Systemi Anatomy Topic 3.1 Protein Interactions PDF

Preview

Summary

Lecture notes based on protein interactions, with definitions, explanations, summaries, etc. ...

Description

Protein Interactions ● Most soluble proteins fall into one of 7 broad categories 1. Enzymes - Speed up chemical reactions 2. Membrane transporters - Move substances in and out of cells via channels in the membrane or binding molecules and carrying them through 3. Signal molecules - Hormones, etc 4. Receptors - Bind signal molecules and initiate cellular responses 5. Binding proteins - Mostly in ECF - Bind and transport molecules through body 6. Regulatory proteins - Turn cell processes on/off or up/down - E.g; transcription factors (bind DNA for gene expression and protein synthesis) 7. Immunoglobins - Extracellular immune proteins = antibodies - immune protection

Common Features of Soluble Proteins ● All bind to other molecules non-covalently - This means other molecules can bind to them and release from them without undergoing a chemical reaction ● Binding site = location on protein molecule where binding takes place ● Binding of a molecule to a protein binding site can initiate a process ● Ligand = any molecule that binds to another molecule ● Substrate = ligand that binds to an enzyme or membrane transporter ● Protein signal molecules and transcription factors are ligands

Induced-Fit Model ● For binding to occur the binding site and the

ligand must be compatible ● In protein binding, when ligand and binding site come close, non-covalent interactions allow the 2 molecules to bind ● The binding site and ligand don’t have to fit exactly, they interact via H-bonds, ionic bonds, and van der Waals forces, then the binding site changes shape - (conformational change) - To fit more closely to the ligand

Binding Site Properties X4 ● Binding site exhibit the following 4 properties 1. Specificity 2. Affinity 3. Competition 4. Saturation

1. Protein Specificity ● = ability of a protein to bind a certain ligand or groups of ligands - Some are very specific, some will bind whole groups - E.g; enzymes (peptidases will break apart any polypeptides peptide bonds regardless of AA) - Amino peptidases will only bind to the terminal end of a peptide chain (specific)

2. Affinity ● = degree to which protein is attracted to ligand ● Higher affinity = more likely to bind

Protein Binding Reactions are Reversible ● Binding of ligand to protein is non-covalent ● Binding can be reversible = P + L ⟷ PL - P = protein - L = ligand - PL = protein bound to the ligand ● Reversible reactions reach a state of equilibrium where rate of binding = rate of unbinding (dissociation)

Equilibrium ● ‘Equilibrium’ is a dynamic steady state in the body ● Concentrations of proteins and ligands are constantly changing in the body as

molecules are synthesised, or broken down, or moved from one body compartment to another ● The amount of ligand bound to protein at any moment in time is dependent on the concentration of all of the components

Law of Mass Action ● In the body, concentrations of ligands or proteins are constantly changing ● Protein-ligand binding reactions are often reversible ● Law of mass action states: - When a reaction is a equilibrium, the ratio of the concentration of products to substrates is always the same - If the ratio is disturbed by adding or removing a product or substrate, the reaction will shift in the direction that restores equilibrium ● So - if you add extra protein or ligand, the reaction will go in the direction of increased binding of the protein to ligand, until equilibrium is restored ● If you take away protein or ligand, the reaction will go in the reverse direction where the protein-ligand complex will unbind until equilibrium is restored

3. Competition ● Related ligands compete for binding sites ● Agonist = a ligand that mimics another ligand’s action - E.g; Nicotine mimics the activity of Acetylcholine (ACh) by binding to the same receptor - Drugs can be designed to be agonists ● Antagonist = a competitive antagonist = an inhibitor - Will bind to a protein and decrease its activity

Modulation of Binding Affinity ● A protein’s affinity for a ligand is not always constant as chemical and physical factors can alter or modulate binding affinity ● Binding affinity can be removed altogether ● Some proteins require activation before they have a functioning binding site ● Modulator = a factor that influences either protein or protein activity

Factors that Alter Protein Binding ● Can be chemical or physical ● Isoforms = closely related proteins with similar functions but different affinities for ligand

Activation ● Some proteins are inactive when synthesised in the cell ● Proteolytic activation = in order for these proteins to become active, enzymes must chop off certain parts of the protein molecule ● Inactive forms of proteins often have the prefix ‘pro’ or suffix ‘ogen’ - E.g; Proinsulin is activated to form insulin, trypsinogen is activated to form trypsin

Activation by Cofactors ● Some proteins require the presence of cofactors to activate binding sites ● Cofactors are ions or small functional groups that must attach to the binding site before the ligand will bind ● Many enzymes can’t function without cofactors

Modulation ● 2 basic mechanisms - modulator either 1. Changes ability of the ligand to bind to the binding site 2. Changes in protein’s activity or ability to create a response ● Factors including temp, pH, and molecules that interact with the protein can all modulate protein activity Chemical Modulators ● = molecules that bind covalently or non-covalently to proteins and alter their binding ability ● Can activate or enhance ligand binding, decrease binding ability, or completely inactivate protein binding ability (inactivation may be reversible or irreversible) ● Antagonist = inhibitors - Bind to a protein and decease its activity Physical Modulators ● pH or temperature - pH is a measure oh hydrogen ion concentration ● Small changes act as modulators to increase or decrease activity ● BUT - a critical control point is reached at which non-covalent bonds are disrupted and tertiary conformation is lost - = denatured - This is usually not reversible hence body closely regulates pH and temp

Regulation of Protein ● The body regulates the number of proteins in cells ● Up-regulation = complex signaling pathways direct cells to make new proteins ● Down-regulation = proteins are removed

[ ] = concentration ● Cells regulate protein [ ] to control physiological processes ● Increased protein [ ] means increased reaction rate and vice versa

4. Saturation ● If protein [ ] is constant then ligand [ ] determines reaction rate ● At low [ligand] response rate is directly proportional to [ligand] ● BUT once the ligand molecules reach a certain level the protein will have no more free binding sites so reaction rate reaches its maximal value = saturation...