Pre-treatment microbial Prevotella-to-Bacteroides ratio, determines body fat loss success during a 6-month randomized controlled diet intervention

On the basis of the abundance of specific bacterial genera, the human gut microbiota can be divided into two relatively stable groups that might have a role in personalized nutrition. We studied these simplified enterotypes as prognostic markers for successful body fat loss on two different diets. A total of 62 participants with increased waist circumference were randomly assigned to receive an ad libitum New Nordic Diet (NND) high in fiber/whole grain or an Average Danish Diet for 26 weeks. Participants were grouped into two discrete enterotypes by their relative abundance of Prevotella spp. divided by Bacteroides spp. (P/B ratio) obtained by quantitative PCR analysis. Modifications of dietary effects of pre-treatment P/B group were examined by linear mixed models. Among individuals with high P/B the NND resulted in a 3.15 kg (95% confidence interval (CI): 1.55; 4.76, P<0.001) larger body fat loss compared with ADD, whereas no differences was observed among individuals with low P/B (0.88 kg (95% CI: −0.61; 2.37, P=0.25)). Consequently, a 2.27 kg (95% CI: 0.09; 4.45, P=0.041) difference in responsiveness to the diets were found between the two groups. In summary, subjects with high P/B ratio appeared more susceptible to lose body fat on diets high in fiber and whole grain than subjects with a low P/B ratio.

Weight loss maintenance in overweight subjects on ad libitum diets with high or low protein content and glycemic index: the DIOGENES trial 12-month results

BACKGROUND

A high dietary protein (P) content and low glycemic index (LGI) have been suggested to be beneficial for weight management, but long-term studies are scarce.

OBJECTIVE

The DIOGENES randomized clinical trial investigated the effect of P and GI on weight loss maintenance in overweight or obese adults in eight centers across Europe. This study reports the 1-year results in two of the centers that extended the intervention to 1 year.

METHOD

After an 8-week low-calorie diet (LCD), 256 adults (body mass index >27 kg m(-)(2)) were randomized to five ad libitum diets for 12 months: high P/LGI (HP/LGI), HP/high GI (HP/HGI), low P/LGI (LP/LGI), LP/HGI and a control diet. During the first 6 months, foods were provided for free through a shop system and during the whole 12-month period, subjects received guidance by a dietician. Primary outcome variable was the change in body weight over the 12-month intervention period.

RESULTS

During the LCD period, subjects lost 11.2 (10.8, 12.0) kg (mean (95% confidence interval (CI))). Average weight regain over the 12-month intervention period was 3.9 (95% CI 3.0-4.8) kg. Subjects on the HP diets regained less weight than subjects on the LP diets. The difference in weight regain after 1 year was 2.0 (0.4, 3.6) kg (P=0.017) (completers analysis, N=139) or 2.8 (1.4, 4.1) kg (P<0.001) (intention-to-treat analysis, N=256). No consistent effect of GI on weight regain was found. There were no clinically relevant differences in changes in cardiometabolic risk factors among diet groups.

CONCLUSION

A higher protein content of an ad libitum diet improves weight loss maintenance in overweight and obese adults over 12 months.

Fatty acid composition of adipose tissue triglycerides after weight loss and weight maintenance: the DIOGENES study

Fatty acid composition of adipose tissue changes with weight loss. Palmitoleic acid as a possible marker of endogenous lipogenesis or its functions as a lipokine are under debate. Objective was to assess the predictive role of adipose triglycerides fatty acids in weight maintenance in participants of the DIOGENES dietary intervention study. After an 8-week low calorie diet (LCD) subjects with > 8 % weight loss were randomized to 5 ad libitum weight maintenance diets for 6 months: low protein (P)/low glycemic index (GI) (LP/LGI), low P/high GI (LP/HGI), high P/low GI (HP/LGI), high P/high GI (HP/HGI), and a control diet. Fatty acid composition in adipose tissue triglycerides was determined by gas chromatography in 195 subjects before the LCD (baseline), after LCD and weight maintenance. Weight change after the maintenance phase was positively correlated with baseline adipose palmitoleic (16:1n-7), myristoleic (14:1n-5) and trans-palmitoleic acid (16:1n-7t). Negative correlation was found with baseline oleic acid (18:1n-9). Lower baseline monounsaturated fatty acids (14:1n-5, 16:1n-7 and trans 16:1n-7) in adipose tissue triglycerides predict better weight maintenance. Lower oleic acid predicts lower weight decrease. These findings suggest a specific role of monounsaturated fatty acids in weight management and as weight change predictors.

Predictors of weight loss maintenance and attrition during a 6-month dietary intervention period: results from the DiOGenes study

There is a need to develop tools to predict individual weight loss maintenance and attrition prognosis. We aimed to identify predictors of weight loss maintenance outcome and attrition in subjects from eight European countries in the DiOGenes project. A total of 932 overweight/obese subjects (body mass index: 27-42 kg m(-2) ) were enrolled in an 8-week low-calorie diet (LCD). The 776 subjects (83%) who achieved at least 8% reduction in their initial body weight were randomized into five dietary arms varying in protein content and glycemic index for a 6-month weight maintenance period. Baseline characteristics, weight loss at weeks 1, 3 and 8 of LCD were assessed as predictors of weight loss maintenance and attrition using multivariate regression and correlation models. The multivariate model showed that the 6-month weight loss maintenance was predicted by: 7.889 - 0.343 × weight loss at week 3 + 1.505 × weight loss at week 8 + 2.422 × gender (0 = male and 1 = female gender) (R(2)  = 51%, P = 0.0001). A greater weight loss at week 8 was associated with a lower attrition during the subsequent 6-month dietary intervention period (OR = 0.92, 95% CI: 0.88-0.97, P = 0.001). Furthermore, the men showed an increased likelihood for attrition during the dietary intervention period (OR = 1.54, 95% CI: 1.07-2.20, P = 0.02). A greater weight loss during 8 weeks of LCD and female gender predict better 6-month weight maintenance of weight loss, whereas the baseline characteristics did not predict outcome. Attrition could be strongly predicted by gender and weight loss during LCD.

Effect of trans fatty acid intake on abdominal and liver fat deposition and blood lipids: a randomized trial in overweight postmenopausal women

Background:

Intake of industrially produced trans fatty acids (TFAs) is, according to observational studies, associated with an increased risk of cardiovascular disease, but the causal mechanisms have not been fully elucidated. Besides inducing dyslipidemia, TFA intake is suspected to promote abdominal and liver fat deposition.

Objective:

We examined the effect of a high intake of TFA as part of an isocaloric diet on whole-body, abdominal and hepatic fat deposition, and blood lipids in postmenopausal women.

Methods:

In a 16-week double-blind parallel intervention study, 52 healthy overweight postmenopausal women were randomized to receive either partially hydrogenated soybean oil providing 15.7 g day⁻¹ of TFA or a control oil with mainly oleic and palmitic acid. Before and after the intervention, body composition was assessed by dual-energy X-ray absorptiometry, abdominal fat by magnetic resonance (MR) imaging, and liver fat by ¹H MR spectroscopy.

Results:

Compared with the control fat, TFA intake decreased plasma high-density lipoprotein (HDL)-cholesterol by 10%, increased low-density lipoprotein (LDL)-cholesterol by 18% and resulted in an increased LDL/HDL-cholesterol ratio (baseline adjusted mean (95% CI) difference between diet groups 0.41 (0.22; 0.60); P<0.001). TFA tended to increase the body fat (0.46 (−0.20; 1.17) kg; P=0.16) and waist circumference (1.1 (−0.1; 2.4) cm; P=0.08) more than the control fat, whereas neither abdominal nor liver fat deposition was affected by TFA.

Conclusion:

The adverse effect of dietary TFA on cardiovascular disease risk involves induction of dyslipidemia, and perhaps body fat, whereas weight gain-independent accumulation of ectopic fat could not be identified as a contributory factor during short-term intake.

Dietary strategy to manipulate ad libitum macronutrient intake, and glycaemic index, across eight European countries in the Diogenes Study

The aim of this study was to describe the development and implementation of a multifaceted, low-fat, weight-loss strategy for a Pan-European randomized controlled dietary intervention study, Diogenes. There were 891 families with at least one overweight/obese parent who underwent screening. Eligible, overweight/obese adults followed an 8-week weight-loss phase with a fixed low-energy diet (800 kcal). On attaining weight loss of > or = 8%, families were randomized to a 6- or 12-month low-fat (25-30%E) diet either based on national dietary guidelines or one of four interventions: low protein (LP)/low glycaemic index (LGI), LP/high GI (HGI), high protein (HP)/LGI and HP/HGI. The impact of each diet in preventing weight (re)gain was tested. A points-based system was used to manipulate dietary protein and carbohydrate. Manipulating carbohydrate composition involved substituting foods with a relatively high or low GI. A questionnaire was designed and completed by study investigators, providing feedback on the dietary intervention methods used to inform future interventions. The points system allowed macronutrient manipulations without compromising dietary flexibility or enforcing energy restrictions. Reported centre/participant differences in the ease of implementing the intervention may reflect dietary diversity and personal preferences for specific weight-management strategies. The points system provides a useful starting point for designing improved experimental paradigms for the manipulation of dietary intake in future trials.

The Diet, Obesity and Genes (Diogenes) Dietary Study in eight European countries - a comprehensive design for long-term intervention

Diogenes is a Pan-European, randomized, controlled dietary intervention study investigating the effects of dietary protein and glycaemic index on weight (re)gain, metabolic and cardiovascular risk factors in obese and overweight families in eight European centres. The article is methodological in character, and the presentation of 'results' will be limited to baseline characteristics of the study populations included. A total of 891 families with at least one overweight/obese parent underwent screening. The parents started an initial 8-week low-calorie diet and families with minimum one parent attaining a weight loss of > or = 8%, were randomized to one of five energy ad libitum, low-fat (25-30 E%) diets for 6 or 12 months: low protein/low glycaemic index, low protein/high glycaemic index, high protein/low glycaemic index, high protein/high glycaemic index or control (national dietary guidelines). At two centres the families were provided dietary instruction plus free foods for 6 months followed by 6-month dietary instruction only. At the remaining six centres the families received dietary instruction only for 6 months. The median weight loss during the low-calorie diet was 10.3 kg (inter-quartile range: 8.7-12.8 kg, n = 775). A total of 773 adults and 784 children were randomized to the 6-month weight (re)gain prevention phase. Despite major cultural and dietary regional differences in Europe, interventions addressing effects of dietary factors are feasible with a reasonable attrition.

Visceral fat loss induced by a low-calorie diet: a direct comparison between women and men

AIM

No studies have assessed if changes in visceral adipose tissue (VAT) during weight loss differ between women and men with comparable amounts of VAT at baseline. The aim of this study was to assess if changes in VAT induced by a low-calorie diet (LCD) differ between women and men.

METHODS

In this post hoc analysis of an existing database, abdominal adipose tissue was evaluated before and after an 8-week LCD (800-1000 kcal/day) by a single-slice magnetic resonance scan performed at the abdominal level. Body composition was measured by dual X-ray energy absorptiometry.

RESULTS

Data from 111 obese subjects (85 women and 26 men) were available. Relative changes in VAT were found to be more pronounced in men [mean (95% CI): -32.6% (-38.7 to -26.6)] than in women [-21.9% (-25.0 to -18.8)] (p = 0.003) after correction for relative changes in fat mass (FM). When analysing only the data from a subgroup of 23 women and 23 men who were matched for similar visceral to abdominal subcutaneous fat ratio at baseline, these differences could not be observed anymore: the change in VAT was -33.7% (-38.7 to -28.7) in men and -26.8% (-31.8 to -21.8) in women (p = 0.07).

CONCLUSIONS

This study suggests that relative changes in VAT during a LCD may be greater in men than in women even after taking relative changes in FM into account. However, these differences disappear when properly matching the subjects for baseline amounts of VAT.

A critical review of the cannabinoid receptor as a drug target for obesity management

The discovery of cannabinoids, with the well-known stimulatory effect of Cannabis sativa on appetite, has offered a new drug target for obesity treatment. Cannabinoids act on two different receptors: CB1 receptors which are sited in the brain and many peripheral tissues, and CB2 receptors which are primarily found in immune system cells. Cannabinoid receptor antagonists act centrally by blocking CB1 receptors, thereby reducing food intake. Moreover, they probably also act peripherally by increasing thermogenesis and therefore energy expenditure, as has been suggested by animal experiments. Despite these promising mechanisms of action, recent clinical studies examining the effect of the two CB1 receptor antagonists rimonabant and taranabant showed that the attained weight loss did not exceed that attained with other currently approved anti-obesity medications. Moreover, potentially severe psychiatric adverse effects limit their clinical use. As several new CB1 receptor antagonists are presently undergoing development, it remains to be elucidated to what extent they differ in terms of efficacy and safety. This review primarily discusses how close cannabinoid receptor antagonists are to the ideal anti-obesity drug, with respect to their mechanisms of action, clinical effectiveness and safety.

Single-transverse-spin asymmetries of identified charged hadrons in polarized pp collisions at sqrt[s]=62.4 GeV

The first measurements of xF-dependent single-spin asymmetries of identified charged hadrons, pi+/-, K+/-, and protons, from transversely polarized proton-proton collisions at 62.4 GeV at RHIC are presented. Large asymmetries are seen in the pion and kaon channels. The asymmetries in inclusive pi+ production, AN(pi+), increase with xF from 0 to approximately 0.25 and AN(pi-) decrease from 0 to approximately -0.4. Observed asymmetries for K- unexpectedly show positive values similar to those for K+, increasing with xF, whereas proton asymmetries are consistent with zero over the measured kinematic range. Comparisons of the data with predictions of QCD-based models are presented.

Production of mesons and baryons at high rapidity and high p(T) in proton-proton collisions at square root[s] = 200 GeV

We present particle spectra for charged hadrons pi(+/-), K(+/-), p, and p[over] from pp collisions at square root[s] = 200 GeV measured for the first time at forward rapidities (2.95 and 3.3). The kinematics of these measurements are skewed in a way that probes the small momentum fraction in one of the protons and large fractions in the other. Large proton to pion ratios are observed at values of transverse momentum that extend up to 4 GeV/c, where protons have momenta up to 35 GeV. Next-to-leading order perturbative QCD calculations describe the production of pions and kaons well at these rapidities, but fail to account for the large proton yields and small p[over]/p ratios.

Charged meson rapidity distributions in central Au+Au collisions at square root(sNN) = 200 GeV

We have measured rapidity densities dN/dy of pi+/- and K+/- over a broad rapidity range (-0.1 < y < 3.5) for central Au + Au collisions at square root(sNN) = 200 GeV. These data have significant implications for the chemistry and dynamics of the dense system that is initially created in the collisions. The full phase-space yields are 1660 +/- 15 +/- 133 (pi+), 1683 +/- 16 +/- 135 (pi-), 286 +/- 5 +/- 23 (K+), and 242 +/- 4 +/- 19 (K-). The systematics of the strange to nonstrange meson ratios are found to track the variation of the baryochemical potential with rapidity and energy. Landau-Carruthers hydrodynamics is found to describe the bulk transport of the pions in the longitudinal direction.

Centrality dependence of charged-particle pseudorapidity distributions from d + Au collisions at sqrt[sNN] = 200 GeV

Charged-particle pseudorapidity densities are presented for the d + Au reaction at sqrt[s(NN)] = 200 GeV with -4.2 < or = eta < or = 4.2. The results, from the BRAHMS experiment at BNL Relativistic Heavy-Ion Collider, are shown for minimum-bias events and 0%-30%, 30%-60%, and 60%-80% centrality classes. Models incorporating both soft physics and hard, perturbative QCD-based scattering physics agree well with the experimental results. The data do not support predictions based on strong-coupling, semiclassical QCD. In the deuteron-fragmentation region the central 200 GeV data show behavior similar to full-overlap d+Au results at sqrt[s(NN)] = 19.4 GeV.

Evolution of the nuclear modification factors with rapidity and centrality in d + Au collisions at (sqrt)[N(S)N]=200 GeV

We report on a study of the transverse momentum dependence of nuclear modification factors R(dAu) for charged hadrons produced in deuteron + gold collisions at sqrt[s(NN)]=200 GeV, as a function of collision centrality and of the pseudorapidity (eta=0, 1, 2.2, 3.2) of the produced hadrons. We find a significant and systematic decrease of R(dAu) with increasing rapidity. The midrapidity enhancement and the forward rapidity suppression are more pronounced in central collisions relative to peripheral collisions. These results are relevant to the study of the possible onset of gluon saturation at energies reached at BNL RHIC.

Nuclear stopping in Au+Au collisions at square root of S(NN)=200 GeV

Transverse momentum spectra and rapidity densities, dN/dy, of protons, antiprotons, and net protons (p-p) from central (0%-5%) Au+Au collisions at square root of S(NN)=200 GeV were measured with the BRAHMS experiment within the rapidity range 0</=y</=3. The proton and antiproton dN/dy decrease from midrapidity to y=3. The net-proton yield is roughly constant for y<1 at dN/dy approximately 7, and increases to dN/dy approximately 12 at y approximately 3. The data show that collisions at this energy exhibit a high degree of transparency and that the linear scaling of rapidity loss with rapidity observed at lower energies is broken. The energy loss per participant nucleon is estimated to be 73+/-6 GeV.

Transverse-momentum spectra in Au+Au and d+Au collisions at sqrt[s(NN)]=200 GeV and the pseudorapidity dependence of high-p(T) suppression

We present spectra of charged hadrons from Au+Au and d+Au collisions at sqrt[s(NN)]=200 GeV measured with the BRAHMS experiment at RHIC. The spectra for different collision centralities are compared to spectra from p+(-)p collisions at the same energy scaled by the number of binary collisions. The resulting ratios (nuclear modification factors) for central Au+Au collisions at eta=0 and eta=2.2 evidence a strong suppression in the high p(T) region (>2 GeV/c). In contrast, the d+Au nuclear modification factor (at eta=0) exhibits an enhancement of the high p(T) yields. These measurements indicate a high energy loss of the high p(T) particles in the medium created in the central Au+Au collisions. The lack of suppression in d+Au collisions makes it unlikely that initial state effects can explain the suppression in the central Au+Au collisions.

Rapidity dependence of charged antihadron to hadron ratios in Au+Au collisions at sqrt[s(NN)]=200 GeV

We present ratios of the numbers of charged antihadrons to hadrons (pions, kaons, and protons) in Au+Au collisions at sqrt[s(NN)]=200 GeV as a function of rapidity in the range y=0-3. While the ratios at midrapidity are approaching unity, the K(-)/K(+) and p;/p ratios decrease significantly at forward rapidities. An interpretation of the results within the statistical model indicates a reduction of the baryon chemical potential from mu(B) approximately 130 MeV at y=3 to mu(B) approximately 25 MeV at y=0.

PPARgamma agonists in the treatment of type II diabetes: is increased fatness commensurate with long-term efficacy?

The nuclear hormone receptor peroxisome proliferator-activated receptor gamma (PPARgamma) is a member of the PPAR family. The endogenous activators of all members of the PPAR family are a variety of fatty acids, which suggests that the PPARs are highly involved in lipid metabolism. In the present paper, the current understanding of the involvement of PPARgamma in adipocyte proliferation and adipose tissue formation is extensively reviewed, and it is stressed that PPARgamma seems to be a major regulator in the differentiation of adipocytes. Thiazoledinediones (TZDs) are a group of PPARgamma-agonists used in the treatment of type 2 diabetes (T2D) since 1997. They are characterized by their ability to decrease insulin resistance, and have been suggested to slow down the progression of insulin resistance. Treatment with TZD requires several weeks of treatment to decrease plasma glucose levels, but in addition they markedly decrease plasma triglycerides and free fatty acids. A major drawback of treatment with TZD is body fat gain, but some evidence suggests that the fat is redistributed in a favourable direction, that is, from visceral to subcutaneous depots. However, the effect of long-term treatment on weight gain following TZD treatment is unknown, and it may be questioned whether the use of these 'adipogenic compounds' is appropriate, considering that excess body fat is almost a prerequisite for the development of type 2 diabetes.

Pseudorapidity distributions of charged particles from Au + Au collisions at the maximum RHIC energy, square root[s(NN)] = 200 GeV

We present charged-particle multiplicities as a function of pseudorapidity and collision centrality for the 197Au+197Au reaction at square root[s(NN)] = 200 GeV. For the 5% most central events we obtain dN(ch)/deta/(eta = 0) = 625+/-55 and N(ch)/(-4.7< or =eta < or =4.7) = 4630 +/- 370, i.e., 14% and 21% increases, respectively, relative to square root[s(NN)] = 130 GeV collisions. Charged-particle production per pair of participant nucleons is found to increase from peripheral to central collisions around midrapidity. These results constrain current models of particle production at the highest RHIC energy.

Rapidity dependence of antiproton-to-proton ratios in Au+Au collisions at square root of (sNN) = 130 GeV

Measurements, with the BRAHMS detector, of the antiproton-to-proton ratio at midrapidities and forward rapidities, are presented for Au+Au reactions at square root of [s(NN)] = 130 GeV, and for three different collision centralities. For collisions in the 0%-40% centrality range, we find N(&pmacr;)/N(p) = 0.64+/-0.04((stat))+/-0.06((syst)) at y approximately 0, 0.66+/-0.03+/-0.06 at y approximately 0.7, and 0.41+/-0.04+/-0.06 at y approximately 2. The ratios are found to be nearly independent of collision centrality and transverse momentum. The antiproton and proton rapidity densities vary differently with rapidity, and indicate a significant degree of collision transparency, although a net-baryon free midrapidity plateau (Bjorken limit) is not yet reached.

Three-dimensional structure of Escherichia coli asparagine synthetase B: a short journey from substrate to product

Asparagine synthetase B catalyzes the assembly of asparagine from aspartate, Mg(2+)ATP, and glutamine. Here, we describe the three-dimensional structure of the enzyme from Escherichia colidetermined and refined to 2.0 A resolution. Protein employed for this study was that of a site-directed mutant protein, Cys1Ala. Large crystals were grown in the presence of both glutamine and AMP. Each subunit of the dimeric protein folds into two distinct domains. The N-terminal region contains two layers of antiparallel beta-sheet with each layer containing six strands. Wedged between these layers of sheet is the active site responsible for the hydrolysis of glutamine. Key side chains employed for positioning the glutamine substrate within the binding pocket include Arg 49, Asn 74, Glu 76, and Asp 98. The C-terminal domain, responsible for the binding of both Mg(2+)ATP and aspartate, is dominated by a five-stranded parallel beta-sheet flanked on either side by alpha-helices. The AMP moiety is anchored to the protein via hydrogen bonds with O(gamma) of Ser 346 and the backbone carbonyl and amide groups of Val 272, Leu 232, and Gly 347. As observed for other amidotransferases, the two active sites are connected by a tunnel lined primarily with backbone atoms and hydrophobic and nonpolar amino acid residues. Strikingly, the three-dimensional architecture of the N-terminal domain of asparagine synthetase B is similar to that observed for glutamine phosphoribosylpyrophosphate amidotransferase while the molecular motif of the C-domain is reminiscent to that observed for GMP synthetase.

Structure of the bis(Mg2+)-ATP-oxalate complex of the rabbit muscle pyruvate kinase at 2.1 A resolution: ATP binding over a barrel

Pyruvate kinase from rabbit muscle has been cocrystallized as a complex with MgIIATP, oxalate, Mg2+, and either K+ or Na+. Crystals with either Na+ or K+ belong to the space group P2(1)2(1)2(1), and the asymmetric units contain two tetramers. The structures were solved by molecular replacement and refined to 2.1 (K+) and 2.35 A (Na+) resolution. The structures of the Na+ and K+ complexes are virtually isomorphous. Each of the eight subunits within the asymmetric unit contains MgIIoxalate as a bidentate complex linked to the protein through coordination of Mg2+ to the carboxylates of Glu 271 and Asp 295. Six of the subunits also contain an alpha,beta,gamma-tridentate complex of MgIIATP, and the active-site cleft, located between domains A and B, is closed in these subunits. In the remaining two subunits MgIIATP is missing, and the active-site cleft is open. Closure of the active-site cleft in the fully liganded subunits includes a rotation of 41 degrees of the B domain relative to the A domain. alpha-Carbons of residues in the B domain undergo movements of up to 17.8 A (Lys 124) in the cleft closure. Lys 206, Arg 119, and Asp 177 from the B domain move several angstroms from their positions in the open conformation to contact the MgIIATP complex in the active site. The gamma-phosphate of ATP coordinates to both magnesium ions and to the monovalent cation, K+ or Na+. A Mg2+-coordinated oxygen from the MgIIoxalate complex lies 3.0 A from Pgamma of ATP, and this oxygen is positioned for an in-line attack on the phosphorus. The side chains of Lys 269 and Arg 119 are positioned to provide leaving-group activation in the forward and reverse directions. There is no obvious candidate for the acid/base catalyst near the 2-si face of the prospective enolate of the normal substrate. A functional group linked through solvent and side-chain hydroxyls may function in a proton relay.

Ligand-induced domain movement in pyruvate kinase: structure of the enzyme from rabbit muscle with Mg2+, K+, and L-phospholactate at 2.7 A resolution

The structure of rabbit muscle pyruvate kinase crystallized as a complex with Mg2+, K+, and L-phospholactate (L-P-lactate) has been solved and refined to 2.7 A resolution. The crystals, grown from solutions of polyethylene glycol 8000 at pH 7.5, belong to the space group P2(1) and have unit cell parameters a = 144.4 A, b = 112.6 A, c = 171.2 A, and beta = 93.7 degrees. The asymmetric unit contains two tetramers. The crystal structure reveals that the eight subunits within the asymmetric unit adopt several different conformations. These conformations are characterized by differences in the relative positions of protein domains A and B, resulting in different degrees of closure of the active site cleft that occupies the interface between these two domains. The global conformational differences may be described as rotations of the B domain with respect to the (beta/alpha)8-barrel of the A domain. Carbon atoms of the backbone in domain B rotate >20 degrees from the most open to the most closed subunit. The different conformations among subunits within the asymmetric unit are accompanied by 3-3.8 A shifts in the position of Mg2+ and a significant change in the orientation of the phenyl ring of Phe 243. In all of the subunits, Mg2+ coordinates to the protein through the carboxylate side chains of Glu 271 and Asp 295. In the subunit having the most closed conformation, Mg2+ also coordinates to the carboxylate oxygen, the bridging ester oxygen, and a nonbridging phosphoryl oxygen of L-P-lactate. Mg2+ to L-P-lactate coordination is missing in subunits exhibiting a more open conformation. K+ coordinates to four protein ligands and to a phosphoryl oxygen of the L-P-lactate. The position and liganding of K+ are unaffected by the different conformations of the subunits. The side chain of Arg 72, Mg2+, and K+ provides a locus of positive charge for the phosphate moiety of the analog in the closed subunit.

Structural and mechanistic studies of enolase

The high-resolution structure of yeast enolase cocrystallized with its equilibrium mixture of substrate and product reveals the stereochemistry of substrate/product binding and therefore the groups responsible for acid/base catalysis and stabilization of the enolate intermediate. Expression and characterization of site-specific mutant forms of the enzyme have confirmed the roles of amino acid side chains in the catalysis of the first and second steps of the reaction. Coordination of both required magnesium ions to the carboxylate of the substrate/product indicates a role for these cations in stabilization of the intermediate.

A carboxylate oxygen of the substrate bridges the magnesium ions at the active site of enolase: structure of the yeast enzyme complexed with the equilibrium mixture of 2-phosphoglycerate and phosphoenolpyruvate at 1.8 A resolution

The equilibrium mixture of yeast enolase with substrate, 2-phospho-D-glycerate (2-PGA), and product, phosphoenolpyruvate (P-enolpyruvate), has been crystallized from solutions of poly(ethylene glycol) (PEG) at pH 8.0. Crystals belong to the space group C2 and have unit cell dimensions a = 121.9 A, b = 73.2 A, c = 93.9 A, and beta = 93.3 degrees. The crystals have one dimer per asymmetric unit. Crystals of the equilibrium mixture and of the enolase complex of phosphonoacetohydroxamate (PhAH) are isomorphous, and the structure of the former complex was solved from the coordinates of enolase-(Mg2+)2-PhAH [Wedekind, J. E., Poyner, R. R., Reed, G. H., & Rayment, I. (1994) Biochemistry 33, 9333-9342]. The current crystallographic R-factor is 17.7% for all recorded data (92% complete) to 1.8 A resolution. The electron density map is unambiguous with respect to the positions and liganding of both magnesium ions and with respect to the stereochemistry of substrate/product binding. Both magnesium ions are complexed to functional groups of the substrate/product. The higher affinity Mg2+ coordinates to the carboxylate side chains of Asp 246, Glu 295, and Asp 320, both carboxylate oxygens of the substrate/product, and a water molecule. One of the carboxylate oxygens of the substrate/product also coordinates to the lower affinity Mg2+-thus forming a mu-carboxylato bridge. The other ligands of the second Mg2+ are a phosphoryl oxygen of the substrate/product, two water molecules, and the carbonyl and gamma-oxygens of Ser 39 from the active site loop. The intricate coordination of both magnesium ions to the carboxylate group suggests that both metal ions participate in stabilizing negative charge in the carbanion (aci-carboxylate) intermediate. The epsilon-amino group of Lys 345 is positioned to serve as the base in the forward reaction whereas the carboxylate side chain of Glu 211 is positioned to interact with the 3-OH of 2-PGA. The structure provides a candid view of the catalytic machinery of enolase.

Structure of rabbit muscle pyruvate kinase complexed with Mn2+, K+, and pyruvate

The molecular structure of rabbit muscle pyruvate kinase, crystallized as a complex with Mn2+, K+, and pyruvate, has been solved to 2.9-A resolution. Crystals employed in the investigation belonged to the space group P1 and had unit cell dimensions a = 83.6 A, b = 109.9 A, c = 146.8 A, alpha = 94.9 degrees, beta = 93.6 degrees, and gamma = 112.3 degrees. There were two tetramers in the asymmetric unit. The structure was solved by molecular replacement, using as the search model the coordinates of the tetramer of pyruvate kinase from cat muscle [Muirhead, H., Claydon, D. A., Barford, D., Lorimer, C. G., Fothergill-Gilmore, L. A., Schiltz, E., & Schmitt, W. (1986) EMBO J.5, 475-481]. The amino acid sequence derived from the cDNA coding for the enzyme from rabbit muscle was fit to the electron density. The rabbit and cat muscle enzymes have approximately 94% sequence identity, and the folding patterns are expected to be nearly identical. There are, however, three regions where the topological models of the cat and rabbit pyruvate kinases differ. Mn2+ coordinates to the protein through the carboxylate side chains of Glu 271 and Asp 295. These two residues are strictly conserved in all known pyruvate kinases. In addition, the density for Mn2+ is connected to that of pyruvate, consistent with chelation through a carboxylate oxygen and the carbonyl oxygen of the substrate. The epsilon-NH2 of Lys 269 and the OH of Thr 327 lie on either side of the methyl group of bound pyruvate. Spherical electron density, assigned to K+, is located within a well-defined pocket of four oxygen ligands contributed by the carbonyl oxygen of Thr 113, O gamma of Ser 76, O delta 1 of Asn 74, and O delta 2 of Asp 112. The interaction of Asp 112 with the side chains of Lys 269 and Arg 72 may mediate, indirectly, monovalent cation effects on activity.

Use of dual wavelength spectrophotometry and continuous enzymatic depletion of oxygen for determination of the oxygen binding constants of hemoglobin

A small stopped-flow cuvette was built into a computer-controlled Cary 210 spectrophotometer. The enzymatic depletion of oxygen in solutions of hemoglobin and myoglobin was initiated by flowing the hemeproteins with the enzyme against a solution of the hemeproteins containing the appropriate substrate. The deoxygenation was homogeneous throughout the solution. Oxygen activity was calculated at each instant of time from the fractional saturation of Mb, determined from observations at the Hb/HbO2 isosbestic wavelength. Fractional saturation of Hb was determined from absorbances at the Mb/MbO2 isosbestic wavelength. The spectrophotometer cycled between these two wavelengths during the deoxygenation. The deoxygenation of HbO2 was largely complete in 20-25 min, whereas the deoxygenation of MbO2 was allowed to proceed for about 1 h. This procedure eliminates equilibration of Hb solutions with a gas phase and replaces oxygen electrode readings with spectrophotometric sensing by Mb, providing essentially instantaneous determinations of oxygen activity and hence 250-500 or more independent data points per run. The Mb and Hb data vectors require several manipulations to correct for small relative displacements in time and for small non-isosbestic effects. Detailed consideration of the enzyme kinetics allowed oxygen activities to be determined in regions where Mb is a poor sensor. Studies of HbO2 deoxygenation as a function of wavelength show that the determination of the four Adair constants requires in addition the determination of three spectroscopic parameters. Values of the apparent Adair constants, determined without these spectroscopic parameters, depend strongly on the monitoring wavelength.

RNA-DNA hybridization analyses of tRNA-Val-3b in Drosophila melanogaster

Transfer RNA was extracted from 50-300 mg of adult flies and specifically labeled in vitro. The level of individual isoacceptors was quantitated by efficient annealing to Drosophila tRNA genes carried on recombinant DNA plasmids immobilized on nitrocellulose filters. The level of tRNAVal3b in the tRNA isolated from flies deficient in the major tRNAVal3b loci has been examined. The results show that deletion of the major tRNAVal3b loci resulted in a reduction of approximately 50% in the level of tRNAVal3b but did not produce the Minute phenotype; furthermore the effects of deficiencies at two loci were approximately additive.