QM/MM for BIO applications

Transcription

1 QM/MM for BIO applications February 9, 2011 I-Feng William Kuo P. O. Box 808, Livermore, CA This work performed under the auspices of the U.S. Department of Energy by under Contract DE-AC52-07NA27344

2 Link atoms IMOMM - (Integrated ab initio & Molecular Mechanics) Maseras and Morokuma J Comp Chem 16, 1170 (1995). Once you have identified the key residues of interest, the ideal place to cut is between the alpha and beta carbon effectively making the whole functional group QM while the backbone is MM. L-α-alanine Preserve the functional property of each amino acid and at the same time, you only have integer charges to account for. Must specify an appropriate alpha parameter. α = = r eq ( QM MM ) r ( QM H ) eq 2

3 Quantum Mechanics / Molecular Mechanics Purpose: Simulate large complex system where only regions of interest are treated with more sophisticated interaction potentials while less interesting zones are treated using cheaper interaction potentials. Most simulation of biological system start with some form of structure provided via the protein data bank. ( Typically, simulations are interested in uncovering the transition from reactants to products with emphasis on the transition state geometry and energetic barrier. Unfortunately, the structures provided via PDB are usually of the protein with/without reactants/products/inhibitors in either the initial or final state. 3

4 Active site Stanton et al. J Phys Chem B, 2007, 111(43), Active sites can be very well defined. Typically contains conserved residues, hydrogen bonding partners and hydrophobic residues that help hold the reactants in place. Choice of what QM atoms to incorporate is relatively straight forward. 4

5 Another example but less well defined active site Guan and Kaback Annu Rev Biophys Bio Struct 2006, 35: There can be a lot of labile water and thus does not show up in the PDB structure. Hence classical equilibration is essential. In addition if a crystal water does appear in the PDB, it s a good idea to verify that it stays there in your simulation!! 5

6 Importance of secondary residues Guan and Kaback Annu Rev Biophys Bio Struct 2006, 35: Lassila, Keeffe, Kast, and Mayo Biochemistry 2007, 46, Enzyme shown here is chorismate mutase (CM) bound to an transition state analog. 6 secondary sites mutate with all 19 possible amino acid substitutions. CM tolerant to 34% of 114 possible mutations. Only 34% of the 114 possible mutants still funcitoning. 6

7 Pressure and temperature effects Balny and Hooper Eur J Biochem 176, (1988). QM region is encapsulated by MM region. Most likely with some pressure differential. How will mechanism and barrier be altered is an open question. Bulk modulus for salt water is 23.4 kbar. Thus 15% change in volume is approximately 3.5 kbar. Ferreon, Ferreon, Bolen, Rosgen Biophy J 92(1) (2007). Hydroxylamine oxidoreductase (HAO) catalyzes NH 2 OH + H 2 O HNO 2 + 2e - + 2H +. The active site is a heme like ferrous chromophore P460. RNase A with inhibitor CMP denaturing agent urea and water. With/without urea 2 M urea are shown as dash/solid lines. 7

8 Even more outstanding issues regarding sampling Klahn, Braun-Sand, Rosta, and Warshel J Phys Chem B 2005, 109(32): QM/MM study of the Ras*GAP system with water attacking a metaphostae in the active site. Utilizes minimization and scanning of PES from representative configurations. Total MM simulation was 1ns, but five representative configurations from the last 500 ps was removed to be used at the starting configuration of QM/MM studies. The same issues are in effect for MD simulations. 8

9 QM size effects Hu, Boone, and Yang J Am Chem Soc 2008, 130(44) Stanton et al. J Phys Chem B, 2007, 111(43), sol exp G = 38.7 G enzyme exp =15. 2 Gexp = G = G =16. 5 G = G = 7 9

10 System size effects Stanton et al. J Phys Chem B, 2007, 111(43), Large Small 10

11 System size effects Stanton et al. J Phys Chem B, 2007, 111(43), sol exp G = 38.7 G enzyme exp =15. 2 Gexp = Small QM G = 16 Large QM G = 7 11

12 Spectral signatures & structures Baer, et al

13 Probing different mechanism 13

14 Schiff base formation Stanton et al. (unpublished). G = 20 / G exp = 17 / 14

15 Nucleophilic addition of Asp G = 13 / Stanton et al. (unpublished). G exp = 17 / 15

16 Minimal additions to input file for QM/MM &FORCE_EVAL METHOD QMMM &QMMM E_COUPL GAUSS USE_GEEP_LIB 7 &CELL ABC &END CELL &QM_KIND &END QM_KIND &END QMMM &END FORCE_EVAL 16

17 section &QM_KIND &QMMM &QM_KIND C MM_INDEX &END QM_KIND &QM_KIND H MM_INDEX MM_INDEX 6 7 MM_INDEX 9 10 MM_INDEX &END QM_KIND &END QMMM 17

18 section &LINK &QMMM &QM_KIND C MM_INDEX &END QM_KIND &QM_KIND H MM_INDEX MM_INDEX 6 7 &END QM_KIND &LINK QM_INDEX 5 MM_INDEX 8 LINK_TYPE IMOMM QM ALPHA_IMOMM 1.38 &END LINK &END QMMM 18

19 DFT Run diagnostic: deca-alanine 19

20 Conclusions 1. What is the thermodynamic state of a QM/MM system? Where are we exactly on the phase diagram? 2. Secondary active site residues can alter kinetic rates. 3. Ergodicity issues with QM/MM simulations. What is the longest mode in our system? 20