Blundell, T. L., and Johnson, L. N. (1976) Protein Crystallography, Academic Press, London.  Home/Search   Document Not in Database   Summary   Related Articles   Check

....correlation matrices, conformational flexibility, macromolecular shape, segmental flexibility, temperature factors. 1. Introduction The main sources of structural information for biological macromolecules is experimental techniques such as X ray crystallography and NMR (nuclear magnetic resonance)[1, 2] . There is, however, also an increasing ability to define structure (or partial structure) with predictive methodologies as well (secondary structure[3, 4] structural class [5] surface vs. buried atoms[6] local conformation [7] approximate fold [8] and others) Both the experimental and ....

....of atomic coordinates. 1.1.2 X ray Crystallography Structures determined using X ray crystallography routinely include information about the temperature factor, or B factor for each atom. The crystallographic B factor is a 3 scalar estimate of signal attenuation derived from electron density maps [1] . Thermal motion of atoms causes a decrease in the intensity of X ray crystallographic readings by a factor of e B K , where B = 8p 3, represents the mean displacement of the atom, and K depends on crystallographic experimental parameters. Atoms which reliably assume the same position ....

Blundell, T.L. and L.N. Johnson, Protein Crystallography. 1976, New York: Academic Press.

....large numbers of sequential data, and there is a need for efficient methods for determining the structures that correspond to these sequences. Experimental methods have been the primary means of structure definition, but are subject to problems of high cost and biased sampling of structure space[1, 2]. Techniques for sequence analysis provide information about likely structural features based on prediction of secondary structure [3, 4] prediction of structural class [5] and prediction of functional class[6] There is also an increasing amount of information available based on the detailed ....

....model of the data and its uncertainty. For molecular structure, the parameters to be estimated are the coordinates of atoms in three dimensional space. We represent the mean positions of each atom as a vector, x, of length 3N for N atoms: x = x 1 y 1 z 1 x 2 y 2 z 2 . x N y N z N ] T [1] The second element of our representation is a variance covariance matrix for vector x. This matrix, C(x) contains the autocovariance information for vector x: the diagonal elements contain the variances of each element of x, whereas the off diagonals contain the covariances among the elements ....

Blundell, T.L. and L.N. Johnson, Protein Crystallography. 1976, New York: Academic Press.

....itself; an example is the prediction of secondary structures of a protein from its primary sequence [25, 80, 82] Finally, a multitude of experimental techniques yields different kinds of structural data. Examples include spatial frequencies of structural features from X ray crystallography [10]; distances from nuclear magnetic resonance (NMR) 88] fluorescent energy transfer (FRET) 23] and cross linking [7] surface proximity information from solvent accessibility [57] and chemical probes [69] and molecular surface shape from electron microscopy [31] Computing the molecular ....

T. L. Blundell and L. N. Johnson, Protein Crystallography, Academic Press, New York, 1976.

....to the data warehouse. In order to exploit this data, a format must be found in which three dimensional comparisons can be made, and algorithms must be written to transform data to that format. The two most common methods for obtaining the 3D structure of a target are X Ray crystallography[6] and nuclear magnetic resonance (NMR) spectroscopy[7] The result of both of these methods is a set of x, y, and z coordinates for every atom in the target. NMR studies produce a family of structures, similar to the conformers of a chemical compound. Certain other experiments, such as ....

Blundell, T.L., and Johnson, L.N., "Protein Crystallography" 1976 Academic Press

....protein and nucleic acid molecules (containing on the order of 500 amino acids or 100 bases) are mature and well understood. The size and flexibility of large macromolecular complexes makes them difficult to study with the primary methods for determining structure (x ray crystallography [1] and nuclear magnetic resonance [2] For now, the structures of large complexes must be probed with experimental methods that provide structural information that is relatively sparse and relatively noisy. Such methods include determination of molecular shape and volume[3] estimating proximity ....

Blundell, T.L. and L.N. Johnson, Protein Crystallography. 1976, New York: Academic Press.

....[11, 12] Our best high resolution view of proteins comes from x ray crystallographic investigations, and these contain information about relative stability as well. The crystallographic B factor (or temperature factor) is typically a scalar estimate of occupancy derived from electron density maps [13]. Thermal motion of atoms causes a decrease in the intensity of X ray crystallographic readings by a factor of e B , where Altman et al. 4 B = 8p 2 2 3 and represents the mean square displacement of atoms. Atoms which reliably assume the same position within the unit cell have a low ....

....the conformations assumed by a segment may vary over the time period of data collection (minutes to hours) In either case, the electron density signal is attenuated. The results of this attenuation is seen in the electron density maps that are generated from the crystallographic structure factors [13]. Atoms with a relatively low occupancy do not have the sharp peaks of electron density contour that characterize high occupancy, rigid sections of the molecule. Instead, the electron density may be entirely absent or present at only low levels of the contour. Unfortunately, the precise ....

Blundell, T.L. and L.N. Johnson, Protein Crystallography. 1976, New York: Academic Press.

....can be computed) are X ray crystallography and nuclear magnetic resonance (NMR) spectroscopy. The applicability of X ray crystallography is limited by the fact that not all proteins crystallize, and that the crystalline forms of molecules are not exactly the same as their forms in solution [5]. NMR spectroscopy does not have these problem, but NMR data can be noisy and sparse. Effective determination of structures solely from NMR data has been limited to small molecules [7] Other sources of information about molecular structure include theoretical considerations and statistical ....

Blundell, T.L. and L.N. Johnson, Protein Crystallography. 1976, New York: Academic Press.

....in a few steps. 3.1 Normalization step The standard Wilson method is applied to native protein data (up to native resolution) to obtain the scale factor K p and the overall thermal factor B p . Estimates of the corresponding factors for the derivative are obtained by a differential Wilson plot [19] through the equation ( ln S S S p H p p d F F 2 2 ( ln K K B B sin p d d p 2 2 2 q l (3) Actually from (3) the ratio R k =K d K p and the difference DB=B d B p are obtained. Then B d and K d are set to B d =B p DB and K d =K p R k . Equation (3) is ....

Blundell, T.L. & Johnson, L.N. (1976). Protein Crystallography, p. 336, London: Academic Press.

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Blundell, T. L., and Johnson, L. N. (1976) Protein Crystallography, Academic Press, London.

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T. L. Blundell and L. N. Johnson, Protein Crystallography, Academic Press, New York, 1976.

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