1. Energetics of protein structure

2. Energetics of protein structures Molecular Mechanics force fields Implicit solvent Statistical potentials

3. Energetics of protein structures Molecular Mechanics force fields Implicit solvent Statistical potentials

4. What is an atom? Classical mechanics: a solid object Defined by its position (x,y,z), its shape (usually a ball) and its mass May carry an electric charge (positive or negative), usually partial (less than an electron)

5. MASS 20 C 12.01100 C ! carbonyl C, peptide backbone MASS 21 CA 12.01100 C ! aromatic C MASS 22 CT1 12.01100 C ! aliphatic sp3 C for CH MASS 23 CT2 12.01100 C ! aliphatic sp3 C for CH2 MASS 24 CT3 12.01100 C ! aliphatic sp3 C for CH3 MASS 25 CPH1 12.01100 C ! his CG and CD2 carbons MASS 26 CPH2 12.01100 C ! his CE1 carbon MASS 27 CPT 12.01100 C ! trp C between rings MASS 28 CY 12.01100 C ! TRP C in pyrrole ring Example of atom definitions: CHARMM

6. RESI ALA 0.00 GROUP ATOM N NH1 -0.47 ! | ATOM HN H 0.31 ! HN-N ATOM CA CT1 0.07 ! | HB1 ATOM HA HB 0.09 ! | / GROUP ! HA-CA--CB-HB2 ATOM CB CT3 -0.27 ! | \ ATOM HB1 HA 0.09 ! | HB3 ATOM HB2 HA 0.09 ! O=C ATOM HB3 HA 0.09 ! | GROUP ! ATOM C C 0.51 ATOM O O -0.51 BOND CB CA N HN N CA BOND C CA C +N CA HA CB HB1 CB HB2 CB HB3 DOUBLE O C Example of residue definition: CHARMM

7. Atomic interactions Torsion angles Are 4-body Angles Are 3-body Bonds Are 2-body Non-bonded pair

8. Forces between atoms Strong bonded interactions b   All chemical bonds Angle between chemical bonds Preferred conformations for Torsion angles: -  angle of the main chain -  angles of the sidechains (aromatic, …)

9. Forces between atoms: vdW interactions 1/r 12 1/r 6 R ij r Lennard-Jones potential

10. Example: LJ parameters in CHARMM

11. Forces between atoms: Electrostatics interactions r Coulomb potential qiqi qjqj

12. Some Common force fields in Computational Biology ENCAD (Michael Levitt, Stanford) AMBER (Peter Kollman, UCSF; David Case, Scripps) CHARMM (Martin Karplus, Harvard) OPLS (Bill Jorgensen, Yale) MM2/MM3/MM4 (Norman Allinger, U. Georgia) ECEPP (Harold Scheraga, Cornell) GROMOS (Van Gunsteren, ETH, Zurich) Michael Levitt. The birth of computational structural biology. Nature Structural Biology, 8, 392-393 (2001)

13. Energetics of protein structures Molecular Mechanics force fields Implicit solvent Statistical potentials

14. Solvent Explicit or Implicit ?

15. Potential of mean force A protein in solution occupies a conformation X with probability: X: coordinates of the atoms of the protein Y: coordinates of the atoms of the solvent The potential energy U can be decomposed as: U P (X): protein-protein interactions U S (X): solvent-solvent interactions U PS (X,Y): protein-solvent interactions

16. Potential of mean force We study the protein’s behavior, not the solvent: P P (X) is expressed as a function of X only through the definition: W T (X) is called the potential of mean force.

17. Potential of mean force The potential of mean force can be re-written as: W sol (X) accounts implicitly and exactly for the effect of the solvent on the protein. Implicit solvent models are designed to provide an accurate and fast estimate of W(X).

18. + + Solvation Free Energy W np W sol

19. The SA model Surface area potential Eisenberg and McLachlan, (1986) Nature, 319, 199-203

20. Surface area potentials Which surface? Molecular Surface Accessible surface

21. Hydrophobic potential: Surface Area, or Volume? (Adapted from Lum, Chandler, Weeks, J. Phys. Chem. B, 1999, 103, 4570.) “Radius of the molecule” Volume effect Surface effect For proteins and other large bio-molecules, use surface

22. Protein Electrostatics Elementary electrostatics Electrostatics in vacuo Uniform dielectric medium Systems with boundaries The Poisson Boltzmann equation Numerical solutions Electrostatic free energies The Generalized Born model

23. Elementary Electrostatics in vacuo Some basic notations: Divergence Gradient Laplacian

24. Elementary Electrostatics in vacuo Coulomb’s law: The electric force acting on a point charge q2 as the result of the presence of another charge q1 is given by Coulomb’s law: q1q1 r u Electric field due to a charge: By definition: q2q2 q1q1 E “radiates”

25. Elementary Electrostatics in vacuo Gauss’s law: The electric flux out of any closed surface is proportional to the total charge enclosed within the surface. Integral form:Differential form: Notes: - for a point charge q at position X 0,  (X)=q  (X-X 0 ) - Coulomb’s law for a charge can be retrieved from Gauss’s law

26. Elementary Electrostatics in vacuo Energy and potential: - The force derives from a potential energy U: - By analogy, the electric field derives from an electrostatic potential  : For two point charges in vacuo: Potential produced by q 1 at at a distance r:

27. Elementary Electrostatics in vacuo The cases of multiple charges: the superposition principle: Potentials, fields and energy are additive For n charges: q1q1 q2q2 qiqi qNqN X

28. Elementary Electrostatics in vacuo Poisson equation: Laplace equation: (charge density = 0)

29. +- Uniform Dielectric Medium Physical basis of dielectric screening An atom or molecule in an externally imposed electric field develops a non zero net dipole moment: (The magnitude of a dipole is a measure of charge separation) The field generated by these induced dipoles runs against the inducing field the overall field is weakened (Screening effect) The negative charge is screened by a shell of positive charges.

30. + Uniform Dielectric Medium Electronic polarization: - - - - - - - - - - - - - + - - - - - - - - - - - - - Under external field Resulting dipole moment Orientation polarization: Under external field Resulting dipole moment

31. Uniform Dielectric Medium Polarization: The dipole moment per unit volume is a vector field known as the polarization vector P(X). In many materials:  is the electric susceptibility, and  is the electric permittivity, or dielectric constant The field from a uniform dipole density is -4  P, therefore the total field is

32. Uniform Dielectric Medium Some typical dielectric constants: MoleculeDipole moment (Debyes) of a single molecule Dielectric constant  of the liquid at 20°C Water1.980 Ethanol1.724 Acetic acid1.74 Chloroform0.864.8

33. Uniform Dielectric Medium Modified Poisson equation: Energies are scaled by the same factor. For two charges:

34. Uniform Dielectric Medium The work of polarization: It takes work to shift electrons or orient dipoles. A single particle with charge q polarizes the dielectric medium; there is a reaction potential  that is proportional to q for a linear response. The work needed to charge the particle from q i =0 to q i =q: For N charges: Free energy

35. System with dielectric boundaries The dielectric is no more uniform:  varies, the Poisson equation becomes: If we can solve this equation, we have the potential, from which we can derive most electrostatics properties of the system (Electric field, energy, free energy…) BUT This equation is difficult to solve for a system like a macromolecule!!

36. The Poisson Boltzmann Equation  (X) is the density of charges. For a biological system, it includes the charges of the “solute” (biomolecules), and the charges of free ions in the solvent: The ions distribute themselves in the solvent according to the electrostatic potential (Debye-Huckel theory): The potential f is itself influenced by the redistribution of ion charges, so the potential and concentrations must be solved for self consistency!

37. The Poisson Boltzmann Equation Linearized form: I: ionic strength

38. Analytical solution Only available for a few special simplification of the molecular shape and charge distribution Numerical Solution Mesh generation -- Decompose the physical domain to small elements; Approximate the solution with the potential value at the sampled mesh vertices -- Solve a linear system formed by numerical methods like finite difference and finite element method Mesh size and quality determine the speed and accuracy of the approximation Solving the Poisson Boltzmann Equation

39. Linear Poisson Boltzmann equation: Numerical solution PP ww Space discretized into a cubic lattice. Charges and potentials are defined on grid points. Dielectric defined on grid lines Condition at each grid point: j : indices of the six direct neighbors of i Solve as a large system of linear equations

40. Electrostatic solvation energy The electrostatic solvation energy can be computed as an energy change when solvent is added to the system: The sum is over all nodes of the lattice S and NS imply potentials computed in the presence and absence of solvent.

41. Approximate electrostatic solvation energy: The Generalized Born Model Remember: For a single ion of charge q and radius R: Born energy For a “molecule” containing N charges, q 1,…q N, embedded into spheres or radii R 1, …, R N such that the separation between the charges is large compared to the radii, the solvation energy can be approximated by the sum of the Born energy and Coulomb energy:

42. Approximate electrostatic solvation energy: The Generalized Born Model The GB theory is an effort to find an equation similar to the equation above, that is a good approximation to the solution to the Poisson equation. The most common model is: a i : Born radius of charge i:  G GB is correct when rij 0 and r ij ∞ Assuming that the charge i produces a Coulomb potential:

43. Approximate electrostatic solvation energy: The Generalized Born Model  G GB

44. Further reading Michael Gilson. Introduction to continuum electrostatics. http://gilsonlab.umbi.umd.edu http://gilsonlab.umbi.umd.edu M Schaefer, H van Vlijmen, M Karplus (1998) Adv. Prot. Chem., 51:1-57 (electrostatics free energy) B. Roux, T. Simonson (1999) Biophys. Chem., 1-278 (implicit solvent models) D. Bashford, D Case (2000) Ann. Rev. Phys. Chem., 51:129-152 (Generalized Born models) K. Sharp, B. Honig (1990) Ann. Rev. Biophys. Biophys. Chem., 19:301-352 (Electrostatics in molecule; PBE) N. Baker (2004) Methods in Enzymology 383:94-118 (PBE)

45. Energetics of protein structures Molecular Mechanics force fields Implicit solvent Statistical potentials

46. Statistical Potentials r a b r(Ǻ) f(r)

47. Ile-Asp Ile-Leu CountsEnergy r(Ǻ)

48. cRMS (Ǻ) Score 1CTF The Decoy Game Finding near native conformations