HomeApplicationsProtein BiologyProtein Structural Analysis

Protein Structural Analysis

PDB ID: 5MU8 from Blevitt et al., Structural Basis of Small-Molecule Aggregate Induced Inhibition of a Protein-Protein Interaction. J. Med Chem. 2017, 60:3511-3517, and AS Rose et al.(2018) NGL viewer: web-based molecular graphics for large complexes. Bioinformatics and RCSB PDB.

The function of a protein is directly dependent on its structure, its interactions with other proteins, and its location within cells, tissues, and organs. The structure and function of proteins is studied on a large scale in proteomics, which enables the identification of protein biomarkers associated with specific disease states and provides potential targets for therapeutic treatment. The understanding of protein structure and mapping of protein location, expression levels, and interactions yield valuable information that can used to infer protein function.

Protein Structure
Protein Structure Determination
Protein Mapping


Related Product Resources

Bulletin: ISOGRO Media


Related Technical Articles

  • Methyl groups are ideal probes for studying protein structure and function by NMR. Choose among user-friendly kits for isotope labeling of a single type or multiple types of methyl groups.
  • Sigma-Aldrich presents an article about the selective protonation of methyl groups in highly deuterated proteins. In which the structural NMR studies of small proteins, a maximum number of proton chemical shifts are usually assigned and NOEs connecting large numbers of sites are subsequently quantified in terms of distance restraints that are then used to obtain an ensemble of structures.
  • Solid-state NMR on Larger Biomolecules; Sigma-Aldrich.com
  • Handling & Storage of Custom Peptides
  • Amino acid reference chart contains the twenty amino acids found in eukaryotes, grouped according to their side chains and charge. Discover our full product line of amino acids, including Alanine, Isoleucine, Leucine, Valine, Phenylalanine, Tryptophan, Tyrosine, Aspargine, Cysteine, Glutamine, Methionine, Serine, Threonine, Aspartic acid, Glutamic acid, Arginine, Histidine, Lysine, Glycine and Proline. Learn more today.
  • Biomolecular NMR: Isotope Labeling Methods for Protein Dynamics Studies
  • Glycan Sequencing Using Exoglycosidases
  • Glycosylphosphatidylinisotol (GPI) anchored proteins are membrane bound proteins found throughout the animal kingdom. GPI anchored proteins are linked at their carboxyterminus through a phosphodiester linkage of phosphoethanolamine to a trimannosyl-non-acetylated glucosamine (Man3-GlcN) core.
  • See All

Related Protocols

  • This page covers the principles and methods of chromatofocusing, a chromatography technique that separates proteins according to differences in their isoelectric point (pI).
  • Selected Protocol from "Protein-Protein Interactions: A Molecular Cloning Manual, 2nd Edition,", Erica A. Golemis and Peter D. Adams. Protein Interactions Captured by Chemical Cross-linking: One-Step Cross-linking with Formaldehyde
  • See All

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.