Protein methods

Protein methods are the techniques used to study proteins.

There are genetic methods for studying proteins, methods for detecting proteins, methods for isolating and purifying proteins and other methods for characterizing the structure and function of proteins, often requiring that the protein first be purified.

Genetic methods

• conceptual translation- many proteins are never directly sequenced, but their sequence of amino acids is known by "conceptual translation" of a known mRNA sequence. See genetic code.
• site-directed mutagenesis allows new variants of proteins to be produced and tested for how structural changes alter protein function.
  • insertion of protein tags such as the His-tag. See also green fluorescent protein.
• evolutionary; analysis of sequence changes in different species using software such as BLAST.
• Proteins that are involved in human diseases can be identified by matching alleles to disease and other phenotypes using methods such as calculation of LOD scores.

Detecting proteins

• microscopy, protein immunostaining
• Protein immunoprecipitation
• Immunoelectrophoresis
• Immunoblotting
• BCA Protein Assay
• Western blot
• Spectrophotometry
• Enzyme assay

Protein purification

• Protein Isolation
  • chromatography methods: Ion exchange, Size-exclusion chromatography or Gelfiltration, Affinity chromatography
• Protein Extraction and Solubilization
• Protein Concentration Determination Methods, Bradford protein assay
• Concentrating Protein Solutions
• Gel electrophoresis
  • Gel Elecdsis Under denaturing conditions
  • Gel Electrophoresis Under non-denaturing conditions
  • 2D Gel Electrophoresis
• Electrofocusing

Protein structures

• X-ray crystallography
• Protein NMR

Protein-Protein interactions

• Yeast two-hybrid system
• Protein-fragment complementation assay
• Co-immunoprecipitation
• Affinity purification and mass spectrometry

Protein-DNA interactions

• ChIP-on-chip
• Chip-Sequencing
• DamID
• Microscale Thermophoresis

Other methods

• Hydrogen-deuterium exchange
• Mass spectrometry
• Molecular dynamics
• Protein structure prediction
• Protein sequencing
• Protein structural alignment
• Protein ontology
• Protein synthesis
• Proteomics
• Peptide mass fingerprinting
• Ligand binding assay
• Eastern blotting
• metabolic labeling
  • heavy isotope labeling
  • radioactive isotope labeling

References

• "Protein Methods", 2nd Edition by Daniel M. Bollag, Michael D. Rozycki and Stuart J. Edelstein (1996) Published by Wiley Publishers ISBN 0-471-11837-0.