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Protein Function

Keratin Collagen

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Hemoglobin Immunoglobulin Myosin .

Fibrous proteins
Keratin (hair) α− helix coiled coils Similar structures also found in intermediate filaments, DNA-binding proteins, membrane-fusion proteins Collagen (bone) Collagen helix: a triple poly-proline II helix Collagen helices also found in some extracellular enzymes Fibroin (silk) β− sheet Found only in arthropods

Polyproline II helix Often occurs with repeating sequence Gly-Pro-Pro No hydrogen bonds Stabilized by steric repulsion of prolines

Long polyproline II helices found in collagen; short segments found in some other proteins

Hemoglobin and myoglobin

Myoglobin Oxygen binding protein in vertebrate muscle Function: facilitates oxygen transport through muscle cells 153 amino acids Prosthetic group = heme (Fe + protoporphyrin IX) Ligand =Oxygen Oxygen binding site = heme iron .

Myoglobin oxygen equilibrium MbO2 Mb + O2 [Mb] [O2] Kd = [MbO2] .

Fraction of myoglobin molecules with O2 bound = Fractional saturation = Y number of Mb molecules with O2 bound total number of Mb molecules [MbO2] [Mb] + [MbO2] Y = Y = .

Y = [MbO2] [Mb] + [MbO2] [Mb] [O2] Kd = [MbO2] .

Y = [MbO2] [Mb] + [MbO2] [Mb] [O2] Kd = [MbO2] [MbO2] = [Mb] [O2] Kd .

Y = [MbO2] [Mb] + [MbO2] [Mb] [O2] Kd = [MbO2] [Mb][O2]/Kd [Mb] + [Mb][O2]/Kd [MbO2] = [Mb] [O2] Kd Y = .

Y = [MbO2] [Mb] + [MbO2] [Mb] [O2] Kd = [MbO2] [Mb][O2]/Kd [Mb] + [Mb][O2]/Kd [MbO2] = [Mb] [O2] Kd Y = .

Y = [MbO2] [Mb] + [MbO2] [Mb] [O2] Kd = [MbO2] [Mb][O2]/Kd [Mb] + [Mb][O2]/Kd [MbO2] = [Mb] [O2] Kd [O2]/Kd 1 + [O2]/Kd Y = = .

Y = [MbO2] [Mb] + [MbO2] [Mb] [O2] Kd = [MbO2] [Mb][O2]/Kd [Mb] + [Mb][O2]/Kd = [O2] Kd + [O2] [MbO2] = [Mb] [O2] Kd [O2]/Kd 1 + [O2]/Kd Y = = .

Mb oxygen dissociation curve Y = 0.5 at p50 O2 concentration is usually expressed in pressure units O2 concentration in venous blood .

How does O2 get into the binding site? .

3-bisphosphoglycerate H+ . β subunits each 16.400 Prosthetic groups: heme (protoporphyrin IX plus iron) Oxygen binding sites: heme iron Homotropic allosterism: oxygen binding Heterotropic allosterism: 2.Hemoglobin Oxygen transporter in red blood cells Molecular weight: 65.000 Quaternary structure: α2β 2 α.

Mb and Hb have similar amino acid sequences .

Mb and α and β subunits of Hb have similar tertiary structures .

Hemoglobin displays cooperative oxygen binding .

At low pO2 Hb has low affinity for O2 At high pO2 Hb has high affinity for O2 As O2 binds. Hb switches from low affinity state to high affinity state .

Hb undergoes a conformational change as it binds O2 .

Ion pairs between subunits stabilize Hb in the T state .

Deoxy heme: iron out of plane .

Heme flattens when oxygen binds .

breaking a H-bond Heme flattens →val moves →H-bond breaks →ion pairs break.Flattened heme pushes against a valine side chain. destabilizing T-state .

How information about O2 binding to one subunit is communicated to other subunits .

Hemoglobin conformational change .

The Hill equation Y = pO2 p50 + pO2 (pO2)n (p50)n + (pO2)n myoglobin Y = hemoglobin .

The Hill equation Y = pO2 p50 + pO2 (pO2)n (p50)n + (pO2)n myoglobin Y = hemoglobin log [Y/(1-Y)] = n log pO2 – n log p50 .

Hill plot: graphical representation of cooperative ligand binding .

BPG: a heterotropic allosteric inhibitor increasing BPG BPG stabilizes the low O2 affinity Hb T state .

the hole between β chains disappears and BPG can’t bind T R .BPG binds to cavity between β chains in deoxy Hb and stabilizes the T state In the R state.

diversity .immunoglobulin secreted in response to recognition of antigen (“foreign” molecule) Bind to invading cell or virus surface. target invader for attack by macrophages or complement cascade Dissociation constants for immunoglobulin-antigen interaction often in the 10-9 to 10-11 M range Unique properties: specificity.Immunoglobulins Produced by B lymphocytes .

1 constant domain Heavy chains: 5 classes . 3 or 4 constant domains . IgD.κ and λ 1 variable domain. IgM 1 variable domain.Immunoglobulin composition: 2 light chains (25 kDa each) + 2 heavy chains (50-60 kDa each) held together by disulfide bonds Immunoglobulin domain: 110 amino acid unit Light chains: 2 classes . IgE.IgA. IgG.

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Two different human λ heavy chain constant sequences (C1 and C2) QPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADS QPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADS Two different human λ light chain variable sequences QSVLTQPPSASGTPGQRVTISCSGGNFDIGRNSVNWYQVHPGTAP QSVLTQPPSVSGTPGQRVTISCSGGSSNGTGNNYVYWYQQLPGTA .

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Topology of the immunoglobulin fold .

Hypervariable regions form loops at the tip of the variable domains .

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Two Ig variable chains bound to a protein antigen .

moves along microtubules •Dynein – bending of cilia Rotory-type •F-ATPase and V-ATPase – ion transport across membranes •Flagellar motor . moves along actin filaments •Kinesin – cargo transport. change in cell shape.Motor proteins Lever-type •Myosin – muscle contraction.

Repeating pattern of sarcomeres .

driven by ATP hydrolysis .Myofibril contracts by filaments sliding past each other.

Myosin is the major protein of the thick filament Heavy chain Regulatory light chain Essential light chain Heavy chains = 220 kDa each (N-terminal "head" containing ATPase activity plus C-terminal α-helical "tail") Light chains = 15-22 kDa each .

Proteolysis of myosin with the enzyme papain produces Subfragment 1 (S1): heavy chain "head" plus both light chains .

Myosin subfragment 1 .

Myosin undergoes large conformational change when ATP is hydrolyzed to ADP and phosphate is released .

Myosin power stroke .

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