Differences between bulk and molecular water are responsible for the following solvation effect:…

1. Differences between bulk and molecular water are responsible for the following solvation effect: (a) hydrogen bonds are destabilized in ?-helical peptides compared to their gas phase stability. (b) the dipole moments in nucleotides increase when solvated. (c) water molecules coat the inside of carbon nanotubes with long dwell times. (d) gas phase and solvated peptides sample different backbone torsion angles. (e) two of the above are correct. 2. SASA (a) is proportional to the solvation free energy. (b) is typically larger than the exposed van der Waals surface area. (c) accounts only for solute interactions with the first solvation shell. (d) is a relatively time consuming portion of calculating the energy of a modeled system. (e) two of the above are true. 3. The following is false about implicit solvation models in general: (a) they tend to account for first solvation shell interactions only. (b) they tend to account for first and second solvation shell interactions only. (c) hydrogen bonding and the molecular character of water is completely accounted for. (d) hydrogen bonding and the molecular character of water is completely ignored. (e) more than one of these statements is false! 4. (3 pts) In terms of the short- and long-range solvation effects discussed in class, which are more likely to be important in simulating the docking of ligands in the binding pocket of acetylcholinesterase, which was also discussed in class? Which might be less important? In both cases, state your logic. 5. (2 pts) Why do the TIP3P, 4P, and 5P explicit solvent models have such different partial charges q1 and q2? 6. (2 pts) Based on the O-H RDF’s shown in lecture for the TIP water models, explain why none of them achieve the O-H RDF line-shape determined by experiment. 7. (3 pts) Assuming that the classical force field you’re using has parameters for them, comment on the likely behavior of the following counterions in simulation with respect to reality: H+, OH-, Li+, Ca2+, I-, Zn+. 8. (3 pts) If a non-Langevin stochastic equation of motion is used to calculate forces (in tandem with an implicit solvent model) and that E.O.M. is characterized by = 0, what does this imply about the realistic nature of the dynamics? 9. (3 pts) What are the three terms that contribute to the calculation of solvation free energy in standard implicit solvent models, such as GB/SA, and which of these terms includes the energetics associated with hydrogen bonding between the solvent and the solute? How about between different atoms in the solute? 10. (2 pts) If the molecular surface area was calculated as the vdW surface, how would this affect the solvation free energy of the following moieties? Na+, CH4, a small (~20 atoms) organic molecule, a large protein (thousands of atoms). 11. How is ionic strength “built into” the Poisson-Boltzmann equation? 12. If the ions A2+ and B+ have the same radius in the gas phase, what is the approximate ratio of their hydrated radii in aqueous solution, rA/rB? 13. Simulation design (3 pts) Your goal is to simulate a moderate sized protein that has three sidechains with +1 charges and two sidechains with -1 charges. The protein also binds a Zn2+ ion in a pocket that does not involve any of these five charged residues. Without considering software limitations and assuming the force field has already been chosen, describe in complete detail the simulation methodology you would use to obtain the most “physically relevant” data from MD simulations in the NPT ensemble. Assume the protein is roughly spherical with a radius of ~15 Å. Don’t concern yourself with simulation speed (yet!). Now state how you could significantly speed up your simulations without opening yourself up to significant potential artifacts or deviations from “real” behavior. (Do not consider implicit solvent!) 14. (5 pts) If two oppositely charged ions have identical Born radii and they are separated by a distance equal to twice that born radius, what is the quantitative value of the GB screening factor fGB? Assuming a shifted cutoff is set too low, and is rcut

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