Protein Function PDF

5 Protein Function © 2021 Macmillan Learning  Proteins Function by Interacting Dynamically with Other Molecules two types of interactions: – protein acting as a reaction catalyst, or enzyme, alters the chemical configuration or composition of a bound molecule – neither t...

5 Protein Function © 2021 Macmillan Learning  Proteins Function by Interacting Dynamically with Other Molecules two types of interactions: – protein acting as a reaction catalyst, or enzyme, alters the chemical configuration or composition of a bound molecule – neither the chemical configuration nor the composition of the bound molecule is changed in this case  Oxygen Can Bind to a Heme Prosthetic Group oxygen: – poorly soluble in aqueous solutions – diffusion through tissues is ineffective over large distances – transition metals have strong tendency to bind (iron, copper)  Heme Prosthetic Group heme = protein prosthetic group – present in myoglobin and hemoglobin – consists of a complex organic ring structure, protoporphyrin, with a bound Fe2+ atom  Coordination Bonds of Iron six coordination bonds: – four to nitrogen atoms in the flat porphyrin ring – two perpendicular to the porphyrin  Perpendicular Coordination Bonds two perpendicular coordination bonds: – one is occupied by a side-chain nitrogen of a highly conserved proximal His residue – one is the binding site for molecular oxygen (O2) Fe2+ binds O2 reversibly Fe3+ does not bind O2 Tetrahedral bipyramid Myoglobin Has a Single Binding Site for Oxygen myoglobin: – 153 residues + one molecule of heme – bends named after the α-helical segments they connect His93 = ninety-third reside from the amino terminal end His F8 = eighth residue in α helix F  Graphical Representations of Ligand Binding binding sites occupied [PL] Y= = total binding sites [PL] + [P] [L] [L] Y= = [L] + 1 [L] +K𝑑𝑑 Ka [L] at which ½ of the available ligand-binding sites are occupied (Y = 0.5) corresponds to Kd Ka: association constant Kd: dissociation constant, Kd=1/Ka Ka [PL] 𝑃𝑃 + 𝐿𝐿 𝑃𝑃𝑃𝑃 Ka= Kd [P] [L] Representative Kd Values  Binding of O2 to Myoglobin substituting the [O2] for [L]: [O2] Y= [O2] + Kd partial pressure of O2 (pO2) is easier to measure than [O2] defining the partial pressure of oxygen at [O2]0.5 as P50: pO2 Y= pO2 + P50 Hemoglobin Transports Oxygen in Blood erythrocytes (red blood cells) transport O2 – formed from hemocytoblasts (precursor stem cells) – main function is to carry hemoglobin arterial blood = ~96% saturated with O2 peripheral blood = ~64% saturated with O2  Hemoglobin Subunits Are Structurally Similar to Myoglobin hemoglobin: – tetrameric protein with 4 heme groups – adult hemoglobin has two globin types: two α chains (141 residues each) and two β chains (146 residues each) strong interactions between unlike subunits (between α and β) – hydrophobic effect – hydrogen bonds – ion pairs (salt bridges) Hemoglobin Undergoes a Structural Change on Binding Oxygen two conformations of Greater number hemoglobin: of ion pairs – R state = O2 has a higher affinity for hemoglobin – T state = more stable when O2 is absent, predominant conformation of deoxyhemoglobin  The T → R Transition R state = O2 has a higher affinity for hemoglobin T state = more stable when O2 is absent O2 binding to hemoglobin in the T state triggers a conformational change to the R state – αβ subunit pairs slide past each other and rotate – the pocket between the β subunits narrow – some ion pairs that stabilize the T state break and some new ones form https://www.youtube.com/watch?v=H3DHvJ_MEtk Changes in Conformation Near Heme  Hemoglobin Binds Oxygen Cooperatively hemoglobin myoglobin hemoglobin has a hybrid sigmoid binding curve for oxygen  Allosteric Proteins allosteric protein (e.g., hemoglobin) = binding of a ligand to one site affects the binding properties of another site on the same protein – modulators = ligands that bind to an allosteric protein to induce a conformational change – homotropic = normal ligand and modulator are identical – heterotropic = modulator is a molecule other than the normal ligand Oxygen Binding to Hemoglobin Is Regulated by 2,3-Bisphosphoglycerate 2,3-bisphosphoglycerate (BPG): – example of heterotropic allosteric modulation – binds to a site distant from O2-binding site – greatly reduces the affinity of hemoglobin for oxygen HbBPG + O2 ⇌ HbO2 + BPG Binding of BPG to Deoxyhemoglobin BPG binds to the cavity between the β subunits in the T state – cavity is lined with positively charged residues – BPG stabilizes the T state  Fetal Hemoglobin fetus synthesizes α2γ2 hemoglobin – lower affinity for BPG than normal adult hemoglobin – higher affinity for O2 than normal adult hemoglobin  Sickle Cell Anemia Is a Molecular Disease of Hemoglobin sickle cell anemia: – homozygous condition – single amino acid substitution (Glu6 to Val6) β chains produces a hydrophobic patch Normal and Sickle Cell Hemoglobin deoxygenated hemoglobin becomes insoluble and forms polymers that aggregate normal hemoglobin remains soluble upon deoxygenation