Thermal dependence of apolipoprotein A-I-phospholipid recombination

Studies of the recombination of apolipoprotein A-I (apo A-I), the major protein constituent of human high-density lipoprotein, and various synthetic phospholipids, both alone and in mixtures, have been performed. Pure diacyl phospholipids containing homologous fatty acids of the C12, C13, C14, and C15 series, as well as the two positional isomers containing C14 and C16 fatty acids in positions 1 and 2, undergo reaction with the apo A-I protein only near their gel-liquid-crystalline transition temperatures; the degree of reactivity of these phospholipids toward recombination was observed to decrease as the transition temperature increased. The presence of lysolecithin in the incubation mixtures at proportions of 5 mol/mol of protein or lower was not found to have a significant effect on the rate of recombination. Binary mixtures of dimyristoylphosphatidylcholine and dipalmitoylphosphatidylcholine at various proportions react maximally with apo A-I at the onset of the phase transition, as judged by comparison with published phase diagrams; in this case also, the rate of recombination was observed to decline for mixtures with higher phase transition temperatures. These results are interpreted in terms of protein insertion at lattice defects arising from the presence of phospholipid clusters undergoing the phase transition; these clusters are derived from the cooperative and simultaneous melting of a number of molecules, the cooperativity being dependent upon the nature of the phospholipid. It is postulated that phospholipids which melt in a more highly cooperative fashion are more capable of interacting with the apolipoproteins since these phospholipids will possess larger lattice defects during the phase transition.     

Dose dependence for radiation-induced allelic recombination in Chlamydomonas reinhardi

The frequency of recombination between the acetate 14A and E alleles of the green alga Chlamydomonas reinhardi can be changed by γ radiation only if germinating zygospores are irradiated during one or other of two short meiotic stages. During the first, which is probably located in preleptotene, the frequency of allelic recombination increased linearly with dose and at 20.3 krad, the highest dose used, recombination frequency was increased by a factor of 7 while zygospore survival was reduced to 58%. During the second stage, probably located in late zygotene or early pachytene, a maximum increase of 1.5–2 times the control frequency was found at doses between 2 and 5 krad, higher doses producing no further increase.

The spontaneous recombination frequencies in zygospores from two different crosses, obtained by mating two different acetate 14A strains to a common acetate 14E stock, differed by a factor of about 10, suggesting that the acetate 14A strains possess different alleles of at least one “recombination” gene. In absolute terms, the cross which had a high spontaneous frequency exhibited a larger response to radiation, particularly at the second stage, though as a proportion of the control frequency the response was smaller. Zygospores of the second cross were also more sensitive to the lethal effects of the radiation.     

The evolutionary role of the dependence of recombination on environment

Summary The recombination frequency (rf) is known to be dependent not only on genetic background, but on the environment as well. In our numerical experiments we examine the role of the dependence of recombination on environment in the evolution of the genetic system. Variable rf-strategies, ensuring mean fitnesses greater than the optimum constant rf^*-level, exist in both cyclical and stochastic environments. The conclusion that environment dependent recombination is evolutionary advantageous can be shown to be valid when variation in the frequency of recombination modifiers rather than mean fitness (which implies the concept of group selection) is used as a criterion for strategy comparisons. In this case, an evolutionary advantageous type of variable rf-strategies is the one ensuring restricted genetic variability dispersion in an optimal environment and an increase in released variation with the deterioration of environmental conditions. Another important result is that, taking into account the dependence of recombination on environment, it is possible to account for the maintenance of a higher level of population recombination than that predicted by models with the constant rf-level. On the whole, the data obtained indicate that the direct influence of external factors upon the rf-value could have been a significant factor in the evolution of the genetic system.     

XPD-dependent activation of apoptosis in response to triplex-induced DNA damage

DNA sequences capable of forming triplexes are prevalent in the human genome and have been found to be intrinsically mutagenic. Consequently, a balance between DNA repair and apoptosis is critical to counteract their effect on genomic integrity. Using triplex-forming oligonucleotides to synthetically create altered helical distortions, we have determined that pro-apoptotic pathways are activated by the formation of triplex structures. Moreover, the TFIIH factor, XPD, occupies a central role in triggering apoptosis in response to triplex-induced DNA strand breaks. Here, we show that triplexes are capable of inducing XPD-independent double strand breaks, which result in the formation of γH2AX foci. XPD was subsequently recruited to the triplex-induced double strand breaks and co-localized with γH2AX at the damage site. Furthermore, phosphorylation of H2AX tyrosine 142 was found to stimulate the signaling pathway of XPD-dependent apoptosis. We suggest that this mechanism may play an active role in minimizing genomic instability induced by naturally occurring noncanonical structures, perhaps protecting against cancer initiation.     

Concentration dependence of IgG-protein A affinity studied by wireless-electrodeless QCM

The binding affinity between human immunoglobulin G (IgG) and protein A was studied by the homebuilt wireless-electrodeless quartz crystal microbalance (QCM). Protein A was immobilized on the electrodeless AT-cut quartz plate of 0.05 mm thick and its fundamental resonance frequency near 34 MHz was measured by a noncontacting manner using a line antenna. The vibrational analysis was performed to ensure higher sensitivity of the electrodeless QCM. A flow-cell system was fabricated to continuously measure the resonance frequency during the injection sequence of the IgG solutions with concentrations of 1-20,000 ng/mL. The exponential frequency changes were recorded to determine the affinity based on the Langmuir kinetics. The equilibrium constant K(A) significantly varied between 6 x 10(6) and 6 x 10(10) M(-1), depending on the IgG concentration, which is attributed to various formations of IgG-protein A complexes.     

Distance dependence of long-range electron transfer through helical peptides.

Helical peptides of 8mer, 16mer, and 24mer carrying a disulfide group at the N-terminal and a ferrocene moiety at the C-terminal were synthesized, and they were self-assembled on gold by a sulfur-gold linkage. Infrared reflection-absorption spectroscopy and ellipsometry confirmed that they formed a monolayer with upright orientation. Cyclic voltammetry showed that the electron transfer from the ferrocene moiety to gold occurred even with the longest 24mer peptide. Chronoamperometry and electrochemical impedance spectroscopy were carried out to determine the standard electron transfer rate constants. It was found that the dependence of the electron-transfer rates on the distance was significantly weak with the extension of the chain from 16mer to 24mer (decay constant beta = 0.02-0.04). This dependence on distance cannot be explained by an electron tunneling mechanism even if increased hydrogen-bonding cooperativity or molecular dynamics is considered. It is thus concluded that this long-range electron transfer is operated by an electron hopping mechanism.     

Context dependence of meiotic recombination hotspots in yeast: the relationship between recombination activity of a reporter construct and base composition

Borde and colleagues reported that a reporter plasmid inserted at different genomic locations in Saccharomyces cerevisiae had different levels of meiotic recombination activity. We show that the level of recombination activity is very significantly correlated with the GC content of DNA sequences flanking the insertion.     

Determining force dependence of two-dimensional receptor-ligand binding affinity by centrifugation.

Analyses of receptor-ligand interactions are important to the understanding of cellular adhesion. Traditional methods of measuring the three-dimensional (3D) dissociation constant (Kd) require at least one of the molecular species in solution and hence cannot be directly applied to the case of cell adhesion. We describe a novel method of measuring 2D binding characteristics of receptors and ligands that are attached to surfaces and whose bonds are subjected to forces. The method utilizes a common centrifugation assay to quantify adhesion. A model for the experiment has been formulated, solved exactly, and tested carefully. The model is stochastically based and couples the bond force to the binding affinity. The method was applied to examine tumor cell adherence to recombinant E-selectin. Satisfactory agreement was found between predictions and data. The estimated zero-force 2D Kd for E-selectin/carbohydrate ligand binding was approximately 5 x 10(3) microm(-2), and the bond interaction range was subangstrom. Our results also suggest that the number of bonds mediating adhesion was small (<5).     

Homology dependence of targeted recombination at the Chinese hamster APRT locus.

Using simple linear fragments of the Chinese hamster adenine phosphoribosyltransferase (APRT) gene as targeting vectors, we have investigated the homology dependence of targeted recombination at the endogenous APRT locus in Chinese hamster ovary (CHO) cells. We have examined the effects of varying either the overall length of targeting sequence homology or the length of 5' or 3' flanking homology on both the frequency of targeted homologous recombination and the types of recombination events that are obtained. We find an exponential (logarithmic) relationship between length of APRT targeting homology and the frequency of targeted recombination at the CHO APRT locus, with the frequency of targeted recombination dependent upon both the overall length of targeting homology and the length of homology flanking each side of the target gene deletion. Although most of the APRT+ recombinants analyzed reflect simple targeted replacement or conversion of the target gene deletion, a significant fraction appear to have arisen by target gene-templated extension and correction of the targeting fragment sequences. APRT fragments with limited targeting homology flanking one side of the target gene deletion yield proportionately fewer target gene conversion events and proportionately more templated extension and vector correction events than do fragments with more substantial flanking homology.     

Homologous recombination in hybridoma cells: dependence on time and fragment length.

Mutant hybridoma-myeloma cell lines that are defective in immunoglobulin production are expected to be useful for defining the molecular requirements of immunoglobulin gene expression. The analysis of such mutants would be greatly facilitated if they could be mapped by marker rescue, i.e., by identifying the segments of wild-type DNA that can restore the normal phenotype by homologous recombination with the mutant chromosomal immunoglobulin gene. To assess the feasibility of this type of mapping, we have measured the efficiency with which fragments of wild-type DNA recombine with a mutant hybridoma immunoglobulin gene and restore normal immunoglobulin production. We found that most if not all recombinants were detectable 2 days after DNA transfer and that the frequency of gene restoration increased with increasing length of the transferred mu gene fragments, between 1.2 and 9.5 kilobases. These results indicate that the available technology should be adequate to map mutations in the mu gene to within approximately 1 kilobase.     

Distance dependence and salt sensitivity of pairwise, coulombic interactions in a protein

Histidine pK(a) values were measured in charge-reversal (K78E, K97E, K127E, and K97E/K127E) and charge-neutralization (E10A, E101A, and R35A) mutants of staphylococcal nuclease (SNase) by (1)H-NMR spectroscopy. Energies of interaction between pairs of charges (DeltaG(ij)) were obtained from the shifts in pK(a) values relative to wild-type values. The data describe the distance dependence and salt sensitivity of pairwise coulombic interactions. Calculations with a continuum electrostatics method captured the experimental DeltaG(ij) when static structures were used and when the protein interior was treated empirically with a dielectric constant of 20. The DeltaG(ij) when r(ij) < or = 10 A were exaggerated slightly in the calculations. Coulomb's law with a dielectric constant near 80 and a Debye-Hückel term to account for screening by the ionic strength reproduced the salt sensitivity and distance dependence of DeltaG(ij) as well as the structure-based method. In their interactions with each other, surface charges behave as if immersed in water; the Debye length describes realistically the distance where interactions become negligible at a given ionic strength. On average, charges separated by distances (r(ij)) approximately 5 A interacted with DeltaG(ij) approximately 0.6 kcal/mole in 0.01 M KCl, but DeltaG(ij) decayed to < or =0.10 kcal/mole when r(ij) = 20 A. In 0.10 M KCl, DeltaG(ij) approximately 0.10 kcal/mole when r(ij) = 10 A. In 1.5 M KCl, only short-range interactions with r(ij) < or = 5 A persisted. Although at physiological ionic strengths the interactions between charges separated by more than 10 A are extremely weak, in situations where charge imbalance exists many weak interactions can cumulatively produce substantial effects.     

Lipid dependence of peptide-membrane interactions: Bilayer affinity and aggregation of the peptide alamethicin

Membrane incorporation and aggregation of the peptide alamethicin have been investigated as a function of lipid type. Head group and acyl chain regions both contribute to modulate alamethicin incorporation. Specifically, the peptide prefers thin membranes and saturated chains; incorporation is reduced by the presence of cholesterol. Aggregation of the peptide in the bilayer is virtually insensitive to changes in lipid composition. These findings show some analogies to results obtained with intrinsic membrane proteins and cast doubt on the use of global membrane parameters for interpreting lipid-peptide interactions.     

Relationship between hexamerization and ssDNA binding affinity in the uvsY recombination protein of bacteriophage T4

In bacteriophage T4, homologous genetic recombination events are catalyzed by a presynaptic filament containing stoichiometric quantities of the T4 uvsX recombinase bound cooperatively to single-stranded DNA (ssDNA). The formation of this filament requires the displacement of cooperatively bound gp32 (the T4 ssDNA-binding protein) from the ssDNA, a thermodynamically unfavorable reaction. This displacement is mediated by the T4 uvsY protein (15.8 kDa, 137 amino acids), which interacts with both uvsX- and gp32-ssDNA complexes and modulates their properties. Previously, we showed that uvsY exists as a hexamer under physiological conditions and that uvsY hexamers bind noncooperatively but with high affinity to ssDNA. We also showed that a fusion protein containing the N-terminal 101 amino acid residues of uvsY lacks interactions with uvsX and gp32 but retains both weak ssDNA-binding activity and a residual ability to stimulate uvsX-catalyzed recombination functions. Here, we present quantitative data on the oligomeric structure and ssDNA-binding properties of a closely related fusion protein designated uvsY. Sedimentation velocity and equilibrium results establish that uvsY, unlike native uvsY, behaves as a monomer in solution (M(app) = 14.2 kDa, = 2.1). Like native uvsY, uvsY binds noncooperatively to an etheno-DNA (epsilonDNA) lattice with a binding site size of 4 nucleotides/monomer; however at physiological ionic strength, the association constant for uvsY-epsilonDNA is decreased 10(4)-fold relative to native uvsY. Nevertheless, the magnitude of the salt effect on the association constant (K) is essentially unchanged between uvsY and uvsY, indicating that disruption of the C-terminus does not disrupt the electrostatic ssDNA-binding determinants found within each protomer of uvsY. Instead, the large difference in ssDNA-binding affinities reflects the loss of hexamerization ability by uvsY, suggesting that a form of intrahexamer synergism or cooperativity between binding sites within the uvsY hexamer leads to its high observed affinity for ssDNA.     

pH dependence of copper geometry, reduction potential, and nitrite affinity in nitrite reductase

Many properties of copper-containing nitrite reductase are pH-dependent, such as gene expression, enzyme activity, and substrate affinity. Here we use x-ray diffraction to investigate the structural basis for the pH dependence of activity and nitrite affinity by examining the type 2 copper site and its immediate surroundings in nitrite reductase from Rhodobacter sphaeroides 2.4.3. At active pH the geometry of the substrate-free oxidized type 2 copper site shows a near perfect tetrahedral geometry as defined by the positions of its ligands. At higher pH values the most favorable copper site geometry is altered toward a more distorted tetrahedral geometry whereby the solvent ligand adopts a position opposite to that of the His-131 ligand. This pH-dependent variation in type 2 copper site geometry is discussed in light of recent computational results. When co-crystallized with substrate, nitrite is seen to bind in a bidentate fashion with its two oxygen atoms ligating the type 2 copper, overlapping with the positions occupied by the solvent ligand in the high and low pH structures. Fourier transformation infrared spectroscopy is used to assign the pH dependence of the binding of nitrite to the active site, and EPR spectroscopy is used to characterize the pH dependence of the reduction potential of the type 2 copper site. Taken together, these spectroscopic and structural observations help to explain the pH dependence of nitrite reductase, highlighting the subtle relationship between copper site geometry, nitrite affinity, and enzyme activity.     

Calmodulin and ATP dependence of the high and low calcium affinity p-nitrophenylphosphatase from human erythrocyte membranes

In calmodulin depleted membranes from human erythrocytes, the Ca2+-dependent phosphatase showed different sensitivity to calmodulin and ATP with variable affinity towards free calcium concentrations: a calmodulin-dependent activity with high calcium affinity, K1/2 = 1.2 X 10(-7) mol/l calcium, that was fully activated at submicromolar calcium concentrations, higher concentrations being rather inhibitory; an ATP-dependent activity with lower calcium affinity, K1/2 = 10(-6) mol/l calcium, that was fully activated at 10(-5) mol/l calcium in the presence of 50-200 mumol/l ATP and was insensitive to calmodulin, and a calcium dependent phosphatase that was active at a wider ranger of free calcium, 10(-8)-10(-5) mol/l, and required the presence of both calmodulin and ATP.     

Distance dependence of interactions between charged centres in proteins with common structural features

Data collected for interactions among redox centres, and interactions between redox centres and acid-base residues in a family of small multihaem cytochromes are analysed. The distance dependent attenuation of the interactions between non-surface charges, for separations that range from 8 to 23 angstroms, can be described by a simple function derived from the Debye-Huckel formalism, fit to 9.5 and 7.6 as values for the relative dielectric constant and Debye length, respectively. However, there is considerable scatter in the data despite the structural similarities among the proteins, which is discussed in the framework of using such simple models in predicting properties of novel proteins.     

Lateral diffusion in an archipelago. Distance dependence of the diffusion coefficient.

An understanding of the distance dependence of the lateral diffusion coefficient is useful in comparing the results of diffusion measurements made over different length scales, and in analyzing the kinetics of mobile redox carriers in organelles. A distance-dependent, concentration-dependent diffusion coefficient is defined, and it is evaluated by Monte Carlo calculations of a random walk by mobile point tracers in the presence of immobile obstacles on a triangular lattice, representing the diffusion of a lipid or a small protein in the presence of immobile membrane proteins. This work confirms and extends the milling crowd model of Eisinger, J., J. Flores, and W. P. Petersen (1986. Biophys J. 49:987-1001). Similar calculations for diffusion of mobile particles interacting by a hard-core repulsion yield the distance dependence of the self-diffusion coefficient. An expression for the range of short-range diffusion is obtained, and the distance scales for various diffusion measurements are summarized.