Slide 1Slide 2Slide 3Slide 4Slide 5Slide 6Exploring Promoter Architecture: Can We Compute How Cells Decide?Slide 8Where we are headed: Can We Compute How Cells Decide?Slide 10Slide 11Slide 12Slide 13Slide 14Slide 15Slide 16Slide 17Slide 18Slide 19Slide 20Slide 21Slide 22Slide 23Slide 24Slide 25Slide 26Slide 27Slide 28Slide 29Slide 30Slide 31Slide 32Slide 33Slide 34Slide 35BE/APh161 – Physical Biology of the CellBE/APh161 – Physical Biology of the CellRob PhillipsApplied Physics and BioengineeringCalifornia Institute of TechnologyIon gating driven by ligandsIon gating driven by ligands• Ligand-gated channels.Ion gated channels: Acetylcholine Ion gated channels: AcetylcholineData for the gating of nicotinic acetylcholine receptorData for the gating of nicotinic acetylcholine receptorStates and weights for binding problemsStates and weights for binding problems• We work out the probability of the binding probability by making a model of the solution as a lattice.Binding curves and binding free energyBinding curves and binding free energy• These simple binding curves illustrate the way in which the binding probability depends upon the Kd or the binding energy.Exploring Promoter Architecture: Can We Compute How Cells Decide?Exploring Promoter Architecture: Can We Compute How Cells Decide?Where we are headed: Can We Compute How Cells Decide?Bintu et al. (2005)Some other examplesSome other examples• Data and fits using our binding formula.Some other examplesSome other examplesGibbs’ second lawGibbs’ second law• One idea only: to find the privileged terminal state of a system, maximize the entropy.• A corollary: minimize the free energy – this is for a system in contact with a heat bath.• My point here is to get us all to think about the chemical potential.The gibbs distributionThe gibbs distributionSystem in contact with an energy reservoirProbability for finding the system in microstate i: Boltzmann distr.- partition f.System in contact with a particle and energy reservoirres. controls av. # of particles <N> in the syst.Gibbs distr.Probability for finding the system in microstate i:grand partition f.Treservoir controls av.energy <E> of the systemligand-receptor binding: State variable description ligand-receptor binding: State variable description • Consider a single receptor in contact with the surrounding heat bath and particle reservoir. • Two-state (b/u), is an indicator of the state of binding• The energy is• Evaluate aver. # of ligands bound, <N>: favorable interaction btw L and RContact of the system with a thermal reservoir Contact with a particle reservoir can also be computed as• Recall that the chem.potential of an ideal solution is=>is the energy difference upon taking the ligand from solution and placing it on the receptorCooperativity and bindingCooperativity and binding• Interestingly, many (if not most) of the real world binding problems we care about in biology do not satisfy the simple binding model (sometimes called the Langmuir adsorption isotherm) we have worked out so far. • The classic example (i.e. the hydrogen atom of binding problems) is hemoglobin.Hemoglobin as a case study in cooperativityHemoglobin as a case study in cooperativityseveral 100s hemoglobin moleculesOxygen binds to heme on the hemoglobin molecules• Hemoglobin - the classic example of ligand-receptor binding• Cooperativity: the binding energy for a given ligand depends upon the # of ligands that are already bound to the receptor• Intuitively: conformational change upon binding => the next ligand experiences a different binding energyapps.uwhealth.orgThe heme group includes a porphyrin ring (gray line) + ironThe protein hemoglobin: 4 polypeptide chains (2 -chains, 2 -chains), each carries a heme group => protein can bind up to 4 molecules of O2The nature of the Hill functionThe nature of the Hill functionHemoglobin as a case study in cooperativityHemoglobin as a case study in cooperativity• Hemoglobin-oxygen binding: language of two-states occupation variables. State of system is described with the vectorwhere i: i = 0 (unbound), i = 1 (bound)• Q.: what is the average # of bound O2 molecules as a function of the O2 concentration (or partial pressure)? A toy model of a dimoglobinA toy model of a dimoglobin• To illustrate the idea of cooperativity: imagine a fictitious dimoglobin [=dimeric hemoglobin] molecule which has 2 O2 binding sites (e.g., clams)• => 4 distinct states • The energy of the system:Energy associated with O2 being bound to one of the 2 sitesmeasure of the cooperativityA toy model of a dimoglobinA toy model of a dimoglobin• The grand partition function (sum over the 4 states):• => compute the probabilities for each classes of states: unoccupied, single occupancy, double occupancySingle occupancy Both sites occupiedParameters used: =–5 kBT, J= –2.5 kBT, c0 = 760 mmHgTalking across the membraneTalking across the membrane• Membrane proteins are characterized in some cases by transmembrane alpha helices and cytosolic domain that passes along the signal.Coupling receptors to enzyme actionCoupling receptors to enzyme action• Receptor binding changes the probability of the “active” state.Doing work to change the protein stateDoing work to change the protein state• A wonderful and important topic for our consideration is that of posttranslational modifications.• One of the tricks performed by the cytoplasmic side of a receptor (or its partners) is to do some posttranslational modification.phosphorylationphosphorylation• In bio systems, changes in envir.conditions => the activity of an enzyme must be rapidly altered • One of the most important regulatory modes in all of biology: regulation of protein activity by covalent attachment of phosphate groups• The substrate for protein phosphorylation: target protein and ATP• The enzyme: protein kinase (transfers the terminal phosphate group from ATP to a chemical group on a protein) • A phosphate group carried 2 “-” charges => causes a dramatic change in the local charge distribution on the surface of the protein => drastic, large scale effect on protein structure and ability to bind• This alteration is reversible: protein phosphataseThe diversity of kinasesThe diversity of kinases• “The whole molecular control network, leading from the receptors at the cell surface to the genes in the nucleus, can
View Full Document
Unlocking...