A molecular mechanics force field for NAD+ NADH, and the pyrophosphate groups of nucleotides

Pavelites, Joseph J.; Gao, Jiali; Bash, Paul A.; MacKerell, Alexander D.

doi:10.1002/(sici)1096-987x(19970130)18:2<221::aid-jcc7>3.0.co;2-x

Cited by 189 publications

(201 citation statements)

References 20 publications

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“…Figure 1 shows the results obtained for the first MD simulation in which the published NADH parameters of Pavelites et al 18 were employed. These show reasonably good agreement with the experimental spectra considering that the assumption of linear response is being used.…”

Section: Resultsmentioning

confidence: 99%

“…The reason for doing this was to investigate how sensitive our method was to the quality of the molecular dynamics parameters. The method detailed above resulted in a force field that, while reasonably good, was not strictly parametrized in the thorough method employed by Pavelites et al 18 The variation between the second and third simulations concerned the parametrization of the amide moiety of the NADH cofactor (atoms N7, O14, C18, H67, and H73, Appendix A, Table 4). Trial calculations showed that the molecular orbitals involved in the excitation corresponding to NADH absorption and emission are highly dependent on the structure of this amide group.…”

Section: Methodsologymentioning

confidence: 99%

“…Hence it was believed that the accurate parametrization of this moiety would be essential to obtaining good results. Thus for the second simulation, we used our simple analogy-based force field but kept the torsions defined by Pavelites et al 18 for the amide moiety. Because the magnitude of these torsions are very small in comparison to, for example, a peptide linkage, we decided to, for the third simulation, simply set these torsions to zero.…”

Section: Methodsologymentioning

confidence: 99%

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Large and Fast Relaxations inside a Protein: Calculation and Measurement of Reorganization Energies in Alcohol Dehydrogenase

et al. 2002

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We have used a recently established quantum mechanics/molecular mechanics (QM/MM) method 1 to calculate the optical absorption and emission spectra for NADH in liver alcohol dehydrogenase. The widths of these spectra are sensitive to the amplitude and time scale of protein fluctuations, while the Stokes shift is a direct measure of the extent of relaxation of the molecular system. Despite the very large Stokes shift in this system (∼0.9 eV), we find that the reorganization energy is recovered with 13% accuracy. Moreover, the spectral widths are within 6% of the experimental values. Our results demonstrate that our QM/MM approach to the calculation of free energy surfaces remains highly viable even for very large and very fast fluctuations and even for systems as complex as proteins. We also show that the quality of the results very much depend on the quality of the molecular dynamics trajectory and as such our method provides a way to validate molecular mechanics force field parameters for chromophores via direct comparison with experiment. IntroductionThe extent of a chemical reaction is determined by the free energy difference between reactants and products. The rate constant for a catalytic step is greatly affected by the free energy of activation. It would be useful therefore to be able to predict the extent, origin, and rate of development of this free energy difference in condensed-phase chemical reactions. A liquid or protein will respond to a rapid change in charge distribution by structural rearrangements that minimize the energy of the system. The energy associated with these rearrangements is generally termed the reorganization energy and has a wellestablished role in, for example, nonadiabatic electron-transfer theory. The reorganization energy also appears in the response of a condensed-phase chemical system to optical excitation. The creation of an excited electronic state rearranges the electron density in the molecule, leading to a rearrangement of the surrounding medium and a lowering of the excited-state energy and concomitant raising of the ground-state energy. In fluorescent systems, reorganization is revealed by the fluorescence Stokes shift, which is proportional to the reorganization energy of the system.In one sense, creation of an excited state and the subsequent Stokes shift of the fluorescence can be regarded as an extremely simple type of chemical reaction. The reactant in this case is the excited state of the molecule initially created by the applied optical field, and the product is the state created by relaxation of the system. The free energy gap between reactants and products is indicated by the shift in the peak of the steady-state absorption band from that of the steady-state emission band. The steady-state emission spectrum is a good representation of the product energy because most of the relaxation is complete well before the excited-state emits a photon. Moreover, the spectral width of the absorption and emission spectra reflect the time scale of the fluctuations, as is app...

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Section: Resultsmentioning

confidence: 99%

Section: Methodsologymentioning

confidence: 99%

Section: Methodsologymentioning

confidence: 99%

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Large and Fast Relaxations inside a Protein: Calculation and Measurement of Reorganization Energies in Alcohol Dehydrogenase

et al. 2002

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“…CHARMM27 protein (33) and CHARMM36 lipid (34) force fields were used. The force field for ATP was from Pavelites et al (35).…”

Section: Methodsmentioning

confidence: 99%

Inter- and intrasubunit interactions between transmembrane helices in the open state of P2X receptor channels

Heymann

Dai

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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P2X receptor channels open in response to the binding of extracellular ATP, a property that is essential for purinergic sensory signaling. Apo and ATP-bound X-ray structures of the detergentsolubilized zebrafish P2X4 receptor provide a blueprint for receptor mechanisms but unexpectedly showed large crevices between subunits within the transmembrane (TM) domain of the ATPbound structure. Here we investigate both intersubunit and intrasubunit interactions between TM helices of P2X receptors in membranes using both computational and functional approaches. Our results suggest that intersubunit crevices found in the TM domain of the ATP-bound crystal structure are not present in membraneembedded receptors but substantiate helix interactions within individual subunits and identify a hot spot at the internal end of the pore where both the gating and permeation properties of P2X receptors can be tuned. We propose a model for the structure of the open state that has stabilizing intersubunit interactions and that is compatible with available structural constraints from functional channels in membrane environments.pore-opening mechanism | transmembrane intersubunit crevices P 2X receptor channels are a family of trimeric cation-selective channels that are activated by extracellular ATP (1, 2). These ligand-gated ion channels are expressed in many tissues, including the central and peripheral nervous systems and the immune system, where they play a range of important roles in sensory signaling and inflammation (1, 3).Recent X-ray structures of the zebrafish P2X4 (zfP2X4) receptor in apo and ATP-bound forms (Protein Data Bank ID codes 4DW0 and 4DW1, respectively) have revealed the molecular design of these proteins (2, 4, 5) and have provided valuable information on how ATP binding triggers the opening of the transmembrane (TM) pore ( Fig. 1 A and B). ATP binds to a cleft between subunits within the large extracellular domain, inducing cleft closure and an accompanying lateral flexing of the β-sheet connecting the extracellular domain to the TM domain (5). The apo structure of the zfP2X4 receptor reveals that the TM1 helix is positioned peripheral to the TM2 helix and that the TM2 helix occludes the pore at the central axis within the outer half of the membrane (4, 5). In accord with this structure, accessibility studies show that the TM2 helix lines the aqueous pore and that the residues forming the gate are positioned within the occlusion in the apo structure (6-8). Lateral fenestrations within the extracellular domain provide a path for ions to enter and exit the extracellular vestibule positioned above this TM2 occlusion, and these fenestrations are thought to change conformation in response to ATP binding (9, 10). The ATP-bound structure shows that pore opening involves widening of the extracellular vestibule and an iris-like expansion of the pore (5). Intersubunit interactions within the TM domain in the apo structure are limited to the gate region of TM2 (5), and thus the pore expansion observed in the ATP-bound struc...

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“…Maestro Molecular Modeling software was used to build the acyl chain for the phosphopantetheine moiety. Force field parameters were the ff99 set for proteins (43) and published parameters (44,45) for NADH. The Amber antechamber module and GAFF force field (46) with am1bcc charges (47) were used to generate the parameters for phosphopantetheine and the attached acyl chain.…”

Section: Methodsmentioning

confidence: 99%

Structure of Acyl Carrier Protein Bound to FabI, the FASII Enoyl Reductase from Escherichia coli

Rafi

Novichenok

Kolappan

et al. 2006

Journal of Biological Chemistry

105

150

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Acyl carrier proteins play a central role in metabolism by transporting substrates in a wide variety of pathways including the biosynthesis of fatty acids and polyketides. However, despite their importance, there is a paucity of direct structural information concerning the interaction of ACPs with enzymes in these pathways. Here we report the structure of an acyl-ACP substrate bound to the Escherichia coli fatty acid biosynthesis enoyl reductase enzyme (FabI), based on a combination of x-ray crystallography and molecular dynamics simulation. The structural data are in agreement with kinetic studies on wild-type and mutant FabIs, and reveal that the complex is primarily stabilized by interactions between acidic residues in the ACP helix ␣2 and a patch of basic residues adjacent to the FabI substrate-binding loop. Unexpectedly, the acyl-pantetheine thioester carbonyl is not hydrogen-bonded to Tyr 156 , a conserved component of the short chain alcohol dehydrogenase/reductase superfamily active site triad. FabI is a proven target for drug discovery and the present structure provides insight into the molecular determinants that regulate the interaction of ACPs with target proteins. Acyl carrier proteins (ACPs)7 play an essential role in a diverse array of metabolic pathways including the biosynthesis of fatty acids (1, 2), polyketides (3), membrane-derived oligosaccharides (4), lipopolysaccharides (5, 6), and phospholipids (7). In each case the growing substrate is attached via a thioester to the ACP phosphopantetheine group. ACPs must therefore be able to recognize and interact, in an acyl group-dependent manner, with a wide variety of enzymes. In eukaryotic type I fatty acid synthesis (FASI) and in polyketide biosynthesis, the ACP occurs as part of a larger polypeptide that is also associated with other catalytic activities. In contrast, in bacterial type II fatty acid biosynthesis (FASII), each of the enzyme activities as well as the ACP are encoded by separate polypeptide chains (2). ACPs that function in FASII-mediated biosynthesis are small, highly soluble, acidic proteins that vary in molecular mass from 7.5 kDa (Escherichia coli) to 13 kDa (Mycobacterium tuberculosis) (1, 8 -11).Despite the central role that ACPs play in metabolism, structural details of their interaction with target proteins are sparse. Whereas the structures of ACPs from a variety of different species have been determined by x-ray crystallography (12) and NMR spectroscopy (see for example, Refs. 13 and 14), only one structure has been determined of ACP in complex with another protein, the holo-ACP synthase (AcpS) (15), and no structural information is available for the interaction between ACP and enzymes of the fatty acid biosynthesis pathway. AcpS attaches the phosphopantetheine to the ACP serine and thus, although valuable, the complex of AcpS and ACP differs fundamentally from other ACP-protein complexes and does not provide insight into the delivery of substrate by ACP.The NMR studies reveal that ACPs are highly flexible, a structural f...

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A molecular mechanics force field for NAD+ NADH, and the pyrophosphate groups of nucleotides

Cited by 189 publications

References 20 publications

Large and Fast Relaxations inside a Protein: Calculation and Measurement of Reorganization Energies in Alcohol Dehydrogenase

Large and Fast Relaxations inside a Protein: Calculation and Measurement of Reorganization Energies in Alcohol Dehydrogenase

Inter- and intrasubunit interactions between transmembrane helices in the open state of P2X receptor channels

Structure of Acyl Carrier Protein Bound to FabI, the FASII Enoyl Reductase from Escherichia coli

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