Highly restricted distributions of hydrophobic and charged amino acids in longitudinal quadrants of alpha-helices

Helix formation in folding proteins is stabilized by binding of recurrent hydrophobic side chains in one longitudinal quadrant against the locally most hydrophobic region of the protein. To test this hypothesis, we fitted sequences of 247 alpha-helices of 55 proteins to the circular (infinite) template (symbol; see text) to maximize the strip-of-helix hydrophobicity index (the mean hydrophobicity of residues in (symbol; see text) positions). These template-predicted configurations closely matched crystallographic structures in 87% of four- or five-turn helices compared. We determined the longitudinal quadrant distributions of amino acids in the template-fitted, sheet projections of alpha-helices with respect to the best longitudinal, hydrophobic strip on each helix and to the N and C termini, interiors, and entire helices. Amino acids Leu, Ile, Val, and Phe were concentrated in one longitudinal quadrant (p less than 0.001). Lys, Arg, Asp, and Glu were not in the quadrant of Leu, Ile, Val, and Phe (p less than 0.001). Significant quadrant distributions for other amino acids and for termini of the helices were also found.     

mtDNA depletion with variable tissue expression: a novel genetic abnormality in mitochondrial diseases.

We studied two related infants with a fatal mitochondrial disease, affecting muscle in one and liver in the other. Quantitative analysis revealed a severe depletion of mtDNA in affected tissues. This genetic abnormality was also observed in muscle of an unrelated infant with myopathy and in muscle and kidney of a fourth child with myopathy and nephropathy. Biochemistry, immunohistochemistry, and in situ hybridization showed that the depletion of mtDNA in muscle fibers was correlated with a respiratory chain defect and with lack of mitochondrially translated proteins. Although the differential tissue involvement in these infants suggests mtDNA heteroplasmy, sequence analysis of mtDNA replication origins did not reveal any abnormality that could account for the low copy number.     

Author index to volume 167

The N-terminal amino acid sequences of two chloroform/methanol soluble globulins from barley and one form wheat are reported. They are homologous with N-terminal sequences previously reported for α-amylase and trypsin inhibitors from cereals and 2 S storage proteins from castor bean and rape. Three albumins were also purified from Aegilops squarrosa and Triticum monococcum. These had N-terminal amino acid sequences most closely related to the α-amylase and trypsin inhibitors. The relationships of this superfamily of seed proteins are discussed.     

Chemoattractant receptor promotion of Ca2+ influx across the plasma membrane of HL-60 cells. A role for cytosolic free calcium elevations and inositol 1,3,4,5-tetrakisphosphate production

The mechanisms by which the chemotactic peptide formyl-methyl-leucyl-phenyl-alanine stimulates Ca2+ influx across the plasma membrane were investigated in the human promyelocytic cell line HL-60, induced to differentiate with dimethyl sulfoxide. Ca2+ influx was determined: (a) from the initial rate of Mn2+ influx, apparent from the quenching of intracellular quin2 or fura-2 fluorescence; (b) from the rate of the elevation of cytosolic free calcium, [Ca2+]i, upon readdition of Ca2+ to cells previously stimulated in the absence of extracellular Ca2+. [3H]Inositol tris-, tetrakis-, and pentakisphosphates were analyzed by a high performance liquid chromatography procedure which was optimized for the separation of inositol tetrakisphosphates, yielding three predominant isomers: inositol 1,3,4,5-tetrakisphosphate (Ins(1,3,4,5)P4), inositol 1,4,5,6-tetrakisphosphate, and inositol 1,3,4, 6-tetrakisphosphate. Both the kinetics and agonist dose dependence of Ca2+ influx stimulation correlated closely with the corresponding receptor-mediated variations of [Ca2+]i either in the presence or in the absence of extracellular Ca2+. Of the different inositol phosphates determined in parallel and under the same conditions, accumulation of [3H]Ins(1,3,4,5)P4 correlated best with Ca2+ influx both temporally and in its dose dependence in the presence or in the absence of extracellular Ca2+; inositol 1,3,4-trisphosphate was also correlated but to a lesser extent. Attenuations of [Ca2+]i elevations by decreasing extracellular Ca2+ or by increasing the cytosolic Ca2+ buffering capacity with quin2 led to parallel inhibition of Ca2+ influx and Ins(1,3,4,5)P4 production. In conclusion: 1) activation of Ca2+ influx by formyl-methionyl-leucyl-phenylalanine depends on the elevation of [Ca2+]i, the latter being initiated by Ca2+ mobilization from intracellular stores; 2) Ins(1,3, 4,5)P4 is a strong candidate for maintaining receptor-mediated activation of Ca2+ influx in differentiated HL-60 cells.     

S1-hypersensitive sites in eukaryotic promoter regions.

We have examined by fine mapping the S1 nuclease-hypersensitivity of the 5' flanking regions of the human beta-globin and rat preproinsulin II genes and of the SV40 origin/enhancer region. In all cases S1-hypersensitive sites are located in known or presumed promoter/regulatory regions. Though a consensus DNA sequence is not evident, all of these sites reside in predominantly homopurine-homopyrimidine stretches. The alternate (non-B) DNA structure which is revealed by the enzymatic probe is a sequence-dependent feature of a short stretch of DNA, which is retained upon transplantation into a foreign environment. The alternate structure exhibits S1-nicking patterns uniquely different from those associated with the presence of Z-DNA.     

Quantitation of Malaria Parasite-Erythrocyte Cell-Cell Interactions Using Optical Tweezers

Erythrocyte invasion by Plasmodium falciparum merozoites is an essential step for parasite survival and hence the pathogenesis of malaria. Invasion has been studied intensively, but our cellular understanding has been limited by the fact that it occurs very rapidly: invasion is generally complete within 1 min, and shortly thereafter the merozoites, at least in in vitro culture, lose their invasive capacity. The rapid nature of the process, and hence the narrow time window in which measurements can be taken, have limited the tools available to quantitate invasion. Here we employ optical tweezers to study individual invasion events for what we believe is the first time, showing that newly released P. falciparum merozoites, delivered via optical tweezers to a target erythrocyte, retain their ability to invade. Even spent merozoites, which had lost the ability to invade, retain the ability to adhere to erythrocytes, and furthermore can still induce transient local membrane deformations in the erythrocyte membrane. We use this technology to measure the strength of the adhesive force between merozoites and erythrocytes, and to probe the cellular mode of action of known invasion inhibitory treatments. These data add to our understanding of the erythrocyte-merozoite interactions that occur during invasion, and demonstrate the power of optical tweezers technologies in unraveling the blood-stage biology of malaria.     

Analysis of family resemblance. IV. Operational characteristics of segregation analysis.

In simulated data, segregation analysis of quantitative traits was found to be powerful for resolving a major locus from polygenic and cultural inheritance. It is reasonably robust against a variety of deviations from the model if and only if a major locus, polygenic heritability, and environment common to sibs are simultaneously included in the model, and heterogeneity tests among mating types are performed. Most of the information in quantitative data about a major locus is lost when reduced to affection status.     

Effect of membrane potential on the mechanical equilibrium of biological membranes

The mechanical equilibrium of a membranous sac, whose wall is sandwiched by two oppositely charged fluid layers, is investigated as a mathematical model of a living cell. In so doing, it is assumed that the space charge density in the inner and the outer charged fluid layer is constant. It is also assumed that the fluid inside and outside of the charged fluid layer is a perfect conductor. By solving Maxwell's equation, the electric field and the thickness of the inner and the outer charged fluid layer is determined as a function of the geometry of the sac. Then, the fluid pressure in the charged fluid layer is derived by considering the body force created by the electrostatic field. The condition of mechanical equilibrium of the sac membrane yields an equation which reveals the inter-relation between the geometry, the sac fluid pressure and the membrane potential. According to this equation, the change of membrane potential causes a deformation of the sac. If the wall of the membranous sac is permeable, increase (decrease) of the absolute value of the membrane potential results in swelling (shrinking) of the sac. On the other hand, the mechanical change of the sac volume results in the change of the membrane potential. This analysis provides also an explanation of how the red blood cell maintains the biconcave shape, when the red blood cell is assumed to be a fluid filled membranous sac with non-zero membrane potential.     

Role of Serine-19 Phosphorylation in Regulating Tyrosine Hydroxylase Studied with Site- and Phosphospecific Antibodies and Site-Directed Mutagenesis

Abstract: The effects of depolarization by elevated potassium concentrations were studied in PC12 cells and in stably transfected AtT-20 cells expressing wild-type or [Leu¹⁹]-recombinant tyrosine hydroxylase (rTH). Changes in the phosphorylation states of Ser¹⁹ and Ser⁴⁰ in tyrosine hydroxylase (TH) were determined immunochemically using antibodies specific for the phosphorylated state of each site and compared with changes in TH activity in PC12 cell lysates and with changes in l -DOPA biosynthesis rates in intact AtT-20 cells. Treatment of either PC12 cells or AtT-20 cells expressing wild-type rTH with elevated potassium produced a transient increase in the phosphorylation state of Ser¹⁹ (up to 0.7 mol of phosphate/mol of subunit) in concert with a more gradual and sustained increase in Ser⁴⁰ phosphorylation. Elevated potassium treatment also increased TH activity in PC12 cell lysates, but these increases paralleled the temporal course of Ser⁴⁰, as opposed to Ser¹⁹, phosphorylation. Similarly, increases in DOPA accumulation produced by elevated potassium in AtT-20 cells expressing wild-type rTH paralleled the increases in the phosphorylation state of Ser⁴⁰ but not Ser¹⁹. Moreover, elevated potassium produced comparable increases in DOPA accumulation in AtT-20 cells expressing rTH in which Ser¹⁹ phosphorylation had been eliminated (by substitution of Leu for Ser¹⁹). Thus, depolarization-induced increases in the stoichiometry of Ser¹⁹ phosphorylation do not appear to influence directly the activity of TH in situ.