Protein chemical structures

B and W J Howe 1991. Computer Design of Bioactive Molecules - A Method for Receptor-Based Novo Ligand Design. Proteins Structure, Function and Genetics 11 314-328. i H L 1965. The Generation of a Unique Machine Description for Chemical Structures - A hnique Developed at Chemical Abstracts Service. Journal of Chemical Documentation 5 107-113. J 1995. Computer-aided Estimation of Symthetic Accessibility. PhD thesis. University of Leeds, itan R, N Bauman, J S Dixon and R Venkataraghavan 1987. Topological Torsion A New )lecular Descriptor for SAR Applications. Comparison with Other Descriptors. Journal of emical Information and Computer Science 27 82-85. 

Alkylating agent, a reactive chemical that forms a covalent bond with chemical moieties on the biological target (usually a protein). For instance, p-haloalkylamines generate an aziridinium ion in aqueous base that inserts into -SH, -CHOH, or other chemical structures in peptides. Once inserted, the effects of the alkylating agent are irreversible. 

Cody, C. W., et al. (1993). Chemical structure of the hexapeptide chro-mophore of the Aequorea green-fluorescent protein. Biochemistry 32 1212-1218. 

Ribosomal Protein Synthesis Inhibitors. Figure 3 The chemical structure of tetracycline and possible interactions with 16S rRNA in the primary binding site. Arrows with numbers indicate distances (in A) between functional groups. There are no interactions obseived between the upper portion of the molecule and 16S rRNA consistent with data that these positions can be modified without affecting inhibitory action (from Brodersen et al. [4] with copynght permission). 

Cluster 2 appears to be unique among Fe-S-containing proteins whose structures have so far been determined, emd it has been termed the hybrid cluster (6) because of its diverse chemical nature. Figure 14 is a schematic drawing of the cluster as interpreted from the final electron density synthesis and the structure refinement. The cluster contains both oxygen and sulfur bridges, and X represents a site whose precise nature has not been determined, but which may contain a partially occupied and/or disordered substrate molecule (see Section III,B,3,b). The environments of the four iron atoms can be described as follows. 

Sequence-specific heteropolymers, as a class of synthetic molecules, are unique in that they must be made by chemical steps that add one monomer unit at a time. Moreover, to create truly protein-like structures, which typically have chain lengths of at least 100 monomers and a diverse set of 20 side chains (or more), extremely efficient and rapid coupHngs under general reaction conditions are necessary. For these reasons, soHd-phase synthesis is typically used, so that excess reagents can be used to drive reactions to completion, and subsequent reaction work-ups are quite rapid. 

This approach can be generalized to all possible types of experimental data that may be generated. All chemical structures available in public databases or internal to a company typically feature at least the in vitro binding assay data and additionally, the three-dimensional structure of the protein and/or bound ligand. A chemical compound C will therefore be ... 

Because of their very complex chemical structures and heterogeneity, melanins are difficult to extract, separate, and characterize from tissues. Eumelanins are insoluble in water and organic solvents. They can be extracted from tissues with strong chemicals that are capable of removing lipids, proteins, and other tissue components but also lead to the formation of degradation products. Enzymatic procedures were developed for the isolation of eumelanins from mammalian hair and irises. The first step is sequential digestion with protease, proteinase K, and papaine in the presence... 

T. Kohno, D. Kohda, M. Haruki, S. Yokoyama, and T. Miyazawa, Non-protein amino acid furanomycin, unlike isoleucine in chemical structure, is changed to isoleucine tRNA by isoleucyl-tRNA synthetase and incorporated into protein. J. Biol. 

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