Interaction of Protein with small molecules

Keywords Biophysical monitors Chemical synthesis of proteins Copper binding Expressed protein ligation Interaction of PrP with small molecules... 

R120 M.-J. Clement, P. Savarin, E. Adjadj, A. Sobel, F. Toma and P. A. Curmi, Probing Interactions of Tubulin with Small Molecules, Peptides, and Protein Fragments by Solution Nuclear Magnetic Resonance , in Methods in Cell Biology, eds. L. Wilson and J. J. Correia, Elsevier Inc., 2010, Vol. 95, Microtubules, in vitro, p. 407. 

The endonucleases are a class of restriction enzymes which cleave doubly stranded DNA by recognition of specific (symmetric) nucleotide sequences [38, 39]. The enzymes are of considerable utility in studying sequence-specific interactions of proteins and small molecules with DNA. 

There are no inherent limitations to the nature of the interaction that can be probed with the FAC method. This too stems from an uncoupling of the binding event and the detector. The method can be applied to simple binary interactions between protein and small molecule, but also to protein-protein interactions, protein-cell interactions and virtually any interaction that can be modeled in a flow system. Some of the more elegant examples include drug interaction with whole cells [12] and membrane-bound receptors from brain homogenates [13]. Ultimately, the limitations are dictated by what can be detected from a stream of column effluent. 

S. K. Burley and G. A. Petsko cover the field of noncovalent interactions of proteins, with particular emphasis on weakly polar interactions. Their presentation of the whole field of electrostatic interactions should be of value to many workers in protein chemistry, but their special concern is with the weaker, but very important, interactions involving aromatic side chains, their orientation relative to one another, to oxygen and sulfur atoms, to amino groups, and to aromatic ligands that may bind to the protein. These interactions, only recently recognized for their influence on protein structure, play an important part in the formation of aromatic clusters in the interior of globular proteins and in other features of structure. The authors provide numerous illustrations of the principles involved, from recently determined structures, of both small molecules and proteins. 

Huang Z. The chemical biology of apoptosis. Exploring protein-protein interactions and the life and death of cells with small molecules. Chem Biol. 2002 9 1059-1072. 

It is clear from the discussion of metal homeostasis that the fuU characterization of a protein requires not only its study in the isolated form but also the investigation of its relevant interactions. Therefore, the interactions of metal-binding proteins with small molecules and other proteins are an obvious perspective in biological inorganic research. This implies the importance of the identification and structure characterization of weak protein-protein complexes that represent the key steps of the biochemical processes discussed here. Moreover, metal-mediated protein-protein interactions are just beginning to be identified and will become an important field of research. 

The potential advantages of selective nitration of tyrosyl residues in native proteins are numerous. The reaction is performed under mild conditions, giving rise to a 3-nitrotyrosyl derivative (pK 7), which in the acid form absorbs intensely at 350 nm. Hence, the nitrotyrosine content may be readily determined spectrophotometrically, as well as by amino acid analysis ( 2.2.3). The absorption spectrum of 3-nitro-tyrosine is highly sensitive to solvent polarity and exhibits significant optical activity in the long wavelength absorption band. Consequently, nitrotyrosyl residues can be utilized as indicators of conformational change, or of interactions of proteins with other macromolecules or small molecules (e.g. Kirschner and Schachman 1973). Any perturbation in the pK of nitrotyrosyl residues is readily determined spectrophotometrically. 

Jacobs et al. (68) that FMN cannot cross the protein coat, and the most probable explanation of the NMR data of Khodr et al. (76), concerning the interaction of ferritin with small amines, is that passage through the coat is severely limited, even for small molecules. 

One advantage of SPRi is the fact that no label is necessary, although the targets are immobilized on a support, often through covalent linkage. The interaction of proteins with any other classes of compounds, such as lipids, small molecules. 

The functional microarray typically consists of a collection of full-length functional proteins or protein domains printed on glass slides that are then exposed to a protein preparation from a cell that represents the entire proteome of that cell. This method is useful in determining protein-protein interactions. In addition, this method is useful in predicting the interaction of proteins with DNA, RNA, phospholipids, and small molecules. RPA includes glass slides on which a cellular protein preparation is fixed and then probed with a known antibody. This method helps in identifying the proteins that are altered and cannot bind with a known antibody in the proteome of diseased cell types. This method also identifies the proteins that are altered as a result of phosphorylation or other posttranslational modifications in normal and disease conditions or under growth conditions. 

Adsorption/absorption of biomolecules primarily results in depletion of necessary factors provided by the medium or secreted by the cells. It is an equilibrium-based phenomenon resulting in partitioning of the biomolecules between the PDMS material and the aqueous phase. Consequently, in a fluidic environment, new biomolecules (in the case of those provided by the medium) continuously arrive and are adsorbed/absorbed while a portion of the previously adsorbed/absorbed ones are detached from the PDMS material. As long as there is a sufficient supply of biomolecules in the medium, cell growth is not hampered. However, small molecules and proteins that are secreted by the cells and necessary for control of cellular functions (autocrine and paracrine factors) can potentially be removed to an extent strongly competing with the cellular capacity to excrete them. Secondly, adsorption of proteins, even if they were supplied by the medium and only transiently adsorbed on the hydrophobic surface of PDMS, causes an even more severe problem. The hydrophobic interaction of proteins with PDMS results in their denaturation due to the exposure of the hydrophobic core of the protein. 

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