Rate of immune elimination of antigen from the circulatory bed of rabbits of different ages

The solubility parameters of a range of saturated hydrocarbons were calculated from vapor pressures and heats of vaporization. Solubilities of testosterone propionate were determined in these solvents at 25 degrees and yielded solute solubility parameters which varied from solvent to solvent. The solubility parameter of testosterone propionate was determined by several other methods, and support was found for the previously published figure of 9.5 cal(1/2) cm(-3/2). The geometric mean coefficient (l(12)) in saturated hydrocarbons was found to be a rectilinear function of the branching ratio (r). The mean l(12) of androstanolone and testosterone propionates was used to calculate the solubilities of other esters, giving good agreement with experimental results. IR data, presented as the sum of the shifts of the 3-keto and 17-ester carbonyl stretching frequencies in polar solvents, correlated rectilinearly with the geometric mean coefficients and the plot extrapolated to the l(12) value of n-hexane, calculated from the branching ratio plot. Attempts to predict solubilities of other esters in polar solvents using l(12) values achieved only limited success.     

Conformation of phosphatidylserine in bilayers as studied by Fourier transform infrared spectroscopy

The 13C labeled lipid 1[1'-13C]DPPS-NH4+ and its metal salts were used to unambiguously assign all carbonyl vibrations in the infrared spectrum of phosphatidylserines. It is shown that the C=O stretching band at 1741 cm-1 of phosphatidylserines previously assigned to the sn-1 C = O vibration contains contributions from both the sn-1 and the sn-2 carbonyls. The C=O stretching band at frequencies between 1715 and 1730 cm-1 previously assigned to the sn-2 C=O vibration also contains contributions from both carbonyl groups. The frequency dependence observed with the ester carbonyls primarily reflects hydrogen bonding and the polarity of the immediate vicinity. Conformational changes are accounted for in terms of frequency shifts if the conformational change involves the disposition of the C=O groups and in turn the hydrogen bonding properties. The infrared spectra of phospholipids dispersed in aqueous medium in the liquid crystalline state are inconsistent with a simple phospholipid conformation, e.g., with a conformation as found in the single-crystal structure of 1,2-dimyristoyl-sn-phosphatidylcholine and 1,2-dilauroyl-rac-phosphatidylethanolamine. The spectra support the hypothesis proposed earlier (Hauser et al., Biochemistry, 1988) on the basis of existing single-crystal phospholipid structures and NMR evidence. The hypothesis states that several conformations are present in liquid crystalline phospholipid dispersions.(ABSTRACT TRUNCATED AT 250 WORDS)     

The orientation of N-H...O=C and N-H...N hydrogen bonds in biological systems: how good is a point charge as a model for a hydrogen bonding atom?

In order to design new ligands for protein-binding sites of unknown structure, it would be useful to predict the likely sites of hydrogen bonding of an unknown protein fragment to a known molecule. The positions of maxima and minima in the electrostatic potential at appropriate distances from the van der Waals surface were calculated for various small molecules, nucleic acid bases, peptide units and amino acid side chains containing groups which can form the biologically important N-H...O=C and N-H...N hydrogen bonds. Their ability to predict the positions of H and O/N in hydrogen bonded complexes, as predicted by optimising the electrostatic interactions of pairs of such molecules constrained by the molecular shapes, was assessed. It is shown that extrema in the electrostatic potential around the isolated molecules give worthwhile predictions for the locations of hydrogen binding partners. For molecules bound by a single N-H...O=C hydrogen bond, the electrostatic maximum associated with the H is usually less than 1 A from an acceptor atom, while a C=O electrostatic minimum is generally less than 1.5 A from the hydrogen bond proton. However, a significant number of hydrogen bonds form to the opposite lone pair from the electrostatic minimum, in which case the separation is up to 3.3 A. This reflects the broad electrostatic potential well around a carbonyl oxygen between the lone pair directions. The model predicts when neighbouring atoms drastically change the hydrogen bonding characteristics of an N-H or C=O group. Although the geometries of hydrogen bonded complexes are influenced by the other van der Waals contacts between the molecules, particularly multiple hydrogen bonds, these influences are constant when considering hydrogen bonding to a specific uncharacterised binding site. Hence, the consideration of sterically accessible electrostatic extrema will be useful in the design of new ligands.     

beta-Lactam antibiotics. Spectroscopy and molecular orbital (MO) calculations. Part I: IR studies of complexation in penicillin-transition metal ion systems and semi-empirical PM3 calculations on simple model compounds

IR studies were preformed to determine possible transition metal ion binding sites of penicillin, the observed changes in spectral position and shape of characteristic IR bands of cloxacillin in the presence of transition metal ions (both in solutions and in the solid state) indicate formation of M-L complexes with engagement of -COO- and/or -CONH- functional groups. The small shift of vC=O towards higher frequencies rules out direct M-L interaction via beta-lactam carbonyl. PM3 calculations on simple model compounds (substituted formamide, cyclic ketones, lactams and substituted monocyclic beta-lactams) have been performed. All structures were fully optimized and the calculated bond lengths, angles, heats of formation and C=O stretching frequencies were discussed to determine the beta-lactam binding sites and to explain its susceptibility towards nucleophilic attack (hydrolysis in vitro) and biological activity. The relative changes of calculated values were critically compared with available experimental data and same correlation between structural parameters and in vivo activity was shown.     

Fourier transform infrared evidence for connectivity between CuB and glutamic acid 286 in cytochrome bo3 from Escherichia coli

Photodissociation of fully reduced, carbonmonoxy cytochrome bo3 causes ultrafast transfer of carbon monoxide (C triple bond O) from heme iron to CuB in the binuclear site. At low temperatures, the C triple bond O remains bound to CuB for extended times. Here, we show that the binding of C triple bond O to CuB perturbs the IR stretch of an un-ionized carboxylic acid residue, which is identified as Glu286 by mutation to Asp or to Cys. Before photodissociation, the carbonyl (C=O)-stretching frequency of this carboxylic acid residue is 1726 cm-1 for Glu286 and 1759 cm-1 for Glu286Asp. These frequencies are definitive evidence for un-ionized R-COOH and suggest that the carboxylic acids are hydrogen-bonded, though more extensively in Glu286. In Glu286Cys, this IR feature is lost altogether. We ascribe the frequency shifts in the C=O IR absorptions to the effects of binding photodissociated C triple bond O to CuB, which are relay ed to the 286 locus. Conversely, the 2065 cm-1 C triple bond O stretch of CuB-CO is markedly affected by both mutations. These effects are ascribed to changes in the Lewis acidity of CuB, or to displacement of a CuB histidine ligand by C triple bond O. C triple bond O binding to CuB also induces a downshift of an IR band which can be attributed to an aromatic C-H stretch, possibly of histidine imidazole, at about 3140 cm-1. The results suggest an easily polarizable, through-bond connectivity between one of the histidine CuB ligands and the carboxylic group of Glu286. A chain of bound water molecules may provide such a connection, which is of interest in the context of the proton pump mechanism of the heme-copper oxidases.     

Delivery of dehydroepiandrosterone to premenopausal women: effects of micronization and nonoral administration

Previous molecular mechanics calculations suggest that strands of peptide nucleic acids (PNAs) and complementary oligonucleotides form antiparallel duplexes stabilized by interresidue hydrogen bonds. In the computed structures, the amide carbonyl oxygen nearest the nucleobase (O7') forms an interresidue hydrogen bond with the backbone amide proton of the following residue, (n + 1)H1'. Of the 10 published two dimensional 1H NMR structures of a hexameric PNA.RNA heteroduplex. PNA(GAACTC).r(GAGUUC), 9 exhibit two to five potential interresidue hydrogen bonds. In our minimized average structure, created from the coordinates of these 10 NMR structures, three of the five possible interresidue hydrogen bond sites within the PNA backbone display the carbonyl oxygen (O7') and the amide proton (n + 1)H1' distances and N1'-H1'-(n - 1)O7' angles optimal for hydrogen bond formation. The finding of these interresidue hydrogen bonds supports the results of our previous molecular mechanics calculations.     

PP7, a plant phosphatase representing a novel evolutionary branch of eukaryotic protein Ser/Thr phosphatases

Theoretical quantum mechanical ab initio Hartree-Fock calculations on molecular systems, modeling processes related to the specificity of thymidylate synthase inactivation are reported. We considered several steps of the methylation of the substrate dUMP and 4- or 5-mono- and 4,5-bisubstituted dUMP analogs, as well. The following reactions were modeled: the cysteine residue (Cys198 in the L.casei enzyme) nucleophilic attack on the substrate and the substrate C(5)-H proton abstraction. The substrate was modeled by the 1-methyluracil molecule and its structural analogs. The cysteine Cys198 residue was modeled by the methylmercaptane molecule. The substrate-enzyme binary complex was modeled by the 1-methyl-5,6-dihydro-6-thiomethyl-uracil (P1) molecule. The present theoretical calculations suggest that the cysteine nucleophilic attack on the substrate may result in the SH-group addition to the pyrimidine C(5)=C(6) bond in the course of a weakly exothermic reaction. The formerly presumed enolate carbanion appeared to be weakly stable or unstable and it can readily split into the thiol and pyrimidine residues. The s2-thio- (P2) and s2,4-dithio- (P3) substrate analogs should form stable thiolate anions after cysteine residue attachment to the C(6) position of the pyrimidine ring. Studies of the deformed P1 molecule interacting with a water molecule bound to the pyrimidine C(4)=O carbonyl residue allow a suggestion that this water molecule may be directly involved in the C(5)-H proton abstraction and may serve as a proton transmitter between the substrate and the proton acceptor residue, possibly located on the cofactor N10-nitrogen. Interaction of the pyrimidine C(4)=O group, or its modification, with the N5,10-methylenetetrahydrofolate N(10) nitrogen atom is suggested as an additional factor influencing the inhibition process.     

Amide modes of the alpha-helix: Raman spectroscopy of filamentous virus fd containing peptide 13C and 2H labels in coat protein subunits

The filamentous virus fd consists of a single-stranded DNA genome sheathed by 2700 copies of a 50-residue alpha-helical subunit (protein pVIII) and serves as a model assembly of alpha-helices. To advance vibrational assignments for the alpha-helix, we have investigated Raman spectra of fd virions containing 13C and 2H (deuterium) labels at various main-chain sites of the pVIII subunits. 13C was introduced at specific peptide carbonyls, while deuterium was introduced at selected alpha-carbon (Calpha) and amide nitrogen positions. Interpretation of the Raman spectra reveals a previously unrecognized alpha-helix band in the spectral interval 730-745 cm-1, tentatively assigned to a carbonyl in-plane bending mode (amide IV). Experimental evidence has also been obtained for a distinctive alpha-helix marker near 1345 cm-1, assigned to a coupled Calpha-H bending and Calpha-C stretching mode. The fd virions containing 13C-labeled carbonyls exhibit unexpectedly complex amide I profiles, consisting of multiple band components. Amide I splitting resulting from 13C substitution of carbonyls is attributed to decoupling of transition-dipole interactions normally occurring in the extended pVIII helix. The present study identifies novel conformation-dependent Raman bands in a native alpha-helix assembly, confirms amide I and amide III assignments proposed previously for filamentous viruses, and facilitates new Raman assignments for the packaged ssDNA. The alpha-helix markers identified here should also be useful in conformation analyses of other proteins by Raman spectroscopy.     

Determination of the gene sequence and the three-dimensional structure at 2.4 angstroms resolution of methanol dehydrogenase from Methylophilus W3A1

The DNA sequences for the genes encoding the heavy and light subunits of methanol dehydrogenase from Methylophilus methylotrophus W3A1 have been determined. The deduced amino acid sequence has enabled the structure of the enzyme to be refined at 2.4 angstrom resolution against X-ray data collected on a Hamlin area detector. The structure was refined using the programs PROFFT and X-PLOR with several model building step interspersed. The final model contains two heavy chains (571 amino acids), two light chains (69 amino acids), two molecules of pyrroloquinoline quinone, two Ca2+ and 521 solvent molecules. Each half molecule contains four disulfide linkages and four cis peptides. One of the disulfides is formed from two adjacent cysteine residues linked by a trans peptide which creates a novel eight-membered ring. The heavy subunit is an 8-fold beta-propeller, each "blade" of which is a four-stranded antiparallel twisted beta-sheet. The light chain is an elongated subunit stretching across the surface of the heavy subunit, with residues 1 to 32 containing four beta-turns and residues 33 to 62 forming a helix; however, it neither interacts with the active site, nor the other HL dimer and its functional role is obscure. Around the 8-fold beta-propeller there is a repeating pattern of tryptophan residues located in the outer strand of seven of the eight beta-leaflets, each packed between adjacent leaflets. Each of these tryptophan residues is centered in the beta-strand and participates in the main chain hydrogen bonding of the sheet. Five of the seven tryptophan residues have closely similar interactions with the adjacent beta-leaflet including stacking of the tryptophan indole rings against a peptide plane and formation of a hydrogen bond from NE1 of the indole ring to a main-chain carbonyl. This repeating pattern is conserved over a number of MEDH sequences. The PQQ is located on the pseudo 8-fold rotation axis of the heavy subunit, in a funnel-shaped internal cavity, sandwiched between the indole ring of Trp237 and the two sulfur atoms of the Cys103-Cys104 vicinal disulfide. A hexacoordinate Ca2+ is bound in the active site by one nitrogen and five oxygen ligands, three from the PQQ and the others from two protein side-chains. In the active site an isolated solvent molecule is bound to the O5 of PQQ and to a nearby aspartate side-chain; its position may be the binding site for methanol. The aspartate might than serve as a general base for proton abstraction from the substrate hydroxyl. The C5 atom of PQQ could be activated by electrophilic catalysis by a nearby argenine side-chain or by the calcium ion bound to PQQ.     

Transmembrane signaling mediated by water in bovine rhodopsin

Unhydrated air-dried films of rhodopsin from bovine rod outer segment membranes do not produce its active state, metarhodopsin II. In order to reveal requirements for its formation, we studied changes in H-bonding of water, peptide carbonyl and carboxylic acid in the photochemical reactions by means of difference Fourier transform infrared spectroscopy, under both hydrated and unhydrated conditions. A water molecule near Glu113, which undergoes H-bonding change in bathorhodopsin, remained in the unhydrated film, but with a weaker H-bonding state than in the hydrated film. The other water molecules, which shfit in lumirhodopsin and metarhodopsin I as well as in bathorhodopsin of the hydrated film, were not observed in the unhydrated film. Effects of the dehydration were detected in all the C=O stretching vibrations of the peptide backbone and of Asp83 in the formation of bathorhodopsin. The C=O stretching band of Asp83 of lumirhodopsin and metarhodopsin I is intensified in the unhydrated film. We propose that structural changes at the intradiscal site in the interaction between the Schiff base and Glu113 affect water molecules, the peptide backbone, Asp83 and Glu122 in helices B and C through consecutive photochemical processes to metarhodopsin II.     

Fourier transform infrared spectroscopy characterization of the lamellar and nonlamellar structures of free lipid A and Re lipopolysaccharides from Salmonella minnesota and Escherichia coli

The structural polymorphism of free lipid A and deep rough mutant lipopolysaccharide (LPS Re) from Salmonella minnesota strain R595 and Escherichia coli strain F515 was characterized by Fourier transform infrared (IR) spectroscopy. For this, the beta <--> alpha phase states and the three-dimensional supramolecular structures, the latter deduced from small-angle synchrotron radiation x-ray diffraction, were investigated at different water contents, Mg2+ concentrations, and temperatures. The analysis of the IR data for vibrations originating from the hydrophobic moiety shows that the beta <--> alpha acyl chain melting is strongly expressed only for the stretching and scissoring modes of the methylene groups. Vibrational groups originating from the interface region sense the acyl chain melting well (ester carbonyl bands) or only weakly (amide bands), and those resulting from the pure polar moiety not at all. From the x-ray data, the existence of lamellar (L), different cubic, and, for lipid A and LPS R595, also inverted hexagonal (HII) structures could be proven in the temperature range 20-80 degrees C with cubic <--> cubic and cubic <--> HII transitions for the Mg(2+)-free and L <--> HII transitions for the Mg(2+)-containing samples. These structural transitions can be characterized most readily by specific changes of the vibrational bands resulting from the interface region: the ester carbonyl and the amide bands. The magnitude of the changes corresponds to that of the structural rearrangement, i.e., is highest for the L <--> HII, lower for the cubic <--> HII, and lowest for the cubic <--> cubic transitions. The structural transitions are only marginally expressed for vibrational bands of the hydrophobic moiety. Similarly, the band contours of vibrations from the hydrophilic region are no indicators of the structural reorientations except for the carboxylate bands of LPS Re. Particularly the stretching vibrations of the phosphate groups are nearly completely invariant; the absolute values of their half bandwidths, however, differ significantly for lipid A and LPS Re, which seems to be of biological relevance. The ability of IR spectroscopy to detect supramolecular changes also beyond the measurability by x-ray diffraction, i.e., at water contents > 95 to 99.5%, is demonstrated.     

Binding of transducin and transducin-derived peptides to rhodopsin studies by attenuated total reflection-Fourier transform infrared difference spectroscopy

Fourier transform infrared difference spectroscopy combined with the attenuated total reflection technique allows the monitoring of the association of transducin with bovine photoreceptor membranes in the dark. Illumination causes infrared absorption changes linked to formation of the light-activated rhodopsin-transducin complex. In addition to the spectral changes normally associated with meta II formation, prominent absorption increases occur at 1735 cm-1, 1640 cm-1, 1550 cm-1, and 1517 cm-1. The D2O sensitivity of the broad carbonyl stretching band around 1735 cm-1 indicates that a carboxylic acid group becomes protonated upon formation of the activated complex. Reconstitution of rhodopsin into phosphatidylcholine vesicles has little influence on the spectral properties of the rhodopsin-transducin complex, whereas pH affects the intensity of the carbonyl stretching band. AC-terminal peptide comprising amino acids 340-350 of the transducin alpha-subunit reproduces the frequencies and isotope sensitivities of several of the transducin-induced bands between 1500 and 1800 cm-1, whereas an N-terminal peptide (aa 8-23) does not. Therefore, the transducin-induced absorption changes can be ascribed mainly to an interaction between the transducin-alpha C-terminus and rhodopsin. The 1735 cm-1 vibration is also seen in the complex with C-terminal peptides devoid of free carboxylic acid groups, indicating that the corresponding carbonyl group is located on rhodopsin.     

Mechanism of aldehyde oxidation catalyzed by horse liver alcohol dehydrogenase

The mechanism of oxidation of benzaldehyde to benzoic acid catalyzed by horse liver alcohol dehydrogenase (HLADH) has been investigated using the HLADH structure at 2.1 A resolution with NAD+ and pentafluorobenzyl alcohol in the active site [Ramaswamy et al. (1994) Biochemistry 33,5230-5237]. Constructs for molecular dynamics (MD) investigations with HLADH were obtained by a best-fit superimposition of benzaldehyde or its hydrate on the pentafluorobenzyl alcohol bound to the active site Zn(II)ion. Equilibrium bond lengths, angles, and dihedral parameters for Zn(II) bonding residues His67, Cys46, and Cys174 were obtained from small-molecule X-ray crystal structures and an ab initio-derived parameterization of zinc in HLADH [Ryde, U. (1995) Proteins: Struct., Funct., Genet. 21,40-56]. Dynamic simulations in CHARMM were carried out on the following three constructs to 100 ps: (MD1) enzyme with NAD+, benzaldehyde, and zinc-ligated HO-in the active site; (MD2) enzyme with NAD+ and hydrated benzaldehyde monoanion bound to zinc via the pro-R oxygen, with a proton residing on the pro-S oxygen; and (MD3) enzyme with NAD+ and hydrated benzaldehyde monoanion bound to zinc via the pro-S oxygen, with a proton residing on the pro-R oxygen. Analyses were done of 800 sample conformations taken in the last 40 ps of dynamics. Structures from MD1 and MD3 were used to define the initial spatial arrangements of reactive functionalities for semiempirical PM3 calculations. Using PM3, model systems were calculated of ground states and some transition states for aldehyde hydration, hydride transfer, and subsequent proton shuttling. With benzaldehyde and zinc-bound hydroxide ion in the active site, the oxygen of Zn(II)-OH resided at a distance of 2.8-5.5 A from the aldehyde carbonyl carbon during the dynamics simulation. This may be compared to the PM3 transition state for attack of the Zn(II)-OH oxygen on the benzaldehyde carbonyl carbon, which has an O...C distance of 1.877 A. HLADH catalysis of the aldehyde hydration would require very little motion aside from that in the ground state. Two simulations of benzaldehyde hydrate ligated to zinc (MD2 and MD3) both showed close approach of the aldehyde hydrate hydrogen to NAD+C4, varying from 2.3 to 3.3 A, seemingly favorable for the hydride transfer reaction. The MD2 configuration does not allow proton shuttling. On the other hand, when the pro-S oxygen is ligated to zinc (MD3), the proton on the pro-R oxygen averages 2.09 A from the hydroxyl oxygen of Ser48 such that initiation of shuttling of protons via Ser48 to the ribose 2'-hydroxyl oxygen to the 3'-hydroxyl oxygen to His51 nitrogen is sterically favorable. PM3 calculations suggest that this proton shuttle represents a stepwise reaction which occurs subsequent to hydride transfer. The PM3 transition state for hydride transfer based on the MD3 configuration has the transferring hydride 1.476 A from C4 of NAD+ and 1.433 A from the aldehyde alpha-carbon.     

Internal chemical bonding in solutions of simple phosphates and vanadates

The chemical bonding within structurally related phosphates and vanadates in aqueous solution is compared on the basis of vibrational frequencies obtained by classical Raman spectroscopy. To do this, an empirical relationship between the stretching frequency of P-O and P-OH or P-OR groups and bond strength is developed such that the sum of the PO bond strengths, expressed in terms of average number of electron pairs per bond, is as close as possible to 5.0 for phosphoric acid and various anions and esters thereof. The same approach is used for the corresponding vanadates. The internal bonding in phosphates involves a greater bond strength for P-OH and a smaller strength for P-O than might be expected from a simple consideration of canonical resonance forms. In vanadates, V-OH and V-O are closer to single and double bonds, respectively, than in phosphates, and the force constant for V = O is considerably smaller than for P = O, although that for V-OH and P-OH is similar. Since treating the P-O and V-O groups of simple tetrahedral phosphates and vanadates as independent diatomic oscillators provides good correlations between the respective frequencies and bond strengths, the same correlations are used to approximate the expected stretching frequencies for distorted phosphates and vanadates. The distortions considered are those that presumably characterize associative and dissociative transition states for a concerted transfer of the (PO3-) fragment of a dianionic phosphate group between donor and acceptor oxygens with similar character.(ABSTRACT TRUNCATED AT 250 WORDS)     

Anisotropic molecular rotational diffusion in 15N spin relaxation studies of protein mobility

The backbone dynamics of the uniformly 15N-labeled N-terminal 63-residue DNA-binding domain of the 434 repressor has been characterized by measurements of the individual 15N longitudinal relaxation times, T1, transverse relaxation times, T2, and heteronuclear 15N[1H]-NOEs at 1H resonance frequencies of 400 and 750 MHz. The dependence of an apparent spherical top correlation time, tauR, on the orientation of the N-H bond vector with respect to the principal axes of the global diffusion tensor of the protein was used to establish the fact that the degree of anisotropy of the global molecular tumbling amounts to 1.2, which is in good agreement with the values obtained from model calculations of the hydrodynamic properties. A model-free analysis showed that even this small anisotropy leads to the implication of artifactual slow internal motions for at least two residues when the assumption of isotropic global motion is used. Additional residues may actually undergo internal motions on the same time scale as the global rotational diffusion, in which case the model-free approach would, however, be inappropriate for quantifying the correlation times and order parameters. Overall, the experiments with 434(1-63) demonstrate that the assumption of isotropic rotational reorientation may result in artifacts of model-free interpretations of spin relaxation data even for proteins with small deviations from spherical shape.     

Theoretical study of the distal-side steric and electrostatic effects on the vibrational characteristics of the FeCO unit of the carbonylheme proteins and their models

The vibronic theory of activation and quantum chemical intermediate neglect of differential overlap (INDO) calculations are used to study the activation of carbon monoxide (change of the C-O bond index and force field constant) by the imidazole complex with heme in dependence on the distortion of the porphyrin ring, geometry of the CO coordination, iron-carbon and iron-imidazole distances, iron displacement out of the porphyrin plane, and presence of the charged groups in the heme environment. It is shown that the main contribution to the CO activation stems from the change in the sigma donation from the 5 sigma CO orbital to iron, and back-bonding from the iron to the 2 pi orbital of CO. It follows from the results that none of the studied distortions can explain, by itself, the wide variation of the C-O vibrational frequency in the experimentally studied model compounds and heme proteins. To study the dependence of the properties of the FeCO unit on the presence of charged groups in the heme environment, the latter are simulated by the homogeneous electric field and point charges of different magnitude and location. The results show that charged groups can strongly affect the strength of the C-O bond and its vibrational frequency. It is found that the charges located on the distal side of the heme plane can affect the Fe-C and C-O bond indexes (and, consequently, the Fe-C and C-O vibrational frequencies), both in the same and in opposite directions, depending on their position. The theoretical results allow us to understand the peculiarities of the effect of charged groups on the properties of the FeCO unit both in heme proteins and in their model compounds.     

Temperature-dependent ultraviolet resonance Raman spectroscopy of the premelting state of dA.dT DNA

Poly(dA).poly(dT) and DNA duplex with four or more adenine bases in a row exhibits a broad, solid-state structural premelting transition at about 35 degrees C. The low-temperature structure is correlated with the phenomena of "bent DNA." We have conducted temperature-dependent ultraviolet resonance Raman measurements of the structural transition using poly(dA).poly(dT) at physiological salt conditions, and are able to identify, between the high and low temperature limits, changes in the vibrational frequencies associated with the C4 carbonyl stretching mode in the thymine ring and the N6 scissors mode of the amine in the adenine ring of poly(dA).poly(dT). This work supports the model that the oligo-dA tracts' solid-state structural premelting transition is due to a set of cross-stand bifurcated hydrogen bonds between consecutive dA. dT pairs.     

Proton transfer in the mechanism of triosephosphate isomerase

Triosephosphate isomerase (TIM) catalyzes the reversible interconversion of dihydroxyacetone phosphate (DHAP) and glyceraldehyde 3-phosphate (GAP), with Glu-165 removing the pro-R proton from C1 of DHAP and neutral His-95 polarizing the carbonyl group of the substrate. During the TIM reaction, approximately 2% of the pro-R tritium from C1 of DHAP is conserved and appears at C2 of GAP [Nickbarg, E. B., and Knowles, J. R. (1988) Biochemistry 27, 5939]. In the "classical" mechanism, 98% of the pro-R tritium exchanges with solvent from Glu-165 at the intermediate state and the remaining 2% is transferred by Glu-165 to C2 of the same substrate molecule. This intramolecular transfer of tritium is therefore predicted to be independent of DHAP concentration. On the basis of NMR detection of a strong hydrogen bond between Glu-165 and the 1-OH of an analogue of the enediol intermediate [Harris, T. K., Abeygunawardana, C., and Mildvan, A. S. (1997) Biochemistry 36, 14661], we have suggested a "criss-cross" mechanism for TIM in which Glu-165 transfers a proton from C1 of DHAP to O2 of the enediol, and subsequently from O1 of the enediol to C2 of the product GAP. Since the pro-R proton is transferred to O2 instead of C2 in the criss-cross mechanism, no intramolecular transfer of label from substrate to product would be expected to occur. However, intermolecular transfer of label could occur if the label exchanges from O2 into a group on the protein and is transferred to GAP in subsequent turnovers. The extent of intermolecular tritium transfer in the criss-cross mechanism would be predicted to be dependent on DHAP concentration. The extent of tritium transfer was studied as a function of initial DHAP concentration using DHAP highly tritiated at the pro-R position. At 50% conversion to GAP, triphasic tritium transfer behavior was found. For phase 1, between 0.03 and 0.3 mM DHAP, a constant extent of tritium transfer of 1.19 +/- 0.03% occurred. For phase 2, between 0.3 and 1.0 mM DHAP, the extent of transfer progressively increased as a function of DHAP concentration to 2.17 +/- 0.15%. For phase 3, between 1.0 and 7.0 mM DHAP, the extent of transfer slightly decreased to 1.68 +/- 0.17%. In a direct test for intermolecular isotope transfer, doubly labeled [1(R)-D, 13C3]DHAP and 13C-depleted [1(R)-H,12C3]DHAP were synthesized, mixed in equal amounts, and incubated at 1 mM total DHAP with TIM, GAP dehydrogenase, NAD+, and arsenate until 50% conversion to 3-phosphoglycerate occurred. Electrospray ionization mass spectral analysis of the stable 3-phosphoglycerate product detected an extent of 1.4 +/- 0.4% of intramolecular D transfer from [13C3]DHAP to the 13C3 product, but no intermolecular transfer (相似文献   

Nonenzymatic and enzymatic hydrolysis of alkyl halides: a theoretical study of the SN2 reactions of acetate and hydroxide ions with alkyl chlorides

The SN2 displacements of chloride ion from CH3Cl, C2H5Cl, and C2H4Cl2 by acetate and hydroxide ions have been investigated, using ab initio molecular orbital theory at the HF/6-31+G(d), MP2/6-31+G(d), and MP4/6-31+G(d) levels of theory. The central barriers (calculated from the initial ion-molecule complex) of the reactions, the differences of the overall reaction energies, and the geometries of the transition states are compared. Essential stereochemical changes before and after the displacement reactions are described for selected cases. The gas phase reactions of hydroxide with CH3Cl, C2H5Cl, and C2H4Cl2 have no overall barrier, but there is a small overall barrier for the reactions of acetate with CH3Cl, C2H5Cl, and C2H4Cl2. A self-consistent reaction field solvation model was used to examine the SN2 reactions between methyl chloride and hydroxide ion and between 1,2-dichloroethane and acetate in solution. As expected, the reactions in polar solvent have a large barrier. However, the transition state structures determined by ab initio calculations change only slightly in the presence of a highly polar solvent as compared with the gas phase. We also calibrated the PM3 method for future study of an enzymatic SN2 displacement of halogen.