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Electrostatic Interactions in Proteins Involved in any process where there is movement of charge

Electrostatic Interactions in Proteins Involved in any process where there is movement of charge. Folding Ligand and Ion Binding Ion conduction Proton transfer (pKa) Salt effects, e.g in protein-DNA binding Electron transfer Spectroscopic Transitions.

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Electrostatic Interactions in Proteins Involved in any process where there is movement of charge

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  1. Electrostatic Interactions in ProteinsInvolved in any process where there is movement of charge • Folding • Ligand and Ion Binding • Ion conduction • Proton transfer (pKa) • Salt effects, e.g in protein-DNA binding • Electron transfer • Spectroscopic Transitions

  2. Calculation of Electrostatic Interactions Given the position and identity of all the atoms • Calculate electrostatic potential distribution • Calculate energy and forces Need to model the response of system (molecule, water, salt etc) to the charges Possible approaches • Quantum mechanics • Explicit, ‘all atom’ approach, such as molecule dynamics • Explicit molecular charges + Effective response

  3. The Finite Difference PB Model } h e=80 Ci,bulk + - Map molecule + solvent onto lattice d+ d- e=4-6 assign q,e,Ci,bulk at each Lattice point Solve FDPB Eqn. at every lattice point Lattice Point Neighbouring Lattice points

  4. Effect of Molecule-Solvent Boundary Field lines ‘pushed’ into higher susceptibility region: • Penalty to bury charges (desolvation) • Buried charges interact more strongly (descreening)

  5. RNA Electrostatics, Molecular interaction and Function Red: - Blue: + Kevin Chin, K. Sharp, B. Honig & A. Pyle. Nature Structural Biology (99)6:1055. http://cpmcnet.columbia.edu/dept/gsas/biochem/labs/pyle

  6. Group I Intron Phosphate groups in red

  7. Group I Intron Ion binding site Red: - Blue: +

  8. Conduction of Synthetic Ion Channel Gregg Dieckman, J. Lear, Q. Zhong, M. Klein, W. DeGrado, Kim Sharp, BPJ(99) 76:618 Ac-(LSSLLSL)3-CONH2 •Helical peptide inserts into bilayer •Forms Ion channels Cation specific Rectify • Model for biological ion channels Nernst-Planck Electrodiffusion model Current at V depends on energy profile of ion through channelf(z)

  9. Ion Desolvation Ion-Backbone Interaction Ion-Sidechain Interation Net Energy Profile for cation/anion

  10. Current at a series of voltages and left/right ion concentrations can be fit with no adjustable parameters using average structure from long MD simulations

  11. Modelling the Response of the Environment Polarization of electrons Reorientation of permanent dipoles Susceptibility: c = 0 (vacuum) c = e -1 79 (water) 3-5 (proteins, nucl. acids) Redistribution of solvent ions (Boltzmann distribution) } induced by Polarization Field

  12. The Poisson-Boltzmann Model + - d+ e=80 Csalt d- e=4-6 Potential distribution satisfies the PB Eqn. Polarizability Solvent ions Molecule Charge

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