Protein-ligand interactions characterization

This experiment provides a nice example of the application of spectroscopy to biochemistry. After presenting the basic theory for the spectroscopic treatment of protein-ligand interactions, a procedure for characterizing the binding of methyl orange to bovine serum albumin is described. 

The book is separated into five major sections One short section on general aspects of spectroscopy, molecular biology and data evaluation is followed by an introduction into the NMR of commonly encountered classes of biomolecules. Thereafter, recent developments in spectroscopic techniques are highlighted. The next section describes experiments and practical aspects useful for the characterization of protein-ligand interactions. The final section presents an account on strategies for drug development using NMR written by experts from pharmaceutical industry. 

ALIS An Affinity Selection-Mass Spectrometry System for the Discovery and Characterization of Protein-Ligand Interactions... 

It is important to note that the same ALIS hardware and software used for combinatorial library screening is applicable to characterizing protein-ligand interactions using the methods described below. 

Advances in chemical synthesis have enabled considerable sophistication in the construction of diverse compound libraries to probe protein function [61, 62). However, few general techniques exist that can directly assess binding mechanisms and evaluate ligand afEnities in a multiplexed format. To realize the full potential of combinatorial chemistry in the drug discovery process, generic and efficient tools must be applied that combine mixture-based techniques to characterize protein-ligand interactions with the strengths of diversity-oriented chemical synthesis. 

Annis A, Chuang C-C, Nazef N An affinity selection-mass spectrometry system for the discovery and characterization of protein-ligand interactions, chapter 3. 

Pellecchia, M., et al., NMR-based structural characterization of large protein-ligand interactions. J Biomol NMR, 2002, 22, 165-173. 

Jahnke, W., Spin labels as a tool to identify and characterize protein-ligand interactions by NMR spectroscopy. ChemBioChem, 2002, 3, 167-173. 

Vajda, S. and Guarnieri, F. (2006). Characterization of protein-ligand interaction sites using experimental and computational methods. Curr. Opin. Drug Discov. Dev. 9, 354—362. 

The first part of this section describes how this interpretation is done and which assumptions have been made to retrieve plausible results. The second part will then describe the algorithms used to compute bond characteristics from geometric information, because the PDB file format and its successors include no means to specify hybridization states or bond orders, which are essential for the characterization of properties of small organic ligands. Ligand bond characteristics interpretation is a prerequisite for the step to follow the detailed description of protein-ligand interactions by pharmacophore models. 

Once a suitable matrix is obtained, with the ligand coupled to it, and properly characterized with regard to ligand concentration, the effectiveness of the protein-ligand interaction can be evaluated. A sample containing the target protein is applied to the column, which is washed and evaluated for retained protein. 

Protein-ligand interactions can not only be secreened or selected in vitro, but also can be directly characterized for particular interaction partners. Nemoto et al. (1999) applied the mRNA-peptide fusion technology to fluorescently label the displayed proteins in order to study protein-protein interactions by fluorescence polarization measurements. 

In the last few years, a number of publications have demonstrated that the GRID/PCA or GRID/CPCA methods can be successfully applied to characterize the structural differences between protein binding sites, and to identify differences in the protein-ligand interactions as well as the regions on the target enzymes which mediate highly selective interactions [4—17]. 

To characterize protein-ligand interactions by F NMR, the ligand or the protein can be labeled with fluorine to produce spectra without overwhelming complexity. Proteins expressed in E.coli and tissue culture have been labeled with fluorine by biosynthetic incorporation of fluoro analogs of tryptophan, phenylalanine and tyrosine. Conformational properties of receptor... 

Molecular modeling techniques are used extensively to supplement biophysical experimental methods for characterization of protein-ligand complexes. Modeling methods are often an essential tool for refinement of detailed structures from raw experimental data, and modeling techniques can provide additional information not readily available from experimental approaches. An overview of some modeling techniques suitable for investigation of protein-ligand interactions will be presented here. 

Sem, D.S., Yu, L., Coutts, S.M., and Jack, R. (2001) Object-oriented approach to drug design enabled by NMR SOLVE First real-time structural tool for characterizing protein-ligand interactions. J. Cell. Biochem. Suppl. 37, 99-105. 

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