Enzyme conformation

Linderstrom-Lang, A., and Schellman, P. (1959). Protein conformation. Enzymes 1 443-471. 

The generalization of the model in Section 8.6 to three or more regulatory sites is quite straightforward. We still assume a two-conformation enzyme (L, H) with one active site and m identical (in the strict sense) regulator sites. 

Table 5 contains ribonucleotides with the common amino and carbonyl structures, with extra substituents, and with totally unsubstituted bases like purine or benzimidazole. Apparent values and velocities do not vary more than about tenfold in the presence of specific effector deoxyribonucleotides. Guanine and cytosine nucleotides have usually fastest and compounds with fewer base substituents show decreased reaction rates. Loss of substrate activity is only observed in syn-oriented nucleotides where the nucleobase is rotated about the glycosidic bond like in 8-bromo-ADP or -ATP. Molecular conformation-enzyme activity relationships have been discussed in detail ... 

Ha T, Ting A Y, Liang J, Caldwell W B, Deniz A A, Chemla D S, Schultz P G and Weiss S 1999 Single-molecule fluorescence spectroscopy of enzyme conformational dynamics and cleavage mechanism Proc. Natl Acad. Sc/. USA 96 893-8... 

Averbukh I Sh, Blumenfeld L A, Kovarsky V A and Perelman N F 1986 A model of the mechanism of enzyme action in terms of protein conformational relaxation Blochim. Blophys. Acta. 873 290-6... 

Blumenfeld L A, Burbajev D S and Davydov R M 1986 Processes of conformational relaxation in enzyme catalysis The Fluctuating Enzyme ed E R Welch (New York Wiley) pp 369-402... 

Calculation of Conformational Free Energies for a Model of a Bilobal Enzyme Protein kinases catalyze the transfer of phosphate from adenosine triphosphate (ATP) to protein substrates and are regulatory elements of most known pathways of signal transduction. 

The lUBMB Commission on Nomenclature has issued a number of recommendations dealing with areas of a more biochemical nature (72), such as peptide hormones (86), conformation of polypeptide chains (87), abbreviations for nucleic acids and polynucleotides (88), iron—sulfur proteins (89), enzyme units (90), etc. The Commission has also produced rules and recommendations for naming enzymes (91,92). 

Several methods are being studied to enhance the stabiUty of peptide mimics and improve their stereochemical similarity to the endogenous peptides. For example, the tetrapeptide Cys—Val—Phe—Met, a potent inhibitor of Ras famesyltransferase, is proposed to exist in a turned conformation, which mimics the endogenous peptide during enzyme binding. This conformation is successhiUy mimicked by 3-amino-l-carboxymethyl-5-phenyl-benzodiazepin-2-onederivatives (198) (142). 

Films or membranes of silkworm silk have been produced by air-drying aqueous solutions prepared from the concentrated salts, followed by dialysis (11,28). The films, which are water soluble, generally contain silk in the silk I conformation with a significant content of random coil. Many different treatments have been used to modify these films to decrease their water solubiUty by converting silk I to silk II in a process found usehil for enzyme entrapment (28). Silk membranes have also been cast from fibroin solutions and characterized for permeation properties. Oxygen and water vapor transmission rates were dependent on the exposure conditions to methanol to faciUtate the conversion to silk II (29). Thin monolayer films have been formed from solubilized silkworm silk using Langmuir techniques to faciUtate stmctural characterization of the protein (30). ResolubiLized silkworm cocoon silk has been spun into fibers (31), as have recombinant silkworm silks (32). 

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