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van Outersterp RE, Martens J, Berden G, Steill JD, Oomens J, Rijs AM. Structural characterization of nucleotide 5'-triphosphates by infrared ion spectroscopy and theoretical studies. Phys Chem Chem Phys 2018; 20:28319-28330. [PMID: 30398499 DOI: 10.1039/c8cp03314e] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The molecular family of nucleotide triphosphates (NTPs), with adenosine 5'-triphosphate (ATP) as its best-known member, is of high biochemical importance as their phosphodiester bonds form Nature's main means to store and transport energy. Here, gas-phase IR spectroscopic studies and supporting theoretical studies have been performed on adenosine 5'-triphosphate, cytosine 5'-triphosphate and guanosine 5'-triphosphate to elucidate the intrinsic structural properties of NTPs, focusing on the influence of the nucleobase and the extent of deprotonation. Mass spectrometric studies involving collision induced dissociation showed similar fragmentation channels for the three studied NTPs within a selected charge state. The doubly charged anions exhibit fragmentation similar to the energy-releasing hydrolysis reaction in nature, while the singly charged anions show different dominant fragmentation channels, suggesting that the charge state plays a significant role in the favorability of the hydrolysis reaction. A combination of infrared ion spectroscopy and quantum-chemical computations indicates that the singly charged anions of all NTPs are preferentially deprotonated at their β-phosphates, while the doubly-charged anions are dominantly αβ-deprotonated. The assigned three-dimensional structure differs for ATP and CTP on the one hand and GTP on the other, in the sense that ATP and CTP show no interaction between nucleobase and phosphate tail, while in GTP they are hydrogen bonded. This can be rationalized by considering the structure and geometry of the NTPs where the final three dimensional structure depends on a subtle balance between hydrogen bond strength, flexibility and steric hindrance.
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Affiliation(s)
- Rianne E van Outersterp
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED, Nijmegen, The Netherlands.
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Schinle F, Crider PE, Vonderach M, Weis P, Hampe O, Kappes MM. Spectroscopic and theoretical investigations of adenosine 5'-diphosphate and adenosine 5'-triphosphate dianions in the gas phase. Phys Chem Chem Phys 2013; 15:6640-50. [PMID: 23258289 DOI: 10.1039/c2cp43808a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Doubly deprotonated adenosine 5'-diphosphate ([ADP-2H](2-)) and adenosine 5'-triphosphate ([ATP-2H](2-)) dianions were investigated using infrared multiple photon dissociation (IR-MPD) and photoelectron spectroscopy. Vibrational spectra acquired in the X-H stretch region (X = C, N, O) and augmented by isotope-labelling were compared to density functional theory (DFT) calculations at the B3LYP/TZVPP level. This suggests that in [ATP-2H](2-) the two phosphate groups adjacent to the ribose ring are preferentially deprotonated. Photoelectron spectra recorded at 4.66 and 6.42 eV photon energies revealed adiabatic detachment energies of 1.35 eV for [ADP-2H](2-) and 3.35 eV for [ATP-2H](2-). Repulsive Coulomb barriers were estimated at ~2.2 eV for [ADP-2H](2-) and ~1.9 eV for [ATP-2H](2-). Time-dependent DFT calculations have been used to simulate the photoelectron spectra. Photodetachment occurs primarily from lone pair orbitals on oxygen atoms within the phosphate chain.
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Affiliation(s)
- Florian Schinle
- Institut für Physikalische Chemie, Karlsruhe Institute of Technology (KIT), 76128 Karlsruhe, Germany
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3
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Harrison CB, Schulten K. Quantum and classical dynamics simulations of ATP hydrolysis in solution. J Chem Theory Comput 2012; 8:2328-2335. [PMID: 23293550 PMCID: PMC3536536 DOI: 10.1021/ct200886j] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
ATP hydrolysis is a key reaction in living cells that drives many cellular processes. The reaction, which involves gamma phosphate cleavage from ATP, converting it to ADP, has been suggested to occur via an associative or dissociative mechanism dependent upon the surrounding environment. Prior quantum chemical studies suffered from short simulation timescales failing to capture free energy contributions due to relaxation of the surrounding aqueous environment. We have developed a highly parallelized QM/MM implementation in the NAMD and OpenAtom simulation packages, using the dual grid, dual length scale method for combined plane-wave and Eular exponential spline-based QM/MM simulations. This approach, using message-driven parallel quantum and classical dynamics, permits sufficient timescale simulations for quantum chemical events such as ATP hydrolysis, and is found to accurately and reliably include the free energy contributions of solvent relaxation to hydrolysis. In this paper we describe the application of the dual grid, dual length plane-wave-based QM/MM method to study both the associative and dissociative mechanisms of ATP hydrolysis, accounting for the free energy contribution from solvent relaxation, as well as for the key role of Mg(2+) in the reaction.
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Affiliation(s)
- Christopher B. Harrison
- Beckman Institute and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Klaus Schulten
- Beckman Institute and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Breslavskaya NN, Dolin SP, Buchachenko AL. phosphate hydrate complexes of singly and doubly charged magnesium ions: Structure, energies, and spin states. RUSS J INORG CHEM+ 2010. [DOI: 10.1134/s0036023610040121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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5
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Pakiari AH, Farrokhnia M, Moradshahi A. Quantum chemical analysis of ATP, GTP and related compounds in gas phase. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2010. [DOI: 10.1007/bf03245859] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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6
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Arabi AA, Matta CF. Where is electronic energy stored in adenosine triphosphate? J Phys Chem A 2009; 113:3360-8. [PMID: 19281210 DOI: 10.1021/jp811085c] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The gas-phase electronic energy of the hydrolysis of methyl triphosphate, a model of adenosine 5'-triphosphate (ATP), is partitioned into local (atomic and group) contributions. A modified definition of Lipmann's "group transfer potential" is proposed on the basis of the partitioning of the total electronic energy into atomic contributions within the framework of the quantum theory of atoms in molecules (QTAIM). The group transfer potential is defined here as the sum of the atomic energies forming the group in ATP minus the sum of the energies of the same atoms in inorganic phosphate. It is found that the transfer potential of the terminal phosphate group in ATP is significantly reduced, from +241.7 to +73.1 kcal/mol, as a result of complexation with magnesium. This is accompanied by a concomitant change in the energy of reaction from -168.6 to -24.9 kcal/mol. Regions within ATP where the electronic energy changes the most upon hydrolysis are identified. The study is conducted at the DFT/B3LYP/6-31+G(d,p) level of theory.
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Affiliation(s)
- Alya A Arabi
- Department of Chemistry and Physics, Mount Saint Vincent University, Halifax, Nova Scotia, Canada B3M 2J6
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7
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Matta CF, Arabi AA, Keith TA. Atomic Partitioning of the Dissociation Energy of the P−O(H) Bond in Hydrogen Phosphate Anion (HPO42-): Disentangling the Effect of Mg2+. J Phys Chem A 2007; 111:8864-72. [PMID: 17713891 DOI: 10.1021/jp0735280] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This paper has three goals: (1) to provide a first step in understanding the atomic basis of the role of magnesium in facilitating the dissociation of the P-O bond in phosphorylated biochemical fuel molecules (such as ATP or GTP), (2) to compare second-order Møller-Plesset perturbation theory (MP2) results with those obtained at the more economical density functional theory (DFT) level for a future study of larger more realistic models of ATP/GTP, and (3) to examine the calculation of atomic total energies from atomic kinetic energies within a Kohn-Sham implemention of DFT, as compared to ab initio methods. A newly described method based on the quantum theory of atoms in molecules (QTAIM), which is termed the "atomic partitioning of the bond dissociation energy" (APBDE), is applied to a simple model of phosphorylated biological molecules (HPO42-). The APBDE approach is applied in the presence and in the absence of magnesium. It is found that the P-O(H) bond in the magnesium complex is shorter, exhibits a higher stretching frequency, and has a higher electron density at the bond critical point than in the magnesium-free hydrogen phosphate anion. Though these data would seem to suggest a stronger P-O(H) bond in the magnesium complex compared to the magnesium-free case, the homolytic breaking of the P-O(H) bond in the complex is found to be easier, i.e., has a lower BDE. This effect is the result of the balance of several atomic contributions to the BDE induced by the magnesium cation, which stabilizes the dissociation product more than it stabilizes the intact model molecule.
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Affiliation(s)
- Chérif F Matta
- Department of Chemistry and Physics, Mount Saint Vincent University, Halifax, Nova Scotia, Canada.
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Maron L, Ramírez-Solís A. New Nonsymmetric P(OH)3 Species. Comparison with the C3 Isomer and Themochemistry at the DFT, MP2, and CCSD(T) Levels of Theory. J Phys Chem A 2007; 111:3173-7. [PMID: 17394296 DOI: 10.1021/jp070020o] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two new less-symmetric P(OH)3 isomers that are more stable than the C3 structure are found at the density functional theory (B3PW91, B3LYP), MP2, and CCSD(T) levels with the large aug-cc-pvdz/pvtz basis sets. The C1 and C3 structures are qualitatively different from those found for the As(OH)3 molecule. An additional lower lying P(OH)3 structure with Cs symmetry has been obtained. With the largest basis set the Cs isomer is predicted to be the most stable. However, the inclusion of zero-point-energy corrections induces an inversion between the Cs and C1 isomers, with the latter becoming the lowest energy structure at the highest correlated level. Increasing inclusion of electronic correlation effects reduces the energy difference between the C1 and Cs structures while the C1-C3 energy difference and C1-Cs interconversion barrier become larger. In all cases, energy differences and barrier heights are around 1 kcal/mol.
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Affiliation(s)
- L Maron
- Laboratoire de Physique Quantique, IRSAMC, Université Paul Sabatier, 118, Route de Narbonne Toulouse 31062 Cedex, France
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Pepi F, Barone V, Cimino P, Ricci A. Gas-Phase Chemistry of Diphosphate Anions as a Tool To Investigate the Intrinsic Requirements of Phosphate Ester Enzymatic Reactions: The [M1M2HP2O7]− Ions. Chemistry 2007; 13:2096-108. [PMID: 17143922 DOI: 10.1002/chem.200601093] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Experimental studies on gaseous inorganic phosphate ions are practically nonexistent, yet they can prove helpful for a better understanding of the mechanisms of phosphate ester enzymatic processes. The present contribution extends our previous investigations on the gas-phase ion chemistry of diphosphate species to the [M(1)M(2)HP(2)O(7)](-) ions where M(1) and M(2) are the same or different and correspond to the Li, Na, K, Cs, and Rb cations. The diphosphate ions are formed by electrospray ionization of 10(-4) M solutions of Na(5)P(3)O(10) in CH(3)CN/H(2)O (1/1) and MOH bases or M salts as a source of M(+) cations. The joint application of mass spectrometric techniques and quantum-mechanical calculations makes it possible to characterize the gaseous [M(1)M(2)HP(2)O(7)](-) ions as a mixed ionic population formed by two isomeric species: linear diphosphate anion coordinated to two M(+) cations (group I) and [PO(3)M(1)M(2)HPO(4)](-) clusters (group II). The relative gas-phase stabilities and activation barriers for the isomerization I-->II, which depend on the nature of the M(+) cations, highlight the electronic susceptibility of P-O-P bond breaking in the active site of enzymes. The previously unexplored gas-phase reactivity of [M(1)M(2)HP(2)O(7)](-) ions towards alcohols of different acidity was investigated by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR/MS). The reaction proceeds by addition of the alcohol molecule followed by elimination of a water molecule.
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Affiliation(s)
- Federico Pepi
- Dipartamento di Studi di Chimica e Tecnologia delle Sostanze Biologicamente Attive, Università degli Studi di Roma La Sapienza, Piazzale A. Moro 5, 00185 Rome, Italy
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10
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Hand CE, Honek JF. Phosphate transfer from inositol pyrophosphates InsP5PP and InsP4(PP)2: A semi-empirical investigation. Bioorg Med Chem Lett 2007; 17:183-8. [PMID: 17045478 DOI: 10.1016/j.bmcl.2006.09.066] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2006] [Revised: 09/20/2006] [Accepted: 09/21/2006] [Indexed: 11/17/2022]
Abstract
A novel phosphate transfer process involving the non-enzymatic transfer of a phosphate group from inositol pyrophosphates to serine residues in proteins has been recently reported. Semi-empirical calculations at the PM3/SM5.2 level were undertaken to explore the effect of inositol pyrophosphate structure and overall charge on the thermodynamics of this phosphate transfer.
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Affiliation(s)
- Christine E Hand
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ont., Canada
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11
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Tulub AA. Molecular dynamics DFT:B3LYP study of guanosinetriphosphate conversion into guanosinemonophosphate upon Mg2+ chelation of alpha and beta phosphate oxygens of the triphosphate tail. Phys Chem Chem Phys 2006; 8:2187-92. [PMID: 16751877 DOI: 10.1039/b517072a] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A molecular dynamics DFT:B3LYP (6-31G(**) basis set) study is used to elucidate the mechanism of guanosinetriphosphate (GTP) conversion into guanosinemonophosphate (GMP) upon the action of Mg(2+) (magnesium cofactor). The computations are carried out at 310 K in a volume of 178 water molecules, which surround the Mg(2+)-GTP complex and imitate the effect of solution. Over 5 ps, Mg(2+)-GTP appears to be fully decomposed, yielding five final products: two hydrated molecules of inorganic phosphate Pi, a hydrated Mg(2+), atomic oxygen (which in the course of a couple of subsequent reactions gains two hydrogens and converts into a water molecule) and a highly active *GMP radical. The radical production is linked to presence of Mg(2+), which initiates a radical mechanism of GTP cleavage. At the initial stage, Mg(2+) undergoes reduction to Mg(+), accompanied by the formation of an ion-radical pair with GTP, (+)Mg*-*GTP(3-). Without Mg(2+), an inert form of GMP (the ionic mechanism of GTP hydrolytic cleavage) rather than GMP is produced. *GMP production, which is similar to that of *AMP (adenosinemonophosphate), *CMP (cytidinemonophosphate), TMP (thymidinemonophosphate) and *UMP (uridinemonophosphate), plays a crucial role in DNA and RNA single chain synthesis.
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Affiliation(s)
- Alexander A Tulub
- Saint-Petersburg State University, Universitetskaya Embankment 7/9, Saint-Petersburg, 199034, Russian Federation.
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12
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Pepi F, Ricci A, Rosi M, Di Stefano M. Effect of Alkali Metal Coordination on Gas-Phase Chemistry of the Diphosphate Ion: The MH2P2O7− Ions. Chemistry 2006; 12:2787-97. [PMID: 16416491 DOI: 10.1002/chem.200500723] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Systematic experimental and theoretical studies on anionic phosphate species in the gas phase are almost nonexistent, even though they could provide a benchmark for enhanced comprehension of their liquid-phase chemical behavior. Gaseous MH(2)P(2)O(7) (-) ions (M=Li, Na, K, Rb, Cs), obtained from electrospray ionization of solutions containing H(4)P(2)O(7) and MOH or M salts as a source of M(+) ions were structurally assayed by collisionally activated dissociation (CAD) mass spectrometry and theoretical calculations at the B3LYP/6-31+G* level of theory. The joint application of mass spectrometric techniques and theoretical methods allowed the MH(2)P(2)O(7) (-) ions to be identified as having a structure in which the linear diphosphate anion is coordinated to the M(+) ion (I) and provides information on gas-phase isomerization processes in the [PO(3)...MH(2)PO(4)](-) clusters II and the [P(2)O(6)...M...H(2)O](-) clusters IV. Studies of gas-phase reactivity by Fourier transform ion cyclotron resonance (FTICR) and triple quadrupole (TQ) mass spectrometry revealed that the MH(2)P(2)O(7) (-) ions react with selected nucleophiles by clustering, proton transfer and addition-elimination mechanisms. The influence of the coordination of alkali metal ions on the chemical behavior of pyrophosphate is discussed.
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Affiliation(s)
- Federico Pepi
- Dip.to di Studi di Chimica e Tecnologia delle Sostanze, Biologicamente Attive, Università di Roma "La Sapienza", P. le A. Moro 5, 00185 Rome, Italy
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13
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Pepi F, Ricci A, Rosi M, Di Stefano M. Gaseous H5P2O8? Ions: A Theoretical and Experimental Study on the Hydrolysis and Synthesis of Diphosphate Ion. Chemistry 2004; 10:5706-16. [PMID: 15472941 DOI: 10.1002/chem.200400293] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The structure and reactivity of gaseous H5P2O8- ions obtained from the chemical ionization (CI) of an H4P2O7/H2O mixture and from electrospray ionization (ESI) of CH3CN/H2O/H4P2O7 solutions were investigated by Fourier transform ion cyclotron (FTICR) and triple quadrupole mass spectrometry. Theoretical calculations performed at the B3LYP/6-31+G* level of theory and collisionally activated dissociation (CAD) mass spectrometric results allowed the ionic population obtained in the CI conditions to be structurally characterized as a mixture of gaseous [H3P2O7...H2O]-, [H3PO4...H2PO4]-, and [PO3...H3PO4...H2O]- clusters. The energy profile emerging from theoretical calculations affords insight into the mechanism of diphosphate ion hydrolysis and synthesis.
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Affiliation(s)
- Federico Pepi
- Dip.to di Studi di Chimica e Tecnologia delle Sostanze Biologicamente Attive, Università di Roma La Sapienza, P.le A. Moro, 5 00185 Rome, Italy
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14
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Range K, McGrath MJ, Lopez X, York DM. The structure and stability of biological metaphosphate, phosphate, and phosphorane compounds in the gas phase and in solution. J Am Chem Soc 2004; 126:1654-65. [PMID: 14871095 DOI: 10.1021/ja0356277] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Density functional calculations of a series of metaphosphates, acyclic and cyclic phosphates and phosphoranes relevant to RNA catalysis are presented. Solvent effects calculated with three well-established solvation models are analyzed and compared. The structure and stability of the compounds are characterized in terms of thermodynamic quantities for isomerization and ligand substitution reactions, gas-phase proton affinities, and microscopic solution pK(a)() values. The large dataset of compounds allows the estimation of bond energies to determine the relative strengths of axial and equatorial P-O phosphorane single bonds and P-O single and double bonds in metaphosphates and phosphates. The relative apicophilicty of hydroxyl and methoxy ligands in phosphoranes are characterized. The results presented here provide quantitative insight into RNA catalysis and serve as a first step toward the construction of a high-level quantum database for development of new semiempirical Hamiltonian models for biological reactions
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Affiliation(s)
- Kevin Range
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455-0431, USA
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Affiliation(s)
- J. Akola
- Institut für Festkörperforschung, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - R. O. Jones
- Institut für Festkörperforschung, Forschungszentrum Jülich, D-52425 Jülich, Germany
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16
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Johnson J, Panas I. Water adsorption and hydrolysis in the Si2O4, P2O5 and P4O10 systems – essential roles of the phosphate system in biosynthesis. Chem Phys 2002. [DOI: 10.1016/s0301-0104(01)00551-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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17
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Wang XB, Vorpagel ER, Yang X, Wang LS. Experimental and Theoretical Investigations of the Stability, Energetics, and Structures of H2PO4-, H2P2O72-, and H3P3O102- in the Gas Phase. J Phys Chem A 2001. [DOI: 10.1021/jp013244u] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xue-Bin Wang
- Department of Physics, Washington State University, 2710 University Drive, Richland, Washington 99352, W. R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, MS K8−88, P.O. Box 999, Richland, Washington 99352, and MSCF Visualization and User Services Group, W. R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, MS K8-91, P.O. Box 999, Richland, Washington 99352
| | - Erich R. Vorpagel
- Department of Physics, Washington State University, 2710 University Drive, Richland, Washington 99352, W. R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, MS K8−88, P.O. Box 999, Richland, Washington 99352, and MSCF Visualization and User Services Group, W. R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, MS K8-91, P.O. Box 999, Richland, Washington 99352
| | - Xin Yang
- Department of Physics, Washington State University, 2710 University Drive, Richland, Washington 99352, W. R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, MS K8−88, P.O. Box 999, Richland, Washington 99352, and MSCF Visualization and User Services Group, W. R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, MS K8-91, P.O. Box 999, Richland, Washington 99352
| | - Lai-Sheng Wang
- Department of Physics, Washington State University, 2710 University Drive, Richland, Washington 99352, W. R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, MS K8−88, P.O. Box 999, Richland, Washington 99352, and MSCF Visualization and User Services Group, W. R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, MS K8-91, P.O. Box 999, Richland, Washington 99352
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André I, Tvaroska I, Carver JP. Effects of the Complexation by the Mg2+ Cation on the Stereochemistry of the Sugar−Diphosphate Linkage. Ab Initio Modeling on Nucleotide−Sugars. J Phys Chem A 2000. [DOI: 10.1021/jp000028x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Isabelle André
- GlycoDesign Inc., 480 University Avenue, Suite 900, Toronto, Ontario, Canada M5G 1V2
| | - Igor Tvaroska
- GlycoDesign Inc., 480 University Avenue, Suite 900, Toronto, Ontario, Canada M5G 1V2
| | - Jeremy P. Carver
- GlycoDesign Inc., 480 University Avenue, Suite 900, Toronto, Ontario, Canada M5G 1V2
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19
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Hutter MC, Helms V. Influence of key residues on the reaction mechanism of the cAMP-dependent protein kinase. Protein Sci 1999; 8:2728-33. [PMID: 10631989 PMCID: PMC2144238 DOI: 10.1110/ps.8.12.2728] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The reaction mechanism of the catalytic phosphoryl transfer of cAMP-dependent protein kinase (cAPK) was investigated by semi-empirical AM1 molecular orbital computations of an active site model system derived from the crystal structure of the catalytic subunit of the enzyme. The activation barrier is calculated as 20.7 kcal mol(-1) and the reaction itself to be exothermic by 12.2 kcal mol(-1). The active site residue Asp166, which was often proposed to act as a catalytic base, does not accept a proton in any of the reaction steps. Instead, the hydroxyl hydrogen of serine is shifted to the simultaneously transferred phosphate group of ATP. Although the calculated transition state geometry indicates an associative phosphoryl transfer, no concentration of negative charge is found. To study the influence of protein mutations on the reaction mechanism, we compared two-dimensional energy hypersurfaces of the protein kinase wild-type model and a corresponding mutant in which Asp166 was replaced by alanine. Surprisingly, they show similar energy profiles despite the experimentally known decrease of catalytic activity for corresponding mutants. Furthermore, a model structure was examined, where the charged NH3 group of Lys168 was replaced by a neutral methyl group. The energetic hypersurface of this hypothetical mutant shows two possible pathways for phosphoryl transfer, which both require significantly higher activation energies than the other systems investigated, while the energetic stabilization of the reaction product is similar in all systems. As the position of the amino acid side chains and the substrate peptide is virtually unchanged in all model systems, our results suggest that the exchange of Asp166 by other amino acid is less important to the phosphoryl transfer itself, but crucial to maintain the configuration of the active site in vivo. The positively charged side chain of Lys168, however, is necessary to stabilize the intermediate reaction states, particularly the side chain of the substrate peptide.
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Affiliation(s)
- M C Hutter
- Max-Planck-Institute of Biophysics, Frankfurt, Germany
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20
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Tvaroska I, André I, Carver JP. Ab initio studies of conformational properties of dimethyl diphosphate dianion and its complex with magnesium. ACTA ACUST UNITED AC 1999. [DOI: 10.1016/s0166-1280(98)00569-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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21
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Saint-Martin H, Vicent LE. Ab Initio Study of the Hydrolysis Reactions of Neutral and Anionic Mg−Pyrophosphate Complexes in the Gas Phase. J Phys Chem A 1999. [DOI: 10.1021/jp9915782] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Humberto Saint-Martin
- Centro de Ciencias Físicas, Universidad Nacional Autónoma de México, Apartado Postal 48-3, Cuernavaca, Morelos 62251, México, and Facultad de Ciencias, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62270, México
| | - Luis E. Vicent
- Centro de Ciencias Físicas, Universidad Nacional Autónoma de México, Apartado Postal 48-3, Cuernavaca, Morelos 62251, México, and Facultad de Ciencias, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62270, México
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McCarthy WJ, Smith DMA, Adamowicz L, Saint-Martin H, Ortega-Blake I. An Ab Initio Study of the Isomerization of Mg− and Ca−Pyrophosphates. J Am Chem Soc 1998. [DOI: 10.1021/ja972715g] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- W. J. McCarthy
- Contribution from the Biotechnology Center, Utah State University, Logan, Utah 84332, Department of Chemistry, University of Arizona, Tucson, Arizona 85721, and Laboratorio de Cuernavaca, Instituto de Física, Universidad Nacional Autónoma de México, Apartado Postal 48-3, Cuernavaca, Morelos 62251, Mexico
| | - D. M. A. Smith
- Contribution from the Biotechnology Center, Utah State University, Logan, Utah 84332, Department of Chemistry, University of Arizona, Tucson, Arizona 85721, and Laboratorio de Cuernavaca, Instituto de Física, Universidad Nacional Autónoma de México, Apartado Postal 48-3, Cuernavaca, Morelos 62251, Mexico
| | - L. Adamowicz
- Contribution from the Biotechnology Center, Utah State University, Logan, Utah 84332, Department of Chemistry, University of Arizona, Tucson, Arizona 85721, and Laboratorio de Cuernavaca, Instituto de Física, Universidad Nacional Autónoma de México, Apartado Postal 48-3, Cuernavaca, Morelos 62251, Mexico
| | - H. Saint-Martin
- Contribution from the Biotechnology Center, Utah State University, Logan, Utah 84332, Department of Chemistry, University of Arizona, Tucson, Arizona 85721, and Laboratorio de Cuernavaca, Instituto de Física, Universidad Nacional Autónoma de México, Apartado Postal 48-3, Cuernavaca, Morelos 62251, Mexico
| | - I. Ortega-Blake
- Contribution from the Biotechnology Center, Utah State University, Logan, Utah 84332, Department of Chemistry, University of Arizona, Tucson, Arizona 85721, and Laboratorio de Cuernavaca, Instituto de Física, Universidad Nacional Autónoma de México, Apartado Postal 48-3, Cuernavaca, Morelos 62251, Mexico
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