Protein-ligand interactions: Enzyme structure and mechanism: · Enzyme + substrate <- > enzyme-substrate complex. Catalysis occurs. · Some interactions more complicated- many molecules, competitors etc. · Interaction between substrate tends to be limiting factor. The equilibrium constant: Kan A + B => Kaff AB · Forward rate constant: kon (rates always small ks). Sometimes called ka- association, or k+1. · Rates affect interactions. · Reverse: Koff/ka/k-1. · Rate constants are always the same for a given set of interactions, not dependent on concentrations. · Rates depend on concentrations. . At equil, rate in forward reaction direction = rate in reverse direction. · Experimentally measure concs of products and reactants or on and off rates to define equil kon [A][B] = koff [AB] units: (M1 s1)(M)(M) = (s1)(M) KA = Km = [AB] [A][B] units: (M)/(M)(M) = (M-1) constant. · Describes tendency of system to be bound- two molecules with high affinity for each other- high amount of AB so KA is large- or unbound- lots of A and B- small KA value (less than one)- tendency to the left. · Equil constant: ratio is the concentration the reaction is going to/concentration it is going from. KA = association- reciprocal concentration. Closer to 1 = to the right, closer to 0 = to the left. · KD = dissociation, reverse equil constant- reciprocal: KA = 1/ Kg Kp = [AB] units (?)x(??(?) = (?) [A]x[B] · Keq: vague and interchangeable for association and dissociation. · KM: related to enzyme substrate concentrations. Equivalent to KD. · In some cases, values of equil constant may be unitless. E + S < -- > ES KM= [ES] [E]x[S] units: (MX(M)(M) = (M) · Keep track of units.
forward A + B -* AB reaction rate reverse reaction rate equilibrium conditions Thermodynamic changes: A + B A + B ·· AB Kom K 5-1 AB K M-1 [A] [B] [AB] Kp = [A] [B] M [AB] KM [E] [S] M [ES] [AB] KA = [A]x[B] AG = - RT In KA units: J mol ** = (J K-1 mol ** ) (K) (M) AG = AH - TAS . Natural logarithm of a KA value of 1 is 0. Gives delta G value of <0 so favourable. · If KA larger than 1, In = positive value. Delta G >0 so unfavourable. · KA smaller than 1, In is negative and negative x negative = positive so unfavourable. · Units of Gibbs free energy are j mol-1. · negative change in delta G is favourable. a reaction coordinate activation energy energy A + B TAG AB · Larger activation energy = slower reaction rate. Energy barrier dictates on and off rates. . Product should be at lower energy than reactants for reactions to be favourable.
· Boltzmann distribution: described by population of molecules in different energy levels. Delta G= 0 means 50:50 ratio. NA/NB = e (-AG/KB ) Concentrations at equilibrium [DHAP] = 220 UM [GA3P] = 10 UM According to the Boltzmann distribution, the