Protein Structural Analysis

Protein structure

Protein structure is determined by the sequence of amino acids that compose the protein and how the protein folds into more complex shapes.

• Primary structure is defined by the amino acid sequence of the protein.
• Secondary structure is defined by local interactions of stretches of the polypeptide chain, which can form α-helices and β-sheets through hydrogen bonding interactions.
• Tertiary structure defines the overall three-dimensional structure of the protein.
• Quaternary structure defines how multiple protein subunits interact to form larger complexes.

Protein Structure Determination

The determination of three-dimensional protein structures at atomic resolution is useful in the elucidation of protein function, structure-based drug design, and molecular docking.

• NMR: Nuclear magnetic resonance (NMR) spectroscopy is used to obtain information about the structure and dynamics of proteins. In NMR, the spatial location of atoms is determined by their chemical shifts. For protein NMR, proteins are typically labeled with stable isotopes (¹⁵N, ¹³C, ²H) to enhance sensitivity and facilitate structural deconvolution. Isotopic labels are typically introduced by supplying isotopically labeled nutrients in the growth medium during protein expression.
• X-ray crystallography: Protein X-ray crystallography can be used to obtain the three-dimensional structure of proteins through X-ray diffraction of crystallized proteins. Crystals are grown by seeding highly concentrated protein in solutions that promote precipitation, with ordered protein crystals forming under suitable conditions. X-rays are aimed at the protein crystal, which scatters the X-rays onto an electronic detector or film. The crystals are rotated to capture diffraction in three dimensions, enabling calculation of the position of each atom in the crystallized molecule by Fourier Transform.

Protein Mapping

Mapping of the location and expression level of proteins in specific cells, tissues, and organs aids in the functional study of the proteome. Spatial distribution of proteins is key to protein function, with improper localization or expression triggering various disease states. Mapping projects such as the Human Protein Atlas provide a proteomic resource for biomarker discovery and aid in the understanding of disease pathology. Mapping of the interactome helps define the molecular interactions that occur on a cellular level, assisting in the understanding of protein function and providing valuable potential drug targets for disease.