Solution-active structural alterations in liganded hemoglobins C (beta6 Glu --> Lys) and S (beta6 Glu --> Val).

Based upon existing crystallographic evidence, HbS, HbC, and HbA have essentially the same molecular structure. However, important areas of the molecule are not well defined crystallographically (e.g. the N-terminal nonhelical portion of the alpha and beta chains), and conformational constraints differ in solution and in the crystalline state. Over the years, our laboratory and others have provided evidence of conformational changes in HbS and, more recently, in HbC. We now present data based upon allosteric perturbation monitored by front-face fluorescence, ultraviolet resonance Raman spectroscopy, circular dichroism, and oxygen equilibrium studies that confirm and significantly expand previous findings suggesting solution-active structural differences in liganded forms of HbS and HbC distal to the site of mutation and involving the 2,3-diphosphoglycerate binding pocket. The liganded forms of these hemoglobins are of significant interest because HbC crystallizes in the erythrocyte in the oxy form, and oxy HbS exhibits increased mechanical precipitability and a high propensity to oxidize. Specific findings are as follows: 1) differences in the intrinsic fluorescence indicate that the Trp microenvironments are more hydrophobic for HbS > HbC > HbA, 2) ultraviolet resonance Raman spectroscopy detects alterations in Tyr hydrogen bonding, in Trp hydrophobicity at the alpha1beta2 interface (beta37), and in the A-helix (alpha14/beta15) of both chains, 3) displacement by inositol hexaphosphate of the Hb-bound 8-hydroxy-1,3,6-pyrenetrisulfonate (the fluorescent 2,3-diphosphoglycerate analog) follows the order HbA > HbS > HbC, and 4) oxygen equilibria measurements indicate a differential allosteric effect by inositol hexaphosphate for HbC approximately HbS > HbA.     

Novel side reaction accompanying cyclization of Glu(R1)‐Glu(R2) dipeptides via lactamization of the Glu(R1) residue

A series of linear peptides with the general formula H‐Glu(R1)‐Glu(R2)‐OH was subjected to cyclization under standard conditions. Formation of respective 2,5‐diketopiperazines was accompanied by transformation of the N‐terminal Glu(R1) to pyroglutamic acid residue. Even in the case R1 is an amino acid residue attached to the N‐terminal γ‐carboxyl group, lactamization leads to its elimination. The observed reaction has not been reported so far in the literature. Correspondingly, an alternative route to Glu(R1)‐Glu(R2)‐containing 2,5‐diketopiperazines was applied to improve the overall yields.     

X-ray structure of Glu 53 human lysozyme.

The three-dimensional structure of a modified human lysozyme (HL), Glu 53 HL, in which Asp 53 was replaced by Glu, has been determined at 1.77 A resolution by X-ray analysis. The backbone structure of Glu 53 HL is essentially the same as the structure of wild-type HL. The root mean square difference for the superposition of equivalent C alpha atoms is 0.141 A. Except for the Glu 53 residue, the structure of the active site region is largely conserved between Glu 53 HL and wild-type HL. However, the hydrogen bond network differs because of the small shift or rotation of side chain groups. The carboxyl group of Glu 53 points to the carboxyl group of Glu 35 with a distance of 4.7 A between the nearest carboxyl oxygen atoms. A water molecule links these carboxyl groups by a hydrogen bond bridge. The active site structure explains well the fact that the binding ability for substrates does not significantly differ between Glu 53 HL and wild-type HL. On the other hand, the positional and orientational change of the carboxyl group of the residue 53 caused by the mutation is considered to be responsible for the low catalytic activity (ca. 1%) of Glu 53 HL. The requirement of precise positioning for the carboxyl group suggests the possibility that the Glu 53 residue contributes more than a simple electrostatic stabilization of the intermediate in the catalysis reaction.     

Intermolecular association and molecular weight of aggregates of a monodisperse homohexapeptide,Nps-[Glu(OBzl)]6-NHEt,in solution

Light scattering from the solutions of Nps-[Glu(OBzl)]₆-NHEt in dioxane or ethylene dichloride has been measured at different concentrations, and a critical concentration of intermolecular association is found to exist, which is equal to the critical concentration of β-form formation. The Debye plot of light scattering leads to the molecular weight of aggregates at the critical concentration, which corresponds to an aggregation number 15 in dioxane and 53 in ethylene dichloride. In the latter solvent the aggregates further associate into a larger aggregate consisting of 330 molecules when the concentration is increased beyond the critical concentration. The content of β-form, which is a measure of number of hydrogen bonds, is derived from the ir data previously obtained. The results on the modes of intermolecular association and hydrogen bonding lead to possible structures of aggregates formed by both hydrogen bonds and other nonbonding side-chain interactions.     

Manganese(II) tri-tert-butoxysilanethiolate complexes with imidazole-based coligands: a neutral complex with four independent ligands and MNOS2 core (M=Mn) related to the liver alcohol dehydrogenase catalytic center (M=Zn)

The reaction of [Mn{SSi(OBu(t))3}2(MeOH)4] with imidazole and its two methyl substituted derivatives leads to different types of heteroleptic manganese(II) thiolate complexes. Reaction with 1-methylimidazole gives the silanethiolate devoid of methanol but with two nitrogen ligands and thus central MnN(2)S(2) core. The reaction with imidazole leads to the methanol solvated complex with only one nitrogen ligand but manganese coordination sphere enlarged to MnO(2)NS(2) due to an O,S-chelation by tri-tert-butoxysilanethiolate ligand. Molecules of this compound interact through a set of N-H...(Me)O-H...S hydrogen bonds with methanol hydroxyl group being simultaneously acceptor and donor. With 2-methylimidazole the product is an assembly of two different neutral complexes joined again by hydrogen bonds, however, this time of N-H...S type. One of these complexes has the previously mentioned MnO(2)NS(2) core. The second neutral complex exhibits four donor atoms (MnNOS(2)core) derived from four independent ligands, i.e., two silanethiolate rests, one N-heterocyclic base and one alcohol. This structure presents similarities with a zinc-based alcohol dehydrogenase active site that have never been obtained before, including with other metals (Zn, Co). It may, therefore, be considered the first neutral structural model of liver alcohol dehydrogenase (LADH).     

Charge-charge interactions are key determinants of the pK values of ionizable groups in ribonuclease Sa (pI=3.5) and a basic variant (pI=10.2)

The pK values of the titratable groups in ribonuclease Sa (RNase Sa) (pI=3.5), and a charge-reversed variant with five carboxyl to lysine substitutions, 5K RNase Sa (pI=10.2), have been determined by NMR at 20 degrees C in 0.1M NaCl. In RNase Sa, 18 pK values and in 5K, 11 pK values were measured. The carboxyl group of Asp33, which is buried and forms three intramolecular hydrogen bonds in RNase Sa, has the lowest pK (2.4), whereas Asp79, which is also buried but does not form hydrogen bonds, has the most elevated pK (7.4). These results highlight the importance of desolvation and charge-dipole interactions in perturbing pK values of buried groups. Alkaline titration revealed that the terminal amine of RNase Sa and all eight tyrosine residues have significantly increased pK values relative to model compounds.A primary objective in this study was to investigate the influence of charge-charge interactions on the pK values by comparing results from RNase Sa with those from the 5K variant. The solution structures of the two proteins are very similar as revealed by NMR and other spectroscopic data, with only small changes at the N terminus and in the alpha-helix. Consequently, the ionizable groups will have similar environments in the two variants and desolvation and charge-dipole interactions will have comparable effects on the pK values of both. Their pK differences, therefore, are expected to be chiefly due to the different charge-charge interactions. As anticipated from its higher net charge, all measured pK values in 5K RNase are lowered relative to wild-type RNase Sa, with the largest decrease being 2.2 pH units for Glu14. The pK differences (pK(Sa)-pK(5K)) calculated using a simple model based on Coulomb's Law and a dielectric constant of 45 agree well with the experimental values. This demonstrates that the pK differences between wild-type and 5K RNase Sa are mainly due to changes in the electrostatic interactions between the ionizable groups. pK values calculated using Coulomb's Law also showed a good correlation (R=0.83) with experimental values. The more complex model based on a finite-difference solution to the Poisson-Boltzmann equation, which considers desolvation and charge-dipole interactions in addition to charge-charge interactions, was also used to calculate pK values. Surprisingly, these values are more poorly correlated (R=0.65) with the values from experiment. Taken together, the results are evidence that charge-charge interactions are the chief perturbant of the pK values of ionizable groups on the protein surface, which is where the majority of the ionizable groups are positioned in proteins.     

Active site residues of human beta-glucuronidase. Evidence for Glu(540) as the nucleophile and Glu(451) as the acid-base residue.

Human beta-glucuronidase (hGUSB) is a member of family 2 glycosylhydrolases that cleaves beta-D-glucuronic acid residues from the nonreducing termini of glycosaminoglycans. Amino acid sequence and structural homology of hGUSB and Escherichia coli beta-galactosidase active sites led us to propose that residues Glu(451), Glu(540), and Tyr(504) in hGUSB are involved in catalysis, Glu(451) being the acid-base residue and Glu(540) the nucleophile. To test this hypothesis, we introduced mutations in these residues and determined their effects on enzymes expressed in COS cells and GUSB-deficient fibroblasts. The extremely low activity in cells expressing Glu(451), Glu(540), and Tyr(504) hGUSBs supported their roles in catalysis. For kinetic analysis, wild type and mutant enzymes were produced in baculovirus and purified to homogeneity by affinity chromatography. The k(cat)/K(m) values (mM(-1).s(-1)) of the E540A, E451A, and Y504A enzymes were 34,000-, 9100-, and 830-fold lower than that of wild type hGUSB, respectively. High concentrations of azide stimulated the activity of the E451A mutant enzyme, supporting the role of Glu(451) as the acid-base catalyst. We conclude that, like their homologues in E. coli beta-galactosidase, Glu(540) is the nucleophilic residue, Glu(451) the acid-base catalyst, and Tyr(504) is also important for catalysis, although its role is unclear. All three residues are located in the active site cavity previously determined by structural analysis of hGUSB.     

A tRNA(Glu) that uncouples protein and tetrapyrrole biosynthesis

Glu-tRNA is either bound to elongation factor Tu to enter protein synthesis or is reduced by glutamyl-tRNA reductase (GluTR) in the first step of tetrapyrrole biosynthesis in most bacteria, archaea and in chloroplasts. Acidithiobacillus ferrooxidans, a bacterium that synthesizes a vast amount of heme, contains three genes encoding tRNA(Glu). All tRNA(Glu) species are substrates in vitro of GluRS1 from A. ferrooxidans.Glu-tRNA(3)(Glu), that fulfills the requirements for protein synthesis, is not substrate of GluTR. Therefore, aminoacylation of tRNA(3)(Glu) might contribute to ensure protein synthesis upon high heme demand by an uncoupling of protein and heme biosynthesis.     

Synthesis and some pharmacological properties of [Glu(OMe)4]oxytocin and [Mpr1, Glu(OMe)4]oxytocin.

[Glu(OMe)4]oxytocin (XVI) and [Mpr1, Glu(OMe)4]oxytocin (XVII) bearing a methyl ester group in place of the carboxamide group in position 4 of oxytocin were synthesized by (3 + 6) segment condensation using the S-trityl group for the protection of the cysteine side chains. Analogue XVI exhibited 10.5 U/mg in vitro uterotonic, and 42 U/mg avian vasodepressor, activity, and analogue XVII 21.4 U/mg and 82 U/mg of the respective activities. Both compounds showed no response in the rat pressor assay.     

Syntheses and characterization of aqua-bridged dimetallic complexes,M2(mu-H2O)(mu-OAc)2(Im)4(OAc)2(M=Mg2+, Mn2+, and Ni2+). Structural models for the active sites of dimetallic hydrolases

Four novel aqua-bridged dinuclear complexes with a formula M2(mu-H2O)(mu-OAc)2(Im)4(OAc)2(Im)4(OAc)2 (where Im=imidazole, M=Mg2+ 1, Mn2+ 2, Ni2+ 3 and Co2+ 4) have been synthesized and characterized. Complexes 1, 2 and 3 have been characterized by X-ray crystallography. Two M2+ ions are bridged by an aqua molecule and two carboxylate anion with M...M=3.635-3.777 A, M-OH(2)=2.109-2.246 A and M-OH(2)-M=114.4-119.0 degrees, respectively. Each complex is further stabilized by two intramolecular hydrogen bonds between the hydrogens of the bridging aqua and the oxygens of the terminal monodentate acetates with a distance of O...O=2.6 A. The terminal monodentate acetates display "reversed" C-O distances, namely the C-O(free) distances are actually longer than the C-O(coordinating) distances. This abnormal geometry of a monodentate carboxylate would be caused by the strong "pulling effect" on the terminal carboxylates by intra- and intermolecular hydrogen bonds. The O-H stretching vibration of the bridging water was identified at ca. 2328 cm(-1) in IR spectra based on the deuterium isotope shift. The solid state 13C and 15N NMR spectra of 1 displayed two sets of peaks for acetate and Im ligands, respectively, consistent with the presence of two types of coordination modes of acetate and the two symmetrically non-equivalent Im as revealed by X-ray structure. 15N chemical shift of NH in Im ligands underwent about 6 ppm downfield shift due to its involvement in an intermolecular hydrogen bond.     

Stabilization of apoflavodoxin by replacing hydrogen-bonded charged Asp or Glu residues by the neutral isosteric Asn or Gln

Knowledge of protein stability principles provides a means to increase protein stability in a rational way. Here we explore the feasibility of stabilizing proteins by replacing solvent-exposed hydrogen-bonded charged Asp or Glu residues by the neutral isosteric Asn or GLN: The rationale behind this is a previous observation that, in some cases, neutral hydrogen bonds may be more stable that charged ones. We identified, in the apoflavodoxin from Anabaena PCC 7119, three surface-exposed aspartate or glutamate residues involved in hydrogen bonding with a single partner and we mutated them to asparagine or glutamine, respectively. The effect of the mutations on apoflavodoxin stability was measured by both urea and temperature denaturation. We observed that the three mutant proteins are more stable than wild-type (on average 0.43 kcal/mol from urea denaturation and 2.8 degrees C from a two-state analysis of fluorescence thermal unfolding data). At high ionic strength, where potential electrostatic repulsions in the acidic apoflavodoxin should be masked, the three mutants are similarly more stable (on average 0.46 kcal/mol). To rule out further that the stabilization observed is due to removal of electrostatic repulsions in apoflavodoxin upon mutation, we analysed three control mutants and showed that, when the charged residue mutated to a neutral one is not hydrogen bonded, there is no general stabilizing effect. Replacing hydrogen-bonded charged Asp or Glu residues by Asn or Gln, respectively, could be a straightforward strategy to increase protein stability.     

Serine and threonine residues bend alpha-helices in the chi(1) = g(-) conformation

The relationship between the Ser, Thr, and Cys side-chain conformation (chi(1) = g(-), t, g(+)) and the main-chain conformation (phi and psi angles) has been studied in a selection of protein structures that contain alpha-helices. The statistical results show that the g(-) conformation of both Ser and Thr residues decreases their phi angles and increases their psi angles relative to Ala, used as a control. The additional hydrogen bond formed between the O(gamma) atom of Ser and Thr and the i-3 or i-4 peptide carbonyl oxygen induces or stabilizes a bending angle in the helix 3-4 degrees larger than for Ala. This is of particular significance for membrane proteins. Incorporation of this small bending angle in the transmembrane alpha-helix at one side of the cell membrane results in a significant displacement of the residues located at the other side of the membrane. We hypothesize that local alterations of the rotamer configurations of these Ser and Thr residues may result in significant conformational changes across transmembrane helices, and thus participate in the molecular mechanisms underlying transmembrane signaling. This finding has provided the structural basis to understand the experimentally observed influence of Ser residues on the conformational equilibrium between inactive and active states of the receptor, in the neurotransmitter subfamily of G protein-coupled receptors.     

Antigen-Specific T-cell factors in the immune response to poly(Tyr,Glu)-poly(Pro)-poly(Lys)

The production by T cells of an antigen-specific factor capable of replacing the T-cell function in specific antibody formation was used as a tool for studying the cellular aspects of the genetic control of immune responses. The ability of different T-cell populations to produce a cooperative signal and the ability of B-cell populations to react to this signal were studied in different mouse strains. The antigen used was the synthetic polypeptide poly(LTyr,LGlu)-poly-(LPro) —poly(lXys), (T,G)-Pro -L, the response to which was found not to beH-2-linked. It was found that the SWR strain of mice, a low responder to (T,G)-Pro -L, is not capable of producing a T-cell factor specific to this antigen, but its B cells react normally to an active factor produced in a high responder strain. In the DBA/1 strain, also a low responder to (T,G)-Pro -L, the bone marrow cells are not able to cooperate with an active T-cell factor to produce anti-(T,G)-Pro —L-specific antibodies, while their T cells do produce a (T,G)-Pro -L-specific factor. The SWR (low responder) B cells can be triggered by DBA/1 (low responder) T cells factor specific to (T,G)-Pro —L to produce an antibody response to this immunogen. These results suggest that the immune response to (T,G)-Pro -L is controlled by two genes which are expressed in different lymphocyte populations.     

Effect of uridine dethiolation in the anticodon triplet of tRNA(Glu) on its association with tRNA(Phe)

The effect of U(34) dethiolation on the anticodon-anticodon association between E. coli tRNA(Glu) and yeast tRNA(Phe) has been studied by the temperature jump relaxation technique. An important destabilization upon replacement of the thioketo group of s2U(34) by a keto group, was revealed by a lowering of melting temperature of about 20 degrees C. The measured kinetic parameters indicated that this destabilization effect was originated in an increase of dissociation and a decrease of association rate constants by a factor of 4 to 5. Modifications in both stacking interactions and flexibility in the anticodon loop would be responsible for this effect.     

Glu(191) and Asp(195) in rat mitochondrial processing peptidase beta subunit are involved in effective cleavage of precursor protein through interaction with the proximal arginine

Mitochondrial processing peptidase (MPP), consisting of alpha and beta subunits, recognizes a large variety of N-terminal extension peptides of mitochondrial precursor proteins, and generally cleaves a single site of the peptide including arginine at the -2 position (P(2)). We obtained evidence that Glu(191) and Asp(195) of rat beta subunit interact with P(2) arginine of precursor protein through ionic and hydrogen bonds, respectively, using recombinant MPP. Mutation to alanines at Glu(191) and Asp(195) reduced processing activity toward precursors with P(2) arginine, but resulted in no loss of activity toward P(2) alanine precursors. Charge-complementary mutation demonstrated that MPP variants with beta Arg(191) exhibited compensatory processing activity for the precursor with acidic residue at the P(2) position. Thus, Glu(191) and Asp(195) are substrate-binding sites required for cleavage of extension peptides through interaction with P(2) arginine.     

Quantitation of gluconeogenesis by (2)H nuclear magnetic resonance analysis of plasma glucose following ingestion of (2)H(2)O

We present a simple (2)H NMR assay of the fractional contribution of gluconeogenesis to hepatic glucose output following ingestion of (2)H(2)O. The assay is based on the measurement of relative deuterium enrichment in hydrogens 2 and 3 of plasma glucose. Plasma glucose was enzymatically converted to gluconate, which displays fully resolved deuterium 2 and 3 resonances in its (2)H NMR spectrum at 14.1 T. The signal intensity of deuterium 3 relative to deuterium 2 in the gluconate derivative as quantitated by (2)H NMR was shown to provide a precise and accurate measurement of glucose enrichment in hydrogen 3 relative to hydrogen 2. This measurement was used to estimate the fractional contribution of gluconeogenesis to hepatic glucose output for two groups of rats; one group was fasted for 7 h and the other was fasted for 29 h. Rats were administered (2)H(2)O to enrich total body water to 5% over the last 4-5 h of each fasting period. For the 7-h fasted group, the hydrogen 3/hydrogen 2 enrichment ratio of plasma glucose was 0.32 +/- 0.09 (n = 7). This indicates that gluconeogenesis contributed 32 +/- 9% of total hepatic glucose output with glycogenolysis contributing the remainder. For the 29-h fasted group, the hydrogen 3/hydrogen 2 enrichment ratio of plasma glucose was 0.81 +/- 0.10 (n = 6), indicating that gluconeogenesis supplied the bulk of hepatic glucose output (81 +/- 10%).     

The role of Glu181 in the photoactivation of rhodopsin

The visual pigment rhodopsin is a prototypical seven transmembrane helical G protein-coupled receptor. Photoisomerization of its protonated Schiff base (PSB) retinylidene chromophore initiates a progression of metastable intermediates. We studied the structural dynamics of receptor activation by FTIR spectroscopy of recombinant pigments. Formation of the active state, Meta II, is characterized by neutralization of the PSB and its counterion Glu113. We focused on testing the hypothesis of a PSB counterion switch from Glu113 to Glu181 during the transition of rhodopsin to the still inactive Meta I photointermediate. Our results, especially from studies of the E181Q mutant, support the view that both Glu113 and Glu181 are deprotonated, forming a complex counterion to the PSB in rhodopsin, and that the function of the primary counterion shifts from Glu113 to Glu181 during the transition to Meta I. The Meta I conformation in the E181Q mutant is less constrained compared with that of wild-type Meta I. In particular, the hydrogen bonded network linking transmembrane helices 1, 2, and 7, adopts a conformation that is already Meta II-like, while other parts of the receptor appear to be in a Meta I-like conformation similar to wild-type. We conclude that Glu181 is responsible, in part, for controlling the extraordinary high pK(a) of the chromophore PSB in the dark state, which very likely decreases upon transition to Meta I in a stepwise weakening of the interaction between PSB and its complex counterion during the course of receptor activation. A model for the specific role in coupling chromophore isomerization to protein conformational changes concomitant with receptor activation is presented.     

Photoinduced reduction of water by tin(IV) and ruthenium(II) porphyrins

In the paper are presented new photoredox systems for the reduction of water in which water- soluble Sn(IV) and Ru(II) porphyrins have been used as photosensitizers It has been found that during the photolysis of water Sn(IV) porphyrin underwent photoreduction whereas Ru(II) porphyrin underwent photooxidation. The successive photo- products of Sn(IV) porphyrin in the reaction from EDTA were, first, Sn(IV) chlorin and, second, Sn(IV) bacteriochlorin. In the experiments on the photo- generation of hydrogen, a correlation between the rates of hydrogen evolution and the reduction potentials of the electron carriers has been observed. The highest rate of hydrogen generation by means of Sn(IV) and Ru(II) porphyrins has been found for those electron carriers whose values of reduction potentials were tau; 0.55 and tau; 0.45 V. In the case of Ru(II) porphyrin, the rate of hydrogen evolution additionally depended on the molecular structure of the electron carrier. It has been found that during the water photolysis, viologens show a tendency to form their respective complexes with Ru(II) porphyrin, but only when they occur in a one-electron reduced form in the solution.     

Metabolism of S-(2-chloro-1,1,2-trifluoroethyl)-L-cysteine to hydrogen sulfide and the role of hydrogen sulfide in S-(2-chloro-1,1,2-trifluoroethyl)-L-cysteine-induced mitochondrial toxicity

The nephrotoxic cysteine S-conjugate S-(2-chloro-1,1,2-trifluoroethyl)-L-cysteine (CTFC) is metabolized by kidney homogenates and subcellular fractions to pyruvate and a reactive thiol, which is cytotoxic and partially decomposes to yield hydrogen sulfide and thiosulfate. Although hydrogen sulfide is a potent mitochondrial poison, the mitochondrial toxicity of CTFC is not attributable to hydrogen sulfide formation, as shown by different sites of inhibition of mitochondrial respiration by CTFC and hydrogen sulfide. The efficient mitochondrial oxidation of hydrogen sulfide apparently serves to protect mitochondria against the toxic effects of hydrogen sulfide generated from CTFC.     

Hydrogen sequential dissociative chemisorption on Nin(n = 2~9,13) clusters: comparison with Pt and Pd

Hydrogen dissociative chemisorption and desorption on small lowest energy Ni_n clusters up to n = 13 as a function of H coverage was studied using density functional theory. H adsorption on the clusters was found to be preferentially at edge sites followed by 3-fold hollow sites and on-top sites. The minimum energy path calculations suggest that H₂ dissociative chemisorption is both thermodynamically and kinetically favorable and the H atoms on the clusters are mobile. Calculations on the sequential H₂ dissociative chemisorption on the clusters indicate that the edge sites are populated first and subsequently several on-top sites and hollow sites are also occupied upon full cluster saturation. In all cases, the average hydrogen capacity on Ni_n clusters is similar to that of Pd_n clusters but considerably smaller than that of Pt_n clusters. Comparison of hydrogen dissociative chemisorption energies and H desorption energies at full H-coverage among the Ni family clusters was made.