Nucleotides complexes

Stability Constants (LogU)K, at 298 K and I = 0.1M) for Phosphate, Phospho-nate, Nucleoside, and Nucleotide Complexes of Selected M2+ Cations... 

The topologically defined region(s) on an enzyme responsible for the binding of substrate(s), coenzymes, metal ions, and protons that directly participate in the chemical transformation catalyzed by an enzyme, ribo-zyme, or catalytic antibody. Active sites need not be part of the same protein subunit, and covalently bound intermediates may interact with several regions on different subunits of a multisubunit enzyme complex. See Lambda (A) Isomers of Metal Ion-Nucleotide Complexes Lock and Key Model of Enzyme Action Low-Barrier Hydrogen Bonds Role in Catalysis Yaga-Ozav /a Plot Yonetani-Theorell Plot Induced-Fit Model Allosteric Interaction... 

Stereochemical probes of the specificity of substrates, products, and effectors in enzyme-catalyzed reactions, receptor-ligand interactions, nucleic acid-ligand interactions, etc. Most chirality probe studies attempt to address the stereospecificity of the substrates or ligands or even allosteric effectors. However, upon use of specific kinetic probes, isotopic labeling of achiral centers, chronfium-or cobalt-nucleotide complexes, etc., other stereospecific characteristics can be identified, aU of which will assist in the delineation of the kinetic mechanism as well as the active-site topology. A few examples of chirality probes include ... 

Chrominm(III) and Cobalt(III) Nucleotide Complexes. Coordination isomers of Cr(III)- and Co(III)-nucleotides can be separated and used to test for specificity. Since Cr(III) is diamagnetic, EPR and NMR experiments can supplement the chirality probes . ... 

Exchange-inert complexes of Cr(III) with nucleotide ligands are very stable toward hydrolysis. Such complexes have proven to be extremely useful as chirality probes in that different coordination isomers can be prepared and separated These nucleotide complexes have also proved useful as dead-end inhibitors of enzyme-catalyzed reactions. Because Cr(lII) is paramagnetic, distances can be measured by measuring the effects of Cr(lll) on the NMR signals of nearby atoms when the Cr(lll)-nucleotide complex binds to the surface of a mac-romolecule. See Exchange-Inert Complexes... 

O Sullivan and Smithersi describe various protocols for determining dissociation constants (or, stability constants) of metal ion-nucleotide complexes. Morrison and Cleland have presented a kinetic method that has... 

A metal-nucleotide complex that exhibits low rates of ligand exchange as a result of substituting higher oxidation state metal ions with ionic radii nearly equal to the naturally bound metal ion. Such compounds can be prepared with chromium(III), cobalt(III), and rhodi-um(III) in place of magnesium or calcium ion. Because these exchange-inert complexes can be resolved into their various optically active isomers, they have proven to be powerful mechanistic probes, particularly for kinases, NTPases, and nucleotidyl transferases. In the case of Cr(III) coordination complexes with the two phosphates of ATP or ADP, the second phosphate becomes chiral, and the screw sense must be specified to describe the three-dimensional configuration of atoms. 

Coordination isomers of metal ion-nucleotide complexes. For most metal ions, for example Mg, the metal... 

Preliminary rate measurements should allow one to make a plot of initial velocity Vq versus [metal ion], and this should provide information on the optimal metal ion concentration. (For many MgATP -dependent enzymes, the optimum is frequently 1-3 mM uncomplexed magnesium ion.) Then, by utilizing pubhshed values for formation constants (also known as stability constants) defining metal ion-nucleotide complexation, one can readily design experiments to keep free metal ion concentration at a fixed level. To compensate properly for metal ion complexation in ATP-dependent reactions, one must chose a buffer for which a stability constant is known. For example, in 25 mM Tris-HCl (pH 7.5), the stability constant for MgATP is approximately 20,000 M Thus, one can write the following equation ... 

The following table lists several frequently used stability constants for metal ion-nucleotide complexes. Because complexation is driven by neutrafization of electric charge on the components, one should immediately appreciate that the values apply only for the specified solution conditions. A more complete list is provided else-where. ... 

In the A series of CrATP, there are two screw-sense isomers, S (pseudoequatorial) and A (pseudoaxial). A number of nucleotide-dependent enzymes have been shown to be specific for one of the screw-sense isomers. See Exchange-Inert Metal-Nucleotide Complexes... 

LAMBDA (or A-) ISOMERS OF METAL ION-NUCLEOTIDE COMPLEXES LANGMUIR ISOTHERM BIOMINERALIZATION MICELLE... 

LAMBDA (or A-j ISOMERS OE METAL ION-NUCLEOTIDE COMPLEXES Metal ion-ligand complex,... 

LASER-FLASH KINETIC ANALYSIS METAL ION CATALYSIS METALLOTHIONEINS Metal-nucleotide complex,... 

SCREW SENSE OF METAL-NUCLEOTIDE COMPLEXES Sea shell formation, BIOMINERALIZATION SECOND... 

Brakoulias A, Jackson RM (2004) Towards a structural classification of phosphate binding sites in protein-nucleotide complexes an automated all-against-all structural comparison using geometric matching. Proteins Struct Funct Bioinformatics 56 250-260... 

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