1
|
Cummins PL. The Coevolution of RuBisCO, Photorespiration, and Carbon Concentrating Mechanisms in Higher Plants. Front Plant Sci 2021; 12:662425. [PMID: 34539685 PMCID: PMC8440988 DOI: 10.3389/fpls.2021.662425] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 07/26/2021] [Indexed: 05/20/2023]
Abstract
Ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase (RuBisCO) is the carbon-fixing enzyme present in most photosynthetic organisms, converting CO2 into organic matter. Globally, photosynthetic efficiency in terrestrial plants has become increasingly challenged in recent decades due to a rapid increase in atmospheric CO2 and associated changes toward warmer and dryer environments. Well adapted for these new climatic conditions, the C4 photosynthetic pathway utilizes carbon concentrating mechanisms to increase CO2 concentrations surrounding RuBisCO, suppressing photorespiration from the oxygenase catalyzed reaction with O2. The energy efficiency of C3 photosynthesis, from which the C4 pathway evolved, is thought to rely critically on an uninterrupted supply of chloroplast CO2. Part of the homeostatic mechanism that maintains this constancy of supply involves the CO2 produced as a byproduct of photorespiration in a negative feedback loop. Analyzing the database of RuBisCO kinetic parameters, we suggest that in genera (Flaveria and Panicum) for which both C3 and C4 examples are available, the C4 pathway evolved only from C3 ancestors possessing much lower than the average carboxylase specificity relative to that of the oxygenase reaction (S C/O=S C/S O), and hence, the higher CO2 levels required for development of the photorespiratory CO2 pump (C2 photosynthesis) essential in the initial stages of C4 evolution, while in the later stage (final optimization phase in the Flaveria model) increased CO2 turnover may have occurred, which would have been supported by the higher CO2 levels. Otherwise, C4 RuBisCO kinetic traits remain little changed from the ancestral C3 species. At the opposite end of the spectrum, C3 plants (from Limonium) with higher than average S C/O, which may be associated with the ability of increased CO2, relative to O2, affinity to offset reduced photorespiration and chloroplast CO2 levels, can tolerate high stress environments. It is suggested that, instead of inherently constrained by its kinetic mechanism, RuBisCO possesses the extensive kinetic plasticity necessary for adaptation to changes in photorespiration that occur in the homeostatic regulation of CO2 supply under a broad range of abiotic environmental conditions.
Collapse
|
2
|
Cummins PL, Gready JE. Kohn-Sham Density Functional Calculations Reveal Proton Wires in the Enolization and Carboxylase Reactions Catalyzed by Rubisco. J Phys Chem B 2020; 124:3015-3026. [PMID: 32208706 DOI: 10.1021/acs.jpcb.0c01169] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Ribulose 1,5-bisphosphate (RuBP) carboxylase-oxygenase (Rubisco) plays a fundamental role in the carbon cycle by fixing the atmospheric CO2 used in photosynthesis. Rubisco is all the more remarkable because it must catalyze some difficult multistep reaction chemistry involving proton transfers within the one active site. In the present study, we have used Kohn-Sham density functional theory at the B3LYP/6-31G* level with basis set superposition error and dispersion corrections (B3LYP-gCP-D3) to examine the possibility that the proton transfers can take place through molecular wires (including active-site water molecules) via the classical Grotthuss proton-shuttle mechanism. The results support an essential role for water molecules found in the crystal structures of Rubisco complexes as facilitators of proton transport in all the rate-limiting (catalytic) reaction steps through a network of short proton wires within the Rubisco active site. We suggest that completion of the initial product turnover (cycle) requires two excess protons produced in the initial carbamylation that is required for Rubisco activation. By use of proton wires, a large number of reaction steps may be accommodated within a single active site without necessitating the input of excessive conformational strain energy arising from the movement of residue side chains into positions where direct protonation of substrates can occur. The involvement of the identified types of proton wires in the kinetic mechanism is capable of providing a unique explanation for various experimental observations, including deuterium isotope effects and the results of site-directed mutagenesis experiments, and may thus provide a realistic solution to the problem of Rubisco's challenging chemistry.
Collapse
Affiliation(s)
- Peter L Cummins
- Department of Genome Sciences, John Curtin School of Medical Research, The Australian National University, Canberra, ACT 0200, Australia
| | - Jill E Gready
- Department of Genome Sciences, John Curtin School of Medical Research, The Australian National University, Canberra, ACT 0200, Australia
| |
Collapse
|
3
|
Cummins PL, Kannappan B, Gready JE. Response: Commentary: Directions for Optimization of Photosynthetic Carbon Fixation: RuBisCO's Efficiency May Not Be So Constrained After All. Front Plant Sci 2019; 10:1426. [PMID: 31824523 PMCID: PMC6884029 DOI: 10.3389/fpls.2019.01426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 10/15/2019] [Indexed: 05/29/2023]
|
4
|
Kannappan B, Cummins PL, Gready JE. Mechanism of Oxygenase-Pathway Reactions Catalyzed by Rubisco from Large-Scale Kohn-Sham Density Functional Calculations. J Phys Chem B 2019; 123:2833-2843. [PMID: 30845802 DOI: 10.1021/acs.jpcb.9b00518] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ribulose 1,5-bisphosphate carboxylase-oxygenase (Rubisco) is the primary carbon-fixing enzyme in photosynthesis, fixing CO2 to a 5-carbon sugar, RuBP, in a series of five reactions. However, it also catalyzes an oxygenase reaction by O2 addition to the same enolized RuBP substrate in an analogous reaction series in the same active site, producing a waste product and loss of photosynthetic efficiency. Starting from RuBP, the reactions are enolization to the enediolate form, addition of CO2 or O2 to form the carboxy or peroxo adduct, hydration to form a gemdiolate, scission of the C2-C3 bond of the original RuBP, and stereospecific or nonstereospecific protonation to form two molecules of the 3-carbon PGA product, or one molecule of PGA, one of 2-carbon PG (waste product), and one water molecule. Reducing the loss of efficiency from the oxygenase reaction is an attractive means to increase crop productivity. However, lack of understanding of key aspects of the catalytic mechanisms for both the carboxylase and oxygenase reactions, particularly those involving proton exchanges and roles of water molecules, has stymied efforts at re-engineering Rubisco to reduce losses from the oxygenation reaction. As the stable form of molecular oxygen is the triplet biradical state (3O2), its reaction with near-universal singlet-state molecules is formally spin forbidden. Although in oxygenase enzymes, 3O2 activation is usually achieved by one-electron transfers using transition-metal ions or organic cofactors, recently, cofactor-less oxygenases in which the substrate itself is the source of the electron for 3O2 activation have been identified, but in all such cases an aromatic ring stabilizes the substrate's negative charge. Here we present the first large-scale Kohn-Sham density functional theory study of the reaction mechanism of the Rubisco oxygenase pathway. First, we show that the enediolate substrate complexed to Mg2+ and its ligands extends the region for charge delocalization and stabilization of its negative charge to allow formation of a caged biradical enediolate-O2 complex. Thus, Rubisco is a unique type of oxygenase without precedent in the literature. Second, for the O2 addition to proceed to the singlet peroxo-adduct intermediate, the system must undergo an intersystem crossing. We found that the presence of protonated LYS334 is required to stabilize this intermediate and that both factors (strongly stabilized anion and protonated LYS334) facilitate a barrier-less activation of 3O2. This finding supports our recent proposal that deoxygenation, that is, reversal of gas binding, is possible. Third, as neither CO2 nor O2 binds to the enzyme, our findings support the proposal from our recent carboxylase study that the observed KC or KO (Michaelis-Menten constants) in the steady-state kinetics reflect the respective adducts, carboxy or peroxo. Fourth, after computing hydration pathways with water addition both syn and anti to C3, we found, in contrast to the results of our carboxylation study indicating anti addition, that in the oxygenation reaction only syn-hydration is capable of producing a stable gemdiolate that facilitates the rate-limiting C2-C3 bond scission to final products. Fifth, we propose that an excess proton we previously found was required in the carboxylation reaction for activating the C2-C3 bond scission is utilized in the oxygenation reaction for the required elimination of a water molecule. In summary, despite its oxygenase handicap, Rubisco's success in directing 75% of its substrate through the carboxylation pathway can be considered impressively effective. Although native C3 Rubiscos are in a fix with unwanted activity of 3O2 hampering its primary carboxylase function, mechanistic differences presented here with findings in our recent carboxylase study for both the gas-addition and subsequent reactions provide some clues as to how creative Rubisco re-engineering may offer a solution to reducing the oxygenase activity.
Collapse
Affiliation(s)
- Babu Kannappan
- John Curtin School of Medical Research , The Australian National University , Canberra ACT 0200 , Australia
| | - Peter L Cummins
- John Curtin School of Medical Research , The Australian National University , Canberra ACT 0200 , Australia
| | - Jill E Gready
- John Curtin School of Medical Research , The Australian National University , Canberra ACT 0200 , Australia
| |
Collapse
|
5
|
Cummins PL, Kannappan B, Gready JE. Ab Initio Molecular Dynamics Simulation and Energetics of the Ribulose-1,5-biphosphate Carboxylation Reaction Catalyzed by Rubisco: Toward Elucidating the Stereospecific Protonation Mechanism. J Phys Chem B 2019; 123:2679-2686. [DOI: 10.1021/acs.jpcb.8b12088] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter L. Cummins
- John Curtin School of Medical Research, The Australian National University, Canberra ACT 0200, Australia
| | - Babu Kannappan
- John Curtin School of Medical Research, The Australian National University, Canberra ACT 0200, Australia
| | - Jill E. Gready
- John Curtin School of Medical Research, The Australian National University, Canberra ACT 0200, Australia
| |
Collapse
|
6
|
Cummins PL, Kannappan B, Gready JE. Revised mechanism of carboxylation of ribulose-1,5-biphosphate by rubisco from large scale quantum chemical calculations. J Comput Chem 2018; 39:1656-1665. [PMID: 29756365 DOI: 10.1002/jcc.25343] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 04/04/2018] [Accepted: 04/06/2018] [Indexed: 01/06/2023]
Abstract
Here, we describe a computational approach for studying enzymes that catalyze complex multi-step reactions and apply it to Ribulose 1,5-bisphosphate carboxylase-oxygenase (Rubisco), the enzyme that fixes atmospheric carbon dioxide within photosynthesis. In the 5-step carboxylase reaction, the substrate Ribulose-1,5-bisphosphate (RuBP) first binds Rubisco and undergoes enolization before binding the second substrate, CO2 . Hydration of the RuBP.CO2 complex is followed by CC bond scission and stereospecific protonation. However, details of the roles and protonation states of active-site residues, and sources of protons and water, remain highly speculative. Large-scale computations on active-site models provide a means to better understand this complex chemical mechanism. The computational protocol comprises a combination of hybrid semi-empirical quantum mechanics and molecular mechanics within constrained molecular dynamics simulations, together with constrained gradient minimization calculations using density functional theory. Alternative pathways for hydration of the RuBP.CO2 complex and associated active-site protonation networks and proton and water sources were investigated. The main findings from analysis of the resulting energetics advocate major revision to existing mechanisms such that: hydration takes place anti to the CO2 ; both hydration and CC bond scission require early protonation of CO2 in the RuBP.CO2 complex; CC bond scission and stereospecific protonation reactions are concerted and, effectively, there is only one stable intermediate, the C3-gemdiolate complex. Our main conclusions for interpreting enzyme kinetic results are that the gemdiolate may represent the elusive Michaelis-Menten-like complex corresponding to the empirical Km (=Kc ) with turnover to product via bond scission concerted with stereospecific protonation consistent with the observed catalytic rate. © 2018 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Peter L Cummins
- John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, 0200, Australia
| | - Babu Kannappan
- John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, 0200, Australia
| | - Jill E Gready
- John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, 0200, Australia
| |
Collapse
|
7
|
Cummins PL, Kannappan B, Gready JE. Directions for Optimization of Photosynthetic Carbon Fixation: RuBisCO's Efficiency May Not Be So Constrained After All. Front Plant Sci 2018; 9:183. [PMID: 29545812 PMCID: PMC5838012 DOI: 10.3389/fpls.2018.00183] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 01/31/2018] [Indexed: 05/19/2023]
Abstract
The ubiquitous enzyme Ribulose 1,5-bisphosphate carboxylase-oxygenase (RuBisCO) fixes atmospheric carbon dioxide within the Calvin-Benson cycle that is utilized by most photosynthetic organisms. Despite this central role, RuBisCO's efficiency surprisingly struggles, with both a very slow turnover rate to products and also impaired substrate specificity, features that have long been an enigma as it would be assumed that its efficiency was under strong evolutionary pressure. RuBisCO's substrate specificity is compromised as it catalyzes a side-fixation reaction with atmospheric oxygen; empirical kinetic results show a trend to tradeoff between relative specificity and low catalytic turnover rate. Although the dominant hypothesis has been that the active-site chemistry constrains the enzyme's evolution, a more recent study on RuBisCO stability and adaptability has implicated competing selection pressures. Elucidating these constraints is crucial for directing future research on improving photosynthesis, as the current literature casts doubt on the potential effectiveness of site-directed mutagenesis to improve RuBisCO's efficiency. Here we use regression analysis to quantify the relationships between kinetic parameters obtained from empirical data sets spanning a wide evolutionary range of RuBisCOs. Most significantly we found that the rate constant for dissociation of CO2 from the enzyme complex was much higher than previous estimates and comparable with the corresponding catalytic rate constant. Observed trends between relative specificity and turnover rate can be expressed as the product of negative and positive correlation factors. This provides an explanation in simple kinetic terms of both the natural variation of relative specificity as well as that obtained by reported site-directed mutagenesis results. We demonstrate that the kinetic behaviour shows a lesser rather than more constrained RuBisCO, consistent with growing empirical evidence of higher variability in relative specificity. In summary our analysis supports an explanation for the origin of the tradeoff between specificity and turnover as due to competition between protein stability and activity, rather than constraints between rate constants imposed by the underlying chemistry. Our analysis suggests that simultaneous improvement in both specificity and turnover rate of RuBisCO is possible.
Collapse
|
8
|
Cummins PL, Gready JE. Prediction of Relative Binding Constants of Cofactors and Designed Ligands to Dihydrofolate Reductase by Computer Simulation. Pteridines 2013. [DOI: 10.1515/pteridines.1991.3.12.137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Peter L. Cummins
- Department of Biochemistry, University of Sydney, Sydney, NSW 2006, Australia
| | - Jill E. Gready
- Department of Biochemistry, University of Sydney, Sydney, NSW 2006, Australia
| |
Collapse
|
9
|
Alonso H, Cummins PL, Gready JE. Methyltetrahydrofolate:corrinoid/iron−sulfur Protein Methyltransferase (MeTr): Protonation State of the Ligand and Active-Site Residues. J Phys Chem B 2009; 113:14787-96. [DOI: 10.1021/jp900181g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hernán Alonso
- Computational Proteomics Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
| | - Peter L. Cummins
- Computational Proteomics Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
| | - Jill E. Gready
- Computational Proteomics Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
| |
Collapse
|
10
|
Cummins PL, Rostov IV, Gready JE. Calculation of a Complete Enzymic Reaction Surface: Reaction and Activation Free Energies for Hydride-Ion Transfer in Dihydrofolate Reductase. J Chem Theory Comput 2007; 3:1203-11. [DOI: 10.1021/ct600313b] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Peter L. Cummins
- Computational Proteomics Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
| | - Ivan V. Rostov
- Computational Proteomics Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
| | - Jill E. Gready
- Computational Proteomics Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
| |
Collapse
|
11
|
Cummins PL, Gready JE. The Influence of Starting Coordinates in Free Energy Simulations of Ligand Binding to Dihydrofolate Reductase. Molecular Simulation 2006. [DOI: 10.1080/08927029508024052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
12
|
Alonso H, Gillies MB, Cummins PL, Bliznyuk AA, Gready JE. Multiple ligand-binding modes in bacterial R67 dihydrofolate reductase. J Comput Aided Mol Des 2005; 19:165-87. [PMID: 16059670 DOI: 10.1007/s10822-005-3693-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2004] [Accepted: 03/11/2005] [Indexed: 11/25/2022]
Abstract
R67 dihydrofolate reductase (DHFR), a bacterial plasmid-encoded enzyme associated with resistance to the drug trimethoprim, shows neither sequence nor structural homology with the chromosomal DHFR. It presents a highly symmetrical toroidal structure, where four identical monomers contribute to the unique central active-site pore. Two reactants (dihydrofolate, DHF), two cofactors (NADPH) or one of each (R67*DHF*NADPH) can be found simultaneously within the active site, the last one being the reactive ternary complex. As the positioning of the ligands has proven elusive to empirical determination, we addressed the problem from a theoretical perspective. Several potential structures of the ternary complex were generated using the docking programs AutoDock and FlexX. The variability among the final poses, many of which conformed to experimental data, prompted us to perform a comparative scoring analysis and molecular dynamics simulations to assess the stability of the complexes. Analysis of ligand-ligand and ligand-protein interactions along the 4 ns trajectories of eight different structures allowed us to identify important inter-ligand contacts and key protein residues. Our results, combined with published empirical data, clearly suggest that multipe binding modes of the ligands are possible within R67 DHFR. While the pterin ring of DHF and the nicotinamide ring of NADPH assume a stacked endo-conformation at the centre of the pore, probably assisted by V66, Q67 and I68, the tails of the molecules extend towards opposite ends of the cavity, adopting multiple configurations in a solvent rich-environment where hydrogen-bond interactions with K32 and Y69 may play important roles.
Collapse
Affiliation(s)
- Hernán Alonso
- Computational Proteomics Group, John Curtin School of Medical Research, The Australian National University, P.O. Box 334, 2601, Canberra, ACT, Australia
| | | | | | | | | |
Collapse
|
13
|
Cummins PL, Gready JE. Computational methods for the study of enzymic reaction mechanisms III: A perturbation plus QM/MM approach for calculating relative free energies of protonation. J Comput Chem 2005; 26:561-8. [PMID: 15726569 DOI: 10.1002/jcc.20192] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We describe a coupling parameter, that is, perturbation, approach to effectively create and annihilate atoms in the quantum mechanical Hamiltonian within the closed shell restricted Hartree-Fock formalism. This perturbed quantum mechanical atom (PQA) method is combined with molecular mechanics (MM) methods (PQA/MM) within a molecular dynamics simulation, to model the protein environment (MM region) effects that also make a contribution to the overall free energy change. Using the semiempirical PM3 method to model the QM region, the application of this PQA/MM method is illustrated by calculation of the relative protonation free energy of the conserved OD2 (Asp27) and the N5 (dihydrofolate) proton acceptor sites in the active site of Escherichia coli dihydrofolate reductase (DHFR) with the bound nicotinamide adenine dinucleotide phosphate (NADPH) cofactor. For a number of choices for the QM region, the relative protonation free energy was calculated as the sum of contributions from the QM region and the interaction between the QM and MM regions via the thermodynamic integration (TI) method. The results demonstrate the importance of including the whole substrate molecule in the QM region, and the overall protein (MM) environment in determining the relative stabilities of protonation sites in the enzyme active site. The PQA/MM free energies obtained by TI were also compared with those estimated by a less computationally demanding nonperturbative method based on the linear response approximation (LRA). For some choices of QM region, the total free energies calculated using the LRA method were in very close agreement with the PQA/MM values. However, the QM and QM/MM component free energies were found to differ significantly between the two methods.
Collapse
Affiliation(s)
- Peter L Cummins
- Computational Proteomics Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
| | | |
Collapse
|
14
|
Gustiananda M, Liggins JR, Cummins PL, Gready JE. Conformation of prion protein repeat peptides probed by FRET measurements and molecular dynamics simulations. Biophys J 2004; 86:2467-83. [PMID: 15041684 PMCID: PMC1304095 DOI: 10.1016/s0006-3495(04)74303-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We report the combined use of steady-state fluorescence resonance energy transfer (FRET) experiments and molecular dynamics (MD) simulations to investigate conformational distributions of the prion protein (PrP) repeat system. FRET was used for the first time to probe the distance, as a function of temperature and pH, between a donor Trp residue and an acceptor dansyl group attached to the N-terminus in seven model peptides containing one to three repeats of the second decarepeat of PrP from marsupial possum (PHPGGSNWGQ)nG, and one and two human PrP consensus octarepeats (PHGGGWGQ)nG. In multirepeat peptides, single-Trp mutants were made by replacing other Trp(s) with Phe. As previous work has shown PrP repeats do not adopt a single preferred stable conformation, the FRET values are averages reflecting heterogeneity in the donor-acceptor distances. The T-dependence of the conformational distributions, and derived average dansyl-Trp distances, were obtained directly from MD simulation of the marsupial dansyl-PHPGGSNWGQG peptide. The results show excellent agreement between the FRET and MD T-dependent distances, and demonstrate the remarkable sensitivity and reproducibility of the FRET method in this first-time use for a set of disordered peptides. Based on the results, we propose a model involving cation-pi or pi-pi His-Trp interactions to explain the T- (5-85 degrees C) and pH- (6.0, 7.2) dependencies on distance, with HW i, i + 4 or WH i, i + 4 separations in sequence being more stable than HW i, i + 6 or WH i, i + 6 separations. The model has peptides adopting loosely folded conformations, with dansyl-Trp distances very much less than estimates for fully extended conformations, for example, approximately 16 vs. 33, approximately 21 vs. 69, and approximately 22 vs. 106 A for 1-3 decarepeats, and approximately 14 vs. 25 and approximately 19 vs. 54 A for 1-2 octarepeats, respectively. The study demonstrates the usefulness of combining FRET with MD, a combination reported only once previously. Initial "mapping" of the conformational distribution of flexible peptides by simulation can assist in designing and interpreting experiments using steady-state intensity methods, and indicating how time-resolved or anisotropy methods might be used.
Collapse
Affiliation(s)
- Marsia Gustiananda
- Computational Proteomics Group, John Curtin School of Medical Research, Australian National University, Canberra ACT 2601, Australia
| | | | | | | |
Collapse
|
15
|
Titmuss SJ, Cummins PL, Rendell AP, Bliznyuk AA, Gready JE. Comparison of linear-scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods for enzymic reactions. II. An energy decomposition analysis. J Comput Chem 2002; 23:1314-22. [PMID: 12214314 DOI: 10.1002/jcc.10122] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
QM/MM methods have been developed as a computationally feasible solution to QM simulation of chemical processes, such as enzyme-catalyzed reactions, within a more approximate MM representation of the condensed-phase environment. However, there has been no independent method for checking the quality of this representation, especially for highly nonisotropic protein environments such as those surrounding enzyme active sites. Hence, the validity of QM/MM methods is largely untested. Here we use the possibility of performing all-QM calculations at the semiempirical PM3 level with a linear-scaling method (MOZYME) to assess the performance of a QM/MM method (PM3/AMBER94 force field). Using two model pathways for the hydride-ion transfer reaction of the enzyme dihydrofolate reductase studied previously (Titmuss et al., Chem Phys Lett 2000, 320, 169-176), we have analyzed the reaction energy contributions (QM, QM/MM, and MM) from the QM/MM results and compared them with analogous-region components calculated via an energy partitioning scheme implemented into MOZYME. This analysis further divided the MOZYME components into Coulomb, resonance and exchange energy terms. For the model in which the MM coordinates are kept fixed during the reaction, we find that the MOZYME and QM/MM total energy profiles agree very well, but that there are significant differences in the energy components. Most significantly there is a large change (approximately 16 kcal/mol) in the MOZYME MM component due to polarization of the MM region surrounding the active site, and which arises mostly from MM atoms close to (<10 A) the active-site QM region, which is not modelled explicitly by our QM/MM method. However, for the model where the MM coordinates are allowed to vary during the reaction, we find large differences in the MOZYME and QM/MM total energy profiles, with a discrepancy of 52 kcal/mol between the relative reaction (product-reactant) energies. This is largely due to a difference in the MM energies of 58 kcal/mol, of which we can attribute approximately 40 kcal/mol to geometry effects in the MM region and the remainder, as before, to MM region polarization. Contrary to the fixed-geometry model, there is no correlation of the MM energy changes with distance from the QM region, nor are they contributed by only a few residues. Overall, the results suggest that merely extending the size of the QM region in the QM/MM calculation is not a universal solution to the MOZYME- and QM/MM-method differences. They also suggest that attaching physical significance to MOZYME Coulomb, resonance and exchange components is problematic. Although we conclude that it would be possible to reparameterize the QM/MM force field to reproduce MOZYME energies, a better way to account for both the effects of the protein environment and known deficiencies in semiempirical methods would be to parameterize the force field based on data from DFT or ab initio QM linear-scaling calculations. Such a force field could be used efficiently in MD simulations to calculate free energies.
Collapse
Affiliation(s)
- Stephen J Titmuss
- Computational Proteomics and Therapy Design Group, Division of Biochemistry and Molecular Biology, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra, ACT 2601, Australia
| | | | | | | | | |
Collapse
|
16
|
Cummins PL, Greatbanks SP, Rendell AP, Gready JE. Computational Methods for the Study of Enzymic Reaction Mechanisms. 1. Application to the Hydride Transfer Step in the Catalysis of Dihydrofolate Reductase. J Phys Chem B 2002. [DOI: 10.1021/jp021070q] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter L. Cummins
- Computational Proteomics and Therapy Design Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia, and Department of Computer Science, Faculty of Engineering and Information Technology, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
| | - Stephen P. Greatbanks
- Computational Proteomics and Therapy Design Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia, and Department of Computer Science, Faculty of Engineering and Information Technology, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
| | - Alistair P. Rendell
- Computational Proteomics and Therapy Design Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia, and Department of Computer Science, Faculty of Engineering and Information Technology, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
| | - Jill E. Gready
- Computational Proteomics and Therapy Design Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia, and Department of Computer Science, Faculty of Engineering and Information Technology, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
| |
Collapse
|
17
|
Cummins PL, Ramnarayan K, Singh UC, Gready JE. Molecular dynamics/free energy perturbation study on the relative affinities of the binding of reduced and oxidized NADP to dihydrofolate reductase. J Am Chem Soc 2002. [DOI: 10.1021/ja00022a008] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
18
|
Cummins PL, Bacskay GB, Hush NS. Ab initio quantum chemical studies of electric field gradients in the hydrogen bonded molecular nitrogen-hydrogen fluoride and molecular nitrogen-hydrogen chloride complexes. ACTA ACUST UNITED AC 2002. [DOI: 10.1021/j100257a005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
19
|
Cummins PL, Titmuss SJ, Jayatilaka D, Bliznyuk AA, Rendell AP, Gready JE. Comparison of semiempirical and ab initio QM decomposition analyses for the interaction energy between molecules. Chem Phys Lett 2002. [DOI: 10.1016/s0009-2614(01)01417-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
20
|
Cummins PL, Gready JE. Energetically most likely substrate and active-site protonation sites and pathways in the catalytic mechanism of dihydrofolate reductase. J Am Chem Soc 2001; 123:3418-28. [PMID: 11472112 DOI: 10.1021/ja0038474] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Despite much experimental and computational study, key aspects of the mechanism of reduction of dihydrofolate (DHF) by dihydrofolate reductase (DHFR) remain unresolved, while the secondary DHFR-catalyzed reduction of folate has been little studied. Major differences between proposed DHF mechanisms are whether the carboxylate group of the conserved active-site Asp or Glu residue is protonated or ionized during the reaction, and whether there is direct protonation of N5 or a proton shuttle from an initially protonated carboxylate group via O4. We have addressed these questions for both reduction steps with a comprehensive set of ab initio quantum chemical calculations on active-site fragment complexes, including the carboxyl side chain and, progressively, all other polar active-site residue groups including conserved water molecules. Addition of two protons in two steps was considered. The polarization effects of the remainder of the enzyme system were approximated by a dielectric continuum self-consistent reaction field (SCRF) model using an effective dielectric constant (epsilon) of 2. Optimized geometries were calculated using the density functional (B3LYP) method and Onsager SCRF model with the 6-31G basis. Single-point energy calculations were then carried out at the B3LYP/6-311+G level with either the Onsager or dielectric polarizable continuum model. Additional checking calculations at MP2 and HF levels, or with other basis sets or values of epsilon, were also done. From the results, the conserved water molecule, corresponding to W206 in the E. coli DHFR complexes, that is H-bonded to both the OD2 oxygen atom of the carboxyl (Asp) side chain and O4 of the pterin/dihydropterin ring, appears critically important and may determine the protonation site for the enzyme-bound substrates. In the absence of W206, the most stable monoprotonated species are the neutral-pair 4-enol forms of substrates with the carboxyl group OD2 oxygen protonated and H-bonded to N3. If W206 is included, then the most stable forms are still the neutral-pair complexes but now for the N3-H keto forms with the protonated OD2 atom H-bonding with W206. A second proton addition to these complexes gives protonations at N8 (folate) or N5 (DHF). Calculated H-bond distances correlate well with those for the conserved W206 observed in many X-ray structures. For all structures with occluded M20 loop conformations (closed active site), OD2-N3 distances are less than OD2-NA2 distances, which is consistent with those calculated for protonated OD2 complexes. Thus, the results (B3LYP; epsilon = 2 calculations) support a mechanism for both folate and DHF reduction in which the OD2 carboxyl oxygen is first protonated, followed by a direct protonation at N8 (folate) and N5 (DHF) to obtain the active cation complexes, i.e., doubly protonated. The results do not support a proposed protonated carboxyl with DHF in the enol form for the Michaelis complex, nor an ionized carboxyl with protonated enol-DHF as a catalytic intermediate. However, as additional calculations for the monoprotonated complete complexes show a reduction in the energy differences between the neutral-pair keto and ion-pair keto (N8- or N5-protonated) forms, we are extending the treatment using combined quantum mechanics and molecular mechanics (QM/MM) and molecular dynamics simulation methods to refine the description of the protein/solvent environment and prediction of the relative stabilization free energies of the various (OD2, O4, N5, and N8) protonation sites.
Collapse
Affiliation(s)
- P L Cummins
- Computational Molecular Biology and Drug Design Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
| | | |
Collapse
|
21
|
Cummins PL, Gready JE. Combined Quantum and Molecular Mechanics (QM/MM) Study of the Ionization State of 8-Methylpterin Substrate Bound to Dihydrofolate Reductase. J Phys Chem B 2000. [DOI: 10.1021/jp993153l] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter L. Cummins
- Computational Molecular Biology and Drug Design Group, John Curtin School of Medical Research, Australian National University, P.O. BOX 334, Canberra ACT, 2601 Australia
| | - Jill E. Gready
- Computational Molecular Biology and Drug Design Group, John Curtin School of Medical Research, Australian National University, P.O. BOX 334, Canberra ACT, 2601 Australia
| |
Collapse
|
22
|
Titmuss SJ, Cummins PL, Bliznyuk AA, Rendell AP, Gready JE. Comparison of linear-scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods applied to enzyme reactions. Chem Phys Lett 2000. [DOI: 10.1016/s0009-2614(00)00215-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
23
|
Cummins PL, Gready JE. QM/MM and SCRF studies of the ionization state of 8-methylpterin substrate bound to dihydrofolate reductase: existence of a low-barrier hydrogen bond. J Mol Graph Model 2000; 18:42-9. [PMID: 10935206 DOI: 10.1016/s1093-3263(00)00034-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Using combined semiempirical quantum mechanics and molecular mechanics (QM/MM) and ab initio self-consistent reaction field (SCRF) calculations, we determined that a low-barrier hydrogen bond (LBHB) is formed when the mechanism-based substrate 8-methylpterin binds to dihydrofolate reductase (DHFR). The substrate initially was assumed bound either in the ion-pair form corresponding to N3-protonated substrate hydrogen (H) bonded to the unprotonated (carboxylate) of the conserved Glu30 residue in the active site, or in the neutral-pair form corresponding to unprotonated substrate H bonded to the neutral (carboxylic acid) from of Glu30. The free energy of interaction of these H-bonded systems with the protein/solvent surroundings was computed using a coordinate-coupled free energy perturbation (FEP) method implemented within the molecular dynamics (MD) simulation scheme and using a semiempirical (PM3) QM/MM force field. The free energy obtained from the QM/MM force-field simulations corresponds most closely with the corresponding free energy component obtained from HF/6-31G* SCRF calculations using a value of 2 for the dielectric constant (epsilon) for the solvated protein. Calculations were performed at levels ranging from HF/6-31G to MP2/6-31G* to B3LYP/6-31 + G**, with varying dielectric constants. The energy-minimized path for motion of the proton in the H bond along a one-dimensional reaction coordinate was calculated at HF/6-31G, HF/6-31G* (epsilon = 1) and B3LYP/6-31G* (epsilon = 2) levels. These calculations identified a second neutral-pair complex, involving the 2-amino group of substrate, which also interacts with Glu30, which is lower in energy than the ion-pair form. A harmonic vibrational analysis shows that the first vibrational state appears to lie near or above the TS connecting potential energy minima corresponding to the two neutral-pair configurations, thus indicating an LBHB. Consequently, the H-bonded system will have a significant probability of being found in the ion-pair form, in agreement with experimental spectral studies indicating an enzyme-bound cation and suggesting that the LBHB would activate substrate towards hydride-ion transfer from NADPH.
Collapse
Affiliation(s)
- P L Cummins
- Computational Molecular Biology and Drug Design Group, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | | |
Collapse
|
24
|
|
25
|
Cummins PL, Gready JE. Investigating Enzyme Reaction Mechanisms with Quantum Mechanical-Molecular Mechanical Plus Molecular Dynamics Calculations. ACTA ACUST UNITED AC 1998. [DOI: 10.1021/bk-1998-0712.ch016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Affiliation(s)
- Peter L. Cummins
- Division of Biochemistry and Molecular Biology, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra, ACT 2601 Australia
| | - Jill E. Gready
- Division of Biochemistry and Molecular Biology, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra, ACT 2601 Australia
| |
Collapse
|
26
|
Cummins PL, Gready JE. Molecular dynamics and free energy perturbation study of hydride-ion transfer step in dihydrofolate reductase using combined quantum and molecular mechanical model. J Comput Chem 1998. [DOI: 10.1002/(sici)1096-987x(199806)19:8<977::aid-jcc15>3.0.co;2-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
27
|
|
28
|
Cummins PL, Gready JE. Thermodynamic integration calculations on the relative free energies of complex ions in aqueous solution: Application to ligands of dihydrofolate reductase. J Comput Chem 1994. [DOI: 10.1002/jcc.540150704] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
29
|
|
30
|
Cummins PL, Gready JE. Computer-aided drug design: a free energy perturbation study on the binding of methyl-substituted pterins and N5-deazapterins to dihydrofolate reductase. J Comput Aided Mol Des 1993; 7:535-55. [PMID: 8294945 DOI: 10.1007/bf00124361] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Molecular dynamics simulation and free energy perturbation techniques have been used to study the relative binding free energies of 8-methylpterins and 8-methyl-N5-deazapterins to dihydrofolate reductase (DHFR). Methyl-substitution at the 5, 6 and 7 positions in the N-heterocyclic ring gives rise to a variety of ring substituent patterns and biological activity: several of these methyl derivatives of the 8-methyl parent compounds (8-methylpterin and 8-methyl-N5-deazapterin) have been identified as substrates or inhibitors of vertebrate DHFR in previous work. The calculated free energy differences reveal that the methyl-substituted compounds are thermodynamically more stable than the primary compounds (8-methylpterin and 8-methyl-N5-deazapterin) when bound to the enzyme, due largely to hydrophobic hydration phenomena. Methyl substitution at the 5 and/or 7 positions in the 6-methyl-substituted compounds has only a small effect on the stability of ligand binding. Furthermore, repulsive interactions between the 6-methyl substituent and DHFR are minimal, suggesting that the 6-methyl position is optimal for binding. The results also show that similarly substituted 8-methylpterins and 8-methyl-N5-deazapterins have very similar affinities for binding to DHFR. The computer simulation predictions are in broad agreement with experimental data obtained from kinetic studies, i.e. 6,8-dimethylpterin is a more efficient substrate than 8-methylpterin and 6,8-dimethyl-N5-deazapterin is a better inhibitor than 8-methyl-N5-deazapterin.
Collapse
Affiliation(s)
- P L Cummins
- Department of Biochemistry, University of Sydney, N.S.W., Australia
| | | |
Collapse
|
31
|
Cummins PL, Gready JE. Novel mechanism-based substrates of dihydrofolate reductase and the thermodynamics of ligand binding: a comparison of theory and experiment for 8-methylpterin and 6,8-dimethylpterin. Proteins 1993; 15:426-35. [PMID: 8460112 DOI: 10.1002/prot.340150409] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Molecular dynamics simulation and free energy perturbation techniques have been used to study the relative binding free energies of the designed mechanism-based pterins, 8-methylpterin and 6,8-dimethylpterin, to dihydrofolate reductase (DHFR), with cofactor nicotinamide adenine dinucleotide phosphate (NADPH). The calculated free energy differences suggest that DHFR.NADPH.6,8-dimethylpterin is thermodynamically more stable than DHFR.NADPH.8-methylpterin by 2.4 kcal/mol when the substrates are protonated and by 1.3 kcal/mol when neutral. The greater binding strength of 6,8-dimethylpterin may be attributed largely to hydration effects. In terms of an appropriate model for the pH-dependent kinetic mechanism, these differences can be interpreted consistently with experimental data obtained from previous kinetic studies, i.e., 6,8-dimethylpterin is a more efficient substrate of vertebrate DHFRs than 8-methylpterin. The kinetic data suggest a value of 6.6 +/- 0.2 for the pKa of the active site Glu-30 in DHFR.NADPH. We have also used experimental data to estimate absolute values for thermodynamic dissociation constants of the active (i.e., protonated) forms of the substrates: these are of the same order as for the binding of folate (0.1-10 microM). The relative binding free energy calculated from the empirically derived dissociation constants for the protonated forms of 8-methylpterin and 6,8-dimethylpterin is 1.4 kcal/mol, a value which compares reasonably well with the theoretical value of 2.4 kcal/mol.
Collapse
Affiliation(s)
- P L Cummins
- Department of Biochemistry, University of Sydney, N.S.W., Australia
| | | |
Collapse
|
32
|
Cummins PL, Gready JE. The effect of codon 31 on the relative affinities for the binding of designed 8-alkyl-pterins to dihydrofolate reductase: a statistical perturbation theory and molecular dynamics simulation study. Adv Exp Med Biol 1993; 338:511-4. [PMID: 8304169 DOI: 10.1007/978-1-4615-2960-6_103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- P L Cummins
- Department of Biochemistry, University of Sydney, N.S.W. Australia
| | | |
Collapse
|
33
|
Gready JE, Cummins PL, Wormell P. Computer-aided design of mechanism-based pterin analogues and MD/FEP simulations of their binding to dihydrofolate reductase. Adv Exp Med Biol 1993; 338:487-92. [PMID: 8304164 DOI: 10.1007/978-1-4615-2960-6_98] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Using a combined theoretical and experimental approach we have been able to predict several chemical properties and the contributions of the many factors which determine the macroscopic binding behaviour of these new mechanism-based compounds with DHFR, and also analyse experimental data to develop structure-activity relationships.
Collapse
Affiliation(s)
- J E Gready
- Department of Biochemistry, University of Sydney NSW, Australia
| | | | | |
Collapse
|
34
|
|
35
|
Cummins PL, Gready JE. Mechanistic aspects of biological redox reactions involving NADH 2: A combined semiempirical andab initio study of hydride-ion transfer between the NADH analogue, 1-methyl-dihydronicotinamide, and folate and dihydrofolate analogue substrates of dihydrofolate reductase. J Comput Chem 1990. [DOI: 10.1002/jcc.540110703] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
36
|
Cummins PL, Gready JE. Computational strategies for the optimization of equilibrium geometries and transition-state structures at the semiempirical level. J Comput Chem 1989. [DOI: 10.1002/jcc.540100712] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
37
|
Cummins PL, Bacskay GB, Hush NS, Jönsson B. On the structure, lattice energy and 14N nuclear quadrupole coupling constant of solid HCN. Chem Phys Lett 1988. [DOI: 10.1016/0009-2614(88)80198-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
38
|
Cummins PL, Backsay GB, Hush NS. The effect of intermolecular interactions on the electric field gradients in solid ammonia, tetrazole and imidazole. Mol Phys 1987. [DOI: 10.1080/00268978700102141] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
39
|
Cummins PL, Bacskay GB, Hush NS. Ab initio quantum chemical studies of the electronic properties of the hydrogen bonded N2HF, N2HCl, (HCN)2 and NH3HCN complexes. Chem Phys 1987. [DOI: 10.1016/0301-0104(87)80046-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
40
|
Cummins PL, Bacskay GB, Hush NS. The prediction of nuclear quadrupole moments fromabinitioquantum chemical studies on small molecules. II. The electric field gradients at the17O,35Cl, and2H nuclei in CO, NO+, OH−, H2O, CH2O, HCl, LiCl, and FCl. J Chem Phys 1987. [DOI: 10.1063/1.453586] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
41
|
|
42
|
Cummins PL, Bacskay GB, Hush NS, Ahlrichs R. The prediction of nuclear quadrupole moments from ab initio quantum chemical studies on small molecules. I. The electric field gradients at the 14N and 2H nuclei in N2, NO, NO+, CN, CN−, HCN, HNC, and NH3. J Chem Phys 1987. [DOI: 10.1063/1.452390] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
43
|
Cummins PL, Rendell APL, Swanton DJ, Bacskay GB, Hush NS. The role of electrostatics in molecular interactions: prediction of shapes and electronic properties of weakly bound complexes. INT REV PHYS CHEM 1986. [DOI: 10.1080/01442358609353375] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
44
|
Cummins PL, Bacskay GB, Hush NS, Halle B, Engström S. The effect of intermolecular interactions on the2H and17O quadrupole coupling constants in ice and liquid water. J Chem Phys 1985. [DOI: 10.1063/1.448384] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
45
|
|