NAD+ and NAD+ analogues in horse liver alcohol dehydrogenase. Relationship between reactivity and conformation simulated with molecular mechanics

Beijer, Nicoline A.; Buck, HM Henk; Sluyterman, L.A.A.E.; Meijer, E. M.

doi:10.1016/0167-4838(90)90190-q

Cited by 15 publications

(11 citation statements)

References 29 publications

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“…The bent structure in the endo configuration maximizes the overlap between the highest occupied molecular orbital (HOMO) of the hydride ion and the owest unoccupied molecular orbital (LUMO) of the hydride acceptor, minimizing the activation energy of the hydride transfer reaction [24,25]. Similarly, the pyridine nucleotide adopts a trans conformation with respect to the carboxamide group, thought to further increase reactivity for hydride transfer [25,28,29]. …”

Section: Resultsmentioning

confidence: 99%

Evolution of Function in the “Two Dinucleotide Binding Domains” Flavoproteins

2007

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Structural and biochemical constraints force some segments of proteins to evolve more slowly than others, often allowing identification of conserved structural or sequence motifs that can be associated with substrate binding properties, chemical mechanisms, and molecular functions. We have assessed the functional and structural constraints imposed by cofactors on the evolution of new functions in a superfamily of flavoproteins characterized by two-dinucleotide binding domains, the “two dinucleotide binding domains” flavoproteins (tDBDF) superfamily. Although these enzymes catalyze many different types of oxidation/reduction reactions, each is initiated by a stereospecific hydride transfer reaction between two cofactors, a pyridine nucleotide and flavin adenine dinucleotide (FAD). Sequence and structural analysis of more than 1,600 members of the superfamily reveals new members and identifies details of the evolutionary connections among them. Our analysis shows that in all of the highly divergent families within the superfamily, these cofactors adopt a conserved configuration optimal for stereospecific hydride transfer that is stabilized by specific interactions with amino acids from several motifs distributed among both dinucleotide binding domains. The conservation of cofactor configuration in the active site restricts the pyridine nucleotide to interact with FAD from the re-side, limiting the flow of electrons from the re-side to the si-side. This directionality of electron flow constrains interactions with the different partner proteins of different families to occur on the same face of the cofactor binding domains. As a result, superimposing the structures of tDBDFs aligns not only these interacting proteins, but also their constituent electron acceptors, including heme and iron-sulfur clusters. Thus, not only are specific aspects of the cofactor-directed chemical mechanism conserved across the superfamily, the constraints they impose are manifested in the mode of protein–protein interactions. Overlaid on this foundation of conserved interactions, nature has conscripted different protein partners to serve as electron acceptors, thereby generating diversification of function across the superfamily.

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Section: Resultsmentioning

confidence: 99%

Evolution of Function in the “Two Dinucleotide Binding Domains” Flavoproteins

2007

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“…However, such gas phase calculations neglect the effects of the solvent or protein environment, which have been shown to play an important role in proton and hydride transfer reactions − In addition, molecular dynamics (MD) calculations using molecular mechanical potentials have been performed on complexes of dehydrogenase enzymes with NAD + and various NAD + analogs. ,, All of these calculations have been used to determine structural information about the complexes and to compare the energetics of different possible mechanisms for the enzyme reactions. These methods, however, do not provide dynamical information on the mechanism of hydride transfer.…”

Section: Introductionmentioning

confidence: 99%

“…16 In order to incorporate these effects, semiempirical and ab initio calculations including portions of the protein active site have been performed for model NADH hydride transfer reactions. [32][33][34][35][36][37][38][39] In addition, molecular dynamics (MD) calculations using molecular mechanical potentials have been performed on complexes of dehydrogenase enzymes with NAD + and various NAD + analogs. 33,39,40 All of these calculations have been used to determine structural information about the complexes and to compare the energetics of different possible mechanisms for the enzyme reactions.…”

Section: Introductionmentioning

confidence: 99%

Development of a Potential Surface for Simulation of Proton and Hydride Transfer Reactions in Solution: Application to NADH Hydride Transfer

Hurley

Hammes‐Schiffer

1997

J. Phys. Chem. A

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This paper presents a new augmented molecular mechanical potential that incorporates significant quantum mechanical effects for proton and hydride transfer reactions in solution and in enzymes. The solvent is treated explicitly, specified covalent bonds in the solute are allowed to break and form, and the charge distribution of the solute is allowed to vary smoothly from that of the reactant to that of the product during the reaction. Moreover, in order to incorporate changes in bond order and hybridization, an efficient constraint dynamics method is combined with switching functions to smoothly vary the structure of the complex from the reactant to the product structure during the reaction. This new methodology is applied to model nicotinamide adenine dinucleotide (NADH) hydride transfer reactions, in particular to the oxidation of ethanol by the NAD+ analog 1-methyl-nicotinamide in acetonitrile and in water. Both cis and trans orientations of the NADH amide sidearm and both protonated and deprotonated forms of the substrate are studied. The structures and charge distributions of the model complexes are obtained from ab initio gas phase geometry optimizations at the Hartree−Fock 6-31G* level and are utilized to parametrize the potential energy surface. Classical free energy curves in both acetonitrile and water are calculated in order to illustrate the solvent effects on the energy gap between the reactant and the product states. The radial distribution functions between the solute and the water molecules together with the orientational distributions of the hydration shell water molecules are also calculated in order to elucidate the nature and extent of hydrogen bonding between the solvent and the solute.

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“…In the past, a molecular mechanics approach has been used to study in detail the interactions of the coenzyme NAD ÷ and a number of analogues in the active site of HLADH, in order to understand the essential factors involved in the productive binding between coenzyme and apo-enzyme [17][18][19]45]. It seemed worthwhile, however, to reconsider their results, utilizing recent X-ray data that show up more water molecules.…”

Section: Modelling Calculationsmentioning

confidence: 99%

“…In the past we have used a molecular mechanics approach to study in detail the interactions of the coenzyme NAD + and a number of analogues in the active site of HLADH, in order to understand the essential factors involved in the productive binding between coenzyme and apo-enzyme [17][18][19][20]. In this paper we present the results of detailed kinetic studies on HLADH with PEG-NAD ÷ as coenzyme, and an extension of our modelling studies including molecular mechanics (MM) and dynamics (MD), to rationalize the kinetic data obtained.…”

Section: Introductionmentioning

confidence: 99%