protein

Examples of protein in the following topics:

• Mapping Protein-Protein Interactions

  • Mapping protein-protein interactions gives us a better understanding of molecular mechanisms inside the cell.
  • The protein complexes formed could be stable (proteins interact for a prolonged period of time) or transient (proteins interact for a brief period of time).
  • The tag serves as a tool to purify the bait protein and associated proteins by affinity chromatography.
  • The identity of the protein associated with a given bait protein is determined by comparing its peptide fingerprint against available databases.
  • Principle of the bait and prey method for the study of protein-protein interaction.

• Proteolytic Degradation

  • The mechanisms of proteolytic degradation are necessary for obtaining amino acids via degradation of digested proteins, preventing accumulation or abnormal concentrations of proteins, and by regulating cellular processes by removing proteins no longer needed.
  • Proteasomes are protein complexes that function in the degradation of unneeded or damaged proteins via proteolysis.
  • The recognition of this ubiquitin signal by the proteasome results in degradation of the protein into its amino acids, which are then recycled and reused for the synthesis of new proteins.
  • The lysosome contains proteases that are able to target and degrade proteins.
  • Once the protein arrives at the proteasome, the protein is degraded into its amino acids which are then reused for synthesis of new proteins.

• Proteomics

  • The proteome is the entire complement of proteins, including the modifications made to a particular set of proteins, produced by an organism or system.
  • Fourth, many proteins form complexes with other proteins or RNA molecules.
  • Finally, protein degradation rate plays an important role in protein content.
  • Most proteins function in collaboration with other proteins.
  • Several methods are available to probe protein–protein interactions.

• Purifying Proteins by Affinity Tag

  • Protein tags are peptide sequences genetically grafted onto a recombinant protein.
  • Protein tags are peptide sequences genetically grafted onto a recombinant protein.
  • These include chitin binding protein (CBP), maltose binding protein (MBP), and glutathione-S-transferase (GST).
  • BCCP (Biotin Carboxyl Carrier Protein), a protein domain recognized by streptavidin
  • Green fluorescent protein-tag, a protein which is spontaneously fluorescent and can be bound by nanobodies

• Two-Hybrid Analysis

  • Several methodologies exist to study the interaction of proteins in vivo.
  • The yeast two-hybrid screening system is an effective and quick tool for the in vivo study of protein–protein interaction both in prokaryotes and eukaryotes.
  • One limitation of classic yeast two-hybrid screens is that they are limited to soluble proteins.
  • It is therefore impossible to use them to study the protein–protein interactions between insoluble integral membrane proteins.
  • These fused proteins are called the bait and prey, respectively.

• Western Blots

  • The Western blot technique determines protein molecular weight and measures protein abundance in different samples.
  • The Western blot (sometimes called the protein immunoblot) is a widely accepted analytical technique used to detect specific proteins in a given sample of tissue homogenate or extract.
  • Assorted detergents, salts, and buffers may be employed to encourage lysis of cells and to solubilize proteins.
  • The technique uses gel electrophoresis to separate native proteins by 3-D structure or denatured proteins by the length of the polypeptide.
  • The proteins are then transferred to a membrane (typically nitrocellulose or PVDF), where they are stained with antibodies specific to the target protein.

• The Heat-Shock Response

  • Heat shock response is a cell's response to intense heat, including up-regulation of heat shock proteins.
  • HSPs are also called 'stress-proteins' and respond to heat, cold and oxygen deprivation by activating several cascade pathways.
  • They also shuttle proteins from one compartment to another inside the cell and target old or terminally misfolded proteins to proteases for degradation.
  • Additionally, heat shock proteins are believed to play a role in the presentation of pieces of proteins (or peptides) on the cell surface to help the immune system recognize diseased cells.
  • Heat shock protein come in many sizes.

• Iron-Binding Proteins

  • Iron binding proteins of the innate immune system include lactoferrin and transferrins.
  • Iron-binding proteins are proteins generally used to play roles in metabolism.
  • Iron-binding proteins are serum proteins, found in the blood, and as their name suggests, are used to bind and transport iron.
  • Lactoferrin (LF), also known as lactotransferrin (LTF), is a multifunctional protein of the transferrin family.
  • Based on PDB (Protein Data Bank) 1b0l

• Immunoblot Procedures

  • Immunoblot is a technique for analyzing proteins via antigen-antibody specific reactions.
  • Immunoblot procedures like protein blotting, or Western blotting, allow individuals to detect specific solubilized proteins from extracts made from cells or tissues, before or after any purification steps.
  • As the proteins migrate out of the gel, they are captured on a membrane.
  • Protein binding to the membrane is an irreversible mechanism.
  • proteins separated by molecular weight and represented by a dark band on a blot.

• DNA Mobility Shifts

  • DNA mobility shift assay is a technique for studying gene regulation and determining protein-DNA interactions.
  • A mobility shift assay is electrophoretic separation of a protein-DNA or protein-RNA mixture on a polyacrylamide or agarose gel for a short period.
  • However, assuming that the protein is capable of binding to the fragment, the lane with protein present will contain another band that represents the larger, less mobile, complex of nucleic acid probe bound to protein, which is "shifted" up on the gel (since it has moved more slowly).
  • If the starting concentrations of protein and probe are known, and if the stoichiometry of the complex is known, the apparent affinity of the protein for the nucleic acid sequence may be determined.
  • This method is referred to as a supershift assay, and is used to unambiguously identify a protein present in the protein-nucleic acid complex.