Validation of the GROMOS force-field parameter set 45A3 against nuclear magnetic resonance data of hen egg lysozyme

The quality of molecular dynamics (MD) simulations of proteins depends critically on the biomolecular force field that is used. Such force fields are defined by force-field parameter sets, which are generally determined and improved through calibration of properties of small molecules against experimental or theoretical data. By application to large molecules such as proteins, a new force-field parameter set can be validated. We report two 3.5 ns molecular dynamics simulations of hen egg white lysozyme in water applying the widely used GROMOS force-field parameter set 43A1 and a new set 45A3. The two MD ensembles are evaluated against NMR spectroscopic data NOE atom–atom distance bounds, ³J_NH and ³J coupling constants, and ¹5N relaxation data. It is shown that the two sets reproduce structural properties about equally well. The 45A3 ensemble fulfills the atom–atom distance bounds derived from NMR spectroscopy slightly less well than the 43A1 ensemble, with most of the NOE distance violations in both ensembles involving residues located in loops or flexible regions of the protein. Convergence patterns are very similar in both simulations atom-positional root-mean-square differences (RMSD) with respect to the X-ray and NMR model structures and NOE inter-proton distances converge within 1.0–1.5 ns while backbone ³J_HN-coupling constants and ¹H– ¹5N order parameters take slightly longer, 1.0–2.0 ns. As expected, side-chain ³J-coupling constants and ¹H– ¹5N order parameters do not reach full convergence for all residues in the time period simulated. This is particularly noticeable for side chains which display rare structural transitions. When comparing each simulation trajectory with an older and a newer set of experimental NOE data on lysozyme, it is found that the newer, larger, set of experimental data agrees as well with each of the simulations. In other words, the experimental data converged towards the theoretical result.     

Biomolecular structure refinement based on adaptive restraints using local-elevation simulation

Introducing experimental values as restraints into molecular dynamics (MD) simulation to bias the values of particular molecular properties, such as nuclear Overhauser effect intensities or distances, dipolar couplings, ³ J-coupling constants, chemical shifts or crystallographic structure factors, towards experimental values is a widely used structure refinement method. Because multiple torsion angle values ϕ correspond to the same ³ J-coupling constant and high-energy barriers are separating those, restraining ³ J-coupling constants remains difficult. A method to adaptively enforce restraints using a local elevation (LE) potential energy function is presented and applied to ³ J-coupling constant restraining in an MD simulation of hen egg-white lysozyme (HEWL). The method succesfully enhances sampling of the restrained torsion angles until the 37 experimental ³ J-coupling constant values are reached, thereby also improving the agreement with the 1,630 experimental NOE atom–atom distance upper bounds. Afterwards the torsional angles ϕ are kept restrained by the built-up local-elevation potential energies.     

Analysis of the 1H-NMR spectra of ferrichrome peptides. II. The amide resonances

The high-resolution ¹H-nmr study of the ferrichrome cyclohexapeptides, in d6 -DMSO solutions, has been extended to the amide NH spectral region. A total of ten diamagnetic analogues of ferrichrome that differ in the coordinated metal ion (Al³⁺, Ga³⁺ or Co³⁺), the primary structure, the nature of the bidentate hydroxamate moiety, or the isotope compositions (¹⁴N, ¹⁵N) have been investigated. The ³J_αNH values reflect regiorous conformational isomorphism throughout the complete suite of analogues, quite independent of the residue occupancy of each site. Totally resolved amide multiplets have been obtained in most cases and the four-line (doublet of doublets) appearances of glycyl NH resonances has been observed for the first times; these data enabled stereospecific assignment and accurate analysis of the NH-CαH proton spin systems. The high resolution was made possible by the use of a suitable spectral deconvolution shceme at 360 MHz. The fine structure, extraordinarily well displayed in the ¹⁵N-peptide spectra, provides a series of parameter values whose consistency has been checked by computer simulation. Since the crystallographic structure for two of the ferric peptides is known to 0.002-Å resolution, a ³J vs θ correspondence could be confidently established. A Karplus curve was derived from the combined x-ray and nmr data: It is suggested that seriously nonplanar amides can exhibit ³J_αNH values higher than predicted by the ferrichrome curve.     

Two-substrate kinetic analysis: a novel approach linking ion and acid-base transport at the gills of freshwater trout,Oncorhynchus mykiss

Summary The novel application of a two-substrate model (Florini and Vestling 1957) from enzymology to transport kinetics at the gills of freshwater trout indicated that Na⁺/acidic equivalent and Cl^-/basic equivalent flux rates are normally limited by the availability of the internal acidic and basic counterions, as well as by external Na⁺ and Cl^- levels. Adult rainbow trout fitted with dorsal aortic and bladder catheters were chronically infused (10–16 h) with isosmotic HCl to induce a persistent metabolic acidosis. Acid-base neutral infusions of isosmotic NaCl and non-infused controls were also performed. Results were compared to previous data on metabolic alkalosis in trout induced by either isosmotic NaHCO₃ infusion or recovery from environmental hyperoxia (Goss and Wood 1990a, b). Metabolic acidosis resulted in a marked stimulation of Na⁺ influx, no change in Cl^- influx, positive Na⁺ balance, negative Cl^- balance, and net H⁺ excretion at the gills. Metabolic alkalosis caused a marked inhibition of Na⁺ influx and stimulation of Cl^- influx, negative Na⁺ balance, positive Cl^- balance, and net H⁺ uptake (=base excretion). Mean gill intracellular pH qualitatively followed extracellular pH. Classical one-substrate Michaelis-Menten analysis of kinetic data indicated that changes in Na⁺ and Cl^- transport during acid-base disturbance are achieved by large increases and decreases in J_max, and by increases in K_m. However, one-substrate analysis considers only external substrate concentration and cannot account for transport limitations by the internal substrate. The kinetic data were fitted successfully to a two-substrate model, using extracellular acid-base data as a measure of internal HCO ₃ ^- and H⁺ availability. This analysis indicated that true J_max values for Na⁺/acidic equivalent and Cl^-/basic equivalent transport are 4–5 times higher than apparent J_max values by one-substrate analysis. Flux rates are limited by the availability of the internal counterions; transport K_m values for HCO ₃ ^- and H⁺ are far above their normal internal concentrations. Therefore, small changes in acid-base status will have large effects on transport rates, and on apparent J_max values, without alterations in the number of transport sites. This system provides an automatic, negative feedback control for clearance or retention of acidic/basic equivalents when acid-base status is changing.Abbreviations Amm total ammonia in water - DMO 55-dimethyl-24-oxyzolidine-dione - J_in unidirectional inward ion movement across the gill - J_out unidirectional outward ion movement across the gill - J_net net transfer of ions (sum of J_in and J_out) across the gill - J_max maximal transport rate for ion - K_m inverse of affinity of transporter for ion - PIO₂ partial pressure of oxygen in inspired water - P_aCO₂ partial pressure of carbon dixide in arterial blood - TAlk titratable alkalinity of the water - PEG polyethylene glycol - NEN New England Nuclear     

Quantitative two-dimensional nmr study of dermenkephalin,a highly potent and selective δ-opioid peptide

Dermenkephalin, H-Tyr-(D ) Met-Phe-His-Leu-Met-Asp-NH₂, a highly potent and selective δ-opioid peptide isolated from frog skin, was studied in DMSO-d₆ solution by two-dimensional nmr spectroscopy, including the determination of NH temperature coefficients, the evaluation of ³J coupling constants from phase-sensitive correlated spectroscopy (COSY) and the volumes of nuclear Overhauser effect (NOE) correlations. The two-dimensional NOE spectroscopy (NOESY) spectrum of dermenkephalin revealed sequential, medium-, and long-range effects. To put this information on a quantitative basis, special attention was devoted to J cross-peak suppression, quantification of the NOE volumes and analysis of the overlaps, normalization of the NOEs against diagonal peaks and H_ββ′ geminal interactions. Although most of the dihedral angles deduced from the ³J_Nα coupling constants together with several N_iα_i and α_iN_{i + 1} NOEs pointed to a partially extended peptide backbone, several N_i N_{i + 1} NOEs and β_i N_{i + 1} interactions argued in favor of a folded structure. Moreover, several long-range correlations of strong intensities were found that supported a close spatial proximity between the side chains of D -Met² and Met⁶, Tyr¹ and His⁴, Tyr¹ and Asp⁷, and His⁴ and the C-terminal amide group. In Phe, the g^? rotamer in the side chain is deduced from the ³J_αβ coupling constants and αβ and Nβ NOE correlations. Whereas the amide proton dependency was not indicative of stable hydrogen bonds, the nonuniform values of the temperature coefficient may reflect an equilibrium mixture of folded and extended conformers. The overall data should provide realistic starting models for energy minimization and modelization studies. © 1993 John Wiley & Sons, Inc.     

Two-Dimensional 1H, 15N NMR investigation of uniformly 15N-labeled Lac Repressor Headpiece

Abstract

¹⁵N uniformly labeled lac repressor and lac repressor headpiece were prepared. ¹⁵N NMR spectra of lac repressor were shown resolution inadequate for detailed study while the data showed that the ¹⁵N labeled N-terminal part of the protein is quite suitable for this type of study allowing future investigation of the specific interaction of the lac repressor headpiece with the lac operator. We report here the total assignment of proton ¹H and nitrogen ¹⁵NH backbone resonances of this headpiece in the free state. Assignments of the ¹⁵N resonances of the protein were obtained in a sequential manner using heteronuclear multiple quantum coherence (HMQC), relayed HMQC nuclear Overhauser and relayed HMQC-HOHAHA spectroscopy. More than 80 per cent of residues were assigned by their ¹⁵NH(i)-N¹H(i+1) and ¹⁵NH(i)-N¹(i-1) connectivities. Values of the ³J_NHα splitting for 39 of the 51 residues of the headpiece were extracted from HMQC and HMQC-J. The observed ¹⁵NH(i)-C^βH cross peaks and the ³J_NHα coupling constants values are in agreement with the three α-helices previously described [Zuiderweg, E.R.P., Scheek, R.M., Boelens, R., van Gunsteren, W.F. and Kaptein, R., Biochimie 67, 707 (1985)]. The ³J_NHα coupling constants can be now used for a more confident determination of the lac repressor headpiece. From these values it is shown that the geometry of the ends of the second and third α-helices exhibit deviation from the canonical α-helix structure. On the basis of NOEs and ³J_NHα values, the geometry of the turn of the helix-turn-helix motif is discussed.     

C-nuclear magnetic resonance studies of 85% C-enriched amino acids and small peptides: pH effects on the chemical shifts, coupling constants, kinetics of cis-trans isomerisation and conformation aspects

The ¹³C chemical shifts of several 85% ¹³C-enriched amino acids and small peptides were studied as a function of pH. The results show that the chemical shifts of carbon atoms of ionizable groups vary significantly within the zone of their pK. Generally with the pH going from 7 to 1 all the δC are shifted more or less upfield with the exception of the carbonyl group of the second last residue which is shifted slightly downfield. This suggests the formation of an hydrogen bond at acid pH involving in a seven-membered ring the C=O in question and the COOH terminal.The percentage of cis and trans conformers of glycyl-l-proline and glycyl-l-prolylglycine were studied as a function of pH. The trans form is always preponderant whatever the pH. The accessibility of the carbonyl group to protonation of the proline residue strongly influences the cis-trans equilibrium. Thus, with the pH varying from 7 to 1, the trans isomer changes from 61 to 85% for glycyl-l-proline and only from 77 to 80% for glycyl-l-prolylglycine.The proton NMR studies underline the important differences existing between the two molecular forms of glycyl-l-proline. The cis conformation is characterized with regard to the trans form by the non-equivalence of the α-protons of the glycine residue, by a lower pK₁ and by a larger ΔδH_α of the proline residue as a function of pH. These results could suggest an end-to-end interaction in the cis form of the glycyl-l-proline molecule.The ¹³C-¹³C coupling constants were also studied as a function of pH. The results show that J_Co-Cα of a C-terminal residue, varying from 5 to 6 Hz and reflecting the pK of the carboxylate group, is a linear function of δ_Co and δ_Cα as in the case of the amino acids. The total variation of the electron density of those two carbons in an amino acid is approximately 40% weaker than in a C-terminal residue. The charge distribution along the C_α−C_o bond, however, is practically the same in both cases.Finally the ratios of the conversion rate constants of the two isomers cis-trans of glycyl-proline were calculated at different pH values; the relations between the isomer percentages and δ_Co, δ_Cα on the one hand and the J_Co-Cα on the other were established.     

Motional timescale predictions by molecular dynamics simulations: Case study using proline and hydroxyproline sidechain dynamics

We propose a new approach for force field optimizations which aims at reproducing dynamics characteristics using biomolecular MD simulations, in addition to improved prediction of motionally averaged structural properties available from experiment. As the source of experimental data for dynamics fittings, we use ¹³C NMR spin‐lattice relaxation times T₁ of backbone and sidechain carbons, which allow to determine correlation times of both overall molecular and intramolecular motions. For structural fittings, we use motionally averaged experimental values of NMR J couplings. The proline residue and its derivative 4‐hydroxyproline with relatively simple cyclic structure and sidechain dynamics were chosen for the assessment of the new approach in this work. Initially, grid search and simplexed MD simulations identified large number of parameter sets which fit equally well experimental J couplings. Using the Arrhenius‐type relationship between the force constant and the correlation time, the available MD data for a series of parameter sets were analyzed to predict the value of the force constant that best reproduces experimental timescale of the sidechain dynamics. Verification of the new force‐field (termed as AMBER99SB‐ILDNP) against NMR J couplings and correlation times showed consistent and significant improvements compared to the original force field in reproducing both structural and dynamics properties. The results suggest that matching experimental timescales of motions together with motionally averaged characteristics is the valid approach for force field parameter optimization. Such a comprehensive approach is not restricted to cyclic residues and can be extended to other amino acid residues, as well as to the backbone. Proteins 2014; 82:195–215. © 2013 Wiley Periodicals, Inc.     

On using oscillating time-dependent restraints in MD simulation

The use of time-dependent restraints in molecular simulation in order to generate a conformational ensemble for molecules that is in accordance with measured ensemble averages for particular observable quantities is investigated. Using a model system consisting of liquid butane and the cyclic peptide antamanide the reproduction of particular average ³ J-coupling constant values in a molecular dynamics simulation is analysed. It is shown that the multiple-valuedness and the sizeable gradients of the Karplus curve relating ³ J-coupling constants measured in NMR experiments to the corresponding torsional-angle values cause severe problems when trying to restrain a ³ J-coupling constant to a value close to the extrema of the Karplus curve. The introduction of a factor oscillating with time into the restraining penalty function alleviates this problem and enhances the restrained conformational sampling.     

Effect of pH on structure,function, and stability of mitochondrial carbonic anhydrase VA

Mitochondrial carbonic anhydrase VA (CAVA) catalyzes the hydration of carbon dioxide to produce proton and bicarbonate which is primarily expressed in the mitochondrial matrix of liver, and involved in numerous physiological processes including lipogenesis, insulin secretion from pancreatic cells, ureagenesis, gluconeogenesis, and neuronal transmission. To understand the effect of pH on the structure, function, and stability of CAVA, we employed spectroscopic techniques such as circular dichroism, fluorescence, and absorbance measurements in wide range of pH (from pH 2.0 to pH 11.5). CAVA showed an aggregation at acidic pH range from pH 2.0 to pH 5.0. However, it remains stable and maintains its secondary structure in the pH range, pH 7.0–pH 11.5. Furthermore, this enzyme has an appreciable activity at more than pH 7.0 (7.0 < pH ≤ 11.5) with maximum activity at pH 9.0. The maximal values of k_cat and k_cat/K_m at pH 9.0 are 3.7?×?10⁶ s^?1 and 5.5?×?10⁷ M^?1 s^?1, respectively. However, this enzyme loses its activity in the acidic pH range. We further performed 20-ns molecular dynamics simulation of CAVA to see the dynamics at different pH values. An excellent agreement was observed between in silico and in vitro studies. This study provides an insight into the activity of CAVA in the pH range of subcellular environment.     

Unblocked statistical-coil tetrapeptides and pentapeptides in aqueous solution: a theoretical study

NMR studies of the molecular conformations of peptides and proteins rely on a comparison of the relevant spectral parameters with the corresponding values for so-called statistical-coilpolypeptides. For this reason, it is necessary to characterize the experimental ensemble of states populated by statistical-coilpeptides. Such a characterization, however, has proven to be both difficult and sensitive to changes in many environmental parameters such as solvent composition, temperature, pH, as well as the neighboring amino acids in the sequence. As a consequence, a series of significant discrepancies has been reported for some experimentally observed parameters, such as chemical shifts, or vicinal coupling constants, ³J_NH, whose values appear to be incompatible with a statistical-coilensemble. In this work, we report the results of a molecular mechanics study of a series of unblocked tetra- and pentapeptides under different pH conditions. These calculations were carried out with explicit consideration of both the coupling between the process of proton binding/release and conformation adopted by the molecule at a given pH and the contribution of the conformational entropy to the total free energy. Good agreement was found between the calculated and experimentally determined values of the vicinal coupling constant, ³J_NH, the -proton chemical shift, and the ¹³Cchemical shift. All the evidence accumulated in these theoretical calculations helps to rationalize some of the unsettled anomalies observed experimentally, and to provide an understanding of the effect of pH and amino acid sequence on the conformational preferences of statistical-coilpeptides.     

An NMR investigation of putative interresidue H-bonding in methyl α-cellobioside in solution

Methyl α-cellobioside (methyl β-d-glucopyranosyl-(1→4)-α-d-glucopyranoside) was labeled with ¹³C at C4′ for use in NMR studies in DMSO-d₆ solvent to attempt the detection of a trans-H-bond J-coupling (^3hJ_CCOH) between C4′ and OH3. Analysis of the OH3 signal at 600 MHz revealed only the presence of two homonuclear J-couplings: ³J_H3,OH3 and a smaller, longer range J_HH. No evidence for ^3hJ_C4′,OH3 was found. The longer range J_HH was traced to ⁴J_H4,OH3 based on 2D ¹H–¹H COSY data and inspection of the H2 and H4 signal lineshapes. A limited set of DFT calculations was performed on a methyl cellobioside mimic to evaluate the structural dependencies of ⁴J_H2,O3H and ⁴J_H4,O3H on the H3–C3–O3–H torsion angle. Computed couplings range from about −0.7 to about +1.1 Hz, with maximal values observed when the C–H and O–H bonds are roughly diaxial.     

pH-Induced Proton Permeability Changes of Plasma Membrane Vesicles

In vivo studies with leaf cells of aquatic plant species such as Elodea nuttallii revealed the proton permeability and conductance of the plasma membrane to be strongly pH dependent. The question was posed if similar pH dependent permeability changes also occur in isolated plasma membrane vesicles. Here we report the use of acridine orange to quantify passive proton fluxes. Right-side out vesicles were exposed to pH jumps. From the decay of the applied ΔpH the proton fluxes and proton permeability coefficients (P_H+) were calculated. As in the intact Elodea plasma membrane, the proton permeability of the vesicle membrane is pH sensitive, an effect of internal pH as well as external pH on P_H+ was observed. Under near symmetric conditions, i.e., zero electrical potential and zero ΔpH, P_H+ increased from 65 × 10⁻⁸ at pH 8.5 to 10⁻¹ m/sec at pH 11 and the conductance from 13 × 10⁻⁶ to 30 × 10⁻⁴ S/m². At a constant pH _i of 8 and a pH _o going from 8.5 to 11, P_H+ increased more than tenfold from 2 to 26 × 10⁻⁶ m/sec. The calculated values of P_H+ were several orders of magnitude lower than those obtained from studies on intact leaves. Apparently, in plasma membrane purified vesicles the transport system responsible for the observed high proton permeability in vivo is either (partly) inactive or lost during the procedure of vesicle preparation. The residue proton permeability is in agreement with values found for liposome or planar lipid bilayer membranes, suggesting that it reflects an intrinsic permeability of the phospholipid bilayer to protons. Possible implications of these findings for transport studies on similar vesicle systems are discussed. Received: 5 April 1995/Revised: 28 March 1996     

The effects of extremely alkaline water (pH 9·5) on rainbow trout gill function and morphology

Rainbow trout that were held under control conditions, at pH8·0, in moderately hard Hamilton tap water, had Cl^? and Na⁺ influx rates (J^CLin and J^Na, respectively) of 270 and 300 μmol kg^?1 h^?1, respectively. Exposure to pH 9·5 water led to an immediate 67% decline in J^CL_in and a 45% reduction in J^Na_in at 0–1 h. Influx rates declined further and by 4–5 h the net decreases in both J^CL_in and J^Na_in approximated 80%. By 24 h J^CL_in had recovered to rates not significantly different from those at pH 8·0; while J^Na_in only partially recovered and remained about 50% lower than control measurements through 72 h. The complete recovery of J^CL_in and partial recovery of J^Na_in may have been related to a fourfold greater branchial chloride cell (CC) fractional surface area observed in rainbow trout exposed to pH 9·5 for 72 h. Ammonia excretion (J_Amm) was about 170 μmol N kg^?1 h^?1 at pH 8·0 but was initially reduced by 90% over the first hour of high pH exposure. J_Amm rapidly recovered and by 24 h it had returned to pre-exposure levels. This recovery tended to parallel the partial recovery of J^Na_in. However, subsequent addition of amiloride (10^?4M) to the water at 75 h led to no change in J_Amm, despite a 50% reduction in J^Na_in. Thus, it does not appear that there is a linkage between Na⁺ influx and the recovery of ammonia excretion under highly alkaline conditions.     

Assignment of the 270 MHz nuclear magnetic resonance spectrum of somatostatin in water

The proton nuclear magnetic resonance spectrum of the 14 residue peptide hormone somatostatin in D₂O at 270 MHz has been assigned by comparing the spectra of synthetic analogs with those of the native peptide. Extensive difference double resonance studies of all somatostatins and pH titrations confirmed all assignments. ³J_NHCH values and conventional NMR hydrogen bonding studies confirm the existence of preferred secondary conformations but not with a predominant conformation possessing a β-turn in either of the sequences 7–8–9–10 or 8–9–10–11. More extensive data treatment is needed before the actual conformation(s) of somatostatin is elucidated, but several NMR criteria for conformations are proposed.     

An intracellular pH gradient in the anammox bacterium Kuenenia stuttgartiensis as evaluated by 31P NMR

The cytoplasm of anaerobic ammonium oxidizing (anammox) bacteria consists of three compartments separated by membranes. It has been suggested that a proton motive force may be generated over the membrane of the innermost compartment, the “anammoxosome”. ³¹P nuclear magnetic resonance (NMR) spectroscopy was employed to investigate intracellular pH differences in the anammox bacterium Kuenenia stuttgartiensis. With in vivo NMR, spectra were recorded of active, highly concentrated suspensions of K. stuttgartiensis in a wide-bore NMR tube. At different external pH values, two stable and distinct phosphate peaks were apparent in the recorded spectra. These peaks were equivalent with pH values of 7.3 and 6.3 and suggested the presence of a proton motive force over an intracytoplasmic membrane in K. stuttgartiensis. This study provides for the second time—after discovery of acidocalcisome-like compartments in Agrobacterium tumefaciens—evidence for an intracytoplasmic pH gradient in a chemotrophic prokaryotic cell.     

Specifically mercurated carbohydrate derivatives: models for determination of the stereospecific dependencies of mercury-199 n.m.r. parameters

The proton and natural-abundance carbon-13 nuclear magnetic resonance spectra of a series of methyl 2-deoxy-2-mercuri-d-pyranosides have been measured and analysed. The ¹⁹⁹Hg-¹H and ¹⁹⁹Hg-¹³C couplings, which were readily obtained from the ¹⁹⁹Hg satellite peaks, delineate the angular dependance of ³J and ⁴J couplings.     

Precise vicinal coupling constants3JHNα in proteins from nonlinear fits of J-modulated [15N,1H]-COSY experiments

Summary Improved experimental schemes for the recently introduced J-modulated [¹⁵N,¹H]-correlation experiment for measurements of the homonuclear amide proton-C proton vicinal coupling constants.³J_HN, in uniformly¹⁵N-labeled proteins are described, and a nonlinear fit procedure is presented for quantitative evaluation of³J_HN. The method was first tested with the N-terminal DNA-binding domain of the 434 repressor (M=7.3 kDa), where at 13 C precise values of³J_HN in the range 2.0–9.5 Hz were obtained for all residues with resolved¹⁵N-¹H cross peaks. It was then applied to theAntennapedia homeodomain complexed to a synthetic 14-base pair DNA fragment (molecular weight of the complex 18 kDa). The³J_HN values measured were found to be in excellent agreement with those predicted from the secondary structure of this protein in the complex.Abbreviations and symbols NOE nuclear Overhauser effect - COSY two-dimensional correlated spectroscopy - ³J_HN or J homonuclear vicinal amide proton-C proton coupling constant - 434 repressor(1–69) N-terminal DNA-binding domain of the 434 repressor comprising 69 residues     

Functional roles of Na+ and H+ in SO 4 2− transport by rabbit ileal brush border membrane vesicles

Summary Sulphate uptake by rabbit ileal brush border membrane vesicles was stimulated by a transmembrane sodium gradient ([Na⁺] _o >[Na⁺] _i ), but not by a similar potassium gradient.³⁵SO ₄ ^2– influx (J _oi ^SO4 ) from outside (o) to inside (i) these vesicles was a hyperbolic function of [SO ₄ ^2– ] _o and the affinity constant for anion transport was strongly influenced by [Na⁺] _o (100mm Na⁺,K _t ^SO4 =0.52mm SO ₄ ^2– ; 10mm Na⁺,K _t ^SO4 =4.32mm SO ₄ ^2– ).J _t ^SO4 was a sigmoidal function of [Na⁺] _o at pH 7.4 for both low (0.2m) and high (4.0mm) [SO ₄ ^2– ] _o . The Na⁺-dependency ofJ _t ^SO4 was examined at pH 6.0, 7.4, and 8.0 (same pH inside and outside). At pH 6.0 and 7.4 sigmoidal Na⁺-dependentJ _t ^SO4 exhibited nonlinear Eadie-Hofstee plots indicative of a transport mechanism capable of binding a variable number of sodium ions over the [Na⁺] _o range used. Hill plots of anion transport under these conditions displayed slopes near unity at low [Na⁺] _o and slopes approximating 2.0 at higher cation concentrations. At pH 8.0, Na⁺-dependentJ _t ^SO4 was hyperbolic and showed linear Eadie-Hofstee and Hill plots, the latter with a single slope near 1.0. When a H⁺ gradient was imposed across the vesicle wall (pH _i =8.0, pH _o =6.0), Na⁺-dependentJ _t ^SO4 was hyperbolic and significantly increased at each [Na⁺] _o over values observed using bilateral pH 8.0. In contrast, a H⁺ gradient oriented in the opposite direction (pH _i =6.0, pH _o =8.0) led to Na⁺-dependentJ _t ^SO4 that was sigmoidal and significantly lower at each [Na⁺] _o than values found using bilateral pH 6.0. Electrogenicity ofJ _t ^SO4 at pH 8.0 for both high and low [Na⁺] _o was demonstrated by using a valinomycin-induced transmembrane electrical potential difference. At pH 6.0, electrogenicJ _t ^SO4 occurred only at low [Na⁺] _o (5mm); anion transfer was electroneutral at 50mm Na⁺. A model is proposed for proton regulation of sodium sulphate cotransport where flux stoichiometry is controlled by [H⁺] _i and sodium binding affinity is modified by [H⁺] _o . Preliminary experiments with rabbit proximal tubular brush border membrane vesicles disclosed similarJ _t ^SO4 kinetic properties and a common transport mechanism may occur in both tissues.     

The secondary structure of a pyrimidine-guanine sequence-specific ribonuclease possessing cytotoxic activity from the oocytes of Rana catesbeiana

Summary RC-RNase is a pyrimidine-guanine sequence-specific ribonuclease and a sialic-acid-binding lectin purified from Rana catesbeiana (bullfrog) oocytes. This 111-amino acid protein exhibits cytotoxicity toward several tumor cell lines. In this paper we report the assignments of proton NMR resonances and the identification of the secondary structure deduced from NOE constraints, chemical shift index, ³J_NH and amide proton exchange rates. The protein was directly isolated from bullfrog oocytes; we were able to assign all but five of the amino acid backbone protons of the unlabeled protein by analyzing a large set of two-dimensional proton NMR spectra obtained at several temperatures and pH conditions. Our results indicate that the structure of RC-RNase is dominated by the presence of two triple-stranded antiparallel -sheets and three -helices, similar to those of the pyrimidine family ribonucleases. Two sets of resonances were observed for 11 amide protons and 8 -protons located in the loop-1 region, an 2 helix, and three -strands (1, 3 and 4), suggesting the presence of nonlocalized multiple conformations for RC-RNase.Abbreviations DQF-COSY double-quantum-filtered correlation spectroscopy - DTT dithiothreitol - NOE nuclear Overhauser enhancement - NOESY nuclear Overhauser enhancement spectroscopy - PE-1 N-terminal pyroglutamate - RC-RNase ribonuclease from the oocyte of Rana catesbeiana - TOCSY total correlation spectroscopy - TPPI time-proportional phase incrementation - TSP sodium 3-trimethylsilylpropionate-2,2,3,3-d ₄