Protein T6

• Globular proteins


  Amino acid chains that fold into compact and rounded shapes. Usually have functional roles.

  
• Globular proteins


  • Increase solubility in water
  • Have polar groups on the surface
  • Have hydrophobic groups in the interior
• The Structural Classification of Proteins (SCOP) is used for algorithms for structure comparison and analysis, including homology modelling of proteins

  
• Myoglobin


  A monomeric protein mainly found in muscle tissue, containing a heme group

  
• Myoglobin


  • Can be present in two forms: oxymyoglobin (oxygen-bound) and deoxymyoglobin (oxygen-free)
  • Tertiary structure consists of 8 α-helices (A through H)

  
• Heme group


  A flat molecule with four cyclic pyrrole rings, containing an iron (Fe) atom

  
• Amino acid arrangement in myoglobin

  • Hydrophilic R-groups on the surface, hydrophobic R-groups in the interior
  • Two histidine residues (E7 and F8) interact with the heme iron

  
• Iron (Fe) in the heme group

  In the ferrous state (Fe2+), can form 6 bonds: 4 with the nitrogen atoms of the pyrrole rings, 1 with the proximal histidine, and 1 with O2
• Heme group in myoglobin


  Stabilizes the tertiary structure of the protein

  
• Distal histidine in myoglobin


  Acts as a gate that opens and closes as O2 enters the hydrophobic pocket to bind to the heme

  
• Hydrophobic interior of myoglobin

  Prevents the oxidation of iron, keeping it in the Fe(II) state to bind O2
• Oxygen binding to myoglobin


  Myoglobin binds O2 with high affinity, with a P50 of ~2.8 torr or mm Hg

  
• Hemoglobin is a tetrameric hemeprotein, with two α and two β chains

  
• Hemoglobin structure


  • The α and β chains contain multiple α-helices, similar to myoglobin

  
• Hemoglobin chain interactions


  Stabilized by hydrophobic interactions, electrostatic interactions (salt bridges), and hydrogen bonds

  
• Oxygen binding to hemoglobin

  Hemoglobin must bind oxygen efficiently and become saturated at the high oxygen pressure in the lungs, then release oxygen in tissues where the pressure is lower

  
• Structural changes of hemoglobin

  • Hemoglobin exists in two conformations: T (taut, deoxygenated) and R (relaxed, oxygenated)
  • The T to R transition requires at least two subunits to be bound by oxygen

  
• Hemoglobin cooperativity


  Conformational changes lead to cooperativity among binding sites, where the binding of one O2 molecule increases the affinity for the next

  
• Carbon monoxide (CO) vs Oxygen (O2)

  CO has a much higher affinity for hemoglobin than O2, leading to carbon monoxide poisoning
• Sickle cell anemia is caused by a mutation in the hemoglobin gene (βGlu6 to Val) that leads to abnormal hemoglobin structure and function
• Immunoglobulins (antibodies)


  Composed of variable (V) regions that encode antigen binding activity, and constant (C) regions that encode immune response and effector functions
• Immunoglobulin structure


  • Naturally occurring immunoglobulins have identical heavy and light chains, giving rise to multiple binding sites with identical specificities
  • There is a conserved glycosylation site in the CH2 domain of the Fc region that influences interactions with effector molecules
• Immunoglobulins


  • Destroy foreign cells, particles, proteins
  • Bind bacterial Protein A, Protein G (used in purification)
• Immunoglobulin domains


  • (antigen-binding fragment)
  • (crystallizable fragment)
• There is a conserved glycosylation site in the CH2 domain of the Fc
• A carbohydrate is covalently attached here by post-translational modification
• These conserved glycosylation sites influence interactions with effector molecules
• Immunoglobulin domains


  • The N-terminus of each chain is situated at the tip
  • Each domain has a similar structure, characteristic of all the members of the immunoglobulin superfamily: composed of between 7 (for constant domains) and 9 (for variable domains) β-strands, forming two beta sheets in a Greek key motif
  • Two types of light chain exist, termed lambda (λ) and kappa (κ)
  • The class, and thus the effector function, of an antibody, is defined by the structure of its heavy chain
  • Five main heavy-chain classes or isotypes exist, determining the functional activity of an antibody molecule: immunoglobulin M (IgM), immunoglobulin D (IgD), immunoglobulin G (IgG), immunoglobulin A (IgA), and immunoglobulin E (IgE)
  • Their heavy chains are denoted by the corresponding lower-case Greek letter (μ, δ, γ, α, and ε, respectively)
• Molecular chaperones


  A large group of unrelated protein families whose role is to stabilize unfolded proteins, unfold them for translocation across membranes or for degradation, and/or to assist in their correct folding and assembly
• Molecular chaperones


  • Interact with unfolded or partially folded protein subunits
  • They stabilize non-native conformation and facilitate correct folding of protein subunits
  • They do not interact with native proteins, nor do they form part of the final folded structures
  • Some chaperones are non-specific, and interact with a wide variety of polypeptide chains, but others are restricted to specific targets
  • They often couple ATP binding/hydrolysis to the folding process

  
• Examples of molecular chaperones

  • Heat shock proteins: HSP104, 90, 70, 60 and small HSPs, HSP47
  • Catalysts of folding: Protein disulfide isomerase, Peptidyl prolyl cis-trans isomerase
  • Nucleoplasmin: nucleosome assembly
  • Prosequences: subtilisin, α-lytic protease (intramolecular chaperones)
• Heat shock protein 47 (HSP47)

  • 47 kDa collagen-specific molecular chaperone
  • A member of the serine protease inhibitor (SERPIN) superfamily, but does not possess the inhibitory activity. Shares structural similarity
  • Essential for the proper folding of collagen triple helix
  • Assists in the biosynthesis of collagen molecules in the endoplasmic reticulum (ER), and in the collagen transport from the ER to the Golgi apparatus
  • HSP47 release from collagen in the transport vesicle is triggered by the lower pH in the cis-Golgi or the ER-Golgi intermediate compartment (ERGIC), before being recycled back to the ER
• HSP47 functions


  1. Procollagen chains

  2. Procollagen trimer formation assisted by HSP47

  3. HSP47 assist in collagen transport from endoplasmic reticulum

  4. Secretion to extracellular space

  5. Secretion of misfolded procollagen is prevented

  
• HSP47 collagen binding and release behaviour

  • H255 and H256: Mutation caused less pronounced pH-dependency of collagen binding
  • H302: Mutation caused disturbed collagen-release characteristics
  • H197 and H198: Mutation allows binding but no apparent pH-switch and are unable to control release
  • H220: Mutation caused no binding with collagen
• HSP47-R222S alters synthesis and stability of type I collagen
• R222S mutation leads to osteogenesis imperfecta
• Polar Groups


  Amino acids on the surface of globular proteins, such as serine, threonine, and asparagine, that form hydrogen bonds with water molecules.
• Hydrophobic Groups


  Amino acids in the interior of globular proteins, such as alanine, valine, and leucine, that are unable to form hydrogen bonds with water molecules and are shielded by surrounding polar groups.