Structure interpretation

Therefore, a substantial portion of the secondary structure elements can be readily identified in 3-D maps calculated to 6- to 8-A resolution by interactive visual inspection of the density volume, using 3-D volumerendering techniques (Fig. 9 see Color Insert). Examination of the density range distribution can also be used as a means to verify secondary structure elements identified on the basis of shaded surface representations. For example, the gray density displays of density sections extracted from a 3-D volume are often useful to verify the assignment based on information such as the relative densities of the identified a helices and (3 

Interpretation of the membrane proteins in an envelope virus can be assisted by the identification of transmembrane a helices. Membrane proteins represent a special class of proteins because of the predominant presence of transmembrane helices connected by extramembrane loops and domains. For example, even at 10.5-A resolution, a pair of transmembrane helices could be identified in the Semliki Forest virus El and E2 proteins (Eig. 10 see Color Insert). 

For more complex structures, it is possible to combine electron cryomicroscopy structures with sequence-based secondary structure predictions to interpret the observed secondary structure elements. In the outer shell protein P8 of rice dwarf virus (RDV), where nine helices were predicted in the domain formed by the N and C termini, it was possible to match the lengths of the helices identified in the 3-D density map to those predicted from a consensus secondary structure analyses (Fig. 13a see Color Insert). The connections between the helical densities can be seen in the lower domain of P8, allowing us to establish a rough backbone model for the lower domain of P8 (Zhou et at, 2001). 

To assess the accuracy of such a prediction, DejaVu (Kleywegt and Jones, 1997) and COSEC (Mizuguchi and Lio, 1995) can be used to perform spatial fold recognition. A successful match in the helix arrangement between the helixHunter results of a structure in the Protein Data Bank 

Toward Near-Atomic Resolution Three-Dimensional modeling 

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This color change was first observed by Duffin and Kendall (1954). A first structural interpretation (Baigrie et al., 1979) was later refuted by Gorelik et al. (1980). 

The structural interpretation of the principal quantum number of nucleonic orbital wave functions and the structural basis provided by the close-packed-spheron theory for the neutron and proton magic numbers are discussed in notes submitted to Phys. Rev. Letters and Nature (L. Pauling, 1965). 

The close-packed-spheron theory leads to a simple structural interpretation of the magic numbers (16) they are the numbers at which each layer of the nucleus achieves completion of... 

The wave functions for the two inner-core spherons can, of course, be described as the symmetric and antisymmetric combinations of l.t and Ip-functions. The Nilsson (19) treatment of neutron and proton orbitals in deformed nuclei is completely compatible with the foregoing discussion, which provides a structural interpretation of it. 

Huxley, H.E. Hanson, J. (1954). Changes in the cross-striations of muscle during contraction and stretch and their structural interpretation. Nature 173,973-976. 

Several computational studies have been abstracted and manipulable three-dimensional images of reactants, transition structures, intermediates, and products provided. This material provides the opportunity for detailed consideration of these representations and illustrates how computational chemistry can be applied to the mechanistic and structural interpretation of reactivity. This material is available in the Digital Resource at springer.com/carey-sundberg. 

Garcia-Moreno EB, Fitch CA (2004) Structural interpretation of pH and salt-dependent processes in proteins with computational methods. Methods Enzymol 380 20—51. 

The author is most grateful to Profs. Harold Hart, Fumio Toda, and Edwin Weber for sharing their original ideas with him, for providing the compounds for structural interpretations, and for their encouragement and collaboration. The cooperation of Dr. Stephen Czerkez in the early stages of the study reviewed here is also appreciated. Special thanks are due to Mrs. Zafra Stein for her invaluable assistance. 

It appears that estimates of the dimensions of the unit cell for the B -modification of starch (or amylose) are reasonably in agreement, but that structural interpretations of these observations are at variance. 

N.A.B. Gray, A. Buchs, D.H. Smith and C. Djerassi, Application of artificial intelligence for chemical inference. Part XXXVI. Computer assisted structural interpretation of mass spectral data, Helv. Chim. Acta, 64 (1981) 458-470. 

An analogous structural interpretation was recently advocated by us to explain the mode of catalytic dehydration of aromatic carbinols by acids [7],... 

Dendrimers represent a model for compact multifunctional precursor of polymer networks. Polymer networks prepared by crosslinking of dendrimers were suggested several years ago [64]. Since then, some experimental work has been performed, but there are still many points in structural interpretation of network formation and network properties that are not well understood. 

Rule Language (Radial). RuleMaster expert systems are expressed in Radial, a block structured interpreted language with a syntax similar to Pascal and ADA. Radial is a simple, easy-to-learn language which supports the full range of expert system capabilities. 

Papoulis, A., 1965, Probability, Random Variables, and Stochastic Processes, McGraw-Hill, New York. Pauling, L., 1935, The oxygen equilibrium of hemoglobin and its structural interpretation, Proc. Natl. 

When working with non-radiolabeled drugs the major challenge is to find metabolites in the biological matrices. Because the enzymes responsible for metabolism are quite well characterized metabolic changes can partially be predicted. For example hydroxylation of the parent drug is in many cases the principal metabolic pathway. From a mass spectrometric point of view it results in an increase of 16 units in the mass spectrum. In the full-scan mode an extracted ion current profile can be used to screen for potential metabolites. In a second step a product ion spectrum is recorded for structural interpretation. Ideally, one would like to obtain relative molecular mass information and the corresponding product ion spectrum in the same LC-MS run. This information can be obtained by data dependant acquisition (DDA), as illustrated in Fig. 1.39. 

The endoxylanase gene from Thermoanaerobacter strain B6A was sequenced and structural interpretations were deduced from computer analysis of the amino acid sequence (see Table VIII). The endoglucanase is hydrophilic and has compact secondary structure with 30 6-tums and five potential glycosylation sites. 

Table Vm. Structural Interpretations Deduced From Amino Acid Sequence Computer Analysis of the Thermoanaerobacter Strain B6A Endoxylanase Gene...

The report of a crystal structure for PtBra (oA-OEt)(oA) (9) has been the basis of much structural interpretation. At the time, however, it was thought by the original workers Kneen and Nyholm that the compound submitted was PtBra (oS-OEt) (oS), and this is now tacitly admitted to be the case (74), although a rather ambiguous "corrected structure is described in the footnote. The fuU structure has been determined 13) the product has a six-membered ring, as shown in Fig. 8. 

Compared to the silicates, only a few systematic physico-chemical measurements have been carried out on the binary borates. Whereas in silica and silicates the Si04 tetrahedron is the only building unit, both B08 and BCb groups are known to be present in crystalline and glassy borates (52, 60). Structural interpretations similar to those for the silicates are thus more difficult. At present, no satisfactory model exists for the binary borates. Some very interesting results arc, however, available and these will be discussed below. 

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