bluuebunny/crossref_metadata_2025_split huggingface dataset:
Relationship between conformation and physicochemical properties of polypeptides. I. Synthesis of homo‐ and co‐oligopeptides by the liquid‐phase method
Authors: El Rahman S. Abd , Anzinger H. , Mutter M. 
Published: December 2004

AbstractThe synthesis of the following oligo‐ and co‐oligopeptides by the liquid‐phase method is described: (L‐Met)15 (I), [L‐Glu(OBzl)]20 (II), (L‐Val)8‐Gly (IV), (L‐Ile)8‐Gly (V), (L‐Ile)4‐Gly‐(L‐Ile)4 (VI), (L‐Ile)4‐Pro‐(L‐Ile)4 (VII), (L‐Met)5‐L‐Pro‐(L‐Met)5 (VIII), [L‐Glu(OBzl)]7‐L‐Pro‐[L‐Glu(OBzl)]7 (IX). The oligomers are covalently bound to bifunctional polyethylene glycol (PEG) and monofunctional PEG‐M of Mr 5 × 103−2 × 104. Analytical controls were carried out after each step of synthesis in order to ensure quantitative coupling yields. All products could be obtained in high purity as indicated by amino acid analysis, thin‐layer chromatography and chiroptical methods. The solubility of the oligomers was strongly enhanced by the presence of the C‐terminal PEG group, enabling conformational investigations in a variety of solvents. A significant relationship between conformation and physicochemical properties of the oligopeptides was observed. Oligomers with tendencies to adopt α‐helical (I, II) or unordered structures (VI–IX) showed no pronounced change in solubility or coupling kinetics during chain elongation, whereas the onset of a β‐structure (IV, V) was paralleled by a drastic decrease in solubility and reactivity of the terminal amino groups. Most notably, the insertion of a proline or glycine in the middle of a β‐forming peptide chain (VI, VII) resulted in a considerable increase in solubility compared to the corresponding homo‐oligomers. The impact of the conformational properties of a peptide chain on strategic considerations of peptide synthesis in solution is delineated.
Circular dichroism and conformational analysis of the membrane‐modifying peptide ‐N‐t‐Boc‐(Aib‐L‐Ala)5‐Gly‐Ala‐Aib‐Pro‐Ala‐Aib‐Aib‐Glu‐(OBzl)‐Gln‐OMe with respect to alamethicin
Authors: Oekonomopulos R. , Jung G. 
Published: December 2004

AbstractThe conformational analysis of the CD spectrum is reported for the synthetic and membrane‐modifying nonadecapeptide analog of alamethicin N‐t‐Boc‐(Aib‐L‐Ala)5‐Gly‐Ala‐Aib‐Pro‐Ala‐Aib‐Aib‐Glu(OBzl)‐ Gln‐OMe. The CD data are evaluated according to three different methods and are discussed with respect to those obtained from natural alamethicin and suitable models such as N‐t‐Boc‐(Aib‐L‐Ala)7‐OPOE, fragments of the synthetic nonadecapeptide, and the hexadecapeptide N‐t‐Boc‐(Aib‐L‐Ala)5‐Pro‐Ala‐Aib‐Aib‐Glu(OBzl)‐Gln‐OMe. The synthetic nonadecapeptide with the longer helical region exhibits membrane activities comparable to those of alamethicin, whereas the hexadecapeptide with the shorter helix is inactive.
Heat capacities of transfer of some amino acids and peptides from water to aqueous urea solution
Authors: Prasad K. P. , Ahluwalia J. C. 
Published: December 2004

AbstractIntegral enthalpies of solution at low concentrations of several amino acids and peptides in 2 and 6M urea solutions have been determined at 25 and 35°C. These data have been used to derive the enthalpies of transfer (at 25 and 35°C) and heat capacities of transfer (at 30°C) of these amino acids and peptides from water to aqueous urea solutions. Furthermore, the enthalpies of transfer and heat capacities of transfer per CH2 group and per peptide group CONH have also been estimated. These results show that while the enthalpies and heat capacities of transfer per CH2 group are positive and negative, respectively, the reverse is true for CONH group. The implications of these results in the mechanism of the denaturation of proteins by urea are discussed.
Synthesis and ordered structure of amphipatic block copolymers with a saccharide and a peptide block
Authors: Douy André , Gallot Bernard 
Published: December 2004

AbstractAmphipatic block copolymers (OβEb) with a hydrophilic saccharide block and a hydrophobic polypeptide block were synthesized. In these copolymers the saccharide block is the glyco‐amino acid Oβ from ovomucoid and the peptide block (Eb) is a poly(γ‐benzyl‐L‐glutamate) block. Copolymers OβEb exhibit, in the solid state and in Me2SO concentrated solutions, mesomorphic lamellar structures where the polypeptide chains are in an α‐helical conformation. Depending on the molecular weight of the polypeptide block, three types of lamellar structures are obtained, and they differ by the mode of organization of the polypeptide chains in their lamellae and by the T or Y conformation of the saccharide block.
Thermoelasticity of swollen elastin networks at constant composition
Authors: Andrady A. L. , Mark J. E. 
Published: December 2004

AbstractThermoelastic (force–temperature) measurements were carried out on elastin networks, swollen with a nonvolatile diluent, in elongation over the temperature range 8–35°C. The experiments were conducted at constant composition (thermodynamically closed system) rather than at swelling equilibrium (open system), thus avoiding the need for approximate corrections to account for the changes in swelling with temperature and with elongation. The results indicate that the elastic force is primarily of entropic origin and thus support the random‐network model rather than the liquid‐drop model for elastin in the rubberlike state. A significant energetic contribution to the force was observed, however, as is usually the case for a variety of elastomeric polymers.
Simulation methods for protein structure fluctuations
Authors: Northrup Scott H. , McCammon J. Andrew 
Published: December 2004

AbstractThree numerical techniques for generating thermally accessible configurations of globular proteins are considered; these techniques are the molecular dynamics method, the Metropolis Monte Carlo method, and a modified Monte Carlo method which takes account of the forces acting on the protein atoms. The molecular dynamics method is shown to be more efficient than either of the Monte Carlo methods. Because it may be necessary to use Monte Carlo methods in certain important types of sampling problems, the behavior of these methods is examined in some detail. It is found that an acceptance ratio close to 1/6 yields optimum efficiency for the Metropolis method, in contrast to what is often assumed. This result, together with the overall inefficiency of the Monte Carlo methods, appears to arise from the anisotropic forces acting on the protein atoms due to their covalent bonding. Possible ways of improving the Monte Carlo methods are suggested.
Fluctuations of protein structure as expressed in the distribution of hydrogen exchange rate constants
Authors: Knox Donald G. , Rosenberg Andreas 
Published: December 2004

AbstractHydrogen exchange kinetics of proteins provide information about the dynamics of their structure. The interpretation of experiments has been limited by difficulty in identifying individual rate constants. In order to invert the kinetic data, and to gain information about the individual reacting sites, we introduce a Laplace inversion technique and obtain the distribution function of rate constants by which the intricate reaction proceeds. A series of carefully overlapped experiments were performed on lysozyme at 25°C, an exchange profile obtained, and a distribution function extracted. This function was composed of a product of two terms, indicating two parallel pathways. The first, a power‐law term, was attributed to exchange from the native state. This part of the distribution function thus describes the scope of the conformational fluctuations in proteins at constant temperature and pressure. The second, an exponential, was seen to be associated with the pathway involving thermal unfolding and subsequent free exchange with the solvent. The influence of trichlorethanol and glycerol on the total distribution function was measured. Trichloroethanol selectively increased the contribution from the thermal unfolding pathway, whereas glycerol, besides decreasing this type of contribution, increased the width of the distribution function attributed to structural fluctuations.
15N‐nmr spectroscopy. 20. Cis/trans isomerism and neighboring residue effects of proline‐containing peptides
Authors: Hull William E. , Kricheldorf Hans R. 
Published: December 2004

AbstractFive N‐protected tetrapeptide esters of the structure Gly‐Pro‐X‐X*‐O‐methyl were synthesized in such a way that one of the two variable amino acid residues (X) was isotopically enriched in 15N (denoted by*). The variable amino acids are glycine, alanine, leucine, valine, and phenylalanine. For the natural abundance 15N‐nmr spectra of these tetrapeptide derivatives in methylene chloride only the signals of the Gly‐Pro trans isomer were found. In a 2:1 mixture of acetone and dimethylsulfoxide, signals for both the cis and trans isomers were observed. Three of the five tetrapeptide derivatives show cis/trans splitting of all four nitrogen signals. The 15N‐nmr spectra of Z‐Pro‐Pro‐OH and of (D,L‐proline)n were measured in a 2:1 mixture of acetone and dimethylsulfoxide as well as in water. The effects of solvents and neighboring residues and the influence of the cis/trans isomerism on the nmr spectra are discussed. The determination of the cis/trans equilibria and the assignment of the 15N‐nmr signals of all oligopeptides were achieved by selective isotopic enrichment and by means of 13C‐nmr spectra.
Effect of counterions on complex coacervation
Authors: Tainaka Kei‐Ichi 
Published: December 2004

AbstractIn a recent paper, we developed a thermodynamic theory on the complex coacervation in the absence of low molecular ions, under the assumption that the coacervation is a condensation phenomenon of aggregates of polyanion and polycation in the aqueous solution, by obtaining the interaction potential US between these aggregates on the basis of Flory's method. In this paper, we have extended the theory to a more complicated phenomenon of the counterion‐containing solutions. This treatment has led the interaction potential having an additional contribution to US resulting from an entropy increase by the counterion distribution. The phase diagram between solution (sol) and separated phase has been obtained as a function of the difference of charges between polyanion and polycation. It has been found that the presence of counterions sensitively suppresses the coacervation.
Thermal stability and renaturation of DNA in dimethyl sulfoxide solutions: Acceleration of the renaturation rate
Authors: Escara June F. , Hutton James R. 
Published: December 2004

AbstractThe thermal stability and renaturation kinetics of DNA have been studied as a function of dimethyl sulfoxide (DMSO) concentration. Increasing the concentration of DMSO lowers the melting temperature of DNA but results in an increased second‐order renaturation rate. For example, in a DNA solution containing 0.20M NaCl, 0.01M Tris (pH 8.0), and 0.001M EDTA, the addition of 40% DMSO lowers the melting temperature of the DNA by 27°C and approximately doubles the optimal renaturation rate. The effect of DMSO on the renaturation rate is shown to be at least partially due to its effect on the solution dielectric constant and to be consistent with the polyelectrolyte counterion condensation theory of Manning [(1976) Biopolymers 15, 1333–1343].
Dynamic light scattering studies of internal motions in DNA. II. Clean viral DNAs
Authors: Thomas J. C. , Allison S. A. , Schurr J. M. , Holder R. D. 
Published: December 2004

AbstractInternal Brownian motions of clean ϕ29 and λ‐DNAs have been studied using photon‐correlation techniques at both visible (λ0 = 632.8 nm) and uv (λ0 = 363.8 nm) wavelengths. The present dynamic light scattering data, which extend to K2 = 19 × 1010 cm−2, can in every case be satisfactorily simulated by a Rouse‐Zimm model polymer with an appropriate choice of the three model parameters. The effects of pH, salt concentration, single‐strand breaks, and molecular weight on those model parameters have also been investigated. Intact clean DNAs exhibit surprisingly little variation with pH from 7.85 to 10.25, with salt concentration from 0.01 NaCl to 5.4M NH4Cl, or with molecular weight or GC content. The single‐strand breaks have no effect at pH 9.46, but produce dramatic changes in the model parameters at pH 10.0 and 10.25, indicating the introduction of titratable joints at those pHs. The failure of either single‐strand breaks or a large change in GC content to alter the model parameters in the neutral pH range is a strong indication that local denaturation is not required for those flexions and torsions that dominate the relaxation of fluctuations in the scattered light. The Langevin relaxation time for the slowest internal mode of a particular Rouse‐Zimm model derived from the dynamic light scattering data is compared with pertinent literature data extrapolated to the same molecular weight. The present algorithm for determining model parameters from the light‐scattering Dapp vs K2 curve actually yields a Langevin time in fairly good agreement with the literature value. For unknown reasons the light‐scattering D0 values generally exceed those obtained from the molecular weight and sedimentation coefficient by about 20%.
Activity coefficients of counterions and conformation in kappa‐carrageenan systems
Authors: Rochas C. , Rinaudo M. 
Published: December 2004

AbstractThe optical rotation and the conductivity of kappa‐carrageenans in aqueous solution have been investigated as functions of temperature in the presence of various electrolytes. The activity coefficients of sodium and potassium have been determined and correlated with the conformation. The potassium activity coefficient under ordered conformation is in agreement with a mechanism of dimerization.
1H‐nmr study of protected methionine homo‐oligopeptides in helix‐supporting environment
Authors: Naider Fred , Ribeiro Anthony A. , Goodman Murray 
Published: December 2004

Abstract1H‐nmr spectra for a series of Boc‐L‐(Met)n‐OMe (n = 2–9) homo‐oligopeptides have been observed in the helix‐supporting solvent trifluoroethanol (TFE) at millimolar concentrations. Interfering solvent peaks were eliminated using two decoupling frequencies to selectively remove the methylene and hydroxyl protons of the solvent. Comparisons with specifically α‐deuterated homo‐oligopeptides gave complete assignments of the NH region of the Boc‐Metn‐OMe oligomers up to the heptapeptide. Analysis of chemical shifts, coupling constants, and temperature dependence of chemical shifts suggests that up to the hexapeptide, similar structures exist in deuterochloroform and TFE. In contrast, nmr parameters at the heptapeptide for several internal residues differ in these solvents. These results suggest that a C7 to α‐helix transition may occur in TFE as the chain length of the methionine oligopeptides increases.
Sedimentation‐equilibrium studies of the polysaccharide components of Pseudomonas aeruginosa
Authors: Horton Derek , Riley David A. , Hansen Poul M. T. 
Published: December 2004

AbstractMild acid hydrolysis of lipopolysaccharide antigens from seven different serotype strains antigen immunotypes nos. 1–7 [in the classification of Fisher, M. W., Devlin, H. B. & Gnabasik, F. J. (1969) J. Bacteriol. 98, 835–836] of Pseudomonas aeruginosa gave polysaccharide components of high molecular weight, which were isolated by gel filtration and dialysis. These components were examined by ultracentrifugation at equilibrium with the Rayleigh interferometric optical system. The partial specific volumes were calculated from densities obtained by using a mechanical oscillator. The average molecular weights (Mn, Mw, and Mz) were calculated and compared to evaluate the polydispersity of the polysaccharides. The nonideality was investigated by varying the rotor speed, the height of the solution column, and the concentrations of the polysaccharide fractions. The molar masses were found to range from 14,000 for the polysaccharide from immunotype two to 24,000 for that from immunotype one, when extrapolated to zero rotor speed and solution column height.
Hydrodynamic resistance and diffusion coefficients of a freely hinged rod
Authors: Wegener William A. 
Published: December 2004

AbstractThe seven‐dimensional hydrodynamic resistance and diffusion tensors are evaluated for a rod which is freely hinged at its center and immersed in a viscous fluid. The hydrodynamic resistance tensor is first determined at the hinge, then transformed to other points and inverted to obtain the diffusion tensor. Hydrodynamic interactions between rod halves are neglected, which is asymptotically correct for long rods. In the long‐rod limit, the diffusion coefficient characterizing translations over macroscopic distances is decreased by 3–6% from that for a rigid straight rod of same total length, while the average end‐over‐end rotational diffusion coefficient for each rod half is increased 4.67 times.
Conformational energy studies on N‐methylated analogs of thyrotropin releasing hormone, enkephalin, and luteinizing hormone‐releasing hormone
Authors: Manavalan Parthasarathy , Momany Frank A. 
Published: December 2004

AbstractEmpirical conformational energy calculations have been carried out for N‐methyl derivatives of alanine and phenylalanine dipeptide models and N‐methyl‐substituted active analogs of three biologically active peptides, namely thyrotropin‐releasing hormone (TRH), enkephalin (ENK), and luteinizing hormone‐releasing hormone (LHRH). The isoenergetic contour maps and the local dipeptide minima obtained, when the peptide bond (ω) preceding the N‐methylated residue is in the trans configuration show that (1) N‐methylation constricts the conformational freedom of both the ith and (i + 1)th residues; (2), the lowest energy position for both residues occurs around ϕ = −135° ± 5° and ψ = 75° ± 5°, and (3) the αL conformational state is the second lowest energy state for the (i + 1)th residue, whereas for the ith residue the C5 (extended) conformation is second lowest in energy. When the peptide bond (ωi) is in the cis configuration the ith residue is energetically forbidden in the range ϕ = 0° to 180° and ψ = −180° to +180°. Conformations of low energy for ωi = 0° are found to be similar to those obtained for the trans peptide bond. In all the model systems (irrespective of cis or trans), the αR conformational state is energetically very high. Significant deviations from planarity are found for the peptide bond when the amide hydrogen is replaced by a methyl group. Two low‐energy conformers are found for [(N‐Me)His2]TRH. These conformers differ only in the ϕ and ψ values at the (N‐Me)His2 residue. Among the different low‐energy conformers found for each of the ENK analogs [D‐Ala2,(N‐Me)Phe4, Met5]ENK amide and [D‐Ala2,(N‐Me)Met5]ENK amide, one low‐energy conformer was found to be common for both analogs with respect to the side‐chain orientations. The stability of the low‐energy structures is discussed in the light of the activity of other analogs. Two low‐energy conformers were found for [(N‐Me)Leu7]LHRH. These conformations differ in the types of bend around the positions 6 and 7 of LHRH. One bend type is eliminated when the active analog [D‐Ala6,(M‐Me)Leu7]LHRH is considered.
Effect of ionic strength on the pKa of ligands bound to DNA
Authors: Jones Robert L. , Wilson W. David 
Published: December 2004

AbstractThe pKa of 3,8‐diamino‐6‐phenyl‐phenanthridine (DAPP), a nonquaternary analog of ethidium bromide, has been determined spectrophotometrically as a function of sodium ion concentration both free in solution and complexed to DNA. Unwinding angle determinations with this compound were determined with Col El DNA using ethidium bromide as a standard. The unwinding angle for DAPP was 24 ± 2° relative to 26° for ethidium, and this suggests that DAPP binds in a manner quite similar to ethidium and with no significant outside bound DAPP under these experimental conditions. Isobestic behavior was obtained on spectrophotometric pH titration above pH 5 as long as the ratio of DNA‐phosphate to ligand was between 100 and 300 and the DNA phosphate concentration was approximately 0.01M or greater. The loss of isosbestic behavior which occurred below pH 5 is probably due to titration of the 8 amino group of the ligand complexed to DNA. To circumvent this problem, pKa values and the extinction coefficient of the acidic species were both determined by a computer program using experimental data obtained above pH 5. The pKa of the free compound has only a minor dependence on ionic strength, while the pKa of the ligand bound to DNA in an intercalated complex depends strongly on the sodium ion concentration. The pKa of the DAPP‐DNA complex is a linear function of –log[Na+] as predicted by the ion‐condensation theory of polyelectrolytes. It was determined that DAPP is essentially completely bound to DNA under the conditions of these experiments by (1) determination of apparent pKa values as a function of total DNA concentration, (2) calculation of binding constants for the neutral species of DAPP, and (3) spectral analysis of the protonated and neutral species of DAPP bound to DNA relative to DAPP free in solution. These results support the ion‐condensation theory; provide an independent method for measuring ψ*, the average number of counterions associated per phosphate of DNA in the intercalated conformation; and illustrate that there are no specific pH effects or absolute pKa values for ligands bound to DNA, but only ionic‐strength‐dependent results.