Abstract
Nuclear magnetic resonance (NMR) is an effective, commonly used experimental approach to screen small organic molecules against a protein target. A very popular method consists of monitoring the changes of the NMR chemical shifts of the protein nuclei upon addition of the small molecule to the free protein. Multidimensional NMR experiments allow the interacting residues to be mapped along the protein sequence. A significant amount of human effort goes into manually tracking the chemical shift variations, especially when many signals exhibit chemical shift changes and when many ligands are tested. Some computational approaches to automate the procedure are available, but none of them as a web server. Furthermore, some methods require the adoption of a fairly specific experimental setup, such as recording a series of spectra at increasing small molecule:protein ratios. In this work, we developed a tool requesting a minimal amount of experimental data from the user, implemented it as an open-source program, and made it available as a web application. Our tool compares two spectra, one of the free protein and one of the small molecule:protein mixture, based on the corresponding peak lists. The performance of the tool in terms of correct identification of the protein-binding regions has been evaluated on different protein targets, using experimental data from interaction studies already available in the literature. For a total of 16 systems, our tool achieved between 79% and 100% correct assignments, properly identifying the protein regions involved in the interaction.
Highlights
Interactions of proteins with other molecules define their cellular functions.[1]
If an extensive assignment of all resonances is available, typically for the free protein, PICASSO infers the assignments for the second peak list and derives the chemical shift perturbation (CSP), using the Sorting Distances Smart (SDS) or Resource Allocation Smart (RAS) algorithms
We developed a tool, called PICASSO, that automatically transfers protein assignments from a 2D heteronuclear Nuclear magnetic resonance (NMR) spectrum, for example, 1H−15N HSQC, of a free protein sample to the corresponding spectrum acquired on a protein:ligand mixture
Summary
Interactions of proteins with other molecules define their cellular functions.[1]. These events are crucial for the proper functions of all processes in biological systems, and they are relevant targets for the modulation of cellular process by drugs.[2,3] An extensively used approach to develop new chemical probes to study biology as well as pharmaceuticals is screening small organic molecules (fragments) against a protein target to identify the interacting ligands and the residues forming the binding sites.[4]. Nuclear magnetic resonance (NMR) spectroscopy is a very effective technique to get information about protein−ligand interactions at atomic resolution.[7−9] In the protein-observed method, the spectrum of the target protein is acquired, and the ligand is titrated into the protein solution. This approach aims to provide information about the residues in the protein that are interacting with the ligand, either directly or through a modification of their environment induced by the binding event. When the 3D structure of the protein is available, CSP data allow the identification of the interaction region on the protein surface and can drive docking calculations to derive a structural model of the protein:ligand adduct.[10−12]
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