Beyond Proteins

The deletion of competing pathways is also a productive route to increasing flux through a desired pathway or at least eliminating potential contaminating products (class 3 above) (Hols et al., 1999). However, the removal of aknown pathwaymaybe insufficient to divert flux through the desired pathway, since flux may be limited by either the kinetic parameters of the pathway enzymes or by external factors. Further, the 

Long before molecular geneticists began tinkering with the structure and function of proteins and metabolic pathways, researchers were ma- 

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Beyond protein-protein interactions—development and use of FRET-based nanosensors... 

Patten et al., 1997 Zhang et al., 1997). Molecular breeding has also been extended beyond proteins to pathways and viruses, as well as partial genomes (Crameri et al., 1997 Soong et al., 1999). 

The concerns of the nutritionist regarding protein extend well beyond protein content and protein density. A major concern in human and anima nutrition is the quality of the protein. The term protein quality refers to the ability of a particular protein to provide a balanced pattern of indispensable amino acids. A hi -quality protein contains high concentrations of the indispensable amino acids. A low-quality protein is deficient or lacking in one or more of these amino acids. Although beans and eggs are similar, as far as protein density is concerned, the quality of egg protein is considerably better than that of protein from beans. 

Beyond protein folding, the discovery of peptidyl prolyl isomerases (PPIases) and related proteins has opened the way to novel concepts in biology the notion of chaperone-assisted receptor binding is an emerging field of research which sheds light on receptor function and protein-protein interactions. The recent discovery of a secondary amide peptide bond cis-trans isomerase (APIase) heralds new advances in this field. 

TECHNICAL SCOPE OF PROTEOMICS - BEYOND PROTEIN IDENTIFICATION... 

H. Lin, V.W. Cornish, In vivo protein-protein interaction assays beyond proteins we would like to thank Tony Siu, Dr. Charles Cho, and the members of our lab for their helpful comments as we were preparing this manuscript, Angew. Chem., Int. Ed. Engl. 2001, 40,... 

The involvement of protein kinase C in the enhancement of malignant cell transformation induced by 2,3,7,8-tetrachlorodibenzo-p-dioxin was studied by W6LFLE and Marquardt (1996). The protein kinase inhibitor H-7 markedly reduced the in vitro promoting activity of 12-0-tetradecanoylphorbol-13-acetate but did not affect the promotion by 2,3,7,8-tetrachlorodibenzo-p-dioxin. In accord with these results, 12-0-tetradecanoylphorbol-13-acetate, but not 2,3,7,8-tetrachlorodibenzo-p-dioxin, enhanced the protein kinase C activity in C3H/M2 fibroblasts. Since 12-0-tetradecanoylphorbol-13-acetate-mediated activation of protein kinase C was not affected by ascorbic acid plus a-tocopherol, that the antioxidants interfere with tumour promotion at a step beyond protein kinase C activation. 

Cyclodextrins have had valuable industrial uses for a considerable time, particularly as agents to bind or release volatile molecules. Accurate predictions concerning the selectivity and stability of cyclodextrin-guest complexes are therefore of considerable interest both academically and practically." MD was used to simulate cyclodextrin hydrates" as a test of the applicability of the GROMOS program package to systems beyond proteins and nucleic acids. Other early MD simulations focused on interactions with guests such as enantiomers of methyl-2-chloropropionate. Comparisons between calculated thermodynamic properties for complexes formed by O -cyclodextrin with para-substituted phenols and the results of MM simulations led to improvements in force fields that described the interactions. MM2 simulations were used to support NMR data for the -cyclodextrin inclusion complex with benzoic acid. " The well-known catalytic effect of cyclodextrins has been modeled. For example, the relative rate increase of hydrolysis of S over R phenyl ester stereoisomers in the presence of -cyclodextrin... 

Standard deviations of differences were typically of the order of 85 BU for maximum resistance and 1.5 cm for extensibility. However, when calibrations were put into practice, it was observed that there was a strong influence of environment on their performance (10). This is most likely due to the fact that extensibility is highly correlated with protein content. Therefore, if NIR calibrations for extensibility measure little or nothing beyond protein content the calibration will fail when the intercorrelation changes. 

Morris, S.M., 2006. Arginine beyond protein. The American Joiunal of Clinical Nutrition 83,508S-512S. 

Morris, S.M., Jr, 2006. Aiginine Beyond protein. Am J Clin Nuir 83, 508S-512S. 

Ion specific effects generally follow direct or reverse order of the so-called Hofineister series, which for monovalent anions is, SCN > CIO4 1 > Br- > Cl- > F. In many cases, interfacial effects appear to play a key role. In the simplest case of ions at the air-water interface for example, the specificity is directly reflected in the stability of foams or in the surface tension and surface potential of aqueous salt solutions. In biology, beyond protein crystallisation, the enzymatic activity can be controlled by addition of alkali halides with large differences between fluoride, chloride, bromide, or iodide. Specific types of cations are also identified together with... 

H. Grubmiiller, N. Ehrenhofer, and P. Tavan. Conformational dynamics of proteins Beyond the nanosecond time scale. In M. Peyard, editor. Proceedings of the Workshop Nonlinear Excitations in BiomoleculesMay 30-June 4, 1994, Houches (Prance), Seiten 231-240. Centre de Physique des Houches (France), Springer-Verlag, 1995. 

G. Ramachandran and T. Schlick. Beyond optimization Simulating the dynamics of supercoiled DNA by a macroscopic model. In P. M. Pardalos, D. Shal-loway, and G. Xue, editors. Global Minimization of Nonconvex Energy Functions Molecular Conformation and Protein Folding, volume 23 of DIM ACS Series in Discrete Mathematics and Theoretical Computer Science, pages 215-231, Providence, Rhode Island, 1996. American Mathematical Society. 

Bioinformatics is a relatively new discipline that is concerned with the collection, organisatic and analysis of biological data. It is beyond our scope to provide a comprehensive overvie of this discipline a few textbooks and reviews that serve this purpose are now available (s the suggestions for further reading). However, we will discuss some of the main rnethoc that are particularly useful when trying to predict the three-dimensional structure and fum tion of a protein. To help with this. Appendix 10.1 contains a limited selection of some of tf common abbreviations and acronyms used in bioinformatics and Appendix 10.2 lists sorr of the most widely used databases and other resources. 

Parallel to the activities in the treatment of pernicious anemia were observations in the 1930s that most farm animals had a requirement for an unknown factor beyond the vitamins then known. The lack of this factor became apparent, eg, when chicks or pigs fed a diet with only vegetable protein evidenced slow growth rate and high mortahty. It became apparent that the requited factor, termed animal protein factor, was present in animal sources such as meat and tissue extracts, milk whey, and cow manure. Subsequent to its isolation, it was rapidly shown that vitamin B 2 is the same as animal protein factor. 

Standard calculation methods developed for small proteins are sufficiently powerful to solve protein structures and complexes in the 30 kDa range and beyond [97,98] and protein-nucleic acid complexes [99]. Torsion angle dynamics offers increased conver-... 

RNA structures, compared to the helical motifs that dominate DNA, are quite diverse, assuming various loop conformations in addition to helical structures. This diversity allows RNA molecules to assume a wide variety of tertiary structures with many biological functions beyond the storage and propagation of the genetic code. Examples include transfer RNA, which is involved in the translation of mRNA into proteins, the RNA components of ribosomes, the translation machinery, and catalytic RNA molecules. In addition, it is now known that secondary and tertiary elements of mRNA can act to regulate the translation of its own primary sequence. Such diversity makes RNA a prime area for the study of structure-function relationships to which computational approaches can make a significant contribution. 

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