Binding small-molecule

They also bind small molecules and can be involved in protein-protein interactions. PAS domains in other proteins commonly function either as protein interaction sites or small molecule binding domains. Occasionally,... 

These studies of protein-bound heterometallic cubanes have amply demonstrated that the heterometal site is redox active and able to bind small molecules. Although they have yet to be identified as intrinsic components of any protein or enzyme (except as part of the nitrogenase FeMo cofactor cluster (254)), they are clearly attractive candidates for the active sites of redox enzymes. 

Vesicle size, bilayer fluidity, membrane permeability, microviscosity, ability to bind small molecules, suseeptibility to pore formation, flip-flop rates, extent of water penetration, lateral amphiphile diffusion, vesiele fusion, and kinetic medium effeets (some of which will be discussed briefly below) all depend on the paeking of... 

Other investigators have also studied similar synthetic polymers.11-17 In our experience no water-soluble polymer binds small molecules with an avidity comparable to serum albumin. A comparison of the latter with two of the best-binding polymers18 is shown in Fig. 1. Neither polymer binds as strongly as serum albumin. Despite its large cationic charge and many apolar (—CH2—CH2—CH2—CH2—) side chains, polylysine shows very weak affinity for anions. Polyvinylpyrrolidone is more effective but not impressive. 

The former binds small molecules in a much more... 

Cytochromes of the b and c groups usually have two strong field axial ligands and are therefore low-spin. These will not bind small molecules. Cytochromes a3 and d, in contrast, bind 02 and act as terminal oxidases. 

Cytochrome a is usually low-spin and six-coordinate, and will therefore be involved in electron transfer. Cytochrome a3 is high-spin and five-coordinate, and is therefore able to bind small molecules such as 02 and CO in the sixth, axial position when present as Fe11. It appears therefore that cytochrome a3 is the component of cytochrome oxidase that binds dioxygen, and it is possible that at some stage the dioxygen species would bridge the a3 iron and CuB. 

Enzymes are a class of macromolecules with the ability both to bind small molecules and to effect reaction. Stabilizing forces such as hydrophobic effects only slightly dominate destabilizing forces such as Coulombic forces of equal polarity thus the Gibbs free enthalpy of formation of proteins, AGformation, is only weakly negative. 

Riboswitches are RNA regulatory elements capable of binding small molecule metabolites to regulate the mRNA in which they are embedded (Montange and Batey, 2008 Winkler and Breaker, 2005). Our lab recently solved the crystal structure of the lysine riboswitch ligand-binding domain... 

Thus one might expect flexible, water-soluble synthetic polymers with suitable side chains to show affinities for small molecules. We have examined, over several decades, the binding ability of poly(vinylpyrrolidone), polyvinylpyridine, polylysine, polyacrylamide, poly(isopropylacrylamide), poly(vinylimidazole), poly(vinylmethyloxazolidi-none), poly(vinylmethyloxazolidinone-vinylimidazole), poly(vinylpyrrolidone-vinyli-midazole), poly(vinylpyrrolidone-vinyl alcohol), poly(vinylpyrrolidone-maleic anhydride), poly(vinylmethyloxazolidinone-maleic anhydride), and poly(2-methylami-noethyl methylacrylate-methacrylic acid). Other investigators have studied similar synthetic polymers [5-12], In our experience no water-soluble polymer binds small molecules with an avidity comparable to serum albumin. 

Finally, the selected compounds are purchased or synthesized and then tested. If the goal is to identify weakly binding small molecules, it is important to ensure that the biological assay is sensitive and robust enough to pick up these molecules. Measurements using 100-1000 pM concentration of the ligand frequently cause problems due to the limited solubility of the ligands in water. To compensate for this, the assay is often carried out in the presence of 1-5% dimethyl sulfoxide (DMSO) (see, e.g.. Ref. 14). 

Considering the synthesis of an artificial system with coordinative or covalent bonds in square planar metal chelates for binding small molecules or catalytic use, main points are donor ligand activation, reduced aggregation, and irreversible oxidation of the chelate. 

Metal containing polyoximes (Chap. 5.6) are interesting compounds for binding small molecules (O2, CO) and activating H2 for catalytic reactions. The reversibility for 02-binding in water seems to be higher than with jxjlymer bound porphyrins. Structurally pure polyoxime chelates are difficult to obtain since other structural elemente are often present. 

Possibilities for preparing polymeric N202-chelates (Chap. 5.6) and their li ds are known. Some work must be done in structure inv tigation by molecular weight and its distribution. Interesting properties are their use as adsorbents. The research about binding small molecules like O2 and application as catalyst k yet missing. 

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