Dose-dependent nonlinear response of the main phase-transition temperature of phospholipid membranes to alcohols

Summary The effect of 1-alkanols upon the main phase-transition temperature of phospholipid vesicle membranes between gel and liquid-crystalline phases was not a simple monotonic function of alkanol concentration. For instance, 1-decanol decreased the transition temperature at low concentrations, but increased it at high concentrations, displaying a minimal temperature. This concentration-induced biphasic effect cannot be explained by the van't Hoff model on the effect of impurities upon the freezing point. To explain this nonlinear response, a theory is presented which treats the effect of 1-alkanols (or any additives) on the transition temperature of phospholipid membranes in a three-component mixture. By fitting the experimental data to the theory, the enthalpy of the phase transition H ^* and the interaction energy, _AB ^* between the additive and phospholipid molecules may be estimated. The theory predicts that when _AB ^* >2 (where _AB ^* = _AB,/RT _o,T _o being the transition temperature of phospholipid), both maximum and maximum transition temperatures should exist. When _AB ^* = 2, only one inflection point exists. When _AB ^* < 2, neither maximum nor minimum exists. The alkanol concentration at which the transition temperature is minimum (X _min) depends on the _AB ^* value: the larger the _AB ^* values, the smaller theX _min. When _AB ^* is large enough,X _min values become so small that the plot T vs.X shows positive T in almost all alkanol concentrations. The interaction energy between 1-alkanols and phospholipid molecules increased with the increase in the carbon chain-length of 1-alkanols. In the case of the dipalmitcylphosphatidylcholine vesicle membrane, the carbon chain-length of 1-alkanols that caused predominantly positive T was about 12.     

Properties of a general model of DNA evolution under no-strand-bias conditions

Under the hypothesis of no-strand-bias conditions, the Watson and Crick base-pairing rule decreases the complexity of models of DNA evolution by reducing to six the maximum number of substitution rates. It was shown that intrastrand equimolarity between A and T (A ^* T ^*) and between G and C (G ^* C ^*) is a general asymptotic property of this class of models. This statistical prediction was observed on 60 long genomic fragments (>50 kbp) from various kingdoms, even when the effect of the two opposite orientations for coding sequences is removed. The practical consequence of the model for estimating the expected number of substitutions per site between two homologous DNA sequences is discussed.Abbreviations BPR Watson and Crick base pairing rule (A:T, G:C) - PRI Intrastrand type-1 parity rule (i j, m(i,j)m( )) - PRII Intra strand type-2 parity rule (A ^* T ^*, G ^* C ^*)     

Molecular dynamics simulation of oligosaccharides containing N-acetyl neuraminic acid

αD -N-acetyl neuraminic acid (Neu5Ac, sialic acid) is a commonly occurring carbohydrate residue in various cell surface glycolipids and glycoproteins. This residue is linked terminally or internally to Gal residues via an α(2 → 3) or α(2 → 6) linkage. In the cell surface receptor, sialyl-Lewis^X, a terminal α(2 → 3) linkage is present. Previous studies from our laboratory have shown that in solution Lewis^X adopts a relatively rigid structure. In order to model the Neu5Ac residue, vacuum molecular dynamics of this monosaccharide were compared with simulations that explicitly include solvent water. The dynamical average of the monosaccharide conformation obtained from the two simulations was similar. Vacuum calculations for the disaccharide Neu5Ac α(2 → 3) Gal β-O-methyl show that a number of low energy minima are accessible to this disaccharide. Molecular dynamics simulations starting from the low energy minima show conformational transitions with a time scale of 10–50 ps among several of the minima while large barriers between other minima prevent transitions on the time scale studied. Simulations of this disaccharide in the presence of solvent show fewer conformational transitions, illustrating a dampening effect of the solvent that has been observed in some other studies. Our results are most consistent with an equilibrium among multiple conformations for the Neu5Ac α(2 → 3) Gal β linkage. © 1994 John Wiley & Sons, Inc.     

Sex determination and phenotype in wood lemmings with XXY and related karyotypic anomalies

Summary The wood lemming, Myopus schisticolor, possesses a unique sex determining system comprising both XX and XY females. Normal female development in the presence of XY is guaranteed by a mutation on the X, apparently associated with a structural rearrangement in Xp. This mutation inactivates the testis-inducing and male-determining factor on the Y and distinguishes X^* from X, and X^*Y females from XY males. Normal fertility of X^*Y females is ensured by a mitotic (double) nondisjunction mechanism which, at an early fetal stage, eliminates the Y from the germ line and replaces it by a copy of the X^*.Numerical sex chromosome aberrations are not infrequent and the trisomics XXY and X^*XY are relatively common. XXY individuals are sterile males with severe suppression of spermatogenesis. Among X^*XY animals, both males and females, as well as a true lateral hermaphrodite have been observed. Primary deficiency of germ cells, impairment of spermatogenesis and sterility are characteristic traits of the X^*XY males, whereas X^*XY females have normal oogenesis and are fertile. Both these extremes (except female fertility) coexist in the true hermaphrodite described in the present study. These apparently contradictory observations are explainable under the assumption that X^* and X in X^*XY individuals are inactivated non-randomly or that the cells are distributed unequally. Inactivation of the X or X^* determines whether or not the H-Y antigen will be expressed. When comparing conditions in Myopus and in man, an additional assumption has to be made in relation to the gene(s) involved in sex determination, located in Xp:In Myopus they do not escape inactivation, whereas in man they have been claimed to remain active.     

Cytological identification of two X-chromosome types in the wood lemming (Myopus schisticolor)

In the wood lemming (Myopus schisticolor) three genetic types of sex chromosome constitution in females are postulated: XX, X^*X and X^*Y (X^*=X with a mutation inactivating the male determining effect of the Y chromosome). Males are all XY. It is shown in the present paper that the two types of X chromosomes, X and X^*, exhibit differences in the G-band patterns of their short arms. In addition, it was demonstrated in unbanded chromosomes that the short arm in X^* is shorter than in X. The origin of these differences is still obscure; but they allow to identify and to distinguish the individual types of sex chromosome constitution, as of XX versus X^*X females and of X^*Y females versus XY males, on the basis of G-banded chromosome preparations from somatic cells.     

Repetitive activity and hopf bifurcation under point-stimulation for a simple FitzHugh-Nagumo nerve conduction model

Summary In response to point-stimulation with a constant current, a neuron may propagate a repetitive train of action potentials along its axon. For maintained repetitive activity, the current strength I must be, typically, neither too small nor too large. For I outside some range, time independent steady behavior is observed following a transient phase just after the current is applied. We present analytical results for a piecewise linear FitzHugh-Nagumo model for a point-stimulated (non-space-clamped) nerve which are consistent with this qualitative experimental picture. For each value of I there is a unique, spatially nonuniform, steady state solution. We show that this solution is stable except for an interval (I _*, I ^*) of I values. Stability for I too small or too large corresponds to experiments with sub-threshold I or with excessive I which leads to nerve block. For I = I _*, I ^* we find Hopf bifurcation of spatially nonuniform, time periodic solutions. We conclude that (I _*, I ^*) lies interior to the range of I values for repetitive activity. The values of I _* and I ^* and their dependence on the model parameters are determined. Qualitative differences between results for the point-stimulated configuration and the space-clamped case are discussed.     

Circling syndrome and inner ear disease in mice infected intraperitoneally or intravenously with Coccidioides immitis spherule-endospore phase cultures

Infection was studied in mice with varying doses of spherule-endospore phase cultures of Coccidioides immitis, administered intraperitoneally, intravenously and intranasally. Stain 46 was compared with strain Silveira. The first of these is relatively avirulent in the mycelial phase, the second, rather virulent. Animals were observed for acute death and for circling. Gross and microscopic pathology was studied in mice sacrificed at appropriate intervals after infection. Numbers of fungi were assayed in spleen, lung, kidney, liver, blood, brain, and ear tissue. Strain 46 endospores administered intraperitoneally in doses from 9 × 10⁶ to 2.5 × 10⁷ produced a high incidence of circling syndrome ataxia attributable to inner ear disease.     

Molecular characterization of HLA-A28*, a novel HLA product,and its relationship to HLA-A28 and HLA-A2

The HLA-A28^* molecule expressed by the B-cell line IDF is serologically distinct and intermediate between HLA-A28 and HLA-A2. Comparative tryptic peptide mapping of biosynthetically labeled HLA-A28^*, A28, and A2 molecules showed that HLA-A28^* is also chemically distinct. Reverse-phase high pressure liquid chromatographic analysis of tryptic peptides labeled with ³H-arginine and ³H-lysine revealed that A28^*. A28, and A2 share 65% of their tryptic peptides. Multiple differences were observed between A28^* and both A28 and A2. No peptides unique to A28^* were detected and 25 peptides were shared with both A28 and A2. These results show that A28^* is a novel HLA product that is closely related to A28 and A2. Tryptic peptide map comparisons of these molecules labeled separately with 11 amino acids confirm these results. The data suggest that HLA-A28 ^* may have arisen from a genetic exchange event involving HLA-A28 and -A2. These data are consistent with the hypothesis that A28^* is identical with A28 in the first extracellular domain ( ₁) and identical with A2 in the second domain ( ₂).Abbreviations used in this paper EDTA ethylenediaminetetraacetic acid - HPLC high-pressure liquid chromatography - MHC major histocompatibility complex - NP40 Nonidet P40 - PMSF phenylmethylsulphonylfluoride - SDS-PAGE sodium dodecyl sulfate-polyacrylamide gel electrophoresis - TPCK L(tosylamido-2-phenyl) ethyl chloromethyl ketone - Tris tris (hydroxymethyl)-aminomethane - A alanine - C cysteine - D aspartic acid - E glutamic acid - G glycine - H histidine - K lysine - L leucine - M methionine - N asparagine - Q glutamine - R arginine - S serine - T threonine - V valine - W tryptophan - Y tyrosine     

Involvement of cyclic AMP and its receptor protein in the sensitivity of Escherichia coli K 12 toward serine: excretion of 2-ketobutyrate, a precursor of isoleucine.

Summary A relationship between serine-induced growth sensitivity and the cAMP-CAP complex is established. Mutants of Escherichia coli K 12 deficient either in the cya or crp gene function exhibit a resistant phenotype on serine media although they harbor a relA allele normally leading to sensitivity toward serine. The presence of a crp ^* allele in a cya rela background restores the sensitivity phenotype, while the analysis of serine resistant mutants selected from a crp ^* cya relA strains shows that the mutation leading to resistance is located at, or very near, the crp gene, giving a more or less Crp^- phenotype. In addition crp ^* cya relA strains excrete large quantities of 2-ketobutyrate when grown on glucose M63 medium. This excretion is unambiguously linked to the presence of the crp ^* allele and is correlated with an enhanced threonine deaminase activity. Besides, the complex regulation exerted on the acetolactate synthase activities is discussed.     

Diagnosing lactic acid fermentation based on specific rates of growth,substrate consumption and product formation

The on-line calculated specific rates of growth, substrate consumption and product formation were used to diagnose microbial activities during a lactic acid fermentation. The specific rates were calculated from on-line measured cell mass, and substrate and product concentrations. The specific rates were more sensitive indicators of slight changes in fermentation conditions than such monitored data as cell mass or product concentrations.List of Symbols 1/h specific rate of cell growth - 1/h specific rate of substrate consumption - 1/h specific rate of product formation - ^* dimensionless specific rate of cell growth - ^* dimensionless specific rate of substrate consumption - ^* dimensionless specific rate of product formation - _max 1/h maximum specific rate of cell growth - _max 1/h maximum specific rate of substrate consumption - _max 1/h maximum specific rate of product formation - X g/l cell mass concentration - S g/l substrate concentration - S ^* dimensionless substrate concentration - S ₀ g/l initial substrate concentration - P g/l product concentration     

Existence and uniqueness of a sharp travelling wave in degenerate non-linear diffusion Fisher-KPP equations

In this paper we use a dynamical systems approach to prove the existence of a unique critical value c ^* of the speed c for which the degenerate density-dependent diffusion equation u _ct = [D(u)u _x ] _x + g(u) has: 1. no travelling wave solutions for 0 < c < c ^*, 2. a travelling wave solution u(x, t) = (x - c ^* t) of sharp type satisfying (– ) = 1, () = 0 ^*; '(^*–) = – c ^*/D'(0), '(^*+) = 0 and 3. a continuum of travelling wave solutions of monotone decreasing front type for each c > c ^*. These fronts satisfy the boundary conditions (– ) = 1, '(– ) = (+ ) = '(+ ) = 0. We illustrate our analytical results with some numerical solutions.     

Temporal Genetic Variation in a Population of Aphanius fasciatus (Cyprinodontidae) from a Brackish-water Habitat at Elba Island (Italy)

Allozyme electrophoresis was used to assess temporal genetic variation in three successive generations of the Mediterranean killifish, Aphanius fasciatus. Samplings were carried out in 1995, 1996 and 1997 in a brackish-water habitat at Elba Island, Italy and a total of 212 specimens were collected. The five loci for which polymorphism has been detected in a previous study were assayed. Mean expected heterozygosity values [H=0.397 (SE 0.077), H=0.336 (SE 0.092) and H=0.313 (SE 0.092) in 1995, 1996 and 1997, respectively] were not significantly different by ANOVA test. Deviations from Hardy–Weinberg equilibrium were minimal, with only one out of the 15 probability tests showing a significant departure from the equilibrium; whereas genotypic linkage disequilibrium was not detected. Values of Nei's genetic distance were lower than 0.04. Temporal genetic variation in the A. fasciatus population at Elba Island was observed, with F-statistics indicating significant genetic divergence among samples (=0.035, SE 0.027, p<0.001). Genetic drift acting on two loci (GPD-1 ^* and LDH-3 ^*) is presumably the main force determining the temporal genetic heterogeneity observed; however, the occurrence of selection on individual loci and/or sampling error cannot be excluded. The observed allelic variation among generations in a single population of A. fasciatus is much less than levels observed among geographically discrete samples in previous studies.     

Identification of an uncommon haptoglobin type using DNA and protein analysis

The inherited variations in haptoglobin phenotypes are attributed to the homozygous and heterozygous combinations of three common autosomal alleles:HP ^* 1F,HP ^* 1S andHP ^* 2.HP ^* 1F andHP ^* 1S encode polypeptides that differ by two amino acids at positions 51 and 53. The formation ofHP ^* 2 is postulated to have resulted from a breakage and subsequent reunion event at non-homologous positions of twoHP ^* 1 alleles. The most common form ofHP ^* 2 isHP ^* 2FS in which the 5 end ofHP ^* 2 resemblesHP ^* 1F and the 3 end resemblesHP ^* 1S. Homologous crossing over betweenHP ^* 2 and either anHP ^* 1F orHP ^* 1S allele inHP ^* 2/HP ^* 1 heterozygotes can change the usual type ofHP ^* 2 to three other forms:HP ^* 2SS,HP ^* 2FF orHP ^* 2SF. We describe a nuclear family in which the uncommon genotypeHP ^* 2SS in one parent caused initial confusion in assigning genotypes to the rest of the nuclear family. The data demonstrate the need for a cautious approach when deducing haptoglobin genotypes from molecular analysis alone.     

The study of a French family with two duplicated C4A haplotypes

Summary The finding of two duplicated C4A haplotypes in a normal French family led to a detailed study of their C4 polymorphism. The father had an extremely rare A^*6A^*11, B^* QO haplotype inherited by all of his children and the mother had the more common A^*3A^*2, B^*QO haplotype. Two HLA identical daughters only have four C4A alleles. The father's A11 allotype expresses Ch: 1 (Chido) rather than Rg:1 (Rodgers) and represents a new Ch phenotype Ch: 1,-2,-3,-4,-5,-6. In order to clarify the genetic background in this unusual family, DNA studies of restriction fragment length polymorphisms (RFLPs) were undertake. The father's rare haplotype, which expresses two C4A allotypes, results from a long and a short C4 gene normally associated with the A^*6, B^*1 that also exhibits the BglII RFLP. As it travels in an extended MHC haplotype HLA A2, B57 (17), C2^*C, BF^*S, DR7 that is most frequently associated with A^*6, B^*1, we postulate that the short C4B has been converted in the chain region to a C4A gene which produces a C4A protein. This report of a short C4A gene is the first example in the complex polymorphism of C4.     

Genetic polymorphism of inter-alpha-trypsin-inhibitor (ITI): Formal genetic and linkage analyses

Summary The polymorphism of inter-alpha-trypsin-inhibitor, ITI, was demonstrated by isoelectric focusing in agarose gels (pH 5–8) followed by protein blotting and immunoassay. Segregation in 239 families with 677 children is consistent with the formal hypothesis that there are two common codominant alleles, ITI^*1, ITI^*2, and one rare codominant allele, ITI^*3, at an autosomal locus ITI. Allele frequencies were calculated as ITI^*1=0.600, ITI^*2=0.393, ITI^*3=0.007. Linkage analysis with 36 markers is presented. Slightly positive lod scores were obtained for PGM3 (z=1,35, =0.10) and AK1 (z=1.34, =0.10).     

A new α2HS-glycoprotein allele (AHS * 5 ⋆) in two Japanese families

Summary Serum specimens of two unrelated Japanese males had a new variant of the ₂HS-glycoprotein phenotypes. They had unusual bands designated AHS 5. Family studies indicated that the new variant phenotypes were determined by a new allele, AHS ^* 5, in combination with a common allele AHS ^* 1 or AHS ^* 2, and that the new allele had an autosomal codominant inheritance with other AHS alleles. The frequency of the new ₂HS-glycoprotein allele, AHS ^* 5, is 0.0005.We use the designation AHS to denote the ₂HS-glycoprotein phenotype and allele in agreement with nomenclature guidelines (Shows et al. 1979)     

Computer simulation of the conformational properties of retro–inverso peptides. I. Empirical force field calculations of rigid and flexible geometries of N-acetylglycine-N′- methylamide,bis(acetamido) methane,and N,N′- dimethylmalonamide and their corresponding Cα-methylated analogs

Rigid and flexible geometry calculations are described for N-acetylglycine-N′-methylamide, N-acetylalanine-N′-methylamide, and their retro-inverso analogs, bis(acetamido) methane, 1,1-bis(acetamido) ethane, N,N′-dimethylmalonamide, and N,N′-dimethyl-2-methyl-malonamide. The significance of relaxing all degrees of freedom, especially angular flexibility is demonstrated. The flexible geometry approach yields energy maps similar to those from rigid geometry, but the energy barriers between minima are substantially reduced, leading in general, to more probable transitions and a higher volume of accessible conformational space. Whereas the glycine and alanine derivatives exhibit their lowest energy minima in the C region, the gem-diaminoalkyl and malonyl residues show their lowest minima in the “α-helical” regions. With respect to the effect of side chains (H versus CH₃), the greatest conformational influence appears with the gem-diaminoalkyl residues. These results indicate significantly different conformational behavior of retro peptides and the implications of these pairwise incorporations of retro-inverso residues in peptide chains, are discussed.     

Ligand-induced conformational changes in a thermophilic ribose-binding protein

Background

Members of the periplasmic binding protein (PBP) superfamily are involved in transport and signaling processes in both prokaryotes and eukaryotes. Biological responses are typically mediated by ligand-induced conformational changes in which the binding event is coupled to a hinge-bending motion that brings together two domains in a closed form. In all PBP-mediated biological processes, downstream partners recognize the closed form of the protein. This motion has also been exploited in protein engineering experiments to construct biosensors that transduce ligand binding to a variety of physical signals. Understanding the mechanistic details of PBP conformational changes, both global (hinge bending, twisting, shear movements) and local (rotamer changes, backbone motion), therefore is not only important for understanding their biological function but also for protein engineering experiments.

Results

Here we present biochemical characterization and crystal structure determination of the periplasmic ribose-binding protein (RBP) from the hyperthermophile Thermotoga maritima in its ribose-bound and unliganded state. The T. maritima RBP (tmRBP) has 39% sequence identity and is considerably more resistant to thermal denaturation ( ^app T _m value is 108°C) than the mesophilic Escherichia coli homolog (ecRBP) ( ^app T _m value is 56°C). Polar ligand interactions and ligand-induced global conformational changes are conserved among ecRBP and tmRBP; however local structural rearrangements involving side-chain motions in the ligand-binding site are not conserved.

Conclusion

Although the large-scale ligand-induced changes are mediated through similar regions, and are produced by similar backbone movements in tmRBP and ecRBP, the small-scale ligand-induced structural rearrangements differentiate the mesophile and thermophile. This suggests there are mechanistic differences in the manner by which these two proteins bind their ligands and are an example of how two structurally similar proteins utilize different mechanisms to form a ligand-bound state.     

The peptide binding specificity of HLA-B27 subtypes

Five HLA-B27 subtypes, B^*2701, B^*2703, B^*2704, B^*2705, and B^*2706, were tested for direct binding with twenty-six synthetic nonapeptides carrying the primary anchor residue motifs (combination of amino residues at positions 2 and 9) relevant to B^*2705. The peptide sequences were derived from human HSP89, P53 and MBP. The alpha chains were immunospecifically isolated from LH (B ^* 2701), CH (B ^* 2703), WE1 (B ^* 2704), BTB (B ^* 2705), and LIE (B ^* 2706) cells and their peptide binding was measured by the HLA class I alpha chain refolding assay. The data obtained indicated that the B27 subtypes tested can bind a common set of peptides carrying several different anchor residue motifs. The motifs, R-K and R-R, reported for B^*2705 and a new motif H-R were accepted by B^*2703, B^*2704, and B^*2706, but not by B^*2701. However, other motifs, including known B^*2702 and/or B^*2705 motifs, R-H, R-L, R-A, and R-F, and a new motif found here, R-G, were apparently accepted by all B27 subtypes tested. The observed cross-peptide binding in the B27 subgroup is compatible with the so-called arthritogenic peptide hypothesis in the pathogenesis of ankylosing spondylitis.     

Structure and function of ALG-2, a penta-EF-hand calcium-dependent adaptor protein

ALG-2 (a gene product of PDCD6) is a 22-kD protein containing five serially repetitive EF-hand structures and belongs to the penta-EF-hand (PEF) family, including the subunits of typical calpains. ALG-2 is the most conserved protein among the PEF family members and its homologs are widely found in eukaryotes. X-ray crystal structures of various PEF proteins including ALG-2 have common features: presence of eight α-helices and dimer formation via paired EF5s that are positioned in anti-parallel orientation. ALG-2 forms a homodimer and a heterodimer with its closest paralog peflin. Like calmodulin, a well-known four-EF-hand protein, ALG-2 interacts with various proteins in a Ca²⁺-dependent fashion, but the binding motifs are completely different. With some exceptions, ALG-2-interacting proteins commonly contain Pro-rich regions, and ALG-2 recognizes at least two distinct Pro-containing motifs: PPYP(X)nYP (X, variable; n=4 in ALIX and PLSCR3) and PXPGF (represented by Sec31A). A shorter alternatively spliced isoform, lacking two residues and designated ALG-2^ΔGF122, does not bind ALIX but maintains binding capacity to Sec31A. X-ray crystal structural analyses have revealed that binding of calcium ions induces the configuration of the side chain of R125 so that it opens Pocket 1, which accepts PPYP, but Pocket 1 remains closed in the case of ALG-2^ΔGF122. ALG-2 dimer has two ligand-binding sites, each in a monomer molecule, and appears to function as a Ca²⁺-dependent adaptor protein to either stabilize a preformed complex or to bridge two proteins on scaffolds in systems of the endosomal sorting complex required for transport (ESCRT) and ER-to-Golgi transport.