bluuebunny/crossref_metadata_2025_split huggingface dataset:
Peptide design 310‐helical conformation of a linear pentapeptide containing two dehydrophenylalanines, Boc‐Gly‐ΔZPhe‐Leu‐ΔZPhe‐Ala‐NHCH3
Authors: Bhandary Krishna K. , Chauhan V. S. 
Published: December 2004

Abstractα, β‐Dehydroamino acids are expected to provide conformational constraint to the peptide backbone. A pentapeptide containing two dehydrophenylalanines (ΔZPhe) separated by one L‐amino acid has been synthesized and its solid state conformation determined. The pentapeptide, Boc‐Gly‐ΔZPhe‐Leu‐ΔZPhe‐Ala‐NHCH3, crystallizes from aqueous methanol in the orthorhombic space group P212121. There are four formula units, C35H46N6O7, in a unit cell of dimensions a = 10.155(3), b = 15.175(1), and c = 23.447(2) Å, at room temperature. The structure was solved by direct methods program, SIR88, and refined to a final R = 0.038 based on 3049 reflections with I > 2σ(I). All the peptide links are trans and the backbone conformation of the pentapeptide can be described as a 310‐helix, with mean ϕ, ψ values of −65.1° and −22.8° (the value is averaged over the first four residues). There are four intramolecular 4 → 1 type hydrogen bonds characteristic of 310‐type helices. In the crystal, the helices are held together by intermolecular NH…︁OC head‐to‐tail and lateral hydrogen bonding between symmetry related molecules. This mode of packing is similar to the packing motifs observed so often in other oligopeptides that adopt a 310‐helical structure. © 1993 John Wiley & Sons, Inc.
X‐ray studies on crystalline complexes involving amino acids and peptides. XXIV. Different ionization states and novel aggregation patterns in the complexes of succinic acid with DL‐and L‐histidine
Authors: Prasad G. Sridhar , Vijayan M. 
Published: December 2004

AbstractDiffusion of acetonitrile into an aqueous solution of DL‐histidine and succinic acid in 1:3 molar proportions results in the crystals of DL‐histidine hemisuccinate dihydrate [triclinic, P1, a = 7.654(1), b = 8.723(1), c = 9.260(1) Å, α = 77.23(1), β = 72.37(1) and γ = 82.32 (1)°]. The replacement of DL‐histidine by L‐histidine in the crystallization experiment under identical conditions leads to crystals of L‐histidine semisuccinate trihydrate [orthorhombic, P212121, a = 7.030 (1), b = 8.773 (1), and c = 24.332 (3) Å]. The structures were solved using counter data and refined to R values of 0.056 and 0.054 for 2356 and 1778 observed reflections, respectively. Histidine molecules in both the complexes exist in open conformation I. Succinate and semisuccinate ions in them are planar, and exactly or nearly centrosymmetric. In the DL‐histidine complex, the amino acid molecules form double ribbons and the succinate ions occupy voids left behind when the double ribbons aggregate, as in inclusion compounds. In the L‐histidine complex, the amino acid molecules form columns; so do the semisuccinate ions and water molecules. The two columns interdigitate to form the complex crystal. There are similarities between the molecular aggregation in the complexes and that in the crystals of L‐ and DL‐histidine. However, the presence of succinic acid has the effect of disrupting, partially or totally, head‐to‐tail sequences involving amino acid molecules. © 1993 John Wiley & Sons, Inc.
Effects of molecular association on structure and dynamics of a collagenous peptide
Authors: Daragan Vladimir A. , Ilyina Elena , Mayo Kevin H. 
Published: December 2004

AbstractPeptide GVKGDKGNPGWPGAPY from the triple‐helix domain of type IV collagen aggregates in solution at a critical aggregation concentration of 18 mM. This molecular self association process is investigated by 1H‐ and 13C‐nmr spectroscopy. As a function of increasing peptide concentration, selective 1H resonances are cooperatively chemically shifted by up to 0.04 ppm to apparently saturable values at high concentration. Pulsed field gradient nmr was used to derive translation diffusion constants that, as the peptide concentration is increased, also cooperatively and monotonically decrease to an apparent limiting value. An average number of 6 monomer units per aggregate have been estimated from diffusion constant and 13C relaxation data. Comparative 1H nuclear Overhauser effect spectroscopy (NOESY) spectra accumulated at high and low peptide concentrations suggest that average internuclear distances are decreased as a result of peptide association. 13C‐nmr multiplet spin‐lattice relaxation and 13C‐ {1H} NOE effects on 13C‐enriched glycine methylene positions in the peptide demonstrate that overall molecular tumbling and backbone internal motions are attenuated in the aggregate state. Lowering the solution pD from pD 6 to pD 2 disrupts the aggregate state, suggesting a role for electrostatic interactions in the association process. Based on thermodynamic considerations, hydrophobic interactions also probably act to stabilize the aggregate state. These data are discussed in terms of an nmr/NOE constrained computer‐modeled structure of the peptide. © 1993 John Wiley & Sons, Inc.
Stereochemical constraints in peptide design: Analysis of the influence of a disulfide bridge and an α‐aminoisobutyryl residue on the conformation of a hexapeptide
Authors: Uma K. , Kishore R. , Balaram P. 
Published: December 2004

AbstractThe competing effects of a disulfide bridge and an α‐aminoisobutyryl residue (Aib) in determining the conformation of a hexapeptide have been investigated, by comparing the cyclic disulfide
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and the acylic peptide Boc‐Cys(SBzl)‐Val‐Aib‐Ala‐Leu‐Cys(SBzl)‐NHMe (2). Previously published nmr and crystallographic studies [R. Kishore, S. Raghothama, and P. Balaram (1987) Biopolymers, Vol. 26, pp. 873–891; I. L. Karle, R. Kishore, S. Raghothama, & P. Balaram, (1988) Journal of the American Chemical Society Vol. 110, pp. 1958–1963] have established an antiparallel β‐hairpin structure for 1 with a central Aib‐Ala β‐turn. A comparison of nmr data for 1 and 2 in chloroform and dimethylsulfoxide reveals that the acyclic peptide is conformationally labile. Evidence for a 310‐helical conformation in CDCl3 is obtained from sensitivity of NH chemical shifts to temperature and solvent perturbation and low JHNCαH values. Studies in solvent mixtures establish a conformational transition on going from CDCl3 to (CD3)2SO. The changes in NH nmr parameters, together with the observation of several interresidue C H‐Ni + 1H nuclear Overhauser effects support a conformation having a central β‐turn with extended arms in (CD3)2SO. A single Aib residue appears to stabilize a helix in apolar solvents, for the acyclic hexapeptide, while the disulfide bridge serves to lock the β‐hairpin conformation. © 1993 John Wiley & Sons, Inc.
Conformational transitions using molecular dynamics with minimum biasing
Authors: Harvey Stephen C. , Gabb Henry A. 
Published: December 2004

AbstractThe molecular dynamics algorithm (MD), which simulates intramolecular motions on the subnanosecond timescale, has been modified to allow the investigation of slow conformational transitions that do not necessarily occur spontaneously in MD simulations. The method is designated CONTRA MD (CONformational TRAnsitions by Molecular Dynamics with minimum biasing). The method requires the prior definition of a single conformational variable that is required to vary monotonically from an initial conformation to a final target conformation. The simulation is broken up into a series of short free MD segments, and we determine, after each segment of MD, whether or not the system has evolved toward the final conformation. Those segments that do not move the system in that direction are deleted. Those that do move it toward the final conformation are patched together sequentially to generate a single representative trajectory along the transition pathway. The CONTRA MD method is demonstrated first by application to the simultaneous C2′‐endo to C3′‐endo repucker and anti to syn N‐glycosidic torsion transitions in 2′‐deoxyadenosine and then to the large‐scale bending in phenylalanine transfer RNA. © 1993 John Wiley & Sons, Inc.
The hydration of proteins in nearly anhydrous organic solvent suspensions
Authors: McMinn J. H. , Sowa M. J. , Charnick S. B. , Paulaitis M. E. 
Published: December 2004

AbstractWater sorption isotherms at 27°C have been measured for lysozyme and chymotrypsin in suspensions of toluene, di(n‐butyl) ether, n‐propanol, and a solution of 1M n‐propanol in benzene. Sorption isotherms for the different suspensions are compared by converting solvent water content to the thermodynamic activity of water in each solvent. The sorption behavior is also compared to that for the two proteins hydrated from the vapor phase. At low water activities, all sorption isotherms are similar when compared on the basis of water activity. However, at higher activities, water sorption by the proteins in the organic suspensions is suppressed relative to the sorption of water vapor. The greatest suppression is observed for n ‐propanol, which suggests that the suppression may be due to a competition for water‐binding sites on the protein by the organic solvent. Sorption isotherms at low water activities have also been predicted using a thermodynamic model in which it is assumed that water binds selectively to the ionizable residues on the surface of the protein. A comparison of predicted and measured sorption isotherms shows that the model can provide reasonable estimates of water sorption in nonpolar or moderately polar organic solvent suspensions at low levels of hydration. © 1993 John Wiley & Sons, Inc.
Stretching and overstretching of DNA in pulsed field gel electrophoresis. II. Coupling of orientation and transport in initial response to the field
Authors: Mayer Pascal , Sturm Jean , Weill Gilbert 
Published: December 2004

AbstractThe rise of the birefringence following the application of an electric field to DNA in an agarose gel has been quantitatively analyzed to demonstrate the major role played by the chain overstretching. By analyzing the field free decay after short times, we demonstrate that the overshoot is completely due to overstretching. Its time of appearance τov varies with the field and DNA length in fair agreement with the E−lN0ln N0 prediction of Lim et al. [ (1990), Journal of Chemical Physics, Vol. 92, pp. 709–721]. The τov is also the time corresponding to one tube renewal after relaxation of the overstretching. © 1993 John Wiley & Sons, Inc.
Energetics of the disulfide bridge: An ab initio study
Authors: Qian Weili , Krimm Samuel 
Published: December 2004

AbstractThe energetics of the χχ3χ portion of the disulfide bridge have been obtained from an ab initio study of diethyl disulfide. Calculations at the 3‐21G* level were done on relaxed structures at every ∼ 30° in χ and χ, and the additional energies for small Δχ3 were obtained. Complete E(χ, χ) and χ(χ, χ) maps were computed from Fourier series expansions. These results have been used to calculate the energetics of 92 disulfide bridges in known protein structures, and to compare ab initio and molecular mechanics energies for some observed and predicted bridges. The differences found in relative energies and in χ values suggest that present energy functions give a limited description of the structural and energetic properties of the disulfide bridge. © 1993 John Wiley & Sons, Inc.
Conformationally readdressed CCK‐B/δ‐opioid pepitide ligands
Authors: Nikiforovich Gregory V. , Kolodziej Stephen A. , Nock Bruce , Bernad Nicole , Martinez Jean , Marshall Garland R. 
Published: December 2004

AbstractThe sequence of a cholecystokinin (CCK) related peptide was modified to obtain analogues, which intereact selectively either with CCK‐B, or with δ‐opioid receptors. Two kinds of peptides were designed, namely, the cyclic peptides of the H‐Tyr‐cyclo(D‐Pen‐Gly‐Trp‐L‐/D‐3‐transmecaptoproline)‐Asp‐Phe‐NH2 sequence (compounds 1a and 1b, respectively), and the linear peptides of the H‐Tyr‐D‐Val‐Gly‐Trp‐L/D‐3‐trans‐methylmercaptoproline‐Asp‐Phe‐NH2 sequence (compounds 2a and 2b, respectively). The only difference between the chemical structures of the linear analogues compared to the cyclic ones is that one covalent bond has been eliminated and a sulfur atom is replaced by a methyl group. Molecular modeling showed that, among low‐energy conformers of cyclic compounds 1, there are three‐dimensional structures compatible to the model for δ‐ receptor‐ bound conformer, suggested earlier[G. V. Nikiforovich. V. J. Hruby. O. Prakash, and C. A. Gehrig (1991) Biopolymers. vol. 31. pp. 941–955]. Results of binding assays fully supported the rationale for the design of compounds 1 and 2. The cyclic analogue 1a has Ki values of 4.5 and > 5000 n M at δ‐ and μ‐opioid receptors, respectively; IC50 values of 3000 n M for both CCK‐A and CCK‐B receptors, whereas its linear counterpart 2a has ki values of 462 and 229 nM at δ‐ and μ‐opioid receptors, respectively; and IC50 values of 1.6 and > 10.000 nM for CCK‐A and CCK‐B receptors, respectively. The results of this study demonstrate a possibility to redirect a peptide sequence that interacts with one type of receptors (CCK‐B receptors) toward interaction with another type (δ‐opioid receptors) belonging to a different physiological system. This redirection could be performed by changing the conformational properties of the peptide with very minimal changes in its chemical structure. © 1995 John Wiley & Sons, Inc.
Intramolecular electronic energy transfer in peptides carrying naphthalene and protoporphyrin molecules: A spectroscopic and conformational statistics investigation
Authors: Pispisa B. , Venanzi M. , Palleschi A. , Zanotti G. 
Published: December 2004

AbstractShort linear peptides, carrying an AA spacer in the backbone chain (AA = Aib or Ala),and naphthalene(N) and protoporphyrin IX(P) covalently bound to ϵ‐amino groups of lysine side chains, were synthesized. The general formula is Boc‐Leu‐Leu‐Lys(P)‐(AA)n‐Leu‐Leu‐Lys(N)‐OtBu, with n = 0–2. The photophysical behavior of these compounds was investigated in water/methanol 75/25(v/v) solution by steady‐state and time‐resolved fluorescence experiments. Quenching of excited naphthyl chromophore lakes place by electronic energy transfer to the porphyrin ground state, and proceeds on a time scale of 3–8 ns, while a minor and slower(≈45 ns) fluorescence lifetime measures the decay of the exciplexes. The results were compared with those earlier obtained with the P(Ala)nN peptides(n = 0–4) in methanol solution, showing that addition of water does not significantly alter the dynamic relaxation behavior of the systems investigated, but affects the dissipation mechanism of the energy transferred to P. Quenching efficiencies from both fluorescence intensity and fluorescence lifetime measurements follow a different trend as the number of AA units increases, depending on whether AA = Aib or Ala, indicating that there are differences in the structural features of the two series of peptides. Consistently, CD spectral results suggest that the former compounds attain ordered conformations, possibly of the 310‐helical type, while the latter populate α‐helical structures to an extent depending on the chain length. The ir data in dilute CD3OD or CDCl3 solution confirm this conclusion in that there is an increased percentage of intramolecular H bonds in the P(Aib)nN as compared to the corresponding P(Ala)nN peptides. The photophysical results can be well described by a long‐range dipole–dipole interaction model, provided the separation distances distribution and mutual orientation of N and P groups are taken into account. The need of using the angular relationships between the probes implies that interconversion among conformational substates of chromophores linkages is slow on the time scale of the transfer process, very likely because of both the amide bond in the linkages and the bulkiness of the donor–acceptor pair. © 1995 John Wiley & Sons, Inc.
Gibberellic acid formation in continuous culture
Authors: Holme Tord , Zacharias Bengt 
Published: December 2004

AbstractThe formation of gibberellic acid in single‐stage continuous cultures was studied. Stirred fermenters of 3 and 20‐l. working volumes were used. Maximum output of gibberellic acid was obtained at a holding time of 200 hr. The rate of formation, calculated on the basis of mycelial nitrogen, was comparable with the highest values reported for batch cultures.
Kinetic studies of the lactic acid fermentation in batch and continuous cultures
Authors: Hanson T. P. , Tsao G. T. 
Published: December 2004

AbstractThe fermentation kinetics of the homofermentative organism Lactobacillus delbrueckii in a glucose‐yeast extract medium is studied in both batch and continuous culture under conditions of controlled pH. From a graphical analysis of the batch data, a mathematical model of the process is derived which relates bacterial growth, glucose utilization, and lactic acid formation. The parameters in the model represent the activity of the organism and are a function of pH, having a maximum value at about 5.90. In a continuous stirred tank fermentor (CSTF), the effect of pH, feed concentration, and residence time is observed. The feed medium is a constant ratio of two parts glucose to one part yeast extract plus added mineral salts. An approximate prediction of the steady‐state behavior of the CSTF can be made using a method based on the kinetic model derived for the batch case. In making step changes from one steady state to another, the transient response is observed. Using the kinetic model to simulate the transient period, the calculated behavior qualitatively predicts the observed response.
Effect of wall growth on scale‐up problems and dynamic operating characteristics of the biological reactor
Authors: Howell J. A. , Chi C. T. , Pawlowsky U. 
Published: December 2004

AbstractIf inhibitory substrates are being utilized in a well‐stirred biological reactor, microbiological growth on the walls of the reactor can create a scale‐up problem. A simple model is proposed which shows that without such growth, of the three existing steady states only one is stable and nontrivial, but with wall growth the trivial, stable, steady state (washout) is impossible. In addition, wall growth reduces the region over which three steady states are feasible and reduces the minimum residence time for which there is only one steady state that corresponds to a high conversion. Thus, a laboratory process with a high surface area to volume ratio can give an over optimistic prediction of both necessary residence; time and stability of the full scale process unless wall growth is accounted for.
Bacteria which attack petroleum hydrocarbons in a saline medium
Authors: Soli Giorgio , Bens E. M. 
Published: December 2004

AbstractBacterial strains were isolated from California coastal areas which showed the ability to oxidize normal paraffins, iso‐paraffins, and aromatic hydrocarbons in a synthetic seawater medium. The ability to utilize a particular hydrocarbon was established not only on the basis of visible bacterial growth but also through a chromatographic technique which was standardized and which could define the amount of each hydrocarbon consumed by the bacteria in a mixture. Some of the strains exhibited vigorous hydrocarbon oxidation when exposed to synthetic mixtures of hydrocarbons as well as crude oil. Under conditions of aeration and agitation, mixed cultures could destroy approximately 50% of a South Louisiana crude oil in a period of 48 hr.
Conversion of deteriorated metal cutting fluids into protein
Authors: Speidel Harold K. , Bennett E. O. 
Published: December 2004

AbstractSix soil isolates were grown on a petroleum sulfonate medium and analyzed chromatographically to determine their amino acid composition. The organisms were also examined to determine their growth rate in the petroleum medium, their per cent conversion of hydrocarbon to dry cell mass, their protein content, and their possible use as a food or food supplement. It was found that the isolates varied extensively as to their amino acid composition. Several of the isolates proved to convert the hydrocarbons to cell mass with relative ease. The proteins of four of the isolates appear to be suitable as a good food source, and the protein of one of the remaining isolates appears to be a very good food supplement.
Sterilization by electrohydraulic discharges
Authors: Holland R. V. , Board P. W. , Richardson K. C. 
Published: December 2004

AbstractHigh voltage electric discharges between two electrodes immersed in a liquid (“electrohydraulic discharges”) inactivate microorganisms suspended in the liquid. The intense pulse of UV radiation emitted from the plasma formed between the electrodes causes most of the bactericidal effects, rather than shock waves, or free radicals or other chemical species formed in the liquid medium. A method of sterilizing materials without contamination from electrode debris is described. Possible applications and limitations of the technique are outlined.
Purification of ten transfer riboiiucleic acids from E. coli K‐12 MO
Authors: Weeren H. O. , Ryon A. D. , Kelmers A. D. 
Published: December 2004

AbstractA flowsheet has been developed which leads to the purification of 10 transfer ribonucleic acids (tRNAs) from E. coli K‐12 MO. Crude tRNAs were recovered by phenol extraction and two ethanol precipitation steps. The initial separation of the crude tRNA mixture was achieved by RPC‐3 reversed‐phase chromatography. Following rechromatography under other conditions, the following tRNAs were recovered at a purity of 70 to 100%: arginine, aspartic acid, glutamic acid, lysine, formylmethionine‐1, formylmethionine‐3, normal methionine, phcnylalanine‐1, phenylalaninc‐2, and valine. Recoveries for these tRNAs ranged from 15 to 60%. The flowsheet was demonstrated with chromatogaphic runs ranging from 1,300 to 250,000 A260 units per run. The chromatographic steps were simple and readily reproducible.
Lysozyme activity in the presence of nonionic detergent micelles
Authors: Bernath F. R. , Vieth W. R. 
Published: December 2004

AbstractThe effect of a nonionic surfactant, polyoxyethylenesorbitan monolaurate (Tween 20), on the hen egg‐white lysozyme catalyzed lysis of a dried cell suspension of Micrococcus lysodeikticus is analysed. A rate enhancement of up to 70% is observed in the presence of surfactant at concentrations above the critical micelle concentration. This activity increase may be explained by postulating the existence of a micelle‐enzyme complex in which enzyme molecules are bound to micelles with preferential orientation of their active sites.The reaction is found to be second order with respect to substrate. A mechanism is postulated in which a substrate particle is assumed to be an energy‐furnishing collision partner to the enzyme‐substrate complex. This mechanism correlated data over a wide range of enzyme and substrate concentrations.Data from kinetic, ultrafiltration, ultraviolet, and fluorescence studies provide convincing evidence for the existence of a micelle‐lysozyme complex. The results suggest that it is possible that immobilized enzymes mat in general be more reactive than corresponding free enzymes.
Large scale synthesis of dinucleoside monophosphates catalyzed by ribonuclease from Aspergillus clavatus
Authors: Bauer S. , Lamed R. , Lapidot Y. 
Published: December 2004

AbstractA gram scale enzymatic synthesis of eight, dinucleoside monophosphates (ApC, ApU, CpC, CpU, GpC, GpU, UpC, and UpU) is described. The synthesis involves a reaction between the appropriate ribonucleoside‐2′,3′‐cyclie phosphates and cytidine or uridine in the presence of ribonuelease from Aspergillus clavatus at 30°C. The enzyme is removed from the reaction mixture by chromatography on Bio‐Gel P–4, and the dinucleoside monophosphate is further purified by chromatography on a DEAE‐Sephadex A–25, column.A procedure for the large scale preparation of the ribonuclease from Aspergillus clavatus is also described.