or nuclear magnetic resonance. However, some proteins are highly elongated, either as a string of small globular domains or stabilized by specialized structures such as coiled coils or the collagen triple helix. Peptides larger than 50 kDa typically form two or more domains that are independently folded. Peptides from 10 to 30 kDa typically fold into a single domain. Most proteins fold into globular domains, which have a minimal surface area. Protein folding is driven largely by the hydrophobic effect, which seeks to minimize contact of the polypeptide with solvent. Most proteins fold into globular domains. A combination of hydrodynamics and electron microscopy is especially powerful. Finally, rotary shadowing and negative stain electron microscopy are powerful techniques for resolving the size and shape of single protein molecules and complexes at the nanometer level. The molecular weight can be determined by combining gradient sedimentation and gel filtration, techniques available in most biochemistry laboratories, as originally proposed by Siegel and Monte. It is recalled that a gel filtration column fractionates proteins on the basis of their Stokes radius, not molecular weight. Instead, a simple guideline is presented, based on the measured sedimentation coefficient and a calculated maximum S, to estimate if a protein is globular or elongated.
Readers are reminded that the Perrin equation is generally not a valid approach to determine the shape of proteins. This review collects a number of simple calculations that are useful for thinking about protein structure at the nanometer level. Sedimentation and gel filtration are hydrodynamic techniques that can be used for this medium resolution structural analysis. The samples have been modeled in ReMagX and the measured TEY signals have been used to generate the needed refractive indices and atomic scattering factors.An important part of characterizing any protein molecule is to determine its size and shape. The change in the LaCoO₃ on SrTiO₃+ sample results in vertical stripes which are believed to have Co ions in mixed valencies and spin-states and were discussed in two models. The uncapped LaCoO₃ thin-films show distinctive reconstructed surfaces with more pronounced densities of Co²+ that are energy-feasible ways of compensating the polar surface. The surface contamination layer appears as a distinctive feature in the measured reflectivities. TEY analysis of the CoO on MgO sample indicates a reduction of symmetry from cubic octahedral to distorted tetragonal with the crystal compressed in the xy plane. The LaCoO₃ thin-films were grown with Pulsed Laser Deposition (PLD), with or without a LaAlO₃ cap, on LaAlO₃, NdGaO₃ or SrTiO₃ substrates as examples of compressive and tensile strain. CoO thin-films were grown with Molecular Beam Epitaxy (MBE) on MgO substrate as an example of compressive strain. The needed samples for the current research were readily available through research collaborators. X-ray Absorption Spectroscopy (XAS) was measured in Total Fluorescence Yield (TFY) and Total Electron Yield (TEY), followed by on- and off-Resonant Soft X-ray Reflectometry (RSXR) at constant energy and at fixed momentum transfer vector in the z-direction (fixed Qz).
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Simulating and fitting the data required a special home-written software “ReMagX”. The experiments were carried out in the newly installed Resonant Soft X-ray Scattering (RSXS) endstation of the 10ID-2 beamline, the Canadian Light Source (CLS). The technique is non-destructive, element specific and depth sensitive. The newly developed Soft X-ray Reflectometry (SXR) has been used to study the electronic structure of Transition Metal Oxide (TMO) thin-films.