Crystallographic analysis protein

What molecular architecture couples the absorption of light energy to rapid electron-transfer events, in turn coupling these e transfers to proton translocations so that ATP synthesis is possible Part of the answer to this question lies in the membrane-associated nature of the photosystems. Membrane proteins have been difficult to study due to their insolubility in the usual aqueous solvents employed in protein biochemistry. A major breakthrough occurred in 1984 when Johann Deisenhofer, Hartmut Michel, and Robert Huber reported the first X-ray crystallographic analysis of a membrane protein. To the great benefit of photosynthesis research, this protein was the reaction center from the photosynthetic purple bacterium Rhodopseudomonas viridis. This research earned these three scientists the 1984 Nobel Prize in chemistry. 

KcsA crystals suitable for X-ray crystallographic analysis using synchrotron radiation were obtained and the data collected and analyzed for multiple crystals and six different data sets as described in the 1998 Science publication (reference 15). The final KcsA pore structure, including amino acid residues 23 to 119 of the K+ channel, refined to 3.2 A. The X-ray data were deposited in the Protein Data Bank with the accession number 1BL8. 

Romo, T.D., Clarage, J.B., Sorensen, D.C., Phillips, G.N. Automatic identification of discrete substates in proteins-singular-value decomposition analysis of time-averaged crystallographic refinements. Proteins 1995, 22, 311-21. 

The x-ray crystallographic analysis of protein structures is a remarkably successful technique. Since the publication of the first protein structure, that of myoglobin in 1958, many other protein structures have been determined. The resulting structural details often approaching atomic level have led to great insights into enzyme catalysis, hormone function, the organisation of the immune system, the molecular architecture of virus particles and protein synthesis. Why then should such an apparently successful technique need synchrotron radiation ... 

An application of the ROCS program has been reported recently (82). New scaffolds for small molecule inhibitors of the ZipA-FtsZ protein-protein interaction have been found. The shape comparisons are made relative to the bioactive conformation of a HTS hit, determined by X-ray crystallography. A followup X-ray crystallographic analysis also showed that ROCS accurately predicted the binding mode of the inhibitor. This result offers the first experimental evidence that validates the use of ROCS for scaffold hopping purposes. 

The product of the crystal density and the unit-cell volume (determined from crystallographic analysis, Chapter 4) gives the total mass within the unit cell. This quantity, expressed in daltons, is the sum of all atomic masses in one unit cell. If the protein molecular mass and the number of protein molecules per unit cell are known, then the remainder of the cell can be assumed to be water, thus establishing the proteinlwater ratio. 

In this chapter, I will discuss the strengths and limitations of molecular models obtained by X-ray diffraction. My aim is to help you to use crystallographic models wisely and appropriately, and realize just what is known, and what is unknown, about a molecule that has yielded up some of its secrets to crystallographic analysis. To demonstrate how you can draw these conclusions for yourself with regard to a particular molecule of interest, I will conclude this chapter by discussing a recent structure determination, as it appeared in a biochemical journal. Here my goals are (1) to help you learn to extract criteria of model quality from published structural reports and (2) to review some basic concepts of protein crystallography. 

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