Wuthrich, K. Nmr of Proteins andNucleic Acids. J. Wiley & Sons, New York, 1986.  Home/Search   Document Not in Database   Summary   Related Articles   Check

....involved are modeled as rigid. Current strucral biology experimental inethods are considerably restricted in the amount of information they can provide regarding protein motions. The two most common inethods in use today are protein X ray crystallography [36] and nuclear magnetic resonance (NMR) [52]. The output of these techniques is a set of x, y, z coordinate values for each atom in a protein. Neither of these inethods is able to provide us with a full description, at atomic resolution, of the structural changes that proteins undergo in a timescale relevant to their fimction. Such ....

....is available, our analysis can be performed directly on the confonnational vector set defined collectively by these structures. This is the case for proteins such as HIV 1 protease. Nuclear MaRnetic Resonance (NMR The second most common method of determining the structure of a protein is NMR [52]. This method is in general not as accurate as X ray crystallography and its use is lhnited to small to medimn sized proteins. However, it provides useful information about protein dynmnics directly and avoids the two biggest problems in X ray crystallography: crystallization and phase ....

Wuthrich, K. Nmr of Proteins andNucleic Acids. J. Wiley & Sons, New York, 1986.

....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 ....

....that, for high resolution structures, most of the B factor is due to thermal motion, and not static (lattice) disorder[11] 1.1. 2 Nuclear Magnetic Resonance Structures determined using nuclear magnetic resonance (NMR) are derived from reconstructing structures from multiple distance measurements [2] . There are, therefore, two sources of uncertainty for these structures. First, the interpretation of the NMR data involves assigning a distance (usually a distance range or distance distribution) for each experimental measurement of atomic proximity. Because the data arise from a population of ....

Wuthrich, K., NMR of Proteins and Nucleic Acids . 1986, John Wiley and Sons.

....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 ....

....for vector x: the diagonal elements contain the variances of each element of x, whereas the off diagonals contain the covariances among the elements within x (for N atoms, C(x) is of size 3N x 3N ) C(x) 1 x s 1 x 1 y . 1 x N z . 1 y . N z 1 x . N z [2] The variance of each coordinate of an atom can be extracted from the diagonal and provides the uncertainty in the location of that atom. The off diagonal elements of the variance covariance matrix contain information about the dependence between the coordinates of two atoms (that is, the ....

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Wuthrich, K., NMR of Proteins and Nucleic Acids. 1986, John Wiley and Sons.

....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 structure from these diverse sources of information can be ....

....be generalizable to similarly structured applications, several of which we briefly describe. 17 3. Moments of Internal Distance Distribution The problem of computing a three dimensional structure from a set of inter atomic distances arises in the interpretation of experimental data such as NMR [88] and biochemical cross linking [41] Most such data sets have predominantly short range distances, so that local neighborhoods are well defined, but errors can accumulate when larger scale features are being estimated. In our own experience with the probabilistic least squares algorithm, these ....

K. Wuthrich, NMR of Proteins and Nucleic Acids, John Wiley and Sons, 1986.

....with, or otherwise affect their functions. The problem of determining molecular structure is usually approached experimentally, using X ray crystallography, nuclear magnetic resonance (NMR) or a variety of biochemical experiments that yield distances, angles, and other structural information [11]. In addition to these experimental data, there is a large body of knowledge from general chemistry: bond lengths, bond angles, and torsion angles between atoms. The quality and abundance of data from these sources can vary significantly. Thus, it is important to combine these sources of ....

Wuthrich, K., NMR of Proteins and Nucleic Acids, John Wiley and Sons, 1986.

....such a correlation map of spectral features, e.g. depicting an amplitude as a function of the frequencies of two applied radio frequency fields. Multidimensional NMR Spectroscopy is a powerful method for the determination of the structure of complex organic macromolecules such as proteins [12]. Proteins are long chains of smaller molecules called amino acids. Approximately 18 different types of amino acids are commonly found in proteins. The first step in analyzing the structure of a protein is to determine its constituent amino acids. One type of NMR spectroscopy used for this purpose ....

Wuthrich, K. "NMR of Proteins and Nucleic Acids". John Wiley & Sons, New York,

.... spectroscopic methods such as two dimensional NMR provide a means for determining a labeled subset of the distances between atoms in large structures such as proteins and RNA, and such methods have therefore proved extremely valuable in conformational studies of such molecules (see e.g. [19, 22]) Mathematics Department and Lab. for Computer Science, MIT. Email: bab theory.lcs.mit.edu. y This work was done while at Laboratory for Computer Science, MIT, Cambridge, MA 02139. Present address: Department of Computer Science, Cornell University, Ithaca NY 14853. Email: ....

....ffi in O(n log n) time. 1.2 Errors in NMR Data In this section we give a brief overview of some basic NMR techniques, both for the sake of background and to give a sense for some of the sources of error in NMR. More detailed descriptions can be found in any of a number of sources; see e.g. [19, 22]. NMR experiments are frequently based on measuring proton resonances, since hydrogen atoms are easily detected by these techniques; this is in general sufficient for conformational studies, since hydrogen atoms are abundant in organic molecules. To determine spatial information, one typically ....

K. Wuthrich, NMR of Proteins and Nucleic Acids, Wiley, 1986.

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