Amino acids

• Proteins


  Biological molecules performing a wide variety of functions, such as catalysing reactions, transporting molecules, or providing structural support
• Proteins


  • Their function is very often tightly linked to their three-dimensional structure
  • They are made of the same constituents: amino acids

  
• Amino acids


  The monomers making up proteins, with a general structure containing a central chiral carbon, an amino group, a carboxylic acid group, and a side chain

  
• Amino acids (except glycine) contain a central chiral carbon
• Zwitterion


  An amino acid in water at pH 7 has a positively charged amino group and a negatively charged acid group, but is neutral overall
• The 20 standard amino acids

  • Aliphatic side chains: Alanine, Valine, Leucine, Isoleucine
  • Non-polar side chains: Glycine, Proline, Cysteine, Methionine
  • Aromatic side chains: Histidine, Phenylalanine, Tyrosine, Tryptophan
  • Polar side chains: Asparagine, Glutamine, Serine, Threonine
  • Charged side chains: Aspartic acid, Glutamic acid, Lysine, Arginine

  
• Peptide bond


  The covalent bond formed between two amino acids by a condensation reaction, joining them together to form a polypeptide chain
• Amino acids are called residues when they are part of a peptide

  
• Levels of protein structure

  • Primary structure: Sequence of amino acids
  • Secondary structure: Local fold of the protein backbone, such as alpha-helices and beta-sheets
  • Tertiary structure: Overall three-dimensional shape of the protein
  • Quaternary structure: Arrangement of multiple polypeptide chains

  
• Peptide bond


  • It has a semi double-bond character, forming a planar amide plane
  • The angles between subsequent amide planes (torsion angles) can only adopt certain values, imposing conformations on the backbone
• Alpha-helix


  • Right-handed helical structure with 3.6 residues per turn, stabilised by hydrogen bonds between backbone atoms
  • Side chains project outward from the tightly packed core
• Beta-sheet


  • Stabilised by hydrogen bonds between backbone atoms of adjacent strands
  • Regions of non-repetitive secondary structure are called coils or loops
• Glycine does not have a side chain and plays a specific role in protein secondary structure
• β-sheet


  • Stabilised by hydrogen bonds between different chains
  • Hydrogen bonds are between backbone N–H and C=O groups

  
• β-sheet


  • Figure 7 shows an example
• Coils or loops


  • Regions of non-repetitive secondary structure in proteins
  • Not as regular as α-helices or β-sheets
  • Have a defined structure, not random coil
• Glycine


  • Does not have a side chain, can adopt many folds
  • Proline has a side chain covalently attached to backbone nitrogen, cannot adopt as many conformations, often disrupts secondary structure
• Tertiary structure


  Overall 3D arrangement of a protein: folding of secondary structure elements and position of side chains

  
• Hydrophobic effect


  Responsible for most of the tertiary structure: it is energetically favourable for the protein to fold and bury its hydrophobic residues within its core, away from surrounding water
• Forces, bonds and interactions involved in tertiary structure

  • Disulphide bonds
  • Salt bridges
  • Hydrogen bonds
  • Van der Waals interactions

  
• Quaternary structure


  Assembly of several polypeptide chains, and sometimes addition of a non-protein element, to form a functional protein
• Quaternary structure


  • Haemoglobin has two copies of the same chain and two copies of another, different chain
  • Antibodies contain two heavy chains and two light chains
• When a protein structure is determined experimentally, the 3D coordinates of its constituting atoms are stored in the Protein Databank (PDB), in a PDB file

  
• Protein Databank (PDB)


  Worldwide effort to collect all known structures of large biological molecules (proteins, DNA and RNA) in standardised files, allowing anyone to visualise them using tools like EzMol
• PDB ID


  Unique 4-character identifier for each PDB file (e.g. 2HHB for deoxyhaemoglobin)
• Different national and international entities collaborate to contribute to the global Protein Databank, including the RCSB PDB in the United States or the PDBe in Europe
• 1. ray crystallography


  1. Protein is crystallised

  2. X-rays are shot at the crystals

  3. Crystals diffract the X-rays

  4. Diffraction pattern is recorded

  5. Structure of the protein is calculated from the diffraction pattern

  
• Nuclear magnetic resonance


  1. Protein is in solution and placed in a magnetic field

  2. Protein is irradiated with electromagnetic waves

  3. Nuclei relax and produce a signal that reveals information about other nuclei around them

  4. Information is pieced together to determine which atoms are near which other atoms in the protein
• Cryo-electron microscopy


  1. Protein is in a thin layer of very cold ice

  2. Electron microscope fires electrons at the protein sample

  3. Electrons are scattered when they hit the sample

  4. Thousands of images are recorded with the protein in all possible orientations

  5. Images are assembled back together to create a 3D model of the protein structure

  
• Resolution


  Smallest distance between two distinguishable features in an experimentally determined protein structure
• Features revealed at different resolutions

  • 6Å: General shape of the protein and some α-helices
  • 4Å: Backbone of the protein, secondary structure
  • 3.5Å: Start to see side chains
  • 2.7Å: Can see side chains and start seeing water molecules
  • 1.5Å: Start reaching atomic resolution, can make out two covalently bonded carbon atoms
  • 1.2Å: Can distinguish almost any two covalently linked atoms, except hydrogen

  
• 2.7Å is a good resolution for a structure solved by X-ray crystallography, but most structures in the PDB are between 1.8Å and 2Å resolution
• With cryo-electron microscopy, it is difficult to achieve such high resolutions and 3.5Å is considered good, as it allows the visualisation of side chains