Proteins distance between, measurement

We tested our new potential by applying a local optimization procedure to the potential of some proteins, starting with the native structure as given in the Brookhaven Protein Data Bank, and observing how far the coordinates moved through local optimization. For a good potential, one expects the optimizer to be close to the native structure. As in Ulrich et al. [34], we measure the distance between optimizer B and native structure A by the distance matrix error... 

Fig. 5.4. Correlation between R0 and FRET efficiency. Exchanging ECFP/ EYFP (R0 = 4.72 nm, dashed line) for the red-shifted VFP FRET-pair mKO/ mCherry (R0 = 6.37 nm, solid line) will increase the measured FRET efficiency, since the distance between donor and acceptor is expected to remain unchanged. A FRET pair with increased R0 yields detectable FRET over longer distances and can be used to measure protein-protein interaction between larger proteins.

Although the stabilizing interactions between the amino acid side chains of PLC/j, and the choline headgroup are readily apparent in the PLC fc-phosphonate inhibitor complex, it is more difficult to identify contacts between the protein and the acyl chains of the inhibitor [45]. In part this is because thermal motion in the acyl side chains, especially the sn-1 chain, renders them somewhat disordered. Consequently, the measured distances between the side chain carbons... 

Energy-transfer measurements are often used to estimate the distances between sites on biological macromolecules such as proteins, and the effects of conformational changes on these distances. In this type of experiment, the efficiency of energy transfer is used to calculate the distance between donor and acceptor fluorophores in order to obtain structural information about the macromolecule. 

Resolution, on the other hand, is a more technical term. It refers to the distance between adjacent bands relative to their bandwidths and acknowledges the fact that proteins are distributed in Gaussian profiles with overlapping distributions. The numerical expression for resolution is obtained by dividing the distance between the centers of adjacent bands by some measure of their average bandwidths. It expresses the distance between band centers in units of bandwidth and gives a measure of the overlap between two adjacent bands. For preparative applications, when maximal purity is desired, two proteins to be isolated should be separated by at least a bandwidth. In many applications it is sufficient to be able to simply discern that two bands are distinct. In this case bands can be less than a bandwidth apart. 

S)-warfarin were used as the templates. This substrate superposition was supported by an NMR study measuring distances between the heme-iron and the substrate protons (66). The model featured (1) anionic heteroatom (A-) at a distance of approx 4 A from a hypothetical cationic site (C+) of the protein,... 

The good agreement between the folded and the experimental structure is also evident from Figure (l)(center), which shows the secondary structure alignment of the native and the folded conformations. The good physical alignment of the helices illustrates the importance of hydrophobic contacts to correctly fold this protein. An independent measure to assess the quality of these contacts is to compare the C -C distances (which correspond to the NOE constraints of the NMR experiments that determine tertiary structure) in the folded structure to those of the native structure. We found that 66 % (80 %) of the C/3-C/3 distance distances agree to within one (1.5) standard deviations of the experimental resolution. 

Double-quantum coherence (DQC) was used to measure interspin distances in eight doubly labelled derivatives of T4 lysozyme.25 Distances between 20 and 47 A with distance distributions of 1.0 to 2.8 A were measured. For some variants two conformations were detected with distances that differed by 5 to 5.4 A. It was shown that a few measurements of large distances provided significant constraints on protein structure. 

Specific applications of FRET and FRET include observation of myosin movement (Fig. 19-14),157 measurement of distances between binding sites on tubulin,161 determining stoichiometry of subunit assembly in a y-aminobutyrate receptor of brain,162 association of proteins in peroxisomes,160 study of hydridization of deoxyribonucleotides,163 verifying the handedness of various forms of DNA,164 and other studies of DNA and RNA.164a b... 

Early protein crystallographers, proceeding by analogy with studies of other crystalline substances, examined dried protein crystals and obtained no diffraction patterns. Thus X-ray diffraction did not appear to be a promising tool for analyzing proteins. In 1934, J. D. Bernal and Dorothy Crowfoot (later Hodgkin) measured diffraction from pepsin crystals still in the mother liquor. Bernal and Crowfoot recorded sharp diffraction patterns, with reflections out to distances in reciprocal space that correspond in real space to the distances between atoms. The announcement of their success was, in effect, a birth announcement for protein crystallography. 

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