Small molecule proteins

Equilibrium constants for protein-small molecule association usually are easily measured with good accuracy it is normal for standard free energies to be known to within 0.5 kcal/mol. Standard conditions define temperature, pressure and unit concentration of each of the three reacting species. It is to be expected that the standard free energy difference depends on temperature, pressure and solvent composition AA°a also depends on an arbitrary choice of standard unit concentrations. 

A microscopic, ordered array of nucleic acids, proteins, small molecules, cells or other substances that enables parallel analysis of complex biochemical samples. 

Taylor RD, Jewsbury PJ, Essex JW. A review of protein-small molecule docking methods. J Comput-Aided Mol Des 2002 16 151-66. 

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. 

The general types of protein-protein interactions that occur in cells include receptor-ligand, enzyme-substrate, multimeric complex formations, structural scaffolds, and chaperones. However, proteins interact with more targets than just other proteins. Protein interactions can include protein-protein or protein-peptide, protein-DNA/RNA or protein-nucleic acid, protein-glycan or protein-carbohydrate, protein-lipid or protein-membrane, and protein-small molecule or protein-ligand. It is likely that every molecule within a cell has some kind of specific interaction with a protein. 

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... 

Application of H/D Exchange to Protein-Small Molecule Ligand Interactions... 

Semenova, M.G., Il in, M.M., Belyakova, L.E., Antipova, A.S. (2003). Protein + small-molecule surfactant mixtures thermodynamics of interactions and functionality. In Dickinson, E., van Vliet, T. (Eds). Food Colloids, Biopolymers and Materials, Cambridge, UK Royal Society of Chemistry, pp. 377-387. 

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). 

Perform molecular dynamics simulations and energy minimizations for the target protein-small molecule complex (2W1T-8-chloro-cAMP) using AMBER 11 (downloaded from http // www.ambermd.org/) simulation package. 

Another difference between protein-protein and protein-small-molecule docking involves the treatment of nonbonded interactions. For the docking of rigid low molecular weight compounds, the receptor s molecular interaction... 

PCA can be used for quantitative pharmocological analysis of protein-protein and protein—small molecule binding in vivo. However, if the mDHFR domains are swapped for complementary fragments of another enzyme, then perhaps a PCA with ligand-dependent interacting domains such as FKBP and FRB can be used to regulate the activity of this enzyme. 

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