Single-site mutation and secondary structure stability: an isodesmic reaction approach. The case of unnatural amino acid mutagenesis Ala-->Lac

A method is described to evaluate backbone interactions in proteins via computational unnatural amino acid mutagenesis. Several N-acetyl polyalanyl amides (AcA(n)NH(2)) were optimized in the representative helical (3(10)-, 4(13)-, and a "hybrid" kappa-helix, n = 7, 9, 10, 14) and hairpin (two- and three-stranded antiparallel beta-sheets with type I turns betaalphaalphaepsilon, n = 6, 9, 10) conformations, and extended conformers of N-acetyl polyalanyl methylamides (n = 2, 3) were used to derive multistranded beta-sheet fragments. Subsequently, each residue of every model structure was substituted, one at a time, with l-lactic acid. The resulting mutant structures were again optimized, and group-transfer energies DeltaE(GT) were obtained as heats of the isodesmic reactions: AcA(n)NHR + AcOMe --> AcA(x)LacA(y)NHR + AcNHMe (R = H, CH(3)). These group-transfer energies correlate with the degree of charge polarization of the substituted peptide linkages as measured by the difference Deltae in H and O Mulliken populations in HN-C=O and with the H-bond distances in the "wild-type" structures. A good correlation obtains for the HF/3-21G and B3LYP/6-31G* group-transfer energies. The destabilization effects are interpreted in terms of loss of interstrand and intrastrand H-bonds, decrease in Lewis basicity of the C=O group, and O...O repulsion. On the basis of several comparisons of Ala --> Lac DeltaE(GT)'s with heats of the NH --> CH(2) substitutions, the latter contribution is estimated (B3LYP/6-31G*) to range between 1.5 and 2.4 kcal mol(-1), a figure close to the recent experimental DeltaDeltaG(o) value of 2.6 kcal mol(-1) (McComas, C. C.; Crowley, B. M.; Boger, D. L. J. Am.Chem. Soc. 2003, 125, 9314). The partitioning yields the following maximum values of the electronic association energy of H-bonds in the examined sample of model structures (B3LYP/6-31G* estimates): 3(10)-helix D(e) = -1.7 kcal mol(-1), alpha-helix D(e) = -3.8 kcal mol(-1), beta-sheet D(e) = -6.1 kcal mol(-1). The premise of experimental evaluations of the backbone-backbone H-bonding that Ala --> Lac substitution in proteins is isosteric (e.g., Koh, J. T.; Cornish, V. W.; Schultz, P. G. Biochemistry 1997, 36, 11314) is often but not always corroborated. Examination of the integrity of H-bonding pattern and phi(i), psi(i) distribution identified several mutants with significant distortions of the "wild-type" structure resulting inter alia from the transitions between i, i + 3 and i, i + 4 H-bonding in helices, observed previously in the crystallographic studies of depsipeptides (Ohyama, T.; Oku, H.; Hiroki, A.; Maekawa, Y.; Yoshida, M.; Katakai, R. Biopolymers 2000, 54, 375; Karle, I. L.; Das, C.; Balaram, P. Biopolymers 2001, 59, 276). Thus, the isodesmic reaction approach provides a simple way to gauge how conformation of the polypeptide chain and dimensions of the H-bonding network affect the strength of backbone-backbone C=O...HN bonds. The results indicate that the stabilization provided by such interactions increases on going from 3(10)-helix to alpha-helix to beta-sheet.     

Structure of starch-bentonite gels

Mixed gels of starch and bentonite are investigated in the interval 0.056–0.089 of total solids/water ratio and 0-100% starch in the solids. The bentonite was a sodium calcium bentonite with a Na/Ca ratio of 1.76. In water it forms gels consisting of a network of band-type structures. Starch forms gels through hydrogen bonds between granules and/or amylose and amylopectin present on the external surfaces of granules and/or in fully stretched form. Mixed gels of bentonite and starch were obtained by adding corn starch granules to the already formed bentonite gels and heating the mixture above the Kofler gelatinization temperature. Amylose and amylopectin were adsorbed on strands of band-type structures of mont-morillonite lamellae. Starch gellation, e.g. diffusion of amylose out of the granule, was facilitated in the presence of bentonite. On the other hand, the presence of starch favored delamination of the montmorillonite particle into thinner lamellae. Maximum gelatinization and polymer adsorption were observed for gels with 20% starch and 80% bentonite. Montmorillonite networks formed the continuous phase for 0-80% starch. At higher starch concentrations, montmorillonite flakes were dispersed within the polymer network. Increase in the water content of the gels caused segregation of the bentonite and starch.     

Thermal degradation of some polymers based on ethylene glycol dimethacrylate

Thermogravimetric analysis and pyrolysis in combination with gas chromatography were used to study the thermal behaviour of some cross-linked polymers of ethylene glycol dimethacrylate. The investigated polymers show a complex thermal degradation mechanism. The complexity of the reaction increases together with increase of the ethylene glycol chain in the macromolecule and with increase of the pyrolysis temperature. At low temperature, the thermal decomposition products of the analyzed polymers are mainly the constituent monomers. At high temperatures, besides the monomer, other decomposition products are formed as a result of thermal cracking reactions, i.e. secondary reactions of decomposition and recombination.

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Zusammenfassung Zur Untersuchung des thermischen Verhaltens einiger quervernetzter Polymere auf Äthylenglykoldimetacrylatbasis wurden thermogravimetrische Analyse und Pyrolyse in Zusammenhang mit der Gaschromatographie angewendet. Die untersuchten Polymere zeigten einen komplexen thermischen Zersetzungsmechanismus. Die Komplexizität der Reaktion nimmt mit Zunahme der Anzahl der Äthylenglykolketten im Makromolekül und mit Zunahme der Pyrolysentemperatur gleichermaßen zu. Bei niedrigeren Temperaturen stellen die Hauptzerfallsprodukte der analysierten Polymere hauptsächlich deren Monomere dar. Bei höheren Temperaturen werden als Ergebnis thermischer Krackreaktionen, z. B. sekundäre Zersetzungs- und Rekombinationsreaktionen, neben den Monomeren auch andere Zersetzungsprodukte gebildet.

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New instanton and meron solutions of a generally covariant four-dimensional sigma model

We construct new solutions of the fourdimensional sigma model coupled to the metric tensor field and having an internalO invariance. Our solutions interpolate continuously between the known instanton and meron solutions depending upon a parameterf. We find that the typical domain for the instantons is 2<f≦3 while for the merons is 0≦f≦2.     

Anomalous NMR behavior of meso compounds with remote stereogenic centers on addition of chiral shift reagent or chiral solvating agent

A problem has arisen in using chiral shift reagents (CSR) and chiral solvating agents (CSA) to determine meso and racemic forms of diastereoisomers in which the stereogenic centers of the molecules are separated by achiral spacers. It is found that NMR signals of both meso and racemic forms of diastereoisomers may exhibit doubling on addition of CSR/CSA, which means that unequivocal assignments cannot be made without characterizing the effects for separate meso and racemic forms; this is particularly important for additions of CSR/CSA at relatively low concentrations, which always result in the splitting of some NMR signals of diastereoisomers. The phenomenon is demonstrated in the (31)P NMR spectra of meso and racemic forms of three spermine-bridged gem-disubstituted cyclotriphosphazatrienes, 1a-c, and compared with analogous achiral molecules, the per-substituted spermine-bridged cyclotriphosphazatrienes 2a-d. As expected, only one set of (31)P NMR signals was observed for the achiral compounds 2a-d, even on addition of CSA. Two sets of (31)P NMR ABX multiplets corresponding to meso and racemic diastereoisomers were observed for compounds 1a-c; on addition of CSA, the signals of at least one of the multiplets for each compound separated into more than the expected groups of three lines with an intensity distribution of 2:1:1. To understand this phenomenon, the meso and racemic forms of 1a and 1b and the meso form of 1c have been separated and characterized by X-ray crystallography. On addition of CSA to the racemic forms of 1a and 1b, the (31)P NMR spectrum shows the expected doubling of signals, but, unexpectedly, the same is observed for each of the meso forms of 1a-c. Analogous results using both CSA and CSR have been obtained for the meso and racemic forms of the diastereoisomeric piperazine-bridged macrocyclic-phosphazene compound, 3, whereas no effect was observed for the two meso forms of the doubly bridged macrocyclic-phosphazene compound 4. The phenomenon of doubling of the (31)P NMR signals of the meso form of singly bridged cyclotriphosphazatrienes, 1a-c and 3, is explained by consideration of the equilibrium in solution of independent complexation of a chiral ligand with molecules that have two chiral cyclophosphazene moieties separated by an achiral spacer group. The results show that the stereogenicity of such diastereoisomeric molecules in solution cannot be characterized unequivocally by NMR measurements on addition of either CSR or CSA.     

Variational Operators,Symplectic Operators,and the Cohomology of Scalar Evolution Equations

For a scalar evolution equation u_t = K(t, x, u, u_x, . . . , u_2m+1) with m ≥ 1, the cohomology space H^1,2() is shown to be isomorphic to the space of variational operators and an explicit isomorphism is given. The space of symplectic operators for u_t = K for which the equation is Hamiltonian is also shown to be isomorphic to the space H^1,2() and subsequently can be naturally identified with the space of variational operators. Third order scalar evolution equations admitting a first order symplectic (or variational) operator are characterized. The variational operator (or symplectic) nature of the potential form of a bi-Hamiltonian evolution equation is also presented in order to generate examples of interest.     

On the difference spaces of almost convergent and strongly almost convergent double sequences

In this paper, we study the difference spaces \({\mathcal {F}}(\varDelta )\), \({\mathcal {F}}_0(\varDelta )\), \({\mathcal {[F]}}(\varDelta )\) and \({\mathcal {[F]}}_0(\varDelta )\) of double sequences obtained as the domain of four-dimensional backward difference matrix \(\varDelta \) in the spaces \({\mathcal {F}}\), \({\mathcal {F}}_{0}\), \({\mathcal {[F]}}\) and \({\mathcal {[F]}}_{0}\) of almost convergent, almost null, strongly almost convergent and strongly almost null double sequences; respectively. We examine general topological properties of those spaces and give some inclusion theorems. Furthermore, we deal with their dual spaces.