Intro to Soluble Transport Proteins | Ligand Binding | PDF

2.1: Intro to Soluble Transport Proteins Part 1: Ligand Binding Many of protein functions involve binding channel what is & proteins...

2.1: Intro to Soluble Transport Proteins Part 1: Ligand Binding Many of protein functions involve binding channel what is & proteins lygate - signaling -what are the pathrags mechanisms ? Y metabolic Binding occurs between: pathways Enzymes & substrates Receptors & signal molecules Transporters & small molecules (for transport) > DNA repair and recombination  specific site of the protein small molecule that binds to & A ligand is a small molecule that binds to a protein Ligand - Affinity l Affinity Binding Site · ligand to proten Protein Specificity an Only specific - · protein to ligant to each binding particular ligant https://kuhnlab.natsci.msu.edu/img/siteinterlock_small.png Reversible process involving Ligand binding is a _______________ noncovalent interactions Conformational change + ⇌ occurs through M Protein Ligand Protein-Ligand Complex noncovalent - interactions this binding induces Product conformation in the protein why do we use weak interactions be should - ligand binding be reversible  - Ka Association constant) is the equilibrium constant ___(____________ for the association (or binding) of the protein and ligand + ⇌ Protein Ligand Protein-Ligand Complex tion P + L ⇌ PL ca - Protein - ligand Assoreaction Keq = Ka = [PL] [P][L] [P] = concentration of protein in M, [L] = concentration of ligand in M, Ka unit: M-1 = Ka Dissociation ___(_____________constant) is the equilibrium constant for the dissociation of ligand from protein-ligand complex ⇌ + Protein-Ligand Complex Protein Ligand PL ⇌ P + L a Dissociation Keq = Kd = [P][L] A larger Kd : Product more of the ___________ (dissociation) [PL] Low ____________affinity - free protein Kd unit: M and ligand - Use More Frequent measurement k = T High affinity ↳ lowky/high Ka for affinity  Kd ranges for different interactions are useful for comparing binding affinities lowest Kd (High Affinity) highest Kd (Low Affinity High Low Lehninger Principles of Biochemistry 6 ed Fractional saturation (θ, theta) is the fraction of occupied protein binding sites [P][L] P + L ⇌ PL Kd = [PL] Protein bound to Ligand ) - -(i)+ occupied binding sites [PL] [] Θ = total binding sites = = Protein bound to Ligand [PL] + [P] - a [23 + 2 t Free protein and Ligand [L] = [L] + Kd & Ligand binding can be represented by a hyperbolic curve Memorize Θ= [L] [L] + Kd & All binding are sites taken by Ligand Increase LigandConcentration will see more occoped Concentration you < Ligand binding sites on proteins Kd can be determined from a binding curve. what is O [L] ~ 0 == A lower Kd means a higher affinity of protein for ligand · 5 =he. 5: hh ide The oxygen binding curve for myoglobin is hyperbolic Fractional Saturation Θ= binding sites occupied total binding sites = t P] € (P50 = pO2 at half saturation) low P50 for O2 binding. Myoglobin has a very _________ Oxygen Concentration (partial pressure) 0-75 = Oz =502 +5 02 - 750z = ( 75) (2 8).. 0(-7st = /75 : 2. 8 75 x 2 8 U = · -.. 25 2.1: Intro to Soluble Transport Proteins Part 2: Globin Structure  Oz binding proteins Myoglobin and hemoglobin are both ___ Myoglobin (Mb) Hemoglobin (Hb) muscle tissue Concentrated in ____________ Major protein in Red Blood ___________cells (i.e., erythrocytes) - RBC ① storage Functions as a ___________ depot for O2 Transport __________ O2 in blood from the lungs to the tissues Myoglobin consists of a _________ single polypeptide chain whereas hemoglobin contains _________ four polypeptides Myoglobin (Mb) Hemoglobin (Hb) D G B A C E F H Mb: monomer Hb: dimer of ab dimers heterodimen g α-helices 7 3 ____ _____ α-helices ↓ I heme ____ _____ hemes B heterotetromer ↓ 2x + 2B -similar 3 Dimensional structise Myoglobin and hemoglobin subunits share the same protein fold called ___________ globin fold 9 and B subunt have same protein folds ↓ globlin (from 8 a helix) 8 a-helix Globin Fold : _____________fold up into a globular structure hame ? Why do we need ↳ None Amino Acids interact with can Oxy Reversibily O2 reversibly binds to an iron atom in heme that is tightly bound to the protein ↳ cofactor called prosthetic group ↳ essentical to protein function ↳ covalently bound (tightly bounded) Heme Iron must be in Fe2+ porphyrin complex Fezt ______(reduced) fur Prosthetic group > - Required v state to bind O2 binds one ligand enzyme activity state allows fo Reduced reversibleO2 binding 4 Nitrogen from proline state bind to iron - > in pheric creduced) The amino acid sequence similarity between myoglobin and either the ⍺ or β subunit of hemoglobin is low used in reversible O2 binding both Myoglobin hemaglobin + The asterisk (*) indicates identical amino acids in all sequences, the colon (:) indicates a conservative substitution HIS Two conserved ____________ residues are important for oxygen binding in globin proteins Stabilize - Distal His forms a H- bond with the O2 the Of binds to Oxygen is bound iron through the sixth > coordination bond. Proximal His forms the coordination bond with the Fe2+.  2.1: Intro to Soluble Transport Proteins Part 3: O2 Binding Curve The O2 binding curve of myoglobin is __________ hyperbolic whereas that of hemoglobin is ___________ sigmoidal hyperbolic sigmoidal  O2Affinity For an effective O2 transport, ___________ must vary with the partial pressure of O2 (pO2) Oxygen binding to hemoglobin produces a sigmoidal curve because of ______________ Cooperative binding How can cooperative binding alter the affinity for O2? Protein has ______________________________ Binding of ______________ induces conformational changes Conformational changes are translated to neighboring ligand binding sites, influencing their _______________ for ligand. It allows protein to shift between two conformations: a _______ and a ______ affinity state.