1
|
Ricard TC, Haycraft C, Iyengar SS. Adaptive, Geometric Networks for Efficient Coarse-Grained Ab Initio Molecular Dynamics with Post-Hartree–Fock Accuracy. J Chem Theory Comput 2018; 14:2852-2866. [DOI: 10.1021/acs.jctc.8b00186] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Timothy C. Ricard
- Department of Chemistry and Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Cody Haycraft
- Department of Chemistry and Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Srinivasan S. Iyengar
- Department of Chemistry and Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| |
Collapse
|
2
|
Haycraft C, Li J, Iyengar SS. Efficient, “On-the-Fly”, Born–Oppenheimer and Car–Parrinello-type Dynamics with Coupled Cluster Accuracy through Fragment Based Electronic Structure. J Chem Theory Comput 2017; 13:1887-1901. [DOI: 10.1021/acs.jctc.6b01107] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Cody Haycraft
- Department of Chemistry and
Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Junjie Li
- Department of Chemistry and
Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Srinivasan S. Iyengar
- Department of Chemistry and
Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| |
Collapse
|
3
|
Li J, Haycraft C, Iyengar SS. Hybrid Extended Lagrangian, Post-Hartree–Fock Born–Oppenheimer ab Initio Molecular Dynamics Using Fragment-Based Electronic Structure. J Chem Theory Comput 2016; 12:2493-508. [DOI: 10.1021/acs.jctc.6b00001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Junjie Li
- Department of Chemistry and
Department of Physics, Indiana University, 800 E. Kirkwood Ave., Bloomington, Indiana 47405, United States
| | - Cody Haycraft
- Department of Chemistry and
Department of Physics, Indiana University, 800 E. Kirkwood Ave., Bloomington, Indiana 47405, United States
| | - Srinivasan S. Iyengar
- Department of Chemistry and
Department of Physics, Indiana University, 800 E. Kirkwood Ave., Bloomington, Indiana 47405, United States
| |
Collapse
|
4
|
Li J, Iyengar SS. Ab Initio Molecular Dynamics Using Recursive, Spatially Separated, Overlapping Model Subsystems Mixed within an ONIOM-Based Fragmentation Energy Extrapolation Technique. J Chem Theory Comput 2015; 11:3978-91. [DOI: 10.1021/acs.jctc.5b00433] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Junjie Li
- Department of Chemistry and
Department of Physics, Indiana University, 800 E. Kirkwood Ave, Bloomington, Indiana 47405, United States
| | - Srinivasan S. Iyengar
- Department of Chemistry and
Department of Physics, Indiana University, 800 E. Kirkwood Ave, Bloomington, Indiana 47405, United States
| |
Collapse
|
5
|
Phatak P, Venderley J, Debrota J, Li J, Iyengar SS. Active Site Dynamical Effects in the Hydrogen Transfer Rate-limiting Step in the Catalysis of Linoleic Acid by Soybean Lipoxygenase-1 (SLO-1): Primary and Secondary Isotope Contributions. J Phys Chem B 2015; 119:9532-46. [PMID: 26079999 DOI: 10.1021/acs.jpcb.5b02385] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using ab initio molecular dynamics (AIMD) simulations that facilitate the treatment of rare events, we probe the active site participation in the rate-determining hydrogen transfer step in the catalytic oxidation of linoleic acid by soybean lipoxygenase-1 (SLO-1). The role of two different active site components is probed. (a) On the hydrogen atom acceptor side of the active site, the hydrogen bonding propensity between the acceptor side hydroxyl group, which is bound to the iron cofactor, and the backbone carboxyl group of isoleucine (residue number 839) is studied toward its role in promoting the hydrogen transfer event. Primary and secondary (H/D) isotope effects are also probed and a definite correlation with subtle secondary H/D isotope effects is found. With increasing average nuclear kinetic energy, the increase in transfer probability is enhanced due to the presence of the hydrogen bond between the backbone carbonyl of I839 and the acceptor oxygen. Further increase in average nuclear kinetic energy reduces the strength of this secondary hydrogen bond which leads to a deterioration in hydrogen transfer rates and finally embrances an Arrhenius-like behavior. (b) On the hydrogen atom donor side, the coupling between vibrational modes predominantly localized on the donor-side linoleic acid group and the reactive mode is probed. There appears to be a qualitative difference in the coupling between modes that belong to linoleic acid and the hydrogen transfer mode, for hydrogen and deuterium transfer. For example, the donor side secondary hydrogen atom is much more labile (by nearly a factor of 5) during deuterium transfer as compared to the case for hydrogen transfer. This appears to indicate a greater coupling between the modes belonging to the linoleic acid scaffold and the deuterium transfer mode and also provides a new rationalization for the abnormal (nonclassical) secondary isotope effect results obtained by Knapp, Rickert, and Klinman in J. Am. Chem. Soc. , 2002 , 124 , 3865 . To substantiate our findings noted in point a above, we have suggested an I839 → A839 or I839 → V839 mutation. This will modify the bulkiness of hydrogen the bonding residue, allowing greater flexibility in the secondary hydrogen bond formation highlighted above and adversely affecting the reaction rate.
Collapse
Affiliation(s)
- Prasad Phatak
- Department of Chemistry and Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Jordan Venderley
- Department of Chemistry and Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - John Debrota
- Department of Chemistry and Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Junjie Li
- Department of Chemistry and Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Srinivasan S Iyengar
- Department of Chemistry and Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| |
Collapse
|
6
|
Li J, Li X, Iyengar SS. Vibrational Properties of Hydrogen-Bonded Systems Using the Multireference Generalization to the “On-the-Fly” Electronic Structure within Quantum Wavepacket ab Initio Molecular Dynamics (QWAIMD). J Chem Theory Comput 2014; 10:2265-80. [DOI: 10.1021/ct5002347] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Junjie Li
- Department of Chemistry and
Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Xiaohu Li
- Department of Chemistry and
Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Srinivasan S. Iyengar
- Department of Chemistry and
Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| |
Collapse
|
7
|
Dietrick SM, Iyengar SS. Constructing Periodic Phase Space Orbits from ab Initio Molecular Dynamics Trajectories to Analyze Vibrational Spectra: Case Study of the Zundel (H5O2+) Cation. J Chem Theory Comput 2012; 8:4876-90. [DOI: 10.1021/ct300695x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Scott M. Dietrick
- Department
of Chemistry and Department of Physics, Indiana University, Bloomington, Indiana
47405, United States
| | - Srinivasan S. Iyengar
- Department
of Chemistry and Department of Physics, Indiana University, Bloomington, Indiana
47405, United States
| |
Collapse
|
8
|
Phatak P, Sumner I, Iyengar SS. Gauging the flexibility of the active site in soybean lipoxygenase-1 (SLO-1) through an atom-centered density matrix propagation (ADMP) treatment that facilitates the sampling of rare events. J Phys Chem B 2012; 116:10145-64. [PMID: 22838384 PMCID: PMC3558621 DOI: 10.1021/jp3015047] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present a computational methodology to sample rare events in large biological enzymes that may involve electronically polarizing, reactive processes. The approach includes simultaneous dynamical treatment of electronic and nuclear degrees of freedom, where contributions from the electronic portion are computed using hybrid density functional theory and the computational costs are reduced through a hybrid quantum mechanics/molecular mechanics (QM/MM) treatment. Thus, the paper involves a QM/MM dynamical treatment of rare events. The method is applied to probe the effect of the active site elements on the critical hydrogen transfer step in the soybean lipoxygenase-1 (SLO-1) catalyzed oxidation of linoleic acid. It is found that the dynamical fluctuations and associated flexibility of the active site are critical toward maintaining the electrostatics in the regime where the reactive process can occur smoothly. Physical constraints enforced to limit the active site flexibility are akin to mutations and, in the cases studied, have a detrimental effect on the electrostatic fluctuations, thus adversely affecting the hydrogen transfer process.
Collapse
Affiliation(s)
- Prasad Phatak
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Ave, Bloomington, IN-47405
| | - Isaiah Sumner
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Ave, Bloomington, IN-47405
| | - Srinivasan S. Iyengar
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Ave, Bloomington, IN-47405
| |
Collapse
|