bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the “filterable aggregates and other particles” interpretation of the extraordinary regime of polyelectrolytes
Authors: Schmitz Kenneth S. 
Published: December 2004

AbstractQuasi‐elastic light scattering studies on some polyelectrolyte systems exhibit a somewhat “bizarre” behavior in the profile of the apparent diffusion coefficient Dapp as a function of the salt concentration Cs. As Cs is decreased, Dapp first increases in accordance with polyelectrolyte theories, and then undergoes a precipitous drop in value by over an order of magnitude at a well‐defined critical value Cs = C. This “transition” from Cs > C (ordinary) to Cs < C (extraordinary) is referred to as the “ordinary‐extraordinary” (o‐e) transition.Ghosh, Peitzsch, and Reed [(1992) Biopolymers, Vol. 32, pp. 1105–1122] proposed a “filterable aggregate” (FA) and “other particle” interpretation for the o‐e transition and its reversibility in regard to ionic strength changes. The present communication examines in detail the FA model as applied to the o‐e transition. It is shown that the FA model fails to account of the established characteristics of the o‐e transition. © 1993 John Wiley & Sons, Inc.
Noncoded residues as building blocks in the design of specific secondary structures: Symmetrically disubstituted glycines and β‐alanine
Authors: Di Blasio Benedetto , Pavone Vincenzo , Lombardi Angela , Pedone Carlo , Benedetti Ettore 
Published: December 2004

AbstractStructural changes can be induced in a peptide by selective substitution of coded α‐amino acid residues by noncoded α‐amino acid residues and the consequent production of analogues with modified structure and conformational preferences.In this review article we summarize the solid state structural results and the conformational preferences of two classes of “building blocks”: (a) the linear and cyclic symmetrically α, α‐disubstituted glycines in which either two identical n‐alkyl groups replace the hydrogen atoms of the glycine residue or a cyclic aliphatic side‐chain system is formed by linking the two α‐carbon side chains, respectively; and (b) the β‐alanine residue. Examples, whenever possible, of the use of these residues for the elucidation of the bioactive conformation in the appropriate biological systems will be given. © 1993 John Wiley & Sons, Inc.
Synthesis and conformational study of peptides possessing helically arranged ΔZPhe side chains
Authors: Inai Yoshihito , Ito Takaaki , Hirabayashi Tadamichi , Yokota Kenji 
Published: December 2004

AbstractZ‐Dehydrophenylalanine (ΔzPhe) possessing four oligopeptides, Boc‐(L‐Ala‐ΔzPhe‐Aib)n‐OCH3 (n = 1–4: Boc, t‐butoxycarbonyl; Aib, α‐aminoisobutyric acid), were synthesized, and their solution conformations were investigated by 1H‐nmr, ir, uv, and CD spectroscopy and theoretical CD calculation. 1H‐nmr (the solvent accessibility of NH groups) and ir studies indicated that all the NH groups except for those belonging to the N‐terminal L‐Ala‐ΔzPhe moiety participate in intramolecular hydrogen bonding in chloroform. This suggests that the peptides n = 2–4 have a 4 → 1 hydrogen‐bonding pattern characteristic of 310‐helical structures. The uv spectra of all these peptides recorded in chloroform and in trimethyl phosphate showed an intense maximum around 276 nm assigned to the ΔzPhe chromophores. The corresponding CD spectra of the peptides n = 2–4 showed exciton couplets with a negative peak at longer wavelengths, whereas that of the peptide n = 1 showed only weak signals. Theoretical CD spectra were calculated for the peptides n = 2–4 of several helical conformations, on the basis of exciton chirality method. This calculation indicated that the three peptides form a helical conformation deviating from the perfect 310‐helix that contains three residues per turn, and that their side chains of Δz Phe residues are arranged regularly along the helix. The center‐to‐center distance between the nearest phenyl pair(s) was estimated to be ∼ 5.5 Å. The chemical shifts of the ΔzPhe side‐chain protons (Hβ and aromatic H) for the peptides n = 2–4 indicated anisotropic shielding effect of neighboring phenyl group(s); the effect also supports a regular arrangement of the Δz Phe side chains along the helical axis. © 1993 John Wiley & Sons, Inc.
The loop problem in proteins: A monte carlo simulated annealing approach
Authors: Carlacci Louis , Englander S. Walter 
Published: December 2004

AbstractA Monte Carlo simulated annealing (MCSA) algorithm was used to generate the conformations of local regions in bovine pancreatic trypsin inhibitor (BPTI) starting from random initial conformations. In the approach explored, only the conformation of the segment is computed; the rest of the protein is fixed in the known native conformation. Rather than follow a single simulation exhaustively, computer time is better used by performing multiple independent MCSA simulations in which different starting temperatures are employed and the number of conformations sampled is varied. The best computed conformation is chosen on the basis of lowest total energy and refined further. The total energy used in the annealing is the sum of the intrasegment energy, the interaction energy of the segment with the local surrounding region, and a distance constraint to generate a smooth connection of the initially randomized segment with the rest of the protein.The rms deviations between the main‐chain conformations of the computed segments in BPTI and those of the native x‐ray structure are 0.94 Å for a 5‐residue α‐helical segment, 1.11 Å for a 5‐residue β‐strand segment, and 1.03, 1.61, and 1.87 Ã for 5‐, 7‐, and 9‐residue loop segments. Side‐chain deviations are comparable to the main‐chain deviations for those side chains that interact strongly with the fixed part of the protein. A detailed view of the deviations at an atom‐resolved level is obtained by comparing the predicted segments with their known conformations in the crystal structure of BPTI. These results emphasize the value of predetermined fixed structure against which the computed segment can nest. © 1993 John Wiley & Sons, Inc.
Electromigration behavior of poly‐(L‐glutamate) conformers in concentrated polyacrylamide gels
Authors: Dolník Vladislav , Novotny Milos , Chmelík Josef 
Published: December 2004

AbstractDuring electrophoretic separation of anionic polyamino acids, resolution according to the number of peptide units can be achieved in capillaries filled with hydrophilic gels. While polyaspartate preparations yield single peaks for the individual oligomers at pH above 8.0, polyglutamates exhibit an anomalous behavior of peak splitting, which is attributed here to the separation of the oligopeptide conformers. An Asp‐Glu (1:1) copolymer yields single peaks under similar conditions. At pH near 4.5, where polyglutamate is expected to exist in its α‐helix form, peak splitting disappears. Upon heating to 95°C for at least 120 h (procedure described to transform the α‐helix into a β form), peak splitting disappeared, but could be reestablished after cooling for several days. When a highly charged cation spermine was added to the operational electrolyte, triple peaks appeared in the electropherogram due to the ion‐pair formation. The largest peak in every triplet has been tentatively assigned to the α‐helix form. The electrophoretic results described have been largely supported by CD spectra. © 1993 John Wiley & Sons, Inc.
Hybrid Monte Carlo simulations theory and initial comparison with molecular dynamics
Authors: Brass A. , Pendleton B. J. , Chen Y. , Robson B. 
Published: December 2004

AbstractA formal partially dynamical approach to ergodic sampling, hybrid Monte Carlo, has been adapted for the first time from its proven application in quantum chromodynamics to realistic molecular systems. A series of simulations of pancreatic trypsin inhibitor were run using temperature‐rescaled molecular dynamics and hybrid Monte Carlo. It was found that simulations run using hybrid Monte Carlo equilibrated an order of magnitude faster than those run using temperature‐rescaled molecular dynamics. Certain aspects of improved performance obtained using hybrid Monte Carlo are probably due to the increased efficiency with which this algorithm explores phase space. To discuss this we introduce the notion of “trajectory stiffness”. © 1993 John Wiley & Sons, Inc.
Conformational analysis of the type II and type III collagen α‐1 chain N‐telopeptides by 1H‐NMR spectroscopy and restrained molecular mechanics calculations
Authors: Otter Albin , Scott Paul G. , Kotovych George 
Published: December 2004

AbstractThe type II and type III collagen α‐1 chain N‐telopeptides are a nonadecamer with the sequence pEMAGGFDEKAGGAQLGVMQ‐NH2 and a tetradecamer with the sequence pEYEAYDVKSGVAGG‐NH2, respectively. Their conformations have been studied in CD3OH/H2O (60/40) solution by means of two‐dimensional proton nmr spectroscopy. Based on double quantum filtered correlation spectroscopy, total correlation spectroscopy, rotating frame nuclear Overhauser enhancement (ROE) spectroscopy, and nuclear Over‐hauser enhancement (NOE) spectroscopy experiments, all resonances were assigned and the conformational properties were analyzed in terms of vicinal NH‐Hα coupling constants, sequential and medium‐range NOEs (ROEs), and amide proton temperature coefficients. The NOE distance constraints as well as dihedral constraints based on the vicinal NH‐Hα coupling constants were used as input parameters for restrained molecular mechanics, consisting of restrained molecular dynamics and restrained energy minimization calculations. The type II N‐telopeptide's conformation is dominated by a fused βγ‐turn between Phe6 and Ala10, stabilized by three hydrogen bonds and a salt bridge between the side‐chain end groups of Glu8 and Lys9. The first 5 amino acids are extended with a much higher degree of conformational freedom. The 2 Gly residues following the turns were found to be highly flexible (hinge‐like), leaving the spatial position of the second half of the molecule relative to the fused βγ‐turn undefined. In the type III telopeptide, a series of sequential NH(i)‐NH(i + 1) ROEs were observed between the amino acids Tyr2 and Ser9, indicating that a fraction of the conformational space is helical. However, the absence of medium‐range ROEs and the lack of regularity of the effects associated with α‐helices suggest the presence of a nascent rather than a complete helix. © 1993 John Wiley & Sons, Inc.
Secondary structure of proteins associated in thin films
Authors: Safar Jiri , Roller Peter P. , Ruben George C. , Gajdusek D. Carleton , Gibbs Clarence J. 
Published: December 2004

AbstractThe solid state secondary structure of myoglobin, RNase A, concanavalin A (Con A), poly(L‐lysine), and two linear heterooligomeric peptides were examined by both far‐uv CD spectroscopy1 and by ir spectroscopy. The proteins associated from water solution on glass and mica surfaces into noncrystalline, amorphous films, as judged by transmission electron microscopy of carbon‐platinum replicas of surface and cross‐fractured layer. The association into the solid state induced insignificant changes in the amide CD spectra of all α‐helical myoglobin, decreased the molar ellipticity of the α/β RNase A, and increased the molar ellipticity of all‐β Con A with no change in the positions of the bands' maxima. High‐temperature exposure of the films induced permanent changes in the conformation of all proteins, resulting in less α‐helix and more β‐sheet structure. The results suggest that the protein α‐helices are less stable in films and that the secondary structure may rearrange into β‐sheets at high temperature. Two heterooligomeric peptides and poly (L‐lysine), all in solution at neutral pH with “random coil” conformation, formed films with variable degrees of their secondary structure in β‐sheets or β‐turns. The result corresponded to the protein‐derived Chou‐Fasman amino acid propensities, and depended on both temperature and solvent used. The ir and CD spectra correlations of the peptides in the solid state indicate that the CD spectrum of a “random” structure in films differs from random coil in solution. Formic acid treatment transformed the secondary structure of the protein and peptide films into a stable α‐helix or β‐sheet conformations. The results indicate that the proteins aggregate into a noncrystalline, glass‐like state with preserved secondary structure. The solid state secondary structure may undergo further irreversible transformations induced by heat or solvent. © 1993 John Wiley & Sons, Inc.
Refined three‐dimensional solution structure of a snake cardiotoxin: Analysis of the side‐chain organization suggests the existence of a possible phospholipid binding site
Authors: Gilquin Bernard , Roumestand Christian , Zinn‐Justin Sophie , Ménez André , Toma Flavio 
Published: December 2004

AbstractThe solution structure of toxin γ (60 residues, 4 disulfides) from Naja nigricollis was determined by proton nmr and molecular modeling with DIANA and X‐PLOR. The structures were calculated using 489 distance and 81 dihedral angle constraints. The average atomic rms deviation between the nine refined structures and the average structure is 0.118 nm for the backbone atoms. Toxin γ has an overall folding consisting of three loops stabilized by the four disulfides and forming a two‐ and a three‐stranded β‐sheet (loop I and loops II, III, respectively). The same type of folding has been observed for two homologous cardiotoxins. The very close similarity of the solution structure of toxin γ and the crystal structure of toxin V includes details of the topological arrangement of numerous side chains. Among these are the conserved residues K12, K18, K35, and Y22, known to be critical for the cytolytic activity of toxin γ. A cluster of hydrophobic side chains organized around Y22 is found on one side of the three‐stranded β‐sheet and is spatially close to a group of three lysines (K12, K18, K35). The side chains of these lysines form a cationic site that can accommodate the binding of a phosphate ion as found in the crystal structure of toxin V. The hydrophobic cluster constitutes a possible binding site for the hydrophobic moiety of phospholipids. Together with the complementary cationic site, this hydrophobic surface can form a conserved site by which cardiotoxins bind to membrane phospholipids. © 1993 John Wiley & Sons, Inc.
Overcrossing spectra of protein backbones: Characterization of three‐dimensional molecular shape and global structural homologies
Authors: Arteca Gustavo A. 
Published: December 2004

AbstractA procedure is developed and applied to characterize the global shape and folding features of the backbone of a chain molecule. The methodology is based on the following concept: the probability of observing a rigid placement of a backbone in 3‐space as a projected curve with N overcrossings. The numerical computation of these probabilities allows one to construct the overcrossing spectrum of a macromolecule at a given configuration. Although the spectrum is built from the knowledge of the nuclear geometry of the main‐chain atoms, the shape descriptor overlooks local geometrical features (such as distances and contacts) and provides a characterization of essential (topological) features of the overall fold, such as its compactness and degree of entanglement. In contrast with other shape descriptors, the present approach gives an absolute characterization of the configuration considered, and not one that is relative to an arbitrarily chosen reference structure. Moreover, it is possible to discriminate between folding features that otherwise may not be distinguished when using other geometrical or topological global descriptors. The overcrossing spectrum is proposed as a tool that complements current structural analyses of macromolecules, especially when monitoring structural homologies within a group of related or unrelated polymers. In this work, we apply the methodology to the analysis of proteins having the globin fold. The results are compared with those of other proteins exhibiting similar size and number of residues. Some basic properties of the spectra as a function of the chain length are also discussed. © 1993 John Wiley & Sons, Inc.
Self‐consistent reaction field computation of the reactive characteristics of DNA bases in water
Authors: Orozco Modesto , Luque F. J. 
Published: December 2004

AbstractThe effect of the solvent in the molecular properties of DNA bases has been explored by using a self‐consistent reaction field (SCRF) method based on the AM1 (Austin Model 1) Hamiltonian and a modified version of the high level Miertus–Scrocco–Tomasi (MST) algorithm. MST/AM1 estimates of free energies of hydration compare qualitatively well with the available experimental data, as well as with the results obtained from molecular dynamic simulations. Furthermore, the changes in the dipole predicted by the MST/AM1 method are in good agreement with Monte Carlo/quantum mechanical data, as well as with AM1‐SM2 (Soluation Model 2) estimates. AM1/MST calculations of Mulliken, and electrostatic charges, dipoles, molecular electrostatic potentials and molecular interaction potentials in both vacuum and solution allowed us to quantify the effect of the water on the reactive characteristics of the DNA bases. This effect is large and complex, and cannot be neglected in theoretical calculations where an accurate representation of the DNA bases is needed. The possibility of including the polarization effect of the water into force‐field simulations of DNA structures is discussed. © 1993 John Wiley & Sons, Inc.
Conformational studies of heterochiral peptides with diastereoisomeric residues: Crystal and molecular structures of linear dipeptides derived from leucine, isoleucine, and allo‐isoleucine
Authors: Di Blasio Benedetto , Saviano Michele , Del Duca Valerio , De Simone Giuseppina , Rossi Filomena , Pedone Carlo , Benedetti Ettore , Lorenzi Gian Paolo 
Published: December 2004

AbstractThe x‐ray diffraction analyses of three N‐ and C‐terminally blocked L, D dipeptides, namely t‐Boc‐D‐Leu‐L‐Leu‐OMe (1), t‐Boc‐L‐Ile‐D‐alle‐OMe (2), and t‐Boc‐D‐aIle‐L‐Ile‐OMe (3) containing enantiomeric or diastereomeric amino acid residues have been carried out. The structures were determined by direct methods and refined anisotropically to final R factors of 0.077. 0.058. and 0.072 for (1) (2) and (3), respectively.Peptides 1–3 all assume a similar U‐shaped structure with ϕ and ψ torsion angles cosrresponding to one of the possible calculated minimum energy regions (regions E and G for L residues, and F*. D* and H* for D residues). The peptide backbones of 1‐3 are almost super‐imposable [provided that the appropriate inversion of the chiral centers of (2) is made].Side‐chain conformations of Leu residues in peptide (1) are g− (tg−) for the L‐Leu residue and the mirrored g+ (tg+) for the D‐Leu residue; however, in peptides (2) and (3) the conformations of the isoconfiguralional side chains of the Ile or allo‐Ile residues are (g−t) t and (tg+) tfor the L‐Ile and the D‐allo‐Ile moieties, respectively. In all cases, these conformations correspond to the more populated conformers of β‐branched residues statistically found in crystal structures of small peptides.The results seem to indicate that, at least in short peptides with enantiomeric or diastereoisomeric residues, the change in chirality in the main‐chain atoms perturbs the backbone conformation to a lesser extent and the side chain conformation to a greater extent. © 1995 John Wiley & Sons, Inc.
Conformation of cyclobradykinin by nmr and distance geometry calculations
Authors: Pellegrini Maria , Mammi Stefano , Gobbo Marina , Rocchi Raniero , Peggion Evaristo 
Published: December 2004

AbstractThe conformation of the head‐to‐tail cyclic analogue of bradykinin in DMSO was investigated by nmr. Three sets of resonances were detected and fully assigned. These were attributed to the presence of three stable conformers, two of which were exchanging on the nmr time scale. A fourth, incomplete set of resonances was detected but not assigned. The three major conformers differ in the conformation at the three X‐Pro bonds present.From nuclear Overhauser effect spectroscopy (NOESY) spectra, three sets of interproton distances were derived and used in NOE‐restrained distance geometry calculations. The resulting structures were refined by energy minimization to yield families of structures. Conformer I is characterized by the presence of two type VIb β‐turns between Arg1 and Gly4 and between Phe5 and Phe8. The first β‐turn is present also in conformer II, while an inverse γ‐turn bridging Pro3 is the most pronounced structural feature of conformer III. © 1995 John Wiley & Sons, Inc.
1‐dehydrogenation of steroids by Septomyxa affinis
Authors: Koepsell H. J. 
Published: December 2004

Abstract1‐Dehydrogenation of steroids by Septomyxa affinis is brought about by an inducible enzyme. Only soluble substrate steroid is attacked. Individual steroids are dehydrogenated at different relative rates. The pH‐activity curve is shallow.
An apparatus for aeration of tissue cells in suspended culture with controlled gas mixtures
Authors: Daniels W. F. , Browning E. W. 
Published: December 2004

AbstractAn apparatus is described for the aeration of a series of tissue cultures at rates which may be varied independently for each vessel. The composition of the aerating gas can be adjusted to any desired percentages of CO2 and O2. While designed particularly for study of the aeration requirements of submerged tissue growth, the equipment is equally adaptable for study of submerged growth of bacterial and other systems. The apparatus has been designed for future scale‐up and is adaptable to both the overlay and bubble‐through types of aeration. Flow rates necessary for producing mixtures of 5.0% CO2 and 95.0% air or 5.6% CO2, 14.0% O2, and 80.4% nitrogen are given. The described system has been operated satisfactorily and has proved to be an inexpensive and useful research tool.
Some effects of turbine size on novobiocin fermentations
Authors: Steel R. , Maxon W. D. 
Published: December 2004

AbstractStudies were made of oxygen transfer and power in 20‐1. novobiocin fermentations with five sizes (23–60% of the tank diameter) of geometrically similar flatblade turbine impellers. The influence of changes in apparent viscosity on oxygen transfer and power was found to be related to impeller diameter. At constant agitator speed the oxygen availability rate (OAR) decreased with increase in apparent viscosity, but the magnitude of the reduction was less with a small impeller than with a large one. At constant power input the small‐diameter impeller (23% of tank diameter) gave an OAR about 8 times that of the large one (60% of tank diameter) when tested in viscous beer, whereas with sulfite or yeast all impeller diameters gave the same OAR. Impeller tip velocity correlated with OAR independently of diameter for the five turbine sizes examined. The power required for optimal novobiocin yields increased with increase in turbine diameter, but the yields were independent of diameter at equal OAR.
Plastic ampoules for liquid smallpox vaccine
Authors: Espmark Åke , Lindner Stig 
Published: December 2004

AbstractManufacturing of plastic (PVC) single‐dose ampoules for liquid smallpox vaccine is described. The green stained vaccine is injected in polyvinyl chloride tubes which are then sealed by high frequency welding to make ampoules of 16 mm. length. The tendency for desiccation of the filled vaccine at elevated temperature is considered as an advantage, since it provides a visible indication of previous improper storage. The ampoule is opened by cutting with scissors and vaccine is squeezed out directly on the skin.