Proteins catalysis

For proponents of an RNA-world , predating protein catalysis, to regard RNA catalysts as mimicking enzymes - rather than vice versa - may seem perverse. We use this classification for consistency, and without prejudice... 

Flavohydroquinone bound to apoproteins plays a very important role in flavo-protein-catalysis, either in the electron-transfer to substrates or other enzymes or in the oxygen activation reaction. The chemical reactivity of 1,5-dihydroflavin bound to apoproteins can differ drastically from that of free flavin. The reactivity is likely governed by factors such as the conformation of the bound flavohydroquinone and the ionization state (cf. below). 

The division of function between DNA (genetic information storage) and protein (catalysis) was, according to the RNA world hypothesis, a later development. New variants of self-replicating RNA molecules developed, with the additional ability to catalyze the condensation of amino acids into peptides. Occasionally, the peptide (s) thus formed would reinforce the self-replicating ability of the RNA, and the pair—RNA... 

FIGURE 11-16 Motion of single phospholipids in a bilayer, (a) Movement from one leaflet to the other is very slow, unless (b) catalyzed by a flippase in contrast, lateral diffusion within the leaflet (c) is very rapid and requires no protein catalysis. 

The chemistry of the metalloenzymes must be considered as a special case of enzymic catalysis since most active sites of enzymes are stereospecific for only one molecule or class of molecules and many do not involve metal ions in catalysis. Since the metal ion is absolutely essential for catalysis in the examples chosen for this review, the mechanisms undoubtedly involve the metal ion and a particular protein microenvironment or reactive group(s) as joint participants in the catalytic event. It is our belief that studies of catalysis by metalloenzymes will have as many, if not more, features characteristic of protein catalysis in general, in a fashion similar to metal ion catalysis, and these studies will be directly applicable to heterogeneous and homogeneous catalytic chemical systems where the metal ion carries most of the catalytic function. 

In a similar approach, pyridoxamine was introduced into an S-peptide at position 8 to maintain the interactions with His12 and HisU9 [30]. Upon formation of the RNase complex, the rate was enhanced 7-fold compared with uncomplexed peptides under single turnover conditions. However, replacing the His residue at position 12 with Ser afforded only a 3-fold rate increase for the S-peptide-S-protein complex. Under catalytic conditions with pyruvate and L-phenylalanine as the substrates, uncomplexed peptides did not show catalytic turnover, suggesting that a hydrophobic microenvironment in the peptide-protein complex is critical for catalysis. However, in the presence of the S-protein, catalysis ensued. Up to 1.5 turnovers were observed in 160 h from the S-peptide-S-protein complex. 

A search for organisms that derive some of their catalytic activity from minerals rather than protein enzymes, including organisms that combine mineral and protein catalysis. 

Volume 4 is dedicated to three important topics Catalysis (Part 4.1), Heterogeneous Systems (Part 4.2), and Gas Phase Systems (Part 4.3). The six chapters of Part 4.1 cover the most important aspects of electron transfer catalysis, from fundamental concepts to organic synthesis, from carbon dioxide fixation to protein catalysis, from redox modulation to biomimetic catalysis. Part 4.2 deals with the basic aspects and the latest developments in electron transfer on semiconductors, dye-sensitized electrodes, mono- and multilayers, intercalated compounds, zeolites, micelles and related systems. Part 4.3 covers gas phase systems, from atoms to small molecules, exciplexes, and supermolecules. 

Song, L., El Sayed, M. A., Lanyi, J. K., Protein Catalysis of the Retinal Subpicosecond Photoisomerization in the Primary Process of Bacteriorhodopsin Photosynthesis, Science 1993, 261, 891 894. 

Our purpose here is to review spectroscopic approaches, optical and vibrational, applied to the determination of enzyme structure and dynamics. We focus on hydride transfer reactions in protein catalysis. Vibrational spectroscopy is especially useful in the study of the molecular mechanism of enzymes because it is structurally specific and is of high resolution bond distortions as small as 0.01-0.001 A can be discerned by vibrational spectroscopy. It is at this level of atomic resolution that enzyme induced bond distortions usually manifest themselves. In addition, both enthalpic and entropic factors can be characterized by vibrational spectroscopy, sometimes in quantitative terms. Although most of the chapter is concerned with the structures of static protein-ligand complexes, the dynamics of how these complexes are formed and depleted has recently become a viable topic for scientific... 

Dynamics of Protein Catalysis and Hydride Transfer Activation... 

Rand, R. Raising Water to New Heights. Science 256, 618 (1992). [A brief perspective on the contribution of hydration to molecular assembly and protein catalysis.]... 

Of all the functions of proteins, catalysis is probably the most important. In the absence of catalysis, most reactions in biological systems would take place far too slowly to provide products at an adequate pace for a metabolizing organism. The catalysts that serve this function in organisms are called enzymes. With the exception of some RNAs (ribozymes) that have catalytic activity (described in Sections 11.7 and 12.4), aU other enzymes are globular proteins (section 4.3). Enzymes are the most efficient catalysts known they can increase the rate of a reaction by a factor of up to 10 ° over uncatalyzed reactions. Non-enzymatic catalysts, in contrast, typically enhance the rate of reaction by factors of 102 to 104... 

Adjunct Professor of Physics at Utah State University. After completing her M. A. in Physics and PhD. in Biophysics at Harvard University, she became a member of the technical staff at AT T Bell Laboratories. She joined the USU faculty in 1988. She has a broad scope of expertise from biochemistry to electrical engineering, and has considerable experience in heme protein catalysis, structural biology, and the design and construction of optical and X-ray instrumentation. She was a pioneer the use of X-ray absorption spectroscopy for the investigation of biological problems and has authored more than 100 technical publications in refereed journals and books. 

Berzelius, Jons Jakob (1779-1848) A physician and chemist born in Sweden, Berzelius was secretary of the Royal Swedish Academy of Sciences for thirty years. He is credited with discovering the law of constant proportions for inorganic substances and was the first to distinguish organic from inorganic compounds. He developed a system of chemical symbols and a table of relative atomic weights that are stiU in use. In addition to coining such chemical terms as protein, catalysis, polymer, and isomer, he identified the elements cerium, selenium, silicon, and thorium. 

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