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At least 1,099 records · Page 61Linked to original sources
PubMed1985

Structure of rabbit muscle aldolase at low resolution.

X-ray diffraction data were measured by x-ray diffractometry to 5-A resolution for both the monoclinic form of rabbit skeletal muscle aldolase (EC 4.1.2.13) and a platinum derivative. The heavy atom difference patterson was solved at 6-A resolution yielding eight distinct heavy atom sites. Choice was made of the enantiomorph and protein phases were calculated on the basis of single isomorphous replacement differences. The electron density map calculated from these phases was averaged according to the non-crystallographic molecular symmetry. Rotational symmetry analysis of native patterson and site symmetry analysis of refined heavy atom positions are consistent with the aldolase tetramer possessing a very high degree of 222 internal symmetry. The subunits in the tetramer are positioned in a tetrahedral configuration displaying a slight square planar deformation. Each subunit is roughly ellipsoidal in shape with the major axis nearly parallel to a local 2-fold axis. Prominent at the surface of each subunit were structural features resembling alpha helices. Each subunit contributes to its boundary surface at least six helices which are arranged in a barrel-like manner and possessing a right handed twist with respect to each other. Density associated with binding of substrate on the enzyme was located on the surface of each subunit. Cooperative aspects of the conformational changes produced upon substrate binding are discussed.

Animals↗
PubMed1989

Elucidation of intermediate (mobile) and slow (solidlike) protein motions in bovine lens homogenates by carbon-13 NMR spectroscopy.

The motional dynamics of lens cytoplasmic proteins present in calf lens homogenates were investigated by two 13C nuclear magnetic resonance (NMR) techniques sensitive to molecular motion to further define the organizational differences between the cortex and nucleus. For the study of intermediate (mobile) protein rotational reorientation motion time scales [rotational correlation time (tau 0) range of 1-500 ns], we employed 13C off-resonance rotating frame spin-lattice relaxation, whereas for the study of slow (solidlike) motions (tau 0 greater than or equal to 10 microseconds) we used the solid-state NMR techniques of dipolar decoupling and cross-polarization. The frequency dependence of the peptide bond carbonyl off-resonance rotating frame spectral intensity ratio of the lens proteins present in native calf nuclear homogenate (42% protein) at 35 degrees C indicates the presence of a polydisperse mobile protein fraction with a tau 0,eff (mean) value of 57 ns. This mean value is consistent with the average value calculated from the known water-soluble nuclear lens protein polydispersity assuming a cytoplasmic viscosity 3 times that of pure water. Lowering the temperature to 1 degree C, a temperature which produces the cold cataract, results in an overall decrease in tau 0,eff to 43 ns, suggesting a selective removal of beta H-, LM-, and possibly gamma s-crystallins from the mobile lens protein population. The presence of solidlike or motionally restricted protein species was established by dipolar decoupling and cross-polarization. The fraction of motionally restricted protein in the nuclear region varied from 0.35 to 0.45 in the temperature range of 35-1 degree C. For native cortical homogenate (25% protein), the off-resonances rotating frame spectral intensity ratio frequency-dependent curves for the protein carbonyl resonance yielded tau 0,eff values of 34 and 80 ns at 35 and 1 degree C, respectively. Both values were reconciled with the known lens cortex soluble protein polydispersity using an assumed cytoplasmic viscosity 1.5 times that of pure water at the same temperature. Comparison of proton dipolar-decoupled and nondecoupled 13C NMR spectra of native cortical homogenate at 20 degrees C indicates the absence of significant contributions from slowly tumbling, motionally restricted species. This interpretation was confirmed by the failure to detect significant lens protein 13C-1H cross-polarization at this temperature. However, at 1 degree C, the fraction of solidlike protein was 0.15. Concentrated cortical homogenates at 20 degrees C (42% protein), by contrast, gave cross-polarization spectra with maximum absolute signal intensities 50-70% of native nuclear homogenates, but with similar magnetization parameters...

Animals↗
PubMed1978

Transient electric dichroism of rod-like DNA molecules.

We report transient electric dichroism studies on monodisperse rod-like DNA molecules. By using restriction fragments and DNAs of known length, it is shown that the orientation time is accurately predicted by the theoretically calculated rotational diffusion coefficient. The field dependence of the steady-state dichroism values is not consistent with the induced electric dipole orientation mechanism, and the time dependence is not consistent with the presence of a permanent dipole moment. In order to explain the dependence of the dichroism on the electric field, the ionic strength of the medium, and the length of the macromolecule, we propose a new model in which anisotropic ion flow produces an asymmetric ion atmosphere around the polyelectrolyte, resulting in an orienting torque. From the limiting dichroism at high field, we estimate that the DNA bases are inclined at an angle of 73 degrees or less relative to the helix axis, in good agreement with the revised model of B-form DNA suggested by Levitt, in which the base pairs have a propeller-like twist. Our results establish transient electric dichroism measurements as a technique well suited for study of alterations in the length and base pair inclination of rod-like DNA molecules.

Anions↗
PubMedDate not supplied

Dielectric dispersion of polypeptide solutions. II. Helix-coil transition of poly(epsilon-carbobenzoxy-L-lysine) in m-cresol.

Dielectric dispersion measurements were made on dilute solutions of poly(epsilon-carbobenzoxy-L-lysine) in m-cresol; this system underwent a very sharp thermal helix-coil transition of inverse type around 30 degrees. Mean-square dipole moments "mu-2" and mean rotational relaxation times t were obtained as functions of molecular weight and helical fraction fN. It was found that "mu-2"-one-half varied almost linearly with fN-one-half over a substantial portion of the transition. The relaxation times corrected for solvent viscosity and temperature changed only slightly with fN except in the region of small fN, while, at fixed fN, they displayed molecular weight dependence characteristic of rod-like molecules. These results can be explained if the transition is assumed to proceed almost in all-or-none fashion. This assumption is consistent with the previous finding from statistical thermodynamic analyses that the transition of the system PCBL-m-cresol is highly cooperative, with standard deviation of population one-half being 0.0025 to 0.0027, where standard deviation of population is the cooperativity parameter. Application of Nagai's theory of "mu-2" for interrupted helices yielded the result that standard deviation of population-one-half was in the range 0.001 to 0.005 and the monomeric dipole moment in the helical conformation was 5.4 to 6.2 D.

Benzyl Compounds↗
PubMed1986

Conformational transmission in the glyceryl backbone of phospholipid model compounds, induced by a P(4-coordinated) into trigonal bipyramidal P(5-coord) transition.

Triesterified phospholipid model compounds have been synthesized and extensively studied with 300-MHz 1H NMR in the monomer phase in order to get additional support for the effect of conformational transmission induced by a P(4-coord) into a trigonal bipyramidal P(5-coord) transition, as was suggested by Merkelbach and Buck. To elucidate any conformational preferences around the C2-C3 bond, the stereospecifically deuterated precursor 1,2-dihexanoyl-(3R)-sn-[3-2H]glycerol was synthesized. The results reveal that a coordinational change of phosphorus from four to five is transmitted in a significant increase in population of the conformer, in which the vicinally substituted oxygens O-2 and O-3 are trans located. The impact of this transmission seems not to be restricted to conformational changes in the adjacent C2-C3 bond, but is also present in specific rotations around the C1-C2 bond, thereby shifting the C1-C2 conformational equilibrium towards a decreased contribution of the trans arrangement of the acyl chains. As a consequence the interchain distance will be reduced and thus van der Waals interactions will be maximized. The results are interpreted in terms of increased electron density on O-3 when axially located in a P(5-coord) trigonal bipyramidal compound, thereby introducing enhanced electrostatic repulsions within the oxygen pairs O-3, O-2 and O-3, O-1. Relaxation of this energetically unfavourable geometry leads to the observed conformational shifts. Absence of conformational transmission, as found in P(5-coord) trigonal bipyramidal compounds with the 2-ester group substituted for an alkyl moiety, can be considered as additional support for the introduced concept. In the alkyl part of the model phospholipids, however, no conformational changes were observed by means of 13C NMR. Extrapolating this outcome to more condensed phases, a proposition could be made about the mechanism by which conformational changes in the head-group and/or glyceryl backbone will be compensated.

Cadmium↗
PubMed1986

Temperature and pH dependence of the haemolytic activity of influenza virus and of the rotational mobility of the spike glycoproteins.

Influenza virus (strain X-47) was labeled with the triplet probe, eosin 5-isothiocyanate. Most of the label was found to be associated with haemagglutinin, the major glycoprotein of the viral envelope. Rotational diffusion of the glycoprotein was investigated by measuring flash-induced transient dichroism of the eosin probe. The anisotropy decay curves showed that mobility of haemagglutinin measured at pH 7.3 increased considerably with temperature with the greatest change occurring over the range 20-30 degrees C. However, at pH 5.2 no mobility was detectable over the time range of the experiment. The activity of the virus was determined by assaying haemolysis of human erythrocytes. The haemolytic activity showed an optimum at pH 5.2 and increased markedly with temperature, being negligible below 20 degrees C. In addition, inactivation of the virus by incubation at pH 5.2 was also strongly temperature dependent. A 15 min incubation at pH 5.2 inactivated the virus above 30 degrees C but had no effect below 20 degrees C. On the basis of these results, it is proposed that mobility of haemagglutinin is significant for its functional properties. When the pH is reduced from 7.3 to 5.2, the mobility observed at higher temperatures is required for the molecular rearrangements which accompany the fusion event. In the absence of an apposing membrane, these rearrangements result in irreversible aggregation of haemagglutinin in the viral membrane, and hence loss of mobility and activity.

Circular Dichroism↗
PubMed1975

Analogs of natural lipids. I. Synthesis and properties of tris-homoacyl derivatives of cyclopentane- 1,2,3-triols.

A new series of analogs of triglycerides has been synthesized, in which the glycerol moiety is replaced by each of the three isomeric cyclopentanetriols. For each of the isomeric cyclopentane-1,2,3-triols (1,2,3/0; DL-1,2/3; and 1,3/2), the tris-homoacyl derivatives of octanoic, decanoic, lauric, myristic, palmitic, stearic, and dihydrosterculic acids were prepared by treatment of the respective triols with the appropriate acyl chloride in pyridine. The dihydrosterculates were prepared by fusing the triols with a mixture of the acyl anhydride and the corresponding potassium salt. It is proposed that because of restricted rotation of the carbon-carbon bonds the cyclopentanoid compounds are analogs of specific rotamers of triglycerides. Infrared spectra (KBr discs) obtained at room temperature show differences in crystal structure from series to series. A band near 720 cm-minus 1 (CH2 rock) is doubled in the 1,2,3/0 and 1,2/3 series and is single in the 1,3/2 series and the triglycerides. In each spectrum with a doublet at 720 cm-minus 1, a band near 1470 cm-minus 1 (CH2 bend) is doubled also. A strong band at 890 cm-minus 1 present in the triglyceride spectra is weak or missing from the spectra of the analogs. A band at 1418 cm-minus 1 (bending of CH2 adjacent to C equal to 0) present in the triglyceride spectra is demonstrable only in the 1,2,3/0 derivatives in comparison with the other three series. In all series the dihydrosterculates show a decrease in apparent polarity, relative to the stearates, significantly greater than expected from the introduction of an additional carbon atom. The potential utility of the analogs as probes of the effects of conformation on the physical properties and enzymatic susceptibility of glycerides is discussed.

Alcohols↗
PubMed1982

Hydrodynamic determination of molecular weight, dimensions, and structural parameters of Pf3 virus.

Measurements of the translational, DT, and rotational, DR, diffusion coefficients of Pf3 virus by low-angle polarized intensity fluctuation spectroscopy and field-free transient electric birefringence, respectively, give a length of 720 +/- 25 nm and diameter of 6.5 +/- 1.5 nm upon simultaneous solution of the Broersma equations for rigid rods. Sedimentation coefficient and density increment values obtained under solvent conditions identical with those of DT give a molecular weight of (13.4 +/- 0.8) x 10(6) g mol-1, which gives a mass per length of 18 600 +/- 1300 g mol-1 nm-1. Combining these results with the molecular weight of Pf3 DNA yields a number of protein subunits of 2500 +/- 160 and 2.38 +/- 0.14 nucleotides/protein subunit. Sedimentation coefficient and density increment values of Xf virus when combined with a value for the Xf translational diffusion coefficient [Chen, F. C., Koopmans, G., Wiseman, R. L., Day, L. A., & Swinney, H. L. (1980) Biochemistry 19, 1373] yield a molecular weight of (17.9 +/- 1.0) x 10(6) g mol-1, a number of protein subunits of 3590 +/- 230, 2.07 +/- 0.15 nucleotides/protein subunit, and a mass per length of 18 300 +/- 1200 g mol-1 nm-1. Thus, despite major differences in the DNA-protein packing between these viruses, as well as fd virus, the mass per lengths are surprisingly similar.

Bacteriophages↗
PubMed1981

[Polarimetric determination of alpha-amylase activity (author's transl)].

In the study of the relatively slow amylase-catalysed hydrolysis of oligosaccharides, it is assumed that the subsequent mutarotation has essentially no effect on the kinetics of the total reaction. Relatively large sampled and long measurement times (slow rate of change in angle of rotation) are necessary for the polarimetric determination of alpha-amylase activity. For these reasons, only urine and duodenal juice are suitable as sample sources. Owing to the absence of coupled reactions and auxilliary enzymes, the polarimetrically determined kinetics are generally more representative of the true kinetics of the amylase reaction, than those obtained with fully enzymic methods; in addition, single determinations by the polarimetric method are less subject to interference by sample components. With measurement times in the order of minutes, the polarimetric method shows excellent linearity, very good proportionality between analytical response and quantity of enzyme, and good precision in series (CV = 1.3%). Comparison of the polarimetric with a chromogenic and a fully enzymic method showed an acceptable correlation (r for each method was about 0.98). T, the polarimetric method shows excellent linearity, very good proportionality between analytical response and quantity of enzyme, and good precision in series (CV = 1.3%). Comparison of the polarimetric with a chromogenic and a fully enzymic method showed an acceptable correlation (r for each method was about 0.98). T, the polarimetric method shows excellent linearity, very good proportionality between analytical response and quantity of enzyme, and good precision in series (CV = 1.3%). Comparison of the polarimetric with a chromogenic and a fully enzymic method showed an acceptable correlation (r for each method was about 0.98). The advantages and disadvantages of the polarimeatric method, with consideration of possible interfering factors, are discussed.

Amylases↗
PubMed1996

Enantiofacial selective reduction of 2-allyl-2-carboethoxy-cyclopentanone mediated by baker's yeast.

Enantioselective reduction of 2-allyl-2-carboethoxy-cyclopentanone (2) was accomplished in high enantiomeric excess (> 99%), using baker's yeast in the presence of CuO, to obtain the (+)-2-allyl-2-carboethoxy-cyclopentanol derivative (6). This methodology also provides an entry to corresponding beta-keto ester (-)-(2), representing an important strategy to prepare chiral functionalized 2-oxabicyclic[3.3.0]octane and 2-oxabicyclic[4.4.0]nonane derivatives, useful synthons to access new bioactive compounds.

Cyclopentanes↗
PubMed1997

Exciton chirality of bilirubin homologs.

Bilirubin, the yellow pigment of jaundice, is a bichromophoric tetrapyrrole that readily adopts either of two enantiomeric, folded conformations shaped like ridge-tiles and stabilized by a network of six intramolecular hydrogen bonds. Interconversion of these M and P helical chirality conformational enantiomers is rapid at room temperature but may be displaced toward either enantiomer by intramolecular non-bonded steric interactions. Introduction of a methyl group at the beta and beta' carbons of the propionic acid chains on the symmetric bilirubin analog, mesobilirubin-XIII alpha, shifts the conformational equilibrium toward the M or the P-chirality intramolecularly hydrogen-bonded conformer, depending only on the S or R stereochemistry at beta and beta', resulting in pigments with intense exciton coupling circular dichroism (CD) for the approximately 430 nm transition(s). Optically active synthetic analogs of bilirubin with propionic acid groups lengthened systematically to heptanoic acid (1-5) were synthesized and examined by spectroscopy to explore the influence of alkanoic acid chain length on conformation and intramolecular hydrogen bonding. In these diacids and their dimethyl esters (6-10), strong exciton chirality CD spectra are observed, and the data are correlated with molecular helicity.

Bilirubin↗
PubMed2000

Raman optical activity characterization of native and molten globule states of equine lysozyme: comparison with hen lysozyme and bovine alpha-lactalbumin.

Vibrational Raman optical activity (ROA) spectra of the calcium-binding lysozyme from equine milk in native and nonnative states are measured and compared with those of the homologous proteins hen egg white lysozyme and bovine alpha-lactalbumin. The ROA spectrum of holo equine lysozyme at pH 4.6 and 22 degrees C closely resembles that of hen lysozyme in regions sensitive to backbone and side chain conformations, indicating similarity of the overall secondary and tertiary structures. However, the intensity of a strong positive ROA band at approximately 1340 cm(-1), which is assigned to a hydrated form of alpha helix, is more similar to that in the ROA spectrum of bovine alpha-lactalbumin than hen lysozyme and may be associated with the greater flexibility and calcium-binding ability of equine lysozyme and bovine alpha-lactalbumin compared with hen lysozyme. In place of a strong sharp positive ROA band at approximately 1300 cm(-1) in hen lysozyme that is assigned to an alpha helix in a more hydrophobic environment, equine lysozyme shows a broader band centered at approximately 1305 cm(-1), which may reflect greater heterogeneity in some alpha-helical sequences. The ROA spectrum of apo equine lysozyme at pH 4.6 and 22 degrees C is almost identical to that of the holo protein, which indicates that loss of calcium has little influence on the backbone and side chain conformations, including the calcium-binding loop. From the similarity of their ROA spectra, the A state at pH 1.9 and both 2 and 22 degrees C and the apo form at pH 4.5 and 48 degrees C, which are partially folded denatured (molten globule or state A) forms of equine lysozyme, have similar structures that the ROA suggests contain much hydrated alpha helix. The A state of equine lysozyme is shown by these results to be more highly ordered than that of bovine alpha-lactalbumin, the ROA spectrum of which has more features characteristic of disordered states. A positive tryptophan ROA band at approximately 1551 cm(-1) in the native holo protein disappears in the A state, which is probably due to the presence of nonnative conformations of the tryptophans associated with a previously identified cluster of hydrophobic residues.

Animals↗
PubMed2002

The separation of racemic crystals into enantiomers by chiral block copolymers.

A series of chiral double hydrophilic block copolymers (DHBCs) was synthesized and employed as additives in the crystallization of calcium tartrate tetrahydrate (CaT). We found that appropriate polymers can slow down the formation of the thermodynamically most stable racemic crystals as well as the formation of one of the pure enantiomeric crystals so that chiral separation by crystallization occurs even when racemic crystals can be formed. In addition, the presence of DHBCs results in major modifications of crystal morphology, creating unusual morphologies of higher complexity. Our study demonstrates the potential application of chiral DHBCs in the control of chirality throughout crystallization, in particular for racemic crystal systems, and also shows that enantiomeric excess of one enantiomer can be maximized by the kinetic control of crystallization.

Amino Acids↗
PubMed2002

Cyclotriveratrylene (CTV) as a new chiral triacid scaffold capable of inducing triple helix formation of collagen peptides containing either a native sequence or Pro-Hyp-Gly repeats.

A new triacid scaffold is described based on the cone-shaped cyclotriveratrylene (CTV) molecule that facilitates the triple helical folding of peptides containing either a unique blood platelet binding collagen sequence or collagen peptides composed of Pro-Hyp-Gly repeats. The latter were synthesized by segment condensation using Fmoc-Pro-Hyp-Gly-OH. Peptides were coupled to this CTV scaffold and also coupled to the Kemp's triacid (KTA) scaffold. After assembly of peptide H-Gly-[Pro-Hyp-Gly]2-Phe-Hyp-Gly-Glu(OAll)-Arg-Gly-Val-Glu (OAll)-Gly-[Pro-Hyp-Gly]2-NH2 (13) by an orthogonal synthesis strategy to both triacid scaffolds, followed by deprotection of the allyl groups, the molecular constructs spontaneously folded into a triple helical structure. In contrast, the non-assembled peptides did not. The melting temperature (Tm) of (+/-) CTV[CH2C(O)N(H)Gly-[Pro-Hyp-Gly]2-Phe-Hyp-Gly-Glu-Arg-Gly-Val-Glu-Gly- [Pro-Hyp-Gly]2-NH2]3 (14) is 19 degrees C, whereas KTA[Gly-Gly-[Pro-Hyp-Gly]2-Phe-Hyp-Gly-Glu-Arg-Gly-Val-Glu-Gly- [Pro-Hyp-Gly]2-NH2]3 (15) has a Tm of 20 degrees C. Thus, it was shown for the first time that scaffolds were also effective in stabilizing the triple helix of native collagen sequences. The different stabilizing properties of the two CTV enantiomers could be measured after coupling of racemic CTV triacid to the collagen peptide, and subsequent chromatographic separation of the diastereomers. After assembly of the two chiral CTV scaffolds to the model peptide H-Gly-Gly-(Pro-Hyp-Gly)5-NH2 (24), the (+)-enantiomer of CTV 28b was found to serve as a better triple helix-inducing scaffold than the (-)-enantiomer 28a. In addition to an effect of the chirality of the CTV scaffold, a certain degree of flexibility between the CTV cone and the folded peptide was also shown to be of importance. Restricting the flexibility from two to one glycine residues resulted in a significant difference between the two collagen mimics 20a and 20b, whereas the difference was only slight when two glycine residues were present between the CTV scaffold and the peptide sequence in collagen mimics 30a and 30b.

Circular Dichroism↗
PubMed2002

Efficient preparation of highly optically active (S)-(-)-2,3-allenols and (R)-(+)-2,3-allenyl acetates by a clean novozym-435-catalyzed enzymatic separation of racemic 2,3-allenols.

Novozym-435 has been found to be an effective biocatalyst for the kinetic resolution of a series of racemic 2,3-allenols, affording highly optically active (S)-(-)-2,3-allenols and (R)-(+)-2,3-allenyl acetates in high yields and with excellent ee values. The reaction of 3-(n-butyl)-3,4-pentadien-2-ol (1 a) was successfully performed on a 10 g scale to afford the corresponding (S)-(-)-2,3-allenol (1 a) and (R)-(+)-2,3-allenyl acetate (2 a) in synthetically useful amounts and with high ee values. The advantages of this reaction are the ready availability of the starting materials, high stereoselectivities for both (-)-2,3-allenols and (+)-2,3-allenyl acetates, the use of a relatively high substrate concentration, and a lower catalyst loading. The resulting (S)-(-)-2,3-allenol 1 a can be converted into the corresponding chiral 2,5-dihydrofuran and the vinylic epoxide.

Acetates↗