bluuebunny/crossref_metadata_2025_split huggingface dataset:
New polymer syntheses. IV. Polypeptides of lysine and ornithine with pending pyrimidine bases
Authors: Kricheldorf Hans R. , Fehrle Martin 
Published: May 2005

AbstractStarting with β‐methoxy methacryloylisocyanate, β‐methoxy methacrylisothiocyanate, and β‐isocyanatopropionyl chloride, on the one hand, and Nα‐Z‐lysine or Nα‐Z‐ornithine, on the other hand, Nα‐Z‐amino acids with pyrimidine bases in the side chain were synthesized. These Z‐protected nucleoamino acids were converted to the corresponding N‐carboxyanhydrides (NCAs) via the silylester method. In the case of 2‐thiothymine derivatives, the reaction intermediate of the NCA synthesis caused benzylation of the thioxo‐ group, so that a new class of 2‐mercaptopyrimidine derivatives was isolated unexpectedly. The poly(nucleoamino acids) obtained by polymerization of the nucleoamino acid NCAs were characterized by elemental analyses, optical rotations 1H‐nmr and 13C‐nmr spectra. Vapor pressure osmometry revealed that the DPs were in the range of 20–30. Their spectra suggest a helical secondary structure. While all homopolypeptides are insoluble in water, copolypeptides containing L‐lysine Nε‐hydrobromide possess good solubility in water.
Vibrational circular dichroism in amino acids and peptides. 7. Amide stretching vibrations in polypeptides
Authors: Lal Brij B. , Nafie Laurence A. 
Published: May 2005

AbstractVibrational circular dichroism (VCD) spectra for the principal amide stretching vibrations, amide A (NH stretch) and amide I (predominantly CO stretch), are presented and analyzed for a variety of polypeptides dissolved in chloroform, as well as for two examples in D2O. Our results for poly(γ‐benzyl‐L‐glutamate) confirm the first and only previous report of VCD in polypeptides carried out by Singh and Keiderling [(1981) Biopolymers 20, 237–240]. Collectively, our spectra show that the sense of the bisignate VCD in these two regions depends on the sense of α‐helicity and not on the absolute configuration of the constituent amino acids. This conclusion is established by obtaining VCD for the two polypeptides, poly(β‐benzyl‐L‐asparate) and poly(im‐benzyl‐L‐histidine), that form left‐handed as opposed to right‐handed α‐helices. A new amide band having significant VCD intensity owing to its Fermi resonance interaction with the NH stretching mode has been identified as a weak shoulder on the low‐frequency side of the amide A band near 3200 cm−1 and is assigned as a combination band of the amide I and amide II vibrations. VCD spectra of polypeptides in D2O solution, although weak, have been successfully measured in the amide I region, where spectra appear to be more complicated due to the presence of solvated and internally hydrogen‐bonded amide groups. Strong monosignate contributions to the VCD in the amide A and amide I regions for some of the polypeptides indicate coupling of an electronic nature between these two regions and is deduced by an application of the concept of local sum rules of rotational strength. It appears that a detailed understanding of the VCD obtained for polypeptides will not only be diagnostic of secondary structure, but also of more subtle structural and vibrational effects that give rise to local, intrinsic chirality in the amide vibrations.
Fibrin polymerization studied by static and dynamic light‐scattering as a function of fibrinopeptide A release
Authors: Wiltzius P. , Dietler G. , Känzig W. , Häberli A. , Straub P. W. 
Published: May 2005

AbstractThe polymerization of fibrin induced by the enzyme thrombin was investigated in the pregelation phase by combining measurements of the release of the fibrinopeptides A with static and dynamic light‐scattering at scattering angles ranging from 5°–150°. Without making any assumptions about the polymer distribution, one is led to the following conclusions: The aggregates are rodlike; the Flory‐Stockmayer model is to be preferred over the percolation model, i.e., cyclic bonds are infrequent; in the early stages the experiments indicate a functionality f = 2 (number of reactive binding sites per monomer) that increases with increasing release of fibrinopeptides A, eventually approaching the value f = 4; the number of binding sites involved in a bond is about twice the number of the released fibrinopeptides A; and in the polymers the monomer units aggregate end‐to‐end in the very early stage and then in a staggered overlap.
1H‐nmr studies of polyoxyethylene‐bound homo‐oligo‐L‐methionines
Authors: Ribeiro Anthony A. , Saltman Robert P. , Goodman Murray , Mutter Manfred 
Published: May 2005

AbstractThe use of 1H‐nmr spectroscopy is demonstrated to be a useful analytical method to characterize the structure of synthetic peptides attached to soluble, macromolecular polyoxyethylene (POE) supports in the liquid‐phase method (LPM) of peptide synthesis. We report an extensive 360‐MHz 1H‐nmr study of POE‐bound homo‐oligo‐L‐methionine peptides. A combination of high field and selective saturation or Redfield pulse methods allows resolution of individual backbone NH and α‐CH resonances of dilute peptides in the presence of strong resonances from macromolecular POE and/or protonated solvents. The nmr spectra for the POE‐bound peptides in CDCl3 are qualitatively similar to those of the low‐molecular‐weight Boc‐L‐Metn‐OMe peptide esters. This corroborates other observations that POE has little effect on peptide stucture. The backbone α‐CH region of peptides is overlapped by signals from the terminal oxyethylene group of POE, but the peptide side‐chain and low‐field backbone NH resonances are well resolved. In trifluoroethanol the Boc‐(L‐Met)n‐NH‐POE heptamer and octamer adopt the right‐handed α‐helical structure, and the present nmr studies provide evidence for two strong intramolecular hydrogen bonds to stabilize the helices. In water, the N‐deblocked derivatives, (L‐Met)n‐NH‐POE oligomers adopt β‐sheet structure and manifest well‐resolved nonequivalent NH resonances with 6–7 Hz 3JNH‐CH coupling constants.
Kinetics of formation of fibrin oligomers. I. Theory
Authors: Janmey Paul A. 
Published: May 2005

AbstractThe course of formation of fibrin oligomers is treated theoretically for the condition that self‐assembly of fibrin monomers is rapid compared with the loss of A peptides by the enzymatic action of thrombin. The rate constant for removal of the second A peptide is taken to be larger than that for the first by an arbitrary factor q; the association of activated A sites with their complementary a sites is assumed to be random and independent of oligomer size. Two types of oligomers are considered: noncovalently bonded protofibrils formed by the staggered overlap of thrombin‐activated monomers and covalently bonded linear oligomers formed by factor XIIIa‐mediated end‐to‐end ligation of adjacent monomers within protofibrils. Oligomers of the first type, if ligated, are dissociated to oligomers of the second type by solubilization in SDS–urea. Theoretical curves are presented for xw and x′w (weight‐average degree of polymerization of staggered overlap and linear ligated oligomers, respectively) and for the weight fractions of monomer, dimer, and decamer of both ligated and unligated species as functions of y, the fraction of A peptide removed; and also for wx and w′x, the weight fractions of x‐mer of the respective oligomer types, as a function of x at y = 0.5. With increasing q, the maximum wx or w′x that a low oligomer will reach during the reaction decreases and the size distribution is broadened toward larger oligomers. Comparison with experiment is made in a companion paper.
On the theory of Ψ‐condensation
Authors: Grosberg A. Yu. , Erukhimovitch I. Ya. , Shakhnovitch E. I. 
Published: May 2005

AbstractWe suggest a theory of Ψ‐condensation, based on the assumption that a compact DNA particle is a globule, and specifically that a polymer solution is a strongly fluctuating system and that double‐stranded DNA is a stiff homopolymer single‐stranded chain. We show the DNA globule as it appears in a dilute poly(ethylene oxide) (PEO) solution. The corresponding phase transition is investigated in detail. Growth of the PEO concentration should lead to a decrease in the size of the compact particle and to an increase in its optical rotatory power. Conditions are defined at which drastic compaction of DNA takes place, accompanied by the loss of its optic rotatory power, in regions of high PEO concentrations.
Microwave absorption of DNA between 8 and 12 GHz
Authors: Swicord Mays L. , Davis Christopher C. 
Published: May 2005

AbstractThe microwave absorption of aqueous solutions of DNA extracted from E. coli has been studied between 8 and 12 GHz by the use of an optical heterodyne technique. By measuring optically the temperature rise produced in an absorbing sample by pulsed microwave radiation, unambiguous, direct measurement of the microwave absorption is possible. Our results show that E. coli DNA absorbs microwaves in the 8–12‐GHz region substantially more efficiently than water, which is itself an extremely efficient absorber. The observed absorption is featureless and decreases slightly with increasing frequency. These observations are consistent with an explanation involving direct absorption by longitudinal acoustic modes of the double helix.
Raman spectra and normal vibrations of dipeptides. II. Glycyl‐L‐proline
Authors: Lagant P. , Loucheux‐Lefebvre M. H. , Huvenne J. P. , Vergoten G. , Fleury G. , Legrand P. 
Published: May 2005

AbstractRaman and ir spectra of the glycyl‐L‐proline (GP) dipeptide were recorded. A normal‐coordinate treatment was performed on the basis of the experimental spectra, using a modified Urey‐Bradley force field (MUBFF). Cyclic redundancies were eliminated, and those due to the ring methylene groups, particularly distorted in regard to the tetrahedral conformation, were treated. An assignment of the experimental frequencies is proposed on the basis of the normal treatment.
Vacuum‐ultraviolet circular dichroism of sodium hyaluronate oligosaccharides and polymer segments
Authors: Cowman Mary K. , Bush C. Allen , Balazs Endre A. 
Published: May 2005

AbstractThe CD spectrum of an enzymatically derived sodium hyaluronate (NaHA) segment preparation with chain length 18 ± 3 disaccharide units [NaHAseg, ( NaGlcUA GlcNAc)15–20°. NaGlcUA, sodium D‐glucuronate; GlcNAc, 2‐acetamido‐2‐deoxy‐D‐glucose] in H2O was recorded to 180 nm using a computer‐controlled vacuum‐uv CD instrument. Near 190 nm the spectrum is of low intensity, similar to the sum of the free monosaccharide contributios, attributed to the π–π* transitions of the acetamido and carboxylate substituents. In contrast, much smaller oligosaccharides, also derived from high‐molecular‐weight NaHA by enzymatic digestions, show CD spectra in H2O with prominent bands centered near 190 nm. The oligosaccharide spectra can be matched as linear combinations of interior sugar residue ( NaHAseg) and end sugar residue CD contributions. End residues from oligosaccharides of the type (NaGlcUA‐GlcNAc)n show a negative CD band near 190 nm. End residues from oligosaccharides of the reverse sequence (GlcNAc‐NaGlcUA)n show a positive CD band near 190 nm. Averaging of the two end‐residue spectral contributions yields an approximate match for the spectrum of NAHAseg below 200 nm. It is proposed that the low intensity CD of NaHA in the π–π* region is the result of large‐magnitude, oppositely signed contributions, which can be visulized by studying oligosaccharides.
Peptaibol antibiotics: Conformational preferences of synthetic emerimicin fragments
Authors: Toniolo Claudio , Bonora Gian Maria , Benedetti Ettore , Bavoso Alfonso , Di Blasio Benedetto , Pavone Vincenzo , Pedone Carlo 
Published: May 2005

AbstractThe ir absorption and CD conformational analyses of solutions of the protected 2–9 fragment of the peptaibol antibiotics emerimicins III and IV \documentclass{article}\pagestyle{empty}\begin{document}$ \rlap{--} (Aib_3 \rlap{--} )L - Val - Gly - L - Leu\rlap{--} (Aib_2 \rlap{--} ) $\end{document} and related short sequences are consistent with the presence of a right‐handed α‐helix for the octapeptide, while the tri‐, tetra‐, and pentapeptides adopt a 310‐helix, either right‐ or left‐handed, depending on the amino acid sequences. The structural preferences of solid‐state \documentclass{article}\pagestyle{empty}\begin{document}$ Z\rlap{--} (Aib_3 \rlap{--} )L - Val - OMe $\end{document} and \documentclass{article}\pagestyle{empty}\begin{document}$ Z\rlap{--} (Aib_3 \rlap{--} )L - Val - Gly - OMe $\end{document} have been determined by x‐ray diffraction. In accord with the solution data, incipient 310‐helices, formed by two and three β‐turns, have been found for the tetra‐ and pentapeptides, respectively. The tetrapeptide helix has the left‐handed screw sense, while that of the pentapetide is right‐handed, thus confirming the conclusions of the CD analysis of the solution.
Molecular structure by the constrained damped least‐squares (CDLS) method
Authors: Subhasini S. , Sundaram K. 
Published: May 2005

AbstractA method for simulating three‐dimensional molecular structure is presented. The method can satisfy any number of constraints on the molecular structure. The constraints can pertain to the constancy of individual distances and angles or be related to point‐group symmetry. A simulated three‐dimonsional model is forced to satisfy the required constraints in the least‐squares sense. The least‐squares optimization is damped to guard against convergence failure. This method is suggested as a tool to obtain approximate molecular structure in situations where a number of quantitative features are known about a molecular structure from preliminary crystallographic results but not the full molecular structure. An application to the structure of enniatin B–K+ complex is given to illustrate such a use.
Band structure of electronic circular dichroism spectra and the born‐oppenheimer approximation
Authors: Dewey T. G. 
Published: May 2005

AbstractTheory is presented for determining the effects of band structure on electronic CD spectra. In this development, the effect of the first‐order correction to the Born‐Oppenheimer approximation is considered. This removes the unrealistic feature of identical CD and absorbance spectral band structures present in previous models. The predicted order of magnitude of this correction is consistent with experimentally observed differences in CD and absorbance band structure. A Green function formalism is used to determine the contribution of the intrinsic CD to the total CD of an aggregate of chromophores. The intrinsic CD can be determined from the monomeric CD that has been corrected for effects of the intermolecular interactions in the aggregate.
Comparative flexibility, extension, and conformation of some simple polysaccharide chains
Authors: Burton Bruce A. , Brant David A. 
Published: May 2005

AbstractRealistic polymer chain models are developed for several polysaccharides to illustrate, using perspective drawings of representative chain conformations, the wide range of configuration, extension, and flexibility found in chains of the polysaccharide class. A method for incorporating the gauche or exo‐anomeric effect into polysaccharide conformational energy functions is described, and a novel measure of directional correlation and pseudohelical persistence is utilized to help distinguish the differences in chain configuration observed among the polysaccharides compared.
Description of collagen fibril formation by a theory of polymer crystallization
Authors: Wallace Donald G. , Thompson Andrea 
Published: May 2005

AbstractA well‐known nucleation‐growth model, used extensively to describe the crystallization of synthetic polymers, has been applied to collagen. The model gives (1) a general representation of the effect of temperature on the rate of collagen fibril formation, (2) a semi‐quantitative description of the effect of collagen concentration on growth rate, and (3) an estimate of fibril diameter that is in agreement with observations made by electron microscopy. The mechanism described is apparently that of the early stages of fibril growth, in which microfibrils are formed. An important parameter required in this approach is the free energy of fibril formation. The free energy was approximated by use of an expression derived by Flory for rodlike polymers. Flory's equation plus experimental data on collagen solubility permitted calculation of the free energy over a range of temperature. The resultant expression was of the same form as one commonly used in describing crystallization of synthetic polymers.
Computer simulation of the conformational properties of retro–inverso peptides. I. Empirical force field calculations of rigid and flexible geometries of N‐acetylglycine‐N′‐ methylamide, bis(acetamido) methane, and N, N′‐ dimethylmalonamide and their corresponding Cα‐methylated analogs
Authors: Stern P. S. , Chorev M. , Goodman M. , Hagler A. T. 
Published: May 2005

AbstractRigid and flexible geometry calculations are described for N‐acetylglycine‐N′‐methylamide, N‐acetylalanine‐N′‐methylamide, and their retro‐inverso analogs, bis(acetamido) methane, 1,1‐bis(acetamido) ethane, N,N′‐dimethylmalonamide, and N,N′‐dimethyl‐2‐methyl‐malonamide. The significance of relaxing all degrees of freedom, especially angular flexibility is demonstrated. The flexible geometry approach yields energy maps similar to those from rigid geometry, but the energy barriers between minima are substantially reduced, leading in general, to more probable transitions and a higher volume of accessible conformational space. Whereas the glycine and alanine derivatives exhibit their lowest energy minima in the C region, the gem‐diaminoalkyl and malonyl residues show their lowest minima in the “α‐helical” regions. With respect to the effect of side chains (H versus CH3), the greatest conformational influence appears with the gem‐diaminoalkyl residues. These results indicate significantly different conformational behavior of retro peptides and the implications of these pairwise incorporations of retro‐inverso residues in peptide chains, are discussed.
Computer simulation of the conformational properties of retro–inverso peptides. II. Ab initio study, spatial electron distribution, and population analysis of N‐formylglycine methylamide, N‐formyl N′‐acetyldiaminomethane, and N‐methylmalonamide
Authors: Stern P. S. , Chorev M. , Goodman M. , Hagler A. T. 
Published: May 2005

AbstractAb initio minimal and split‐valence basis set calculations have been performed on compounds that are involved in retro–inverso modifications, i.e., gem‐diaminoalkyl and malonyl structures. These calculations are compared with empirical force field calculations and the minor differences discussed. All calculations agree that the preferred helical conformation of the isolated gem‐diaminoalkyl and malonyl derivatives of residues found in the retro‐inverso modified peptides is 5–8 kcal/mol lower than the C conformation preferred by the isolated peptide residues. Population analysis and contour plots of the charge distribution are used to help explain the differences between the model compounds.
Fluorescence correlation spectroscopy and photobleaching recovery of multiple binding reactions. I. Theory and FCS measurements
Authors: Icenogle R. D. , Elson E. L. 
Published: May 2005

AbstractFluorescence correlation spectroscopy (FCS) and fluorescence photobleaching recovery (FPR) are two methods that may be used to measure diffusion and chemical reaction kinetics in small, labile systems such as biological cells. These methods are here applied to systems in which a fluorescent ligand can bind to a polyvalent substrate molecule in a multistep reaction sequence. The analytical theory for both FCS and FPR is extended to allow analysis of these kinds of systems. Experimental measurements of the binding of ethidium bromide to DNA by FCS confirm the theoretical analysis. (FPR measurements on the same system are reported in the accompanying paper.) The analysis shows that FCS and FPR perceive multivalent binding reactions differently. This difference results from the selective effect of the photobleaching process in the chemical reaction system. The development and results we report could have useful applications to a wide range of biopolymeric binding and assembly process.
Correlation of Tm, sequence, and ΔH of complementary RNA helices and comparison with DNA helices
Authors: Ornstein Rick L. , Fresco Jacques R. 
Published: May 2005

AbstractTm values of 16 fully complementary RNA duplexes with repeating base sequence have been employed as the empirical basis for developing a reliable and practical method for computing apparent enthalpies (ΔHcalc) for their helix → coil transitions. The approach taken is the same as in the accompanying investigation of DNA duplexes, although some of the computational variables of the “best‐fit” function are necessarily different due to the distinguishing structural properties of the RNA‐type helix. An excellent linear correlation was thus obtained between experimental Tm and ΔHcalc values. An equally good fit was obtained between Tm and ΔHcalc for five unrelated (to the 16 RNAs) decaribonucleotide duplexes. The differences in computational variables between the best‐fit methods for RNA and DNA duplexes are shown to be a reflection of differences in cation binding and the effective local dielectric. The greater Tm dependence on G·C content of RNA helices than of DNA helices is shown to be due to a greater latitude of stacking stabilities of complementary dinucleotide fragments containing A·T than A·U base pairs.
Stereochemistry of α‐aminoisobutyric acid peptides in solution: Helical conformations of protected decapeptides with repeating Aib‐L‐Ala and Aib‐L‐Val sequences
Authors: kumar E. K. S. Vijaya , Balaram P. 
Published: May 2005

AbstractThe decapeptides Boc‐(Aib‐L‐Ala)5‐OMe and Boc‐(Aib‐L‐Val)5‐OMe have been studied by 270‐MHz 1H‐nmr in CDCl3 and (CD3)2SO solutions. Intramolecular hydrogen‐bonded NH groups have been delineated using the temperature and solvent dependence of the NH chemical shifts and differential broadening of the NH resonances, induced by addition of a nitroxide radical. Both peptides have eight solvent‐shielded NH groups, suggesting that 310‐helical conformations are maintained in the two solvents. In alternating Aib‐X sequences, the Aib residues appear to play a dominant role in determining the preferred conformations, overriding the intrinsic stereochemical preferences of the X residues.