The C-terminal extrahelical peptide of type I collagen and its role in fibrillogenesis in vitro: effects of ethylurea

Ethylurea was used to weaken hydrophobic interactions during collagen fibrillogenesis in vitro. Intact and enzyme-digested type I collagen was studied. In all preparations, ethylurea decreased the extent and rate of fibril formation, inhibition being greatest in the enzyme-digested collagens. With intact collagen (and probably also with carboxypeptidasedigested collagen), there was no evidence the ethylurea altered the mechanism of fibril growth; in pepsin-digested collagen, however, the growth mechanism was altered by ethylurea, possibly reflecting a conformational change of the “hydrophobic cluster” in the C-terminal peptide. Such a structural change could occur in a hydrophobic environment once the distal portion of the C-terminal peptide (presumed to be essential for its structural stability) is removed by pepsin. The results further emphasize the importance of hydrophobic interactions in collagen fibril nucleation and growth in vitro.     

What Drives Amyloid Molecules To Assemble into Oligomers and Fibrils?

We develop a theory for three states of equilibrium of amyloid peptides: the monomer, oligomer, and fibril. We assume that the oligomeric state is a disordered micellelike collection of a few peptide chains held together loosely by hydrophobic interactions into a spherical hydrophobic core. We assume that fibrillar amyloid chains are aligned and further stabilized by steric zipper interactions—hydrogen bonding, steric packing, and specific hydrophobic side-chain contacts. The model makes a broad set of predictions that are consistent with experimental results: 1), Similar to surfactant micellization, amyloid oligomerization should increase with peptide concentration in solution. 2), The onset of fibrillization limits the concentration of oligomers in the solution. 3), The extent of Aβ fibrillization increases with peptide concentration. 4), The predicted average fibril length versus monomer concentration agrees with data on α-synuclein. 5), Full fibril length distributions agree with data on α-synuclein. 6), Denaturants should melt out fibrils. And finally, 7), added salt should stabilize fibrils by reducing repulsions between amyloid peptide chains. It is of interest that small changes in solvent conditions can tip the equilibrium balance between oligomer and fibril and cause large changes in rates through effects on the transition-state barrier. This model may provide useful insights into the physical processes underlying amyloid diseases.     

Dielectric properties of slightly hydrated collagen: time-water content superposition analysis

The frequency dependences of the dielectric constant, ε′, and the loss factor, ε″, in collagen were measured at several water contents from 0.1 to 0.3 g/g collagen over a frequency range of 30 Hz to 100 kHz and at a temperature of 20°C. Remarkable dispersion was observed at the lower frequencies for higher water contents. According to accumulated results on the thermodynamic and structural investigations, the dispersion has some analogy to the surface conduction proposed by B. V. Hamon [(1953) Aust. J. Phys. 6 , 304–315]. An empirical relation bewteen ε″ and frequency, f, ε″ ∝? fⁿ, where 0 < n < 1, suggests that the dielectric and conductive properties of hydrated collagen are related to carrier jumps between neighboring sites. For the polarization mechanism of this dispersion, we supposed a model of the transfer of protons between absorbed water molecules, and found that the time–water content superposition procedure is applicable to slightly hydrated collagen. The results derived from the superposition procedure show that the water content, ?, is related to the conductivity, σ, or the dielectric loss factor by the following equations: σ (?, f) = const. × ?^nm?1f^1?n and ε″ (?, f) = const. ?^nmf^?n, respectively, where m is a constant independent of ? and f. These results agree with that derived by another treatment of the same data. The role of water molecules in the conduction and polarization in slightly hydrated collagen is considered to be not far from that assumed in the model.     

Three dimensional patient-specific collagen architecture modulates cartilage responses in the knee joint during gait

Site-specific variation of collagen fibril orientations can affect cartilage stresses in knee joints. However, this has not been confirmed by 3-D analyses. Therefore, we present a novel method for evaluation of the effect of patient-specific collagen architecture on time-dependent mechanical responses of knee joint cartilage during gait. 3-D finite element (FE) models of a human knee joint were created with the collagen architectures obtained from T₂ mapped MRI (patient-specific model) and from literature (literature model). The effect of accuracy of the implementation of collagen fibril architecture into the model was examined by using a submodel with denser FE mesh. Compared to the literature model, fibril strains and maximum principal stresses were reduced especially in the superficial/middle regions of medial tibial cartilage in the patient-specific model after the loading response of gait (up to ?413 and ?26%, respectively). Compared to the more coarsely meshed joint model, the patient-specific submodel demonstrated similar strain and stress distributions but increased values particularly in the superficial cartilage regions (especially stresses increased >60%). The results demonstrate that implementation of subject-specific collagen architecture of cartilage in 3-D modulates location- and time-dependent mechanical responses of human knee joint cartilage. Submodeling with more accurate implementation of collagen fibril architecture alters cartilage stresses particularly in the superficial/middle tissue.     

The role of extrahelical peptides in stabilization of collagen fibrils

A quantitative model for fibril assembly of type I collagen was extended to include the explicit effect of extrahelical peptides. The collagen molecule was simulated by rod-like sequences to which short, rigid tails were connected by "nondimensional" flexible joints. Three collagen structures were studied: (1) intact collagen, simulated by a rod of axial ratio 200 (The axial ratio x was taken as a segment length) with two tails of length x = 1 and x = 2, respectively, appended to each end; (2) pepsin-digested collagen, simulated by one rigid segment of length 200 and one tail of length 1; and (3) pronase-digested collagen, by a single rigid segment of length x = 200. Phase equilibria of such structures were calculated, using a lattice theory of Matheson and Flory, and the relation of the polymer-solvent interaction parameter chi to the equilibrium solubility was determined. The chi for each collagen species was then related to temperature (T) and ionic strength (I), based on the approximation that local (per segment) stabilization of collagen fibrils was due to hydrophobic and electrostatic forces only. Solubility vs temperature curves for all three collagen species were computed and compared to published experimental data. From the chi factors for each species, the composite chi was resolved into components representing energetic contributions of the extrahelical peptides relative to the helix, which were interpreted in terms of hydrophobic or electrostatic interactions stabilizing the collagen fibril.     

Manipulating the Length of the <Emphasis Type="Italic">b</Emphasis> Subunit F<Subscript>1</Subscript> Binding Domain in F<Subscript>1</Subscript>F<Subscript>0</Subscript> ATP Synthase from <Emphasis Type="Italic">Escherichia coli</Emphasis>

The peripheral stalk of F₁F₀ ATP synthase is composed of a parallel homodimer of b subunits that extends across the cytoplasmic membrane in F₀ to the top of the F₁ sector. The stalk serves as the stator necessary for holding F₁ against movement of the rotor. A series of insertions and deletions have been engineered into the hydrophilic domain that interacts with F₁. Only the hydrophobic segment from {val-121} to {ala-132} and the extreme carboxyl terminus proved to be highly sensitive to mutation. Deletions in either site apparently abolished enzyme function as a result of defects is assembly of the F₁F₀ complex. Other mutations manipulating the length of the sequence between these two areas had only limited effects on enzyme function. Expression of a b subunit with insertions with as few as two amino acids into the hydrophobic segment also resulted in loss of F₁F₀ ATP synthase. However, a fully defective b subunit with seven additional amino acids could be stabilized in a heterodimeric peripheral stalk within a functional F₁F₀ complex by a normal b subunit.     

Bifurcation Analysis of Genetically Engineered Pacemaking in Mammalian Heart

Genetically engineered pacemaking in ventricular cells has been achieved by down-regulation of the time independent inward rectifying current (I _K1), or insertion of the hyperpolarisation-activated funny current (I _f). We analyse the membrane system (i.e. ionic concentrations clamped) of an epicardial Luo-Rudy dynamic cell model using continuation algorithms with the maximum conductance () of I _K1 and I _f as bifurcation parameters. Pacemaker activity can be induced either via Hopf or homoclinic bifurcations. As _K1 is decreased by ≈74%, autorhythmicity emerged via a homoclinic bifurcation, i.e., the periodicity first appear with infinitely large periods. In contrast, the insertion of _f induced periodicity via a subcritical Hopf bifurcation at _f≈ 0.25 mSμF⁻¹. Stable autorhythmic action potentials occurred at _f > 0.329 mSμF⁻¹.     

CORRELATION OF PAIRWISE GENETIC AND GEOGRAPHIC DISTANCE MEASURES: INFERRING THE RELATIVE INFLUENCES OF GENE FLOW AND DRIFT ON THE DISTRIBUTION OF GENETIC VARIABILITY

Attempts to relate estimates of regional F_ST to gene flow and drift via Wright's (1931) equation F_ST ≈ 1/ (4Nm + 1) are often inappropriate because most natural sets of populations probably are not at equilibrium (McCauley 1993), as assumed by the island model upon which the equation is based, or ineffective because the influences of gene flow and drift are confounded in the product Nm. Evaluations of the association between genetic (F_ST) and geographic distances separating all pairwise populations combinations in a region allows one to test for regional equilibrium, to evaluate the relative influences of gene flow and drift on population structure both within and between regions, and to visualize the behavior of the association across all degrees of geographic separation. Tests of the model using microsatellite data from 51 populations of eastern collared lizards (Crotaphytus collaris collaris) collected from four distinct geographical regions gave results highly consistent with predicted patterns of association based on regional differences in various historical and ecological factors that affect the amount of drift and gene flow. The model provides a prerequisite for and an alternative to regional F_ST analyses, which often simply assume regional equilibrium, thus potentially leading to erroneous and misleading inferences regarding regional population structure.     

The potential inhibitory effect of β-casein on the aggregation and deposition of Aβ1-42 fibrils in Alzheimer’s disease: insight from in-vitro and in-silico studies

Aβ_1-40 and Aβ_1-42 have been shown to be the main components of the amyloid plaques found in the extracellular environment of neurons in Alzheimer’s disease. β-Casein, a milk protein, has been shown to display a remarkable chaperone ability in preventing the aggregation of proteins. In this study, the ability of β-casein to suppress the amyloid fibril formation of Aβ_1-42 has been examined through in vitro studies and molecular docking simulation. The results demonstrate the inhibitory effect of β-casein on fibril formation in Aβ_1-42, in a concentration dependent manner, suggesting that the chaperone binds to the Aβ_1-42 and prevents amyloid fibril formation. Molecular docking results show that the inhibitory effect of the β-casein may be due to binding of the chaperone with the aggregation-prone region of the Aβ_1-42 mainly via hydrophobic interactions. β-Casein probably binds to the CHC and C-terminal domain of the Aβ_1-42, and stabilizes proteins by inhibiting the conversion of monomeric Aβ_1-42 into fibrils. Thus our data suggests that the hydrophobic interactions between β-casein and Aβ_1-42 play an important role in the burial of the hydrophobic part of the Aβ_1-42. This means that β-casein maybe considered for use in preventing amyloid fibril formation in degenerative diseases such as Alzheimer.     

Interaction of bacterial F1-ATPase with octyl glucoside and deoxycholate

Purified F₁-ATPase from Micrococcus lysodeikticus (Micrococcus luteus) contains extensive and easily accessible areas capable of hydrophobic interaction. These hydrophobic areas were demonstrated by the binding of a non-ionic and a mild anionic detergent to this protein, evidenced by charge shift electrophoresis and measured by equilibrium gel chromatography with labelled detergents. F₁-ATPase bound 0.06 ± 0.01 g octyl glucoside per g protein and 0.12 ± 0.01 g deoxycholate per g protein, which amount to 81 and 119 amphiphile molecules per protein molecule, respectively. Deoxycholate and octyl glucoside inhibited the Ca²⁺- and Mg²⁺-dependent ATP hydrolytic activity of the enzyme. The inhibition by octyl glucoside was moderately cooperative. Binding of these detergents to the enzyme did not seem to induce any disruption of its quaternary structure, although the spontaneous dissociation of the δ subunit, which is not essential for the enzyme activity, increased during deoxycholate treatment. These results suggest that hydrophobic domains play a role in the enzymatic activity of this coupling factor and / or in its interaction with the membrane.     

Determining the critical nucleus and mechanism of fibril elongation of the Alzheimer's Abeta(1-40) peptide

We use a coarse-grained protein model to characterize the critical nucleus, structural stability, and fibril elongation propensity of Aβ_1-40 oligomers for the C_2x and C_2z quaternary forms proposed by solid-state NMR. By estimating equilibrium populations of structurally stable and unstable protofibrils, we determine the shift in the dominant population from free monomer to ordered fibril at a critical nucleus of ten chains for the C_2x and C_2z forms. We find that a minimum assembly of 16 monomer chains is necessary to mimic a mature fibril, and show that its structural stability correlates with a plateau in the hydrophobic residue density and a decrease in the likelihood of losing hydrophobic interactions by rotating the fibril subunits. While Aβ_1-40 protofibrils show similar structural stability for both C_2x and C_2z quaternary structures, we find that the fibril elongation propensity is greater for the C_2z form relative to the C_2x form. We attribute the increased propensity for elongation of the C_2z form as being due to a stagger in the interdigitation of the N-terminal and C-terminal β-strands, resulting in structural asymmetry in the presented fibril ends that decreases the amount of incorrect addition to the N terminus on one end. We show that because different combinations of stagger and quaternary structure affect the structural symmetry of the fibril end, we propose that differences in quaternary structures will affect directional growth patterns and possibly different morphologies in the mature fiber.     

In vitro collagen fibril assembly: thermodynamic studies

The in vitro fibril assembly of calf skin collagen was examined as a function of ionic strength and temperature. In a 0.03 M NaPi, pH 7.0, buffer, fibril assembly required a minimum critical concentration of collagen. At nearly physiological ionic strengths and temperatures, the critical concentration was less than 1 microgram/mL and required a very sensitive method for measurement. Raising the ionic strength of the buffer resulted first in higher and then lower critical concentrations. Raising the temperature led to lower critical concentrations. A van't Hoff plot of the fibril growth constant calculated from the critical concentration gave positive enthalpy changes and positive heat capacity changes which indicate that the fibril growth is driven by both hydrophobic and ionic inter-collagen interactions. Sedimentation equilibrium studies showed the collagen to be monomeric at subcritical concentrations. Differential scanning microcalorimetric studies showed only one very sharp heat absorption peak for the fibril assembly which coincided with the appearance of solution turbidity. Within experimental error, the enthalpy changes of the fibril assembly measured with the microcalorimeter were of the same magnitude as the van't Hoff enthalpy changes. These results are discussed in light of a cooperative nucleation-growth mechanism of collagen fibril assembly proposed earlier.     

Adaptation of sorghum: characterisation of genotypic flowering responses to temperature and photoperiod

Sorghum [Sorghum bicolor (L.) Moench] is an important cereal crop grown in a wide range of tropical and temperate environments. This study was conducted to characterise the photothermal flowering responses of sorghum genotypes and to examine relationships between photothermal characteristics and environment of origin in order to better understand the phenological basis of adaptation to environment in sorghum. Twenty-four germplasm accessions and one hybrid from 24 major sorghum-growing areas were grown in a wide range of environments varying in temperature and photoperiod in India, Kenya and Mali between 1992 and 1995. Times from sowing to flowering (f) were recorded, and the responsiveness of 1/f to temperature and photoperiod was quantified using photothermal models. Times from sowing to flowering were accurately predicted in a wide range of environments using a multiplicative rate photothermal model. Significant variation in the minimum time to flower (F_m) and photoperiod sensitivity (critical photoperiod, P_c, and photoperiod-sensitivity slope, P_s) was observed among the genotypes; in contrast there was little variation in base temperature (T_b). Adaptation of sorghum to the diverse environments in which it is grown was largely determined by photoperiod sensitivity and minimum time to flower; photoperiod sensitivity determines broad adaptation to latitude (daylength), while variation in the minimum time to flower determines specific adaptation within smaller ranges of latitude, e.g. within the humid and sub-humid tropics. Received: 16 January 1999 / Accepted: 11 March 1999     

Equilibrium between Genetic Drift and Migration at Various Mutation Rates: Simulation Analysis

Rates of approach to equilibrium values of F _ST /R _ST at various mutation rates and using different mutation models (K-allele model KAM and stepwise model SMM) were analyzed numerically for the finite island model and the one-dimensional stepping stone models of migration, using simulation. In the island model of migration and the KAM mutation model, the rate of approach to the equilibrium F _ST value was appreciably higher and the equilibrium value was almost twofold lower at μ (mutation rate) = m (migration rate) than at μ ≪ m. In the one-dimensional stepping stone model of migration and the KAM model of mutation, the mutation rate significantly affected both the rate of approaching F _ST equilibrium and the equilibrium value. In both island and one-dimensional stepping stone models and SMM, R _ST was not influenced by various mutation rates. The rate of approach to the equilibrium values of both F _ST and R _ST was lower for the stepping stone model than to the island model. R _ST was rather resistant to deviations from the SMM mutation model. __________ Translated from Genetika, Vol. 41, No. 9, 2005, pp. 1283–1288. Original Russian Text Copyright ? 2005 by Efremov.     

Hydrolysis of cellulose in a cellulase-bead fluidized bed reactor

Cellulase was immobilized in a collagen fibril matrix, and no leakage of cellulase from the collagen fibril matrix was observed. The immobilized cellulase was more stable than the native cellulase. The substrate cellulose was hydrolyzed quantitatively with immobilized cellulase. The final reaction product was identified as glucose. Immobilized cellulase was used in a fluidized bed reactor where the pressure drop of the fluidized bed reactor was low and constant. Cellulose was hydrolyzed to glucose by the cellulase-bead fluidized bed reactor. The minimum flow velocity (U_mf) was 0.5 cm/sec and the optimum flow velocity of the cellulose hydrolysis was 1 cm/sec.     

Comparative study on the thermostability of collagen I of skin and bone: Influence of posttranslational hydroxylation of prolyl and lysyl residues

Pepsin-solubilized collagen I from skin and bone was analyzed with regard to its thermal stability as a triple helical molecule in solution and afterin vitro fibril formation. Collagen I from human control bone was compared with samples showing deficiencies or surplus in the degree of hydroxylation of lysine. The helix to coil transitions were studied by circulardichroism measurements and limited trypsin digestion. Melting of fibrils from standardizedin vitro self-assembly was investigated turbidimetrically. Human control bone collagen I has a maximum transition rate (T _m ) at 43.3°C in 0.05% acetic acid. This is 1.9°C above control skin (T _m =41.4°C), most likely, due to a higher degree of prolyl hydroxylation—0.48 in bone vs. 0.41 in skin collagen I. Lysyl overhydroxylation of human and mouse bone collagen I appears to reduce theT _m slightly (1°C). Underhydroxylated bone collagen has aT _m which is 2°C below control. Melting temperatures ofin vitro formed fibrils are an indication for higher thermostability in parallel with an increase of lysyl hydroxylation. Accordingly, the melting temperature of such fibrils from human control skin, 49.3°C, exceeds control bone by 1.4°C. The degree of lysyl hydroxylation in these samples is 0.14 and 0.10, respectively. Further underhydroxylation (0.06) reduced it down to 45.4°C, while extensive overhydroxylation did not continue to increase the thermal stability of fibrils.     

Frequency dependent selection: I. Rare male phenomenon in D. subobscura dependent on the proportion of Amy genotypes and substrate composition

Analysis of the rare male mating advantage in D. subobscura, as a type of frequency dependent selection on maltose and starch media, was done by applying different statistical approaches (χ², cross-product ratio, variance and regression analysis). They reveal that mating occurs at random when proportions of prospective mates are equal, and that mating success of the males homozygous for Amy-locus genotypes (S/S and F/F) depends on their proportion. Regression analysis showed that the F/F males are sexually more active (have higher vigour) than S/S males. Rare male effect is one-sided and appears in F/F males that partake in more heterogamic matings. Comparison of the number of observed and expected homo- and heterogamic matings shows that homogamic matings are more frequent. Multifactorial analysis of variance shows that the number of matings are different for nine pairs of lines and four possible mating types (S_fS_m, S_fF_m, F_fS_m, F_fF_m). The rare male phenomenon is not dependent on different food composition, but is associated with variations in individual genotypes.     

Effects of water on the mechanical properties of gelatin films

The mechanical properties of gelatin films were studied in relation to the effect of water, and compared with those of collagen films. The S-shaped sorption isotherm was separated into an adsorption curve C₁ and dissolution curve C₂. From the C₂ curve, the interaction parameter χ₁ of Flory–Huggins' equation was calculated. The χ₁ of gelatin were larger than those of collagen at low relative humidities (RH), while they coincided with each other at high RH. It was found that a composite curve was made by shifting stress relaxation curves obtained at different humidities along the log time axis. The shift factor for the formation of the composite curve was analyzed by Fujita–Kishimoto's equation, which was based on the free volume theory. The parameter β, which expressed the extent of the contribution of sorbed water to the increase in the free volume of the system, was 0.05 in the range of C₂ from 0 to 0.08 (0–65% RH). This value was much smaller than 0.16 for collagen. The value was 0.16 in the range of C₂ higher than 0.08, which was equal to that of the collagen. Dynamic shear modulus G′, loss modulus G″, and tan δ were determined as functions of RH. The gelatin film extended more than 100% at 73% RH under the very small stress of about 10⁷ dyn/cm². This corresponds to the region where β changes from 0.05 to 0.16, although such a phenomenon was not observed in the collagen film. The wide-angle X-ray pattern of extended gelatin was similar to that of renatured collagen fiber.     

Correlation between Photoinhibition Sensitivity and the Rates and Relative Extents of Xanthophyll Cycle De-epoxidation in Chlorina Mutants of Barley (Hordeum vulgare L.)

We compared photoinhibition sensitivity to high irradiance (HI) in wild-type barley (wt) and both its chlorina f ₁₀₄-nuclear gene mutant, that restricts chlorophyll (Chl) a and Chl b synthesis, and its f ₂-nuclear gene mutant, that inhibits all Chl b synthesis. Both F_v/F_m and _PS2 decreased more significantly in f ₂ than f ₁₀₄ and wt with duration of HI exposure. Chl degraded more rapidly in the f ₂ than in either f ₁₀₄ or wt. Most sensitivity to photoinhibition was exhibited for f ₂, whereas there was little difference in response to HI between the f ₁₀₄ and wt. The highest de-epoxidation (DES) value at every time point of exposure to HI was measured for f ₂, whereas the wt had the lowest value among the three strains. There were two lifetime components resolved for the conversion of violaxanthin (V) to zeaxanthin plus antheraxanthin (Z + A). The most rapid lifetime was around 6 min and the slower lifetime was >140 min, in both the mutants and wt. However, the wt and f ₁₀₄ both displayed larger amplitudes of both de-epoxidation lifetimes than f ₂. The difference between the final de-epoxidation state (DES = [Z + A]/[V + A + Z]) in the light compared to the dark expressed as DES for wt, f ₁₀₄, and f ₂ was 0.630, 0.623, and 0.420, respectively. The slow lifetime component and overall larger DES in the wt and f ₁₀₄ correlated with more photoprotection, as indicated by relatively higher F_v/F_m and _PS2, compared to the f ₂. Hence the photoprotection against photoinhibition has no relationship with the absolute DES value, but there is a strong relationship with de-epoxidation rate and relative extent or DES.