Protein rotation and chromophore orientation in reconstituted bacteriorhodopsin vesicles

Bacteriorhodopsin has been reconstituted into lipid vesicles with dipalmitoyl and dimyristoyls phosphatidylcholine. Circular dichroism (CD) measurements show that the proteins are in a monomeric state above the main lipid phase transition temperature (T_c), 41 and 23°C for dipalmitoyl and dimyristoyl phosphatidylcholine, respectively. Below T_c, the CD spectrum is the same as that found for the purple membrane. The latter result implies that the orientation of the chromophore at these temperatures is most likely the same as in the purple membrane ($\text{70° ± 5°}$ from the normal to the membrane plane).Transient dichroism measurements show that below T_c the proteins are immobile, while above this temperature protein rotation around an axis normal to the plane of the membrane is occurring. In addition, from the data the angle of the chromophore for the rotating proteins with respect to the rotational diffusion axis can be calculated. This angle is found to be $\text{30° ± 3°}$ and $\text{29° ± 4°}$ in dimyristoyl phosphatidylcholine and dipalmitoyl phosphatidylcholine, respectively. This is considerably smaller than the value of $\text{70° ± 5°}$ for the natural biomembrane. A reversible reorientation of the chromophore above and below the respective main T_c transition temperature could explain the change of angle observed provided that all the molecules rotate above T_c.     

The nature of the light-harvesting complex as defined by sodium dodecyl sulfate polyacrylamide gel electrophoresis

Reelectrophoresis of the oligomer form (CP II1) of the chlorophyll $\text{a}\text{b}$ light-harvesting complex (LHC) from the green alga Acetabularia yields two green bands which run at the position typical of the monomer (CP II). The upper green band (CP II₁) is enriched in the 27 kDa polypeptide of the LHC, while the lower is enriched in the 26 kDa polypeptide. The fact that both bands have both chlorophyll (Chl) a and b, and in the same ratio, implies that the LHC is made up of two Chl $\text{a}\text{b}$ proteins. Neither of these bands can be attributed to the Chl $\text{a}\text{b}$ complex ‘CP 29’ (Camm, E.L. and Green, B.R. (1980) Plant Physiol. 66, 428–432). Resolution of CP II₁ and CP II₂ of spinach can be obtained if sucrose gradient fractions of an octylglucoside extract are subjected to SDS-polyacrylamide gel electrophoresis. CP II₁ and CP II₂ are interpreted as being fundamental subunits of the light-harvesting complex as it is defined on SDS-polyacrylamide gels.     

Characterization of two crystal forms of neutrophil cationic protein NP2, a naturally occurring broad-spectrum antimicrobial agent from leukocytes

A hexagonal crystal form (P6₃22, $\text{a = b = 34.0}\text{A}\text{?}\text{, c = 113.5}\text{A}\text{?}$) and a monoclinic form (P2₁, $\text{a = 37.1}\text{A}\text{?}\text{, b = 32.2}\text{A}\text{?}\text{, c = 32.4}\text{A}\text{?}\text{, β = 110 °}$) of neutrophil cationic protein NP2, isolated from rabbit leukocytes, have been characterized. The monoclinic form, containing two promoters (M_r = 3844) per asymmetric unit, diffracts to at least 1.8 Å and is suitable for high-resolution structural studies.     

Trichinella spiralis: genetic basis for differential expression of phase-specific intestinal immunity in inbred mice

Responsiveness of mouse strains after phase-specific immunization with Trichinella spiralis is compared. Two strains ($\text{NFR}\text{N, NFS/N}$) showed strong overall responsiveness. The response type could be characterized in phase-specific terms as: strongly anti-adult, weakly to moderately anti-preadult, and strongly antifecundity. By comparison, congenic mice of the C₅₇B1 $\text{10}\text{Sn}$ background (B10·A, B10·D₂, B10·S, B10·Q) displayed poor total responses that could be characterized as: weakly anti-adult, very weakly anti-preadult, weakly anti-fecundity after preadult immunization, and mixed (weak and strong) after adult immunization. The $\text{C}{}_3\text{H}\text{HeJ}$ mouse appeared to be intermediate between the B10·BR and the $\text{NFR}\text{N}$ strains in overall responsiveness. Genetic determinants of anti-preadult or anti-adult responses of $\text{NFR}\text{N}$ strain mice were dominant over their B10 congenic counterparts as shown in F₁, crosses of $\text{NFR}\text{N}$ × B1O·BR mice. Since the $\text{NFR}\text{N}$ (predominantly H-2^q) and the $\text{NFS}\text{N}$ (H-2^S) are both strong responders, while the B10·Q(H-2^q) and B10·S (H-2^S) are weak, it is suggested that the major genes controlling anti-preadult and anti-adult responses are not linked to the major histocompatibility complex. However, variations in anti-adult immunity and anti-fecundity in the B10 congenic mice (B10·Q and B10·S are the strongest responders) suggest that minor genes linked to the MHC exert some control over these responses. Some evidence was obtained for gene complementation as the F₁ cross of $\text{NFR}\text{N}$ and $\text{NFS}\text{N}$ mice responded more vigorously than the parental lines. We conclude that multiple genes determine anti-T. spiralis intestinal responses in mice. The major genes are unlinked to the major histocompatibility complex whereas several minor genes are linked.     

Crystallographic study of beef liver catalase

An orthorhombic form of beef liver catalase crystals has been examined by X-ray diffraction and electron microscopy. The space group is P2₁2₁2₁ with $\text{a = 89}\text{A}\text{?}\text{, b = 140}\text{A}\text{?}\text{, and}\text{c = 231}\text{A}\text{?}$. Electron micrographs show the presence of broad channels arrayed in a hexagonal manner. The solvent content of these orthorhombic crystals is considerably less than that for previously reported trigonal crystals of beef liver catalase although the packing arrangement appears to be virtually the same, suggesting a possible symmetry transition upon dehydration.     

Crystallography of Bacillus subtilis levansucrase

Levansucrase, an exocellular enzyme, has been isolated from a high producer mutant, the BS5C4 constitutive strain, of Bacillus subtilis. Three crystalline forms have been obtained, all three belonging to the orthorhombic space group P2₁2₁2₁. The most suitable form for a three-dimensional structure investigation has cell dimensions, $\text{a = 68}\text{A}\text{?}$, $\text{b = 125}\text{A}\text{?}$, $\text{c = 54}\text{A}\text{?}$. There is one molecule in the asymmetric unit.     

Trichinella spiralis: Genetics of worm expulsion in inbred and F1 mice infected with different worm doses

The nematode Trichinella spiralis is rejected from the intestine at a time that is characteristic for each inbred strain of mouse. Previous work (R. G. Bell et al. 1982a) had empirically identified strong, intermediate, and weak phenotypes (NFR, $\text{C}\text{H}\text{He}$, and $\text{C57}\text{10}$ mice, respectively) in mice infected with 400 muscle larvae. It is shown that this classification applies to another eight inbred strains: SWR, $\text{DBA}\text{2}$, $\text{DBA}\text{1}$, LP, $\text{Bub}\text{Bn}$—all intermediate, and $\text{NZB}\text{BIN}$, C57L, A, and Mus molossinus—all weak. This phenotypic classification consistently applies with infections of 400–800 muscle larvae. Below doses of 300 muscle larvae, the strain designation of phenotype does not consistently apply. By this it is meant that the relative rejection rate changes for certain strains so that eventually some strains that were strong (NFR) or intermediate (AKR) responders to 400 muscle larvae become weak responders to 50 muscle larvae. Other strains increase their relative rejection time (B10 · BR, B10 · Q) while many do not change (NFS, $\text{C}\text{3}\text{Heb}\text{Fe}$, $\text{DBA}\text{2}$, $\text{DBA}\text{1}$). The phenomenon is most apparent in inbred parental strains rather than in F₁ crosses, and it represents a phenotypic variation in rejection time that is dependent on dose. It is also demonstrated that time of rejection is directly proportional to dose in all inbred and F₁ mouse strains that we have examined. Analysis of F₁ crosses shows that most have the rejection time of the strongest responding parental line, suggesting simple genetic control of strong, intermediate, and weak responses. Two F₁ crosses invalidated this theory. The $\text{DBA}\text{1}\text{×}\text{C3}\text{H}\text{He}$ (intermediate × intermediate) showed a strong response. The additive effects of parental rejection phenotype indicated that these lines could not be genetically identical for intermediate responsiveness. Similarly, the NFR (strong) × B10 · BR (weak) F₁ showed intermediate rejection, indicating partial dominance of $\text{C}\text{57}\text{B}\text{1}\text{10}$ genes over the strong responder NFR strain. Neither the primary expulsion time phenotype, phenotypic variation to low doses, or the rejection characteristics of F₁ crosses could be ascribed to genes linked to the major histocompatibility complex.     

Characterization of the sub-transition of hydrated dipalmitoylphosphatidylcholine bilayers: X-ray diffraction study

The structural changes accompanying the recently described sub-transition of hydrated dipalmitoylphosphatidylcholine (Chen, S.C., Sturtevant, J.M. and Gaffney, B.J. (1980) Proc. Natl. Acad. Sci. USA 77, 5060–5063) have been defined using X-ray diffraction methods. Following prolonged storage at ?4°C the usual L_β′ gel form of hydrated dipalmitoylphosphatidylcholine (DPPC) is converted into a more ordered stable ‘crystal’ form. The bilayer periodicity is 59.1 Å and the most striking feature is the presence of a number of X-ray reflections in the wide angle region. The most prominent of these are a sharp reflection at $\text{1}\text{4.4}\text{A}\text{?}{}^{\mathrm{?1}}$ and a broader reflection at $\text{1}\text{3.9}\text{A}\text{?}{}^{\mathrm{?1}}$. This diffraction pattern is indicative of more ordered molecular and hydrocarbon chain packing modes in this low temperature ‘crystal’ bilayer form. At the sub-transition (T_rmsub = 15–20°C) an increase in the bilayer periodicity occurs ($\text{d=63.6}\text{A}\text{?}$) and a strong reflection at approx. $\text{1}\text{4.2}\text{A}\text{?}{}^{\mathrm{?1}}$ with a shoulder at approx. $\text{1}\text{4.1}\text{A}\text{?}{}^{\mathrm{?1}}$ is observed. This diffraction pattern is identical to that of the bilayer gel (L_β′) form of hydrated DPPC. Thus, the sub-transition corresponds to a bilayer ‘crystal’ → bilayer L_β′ gel structural rearrangement accompanied by a decrease in the lateral hydrocarbon chain interactions. Differential scanning calorimetry and X-ray diffraction show that on further heating the usual structural changes L_β′ → P_β′ and P_β′ → L_α occur at the pre- and main transitions, at approx. 35°C and 41°C, respectively.     

Estimation of mutation rates in cultured mammalian cells

The factors that affect reliable estimations of mutation rates (μ) in cultured mammalian somatic cell populations by fluctuation analysis are studied experimentally and statistically. We analyze the differential effect of the final cell population size in each culture (N_t) and the number of parallel cultures (C) on the variation in the rate estimates ($\text{μ}$) inferred from the P₀ method. The analysis can be made after the derivation of the variance of $\text{μ}$, which is a measure of variation of $\text{μ}$ for a given combination of N_t and C in a number of repeat experiments. The variance of $\text{μ}$ is inversely proportional to C and to the square of N_t. N_t determines the probability of occurrence of mutation in a cell culture. By influencing the size of P₀, N_t also determines whether a rate estimate is obtainable from the experiment. Since P_o is estimated from the fraction of cultures containing no mutation in a set of C cultures, C becomes a determining factor for the accuracy of $\text{μ}$. The rate estimated from $\text{P}\text{?}{}_0$ is biased, but the bias is in general 2 orders of magnitude smaller than $\text{μ}$. By the selection of an appropriate combination of N_t and C for the experiment, this bias can be reduced even further.Based on the notion of comparing two proportions, we propose a test statistic and have applied it to experimental results for a test of equality of mutation rates in different cell lines. This development places the comparison of mutation rates on a statistical basis.     

Evaluation of the water environments in deoxygenated sickle cells by longitudinal and transverse water proton relaxation rates

The longitudinal and transverse water proton relaxation rates of oxygenated and deoxygenated erythrocytes from both normal adults and individuals with sickle cell disease were measured as a function of temperature at two different frequencies. The simplest model which fits all of the data consists of three different environments for water molecules. The majority of the water (98%) has a correlation time indistinguishable from bulk water (3 × 10^?11 sec). Secondly, there is a small amount of water (1.3–1.5%) present which has a correlation time of 2–4 × 10 ^?9 sec and is apparently independent of the erythrocyte sample studied. Presumably this water is the hydration sphere around the hemoglobin molecules and its correlation time is significantly slower than bulk water. The third environment contains approximately 0.2% of the water present and has a correlation time≥ 10^?7 sec. This third environment is considered tightly bound to the hemoglobin because the water proton correlation time is very similar to the expected rotational correlation time for the hemoglobin molecules. The value of the transverse relaxation rate, f_b(T_2b)^?1, for the tightly bound water fraction decreases in oxy ($\text{S}\text{S}$), deoxy ($\text{A}\text{A}$), and oxy ($\text{A}\text{A}$) erythrocyte samples as the temperature is increased as expected for a rotational correlation time process. In dramatic contrast,f_b (T_2b)^?1 increases almost linearly as the temperature is increased over the whole 4 ° to 37 °C temperature range in samples of deoxy ($\text{S}\text{S}$) erythrocytes. The observation suggests a continual increase in the formation of deoxyhemoglobulin S polymers rather than a sudden transition from a homogeneous solution of deoxyhemoglobin S molecules to a solid gel.     

Tyrosyl-tRNA synthetase forms a mononucleotide-binding fold

Tyrosyl-tRNA synthetase from Bacillus stearothermophilus is a dimeric molecule of approximately 90,000 M_r. The crystal structure originally reported by Irwin et al. (1976) has been re-interpreted using a new density-modification technique. The reinterpretation is confirmed by the complete amino acid sequence (D. Barker & (G. Winter, personal communication). The structure consists of an amino-terminal $\text{α}\text{β}$ domain, a domain containing five α-helices, and a region of 99 amino acids at the carboxyl terminus, which appears to be disordered. The re-interpretation reveals two new α-helices in the $\text{α}\text{β}$ domain, and some changes in chain connections. The strands of the β-sheet are in the order A, F, E, B, C, D, with A antiparallel to the others. The arrangement of strands B to F is topologically identical to arrangements found in many other proteins, including the first five strands of the sheet in the NAD-binding domain of the dehydrogenases. Strands B, C, D form a mononucleotide-binding fold.In the complex with tyrosyl adenylate (Rubin & Blow, 1981), an intermediate in the reaction catalysed by the enzyme, the adenine lies near the carboxyl-terminal end of strand F of the β-sheet, with the ribose between the ends of strands B and E. This is similar to the nicotinamide position in dehydrogenases. The tyrosine moiety occupies a pocket at one side of the sheet, close to strands B and C. This tyrosine orientation is quite different from any part of the coenzyme in dehydrogenases. The ends of strands C and D of the sheet are buried, and binding of a nucleotide to the mononucleotide-binding fold formed by strands B, C, D would require a substantial structural change.     

Preliminary crystallographic data for a chloramphenicol acetyltransferase from Escherichia coli.

A type I chloramphenicol acetyltransferase from Escherichia coli has been crystallized as trigonal prisms, in a form suitable for diffraction studies. The space group is P3₁, or P3₂, cell dimensions $\text{a = b = 116.3, c = 147}\text{A}\text{?}$.     

Determination of the multiplicity of the silk fibroin gene and detection of fibroin gene-related DNA in the genome of Bombyx mori.

The number of silk fibroin genes per genome in the silkworm Bombyx mori has been determined by hybridization using fibroin [¹²⁵I]mRNA. The purified [¹²⁵I]mRNA had an oligonucleotide pattern after RNAase T₁ digestion which was characteristic of fibroin mRNA (Suzuki &; Brown, 1972) and it hybridized specifically to DNA with a G + C content expected for a fibroin gene. Thermal denaturations indicated that these hybrids were mismatched by about 3%, which probably indicates some variation among the sequences encoding the internal repetitions of the fibroin protein.The concentration of fibroin gene sequences in B. mori DNA was measured by saturation hybridization of [¹²⁵I]mRNA to filter bound DNA. The same saturation level of 1.8 × 10^?5 μg mRNA per μg DNA was calculated from data obtained with unfractionated DNA and with fibroin gene sequences which had been separated from bulk B. mori DNA by actinomycin $\text{D}\text{CsCl}$ centrifugation. Scatchard plots of the subsaturation data extrapolated to an identical saturation value. Internal reiteration of the fibroin mRNA molecule was apparent from the high association constant of hybridization. An exhaustive hybridization experiment showed that such repetitions comprise at least 90% of each mRNA molecule. The saturation value, in conjunction with the genome DNA content and the mRNA size, indicated the presence of only one fibroin gene per haploid B. mori genome.Hybridization of actinomycin $\text{D}\text{CsCl}$ fractionated DNA indicated that fibroin mRNA can form hybrids with DNA that bands with bulk B. mori DNA. These hybrids appear to involve DNA which is related to, but distinguishable from, true fibroin gene sequences. The fibroin gene-related sequences form mismatched hybrids with the mRNA, are much shorter than the fibroin gene and are dispersed in B. mori DNA of much lower G + C content, and there are many copies of these sequences per B. mori genome.     

The effect of α1-acid glycoprotein (orosomucoid) on triglyceride metabolism in the nephrotic syndrome

We have identified α₁-acid glycoprotein as a new co-factor in the lipoprotein lipase reaction. We isolated an active form of the compound from nephrotic urine that is effective both $\text{in vitro}$ and $\text{in vivo}$. α₁-acid glycoprotein increased lipolysis 100% in the presence of C-II apolipoprotein in a lipoprotein lipase assay system. Rats with induced nephrotic syndrome showed a decrease in triglyceride clearance. $\text{T}\text{1}\text{2}$ was increased from 14 min to 43 min. The injection of α₁-acid glycoprotein restored the lipid clearance to normal. These findings suggest that elevated plasma triglycerides in human nephrotic patients is the direct result of excessive loss of α₁-acid glycoprotein from plasma into urine. We propose that replacement therapy may be possible.     

Favin, a crystalline lectin from Vicia faba

A lectin from the fava bean (Vicia faba) has been purified and crystallized in a form suitable for high-resolution crystallographic structure analysis. This protein binds glucose- and mannose-like saccharides, and it is mitogenic for lymphocytes. The fava lectin crystallizes in the orthorhombic space group. P2₁2₁2₁ with unit cell dimensions $\text{a = 90.0, b = 89.3,}\text{and}\text{c = 67.4}\text{A}\text{?}$. The mass of protein in the asymmetric unit is 53,000 daltons, corresponding to the molecular weight of the protein in solution.     

Crystals of glutamine synthetase from Escherichia coli.

Further details are given of crystals of glutamine synthetase prepared from Escherichia coli. Crystals of two kinds have been observed: (1) rhombic dodecahedra which correspond to the morphology of the crystals studied by Eisenberg et al. (1971) (and which were found by them to contain dodecamers), and (2) rhombohedra, reported here. Cell dimensions and packing considerations led to the consideration of two possible structures for the rhombohedral crystals. These we have called the “T = 7 structure” and the “B.C.C. structure”. The T = 7 structure would be related to that derived by Eisenberg and would contain dodecamers, but is inconsistent with our X-ray intensity data. The B.C.C. structure is considered more probable. It is built of cubic octomers or square tetramers. Electron micrographs of our glutamine synthetase preparations show a wide variety of aggregates, including dodecamers and tetramers. The unit cell dimensions of our crystals are $\text{a = 140 ± 2}\text{A}\text{̊}$, and $\text{c = 148 ± 2}\text{A}\text{̊}$. The Laue symmetry group is $\text{3}\text{̄}$m P3₁.     

Crystallization of cow α-lactalbumin

Three new crystal forms of cow α-lactalbumin are described. A trigonal form in space group P3₁21 or P3₂21 has unit cell dimensions: $\text{a = b = 57.4}\text{A}\text{?}\text{, c = 75.0}\text{A}\text{?}$. A hexagonal form in space group P622 has unit cell dimensions: $\text{a = b = 94.0}\text{A}\text{?}\text{, c = 67.1}\text{A}\text{?}$. A second trigonal form grown in the presence of calcium ions belongs to space group P321 with unit cell dimensions: $\text{a = b = 93.7}\text{A}\text{?}\text{, c = 66.9}\text{A}\text{?}$. The significance of these new crystal forms to the structure determination of cow α-laetalbumin is discussed.