An energetic evaluation of a “Smith” collagen microfibril model

An energy minimized three-dimensional structure of a collagen microfibril template was constructed based on the five-stranded model of Smith (1968), using molecular modeling methods and Kollman force fields (Weiner and Kollman, 1981). For this model, individual molecules were constructed with three identical polypeptide chains ((Gly-Pro-Pro) _n , (Gly-Prop-Hyp) _n , or (Gly-Ala-Ala) _n , wheren=4, 12, and 16) coiled into a right-handed triple-helical structure. The axial distance between adjacent amino acid residues is about 0.29 nm per polypeptide chain, and the pitch of each chain is approximately 3.3 residues. The microfibril model consists of five parallel triple helices packed so that a left-handed superhelical twist exists. The structural characteristics of the computed microfibril are consistent with those obtained for collagen by X-ray diffraction and electron microscopy. The energy minimized Smith microfibril model for (Gly-Pro-Pro)₁₂ has an axial length of about 10.2 nm (for a 36 amino acid residue chain), which gives an estimated D-spacing (234 amino acids per chain) of approximately 66.2 nm. Studies of the microfibril models (Gly-Pro-Pro)₁₂, (Gly-Pro-Hyp)₁₂, and (Gly-Ala-Ala)₁₂ show that nonbonded van der Waals interactions are important for microfibril formation, while electrostatic interactions contribute to the stability of the microfibril structure and determine the specificity by which collagen molecules pack within the microfibril.     

Mechanisms of β-Adrenergic Modulation of IKs in the Guinea-Pig Ventricle: Insights from Experimental and Model-Based Analysis

Detailed understanding of I_Ks gating complexity may provide clues regarding the mechanisms of repolarization instability and the resulting arrhythmias. We developed and tested a kinetic model to interpret physiologically relevant I_Ks properties, including pause-dependence and modulation by β-adrenergic receptors (β-AR). I_Ks gating was evaluated in guinea-pig ventricular myocytes at 36°C in control and during β-AR stimulation (0.1 μmol/L isoprenaline (ISO)). We tested voltage dependence of steady-state conductance (Gss), voltage dependence of activation and deactivation time constants (τ_act, τ_deact), and pause-dependence of τ_act during repetitive activations (τ_react). The I_Ks model was developed from the Silva and Rudy formulation. Parameters were optimized on control and ISO experimental data, respectively. ISO strongly increased Gss and its voltage dependence, changed the voltage dependence of τ_act and τ_deact, and modified the pause-dependence of τ_react. A single set of model parameters reproduced all experimental data in control. Modification of only three transition rates led to a second set of parameters suitable to fit all ISO data. Channel unitary conductance and density were unchanged in the model, thus implying increased open probability as the mechanism of ISO-induced Gss enhancement. The new I_Ks model was applied to analyze ISO effect on repolarization rate-dependence. I_Ks kinetics and its β-AR modulation were entirely reproduced by a single Markov chain of transitions (for each channel monomer). Model-based analysis suggests that complete opening of I_Ks channels within a physiological range of potentials requires concomitant β-AR stimulation. Transient redistribution of state occupancy, in addition to direct modulation of transition rates, may underlie β-AR modulation of I_Ks time dependence.     

A robust all-atom model for LCAT generated by homology modeling

LCAT is activated by apoA-I to form cholesteryl ester. We combined two structures, phospholipase A₂ (PLA₂) that hydrolyzes the ester bond at the sn-2 position of oxidized (short) acyl chains of phospholipid, and bacteriophage tubulin PhuZ, as C- and N-terminal templates, respectively, to create a novel homology model for human LCAT. The juxtaposition of multiple structural motifs matching experimental data is compelling evidence for the general correctness of many features of the model: i) The N-terminal 10 residues of the model, required for LCAT activity, extend the hydrophobic binding trough for the sn-2 chain 15–20 Å relative to PLA₂. ii) The topography of the trough places the ester bond of the sn-2 chain less than 5 Å from the hydroxyl of the catalytic nucleophile, S181. iii) A β-hairpin resembling a lipase lid separates S181 from solvent. iv) S181 interacts with three functionally critical residues: E149, that regulates sn-2 chain specificity, and K128 and R147, whose mutations cause LCAT deficiency. Because the model provides a novel explanation for the complicated thermodynamic problem of the transfer of hydrophobic substrates from HDL to the catalytic triad of LCAT, it is an important step toward understanding the antiatherogenic role of HDL in reverse cholesterol transport.     

Regulation of membrane proteins by dietary lipids: effects of cholesterol and docosahexaenoic acid acyl chain-containing phospholipids on rhodopsin stability and function

Purified bovine rhodopsin was reconstituted into vesicles consisting of 1-stearoyl-2-oleoyl phosphatidylcholine or 1-stearoyl-2-docosahexaenoyl phosphatidylcholine with and without 30 mol % cholesterol. Rhodopsin stability was examined using differential scanning calorimetry (DSC). The thermal unfolding transition temperature (T_m) of rhodopsin was scan rate-dependent, demonstrating the presence of a rate-limited component of denaturation. The activation energy of this kinetically controlled process (E_a) was determined from DSC thermograms by four separate methods. Both T_m and E_a varied with bilayer composition. Cholesterol increased the T_m both the presence and absence of docosahexaenoic acid acyl chains (DHA). In contrast, cholesterol lowered E_a in the absence of DHA, but raised E_a in the presence of 20 mol % DHA-containing phospholipid. The relative acyl chain packing order was determined from measurements of diphenylhexatriene fluorescence anisotropy decay. The T_m for thermal unfolding was inversely related to acyl chain packing order. Rhodopsin kinetic stability (E_a) was reduced in highly ordered or disordered membranes. Maximal kinetic stability was found within the range of acyl chain order found in native bovine rod outer segment disk membranes. The results demonstrate that membrane composition has distinct effects on the thermal versus kinetic stabilities of membrane proteins, and suggests that a balance between membrane constituents with opposite effects on acyl chain packing, such as DHA and cholesterol, may be required for maximum protein stability.     

En bloc transfer of polyubiquitin chains to PCNA in vitro is mediated by two different human E2�CE3 pairs

Post-replication DNA repair in eukaryotes is regulated by ubiquitination of proliferating cell nuclear antigen (PCNA). Monoubiquitination catalyzed by RAD6–RAD18 (an E2–E3 complex) stimulates translesion DNA synthesis, whereas polyubiquitination, promoted by additional factors such as MMS2–UBC13 (a UEV–E2 complex) and HLTF (an E3 ligase), leads to template switching in humans. Here, using an in vitro ubiquitination reaction system reconstituted with purified human proteins, we demonstrated that PCNA is polyubiquitinated predominantly via en bloc transfer of a pre-formed ubiquitin (Ub) chain rather than by extension of the Ub chain on monoubiquitinated PCNA. Our results support a model in which HLTF forms a thiol-linked Ub chain on UBC13 (UBC13∼Ub_n) and then transfers the chain to RAD6∼Ub, forming RAD6∼Ub_n+1. The resultant Ub chain is subsequently transferred to PCNA by RAD18. Thus, template switching may be promoted under certain circumstances in which both RAD18 and HLTF are coordinately recruited to sites of stalled replication.     

Crystal structure and linear chain antiferromagnetism in Mn(tricyanomethanide)2(4,4-bipyridine)2

A new linear chain antiferromagnet, namely Mn(tcm)₂(4,4^′-bipy)₂ (tcm=tricyanomethanide and bipy=bipyridine) has been synthesized and characterized by X-ray crystallography and magnetic susceptibility measurements. Each Mn²⁺ is high-spin S=5/2 and linked to nearest-neighbor spin sites via μ-bridged tcm ligands to form a 1D linear chain while the bipy ligands are monodentate and segregate the chains. Magnetically, a broad maximum in χ^′(T) is observed at 2.1 K and likely signifies short-range magnetic order within the chains. A least-squares fit of the χT(T) data to a classical-spin Fisher chain model yielded good agreement for g=2.008(1) and J=−0.217(4) K. No long-range magnetic ordering is observed above 1.6 K due to the presence of very weak interchain magnetic interactions as indicated by inclusion of a mean-field model that gave zJ^′=−0.009(1) K.     

Determination of enantiomeric purity of glycerides with a chiral PMR shift reagent.

Tris(3-heptafluorobutyryl-d-camphorato)europium(III), Eu(hfbc)₃ was used to determine the optical purities of enantiomeric mixtures of tri-, di- and monoglycerides with various fatty acid chain lengths by proton magnetic resonance (PMR). Synthesized model enantiomers were used to assign PMR signals. Enantiomeric signal separation becomes more difficult if the chain length difference between the fatty acids in the 1- and 3-positions of glycerol becomes smaller. The sign of the enantiomeric shift difference (ΔΔδ) of the terminal acyl CH₃ group of 1-acyl-2,3-distearoyl-sn-glycerol vs its enantiometer remains the same in the series acyl is hexanoyl, butyryl, propionyl, but is reversed for acetyl.The absolute configuration of the main triglyceride of the seed oil of Euonymus alatus was determined to be 3-acetyl-1,2-distearoyl-sn-glycerol and that of a monobutyryl triglyceride fraction from hydrogenated bovine butterfat was confirmed to be mainly 1,2-diacyl-3-butyryl-sn-glycerol. The enantiotopic behaviour of the glycerol CH₂ groups in (nearly) symmetric di- and triglycerides is discussed.     

The electron transport system of Alcaligenes eutrophus H16

In a previous work (Kömen et al. 1991) it has been concluded that membrane fragments isolated from autotrophically grown Alcaligenes eutrophus H16 contain several iron-sulphur centres along with haems of a-, b-, c-, and d-type. These redox components have been proposed to be part of a branched respiratory chain leading to multiple membrane bound oxidases. Here, some of the respiratory activities catalyzed by membrane fragments from wild type cells of A. eutrophus (H16) and, for comparison, Paracoccus denitrificans, have been investigated through the use of electron transport inhibitors. Cyanide (CN^-) titration curves indicated that in A. eutrophus H16 oxidation of succinate and H₂ preferentially proceeds via the cytochrome c oxidase(s) branch (I ₅₀=2 · 10^-5 M) whereas the NADH dependent respiration started being inhibited at higher CN^- concentrations (I ₅₀=5 · 10^-4 M). In membranes isolated from both, cells harvested at late growth-phase (OD 12) and from a mutant deficient in cytochrome c oxidase activity (A. eutrophus RK1), respiration was insensitive to low CN^- concentrations (< 10^-4 M), and it was sustained by the high catalytic activities of two quinol oxidases. These alternative oxidases of b- (formally o-) and d-type showed different sensitivities to KCN (I ₅₀=10^-3 M and 10^-2 M, respectively). Interestingly, the cytochrome c oxidase(s) dependent respiration of H16 membranes was insensitive to antimycin A but largely inhibited by myxothiazol (10^-6 M). This, and previous work (Kömen et al. 1991), suggest that although the respiratory chain of A. eutrophus is endowed with a putative bc ₁ complex, its biochemical nature and role in respiration of this organism are apparently different from those of P. denitrificans. The peculiarity of the respiratory chain of A. eutrophus is confirmed by the rotenone insensitivity of the NADH oxidation in both protoplasts and membrane fragments from wild type and soluble hydrogenase deficient cells (HF14 and HF160). A tentative model of the respiratory chain of autotrophically grown A. eutrophus is presented.     

The essentiality of B chain in stabilizing the structure of the A chain in β1-bungarotoxin fromBungarus multicinctus venom

The dynamic of Trp residue inΒ ₁-bungarotoxin (gb ₁-Bgt), the A chain ofΒ ₁-Bgt and phospholipase A₂ (PLA₂) was assessed by fluorescence measurement. Acrylamide quenching studies showed that the exposure degree of the Trp in PLA₂ is higher than the Trp inΒ ₁-Bgt. The Trp ofΒ ₁-Bgt had a higher accessibility for iodide, reflecting that the basic nature of the B chain might exert an attractive electrostatic force for iodide and increase the susceptibility of Trp in the A chain to iodide. Removal of the B chain ofΒ ₁-Bgt did not significantly affect the exposure degree of Trp in the A chain. Alternatively, the polarity of the environment around the Trp and the hydrophobic character of ANS and substrate binding sites in the separated A chain changed. Measurement of Trp fluorescence with increasing temperature showed that the stability of structure ofΒ ₁-Bgt was higher than those of the separated A chain and PLA₂. These results suggest that the B chain might interact with the A chain and stabilize the conformation of the A chain inΒ ₁-Bgt.     

Production of the human immunoglobulin γ1 chain constant region polypeptides in Escherichia coli

We have determined the nucleotide sequence of the constant region exons of the rearranged human immunoglobulin γ₁ chain gene cloned from a human plasma cell leukemia line, ARH-77. The amino acid sequence deduced from the nucleotide sequence revealed that the allotype of the ARH-77 γ₁ chain was Glm (−1, −2, 3).Recombinant plasmids were then constructed in order to express the human γ₁ chain constant region genes (the Fc region gene and the C_H2-C_H3 domains gene) in Escherichia coli. The human γ₁ chain constant region genes without introns were derived from the genomic gene using synthetic DNA fragments. E. coli carrying each expression plasmid produced antigenically active constant region polypeptides as soluble proteins. In the case of the E. coli-derived Fc region polypeptides, they were generated as monomeric forms in the cytoplasm.     

Hemoglobins Austin and Waco: two hemoglobins with substitutions in the alpha 1 beta 2 contact region.

Hemoglobins (Hbs) Austin and Waco were detected by their electrophoretic migration on cellulose acetate (pH 8.4) and citrate agar (pH 6.2). By these methods, both variants migrated between Hbs A and F. Globin chain analysis at pH 8.6 indicated that the mutant β chain of Hb Austin was faster moving than the β^A chain; however, the mutant chain of Hb Waco was indistinguishable from the β^A chain by this technique. The two variants were isolated by ion-exchange column chromatography. Sequence studies demonstrated a substitution of serine (Hb Austin) and lysine (Hb Waco) for arginine at position 40 in the β chain. These mutations involve an amino acid residue in the α₁β₂ contact region, which, before this report, had been considered invariant in all hemoglobin sequences. Hb Austin was found to exist as dimers when oxygenated and as tetramers when deoxygenated. The equilibrium constant (K_d) for the tetramer to dimer transition was approximately 300 × 10^?6m, as calculated from sedimentation velocity studies. This variant also had high oxygen affinity, a much reduced heme-heme interaction, and a normal Bohr effect. The functional properties of Hb Waco were similar to those of Hb A.     

A potentiometric and kinetic study on the respiratory chain of ferrous-iron-grown Thiobacillus ferrooxidans

The type and number of respiratory chain components present in membranes of Thiobacillus ferrooxidans have been investigated. These redox components were resolved potentiometrically and kinetically. Using optical techniques two cytochromes a₁, multiple cytochromes c and two cytochromes b were detected. By using electron paramagnetic resonance, two copper-containing centres, high and low spin ferric haems and a ferredoxin centre were detected. Based on the combination of a potentiometric resolution and a kinetic study a model for the sequence of the respiratory chain components in the Fe²⁺ to O₂ branch of the T. ferrooxidans respiratory chain is proposed.     

On the problems of the evolutionary optimization of life history. I. Markov model of Leslie life cycle and optimization of fertility

The paper considers the properties of individual life history corresponding to the Leslie model of age-structured population. The life history is modelled as a finite Markov chain with absorption at a death state of individual. In this model, individual longevity, average number of offspring R _L (produced by an individual over the entire life), and some other known characteristics of the life history have been derived using simple probability methods that do not involve matrix calculus and their individual components have been interpreted. In the linear Leslie population model (derived by simple modification of a Markov chain), R _L determines the growth or decline of a population. Individuals with higher R _L values have evolutionary advantages in the population due to accelerated growth in their number. The selection of fertility as a factor of the increase in R _L is considered. In the Leslie model, fertility is a set of correlated quantitative traits, where the age-specific fertility components are determined both by multiple loci and the environment. According to the genetic theory of quantitative trait selection, they evolve towards an increase in R _L . Taking into account the limited resources for reproduction, selection optimizes the fertility distribution according to age. Optimal distribution corresponds to the attainment of the maximum R _L . This complies with the maximization of the rate of population growth (r-selection), which is characteristic of linear population models. The search for the R _L maximum and optimal distribution of fertility belongs to the field of linear programming.     

Hydrogen-bonded supramolecular manganese(II) complexes with network and sheet structures bridged by terephthalate unit

Two 1D complexes [Mn(4- methylpyrazole)₃(H₂O)(tp)]_n (2) and [Mn(4-methylpyrazole)₄(tp)]_n (3) (tp = terephthalate) were synthesized and characterized by means of X-ray analysis and magnetic studies. The molecular structure of 2 reveals that Mn(II) centers with asymmetric coordination surroundings are bridged by crystallographically different tp ligands, forming a 1D chain. The 1D coordination chains are interconnected by hydrogen bonds between free carboxylate oxygen atoms in a chain and hydrogens of pyrazole nitrogen atoms in neighboring chains, leading to a 3D framework. Compound 3 also exhibits a 1D coordination chain which is hydrogen-bonded to adjacent chains, providing a 2D sheet structure. Interestingly, the structures include intra- and interchain hydrogen bonds contributed from N-H groups of the capping 4-methylpyrazole ligands. Magnetic measurements show weak antiferromagnetic interactions with exchange coupling parameters of J = −0.018 cm⁻¹ for 2 and J = −0.062 cm⁻¹ for 3 through the extended tp ligand on the basis of an infinite chain model (H = −J∑S_i · S_i + 1).     

cDNA sequence analysis and mutagenesis studies on the a chain of Β-bungarotoxin from Taiwan banded krait

The cDNA encoding the A chain ofΒ-bungarotoxin (Β-Bgt) was constructed from the cellular RNA isolated from the venom glands ofBungarus multicinctus (Taiwan banded krait). The deduced amino acid sequence encoding the A chain revealed that the determined chain was different from the known A chains (A1, A2, A3, A4, and A5). Nevertheless, the amino acid sequence and the cDNA sequence of the novel A chain were highly homologous with those of other A chains. The gene encoding the A chain ofΒ-Bgt was subjected to mutagenesis, and the Tyr-11, Cys-15, and Leu-72 of the A chain were substituted by Cys-11, Ser-15, and Cys-72, respectively. Instead of the six disulfide bonds observed with the A chain, the resulting mutant contained seven disulfide linkages in its molecular structure which simulated those of presynaptic PLA₂ neurotoxins and PLA₂ enzymes. However, the mutant did not exhibit a higher phospholipase activity than that noted with the recombinant A chain. These results seem to suggest that, in the absence of the B chain, the six pairs of disulfide bonds in the recombinant A-chain molecule are enough to maintain its active conformation for exerting the phospholipase activity.     

The lysis of isolated fish (Oncorhynchus mykiss) gill epithelial cells by surfactants

1. The interaction of a wide range of surfactants with isolated gill epithelial cells of rainbow trout (Oncorhynchus mykiss) was investigated as a function of the surfactant concentration up to and above the critical micelle concentration (cmc). The surfactants included a homologous series of n-alkyl sulphates, single and double chain tri and dimethylammonium bromides (TABs and DABs), cholates and the nonionics n-octylglucoside and Triton X-100.2. With the exception of the C₂₂ alkyl chain TAB and the double chain [(C₁₂)₂] DAB, the surfactants solubilized between 84 and 100% of the cell protein at high concentrations (>cmc).3. At low concentrations n-dodecyltrimethylammonium bromide and, to a lesser extent, Triton X-100 and sodium n-dodecylsulphate release a larger proportion of cell protein than they solubilize lipid in contrast to sodium cholate which initially preferentially solubilizes cell lipid. This differential pattern of solubilization is similar to that observed for other plasma membranes such as those of human erythrocytes and platelets.4. The surfactant concentration required to solubilize 50% (S_50%) of cell protein increases with the cmc. There is an approximately linear relationship between log(S_50%) and log cmc.5. Light microscopy shows that the surfactants at high concentrations (>cmc) fragment the secondary lamellae of the gill filaments.     

Genetic control of antibody specificity in the mouse

Genetic markers related to the antigen binding specificity of mouse immunoglobulins (idiotypes and fine specificity characteristics) are used to investigate the polymorphism of genes encoding heavy chain variable regions (V _H genes). The distribution of eight such specificity related markers in inbred strains and their segregation together with allotype indicate linkage to genes that specify the heavy chain constant regions (C _H genes). A number of recombinant mice allowed the construction of a chromosomal map consisting of threeV _H subloci, oneC _h sublocus, and a region which contains nonimmunoglobulin coding genes. All data are consistent with a linear arrangement of genes in this linkage group so thatV _H andC _H genes are discontinuous. Each of theV _H subloci is correlated to a particular set of antigen binding specificities which include protein antigens, polysaccharides, and haptens. This suggests that specific complementarity determining sequence portions are conserved in the germ line of the mouse.     

Heterogeneity in branching of amylopectin

The angular dependence of scattered light from amylopectin and its β-limit dextrin, the mean square radius of gyration and the molecular weights M_w and M_n have been calculated on the basis of the cascade branching theory for the homogeneously branched model by Meyer &; Bernfeld (1940) (Model I) and for the two heterogeneously branched structures suggested by French (1972) (Model II) and by Robin et al. (1974, 1975) (Model III). The calculations take into account the particularities of topology in branched molecules and the experimentally determined ratio of the number of A- and B-chains, A/B = 1. Furthermore, an average branching density of 4% and an interconnecting chain length of ovbar|n_i2 = 22, found by gel permeation chromatography (GPC) after debranching, were used. The constraints lead to the conclusion that amylopectin is heterogeneously branched. Densely branched clusters containing 3·22 branching units are interconnected by longer chains of 22 units in length. Comparison of the calculated angular dependence of light scattering with measurements from a maize amylopectin β-limit dextrin in 1 n NaOH solution gives strong evidence for a modified Robin-Mercier model. The modification consists of the conclusion that the interconnecting chains are preferentially B-chains, such that these chains carry on the average 1·4 clusters, while Robin and Mercier assume exactly 2 clusters. Our result is in agreement with the distribution of chain length found after debranching the amylopectin β-limit dextrin.     

Barotropic and thermotropic bilayer phase behavior of positional isomers of unsaturated mixed-chain phosphatidylcholines

The bilayer phase transitions of six kinds of mixed-chain phosphatidylcholines (PCs) with an unsaturated acyl chain in the sn-1 or sn-2 position, 1-oleoyl-2-stearoyl- (OSPC), 1-stearoyl-2-oleoyl- (SOPC), 1-oleoyl-2-palmitoyl- (OPPC), 1-palmitoyl-2-oleoyl- (POPC), 1-oleoyl-2-myristoyl- (OMPC) and 1-myristoyl-2-oleoyl-sn-glycero-3-phosphocholine (MOPC), were observed by means of differential scanning calorimetry (DSC) and high-pressure light transmittance measurements. Bilayer membranes of SOPC, POPC and MOPC with an unsaturated acyl chain in the sn-2 position exhibited only one phase transition, which was identified as the main transition between the lamellar gel (L_β) and liquid crystalline (L_α) phases. On the other hand, the bilayer membranes of OSPC, OPPC and OMPC with an unsaturated acyl chain in the sn-1 position exhibited not only the main transition but also a transition from the lamellar crystal (L_c) to the L_β (or L_α) phase. The stability of their gel phases was markedly affected by pressure and chain length of the saturated acyl chain in the sn-2 position. Considering the effective chain lengths of unsaturated mixed-chain PCs, the difference in the effective chain length between the sn-1 and sn-2 acyl chains was proven to be closely related to the temperature difference of the main transition. That is, a mismatch of the effective chain length promotes a temperature difference of the main transition between the positional isomers. Anomalously small volume changes of the L_c/L_α transition for the OPPC and OMPC bilayers were found despite their large enthalpy changes. This behavior is attributable to the existence of a cis double bond and to significant inequivalence between the sn-1 and sn-2 acyl chains, which brings about a small volume change for chain melting due to loose chain packing, corresponding to a large partial molar volume, even in the L_c phase. Further, the bilayer behavior of unsaturated mixed-chain PCs containing an unsaturated acyl chain in the sn-1 or sn-2 position was well explained by the chemical-potential diagram of a lipid in each phase.