Structural Insights into the Trp‐Cage Folding Intermediate Formation

The 20 residue long Trp‐cage is the smallest protein known, and thus has been the subject of several in vitro and in silico folding studies. Here, we report the multistate folding scenario of the miniprotein in atomic detail. We detected and characterized different intermediate states by temperature dependent NMR measurements of the ¹⁵N and ¹³C/¹⁵N labeled protein, both at neutral and acidic pH values. We developed a deconvolution technique to characterize the invisible—fully folded, unfolded and intermediate—fast exchanging states. Using nonlinear fitting methods we can obtain both the thermodynamic parameters (ΔH^F–I, T_m^F–I, ΔC_p^F–I and ΔH^I–U, T_m^I–U, ΔC_p^I–U) and the NMR chemical shifts of the conformers of the multistate unfolding process. During the unfolding of Trp‐cage distinct intermediates evolve: a fast‐exchanging intermediate is present under neutral conditions, whereas a slow‐exchanging intermediate‐pair emerges at acidic pH. The fast‐exchanging intermediate has a native‐like structure with a short α‐helix in the G¹¹–G¹⁵ segment, whereas the slow‐exchanging intermediate‐pair presents elevated dynamics, with no detectable native‐like residue contacts in which the G¹¹? P¹² peptide bond has either cis or trans conformation. Heteronuclear relaxation studies combined with MD simulations revealed the source of backbone mobility and the nature of structural rearrangements during these transitions. The ability to detect structural and dynamic information about folding intermediates in vitro provides an excellent opportunity to gain new insights into the energetic aspects of the energy landscape of protein folding. Our new experimental data offer exceptional testing ground for further computational simulations.     

Inversion of the Kirkwood–Buff Theory of Solutions: Application to Tetrahydrofuran + Aromatic Hydrocarbon Binary Liquid Mixtures

The Kirkwood–Buff (K-B) integrals play an important role in characterizing the intermolecular interactions in liquid mixtures. The interaction is represented by the K-B parameters, G _AA,G _BB, and G _AB, which reflect correlation between like-like and like-unlike species in the mixture. The K-B integrals of binary mixtures of tetrahydrofuran with benzene, toluene, o-xylene, m-xylene, p-xylene and mesitylene at 298.15 K and atmospheric pressure have been computed from the experimental data of ultrasonic speed and density. We have used the similar inverse procedure (as proposed by Ben-Naim) to compute the K-B parameters of the mixture, in which thermodynamic information on mixtures, such as partial molar volumes, isothermal compressibility and experimental data of partial vapor pressures were used. A new route has been incorporated by using regular solution theory in the computation of excess Gibbs energy for obtaining the partial vapor pressures of binary liquid mixtures. The low values of excess entropy, S ^E≈0, obtained for these mixtures indicate the applicability of regular solution theory to the mixtures. The values of the K-B parameter, G _AB, obtained using this procedure indicate that the correlation/affinity between THF and aromatic hydrocarbon molecules follows the order: benzene > toluene > o-xylene > m-xylene > p-xylene > mesitylene, which is in good agreement with the results obtained from the trends exhibited by the excess functions of these mixtures.     

Aggregate morphology and flow behaviour of micellar alkylglycoside solutions

Solutions of n-nonyl-β-D-glucoside (C₉G₁), n-decyl-β-D-glucoside (C₁₀G₁), n-dodecyl-β-D-maltoside (C₁₂G₂), n-tetradecyl-β-D-maltoside (C₁₄G₂) and C₉G₁/C₁₀G₁ mixtures have been characterised by capillary viscometry and rheology in H₂O and D₂O, in order to map the influence of surfactant characteristics on micellisation over a wide concentration range. For the maltosides, the micellar solutions are shear thinning with a zero-shear viscosity that scales with concentration according to a power law with an exponent of about 5.8. In contrast, solutions of the glucosides C₉G₁, C₁₀G₁ and their mixtures show Newtonian flow behaviour and a much lower scaling exponent (<2.4). In C₉G₁/C₁₀G₁ mixtures, the scaling exponent decreases monotonously with increasing C₁₀G₁ content. The flow behaviour correlates with the packing requirements of the various surfactants, and are compatible with the idea that the maltosides form worm-like micelles, whereas the glucosides form branched, interconnected micelles (C₉G₁) and space-filling micellar networks (C₁₀G₁).     

Relationship Between Heat Capacity and Thermal Expansion Derived from the Lennard–Jones Potential

The relationship between heat capacity (C _p) and linear thermal expansion (α) derived from the Lennard–Jones potential is C _p=Aα(U ₀–E), where U ₀ is the heat of sublimation at T=0, E is the enthalpy and A is the coefficient. The values of A for different solidified inert gases coincide with one another within the limits of experimental error (±2%). The relationship is shown to be valid for various substances: solidified rare gases, diamond, halite and copper. This revised version was published online in July 2006 with corrections to the Cover Date.     

Molecular orbital calculations on the conformation of polypeptides and proteins

Quantum mechanical calculations using the PCILO method have been performed on the tripeptide model CH₃CO-X-Y-NHCH₃. Competition between C₅, C₇, C₁₀ rings and open structures has been investigated through mapping of the whole {φ, Ψ} conformational space and energy minimization. From these results, it appears that the C₁₀ ring simulating the folding named U-turn, involving a hydrogen bond between the i...i + 3 residues, is the most probable structure although not the most stable in energy. The results are used for predicting the frequency of U-turns in proteins, α-chymotrypsin is given as an example.     

Micellization behavior of [C16-12-C16], 2Br gemini surfactant in binary aqueous-solvent mixtures

The micellization behavior of bis cationic gemini surfactant, N,N′-dihexadecyl-N,N,N′,N′-tetramethyl-1,12-dodecanediammonium dibromide [C₁₆H₃₃N⁺(CH₃)₂-(CH₂)₁₂-N⁺(CH₃)₂C₁₆H₃₃, 2Br⁻] has been studied in binary aqueous mixtures of dimethyl sulfoxide, methanol, 1,4-dioxane, glycerol and ethylene glycol by conductivity and surface tension measurements at 300 K. The critical micellar concentration, degree of micelle ionization (α), surface excess concentration (Г_max), minimum surface area per molecule of surfactant (A_min), Gibbs free energy of micellization (ΔG_m°), the surface pressure at cmc (π_cmc), and the Gibbs energy of adsorption (ΔG_ad°) of the gemini surfactant have also been determined. The cmc, α, A_min increases where as (ΔG_m°), Г_max, and π_cmc decreases with increasing volume percentage of the solvents in the solvent–water binary mixture. The interfacial properties of the gemini surfactant, solute–solute, solvent–solute interactions and the effectiveness of a surface-active molecule in binary solvent systems have been discussed.     

On unicyclic conjugated molecules with minimal energies

The energy of a graph is defined as the sum of the absolute values of all the eigenvalues of the graph. Let U(k) be the set of all unicyclic graphs with a perfect matching. Let C _g(G) be the unique cycle of G with length g(G), and M(G) be a perfect matching of G. Let U ⁰(k) be the subset of U(k) such that g(G)≡ 0 (mod 4), there are just g/2 independence edges of M(G) in C _g(G) and there are some edges of E(G)\ M(G) in G\ C _g(G) for any G∈U ⁰(k). In this paper, we discuss the graphs with minimal and second minimal energies in U ^*(k) = U(k)\ U ⁰(k), the graph with minimal energy in U ⁰(k), and propose a conjecture on the graph with minimal energy in U(k).      

Selective deacylation of peracylated ribonucleosides

A protocol for chemoselective deprotection of N,O-acylated ribonucleosides has been developed. Peracylated pyrimidine ribonucleosides subjected to guanidinium nitrate and NaOMe in MeOH/CH₂Cl₂ at 0 °C undergo high yielding O-deacylation, while even more pronounced chemoselectivity is observed with peracylated purine ribonucleosides as O5′-acyl groups are preserved. Nucleobase-protecting groups (A^Bz, C^Bz, G^iBu, and U^Bz) are stable to these conditions, rendering this reagent mixture as a valuable addition to the collection of protecting group protocols in nucleoside chemistry.     

The hard-sphere model for linear and regular star polybutadienes

The dilute solution properties of linear, 18-arm, and 270-arm star polybutadienes have been studied in a theta solvent and in a good solvent. Values of the radius of gyration R_G, the second virial coefficient A₂, the intrinsic viscosity [η], and the diffusion coefficient D₀ have been measured for each polymer. The ratios R_T/R_G, R_V/R_G, and R_H/R_G for each type of polymer are used to compare the four dilute solution properties. R_T is termed the “thermodynamic radius.” It is the radius of the hard sphere with the same excluded volume as the polymer coil. R_T is calculated from A₂ by R_T = (3A₂M₂/16ηN_A)^1/3. R_V and R_H are equivalent hard spheres defined for the intrinsic viscosity and translational diffusion coefficient, respectively. R_T/R_G, R_V/R_G, and R_H/R_G increase from about 0.7 for linear polymer coils as the number of arms in the star increases. Values of the ratios for the 18-arm stars are less than the value for the hard-sphere, but the values of the ratios of the 270-arm stars are equal to the hard-sphere limit within experimental error.     

An exact expression for the wiener index of a TUC<Subscript>4</Subscript>C<Subscript>8</Subscript>(R) nanotorus

The Wiener index of a graph G is defined as , where V(G) is the set of all vertices of G and for denotes the length of a minimal path between x and y. A C ₄ C ₈ net is a trivalent decoration made by alternating squares C ₄ and octagons C ₈. It can cover either a cylinder or a torus. In this paper, an algorithm for computing the distance matrix of a C ₄ C ₈(R) nanotorus T = T[p,q] is given. Using this matrix, the Wiener index of T is computed.     

On molecular topological properties of hex‐derived networks

Topological indices are numerical parameters of a molecular graph, which characterize its topology and are usually graph invariant. In quantitative structure–activity relationship/quantitative structure–property relationship study, physico‐chemical properties and topological indices such as Randić, atom–bond connectivity (ABC), and geometric–arithmetic (GA) index are used to predict the bioactivity of chemical compounds. Graph theory has found a considerable use in this area of research. In this paper, we study hex‐derived networks HDN1(n) and HDN2(n), which are generated by hexagonal network of dimension n and derive analytical closed results of general Randić index R_α(G) for different values of α, for these networks of dimension n. We also compute the general first Zagreb, ABC, GA, ABC₄, and GA₅ indices for these hex‐derived networks for the first time and give closed formulae of these degree‐based indices for hex‐derived networks. Copyright © 2016 John Wiley & Sons, Ltd.     

Adsorption and thermodynamic properties of dissymmetric gemini imidazolium surfactants with different spacer length

A series of dissymmetric gemini imidazolium surfactants with different spacer length ([C_mC_sC_nim]Br₂, m + n = 24, m = 12, 14, 16, 18; s = 2, 4, 6) were synthesized and characterized by ¹H NMR and ESI-MS spectroscopy. Their adsorption and thermodynamic properties were investigated by the surface tension and electrical conductivity methods. Consequently, the surface activity parameters (cmc, γ_cmc, π_cmc, pC₂₀, cmc/C₂₀, Γ_max, A_min) and thermodynamic parameters (ΔG_m^θ, ΔH_m^θ, ΔS_m^θ) were obtained. The effects of the dissymmetry (m/n) and the spacer length (s) on the surface activity and micellization process of surfactants have been discussed in detail.     

The spread of unicyclic graphs with given size of maximum matchings

The spread s(G) of a graph G is defined as s(G) = max _i,j |λ _i − λ _j |, where the maximum is taken over all pairs of eigenvalues of G. Let U(n,k) denote the set of all unicyclic graphs on n vertices with a maximum matching of cardinality k, and U ^*(n,k) the set of triangle-free graphs in U(n,k). In this paper, we determine the graphs with the largest and second largest spectral radius in U ^*(n,k), and the graph with the largest spread in U(n,k).      

Protein–Nucleic acid interactions: Investigations on the peptide backbone interaction with polynucleotides

Model building, difference spectroscopy, and ¹H and ¹³C NMR experiments have been carried out to study the binding of poly(L -Ser) with the polyribonucleotides poly(A) and poly(U) at pH 7.1. Studies have also been carried out with base paired duplexes poly(A)?poly(U). Peak doubling of C^α and carbonyl resonances in the ¹³C NMR spectrum of poly(L -Ser) in presence of polyribonucleotides is observed. From the chemical shifts and the linewidth, it is concluded that the interaction occurs through hydrogen bonding between the nucleic acid bases and the peptide backbone. In case of poly(A) and poly(U) the hydrogen bonding scheme with peptide backbone is different from that in the base paired poly(A)?poly(U). The possible binding schemes of double stranded DNA and peptide backbone have been investigated using model building and potential energy calculations. The hydrogen bonding schemes discriminate between various base pairs and their sequence. It is concluded that protein backbone can play an important role in protein–nucleic acid recognition schemes.     

Further Experiments in the Separation of Globin Chains by High Performance Liquid Chromatography

Abstract

The applicability of various column packings, solvents, and gradients for the separation of globin chains by high performance liquid chromatography has been examined. Although numerous combinations may be applied to advantage in special situations, a particularly effective system uses a Waters μBondepak C₁₈ packing with a slight gradient of perchlorate-phosphate-methanol-acetonitrile mixtures. A chromatogram with human β, α, ^Aγ^T, ^Gγ, and ^Aγ^I chains is finished in 80 min, and quantitation of the various chains is possible.     

The study of alanine oscillating reaction catalyzed by tetraazamacrocyclic nickel(II) complex

A closed oscillation system comprised of alanine, KBrO₃, H₂SO₄ and acetone catalyzed by tetraazamacrocyclic nickel(II) complex is introduced, and quantitatively characterized with kinetic parameters, namely the rate constant (k _in, k _p), the apparent activation energy (E _in, E _p) and pre-exponential constant (A _in, A _p) and thermodynamic functions (ΔH _in, ΔG _in, ΔS _in and ΔH _p, ΔG _p, ΔS _p), where indexes “in” and “p” mean “induction period” and “oscillation period,” respectively. The results indicate that tetraazamacrocyclic nickel(II) complex can catalyze alanine oscillating reaction and the reaction corresponds exactly to the feature of irreversible thermodynamics as the entropy of system is negative.     

Influence of Electrochemical Parameters on the Etching of Macropores in Silicon

The process of formation of macropores in silicon with stationary irradiation and a constant current density during the electrochemical process in dependence on the initial bias on the silicon anode, U ₀, has been studied. Stable formation of macropores began when the bias reached U _c, corresponding to a critical concentration of holes p _c at the silicon–electrolyte interface. The process of macropore formation is unstable with U ₀ > U _c.     

The Effect of Anomeric Head Groups, Surfactant Hydrophilicity, and Electrolytes onn-Alkyl Monoglucoside Microemulsions

The effects of the variables of head group structure and salt concentration on microemulsions formed in mixtures of water, alkyl ethylene glycol ethers (C_kOC₂OC_k), andn-alkyl β- -glucopyranosides (C_mβG₁) are explored. Phase behavior of mixtures containing an anomer of the surfactant (n-alkyl α- -glucopyranoside, C_mαG₁), or surfactants with long head groups (n-alkyl maltopyranosides, C_mG₂), or NaCl or NaClO₄as electrolyte are systematically reported as a function of temperature and composition. The substitution ofn-alkyl α- -glucopyranosides forn-alkyl β- -glucopyranosides causes precipitation under some conditions in all mixtures studied. These solubility boundaries begin in the water–surfactant binary mixture at the Krafft boundary, then extend to high concentrations of both surfactant and oil. Increasing the effective length of the surfactant head group by adding C_mG₂to water–C_kOC₂OC_k–C_mβG₁mixtures moves the phase behavior dramatically up in temperature when even small amounts of C_mG₂are used. Adding a lyotropic electrolyte, NaCl, to water–C_kOC₂OC_k–C_mβG₁mixtures moves the phase behavior down in temperature, while the hydrotropic electrolyte NaClO₄moves the phase behavior up in temperature.     

Liquid crystalline behaviour of mixtures of structurally dissimilar mesogens in binary systems

We have studied four binary systems comprising four ester components, viz. 4-nitrophenyl-4′-n-alkoxybenzoates (wheren-alkoxy isn-butoxy, C₄,n-hexyloxy, C₆,n-octyloxy, C₈ andn-decyloxy, C₁₀) and one azo component, 4-n-decyloxy phenylazo-4′-isoamyloxy benzene. A variety of mesomorphic properties are observed in these mixtures. The properties of these systems are discussed on the basis of phase diagrams.