Protein methods are the techniques used to study protein

Protein

Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...

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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
  Genetic code
  The genetic code is the set of rules by which information encoded in genetic material is translated into proteins by living cells....
  
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• site-directed mutagenesis
  Site-directed mutagenesis
  Site-directed mutagenesis, also called site-specific mutagenesis or oligonucleotide-directed mutagenesis, is a molecular biology technique in which a mutation is created at a defined site in a DNA molecule. In general, this form of mutagenesis requires that the wild type gene sequence be known...
  
   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
    Green fluorescent protein
    The green fluorescent protein is a protein composed of 238 amino acid residues that exhibits bright green fluorescence when exposed to blue light. Although many other marine organisms have similar green fluorescent proteins, GFP traditionally refers to the protein first isolated from the...
    
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• evolutionary; analysis of sequence changes in different species using software such as BLAST
  BLAST
  In bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences...
  
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• Proteins that are involved in human diseases can be identified by matching allele
  Allele
  An allele is one of two or more forms of a gene or a genetic locus . "Allel" is an abbreviation of allelomorph. Sometimes, different alleles can result in different observable phenotypic traits, such as different pigmentation...
  
  s to disease and other phenotypes using methods such as calculation of LOD scores
  Genetic linkage
  Genetic linkage is the tendency of certain loci or alleles to be inherited together. Genetic loci that are physically close to one another on the same chromosome tend to stay together during meiosis, and are thus genetically linked.-Background:...
  
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Detecting proteins

• microscopy, protein immunostaining
  Immunostaining
  Immunostaining is a general term in biochemistry that applies to any use of an antibody-based method to detect a specific protein in a sample. The term immunostaining was originally used to refer to the immunohistochemical staining of tissue sections, as first described by Albert Coons in 1941...
  
  
• Protein immunoprecipitation
  Immunoprecipitation
  Immunoprecipitation is the technique of precipitating a protein antigen out of solution using an antibody that specifically binds to that particular protein. This process can be used to isolate and concentrate a particular protein from a sample containing many thousands of different proteins...
  
  
• Immunoelectrophoresis
  Immunoelectrophoresis
  Immunoelectrophoresis is a general name for a number of biochemical methods for separation and characterization of proteins based on electrophoresis and reaction with antibodies. All variants of immunoelectrophoresis require immunoglobulins, also known as antibodies reacting with the proteins to be...
  
  
• Immunoblotting
• BCA Protein Assay
  Bicinchoninic acid assay
  The bicinchoninic acid assay , also known as the Smith assay, after its inventor, Paul K. Smith at the Pierce Chemical Company, is a biochemical assay for determining the total level of protein in a solution , similar to Lowry protein assay, Bradford protein assay or biuret reagent...
  
  
• Western blot
  Western blot
  The western blot is a widely used analytical technique used to detect specific proteins in the given sample of tissue homogenate or extract. It uses gel electrophoresis to separate native proteins by 3-D structure or denatured proteins by the length of the polypeptide...
  
  
• Spectrophotometry
  Spectrophotometry
  In chemistry, spectrophotometry is the quantitative measurement of the reflection or transmission properties of a material as a function of wavelength...
  
  
• Enzyme assay
  Enzyme assay
  Enzyme assays are laboratory methods for measuring enzymatic activity. They are vital for the study of enzyme kinetics and enzyme inhibition.-Enzyme units:...
  
  

Protein purification

Protein purification

Protein purification is a series of processes intended to isolate a single type of protein from a complex mixture. Protein purification is vital for the characterization of the function, structure and interactions of the protein of interest. The starting material is usually a biological tissue or...

• Protein Isolation
  • chromatography methods: Ion exchange
    Ion exchange
    Ion exchange is an exchange of ions between two electrolytes or between an electrolyte solution and a complex. In most cases the term is used to denote the processes of purification, separation, and decontamination of aqueous and other ion-containing solutions with solid polymeric or mineralic 'ion...
    
    , Size-exclusion chromatography or Gelfiltration, Affinity chromatography
    Affinity chromatography
    Affinity chromatography is a method of separating biochemical mixtures and based on a highly specific interaction such as that between antigen and antibody, enzyme and substrate, or receptor and ligand.-Uses:Affinity chromatography can be used to:...
    
    
• Protein Extraction and Solubilization
• Protein Concentration Determination Methods, Bradford protein assay
  Bradford protein assay
  The Bradford protein assay is a spectroscopic analytical procedure used to measure the concentration of protein in a solution. It is subjective, i.e., dependent on the amino acid composition of the measured protein. The Bradford protein assay was developed by Marion M...
  
  
• Concentrating Protein Solutions
• Gel electrophoresis
  Gel electrophoresis
  Gel electrophoresis is a method used in clinical chemistry to separate proteins by charge and or size and in biochemistry and molecular biology to separate a mixed population of DNA and RNA fragments by length, to estimate the size of DNA and RNA fragments or to separate proteins by charge...
  
  
  • Gel Elecdsis Under denaturing conditions
  • Gel Electrophoresis Under non-denaturing conditions
  • 2D Gel Electrophoresis
• Electrofocusing

Protein-DNA interactions

• ChIP-on-chip
  ChIP-on-chip
  ChIP-on-chip is a technique that combines chromatin immunoprecipitation with microarray technology . Like regular ChIP, ChIP-on-chip is used to investigate interactions between proteins and DNA in vivo...
  
  
• Chip-Sequencing
  Chip-Sequencing
  ChIP-Sequencing, also known as ChIP-Seq, is used to analyze protein interactions with DNA. ChIP-Seq combines chromatin immunoprecipitation with massively parallel DNA sequencing to identify the cistrome of DNA-associated proteins. It can be used to precisely map global binding sites for any...
  
  
• DamID
  DamID
  DamID is a molecular biology protocol used to map the binding sites of DNA- and chromatin-binding proteins in eukaryotes. DamID identifies binding sites by expressing the proposed DNA-binding protein as a fusion protein with DNA methyltransferase...
  
  
• Microscale Thermophoresis
  Microscale Thermophoresis
  Microscale Thermophoresis is a technology for the analysis of biomolecules. Microscale Thermophoresis is the directed movement of particles in a microscopic temperature gradient...
  
  

Other methods

• Hydrogen-deuterium exchange
  Hydrogen-deuterium exchange
  Hydrogen–deuterium exchange is a chemical reaction in which a covalently bonded hydrogen atom is replaced by a deuterium atom, or vice versa. Usually the examined protons are the amides in the backbone of a protein. The method gives information about the solvent accessibility of various parts of...
  
  
• Mass spectrometry
  Mass spectrometry
  Mass spectrometry is an analytical technique that measures the mass-to-charge ratio of charged particles.It is used for determining masses of particles, for determining the elemental composition of a sample or molecule, and for elucidating the chemical structures of molecules, such as peptides and...
  
  
• Molecular dynamics
  Molecular dynamics
  Molecular dynamics is a computer simulation of physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a period of time, giving a view of the motion of the atoms...
  
  
• Protein structure prediction
  Protein structure prediction
  Protein structure prediction is the prediction of the three-dimensional structure of a protein from its amino acid sequence — that is, the prediction of its secondary, tertiary, and quaternary structure from its primary structure. Structure prediction is fundamentally different from the inverse...
  
  
• Protein sequencing
  Protein sequencing
  Protein sequencing is a technique to determine the amino acid sequence of a protein, as well as which conformation the protein adopts and the extent to which it is complexed with any non-peptide molecules...
  
  
• Protein structural alignment
• Protein ontology
• Protein synthesis
• Proteomics
  Proteomics
  Proteomics is the large-scale study of proteins, particularly their structures and functions. Proteins are vital parts of living organisms, as they are the main components of the physiological metabolic pathways of cells. The term "proteomics" was first coined in 1997 to make an analogy with...
  
  
• Peptide mass fingerprinting
  Peptide mass fingerprinting
  Peptide mass fingerprinting is an analytical technique for protein identification that was developed in 1993 by several groups independently. In this method, the unknown protein of interest is first cleaved into smaller peptides, whose absolute masses can be accurately measured with a mass...
  
  
• Ligand binding assay
  Ligand binding assay
  In medicine and pharmacology, a ligand binding assay is a technique to identify the presence of a molecule and quantify it. There are numerous types of ligand binding assays, both radioactive and non-radioactive. As such, ligand binding assays are superset of radiobinding assays, which are the...
  
  
• Eastern blotting
  Eastern blotting
  Eastern blotting is a biochemical technique used to analyze protein post translational modifications such as lipids and glycoconjugates. It is most often used to detect carbohydrate epitopes. Thus, Eastern blotting can be considered an extension of the biochemical technique of Western blotting...
  
  
• metabolic labeling
  • heavy isotope labeling
  • radioactive isotope labeling
    Radioactivity in biological research
    Radioactivity can be used in life sciences as a radiolabel to visualise components or target molecules in a biological system. Some radionuclei are synthesised in particle accelerators and have short half-lives, giving them high maximum theoretical specific activities. This lowers the detection...