A hypothesis on the role of hydroxyproline in stabilizing collagen structure

The possibility of hydroxyproline residues stabilizing the collagen triple-helical structure by the formation of additional hydrogen bonds through their γ-hydroxyl group has been studied from structural considerations. It is not possible for this hydroxyl group to form a direct hydrogen bond with a suitable group in a neighbouring chain of the triple-helical protofibril. However, in the modified one-bonded structure, which is stabilized by additional hydrogen bonds being formed through water molecules as intermediaries (put forward in 1968 by Ramachandran, G. N. and Chandrasekharan, R.), it is found that the γ-hydroxyl group of hydroxyproline can form a good hydrogen bond with the water oxygen as acceptor, the hydrogen bond length being 2.82 Å. It is proposed that, in addition to stabilizing the collagen triple-helical structure due to the stereochemical properties of the pyrrolidine ring, hydroxyproline gives added stability by the formation of an extra hydrogen bond. Experimental studies on the determination of shrinkage and denaturation temperatures of native collagen and its synthetic analogues, as a function of their hydroxyproline content, are being undertaken to test this hypothesis.

Effect of the pyrethroid insecticide fenvalerate on sodium current of rat dorsal root ganglion neuron

Fenvalerate is a widely used pyrethroid insecticide. The report presents our findings on the effect of fenvalerate on isolated whole-cell sodium currents in single rat dorsal root ganglionic neurons in culture, studied with patch-clamp technique. Fenvalerate decreased the amplitude of whole-cell sodium current and slowed the inactivation and tail current kinetics.

Improved root t method to evaluate consolidation test results - Discussion

Taylor (1948) suggested the method for determination of the settlement, d, corresponding to 90% consolidation utilizing the characteristics of the degree of consolidation, U, versus the square root of the time factor, square root of T, plot. Based on the properties of the slope of U versus square root of T curve, a new method is proposed to determine d corresponding to any U above 70% consolidation for evaluation of the coefficient of consolidation, Cn. The effects of the secondary consolidation on the Cn value at different percentages of consolidation can be studied. Cn, closer to the field values, can be determined in less time as compared to Taylor's method. At any U in between 75 and 95% consolidation, Cn(U) due to the new method lies in between Taylor's Cn and Casagrande's Cn.

Ion conductance in electrolyte solutions

We develop a new theoretical formulation to study ion conductance in electrolyte solutions, based on a mode coupling theory treatment of the electrolyte friction. The new theory provides expressions for both the ion atmosphere relaxation and electrophoretic contributions to the total electrolyte friction that acts on a moving ion. While the ion atmosphere relaxation term arises from the time-dependent microscopic interaction of the moving ion with the surrounding ions in the solution, the electrophoretic term originates from the coupling of the ion's velocity to the collective current mode of the ion atmosphere. Mode coupling theory, combined with time-dependent density functional theory of ion atmosphere fluctuations, leads to self-consistent expressions for these two terms which also include the effects of self-motion of the ion under consideration. These expressions have been solved for the concentration dependence of electrolyte friction and ion conductance. It is shown that in the limit of very low ion concentration, the present theory correctly reduces to the well-known Debye-Huckel-Onsager limiting law which predicts a linear dependence of conductance on the square root of ion concentration (c). At moderate and high concentrations, the present theory predicts a significant nonlinear and weaker dependence on root c which is in very good agreement with experimental results. The present theory is self-contained and does not involve any adjustable parameter.

Alamethicin and related membrane channel forming polypeptides

Alamethicin and several related microbial polypeptides, which contain a high proportion of agr-aminoisobutyric acid (Aib) residues, possess the ability to modify the permeability properties of phospholipid bilayer membranes. Alamethicin induces excitability phenomena in model membranes and has served as an excellent model for the study of voltage sensitive transmembrane channels. This review summarizes various aspects of the structural chemistry and membrane modifying properties of alamethicin and related Alb containing peptides. The presence of Aib residues in these sequences, constrains the polypeptides to 310 or agr-helical conformations. Functional membrane channels are formed by aggregation of cylindrical peptide helices, which span the lipid bilayer, forming a scaffolding for an aqueous column across the membrane. After consideration of the available data on the conductance characteristics of alamethicin channels, a working, hypothesis for a channel model is outlined. Channel aggregates in the lipid phase may be stabilized by intermolecular hydrogen bonding, involving a central glutamine residue and also by interactions between the macro-dipoles of proximate peptide helices. Fluctuations between different conductance states are rationalized by transitions between states of different aggregation and hence altered dimensions of the aqueous core or by changes in net dipole moment of the aggregate. Ion fluxes through the channel may also be affected by the electric field within the aqueous core.

A linear root water uptake model

A model of root water extraction is proposed, in which a linear variation of extraction rate with depth is assumed. Five crops are chosen for simulation studies of the model, and soil moisture depletion under optimal conditions from different layers for each crop is calculated. Similar calculations are also made using the constant extraction rate model. Rooting depth is assumed to vary linearly with potential evapotranspiration for each crop during the vegetative phase. The calculated depletion patterns are compared with measured mean depletion patterns for each crop. It is shown that the constant extraction rate model results in large errors in the prediction of soil moisture depletion, while the proposed linear extraction rate model gives satisfactory results. Hypothetical depletion patterns predicted by the model in combination with a moisture tension-dependent sink term developed elsewhere are indicated.

Sex Determination - A Hypothesis Based On Noncoding Dna

Certain recent models of sex determination in mammals, Drosophila melanogaster, Caenorhabditis elegans, and snakes are examined in the light of the hypothesis that the relevant genetic regulatory mechanisms are similar and interrelated. The proposed key element in each of these instances is a noncoding DNA sequence, which serves as a high-affinity binding site for a repressor-like molecule regulating the activity of a major "sex-determining" gene. On this basis it is argued that, in several eukaryotes, (i) certain DNA sequences that are sex-determining are noncoding, in the sense that they are not the structural genes of a sex-determining protein; (ii) in some species these noncoding sequences are present in one sex and absent in the other, while in others their copy number or accessibility to regulatory molecules is significantly unequal between the two sexes; and (iii) this inequality determines whether the embryo develops into a male or a female.

Tubulin synthesis and auxin-induced root initiation in phaseolus

The auxin-induced formation of roots in the hypocotyls of Phaseolus vulgaris can be prevented by treatment with actinomycin D, colchicine or cytochalasin B if applied within 40 hr of initiation. Shortly after auxin pretreatment, there is an increase in translatable messenger RNA activity. Analysis of the labelled cell-free products indicate, among other changes, a striking increase in a protein co-migrating with tubulin, in the case of RNA isolated from indolebutyric acid (IBA) pretreated hypocotyls. An increase in tubulin content in vivo can also be demonstrated on the basis of SDS-polyacrylamide gel analysis of membrane proteins and functional assays for tubulin polymerization. An increase in the synthesis of tubulin in vivo can also be demonstrated after IBA pretreatment. In addition, the auxin is also able to promote tubulin polymerization when added in vitro. It is suggested that tubulin synthesis and microtubule assembly are early events in auxin-mediated root differentiation.

A new kinetic model for bulk polymerization of vinyl chloride based on two-phase hypothesis

A kinetic model has been developed for the bulk polymerization of vinyl chloride using Talamini's hypothesis of two-phase polymerization and a new concept of kinetic solubility which assumes that rapidly growing polymer chains have considerably greater solubility than the thermodynamic solubility of preformed polymer molecules of the same size and so can remain in solution even under thermodynamically unfavourable conditions. It is further assumed that this kinetic solubility is a function of chain length. The model yields a rate expression consistent with the experimental data for vinyl chloride bulk polymerization and moreover is able to explain several characteristic kinetic features of this system. Application of the model rate expression to the available rate data has yielded 2.36 × 108l mol−1 sec−1 for the termination rate constant in the polymer-rich phase; as expected, this value is smaller than that reported for homogenous polymerization by a factor of 10–30.

The mean geometry of the peptide unit from crystal structure data

The average dimensions of the peptide unit have been obtained from the data reported in recent crystal structure analyses of di- and tripeptides. The bond lengths and bond angles agree with those in common use, except for the bond angle C---N---H, which is about 4° less than the accepted value, and the angle C2α---N---H which is about 4° more. The angle τ (Cα) has a mean value of 114° for glycyl residues and 110° for non-glycyl residues. Attention is directed to these mean values as observed in crystal structures, as they are relevant for model building of peptide chain structures.

The non-planar peptide unit II. Comparison of theory with crystal structure datastar, open

The theoretical results derived in Part I (Ramachandran, G.N., Lakshminarayan, A.V. and Kolaskar, A.S. (1973) Biochim. Biophys. Acta 303, 8–13) that the three bonds of the peptide unit meeting at N can have a pyramidal structure is confirmed by an analysis of 14 published crystal structures of small peptides. It is shown that the dihedral angles θN and Δω are correlated, while θC, is small and is uncorrelated with Δω, showing that the non-planar distortion at C′ is generally small.

Microscopic modelling of adsorption and the generalised surface layer hypothesis

Two- and three-state models for the adsorption of organic compounds at the electrodelelectrolyte interface are proposed. Different size requirements, if any, for the neutral molecule and the adsorbing solvent are also considered. It is shown how the empirical, generalised surface layer (GSL) relationship (between the potential difference and the electrode charge) formulated by Damaskin et a / . can be understood at the molecular level.

The nonplanar peptide unit III. Quantum chemical calculations for related compounds and experimental X-ray diffraction data

The possible nonplanar distortions of the amide group in formamide, acetamide, N-methylacetamide, and N-ethylacetamide have been examined using CNDO/2 and INDO methods. The predictions from these methods are compared with the results obtained from X-ray and neutron diffraction studies on crystals of small open peptides, cyclic peptides, and amides. It is shown that the INDO results are in good agreement with observations, and that the dihedral angles N and defining the nonplanarity of the amide unit are correlated approximately by the relation N = -2, while C is small and uncorrelated with . The present study indicates that the nonplanar distortions at the nitrogen atom of the peptide unit may have to be taken into consideration, in addition to the variation in the dihedral angles (,), in working out polypeptide and protein structures.

The denaturation of β-lactoglobulin-A at pH 2

The denaturation of β-lactoglobulin-A by heat and guanidine hydrochloride at pH 2 has been investigated. The effect of ethylene glycol on the thermal denaturation at this pH has also been studied. The conditions of the experiments have been chosen so as to eliminate complications arising out of disulfide interchange, changes in the degree of association of the protein during denaturation, and intermolecular aggregation. The physical parameters characterizing the denatured states of the protein which are produced by heat and guanidine hydrochloride have been determined. The thermodynamic parameters for these transitions have been estimated using a two-state hypothesis in each case. Both the physical and thermodynamic parameters indicate that the heat-denatured state of β-lactoglobulin-A retains about 15-20% of residual structure which is destroyed on adding guanidine hydrochloride.

The Out-of-India hypothesis: What do molecules suggest?

The remarkable geological and evolutionary history of peninsular India has generated much interest in the patterns and processes that might have shaped the current distributions of its endemic biota. In this regard the Out of India hypothesis, which proposes that rafting peninsular India carried Gondwanan forms to Asia after the break-up of Gondwana super continent, has gained prominence. Here we have reviewed molecular studies undertaken on a range of taxa of supposedly Gondwanan origin to better understand the Out-of-India scenario. This re-evaluation of published molecular studies indicates that there is mounting evidence supporting Out-of-India scenario for various Asian taxa. Nevertheless, in many studies the evidence is inconclusive due to lack of information on the age of relevant nodes. Studies also indicate that not all Gondwanan forms of peninsular India dispersed out of India. Many of these ancient lineages are confined to peninsular India and therefore are relict Gondwanan lineages. Additionally for some taxa an Into India rather than Out-of-India scenario better explains their current distribution. To identify the Out-of-India component of Asian biota it is imperative that we understand the complex biogeographical history of India. To this end, we propose three oversimplified yet explicit phylogenetic predictions. These predictions can be tested through the use of molecular phylogenetic tools in conjunction with palaeontological and geological data.