Showing papers in "Biopolymers in 1980"
TL;DR: 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.
Abstract: The 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) Biopolymers15, 1333–1343].
291 citations
TL;DR: In this article, the optical rotation and conductivity of kappa-carrageenans in aqueous solution have been investigated as functions of temperature in the presence of various electrolytes.
Abstract: The 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.
241 citations
TL;DR: In this paper, 13C-nmr spectra of red seaweed galactans, belonging to the agar and carrageenan groups or having the intermediate type of structure, were interpreted on the basis of 13Cnm r spectra for model compounds.
Abstract: 13C-nmr spectra of red seaweed galactans, belonging to the agar and carrageenan groups or having the “intermediate” type of structure, were interpreted on the basis of 13C-nmr spectra of model compounds. Signal assignments have been made for most of the known extreme structures of such galactans. 13C-nmr spectroscopy was shown to be a rapid and convenient method of structural analysis, which permits one to determine the type of galactan structure, the absolute configurations of its constituents (galactose and 3,6-anhydrogalactose), and the positions of the sulfate and O-methyl groups in a polysaccharide molecule.
186 citations
TL;DR: In this article, the Poisson-Boltzmann distribution of counterions around polyelectrolytes in solutions containing finite salt concentrations was computed and site binding was shown to be significant.
Abstract: We have computed the Poisson-Boltzmann distribution of counterions around polyelectrolytes in solutions containing finite salt concentrations. The polyelectrolytes considered here are highly charged in the sense that ξ > 1, ξ being the linear charge density parameter for cylinders, which is generalized by us to other shapes.
Contrary to the situation at zero salt concentration, the counterion distribution is not strongly shape dependent, being similar for cylinders or spheres which have the same superficial charge density and radius of curvature Rc. The distribution resembles that in the neighborhood of a plane with the same charge density.
Three regions are distinguished. (1) In the “inner region” which extends up to a distance Rc/2ξ from the surface, the counterion distribution is essentially salt independent. The counterion concentration in the immediate vicinity of the polyelectrolyte surface (CIV) is quite high, typically 1–10M, and proportional to the square of the surface charge density, which is its main determinant. (2) An intermediate region extends out to a distance where the electrostatic potential is equal to κT/e. This distance is comparable to λ for plane and cylinder, and smaller for the sphere. (3) In the outer region, the distribution is hardly influenced by the details of the inner region, on which it cannot, therefore, give much information. Colligative properties are dependent on the distribution in the outer region and are fairly well predicted even by a rudimentary theory.
The large value of the CIV implies that site binding must often be significant. It can be computed by applying the mass-action law to site-bound counterions in equilibrium with the counterions in the neighborhood, whose concentration is the CIV, the relevant equilibrium constant being that for the binding of counterions to isolated monomer sites. Because the CIV is insensitive to salt concentration, this will also be the case for site binding. With the graphs provided, one can compute the extent of sitebinding within the Poisson-Boltzmann framework.
The “condensation radius,” i.e., the radius encompassing a counterionic charge 1 − ξ−1 around a cylinder, is found to be large. It varies with salt concentration and tends to infinity as the salt is diluted. Neither this radius nor the charge fraction 1 − ξ−1 of condensation theory plays any special role in the counterion distribution.
The “finite-salt” results apply to salt concentrations, typically as low as 1–10 mM. This encompasses, among others, all experiments on biological polyelectrolytes.
163 citations
TL;DR: The results show that in the amide I region, β‐turn frequencies can overlap with those of the α‐helix and β‐sheet structures, and therefore caution must be exercised in the interpretation of protein bands in this region.
Abstract: modes are given for the latter three structures. Calculations have been done for structures with standard dihedral angles, as well as for structures whose dihedral angles differ from these by amounts found in protein structures. The force field was that refined in our previous work on polypeptides. Transition dipole coupling was included, and is crucial to predicting frequency splittings in the amide I and amide I1 modes. The results show that in the amide I region, P-turn frequencies can overlap with those of the cu-helix and @-sheet structures, and therefore caution must be exercised in the interpretation of protein bands in this region. The amide I11 modes of 0-turns are predicted at significantly higher frequencies than those of (?-helix and 0-sheet structures, and this region therefore provides the hest possibility of identifying 0-turn structures. Amide V frequencies of fl-turns may also he distinctive for such structures.
152 citations
TL;DR: It is demonstrated from a theoretical analysis of the ionic‐strength dependence of the rate of denaturation of DNA that the above statements are restricted in their validity to radii of curvature greater than 170 Å; beyond this limit, the steeply rising repulsive energy of tightly packed atoms dominates the bending free energy.
Abstract: A thermodynamic analysis of the bending free energy of DNA, initiated previously, is extended. It was demonstrated that the ionic-strength dependence of the persistence length of DNA in aqueous NaCl can be understood by postulating (1) a rigid-rod 60 base-pair unit and (2) a negative contribution from nonelectrostatic sources to the bending free energy of this unit. On electrostatic neutralization of the phosphate charge, the latter term alone survives, and bending becomes a spontaneous process. In this paper it is demonstrated from a theoretical analysis of the ionic-strength dependence of the rate of denaturation of DNA that the above statements are restricted in their validity to radii of curvature greater than 170 A; beyond this limit, the steeply rising repulsive energy of tightly packed atoms dominates the bending free energy. Therefore, spontaneous bending on charge neutralization proceeds up to, but not beyond, this barrier to curvature. It is noted that doughnut forms of DNA induced by binding of cationic spermidine, or mixtures of Mg2+ and polyamines are observed to possess maximum curvatures, corresponding to the radius of the “hole in the middle,” in the range 1/150–1/200 A.
99 citations
TL;DR: Empirical 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‐re releasing hormone (LHRH).
Abstract: Empirical 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.
98 citations
TL;DR: Calculated amide III frequencies extend above 1300 cm−1, providing a compelling assignment of the 1303‐cm−1 band in insulin and similar bands in other globular proteins.
Abstract: The normal modes have been calculated for structures having the dihedral angles of the four β-turns of insulin. Frequencies are predicted in the amide I region near 1652 and 1680 cm−1. The former overlaps the α-helix band at 1658 cm−1 in the Raman spectrum, while the latter accounts for the hitherto unassignable band at 1681 cm−1. Calculated amide III frequencies extend above 1300 cm−1, providing a compelling assignment of the 1303-cm−1 band in insulin and similar bands in other globular proteins.
94 citations
TL;DR: In this paper, a simplified model of a polypeptide chain is described, where each residue is represented by a single interaction center and the energy of the chain and the force acting on each residue are given as a function of the residue coordinates.
Abstract: A simplified model of a polypeptide chain is described. Each residue is represented by a single interaction center. The energy of the chain and the force acting on each residue are given as a function of the residue coordinates. Terms to approximate the effect of solvent and the stabilization energy of helix formation are included. The model is used to study equilibrium and dynamical aspects of the helix–coil transition. The equilibrium properties examined include helix–coil equilibrium constants and their dependence on chain position. Dynamical properties are examined by a stochastic simulation of the Brownian motion of the chain in its solvent surroundings. Correlations in the motions of the residues are found to have an important influence on the helix–coil transition rates.
91 citations
TL;DR: In this article, light-scattering, viscosity, and sedimentation experiments on aqueous solutions of k-carrageenan were conducted to show that this sulfated polygalactose is an expanded flexible random coil.
Abstract: Light-scattering, viscosity, and sedimentation experiments on aqueous solutions of k-carrageenan show that this sulfated polygalactose is an expanded flexible random coil. This expansion is due to long-range interactions that are predominantly electrostatic. Extrapolation of viscosity data to infinite ionic strength provided values for the intrinsic viscosity which were subjected to the Stockmayer-Fixman analysis, giving a value for the Mark-Houwink coefficient under theta-conditions, Kθ, of 0.27. The characteristic ratio, C∞, under these conditions is 7.8, and the conformation factor σ is 2. In a solution of 0.118 ionic strength, where a Mark-Houwink exponent aη of 0.86 is found, the radii of gyration calculated from viscosity data are lower than those found from the angular dependence of scattered light. On the other hand, the radius of gyration found from the sedimentation rate agrees well with the light-scattering radius. The relations between molecular parameters are corrected for the poly-dispersity of the sample.
89 citations
TL;DR: Double bends, in which the signs of two successive virtual‐bond dihedral angles differ, have conformations that are very different from an α‐helix and may play an important role in protein folding because they occur fairly frequently in proteins and cause major changes in the direction of the polypeptide chain.
Abstract: The concept of bends or chain reversals [nonhelical dipeptide sequences in which the distance R3 (i,i+3) between the Cα atoms of residues i and i+3 is ≦ 7.0 A] has been extended to define double bends as tripeptide sequences, not in an α-helix, in which two successive distances R3(i,i+3) and R3 (i+1, i+4) are both ≦7.0 A, with analogous definitions for higher-order multiple bends. A sample of 23 proteins, consisting of 4050 residues, contains 235 single, 58 double, and 11 higher-order multiple bends. Multiple bends may occur as combinations of the “standard” type I, II, and III chain reversals (as well as their mirror images), but usually they require distortions from these well-defined conformations. The frequency of occurrence of amino acids often differs significantly between single and multiple bends. The probability distribution of R3 distances does not differ in single and multiple bends. However, R4 (the distance between the Cα atoms of residues i and i+4) in multiple bends is generally shorter than in tripeptide sequences containing single bends. The value of R4 in many multiple bends is near those for α-helices. In some other multiple bends, R4 is even shorter, indicating that these structures are very compact. The signs of the dihedral angles about the virtual bonds connecting Cα atoms and the values of curvature and torsion, as defined by means of differential geometry, indicate that there is a preference for single and multiple bends to be right-handed (like an α-helical sequence, for example) and that there is a strong tendency to conserve the handedness in both single-bend components of many multiple bends. These often have a strong resemblance to distorted single turns of an α-helix and do not constitute chain reversals. Double bends, in which the signs of two successive virtual-bond dihedral angles differ, have conformations that are very different from an α-helix. They act as chain reversals occuring over three residues. These chain reversals have not been described previously. Multiple bends may play an important role in protein folding because they occur fairly frequently in proteins and cause major changes in the direction of the polypeptide chain.
TL;DR: In this paper, closed random Gaussian polygonal chains of equal length b and thickness d have been generated on a computer and the knot type, the writhing number w, the radius of gyration, and the average of the inverse of the distance between two apices have been determined for each chain.
Abstract: Closed random Gaussian polygonal chains of N (6 < N < 150) bonds of equal length b and thickness d have been generated on a computer. The knot type, the writhing number w, the radius of gyration, and the average of the inverse of the distance between two apices have been determined for each chain. For all the studied knot types—0, 31, 41, 51, and 52—the probability density of finding a given w is Gaussian. The Gaussian is centered about 0 for the amphichiral knots. Therefore, for long circular DNAs, the contribution to the supercoiling energy, which depends on w only, may be considered as purely entropic and may be expressed as ARTw2/N, in agreement with previous semiempirical considerations. The parameter A increases with chain thickness, it decreases as N gets larger but rapidly reaches a plateau. Comparison with experimental data from the literature would suggest that the ratio of the writhing to the constraint increases with ionic strength. The ratio of sedimentation constant of the supercoiled DNA to the sedimentation constant of the nicked DNA varies as N1/4 (w/N)2, and therefore depends on the writhing density and on the length of the DNA.
TL;DR: A general formalism for calculating translational and rotational transport properties, as well as intrinsic viscosities, of rigid macromolecules with an arbitrary shape is proposed in this paper, which can be regarded as a generalization of the one proposed by Nakajima and Wada.
Abstract: A general formalism, which includes translation–rotation coupling, is proposed for calculating translational and rotational transport properties, as well as intrinsic viscosities, of rigid macromolecules with an arbitrary shape. This formalism is based on Brenner's theory of translational–rotational dynamics and on methods for the calculation of hydrodynamic properties that have been already presented, and can be regarded as a generalization of the one proposed by Nakajima and Wada. The calculated transport properties depend on the origin as predicted by Brenner's theory, but in a disagreement with him, the center of resistance and the center of diffusion do not coincide. As one can define several hydrodynamic centers, which in practice turn out to be located at different points, the influence of the choice of the center on the calculated transport properties is discussed. An analysis of the translation–rotation coupling effects in translational diffusion reveals that they arise exclusively from hydrodynamic interactions and are rather small in some cases of interest. Finally, we present a study of the rotational diffusion of rigid bent rods with a fixed length-to-diameter ratio. The diffusion coefficients obtained can be useful to estimate changes with respect to a straight rod.
TL;DR: In this article, the authors developed a thermodynamic theory on the complex coacervation in the absence of low molecular ions, under the assumption that the co-acervation 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.
Abstract: In 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.
TL;DR: In this article, the dependence of the apparent pK with the degree of neutralization and the nature of counterions (Na or Ca) of galacturonic oligomers and polymers is discussed.
Abstract: The potentiometric data concerning the dependence of the apparent pK with the degree of neutralization and the nature of counterions (Na or Ca) of galacturonic oligomers and polymers are discussed. They are characterized by an apparent charge density λapp which predicts their electrostatic behavior. The calculated osmotic coefficients from Katchalsky and Manning's theories are in good agreement with the experimental data obtained by potentiometry. The dependence of the osmotic coefficient (ϕCa) as a function of the polymer concentration is established by potentiometry and interpreted in terms of a multichain aggregation. In addition, it is proven that no Ca2+ is ever fixed in excess of stoichiometry. The dependence of CD spectra obtained under the same conditions as the pK measurements shows analogies between the two sets of results. The CD data, in agreement with 13C-nmr measurements, suggest that in dilute solutions the polymer adopts two conformations: one (acidic form) which may be represented by threefold screw symmetry and a second (Na or Ca form) which can be related to a twofold screw symmetry. The twofold screw symmetry is known to allow the formation of cooperative “egg-box” fixation of Ca without conformation change.
TL;DR: The effect of solvent, temperature, and ionic strength on the dimerization process is investigated and the results obtained differ markedly from previously published results, and possible reasons for this difference are discussed.
Abstract: The self-association of daunorubicin in aqueous solution has been examined using visible absorption, fluorescence, and CD measurements. Spectral changes in the concentration range 10−6 to 1.5 × 10−3M have been interpreted in terms of a monomer–dimer equilibrium for daunorubicin. The data have been analyzed using a nonlinear curve-fitting technique. The results obtained in this study differ markedly from previously published results, and possible reasons for this difference are discussed. The effect of solvent, temperature, and ionic strength on the dimerization process is investigated.
TL;DR: In this paper, a comparison of the light-scattering and viscosity data indicated that Φ in the Flory-Fox equation is lower than for more flexible polymers and increases with molecular weight, probably due to decreasing hydrodynamic permeability.
Abstract: Sodium alginate fractions derived from three different sources—Laminaria hyperboria (75% guluronate), Fucus vesicularus (95% mannuronate), and Azotobacter vinelandii (85% mannuronate)—were investigated in aqueous solution over a wide range of ionic strength and pH using the techniques of light scattering, viscometry, and osmometry. Light-scattering data extrapolated to infinite ionic strength yielded b0 = 4.7 ± 0.3 and 3.0 ± 0.2 nm for the unperturbed effective bond lengths of the guluronate- and mannuronate-rich samples, respectively. These values are in the same ratio as predicted by conformational analysis, although lower by a factor of 0.7, probably due, in part at least, to the fact that measurements cannot be made on pure homopolymers. A comparison of the light-scattering and the viscosity data indicated that Φ in the Flory-Fox equation is lower than for more flexible polymers and increases with molecular weight, probably due to decreasing hydrodynamic permeability. Mark-Houwink exponents obtained from data extrapolated to infinite ionic strength were found to be considerably greater than 0.5, and we attribute this entirely to a variation in Φ. Comparison of the results obtained for the two mannuronate-rich samples indicated that the value of Φ and its variation with molecular weight can, in the case of alginates, differ markedly for chains, which, although having chemical differences, have similar chain statistics.
TL;DR: The molecular dynamics method is shown to be more efficient than either of the Monte Carlo methods, and an acceptance ratio close to 1/6 yields optimum efficiency for the Metropolis method, in contrast to what is often assumed.
Abstract: Three 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.
TL;DR: The probability of occurrence of helix and β‐sheet residues in 47 globular proteins was determined as a function of local hydrophobicity, which was defined by the sum of the Nozaki‐Tanford transfer free energies at two nearest‐neighbors on both sides of the amino acid sequence.
Abstract: The probability of occurrence of helix and ..beta..-sheet residues in 47 globular proteins was determined as a function of local hydrophobicity, which was defined by the sum of the Nozaki-Tanford transfer free energies at two nearest-neighbors on both sides of the amino acid sequence. In general, hydrophilic amino acids favor neither helix nor ..beta..-sheet formations when neighbor residues are also hydrophilic but favor helix formation at higher local hydrophobicity. On the other hand, some hydrophobic amino acids such as Met, Leu, and Ile favor helix formation when neighbor residues are hydrophilic. None of the hydrophobic amino acids favor ..beta..-sheet formation with hydrophilic neighbors, but most of them strongly favor ..beta..-sheet formation at high local hydrophobicity. When the average of 20 amino acids is taken, both helix and ..beta..-sheet residue probabilities are higher at higher local hydrophobicity, although the increase is steeper for ..beta..-sheets. Therefore, ..beta..-sheet formation is more influenced by local hydrophobicity than helix formation. Generally, helices are nearer the surface and tend to have hydrophilic and hydrophobic faces at opposite sides. The tendency of alternating regions of hydrophilic and hydrophobic residues in a helical sequence was revealed by calculating the correlation of the Nozaki-Tanford values. Such amphipathic helices maymore » be important in protein-protein-lipid interactions and in forming hydrophilic channels in the membrane. The choice of 30 nonhomologous proteins as the data set did not alter the above results.« less
TL;DR: Comparison of the interaction occurring between chondroitin 6‐sulfate and collagen under acidic conditions and that occurring under physiological conditions showed that markedly different interaction products were formed under the different conditions.
Abstract: The effects of three glycosaminoglycans (chondroitin 6-sulfate, dermatan sulfate, and hyaluronate) and a proteoglycan on the kinetics of fibril formation and on the thermal stability of the in vitro assembled collagen fibrils, under physiological conditions of ionic strength and pH, have been examined. The glycosaminoglycans were found to influence the kinetics of collagen precipitation but not the thermal stability of the in vitro assembled fibrils. The proteoglycan was found to influence the kinetics of collagen precipitation and to reduce the thermal stability of the in vitro assembled fibrils. Comparison of the interaction occurring between chondroitin 6-sulfate and collagen under acidic conditions (0.05M acetic acid) and that occurring under physiological conditions showed that markedly different interaction products were formed under the different conditions.
TL;DR: A detailed assignment of the 13C chemical shifts of κ- and ι-carrageenans in their Na+ and K+ forms in D2O and dimethylsulfoxide is given in this article.
Abstract: A detailed assignment of the 13C chemical shifts of κ- and ι-carrageenans in their Na+ and K+ forms in D2O and dimethylsulfoxide is given Evidence of the conformational transition induced by temperature variation in the absence of any gel formation on κ-carrageenans is also presented This evidence is based on 13C-nmr and optical rotation experiments
TL;DR: 31P‐Nmr relaxation parameters (spin‐lattice relaxation time, linewidth, and nuclear Overhauser effect) were obtained at three different frequencies for poly(U) and a well‐defined fragment of DNA in solution and suggested that significant torsional and bending motions may also take place for this DNA.
Abstract: 31P-Nmr relaxation parameters (spin-lattice relaxation time, linewidth, and nuclear Overhauser effect) were obtained at three different frequencies for poly(U) and a well-defined (145 ± 3 base-pair) fragment of DNA in solution. Data sets for the two samples were analyzed by theories which included relaxation by the mechanisms of 31P chemical shift anisotropy as well as by 1H-31P dipole–dipole interaction. Neither data set could be satisfactorily described by a single correlation time. A model of a rigid rotor most nearly fits the data for the DNA molecule. Parameters obtained from the least-square fit indicate (1) that the DNA undergoes anisotropic reorientation with a correlation time τ0 = 6.5 × 10−7 sec for the end-to-end motion, (2) the ratio of diffusion constants D∥/D⊥ is 91, and (3) that the linewidth is due to chemical shift dispersion to the extent of 0.5 ppm. Some deviations of the calculated from the observed values suggested that significant torsional and bending motions may also take place for this DNA. Another model which contains isotropic motion but with a broad distribution of correlation times was required to fit the data for poly(U). A log − χ2 distribution function of correlation times [Scheafer, J. (1973) Macromolecules6, 881–888] described well the motion of poly(U) with the average correlation time τ = 3.3 × 10−9 sec and a distribution parameter p = 14.
TL;DR: 31P Nmr parameters (δ, T1, W1/2, and NOE) were measured for the DNA in nucleosome core particles at three frequencies and compared with similar data for the histone‐free DNA, suggesting the presence of different environments for phosphorus atoms in the core particles.
Abstract: 31P Nmr parameters (δ, T1, W1/2, and NOE) were measured for the DNA in nucleosome core particles at three frequencies and compared with similar data for the histone-free DNA. An essentially linear relationship was found between the frequency of observation and line-width for the single broad envelope of 31P resonances of the DNA in the nucleosome cores. We attributed this largely to chemical shift dispersion, with smaller contributions from chemical shift anisotropy and dipolar broadening. These results suggest the presence of different environments for phosphorus atoms in the core particles. However, within the accuracy of the method, no asymmetry in the resonance could be detected, which would tend to rule out any significant degree of DNA “kinking.” To investigate the interactions of the DNA and histones within the core particles we also studied transitions induced by urea and by temperature. Urea caused two stepwise increases in linewidth, which we attributed to conformational changes. A biphasic transition was also observed in the temperature profile, consistent with previous optical studies [Weischet et. al. (1978) Nucleic Acids Res.5, 139]. Various models with different types of local mobility were examined by the relaxation theory. A model of isotropic motion having a broad distribution of correlation times gave a fairly good fit to the 31P-nmr data.
TL;DR: The 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‐Al a‐Aib-Aib'Glu(OBzl)‐ Gln‐OMe.
Abstract: The 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.
TL;DR: A Laplace inversion technique is introduced and the distribution function of rate constants by which the intricate reaction proceeds is obtained, describing the scope of the conformational fluctuations in proteins at constant temperature and pressure.
Abstract: Hydrogen 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.
TL;DR: The thermal triple helix-coil transition of covalently bridged collagen-like peptides with repeating sequences of (Ala-Gly-Pro)n, n = 5−15, was studied optically as mentioned in this paper.
Abstract: The thermal triple helix–coil transition of covalently bridged collagenlike peptides with repeating sequences of (Ala-Gly-Pro)n, n = 5–15, was studied optically. The peptides were soluble in water/acetic acid (99:1) and were found to form triple-helical structures in this solvent system beginning with n = 8. The thermodynamic analysis of the transition equilibrium curves for n = 9–13 yielded the parameters ΔH°s = −7.0 kJ per tripeptide unit, ΔS°s = −23.1 J deg−1 mol−1 per tripeptide unit for the coil-to-helix transition, and the apparent nucleation parameter σ ≃ 5 × 10−2. It was suggested through double-jump temperature experiments that the rate-limiting step during refolding is not only influenced by the difficulties of nucleation, but also by cis–trans isomerization of the Gly-Pro peptide bond.
TL;DR: A significant relationship between conformation and physicochemical properties of the oligopeptides was observed and the impact of the conformational properties of a peptide chain on strategic considerations of peptide synthesis in solution is delineated.
Abstract: The 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.
TL;DR: In this article, tetrapeptides with proline in position 2, asparagine or leucine in position 3, and glycine in positions 1 and 4, with end groups free or blocked on the N-terminal side were studied in their various ionic states in 2H2O and in Me2SO-d6 by 1H- and 13C-nmr.
Abstract: Tetrapeptides with proline in position 2, asparagine or leucine in position 3, and glycine in positions 1 and 4, with end groups free or blocked on the N-terminal side, were studied in their various ionic states in 2H2O and in Me2SO-d6 by 1H- and 13C-nmr. In order to clarify or refine some details, successive substitutions of the residues in these peptides with amino acids enriched to 85% in 13C, or to 85% 13C plus 97% 2H were carried out. The 1H and 13C chemical shifts as well as the 1H-1H, 13C-13C, and 13C-1H coupling constants and the signal intensities show strong similarity of behavior between the tetrapeptides of asparagine and leucine. The main conformational characteristics are (1) the almost total stabilization of the trans conformer in the type I β-turn structure when the peptide is in the zwitterion state dissolved in Me2SO. This is deduced from the 3J and the 3J coupling constants, which both furnish a dihedral angle of ϕ3 = −90°, and from the positive value of the temperature coefficient of the glycine-4 amide protons, which suggests a type 4 1 hydrogen bond; (2) the evolution of cis and trans isomer fractions which change with the ionic state of the peptides in Me2SO, whereas they remain constant in aqueous solution; and (3) the conformation of the pyrrolidine ring as it follows the variations in cis:trans isomer populations together with the side-chain rotamer fractions of the residue in position 3. In the β-turn conformation the isomer cis is less abundant and the pyrrolidine ring is more flexible; this explains the perfect accommodation of the proline residue in position 2 of a bend. The interdependence of these phenomena where interactive forces play a predominant role underlines the importance of cooperative effects in the molecule. The results also suggest that the cis isomer of proline can adapt itself just as well as the trans isomer to position 2 of a type I β-turn.
TL;DR: 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.
Abstract: Internal 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%.
TL;DR: In this article, 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 rubber-like state.
Abstract: Thermoelastic (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.