L4 PTMs (PF2)

• Post-translational modifications (PTM) serve as important contributions to proteomic diversity and complexity and are essential for regulation of protein function and cellular signaling
• Different types of modifications include: cleavage into smaller proteins by peptidases, covalent modification of N-terminus, and covalent modification of side chains introducing functional groups to proteins
• PTM are specific for certain amino acids
• Side chain modifications can change a protein from active to inactive, inactive to active, or have different functions in the cell causing a cascade of events
• Many side chain modifications are regulated, reversible, fast, and useful as switches
• Main types of modifications are: phosphorylation, methylation, acetylation, glycosylation, sumoylation, and ubiquitination
• Phosphorylation:

  • Acts on hydroxyl groups of serine, threonine, and tyrosine
  • Adds a phosphoryl group, changing charge (polar to negative) and size of the amino acid (makes amino acid bigger)
  • Phosphorylation can indicate degradation and ubiquitination, influencing protein stability
• Acetylation of lysine:

  • Increases size and changes charge of lysine
  • Important for regulation of transcription, chromatin, and DNA repair
• Methylation:

  • Important for regulation of transcription, chromatin, and DNA repair
  • Methylation of arginine involves addition of 1 or 2 methyl groups
  • Methylation of lysine can be mono, di, or trimethylated
• Protein folding:

  • Folded structure depends on hydrophobic interactions in the interior
  • Post-translational modifications occur after the protein is folded
• Types of bonds for protein folding:

  • Hydrophobic interactions are many and very strong
  • Hydrogen bonds are moderate and many. these bonds stabilize secondary structure.
  • Van der Waals interactions are weak and many
  • Ionic bonds and disulfide bonds are very strong and few
• Amino acid sequence determines tertiary structure of a protein
• Protein misfolding:

  • Occurs due to mutations, harmful environmental conditions, or aging
  • Mutations can lead to changes in polypeptide sequences
• Protein quality control mechanisms and assisted folding by chaperones:

  • Chaperones are essential for protein homeostasis and quality control
  • Chaperones recognize hydrophobic patches and assist in proper protein folding
  • Chaperones are not part of the native state of the protein
• Post-translational modifications of amino acids are essential for the regulation of protein function and cellular signaling
• Different types of modifications include cleavage into smaller proteins by peptidases, covalent modification of N-terminus, and covalent modification of side chains introducing functional groups to proteins
• Side chain modifications change a protein from active to inactive, or vice versa, causing a cascade of events in the cell
• Main types of modifications are phosphorylation, methylation, acetylation, glycosylation, sumoylation, and ubiquitination
• Kinases transfer phosphates from ATP, while phosphatases remove phosphates in phosphorylation processes
• Acetylation of lysine leads to an increase in size and change in charge, important for regulation of transcription, chromatin, and DNA repair
• Methylation of arginine and lysine is crucial for the regulation of transcription, chromatin, and DNA repair
• Protein folding depends on hydrophobic, hydrogen, van der Waals, ionic, and disulfide bonds
• Amino acid sequence determines the native structure of a protein, and the folding process is thermodynamically favored
• Protein misfolding can occur due to mutations, environmental conditions, or aging, leading to protein quality control mechanisms
• Chaperones assist in protein folding by recognizing hydrophobic patches and protecting proteins during the folding process
• all PTMs are mediated by enzymes
• with phosphorylation, phosphoserine can now interact in electrostatic and ionic interactions that it could not have before. phosphorylation of serine and other amino acids depends on the surrounding environment of the amino acids
• the phosphoryl group that kinase is adding is coming from ATP, this interaction is reversible
• • kinases transfer phosphates from ATP, there are different kinases for specific side chains and the surrounding peptide sequence
  • the different kinase families are:
  • serine/threonine kinases → very similar in structure
  • thyrosine kinases
  • dual specificity kinases → can phosphorylate all of them
• • phosphatatases remove the phosphates
  • the different phosphatase families are: serine/threonine phosphatases, protein tyrosine phosphatases and dual specificity phosphatases
• two ways to study amino acids that are phosphorylated include: 1) phosphomimic: finding an amino acid that mimics if that amino acid were always phosphorylated by comparing to another amino acid that is negatively charged and similar in structure 2) de-phosphorylated: finding an amino acid that is similar to if the amino acid was not phsophorylated ever
• example of acetylation of lysine is the acetylation of histones that regulate translational modification. when lysine is acetylated, the electrostatic interaction between lysine and DNA is gone, allowing the DNA to be transcribed.
• acetyl-CoA gives the acetyl group to lysine
• methylarginines add methyl groups. the removal of methyl groups for arginine is not well understood.
• lysine methyltransferases mediate the methylation of lysine. lysine demethylases remove the methyl groups of lysine.
• primary structure of a protein is very flexible, the secondary structure is less and the tertiary structure of a protein usually only has one form
• some proteins need a ligand partner to stablize into native state, for example the cytochrome needs a haem cofactor to properly fold