Protein Ligand

In biochemistry, a protein ligand is an atom, a molecule or an ion which can bind to a specific site (the binding site) on a protein. Alternative names used to mean a protein ligand are affinity reagents or protein binders. To date, antibodies are the most widely used protein ligands in life-science investigations, however, other molecules such as protein scaffolds, nucleic acids, peptides are also being used.

Main methods to study protein–ligand interactions are principal hydrodynamic and calorimetric techniques, and principal spectroscopic and structural methods such as

• Fourier transform spectroscopy
• Raman spectroscopy
• Fluorescence spectroscopy
• Circular dichroism
• Nuclear magnetic resonance
• Mass spectrometry
• Atomic force microscope
• Paramagnetic probes
• Dual Polarisation Interferometry

Other techniques include: fluorescence intensity, bimolecular fluorescence complementation, FRET (fluorescent resonance energy transfer) / FRET quenching surface plasmon resonance, Bio-Layer Interferometry, Coimmunopreciptation indirect ELIS, equilibrium dialysis, gel electrophoresis, far western blot, fluorescence polarization anisotropy, electron paramagnetic resonance, Microscale Thermophoresis

The dramatically increased computing power of supercomputers and personal computers has made it possible to study protein–ligand interactions also by means of computational chemistry. For example, a worldwide grid of well over a million ordinary PCs was harnessed for cancer research in the project grid.org, which ended in April 2007. Grid.org has been succeeded by similar projects such as World Community Grid, Human Proteome Folding Project, Compute Against Cancer and Folding@Home.