Small molecule-protein interactions

The ProCode technology analyzes libraries of expressed proteins to identify protein-protein and protein-small molecule interactions. Data of genes that interact with existing compounds is then achieved. This accelerates the discovery process by profiling performance prior to expensive testing in vivo. 

MacBeath, G. (2007) Protein Arrays Labeling the Compounds and Probing the Array for Protein-Small Molecule Interactions. CSH Protocols, 2007 pdb.prot4631. 

Functional array Purified proteins are arrayed on the surface and used to detect and characterize protein - protein, protein - DNA or protein - small molecule interactions... 

Canonical Protein - Small Molecule Interactions in the Kinase Family... 

In other work, using a range of different protein function microarrays, each fabricated in the form of BCCP fusion proteins as described here, we have been able to monitor a wide range of protein activities, including protein-protein interactions and protein-small molecule interactions, as well as carrying out on-chip phosphorylation assays (6) (see Note 15). 

Have mastered the workings of hormones on the cellular and molecular levels the concept of membrane and intracellular receptors, nuclear receptors, the various types of second messengers, and the details of their mode of action. Be able to use the Scatchard equation to solve protein-small molecule interaction problems. 

There are many ways in which hormone-receptor interactions may be studied, the classic method being the Scatchard technique, named in honor of George Scatchard. This technique is applicable to any protein-small molecule interaction, and it provides a means of determining the heterogeneity of binding sites, dissociation constants, and the number of binding sites per receptor unit. The last may be a protein molecule, a cell, a cell membrane fragment, or a unit volume of cytosol with a known protein content. 

Fig. 7.1. Different yeast n-hybrid systems that have been developed to study protein-protein, protein-DNA, protein-RNA, and protein - small molecule interactions. A. In the original version of the Y2H system, transcriptional activation of the reporter gene is reconstituted by recruitment of the activation domain (AD) to the promoter region through direct interaction of protein X and Y, since protein X is fused to a DNA-binding domain (DBD) and protein Y is fused to the AD [1], B. In the Y1 H assay, the AD is fused directly to the DBD [109]. This assay can be used to screen either DBDs that can bind to a specific DNA sequence or the in vivo binding site for a given DBD. C.

Because our first two examples have emphasized protein-small molecule interactions, we... 

Proteins, not mRNAs, are the true functional components of cells. Unlike DNA microarrays, on which interactions are based on Watson-Crick base pairing, biomo-lecular interactions on protein microarrays are determined by complex associations between the probe proteins and the target molecules. Individual protein-ligand pairs could differ greatly in their affinities. Furthermore, unlike DNA whose structure is relatively simple, proteins are extremely diverse in structure and functions, and often display many variables, such as posttranslational modifications. Protein microarrays are useful for determining numerous protein interactions including protein-protein [59], protein-DNA [26], and protein-small molecule interactions [30], or identifying the substrates of protein kinases [58]. 

Piezoelectric sensors have become a versatile tool in biosensorics to study protein-protein and protein-small molecule interactions. Here we present theoretical background on piezoelectric sensors and instructions, how to modify their surface with various recognition elements for cholinesterases. These recognition elements comprise an organophosphate (paraoxon), a cocaine derivative (BZE-DADOO), and a tricyclic, aromatic compound (propidium). Additionally, a guide to the kinetic evaluation of the obtained binding curves is given in this chapter. 

When an acridonylalanine (acdAla) was incorporated at different positions of camel single-chain antibody against hen-lysozyme, the Tyrl06acdAla mutant sensitively responded to the binding of nanomolar concentration of the antigen, whereas the Trpl23acdAla mutant was insensitive to the binding (Fig. 5.1-16) [71]. When the same fluorescent amino acid was incorporated into streptavidin, some mutants responded to even a picomolar quantity of biotin [71]. The lower limit of the detectable concentration is determined not by the fluorescence sensitivity, but by the dissociation constants of the protein-small molecule interactions. 

Mann, G., Hermans, J. Modeling protein-small molecule interactions Structure and thermodynamics of noble gases binding in a cavity in mutant phage T4 lysozyme L99A, J. Mol. Biol. 2000, 302, 979-89. 

Protein kinetics analysis as well as studies of protein-small molecule interactions... 

Numerous reports have been published about the three-dimensional structure of proteins determined by X-ray crystallography and/or NMR, and by computational chemical calculation from the results of amino acid sequencing. An empirical approach to identifying catalytic sites, the location of metal ion and carbohydrate binding sites, and folding and unfolding, has been studied with molecular dynamics simulations. Once the binding site of a protein, the structure of the protein-small molecule interaction, is... 

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