Break Desired Compound into 3 Smaller Ones

Transcription

1 Break Desired Compound into 3 Smaller nes A B C Indole ydrazine Phenol When creating a covalent link between model compounds move the charge on the deleted into the carbon to maintain integer charge (i.e. methyl (q C =-0.27, q =0.09) to methylene (q C =-0.18, q =0.09) From MacKerell

2 From top_all22_model.inp RESI PE 0.00! phenol, adm jr. GRUP ATM CG CA ! ATM G P 0.115! D1 E1 GRUP! ATM CD1 CA ! CD1--CE1 ATM D1 P 0.115! // \\ GRUP! G--CG CZ-- ATM CD2 CA ! \ / \ ATM D2 P 0.115! CD2==CE2 GRUP! ATM CE1 CA ! D2 E2 ATM E1 P GRUP ATM CE2 CA ATM E2 P GRUP ATM CZ CA ATM ATM BD CD2 CG CE1 CD1 CZ CE2 CG G CD1 D1 BD CD2 D2 CE1 E1 CE2 E2 CZ DUBLE CD1 CG CE2 CD2 CZ CE1 Top_all22_model.inp contains all protein model compounds. Lipid, nucleic acid and carbohydate model compounds are in the full topology files. G will ultimately be deleted. Therefore, move G (hydrogen) charge into CG, such that the CG charge becomes 0.00 in the final compound. Use remaining charges/atom types without any changes. Do the same with indole From MacKerell

3 Creation of topology for central model compound RESI Mod1! Model compound 1 Group ATM C1 CT ATM 11 A ATM 12 A ATM 13 A GRUP ATM C2 C 0.51 ATM GRUP ATM ATM ATM 4 R1 0.16!new atom ATM C5 CEL ATM 51 EL ATM C6 CT ATM 61 A 0.09 ATM 62 A 0.09 ATM 63 A 0.09 BD C1 11 C1 12 C1 13 C1 C2 C2 2 C BD 3 4 C5 51 C5 C6 C6 61 C6 62 C6 63 DUBLE 4 C5 (DUBLE only required for MMFF) Start with alanine dipeptide. ote use of new aliphatic LJ parameters and, importantly, atom types. R1 from histidine unprotonated ring nitrogen. Charge (very bad) initially set to yield unit charge for the group. ote use of large group to allow flexibility in charge optimization. From MacKerell

4 Partial Charge Assignment Most important aspect for ligands Different force fields might take different philosophies AMBER: RESP charges at the F/6-31G level verestimation of dipole moments Easier to set up CARMM: Interaction based optimization TIP3P water representing the environment Could be very difficult to set up Conformation dependence of partial charges Lack of polarization Try to be consistent within the force field pka calculations for titratable residues

5 C 3 Starting charges?? Mulliken population analysis Analogy comparison C 3 Final charges (methyl, vary q C to maintain integer charge, q = 0.09) interactions with water (F/6-31G*, monohydrates!) From MacKerell

6 Comparison of analogy and optimized charges ame Type Analogy ptimized C1 CT A A A C2 C R C5 CEL EL C6 CT A A A

7 Dihedral optimization based on QM potential energy surfaces (F/6-31G* or MP2/6-31G*). 2 From MacKerell

8 Parameterization of unsaturated lipids All C=C bonds are cis, what does rotation about neighboring single bonds look like? Courtesy of Scott Feller, Wabash College

9 DA conformations from MD rotational barriers are extremely small many conformers are accessible w/ short lifetimes Courtesy of Scott Feller, Wabash College

10 Dynamics of saturated vs. polyunsaturated lipid chains sn1 stearic acid = blue sn2 DA = yellow 500 ps of dynamics Movie courtesy of Mauricio Carrillo Tripp Courtesy of Scott Feller, Wabash College

11 Lipid-protein interactions Radial distribution around protein shows distinct layering of acyl chains DA penetrates deeper into the protein surface Courtesy of Scott Feller, Wabash College

12 Lipid-protein interactions Decomposition of non-bonded interaction shows rhodopsin is strongly attracted to unsaturated chain All hydrophobic residues are stabilized by DA resname U DA U stearic ratio PE ILE VAL LEU MET TYR ALA TRP Courtesy of Scott Feller, Wabash College

13 rigin of protein:da attraction Flexibility of the DA chain allows solvation of the rough protein surface to occur with little intra-molecular energy cost Courtesy of Scott Feller, Wabash College

14 Major Recent Developments ew set of lipid force field parameters for CARMM (CARMM32 + ) Pastor, B. Brooks, MacKerell Polarizable force field Roux, MacKerell

15 Retinal Proteins -- Rhodopsins Me Me Me Me Me Me Me Me Me Me Chromophore Covalently linked to a lysine Usually protonated Schiff base all-trans and 11-cis isomers

16 Unconventional chemistry Me Me Me Me Me Me Me Me Me Me

17 Isomerization Barriers in retinal Lys C 15 C 14 C 13 C 12 C 11 C 10 C 9 C 8 C 7 C 5 C 6 C 4 C 1 C 2 C 3 DFT/6-31G**

18 Coupling of electronic excitation and conformational change in br S 1 S 0 BR K C 13 =C 14 -trans C 13 =C 14 -cis Me Me Me Me Me 13 15

19 Inducing isomerization 500 nm ~50 kcal/mole

20 Classical Retinal Isomerization in Rhodopsin Twist Propagation

21 QM/MM calculations MM MM Lys216-RET QM QM QM ˆ = p 2 i i + + V 1 2 q r i p ip MM QM MM + p + + V i A ia A p Ap MM MM Z r A Z A r + q i> j ij A> B p 1 r + Z AZ r AB B dummy atom MM Asp85, 212 QM

22 Ab Initio QM/MM Excited State MD Simulation QM Quantum mechanical (QM) treatment of the chromophore, and force field (MM) treatment of the embedding protein

23 QM/MM calculation of ATP hydrolysis

24 Coarse grain modeling of lipids 150 particles 9 particles!