Dissociative Transition State Research Articles

Phosphoryl Transfer Transition State Computationally Modeled by Mgf3(-) in the Oncogenetically Indicated Gtpase Protein Rhoa and it's Activating Protein Rhoa.Gap

GTPase enzymes, which hydrolyze guanosine triphosphate (GTP) to guanosine diphosphate (GDP) and inorganic phosphate (Pi), are involved in a large number of critical cellular processes including proliferation. GTPase Activating Protein (GAP) is responsible for the regulation of GTPase. GTPase proteins, when poorly regulated, can signal for uncontrolled cellular growth and are indicated in oncogenesis [1]. I present a computational model of the GTPase protein RhoA in solution and bound to the regulating protein RhoA.GAP. I have modeled a transition state analog of the GTP to GDP phosphoryl transfer reaction based on the crystal structure of the RhoA:RhoGAP protein complex with GDP and MgF3- [2]. Hybrid QM/MM Car-Parrinello MD simulations were performed on the protein complex with the transition state analog, all in explicit water. The reaction was modeled using thermodynamic integration by increasing the terminal phosphate-oxygen bond. These simulations provide evidence for a dissociative transition state and suggest that MgF3- is the best adduct to date to model the transition states of these types of enzymatic phosphoryl transfer reactions. This model could be further exploited to design transition state mimics for many families of GTPase proteins. Finally, this model has shown some structural effects of binding the RhoA.GAP protein to RhoA. These preliminary results indicate that we can understand better the RhoGAP:RhoA protein interface using computational methods. This model could be further exploited to identify ways to dissociate the errant GTPase:GAP complex by targeting the GTP binding site or even the protein-protein interface itself.

Transition State Analogues of Plasmodium falciparum and Human Orotate Phosphoribosyltransferases

The survival and proliferation of Plasmodium falciparum parasites and human cancer cells require de novo pyrimidine synthesis to supply RNA and DNA precursors. Orotate phosphoribosyltransferase (OPRT) is an indispensible component in this metabolic pathway and is a target for antimalarials and antitumor drugs. P. falciparum (Pf) and Homo sapiens (Hs) OPRTs are characterized by highly dissociative transition states with ribocation character. On the basis of the geometrical and electrostatic features of the PfOPRT and HsOPRT transition states, analogues were designed, synthesized, and tested as inhibitors. Iminoribitol mimics of the ribocation transition state in linkage to pyrimidine mimics using methylene or ethylene linkers gave dissociation constants (Kd) as low as 80 nM. Inhibitors with pyrrolidine groups as ribocation mimics displayed slightly weaker binding affinities for OPRTs. Interestingly, p-nitrophenyl riboside 5'-phosphate bound to OPRTs with Kd values near 40 nM. Analogues designed with a C5-pyrimidine carbon-carbon bond to ribocation mimics gave Kd values in the range of 80-500 nM. Acyclic inhibitors with achiral serinol groups as the ribocation mimics also displayed nanomolar inhibition against OPRTs. In comparison with the nucleoside derivatives, inhibition constants of their corresponding 5'-phosphorylated transition state analogues are largely unchanged, an unusual property for a nucleotide-binding site. In silico docking of the best inhibitor into the HsOPRT active site supported an extensive hydrogen bond network associated with the tight binding affinity. These OPRT transition state analogues identify crucial components of potent inhibitors targeting OPRT enzymes. Despite their tight binding to the targets, the inhibitors did not kill cultured P. falciparum.

Distortional binding of transition state analogs to human purine nucleoside phosphorylase probed by magic angle spinning solid-state NMR.

Transition state analogs mimic the geometry and electronics of the transition state of enzymatic reactions. These molecules bind to the active site of the enzyme much tighter than substrate and are powerful noncovalent inhibitors. Immucillin-H (ImmH) and 4'-deaza-1'-aza-2'-deoxy-9-methylene Immucillin-H (DADMe-ImmH) are picomolar inhibitors of human purine nucleoside phosphorylase (hPNP). Although both molecules are electronically similar to the oxocarbenium-like dissociative hPNP transition state, DADMe-ImmH is more potent than ImmH. DADMe-ImmH captures more of the transition state binding energy by virtue of being a closer geometric match to the hPNP transition state than ImmH. A consequence of these similarities is that the active site of hPNP exerts greater distortional forces on ImmH than on DADMe-ImmH to "achieve" the hPNP transition state geometry. By using magic angle spinning solid-state NMR to investigate stable isotope-labeled ImmH and DADMe-ImmH, we have explored the difference in distortional binding of these two inhibitors to hPNP. High-precision determinations of internuclear distances from NMR recoupling techniques, rotational echo double resonance, and rotational resonance, have provided unprecedented atomistic insight into the geometric changes that occur upon binding of transition state analogs. We conclude that hPNP stabilizes conformations of these chemically distinct analogs having distances between the cation and leaving groups resembling those of the known transition state.

Dissociation of multiple hydrogen molecules on the three-dimensional aluminium cluster: theoretical study

Compared to hydrogen activation on bare transition metal clusters, such reactions involving main group metal clusters have been less studied. Here, dissociative addition of multiple H2 to the group 13 metal cluster Al6 is investigated theoretically to examine the viability of generating Al6H8, the novel alane proposed experimentally by Li et al. Coupled-cluster CCSD(T) calculations with the aug-cc-pVTZ basis set are employed to determine the energetics of these additions, and density functional calculations are used to extensively probe the relevant potential energy surfaces. We find the sequential hydrogenations of Al6 via Al6H2k−2 + H2 → Al6H2k (k = 1–4) exothermic, where the Al6H2k cluster global minima structures exhibit the same ‘H-bridging motif’ with two hydrogens sitting on the neighbouring threefold-bridged sites. Of various H2 dissociation modes probed including octahedral- and trigonal prism-like clusters, we find those involving dissociation transition states with the octahedral-like Al6 cores as kinetically most favoured. A correlation is identified between the H2 dissociation barriers and highest occupied molecular orbital–lowest unoccupied molecular orbital gaps of the Al6H2k−2 clusters versus k. For k = 1, the H2 dissociation is predicted to have no enthalpy barrier at the CCSD(T)/aug-cc-pVTZ level, and a good agreement is found between the coupled cluster and G4-calculated energetics. For k = 2, 3 and 4, the lowest enthalpic hydrogen dissociation barriers are determined to be 12, 14 and 20 kcal/mol, respectively, as measured relative to the Al6H2k−2 cluster global minimum isomer plus H2 reactants. According to our calculations, the entropy contribution (−TS) to the free energy dissociation barrier is 8 kcal/mol per H2.

Bond breaking in a Morse chain under tension: Fragmentation patterns, higher index saddles, and bond healing

We investigate the fragmentation dynamics of an atomic chain under tensile stress. We have classified the location, stability type (indices), and energy of all equilibria for the general n-particle chain, and have highlighted the importance of saddle points with index >1. We show that for an n = 2-particle chain under tensile stress the index 2 saddle plays a central role in organizing the dynamics. We apply normal form theory to analyze phase space structure and dynamics in a neighborhood of the index 2 saddle. We define a phase dividing surface (DS) that enables us to classify trajectories passing through a neighborhood of the saddle point using the values of the integrals associated with the normal form. We also generalize our definition of the dividing surface and define an extended dividing surface (EDS), which is used to sample and classify all trajectories that pass through a phase space neighborhood of the index 2 saddle at total energies less than that of the saddle. Classical trajectory simulations are used to study fragmentation patterns for the n = 2 chain under tension. That is, we investigate the relative probability for breaking one bond versus concerted fission of several (two, in this case) bonds. Initial conditions for trajectories are obtained by sampling the EDS at constant energy. We sample trajectories at fixed energies both above and below the energy of the saddle. The fate of trajectories (single versus multiple bond breakage) is explored as a function of the location of the initial condition on the EDS, and a connection made to the work of Chesnavich on collision-induced dissociation. A significant finding is that we can readily identify trajectories that exhibit bond healing. Such trajectories pass outside the nominal (index 1) transition state for single bond dissociation, but return to the potential well region, possibly several times, before ultimately dissociating.

DNA Translocation by Human Uracil DNA Glycosylase: Role of DNA Phosphate Charge

Human DNA repair glycosylases must encounter and inspect each DNA base in the genome to discover damaged bases that may be present at a density of <1 in 10 million normal base pairs. This remarkable example of specific molecular recognition requires a reduced dimensionality search process (facilitated diffusion) that involves both hopping and sliding along the DNA chain. Despite the widely accepted importance of facilitated diffusion in protein-DNA interactions, the molecular features of DNA that influence hopping and sliding are poorly understood. Here we explore the role of the charged DNA phosphate backbone in sliding and hopping by human uracil DNA glycosylase (hUNG), which is an exemplar that efficiently locates rare uracil bases in both double-stranded DNA and single-stranded DNA. Substitution of neutral methylphosphonate groups for anionic DNA phosphate groups weakened nonspecific DNA binding affinity by 0.4-0.5 kcal/mol per substitution. In contrast, sliding of hUNG between uracil sites embedded in duplex and single-stranded DNA substrates persisted unabated when multiple methylphosphonate linkages were inserted between the sites. Thus, a continuous phosphodiester backbone negative charge is not essential for sliding over nonspecific DNA binding sites. We consider several alternative mechanisms for these results. A model consistent with previous structural and nuclear magnetic resonance dynamic results invokes the presence of open and closed conformational states of hUNG. The open state is short-lived and has weak or nonexistent interactions with the DNA backbone that are conducive for sliding, and the populated closed state has stronger interactions with the phosphate backbone. These data suggest that the fleeting sliding form of hUNG is a distinct weakly interacting state that facilitates rapid movement along the DNA chain and resembles the transition state for DNA dissociation.

Base-Catalyzed Decarboxylation of Mandelylthiamin: Direct Formation of Bicarbonate as an Alternative to Formation of CO2

The decarboxylation of mandelylthiamin is subject to general base catalysis (β = 0.26), an outcome that is inconsistent with the expected dissociative transition state in which CO(2) forms along with a residual carbanion. The results implicate a previously unrecognized associative route in which addition of water to a carboxylate followed by base-catalyzed proton transfer and C-C cleavage produces bicarbonate directly. Various reports of the presence or absence of base catalysis in decarboxylation reactions are consistent with the associative route's occurrence in cases where nucleophiles would be generated along with CO(2) in the usual dissociative route.

Gold(I)-Catalyzed Claisen Rearrangement of Allenyl Vinyl Ethers: Missing Transition States Revealed through Evolution of Aromaticity, Au(I) as an Oxophilic Lewis Acid, and Lower Energy Barriers from a High Energy Complex

Curtin-Hammett analysis of four alternative mechanisms of the gold(I)-catalyzed [3,3] sigmatropic rearrangement of allenyl vinyl ethers by density functional theory calculations reveals that the lowest energy pathway (cation-accelerated oxonia Claisen rearrangement) originates from the second most stable of the four Au(I)-substrate complexes in which gold(I) coordinates to the lone pair of oxygen. This pathway proceeds via a dissociative transition state where the C-O bond cleavage precedes C1-C6 bond formation. The alternative Au(I) coordination at the vinyl π-system produces a more stable but less reactive complex. The two least stable modes of coordination at the allenyl π-system display reactivity that is intermediate between that of the Au(I)-oxygen and the Au(I)-vinyl ether complexes. The unusual electronic features of the four potential energy surfaces (PESs) associated with the four possible mechanisms were probed with intrinsic reaction coordinate calculations in conjunction with nucleus independent chemical shift (NICS(0)) evaluation of aromaticity of the transient structures. The development of aromatic character along the "6-endo" reaction path is modulated via Au-complexation to the extent where both the cyclic intermediate and the associated fragmentation transition state do not correspond to stationary points at the reaction potential energy surface. This analysis explains why the calculated PES for cyclization promoted by coordination of gold(I) to allenyl moiety lacks a discernible intermediate despite proceeding via a highly asynchronous transition state with characteristics of a stepwise "cyclization-mediated" process. Although reaction barriers can be strongly modified by aryl substituents of varying electronic demand, direct comparison of experimental and computational substituent effects is complicated by formation of Au-complexes with the Lewis-basic sites of the substrates.

A first-principles study of hydrogen interaction and saturation on ScAl3

Complex metal hydrides are promising hydrogen storage material for mobile applications. The presence of scandium catalysts in complex metal hydrides is found to improve significantly the kinetics of H2 adsorption and desorption. The exact role of these additives is not completely understood. NMR studies suggests the presence of distorted ScAl3 phase which is attributed to the enhancement of reversible uptake and release rates of H2. In this study, we have investigated the hydrogen interaction and saturation on stable ScAl3 cluster at various sites using the density functional theory by employing unrestricted B3LYP/6-311++G(d,p) and the GGA-PW91/DNP methods. From natural bond orbital charge analysis and electrostatic potential superimposed on electron density plots, ScAl3 is found to be more polarized and Sc atom in ScAl3 cluster has higher negative charge and electron density over Al atoms. H2 undergoes dissociative chemisorption on the Sc atop site in ScAl3 resulting in Sc–H–Al bridge structure. The hydrogen saturation is studied by sequential H2 adsorption on ScAl3 cluster. In the Sc site, the first H2 molecule undergoes dissociative chemisorption and further addition results in H2 physisorption with the maximum loading of 6 H2 molecules resulting in stable ScAl3H12 structure. To obtain mechanistic insights into the hydrogenation process, the transition state and activation energy of H2 dissociation on the ScAl3 system has been determined.

Kinetic Stability of the Streptavidin–Biotin Interaction Enhanced in the Gas Phase

Results of the first detailed study of the structure and kinetic stability of the model high-affinity protein-ligand interaction between biotin (B) and the homotetrameric protein complex streptavidin (S(4)) in the gas phase are described. Collision cross sections (Ω) measured for protonated gaseous ions of free and ligand-bound truncated (residues 13-139) wild-type (WT) streptavidin, i.e., S(4)(n+) and (S(4)+4B)(n+) at charge states n = 12-16, were found to be independent of charge state and in agreement (within 10%) with values estimated for crystal structures reported for S(4) and (S(4)+4B). These results suggest that significant structural changes do not occur upon transfer of the complexes from solution to the gas phase by electrospray ionization. Temperature-dependent rate constants were measured for the loss of B from the protonated (S(4)+4B)(n+) ions. Over the temperature range investigated, the kinetic stability increases with decreasing charge state, from n = 16 to 13, but is indistinguishable for n = 12 and 13. A comparison of the activation energies (E(a)) measured for the loss of B from the (S(4)+4B)(13+) ions composed of WT streptavidin and five binding site mutants (Trp79Phe, Trp108Phe, Trp120Phe, Ser27Ala, and Tyr43Ala) suggests that at least some of the specific intermolecular interactions are preserved in the gas phase. The results of molecular dynamics simulations performed on WT (S(4)+4B)(12+) ions with different charge configurations support this conclusion. The most significant finding of this study is that the gaseous WT (S(4)+4B)(n+) ions at n = 12-14, owing to a much larger E(a) (by as much as 13 kcal mol(-1)) for the loss of B, are dramatically more stable kinetically at 25 °C than the (S(4)+4B) complex in aqueous neutral solution. The differences in E(a) values measured for the gaseous (S(4)+4B)(n+) ions and solvated (S(4)+4B) complex can be largely accounted for by a late dissociative transition state and the rehydration of B and the protein binding cavity in solution.

TTR Fibril Formation Inhibitors: Is there a SAR?

Transthyretin is a homotetrameric protein that carries thyroxine and retinol binding protein in plasma and is associated with a variety of amyloid diseases. One approach to the potential treatment of TTR amyloidosis is the stabilization of the native tetramer, over the dissociative transition state, through the binding of small molecules; this increases the kinetic barrier for tetramer dissociation and prevents protein misfolding. Several molecules discovered through focused screening, or created utilizing the structure-based design, were studied to identify the structural features that could make up for a good candidate drug. In this review, we examine several different chemical classes of TTR fibril formation inhibitors, highlighting the structural modifications that have led to an improvement or to a decrease of their potency and/or selectivity.

Deuterium Kinetic Isotope Effects on the Dissociation of a Protein–Fatty Acid Complex in the Gas Phase

Deuterium kinetic isotope effects (KIEs) are reported for the first time for the dissociation of a protein-ligand complex in the gas phase. Temperature-dependent rate constants were measured for the loss of neutral ligand from the deprotonated ions of the 1:1 complex of bovine β-lactoglobulin (Lg) and palmitic acid (PA), (Lg + PA)(n-) → Lg(n-) + PA, at the 6- and 7- charge states. At 25 °C, partial or complete deuteration of the acyl chain of PA results in a measurable inverse KIE for both charge states. The magnitude of the KIEs is temperature dependent, and Arrhenius analysis of the rate constants reveals that deuteration of PA results in a decrease in activation energy. In contrast, there is no measurable deuterium KIE for the dissociation of the (Lg + PA) complex in aqueous solution at pH 8. Deuterium KIEs were calculated using conventional transition-state theory with an assumption of a late dissociative transition state (TS), in which the ligand is free of the binding pocket. The vibrational frequencies of deuterated and non-deuterated PA in the gas phase and in various solvents (n-hexane, 1-chlorohexane, acetone, and water) were established computationally. The KIEs calculated from the corresponding differences in zero-point energies account qualitatively for the observation of an inverse KIE but do not account for the magnitude of the KIEs nor their temperature dependence. It is proposed that the dissociation of the (Lg + PA) complex in aqueous solution also proceeds through a late TS in which the acyl chain is extensively hydrated such that there is no significant differential change in the vibrational frequencies along the reaction coordinate and, consequently, no significant KIE.

Pressure-Accelerated Dissociation of Amyloid Fibrils in Wild-Type Hen Lysozyme

The dynamics of amyloid fibrils, including their formation and dissociation, could be of vital importance in life. We studied the kinetics of dissociation of the amyloid fibrils from wild-type hen lysozyme at 25°C in vitro as a function of pressure using Trp fluorescence as a probe. Upon 100-fold dilution of 8 mg ml−1 fibril solution in 80 mM NaCl, pH 2.2, no immediate change occurred in Trp fluorescence, but at pressures of 50–450 MPa the fluorescence intensity decreased rapidly with time (kobs = 0.00193 min−1 at 0.1 MPa, 0.0348 min−1 at 400 MPa). This phenomenon is attributable to the pressure-accelerated dissociation of amyloid fibrils into monomeric hen lysozyme. From the pressure dependence of the rates, which reaches a plateau at ∼450 MPa, we determined the activation volume ΔV0‡ = −32.9 ± 1.7 ml mol(monomer)−1 and the activation compressibility Δκ‡ = −0.0075 ± 0.0006 ml mol(monomer)−1 bar−1 for the dissociation reaction. The negative ΔV0‡ and Δκ‡ values are consistent with the notion that the amyloid fibril from wild-type hen lysozyme is in a high-volume and high-compressibility state, and the transition state for dissociation is coupled with a partial hydration of the fibril.

From Nondissociative to Dissociative Adsorption of Benzene-thiol on Au(111): A Density Functional Theory Study

The adsorption of the benzene-thiol (C6H5SH) molecule on an Au(111) surface was investigated using the density functional theory method. Unlike prior studies that assume the dissociation of C6H5SH to C6H5S + H and the subsequent chemisorption of C6H5S/Au, the present computational work first clarifies the sites and energetics of both the nondissociative molecular adsorption and the dissociative adsorption and then charts the dissociative chemisorption pathways and transition states. The calculations took into account of the reaction steps in these processes, steps including S–H cleavage, C6H5S/Au formation, H/Au diffusion, and H2 desorption. The thoroughness of this approach yields the discovery of a molecular nondissociative chemisorption state with the S atom sitting on top of a gold atom. This state is stable at room temperature as its adsorption energy amounts to 0.28 eV. Its direct molecular dissociation to form C6H5S/Au and H/Au is barred by an activation barrier of 0.58 eV, and the dissociation is ...

Effect of Ag on the control of Ni-catalyzed carbon formation: A density functional theory study

First-principles calculations have been performed to examine the effect of doped Ag on the kinetics of Ni-catalyzed methane dissociation and coke formation. The close-packed Ag/Ni(111) and stepped Ag/Ni(211) surfaces as well as the defect facets with step sites blocked by Ag or C atoms are constructed to investigate the role of the coordinatively unsaturated sites in the catalytic performance of Ni nanoparticles. The most stable CHx (x=0–4) adsorption configurations and transition states for methane dissociation have been identified on both Ni and Ag/Ni surfaces. The calculated results indicate that the activation energy for methane dissociation is increased with the Ag coverage on Ni(111), and the C atoms deposited on the catalyst surface can be readily separated into small islands by Ag. On Ni(211) Ag atoms are predicted to bind preferentially to the middle-step sites which act as the nucleation center for the growth of filamentous carbon and therefore have the potential to prevent catalyst particles from being destroyed. Meanwhile, as the energy barrier for methane dissociation on the Ag-blocked Ni(211) surface is even higher than that on pure Ni(111), the active center is transferred from the stepped surface to the close-packed surface. These findings provide a rational interpretation of the experimental observations that Ag/Ni catalyst exhibits lower catalytic activity towards steam methane reforming but high resistance to coke deposition.

Mechanistic evidence for a front-side, SNi-type reaction in a retaining glycosyltransferase

A previously determined crystal structure of the ternary complex of trehalose-6-phosphate synthase identified a putative transition state-like arrangement based on validoxylamine A 6'-O-phosphate and uridine diphosphate in the active site. Here linear free energy relationships confirm that these inhibitors are synergistic transition state mimics, supporting front-face nucleophilic attack involving hydrogen bonding between leaving group and nucleophile. Kinetic isotope effects indicate a highly dissociative oxocarbenium ion-like transition state. Leaving group (18)O effects identified isotopically sensitive bond cleavages and support the existence of a hydrogen bond between the nucleophile and departing group. Brønsted analysis of nucleophiles and Taft analysis highlight participation of the nucleophile in the transition state, also consistent with a front-face mechanism. Together, these comprehensive, quantitative data substantiate this unusual enzymatic reaction mechanism. Its discovery should prompt useful reassessment of many biocatalysts and their substrates and inhibitors.

RgBF2+ complexes (Rg = Ar, Kr, and Xe): The cations with large stabilities

Rare gas containing cations with general formula [Rg, B, 2F](+) have been investigated theoretically by second-order Mo̸ller-Plesset perturbation, coupled cluster, and complete active space self-consistent field levels of theory with correlation-consistent basis sets. Totally two types of minima, i.e., boron centered C(2) (v) symmetried RgBF(2) (+) (Rg = Ar, Kr, and Xe) which can be viewed as loss of F(-) from FRgBF(2) and linear FRgBF(+) (Rg = Kr and Xe) are obtained at the CCSD(T)∕aug-cc-pVTZ∕SDD and CASSCF(10,8)∕aug-cc-pVTZ∕SDD levels, respectively. It is shown that the RgBF(2) (+) are global minima followed by FRgBF(+) at 170.9 and 142.2 kcal∕mol on the singlet potential-energy surfaces of [Rg, B, 2F](+) (Rg = Kr and Xe) at the CASPT2(10,8) ∕aug-cc-pVTZ∕SDD∕∕CASSCF(10,8)∕aug-cc-pVTZ∕SDD, respectively. The interconversion barrier heights between RgBF(2) (+) and FRgBF(+) (Rg = Kr and Xe) are at least 39 kcal∕mol. In addition, no dissociation transition state associated with RgBF(2) (+) and FRgBF(+) can be found. This suggests that RgBF(2) (+) (Rg = Ar, Kr, and Xe) can exist as both thermodynamically and kinetically stable species, while linear FRgBF(+) (Rg = Kr and Xe) can exist as metastable species compared with the lowest dissociation limit energies just like isoelectronic linear FRgBO and FRgBN(-). From natural bond orbital and atoms-in-molecules calculations, it is found that the positive charge is mainly located on Rg and boron atoms for both types of minima, the Rg-B bonds of ArBF(2) (+), KrBF(2) (+), and XeBF(2) (+) are mostly electrostatic, thus can be viewed as ion-induced dipole interaction; while that of linear FKrBF(+) and FXeBF(+) are covalent in nature. The previous experimental observation of ArBF(2) (+) by Pepi et al. [J. Phys. Chem. B. 110, 4492 (2006)] should correspond to C(2) (v) minimum. The presently predicted spectroscopies of KrBF(2) (+), XeBF(2) (+), FKrBF(+), and FXeBF(+) should be helpful for their experimental identification in the future.

Theoretical Study of Isomerization and Dissociation Transition States of C3H5O Radical Isomers: Ab Initio Characterization of the Critical Points and Statistical Transition-State Theory Modeling of the Dynamics

I use coupled-cluster theory and a modest basis set, aug-cc-pVDZ, to calculate structures and harmonic vibrational frequencies of local minima and transition states on the C(3)H(5)O potential energy surface. Accurate energies are computed using explicitly correlated coupled-cluster methods and a large basis set, cc-pVQZ-F12, to approach the one-particle basis set limit. My computations characterize eight additional stable radical structures on the global potential energy surface for this system. Additionally, this study encompasses many more isomerization and dissociation pathways, both between previously known intermediates and ones first characterized here. Analysis of the transition states and statistical transition-state theory results shows that energetically small barriers connect many of the alkenol and epoxide intermediates to the straight-chain alkoxy isomers, leading to significant branching to these alkoxy radical intermediates. Facile isomerization to these alkoxy intermediates is significant because the barrier heights leading to H + acrolein and HCO + C(2)H(4) product channels are energetically accessible even at low vibrational energies. The low dissociation barrier heights and loose transition states of these pathways result in unimolecular dissociation as opposed to isomerization to a different C(3)H(5)O intermediate.

Methylthioinosine Phosphorylase fromPseudomonas aeruginosa. Structure and Annotation of a Novel Enzyme in Quorum Sensing

The PA3004 gene of Pseudomonas aeruginosa PAO1 was originally annotated as a 5'-methylthioadenosine phosphorylase (MTAP). However, the PA3004 encoded protein uses 5'-methylthioinosine (MTI) as a preferred substrate and represents the only known example of a specific MTI phosphorylase (MTIP). MTIP does not utilize 5'-methylthioadenosine (MTA). Inosine is a weak substrate with a k(cat)/K(m) value 290-fold less than MTI and is the second best substrate identified. The crystal structure of P. aeruginosa MTIP (PaMTIP) in complex with hypoxanthine was determined to 2.8 Å resolution and revealed a 3-fold symmetric homotrimer. The methylthioribose and phosphate binding regions of PaMTIP are similar to MTAPs, and the purine binding region is similar to that of purine nucleoside phosphorylases (PNPs). The catabolism of MTA in P. aeruginosa involves deamination to MTI and phosphorolysis to hypoxanthine (MTA → MTI → hypoxanthine). This pathway also exists in Plasmodium falciparum, where the purine nucleoside phosphorylase (PfPNP) acts on both inosine and MTI. Three tight-binding transition state analogue inhibitors of PaMTIP are identified with dissociation constants in the picomolar range. Inhibitor specificity suggests an early dissociative transition state for PaMTIP. Quorum sensing molecules are associated with MTA metabolism in bacterial pathogens suggesting PaMTIP as a potential therapeutic target.

Evidence that Water Can Reduce the Kinetic Stability of Protein−Hydrophobic Ligand Interactions

The first quantitative comparison of the thermal dissociation rate constants measured for protein-ligand complexes in their hydrated and dehydrated states is described. Rate constants, measured using surface plasmon resonance spectroscopy, are reported for the dissociation of the 1:1 complexes of bovine β-lactoglobulin (Lg) with the fatty acids (FA), palmitic acid (PA), and stearic acid (SA), in aqueous solution at pH 8 and at temperatures ranging from 5 to 45 °C. The rate constants are compared to values determined from time-resolved blackbody infrared radiative dissociation measurements for the gaseous deprotonated (Lg+FA)(n-) ions, where n = 6 and 7, at temperatures ranging from 25 to 66 °C. Notably, the hydrated (Lg+PA) complex is kinetically less stable than the corresponding gas phase (Lg+PA)(n-) ions at all temperatures investigated; the hydrated (Lg+SA) complex is kinetically less stable than the gaseous (Lg+SA)(n-) ions at temperatures <45 °C. The greater kinetic stability of the gaseous (Lg+FA)(n-) ions originates from significantly larger, by 11-12 kcal mol(-1), E(a) values. It is proposed that the differences in the dissociation E(a) values measured in solution and the gas phase reflect the differential hydration of the reactant and the dissociative transition state.