Cytoskeletal proteins used as marker of differentiation in mouse terato;carcinoma cells

The cyclic AMP receptor protein (CRP) of Escherichia coli has been crystallized. The crystals are orthorhombic, space group $\text{P2}{}_1\text{2}{}_1\text{2}{}_1\text{, a = 46.5}\text{A}\text{?}$, b = 97.1 Å, $\text{c = 105.4}\text{A}\text{?}$, with one dimeric CRP molecule per asymmetric unit.     

Characterization of two new crystal forms of uteroglobin.

Two new crystal forms of oxidized uteroglobin have been obtained. An orthorhombic one ($\text{P2}{}_1\text{2}{}_1\text{2, Z = 2, a = 44.48 (5)}\text{A}\text{?}\text{, b = 36.93 (5)}\text{A}\text{?}\text{, c = 32·34 (5)}\text{A}\text{?}$) and a monoclinic one ($\text{P2}{}_1\text{, Z = 2, a = 44.56 (5)}\text{A}\text{?}\text{, b = 46.06 (5)}\text{A}\text{?}\text{, c = 37.43 (4)}\text{A}\text{?}\text{, β = 120.92 ° (5)}$). Both were grown at pH ~7.0 and diffract to a resolution of 2·1 to 2·2 Å. Data collections for native crystals have been recorded with an automatic four-circle diffractometer.     

Preliminary x-ray crystallographic data for the semisynthetic non-covalent complex of residues 1 to 118 and 111 to 124 of bovine pancreatic ribonuclease

The enzymically active, semisynthetic complex formed by residues 1 through 118 and residues 111 through 124 of bovine pancreatic ribonuclease has been crystallized at pH 5.7 from $\text{(}\text{NH}{}_4\text{)}{}_2\text{SO}{}_4\text{CsCl}$ solutions. The crystals belong to space group P3₂21, have unit cell dimensions $\text{a}\text{and}\text{b = 64.4}\text{A}\text{?}\text{, c = 64.5}\text{A}\text{?}\text{,}\text{and}$ γ = 120° and are isomorphous with form M of ribonuclease A as well as forms W and R of ribonuclease S. They diffract well and may be expected to yield a structure defined to at least 3.0 Å resolution.     

Yeast transfer RNAasp: a new high-resolution x-ray diffracting crystal form of a transfer RNA.

Systematic crystallization studies on brewer's yeast aspartic acid transfer RNA have yielded different crystal forms, one of them diffracting to 3 Å resolution. The high resolution crystal form is orthorhombic ($\text{C222}{}_1\text{, a = 61}\text{A}\text{?}\text{, b = 68}\text{A}\text{?}\text{, c = 148}\text{A}\text{?}$ with one molecule per asymmetric unit) and is stable for over four days under X-rays.     

Location of iron in the Fe2+-bleomycin complex as observed by 13C NMR spectroscopy.

The antineoplastic action of bleomycin is currently thought to arise from the degradation of cellular DNA by the iron-bleomycin complex. Bleomycin A₂ has one iron binding site as revealed by the iron-titrations of bleomycin monitored optically. To probe the structure of the Fe²⁺-bleomycin complex, we studied the paramagnetic effects of its high spin ferrous iron on the nuclear relaxation rates ($\text{1}\text{T}{}_1$) of the natural abundance carbon-13 atoms in the molecule. The presence of Fe²⁺ in bleomycin predominantly enhances the $\text{1}\text{T}{}_1$ of only four protonated carbon atoms in the molecule (C2, C3, C5, and C6). No other protonated carbon atoms are affected significantly. From the magnitudes of the paramagnetic effects of Fe²⁺ on the ¹³C relaxation rates, we obtain distances of 3.6, 4.1, 4.0, and 3.6 Å from the metal to the C2, C3, C5, and C6 carbon atoms, respectively. These results are consistent with the metal ion-chelation of the α-amino group of the terminal diaminopropionic acid residue and the pyrimidine ring but do not implicate any other parts of the bleomycin molecule in binding to iron.     

Ubisemiquinone radicals from the cytochrome b-c1 complex of the mitochondrial electron transport chain--demonstration of QP-S radical formation

Stable ubisemiquinone radical(s) in the cytochrome $\text{b}\text{?}\text{c}{}_1$-II complex of bovine heart was observed following reduction by succinate in the presence of catalytic amounts of succinate dehydrogenase. The radical was abolished by addition of antimycin A, but a residual radical remained in the presence of excess exogenous Q₂. The radical showed an EPR signal of g = 2.0046 ± .003 at X band (～9.4 GHz) with no resolved hyperfine structure and had a line width of 8.1 ± .5 Gauss at 23°C. The Q band (35 GHz) spectra showed wellresolved $\text{g}$-anisotropy and had a field separation between derivative extrema of 26 ± 1 Gauss. This radical is evidently from QP-C. These observations substantiate that the radical is immobilized and bound to a protein. The QP-S radical was demonstrated in the cytochrome $\text{b}\text{-}\text{c}{}_1$-II complex only in the presence of more than a catalytic amount of succinate dehydrogenase and cytochrome $\text{b}\text{-}\text{c}{}_1$. This signal was not antimycin a inhibitory. The signal amplitude paralleled the reconstitutive enzymic activity of succinate-cytochrome $\text{c}$ reductase from succinate dehydrogenase and the cytochrome $\text{b}\text{-}\text{c}{}_1$-II complex.     

Conversion of thyroxine to 3,3',5'-triiodothyronine (reverse-T3) by a soluble enzyme system of rat liver

Infrared spectra of N₂O in a variety of solvents and in the brain of a dog under typical conditions of halothane-N₂O anesthesia have been determined. The appearance or disappearance of N₂O in the brain was readily followed as N₂O was administered or withdrawn. The sites in brain were of two major types; one, with ν₃ = 2229.8 ± 0.4 cm^?1 and $\text{Δν}{}_{\mathrm{<mtext>1</mtext><mtext>2</mtext>}}\text{= 13.0 ± 0.6}\text{cm}{}^{\mathrm{?1}}$, is rather like the polar site in water and the other, with ν₃ = 2216.8 ± 0.8 cm^?1 and $\text{Δν}{}_{\mathrm{<mtext>1</mtext><mtext>2</mtext>}}\text{= 9.6 ± 1.0}\text{cm}{}^{\mathrm{?1}}$, is non-polar and is probably associated with membrane lipid. The significant variations in the antisymmetric stretch (ν₃) of N₂O as the polarity and other properties of the medium (solvent) vary make possible the characterization of $\text{in tissue}$ sites occupied by this anesthetic.     

Lipid-protein interactions in membrane models fluorescence polarization study of cytochrome b5-phospholipids complexes

According to previous authors, cytochrome $\text{b}{}_5$, when extracted from bovine liver by a detergent method, is called cytochrome $\text{d-b}{}_5$. On the other hand, the protein obtained after trypsin action, which eliminates an hydrophobic peptide of about 54 residues, is called cytochrome $\text{t-b}{}_5$.Fluorescence polarization of the dansyl phosphatidylethanolamine probe inserted into phospholipid vesicles is very senstive to the binding of proteins, and so is a useful method to study lipid-protein interactions.The chromophore mobility, $\text{R}$, decreases markedly when dipalmitoyl phosphatidylcholine vesicles are incubated with cytochrome $\text{d-b}{}_5$, whereas $\text{R}$ does not change for cytochrome $\text{c}$ and cytochrome $\text{t-b}{}_5$. This can be interpreted as a strengthening of the bilayer, only due to the interaction of the hydrophobic peptide tail.Interaction of dipalmitoyl phosphatidylcholine vesicles with cytochrome $\text{d-b}{}_5$ occurs either below or above the melting temperature of the aliphatic chains (41 °C). Even for a high protein to lipid molar ratio (1 molecule of protein for 40 phospholipid molecules), the melting temperature is apparently unaffected.Phosphatidylserine and phosphatidylinositol do not interact at pH 7.7 with cytochrome $\text{d-b}{}_5$, because electrostatic forces prevent formation of complexes. At low pH, the interaction with the protein occurs, but the binding is mainly of electrostatic nature.     

Hydrolysis of a thiopeptide by cadmium carboxypeptidase A

Substitution of the active site zinc ion of carboxypeptidase A by cadmium yields an enzyme inactive towards ordinary peptide substrates. However, a substrate analog (BzGlyNHCH₂CSPheOH) containing a thioamide linkage at the scissile position is cleaved to the thioacid. The kinetic parameters and their pH dependencies are $\text{k}{}_{\mathrm{cat}}\text{K}{}_{\mathrm{m}}\text{= 5.04 × 10}{}^4\text{min}{}^{\mathrm{?1}}\text{M}{}^{\mathrm{?1}}$, decreasing with either acid or base (PK_E1 = 5.64, pK_E2 = 9.55), and k_cat = 1.02 × 10² min^?1, decreasing with acid (pK_ES = 6.61). The thiopeptide is less efficiently cleaved by native (zinc) carboxypeptidase A. This cadmium-sulfur synergism supports a mechanism wherein the substrate amide is activated by metal ion coordination to its (thio) carbonyl.     

The structure of the fluorophosphate-pyruvate kinase complex investigated by 31P relaxation rate studies

The interaction of fluorophosphate with muscle pyruvate kinase was investigated by ³¹P nuclear relaxation rate measurements. The fluorophosphate samples were highly purified and were first monitored by ¹⁹F and ³¹P relaxation rate measurements in the formation of the binary FPO₃-Mn complex. The results of the binary complex demonstrated that FPO₃^2? binds in the first coordination sphere of Mn²⁺ via the oxygen atoms but not via the fluorine. The enzyme experiments were designed under conditions where a significant fraction of the ligand is in the ternary enzyme-Mn-FPO₃ complex. These studies demonstrate that the ³¹P relaxation rate of bound FPO₃ ($\text{1}\text{T}{}_{\mathrm{<mtext>1</mtext><mtext>m</mtext>}}\text{= 1.58 ± 0.05 × 10}{}^5\text{s}{}^{\mathrm{?1}}$) is consistent with the binding of this ligand in the first coordination sphere of enzyme-bound Mn²⁺ with an elongated Mn-O-P distance ($\text{r}{}_{\mathrm{<mtext>Mn-P</mtext>}}\text{= 3.3 ± 0.2}\text{A}\text{?}$). Such a structure is demonstrated in the ternary enzyme-Mn-FPO₃ complex, in the complex containing HCO₃^?, and in the complex also containing HCO₃^? and ADP. The data further substantiate the binding of phosphoenolpyruvate analogs in the first coordination sphere of pyruvate kinase-bound Mn²⁺.     

Studies on coenzyme binding to glyceraldehyde-3-phosphate dehydrogenase.

Tyrosyl-transfer RNA synthetase from Bacillus stearothermophilus has been crystallized as hexagonal plates, $\text{P3}{}_1\text{21, a = b = 64.6}\text{A}\text{?}\text{, c = 238.8}\text{A}\text{?}$, with the dimeric molecule (molecular weight, 90,000) occupying two crystallographic asymmetric units (Reid et al., 1973). Three heavy-atom derivatives have been identified and X-ray diffraction measurements have been made to 2.7 Å resolution, using the oscillation method. The three heavy-atom derivatives were methyl mercury (two sites, half occupied, 3 Å apart), uranyl acetate (single fully occupied site) and chloroplatinite PtCl₄^2? (three sites of differing occupancy). The results were used to compute an electron density map at 2.7 Å resolution, which shows the monomer as a unit of about 60 Å × 60 Å × 40 Å. The maximum dimension of the dimer is about 130 Å. Most of the polypeptide chain has been traced uniquely. It includes five α-helices more than 12 Å long and several shorter helices. A six-stranded pleated-sheet structure lies in the centre of each subunit. The catalytic site of the enzyme is believed to be adjacent to the mercury-binding group.     

Isolation of bovine cytochrome c1 as a single non-denatured subunit using gel filtration or high pressure liquid chromatography in deoxycholate

The non-denatured cytochrome $\text{c}{}_1$ subunit of bovine ubiquinone-cytochrome $\text{c}$ reductase was isolated using either gel filtration or high pressure liquid chromatography in 1% deoxycholate. The preparation was a single band on polyacrylamide gel electrophoresis in dodecyl sulfate, had a heme content of 31 nmol heme/mg protein, had an absorbance ratio $\text{A}{}_{417}\text{A}{}_{278}\text{= 2.65}$, a visible spectrum with maxima at 553, 530, 523.5, 417, 317, and 277 nm for the reduced protein, and an amino acid analysis identical to that previously reported for the isolated denatured protein. The Stokes' radius of this non-denatured deoxycholate solubilized protein was 34Å, indicating that the protein either is a dimer in deoxycholate, is asymmetric, or binds large amounts of detergent.     

Polar group interaction and molecular packing of membrane lipids: The crystal structure of lysophosphatidylethanolamine

The conformation and molecular packing of 3-palmitoyl-dl-glycerol-1-phosphoryl-ethanolamine has been determined by a single crystal analysis (R = 0.115); it crystallizes in the monoclinic space group $\text{P2}{}_1\text{a}$ with a unit cell of $\text{a = 7.66}\text{A}\text{?}\text{, b = 9.08}\text{A}\text{?}\text{, c = 37.08}\text{A}\text{?}\text{and}\text{β = 90.2 °}$, with four molecules per unit cell. The molecules exist as configurational and conformational enantiomers and pack in a bilayer arrangement. The phosphorylethanolamine groups have an orientation parallel to the layer surface. The hydrocarbon chains are arranged according to the T∥ chain packing mode and adopt an extreme tilt of 57.5 ° with respect to the layer normal. The free glycerol hydroxyl group forms an intramolecular hydrogen bond with, a phosphate oxygen and thus affects the conformation and orientation of the head group. The phosphorylethanolamine dipoles are oriented parallel to each other in double rows, while they are antiparallel and form a continuous network in dilauroylphosphatidylethanolamine (Elder et al., 1977). The area per molecule in 3-palmitoyl-dl-glycerol-1-phosphorylethanolamine (34.8 Ų) is less than in diacylphosphatidylethanolamine (38.6 Ų), indicating that in the latter the hydrocarbon chains determine the molecular cross-section. The significance of the interaction and space requirement of the phosphorylethanolamine group for the phase behaviour of phosphatidylethanolamine is discussed.     

Evidence for a protonmotive Q cycle mechanism of electron transfer through the cytochrome b-c1 complex.

A protein named oxidation factor can be reversibly removed from succinate-cytochrome $\text{c}$ reductase complex and shown to be required for electron transfer between succinate and cytochrome $\text{c}$. This protein is required for reduction of cytochrome $\text{c}{}_1$ and, in the presence of antimycin, for reduction of both cytochromes $\text{b}$ and $\text{c}{}_1$. These results are consistent with a protonmotive Q cycle mechanism in which the oxidation factor catalyzes electron transfer from reduced quinone to cytochrome $\text{c}{}_1$ and thus liberates from reduced quinone one of two protons required for energy conservation during electron transfer through the cytochrome $\text{b}\text{-}\text{c}{}_1$ complex.     

Respiration-driven proton translocation with nitrite and nitrous oxide in Paracoccus denitrificans

(1) $\text{H}$⁺/electron acceptor ratios have been determined with the oxidant pulse method for cells of denitrifying Paracoccus denitrificans oxidizing endogenous substrates during reduction of O₂, NO^?₂ or N₂O. Under optimal H⁺-translocation conditions, the ratios $\text{H}{}^{\mathrm{+}}\text{O}$, $\text{H}{}^{\mathrm{+}}\text{N}{}_2\text{O}$, $\text{H}{}^{\mathrm{+}}\text{NO}{}^{\mathrm{?}}{}_2$ for reduction to N₂ and $\text{H}{}^{\mathrm{+}}\text{NO}{}^{\mathrm{?}}{}_2$ for reduction to N₂O were 6.0–6.3, 4.02, 5.79 and 3.37, respectively. (2) With ascorbate/N,N,N′,N′-tetramethyl-p-phenylenediamine as exogenous substrate, addition of NO^?₂ or N₂O to an anaerobic cell suspension resulted in rapid alkalinization of the outer bulk medium. $\text{H}{}^{\mathrm{+}}\text{N}{}_2\text{O}$, $\text{H}{}^{\mathrm{+}}\text{NO}{}^{\mathrm{?}}{}_2$ for reduction to N₂ and $\text{H}{}^{\mathrm{+}}\text{NO}{}^{\mathrm{?}}{}_2$ for reduction to N₂O were ?0.84, ?2.33 and ?1.90, respectively. (3) The $\text{H}{}^{\mathrm{+}}\text{oxidant}$ ratios, mentioned in item 2, were not altered in the presence of $\text{valinomycin}\text{K}{}^{\mathrm{+}}$ and the triphenylmethylphosphonium cation. (4) A simplified scheme of electron transport to O₂, NO^?₂ and N₂O is presented which shows a periplasmic orientation of the nitrite reductase as well as the nitrous oxide reductase. Electrons destined for NO^?₂, N₂O or O₂ pass two H⁺-translocating sites. The $\text{H}{}^{\mathrm{+}}\text{electron}$ acceptor ratios predicted by this scheme are in good agreement with the experimental values.     

Electron diffraction study on single crystals of l-type and dl-type lecithins

An electron diffraction study was carried out on thin single micro-crystals of l-type and dl-type dipalmitoyl lecithins grown in xylene suspensions and fine net patterns were obtained and the mechanism of the thermotropic phase transitions of them was clarified.From the apparent structure of diffraction patterns in low temperature, it is confirmed that the two dimensional lattices have p mm symmetry in l-type and in dl-type lecithins. Lattice parameters from the [001] projection are $\text{d}{}_{100}\text{= 9.9}\text{A}\text{?}$ and $\text{d}{}_{010}\text{= 8.8}\text{A}\text{?}$ in l-type, and $\text{d}{}_{100}\text{= 17.2}\text{A}\text{?}$ and $\text{d}{}_{010}\text{= 8.9}\text{A}\text{?}$ in dl-type.With anisotropic variation of dimensions along a and b axes, i.e. contraction for a and expansion for b, induced by temperature rise by electron irradiation during the observation, these diffraction patterns of the lattices of l-type and dl-type were transformed into those characterized by the six diffraction spots having nearly the same spacings. Four of them are observed on slightly outer and two are slightly inner positions as compared with their mean spacings of about (4.1 Å)^?1 in l-type and about (4.2 Å)^?1 in dl-type. The changes in the patterns observed indicate that at low temperatures the hydrocarbon chains are nearly perpendicular to the layer in dl-type lipid, and tilted with a more complicated packing in l-type ones. The dimension along a in dl-type is twice as large as that in l-type.     

Structure of the semiquinone form of flavodoxin from Clostridum MP. Extension of 1.8 A resolution and some comparisons with the oxidized state

As part of a series of comparisons of the structures of the three oxidation states of flavodoxin from Clostridium MP, phases for the semiquinono form were determined to 2.0 Å resolution by isomorphous replacement (〈m 〉 = 0.725). Subsequently, the structure was refined at 1.8 Å resolution by a combination of difference Fourier, real space and reciprocal space methods. After refining to an R of 0.194, we explored the conformation of the FMN binding site by real space refinement versus maps with Fourier coefficients of the form ($\text{2¦F}{}_{\mathrm{<mtext>o</mtext>}}\text{¦? ¦F}{}_{\mathrm{<mtext>c</mtext>}}\text{¦)}\text{exp}\text{(iα}{}_{\mathrm{<mtext>c</mtext>}}$). To minimize bias in the fitting, groups of atoms were systematically omitted from the structure factors used in computation of the ($\text{2¦F}{}_{\mathrm{<mtext>o</mtext>}}\text{? ¦F}{}_{\mathrm{<mtext>c</mtext>}}\text{¦}$) maps.One-electron reduction of oxidized flavodoxin is accompanied by several changes at the FMN binding site: the conformation of residues in the reverse bend formed by Met56-Gly57-Asp58-Glu59 differs in the crystal structures of the oxidized and semiquinone species; further, backbone atoms in residues 55 and 89 shift by more than 0.5 Å and the indole ring of Trp90 undergoes a significant displacement. The orientation of the peptide unit connecting Gly57 and Asp58 is consistent with the presence of a hydrogen bond between the carbonyl oxygen of Gly57 and the flavin N(5) in flavodoxin semiquinone. No equivalent bond is found in oxidized flavodoxin. In both the oxidized and semiquinone species of clostridial flavodoxin, the isoalloxazine ring is essentially planar : the bending angles about N(5)N(10) are ~2.5 ° for the semiquinone structure and ~0 ° in oxidized flavodoxin.The intensity changes resulting from the oxidized agsemiquinone conversion (R_I = 0.33) arise in part from changes in molecular packing. Intermolecular contacts, including neighbors of the prosthetic group, are altered in the repacking. Maps or models of the two oxidation states can be brought into approximate coincidence by a rigid body motion. The required transformation, determined for the isomorphous replacement maps by the method of Cox (1967), is equivalent to a screw motion with a rotation of 1.18 ° and a translation of ?0.34 Å. The molecular structures of oxidized and semiquinone flavodoxins have been compared after superposition of models with idealized co-ordinates and discrepancy indices Rox = 0.213 and Rsq = 0.200. The root-mean-square distance between 523 backbone atoms (excluding sequences 56 to 59 and 89 to 91) is 0.308 Å.     

Carnitine movement across muscle cell membranes. Studies in isolated rat muscle

l-Carnitine uptake and exodus was studied in rat extensor digitorum longus muscle in vitro. A saturable transport process was observed, which had an apparent $\text{K}{}_{\mathrm{<mtext>m</mtext>}}$ of 60 μM and $\text{V}$ of 22 nmol/h per g tissue. Transport was inhibited by 2,4-dinitrophenol, sodium azide, anaerobiosis, ouabain, and sodium ion depletion. Analogs of l-carnitine containing a quarternary ammonium group were found to inhibit uptake (d-carnitine, $\text{K}{}_{\mathrm{<mtext>i</mtext>}}\text{= 400 μ}\text{M}$ γ-butyrobetaine, $\text{K}{}_{\mathrm{<mtext>i</mtext>}}\text{= 60 μ}\text{M}$, choline chloride, $\text{K}{}_{\mathrm{<mtext>i</mtext>}}\text{= 14}\text{mM}$), while those not containing this functional group (γ-aminobutyrate, d,l-β-hydroxybutyrate) had no significant effect at concentrations 100 times the apparent $\text{K}{}_{\mathrm{<mtext>m</mtext>}}$ of l-carnitine. Carnitine exodus from rat extensor digitorum longus muscle consisted of two phases. The rapid initial phase was attributed to leakage of l-carnitine from damaged muscle fibers, as it proceeded at nearly the same rate at 0° and 37°C, and leveled off to a rate of near zero after 1 h of incubation in vitro. The quantitatively more important phase of exodus showed a latency of 1–2 h and then proceeded at a linear rate of 40–45 nmol/h per g tissue. The results of this study support the contention that l-carnitine is taken up by a carrier-mediated, active transport system in rat extensor digitorum longus muscle. Functionally, the transport system for uptake is distinct from the process by which carnitine is lost from this muscle.     

Preliminary crystallographic data for actinidin,a thiol protease from Actinidia chinensis

Crystals of actinidin, a thiol protease from the fruit of Actinidia chinensis, which are suitable for high-resolution X-ray diffraction studies, have been obtained. The space-group is $\text{P2}{}_1\text{2}{}_1\text{2}{}_1\text{,}\text{with}\text{a = 78.1}\text{A}\text{?}\text{, 6 = 81.2}\text{A}\text{?}\text{and}\text{c = 33.0}\text{A}\text{?}$. The asymmetric unit contains one molecule, of molecular weight about 26,000.