Showing papers in "Biopolymers in 1988"
TL;DR: Temperature and conformationally dependent changes in the fine structure of the amide I band from dilute solutions of collagen can be monitored in a reproducible and quantitative fashion.
Abstract: The ir spectra of lathyritic rat skin collagen and calf skin gelatin solutions at a variety of temperatures were obtained using Fourier transform ir spectroscopy and a 9-reflection, 2-pass ZnSe prism sample cell. The spectra were then deconvolved (based on Kauppinnen's method) and the behavior of the amide I band at ∼ 1650 cm−1 observed in detail. Throughout the temperature range studied (4–50°C), three component absorption peaks within the amide I band (at 1633, 1643, and 1660 cm−1) are common to the spectra irrespective of the degree of triple helix content of the sample. Changes in the relative intensities of these component peaks are, however, conformationally dependent. During denaturation of the triple helix, the dominant 1660-cm−1 component in the native collagen spectrum diminishes and the 1633-cm−1 peak becomes relatively intensified. The inherently strong basicity of the carbonyl group of the proline residues together with the frequent occurrence of this imino acid in the X position of the Gly-X-Y triplet of collagen largely accounts for the −30-cm−1 shift of the amide I band during denaturation. Temperature and conformationally dependent changes in the fine structure of the amide I band from dilute solutions of collagen can be monitored in a reproducible and quantitative fashion.
564 citations
TL;DR: Wu et al. as mentioned in this paper proposed a new three-dimensional structure of B-starch in which the unit cell contains 12 glucose residues located in two left-handed, parallel-stranded double helices packed in a parallel register; 36 water molecules are located between these helices.
Abstract: A new three-dimensional structure of B-starch is proposed in which the unit cell contains 12 glucose residues located in two left-handed, parallel-stranded double helices packed in a parallel register; 36 water molecules are located between these helices. Chains are crystallized in the hexagonal space group P61, with lattice parameters a = b = 1.85 nm, c = 1.04 nm. The space group symmetry was derived from an exhaustive analysis of the large body of structural studies published so far. Diffraction data used in this work were taken from the previously reported x-ray fiber diffractogram [H.C. Wu and A. Sarko (1978), Carbohydrate Research, 61, 7–25] after adequate reindexing. The final R factor is 0.145 for the three-dimensional data. The repeating unit consists of a maltose molecule where the glucose residues have the 4C1 pyranose conformation and are α(1 → 4) linked. The conformation of the glycosidic linkage is characterized by torsion angles (Φ, Ψ) that take the values (83.8°, −144.6°) and (84.3°, −144.1°), whereas the valence angles at the glycosidic bridge have a magnitude of 115.8° and 116.5°, respectively. The primary hydroxyl groups exist in a gauche–gauche conformation. There is no intramolecular hydrogen bond. Within the double helix, interstrand stabilization is achieved without any steric conflict and through the occurrence of O(2)…O(6) type of hydrogen bonds. The model presented here, with an hydration around 27% w/w, corresponds to a well-ordered crystalline sample, since all the water molecules could be located with no apparent sign of a disorder. Half of the water molecules are tightly bound to the double helices; the remainder forms a complex network centered around the sixfold screw axis of the unit cell. The consistency of the present structural model, with both physicochemical and biochemical aspects of the crystalline component of tuber starch granules, is analyzed.
493 citations
TL;DR: A new approach to the multiple‐minima problem in protein folding is presented, and its effectiveness by computations on different arbitrary starting conformations of a terminally blocked 19‐residue chain of poly(L‐alanine) for which the global minimum apparently corresponds to the right‐handed α‐helix is illustrated.
Abstract: A new approach to the multiple-minima problem in protein folding is presented. It is assumed that the molecule is driven toward the native structure by three types of mechanism. The first one involves an optimization of the electrostatic interactions, whereby the molecule evolves toward conformations in which the charge distribution becomes energetically more favorable. The second mechanism involves a Monte Carlo–energy minimization approach, and the third one is a backtrack mechanism that acts in the opposite direction, increasing the energy—the third type of movement provides a means to perturb the molecule when it is trapped in a stable but energetically unfavorable local energy minimum. This paper describes the implementation of a model based on these mechanisms, and illustrates its effectiveness by computations on different arbitrary starting conformations of a terminally blocked 19-residue chain of poly(L-alanine) for which the global minimum apparently corresponds to the right-handed α-helix. In all cases, the global minimum was attained, even when the starting conformation was a left-handed α-helix. In the latter case, the trajectory of conformations passed through partially melted forms of the left-handed α-helix (because of electrostatic defects at the ends), and then through the formation of structures leading to the more stable right-handed α-helix.
157 citations
TL;DR: The onset of reptation and of stretching of DNA chains in gel electrophoresis are described quantitatively for the first time, and a phase diagram for the dynamics of DNA during electrophoreis is presented.
Abstract: An extensive series of experiments has been performed to study the mobility of DNA fragments ranging in size from 2.0 to 48.5 kilobose pairs. By varying the agarose concentration in the gels and the electric field strength, three DNA electrophoresis regimes were clearly identified: the Ogston regime (small DNA fragments in large pores of agarose), the reptation regime without DNA chain stretching (small pores of agarose and weak electric fields), and the reptation regime with DNA chain stretching (small pores of agarose, strong electric fields, and large DNA fragments). Here we report on the experimental identification of these regimes and on the conditions governing the transition between each of them. The onset of reptation and of stretching of DNA chains in gel electrophoresis are described quantitatively for the first time, and a phase diagram for the dynamics of DNA during electrophoresis is presented.
147 citations
TL;DR: The high‐frequency Raman spectra of highly ordered and disordered films are compared to show that the extent of crystallinity controls the amount of A‐DNA formed when ethanol is used to dehydrate the films, and it is shown that rapid dehydration does not result in a B to A transition.
Abstract: We have studied the hydration of Na-DNA and Li-DNA fibers and films, measuring water contents, x-ray fiber diffraction patterns, low-frequency Raman spectra (below 100 cm−1), high-frequency Raman spectra (600–1000 cm−1), and swelling, as a function of relative humidity. Most samples gain weight equilibrium (though not conformational equilibrium) in one day. The volume occupied by a base pair as the DNA is hydrated (obtained from the x-ray and swelling data) shows anomalies for the case of Na-DNA in the region where the A-form occurs. Our Raman and x-ray data reproduce the well-known features of the established conformational transitions, but we find evidence in the Raman spectra and optical properties of a transition to what may be a disordered B-like conformation in Na-DNA below 40% relative humidity. We have studied the effects of crystallinity on the A to B transition. We find that the transition to the B-form is impeded in highly crystalline samples. In most samples, the transition occurs in three days (after putting the sample at 92% relative humidity) but in highly crystalline samples, the transition may take months. By comparing the high-frequency Raman spectra of highly ordered and disordered films, we show that the extent of crystallinity controls the amount of A-DNA formed when ethanol is used to dehydrate the films. We show that rapid dehydration (by laser heating) does not result in a B to A transition. A fiber that gives A-type x-ray reflections probably contains B-like material in noncrystalline regions. The low-frequency Raman spectrum is dominated by a band at about 25 cm−1 in both Na- and Li-DNA. Another band is seen near 35 cm−1 in Na-DNA at humidities where the sample is in the A-form. In contrast to earlier reports, we find that the Raman intensity does not depend on fiber orientation relative to the scattering vector. The “35-cm−1” band is largely depolarized (i.e. vertical polarization incident and horizontal polarization scattered, VH, or vice versa, HV) while the “25-cm−1” band appears in both VV, VH and HV polarizations. These bands are all weaker in HH polarization. The “25-cm−1” band may be due to a shearing motion of the phosphates and their associated counterions, while the “35-cm−1” band may be characteristic of A-DNA crystallites. We consider mass-loading, relaxational coupling to the hydration shell, and softening of interatomic potentials as possible explanations of the observed softening of the low-frequency Raman bands on hydration. Relaxation data suggest that the added water binds tightly (on these time scales) and a mass-loading model accounts for the observed softening rather well.
We conclude that the A to B transition is not driven by softening of the “25-cm−1” band. Rather, it is most probably a consequence of crystal-packing forces, with the more regular A-form favored in crystals when these forces are strong.
133 citations
TL;DR: Constrained conformational energy minimizations have been used to calculate an adiabatic potential energy surface for the disaccharide β‐maltose and the inclusion of molecular flexibility was found to significantly lower the barriers to conformational transitions, as has been observed previously for other systems.
Abstract: Constrained conformational energy minimizations have been used to calculate an adiabatic (Φ, ψ) potential energy surface for the disaccharide β-maltose. The inclusion of molecular flexibility in the conformational energy analysis of the disaccharide was found to significantly lower the barriers to conformational transitions, as has been observed previously for other systems. Several low energy wells were identified on the adiabatic surface which differ in energy by small amounts and with low absolute barriers separating them, indicating the possibility of a non-negligible equilibrium population distribution in each well. If such a distribution of conformations existed in the physical system, the conformation observed by NMR NOE measurements would thus be a “virtual” conformation. Molecular dynamics simulations of the motions of this molecule in vacuum were also conducted and indicate that the rate of relaxation of the molecule to the adiabatic surface may be slower than the typical timescale of conformational fluctuations. This effect is apparently due to an unphysical persistence of hydrogen bond patterns in vacuum which does not occur in aqueous solution. Trajectories undergoing transitions between wells were calculated and the effects of such conformational transitions upon the ensemble mean structure, such as might be observed in an NMR experiment, were demonstrated.
126 citations
TL;DR: It is found that if only protein atoms are included in the calculation, no reasonable range atomic of radii can reproduce the experimental translational diffusion constant to better than 20% for lysozyme and 5% for ribonuclease.
Abstract: As a first step toward a systematic parametrization of friction constants of atoms in proteins, a model in which frictional resistance is placed explicitly on each atom accessible to solvent is used to calculate overall translational and rotational diffusion constants. It is found that these quantities are relatively insensitive to the precise value of the atomic friction constant, as long as the effective hydrodynamic radius of the surface atoms is approximately 1 A. However, if only protein atoms are included in the calculation, no reasonable range atomic of radii can reproduce the experimental translational diffusion constant to better than 20% for lysozyme and 5% for ribonuclease. When a hydration shell of approximately 70% coverage for lysozyme and 20% for ribonuclease is included, there is quantitative agreement with experimental results. The sensitivity of peptide diffusion to levels of hydration is also investigated; it is found that for glycine, two bound waters are required to provide agreement with experiment. These findings imply that the effects of solvent damping will be underestimated in stochastic simulations of proteins and peptides unless bound waters are taken into account.
112 citations
TL;DR: Energy minimizations carried out for DNA–drug complexes indicate that, for most drugs, a distortion or disruption of 2 to 4 base pairs occurs at the intercalation site in DNA molecules.
Abstract: The effects of collective motion in DNA as reflected by resonance coupling among its intact segments have been discussed for both linear and circular DNA molecules. The results indicate that due to the effects of this kind of internal collective motion, the energy will be at times highly concentrated at some spots. As a result of the overfocus of energy, the stress built up along the direction of hydrogen bonds between complementary base pairs will be dramatically increased, rupturing a series of consecutive hydrogen bonds simultaneously and resulting in a suddenly free jerk, such that the DNA molecule will undergo a local “quake.” The “hole” formed by this kind of quake-like motion will be large enough for bulky drugs to gain entrance and intercalate into DNA. Even for smaller drugs, this local quake-like motion can also provide a significant mode of entry for intercalation. Energy minimizations carried out for DNA–drug complexes indicate that, for most drugs, a distortion or disruption of 2 to 4 base pairs occurs at the intercalation site in DNA molecules.
106 citations
TL;DR: Four‐arm DNA branched junctions are stable analogs of Holliday recombination intermediates, constructed from oligonucleotides, and macrocyclic closure is observed in a regular ligation ladder, starting from tetramers.
Abstract: Four-arm DNA branched junctions are stable analogs of Holliday recombination intermediates, constructed from oligonucleotides. The conformational flexibility of junctions can be estimated by ligating them together and determining the set of closed macrocyclic products that are obtained among the linked units. We have performed a series of these experiments, using pairs of sticky ends that flank each of the six angles of a four-arm junction. In every case, the ligated junctions are separated by 20 nucleotide pairs, about two turns of DNA. All expected short linear products, starting with dimers, are observed for all ligations. All ligations result in a macrocyclic series that begins with trimers. Thus, over the time scale of these reactions, the arms of this junction can form angles as low as 60°. The response of this junction to torsional stress has been tested in a companion experiment. A smaller version of this same four-arm junction has been oligomerized so that successive junctions are separated by 16 nucleotide pairs, approximately 1.5 turns of DNA. If junctions were as rigid as linear duplex DNA, this system would not be expected to form macrocycles until the continuous chain approaches the Shore–Baldwin limit, ca. 160 base pairs. However, macrocyclic closure is observed in a regular ligation ladder, starting from tetramers. Model building suggests that the most likely explanation for the observed closure is that the junction adopts two different conformations, which bend the continuous strand toward opposite grooves. The junction structures formed by these ligations represent fluctuations from equilibrium structures.
101 citations
TL;DR: In this article, conformational energy computations on a derivative and a homo-dipeptide of Cα,α-diethylglycine were performed and it was found that the residues are conformationally restricted and that the minimum energy conformation corresponds to the fully extended C5 structure when the NCαC′ bond angle is smaller than 108° (as experimentally observed).
Abstract: Conformational energy computations on a derivative and a homo-dipeptide of Cα,α-diethylglycine were performed. In both cases the N- and C-terminal groups are blocked as acetamido and methylamido moieties, respectively. It was found that the Cα,α-diethylglycine residues are conformationally restricted and that the minimum energy conformation corresponds to the fully extended C5 structure when the NCαC′ bond angle is smaller than 108° (as experimentally observed). The results of the theoretical analysis are in agreement with the crystal-state structural propensity of the complete series of N-trifluoroacetylated homo-peptides of this Cα,α-dialkylated residue from monomer to pentamer, determined by x-ray diffraction and also described in this work. Interestingly, for the first time, a crystallographically planar peptide backbone was observed (in the protected tripeptide). A comparison with peptides of Cα,α-dimethylglycine, Cα-methyl, Cα-ethylglycine, and Cα,α-di-n-propylglycine indicates that the fully extended conformation becomes more stable than the helical structures when both amino acid side-chain Cβ atoms are substituted.
96 citations
TL;DR: A method for in situ study of orientation of DNA during gel electrophoresis has been developed and the theory of Slater and Noolandi predicts an orientational length dependence that is an order of magnitude less than the experimental one, and a field dependence that agrees neither with the sigmoidal shape observed in agarose nor with the linear dependence in polyacrylamide.
Abstract: A method for in situ study of orientation of DNA during gel electrophoresis has been developed. Linear dichroism spectra measured by this phase-modulation technique can sensitively and selectively detect orientation of DNA during electrophoretic migration in gel. [Measurement of “electrophoretic orientation” was first reported in 1985 by B. Akerman, M. Jonsson, and B. Norden (1985) (J. Chem. Soc. Chem. Commun. 422–423)]. Restriction fragments of duplex DNA of lengths in the ranges of 300–2319 base pairs (bp) and 4361–23130 bp have been studied in 5% polyacrylamide and 1% agarose gels, respectively. The fragments become preferentially oriented with the DNA helix axis parallel to the migration direction. In agarose the orientation is found to increase sigmoidally, and in polyacrylamide, linearly, with the electric field strength, within the field ranges accessible to measurement (0–40 and 5–40 V/cm, respectively). In both types of gels a considerable increase in orientation with length of DNA was observed. Compared to dipole orientation in electric fields, the electrophoretic orientation is high: orientation factor S = 0.027 in agarose for 23130 bp at 10 V/cm and S = 0.004 in polyacrylamide for 2319 bp at 10 V/cm. In addition to orientation of DNA, the electrophoresis also leads to orientation effects in the gel structure owing to Joule heating. In agarose there is also an effect that is associated with the migrating DNA zones and that produces different orientations of the gel at the front and rear parts of a zone. Evidence is presented that this effect is due to a DNA-induced electroosmotic flow causing a contraction of the gel in the front of the zone and an expansion in the rear. The experimental results on DNA orientation are compared with the reptation theories for gel electrophoresis. The theory of Lumpkin et al. [O. J. Lumpkin, P. Dejardin, and B. H. Zimm (1985) Biopolymers24, 1573–1593] predicts no orientation length dependence, but it does predict a shape of the field dependence that resembles the shape observed in agarose. The theory of Slater and Noolandi [G. W. Slater and J. Noolandi (1986) Biopolymers25, 431–454] predicts an orientational length dependence that is an order of magnitude less than the experimental one, and a field dependence that agrees neither with the sigmoidal shape observed in agarose nor with the linear dependence in polyacrylamide.
TL;DR: It is demonstrated that protein α‐helix content can be predicted from an autocorrelation analysis of the protein hydrophobicity sequence using sequence and secondary structure data from more than 160 proteins and domains.
Abstract: It is demonstrated that protein α-helix content can be predicted from an autocorrelation analysis of the protein hydrophobicity sequence. The Fourier transform of the autocorrelation function yields the spectral densities or weights of the various frequencies contributing to the autocorrelation function. Using sequence and secondary structure data from more than 160 proteins and domains, a linear relationship was found between spectral density at periodicity 3.7 and protein α-helix content (r = 0.83). This relation permits prediction of the helix content (x) of proteins of known sequence to within ± 15%, i.e., as (x ± 15)%. Predictions based on the autocorrelation procedure are compared with values obtained by other methods.
TL;DR: The conformational preferences of the N-trifluoroacetylated homo-peptides of Cα,α-diethylglycine from monomer to pentamer in chloroform solution were determined by using ir absorption and 1H-nmr as discussed by the authors.
Abstract: The conformational preferences of the N-trifluoroacetylated homo-peptides of Cα,α-diethylglycine from monomer to pentamer in chloroform solution were determined by using ir absorption and 1H-nmr. Intramolecular hydrogen bonding was found to be the dominant factor for all NH groups. The likely absence of a conformational transition upon increasing main-chain length, and the remarkable stability to dilution, heating, and addition of perturbing agents, are additional relevant findings of this study. These results are in agreement with those of the fully extended, C5-conformation-forming homo-peptides from the higher homolog Cα,α-di-n-propylglycine, but contrast dramatically to those of the homo-peptides from the lower homolog Cα,α-dimethylglycine, which have been shown to adopt the 310-helical structure.
TL;DR: It is demonstrated that the desired thermal stability of the collagen triple helix requires the “clustered” arrangement of helix‐promoting tripeptides, especially of Gly‐Pro‐Hyp.
Abstract: Variations I–XVIII of a trimerlike cross-linked collagen model peptide were synthesized and used to investigate the cooperation of different neighboring Gly-X-Y tripeptides. The carboxy-terminal decapentapeptide of the tripe-helical part of collagen type I was chosen as the starting point of sequentially modified elongations. The transition temperatures determined by CD measurements show that the incorporation of the imino acid free tripeptides Gly-Ala-Ala and Gly-Ile-Ala results in a weakening of the triple-helical structure. It is demonstrated that the desired thermal stability of the collagen triple helix requires the “clustered” arrangement of helix-promoting tripeptides, especially of Gly-Pro-Hyp.
TL;DR: In solutions containing DNA and cations of more than one type, the competitive interactions of these cations with DNA can be modeled as an ion exchange process that can be described quantitatively by means of the theoretical approach reported in this paper.
Abstract: In solutions containing DNA and cations of more than one type, the competitive interactions of these cations with DNA can be modeled as an ion exchange process that can be described quantitatively by means of the theoretical approach reported in this paper. Under conditions of experimental interest the radial distribution function of each type of counterion is calculated from the results of canonical Monte Carlo (MC) simulations using the primitive model for DNA (having a helical charge distribution) and for the electrolyte ions. These ions consist of monovalent coions, monovalent counterions intended to represent Na+, and counterions of a second type designated Mz+, having variable size and charge (z ≥ 1). The competitive association of these counterions with DNA is described in terms of D, a parameter analogous to an ion exchange equilibrium quotient. Values of D are calculated from the results of our MC simulations and compared with corresponding predictions of the Poisson–Boltzmann (PB) cell model and with results inferred from analyses of previously published nmr measurements. Over typical experimental concentration ranges (0.02M < [Na+] < 0.20M, 0.001 < [Mz+] < 0.160M), DMC and DPB both are predicted to be relatively independent of the bulk ion concentrations. For various specifications of the size and charge of the competing cation (Mz+), DMC and DPB exhibit similar trends, although the MC simulations consistently predict that the cations bearing a higher charge density than that of Na+ are somewhat stronger competitors than indicated by the PB calculations. For monovalent and divalent competitors of varying radii, theoretical predictions of D are compared with values obtained by fitting nmr measurements. If the hard-sphere radii specified in the simulations are the (hydrated) ionic radii determined from conductance measurements, then the MC predictions and the corresponding nmr results are in reasonable agreement for various monovalent competitors and for a divalent polyamine, but not for Ca2+ and Mg2+.
TL;DR: In this paper, normal mode calculations have been carried out for parallel-chain β-sheet structures and the effects of parallel-sheet and antiparallel-sheet arrangements of varying separation have been examined for the poly(L-alanine) case.
Abstract: Normal mode calculations have been carried out for parallel-chain β-sheet structures These include the parallel-chain pleated sheet of poly(L-alanine) and the parallel-chain rippled sheet of polyglycine Dipole derivative coupling has been included for amide I and II modes, and the effects of parallel-sheet and antiparallel-sheet arrangements of varying separation have been examined for the poly(L-alanine) case Some amide and nonamide modes are distinctly different from their antiparallel-chain counterparts, thus providing a basis for distinguishing between such structures from their ir and Raman spectra As in our previous studies, these results emphasize the need for both kinds of spectral data in order to draw definitive conclusions about conformation
TL;DR: In this article, electron microscopy has been carried out on sections of beaded agarose with a wide range of thicknesses, and the results have been analyzed by means of stereological theory using computer graphics.
Abstract: Electron microscopy has been carried out on sections of beaded agarose with a wide range of thicknesses, and the results have been analyzed by means of stereological theory using computer graphics The results agree with a randomly orientated system in which, for 4% gels, the mean molecular weight per unit length of the fiber system is 110 kg mol−1 nm−1, and the number average interjunction length is 37 nm, with an asymmetrical distribution resembling a Maxwell-Boltzmann distribution The spatial distribution of the structure is not uniformly random and there seem to be mi microvoids
TL;DR: In this article, the chemical structure of the β(1 → 3) glycosidically linked D-glucopyranosyl units of the yeast Saccharomyces cerevisiae and Canadida albicans was investigated in dilute alkaline solutions and at neutral pH.
Abstract: By means of alkaline extraction of the cell walsl of the yeasts Saccharomyces cerevisiae and Canadida albicans, water-insoluble glucans were obtained. Methylation analysis and 13C-nmr investigation in dimethyl sulfoxide solution revealed the similar chemical structure of these glucans, being composed of β(1 → 3) glycosidically linked D-glucopyranosyl units with a small amount of β(1 → 6) linkages. More detailed study in dilute alkaline solutions and in the gel state at neutral pH, however, showed that an ordered helical conformation of the glucan chain is less stable in the case of the S. cerevisiae glucan in comparison with that of C. albicans. Measurements of the shift of the absorption maximum of the glucan complexes with Congo Red also demonstrated such difference. The S. cerevisiae glucan was also inable to form a gel at neutral pH. The difference in stability of helical conformation of the glucans is explained on the basis of the methylation analysis, so that the S. cerevisiae glucan possesses longer side chains, which hinder its adoption of a stable helical conformation.
TL;DR: The matrix‐generator methods set forth in the preceding paper for treating rodlike DNA are adapted here to the calculation of average chain extension, macroscopic flexibility, and terminal residue orientation in curved duplexes.
Abstract: The matrix-generator methods set forth in the preceding paper for treating rodlike DNA are adapted here to the calculation of average chain extension, macroscopic flexibility, and terminal residue orientation in curved duplexes. The different characteristics of curved vs rodlike chains are illustrated with the hypothetical poly[d(A5G5)] · poly[d(T5C5)] duplex. The curved helix is both more compact and macroscopically stiffer than either the poly(dA) · poly(dT) or the poly(dG) · poly(dC) chain. The calculations have also been extended to simple repetitive DNA sequences generated by synthetic ligation studies and the computed average chain properties compared with observed gel mobilities. The predicted chain extension is also checked against the measured persistence lengths of the rodlike poly[d(GC)] and poly[d(AT)] alternating copolymers, and the known cyclization tendencies of selected repeating sequences. Chains are generated from local potential energy maps describing the morphology and flexibility of adjacent base pairs. The energy maps, while approximate, are more accurate descriptors of local structure than many of the intuitive models of DNA curvature offered to date. According to the energy surfaces, the intrinsic bending of curved DNA can be traced to asymmetry in the bending of the Gs and Cs that join half-helical turn stretches of adenines in these chains. The oligo A stretches are analogous to residues of a perfectly elastic DNA that bend with equal likelihood in opposing directions. In other models of DNA curvature, the (G · C) base pairs are presumed to adopt the classical B-DNA structure, while the (A · T) base pairs are thought to be in some perturbed conformation.
TL;DR: The mean‐square radius 〈S2〉N of gyration of the DNA topoisomer with the linking number N is evaluated as a function of N and chain length L on the basis of a (circular) twisted wormlike chain.
Abstract: The mean-square radius 〈S2〉N of gyration of the DNA topoisomer with the linking number N is evaluated as a function of N and chain length L on the basis of a (circular) twisted wormlike chain, ie, a special case of the helical wormlike chain Evaluation of 〈S2〉N and also of the moment 〈Wr2〉 of the writhe Wr is carried out over a wide range of L, following the Monte Carlo procedure of Frank-Kamenetskii et al It is found that the present Monte Carlo values of 〈Wr2〉 for large L are appreciably larger than the known Monte Carlo values for freely jointed chains Thus, the empirical interpolation formula for 〈Wr2〉 previously constructed on the basis of the theoretical values for small L along with the latter Monte Carlo values for large L is revised with the present Monte Carlo values By the use of the revised formula, a reanalysis of the experimental data for the distribution of topoisomers is made, and it is found that the present estimates of the torsional constant and the stiffness parameter are equal to and somewhat larger than the previous ones, respectively It is shown that 〈S2〉N decreases with increasing |ΔN|, where ΔN = N − N, with N the number of helix turns in the linear DNA chain in its undeformed state The mean-square radii of gyration 〈S2〉Wr and 〈S2〉 of the original circular Kratky–Porod wormlike chain with and without Wr fixed are also evaluated
TL;DR: In this paper, the basic relations between the molar fractions and the scanning calorimetry data for the system that includes self-dissociation/association process are presented, where mi is the stoichiometric coefficient of the ith state Ai.
Abstract: The basic relations between the molar fractions and the scanning calorimetry data for the system that includes self-dissociation/association process such as
are presented, where mi is the stoichiometric coefficient of the ith state Ai. The relations are described for each state j as
where fj(T) is the molar fraction function of state j and ΔHj(T) is the difference enthalpy function of the system referred to the state j, which can be obtained by scanning calorimetry; R is the gas constant; and T is the absolute temperature. By these relations, scanning calorimetry data can be deconvoluted in order to determine the thermodynamic functions by means of single and double deconvolution. The concentration dependence of the data is analyzed by a method presented in this paper. The nonlinear least squares fitting method for the determination of the functions is discussed. For an example of the application of this method to the actual scanning calorimetry data, thermodynamic data of multistate thermal transition of Vibrio parahaemolyticus hemolysin are analyzed.
TL;DR: The ability to recover distance distributions will have numerous applications in the characterization of biological macromolecules as well as time‐dependent fluorescence energy transfer.
Abstract: We used time-dependent fluorescence energy transfer to determine the distribution of donor-to-acceptor distances in native and denatured troponin I(TnI). The single tryptophan residue (Trp 158) of TnI served as the donor (D), and the acceptor (A) was a labeled cysteine residue (Cys 133). The time-dependent intensity decays of the donor were measured by the frequency-domain method from 10 to 320 MHz. The frequency response of the donor emission, in the absence and presence of acceptor, was used to recover the distribution of D to A distances, using an algorithm that accounts for the intrinsic multiexponential decay of the donor. In the native state the D–A distribution is characterized by an average distance of 23 A and a half-width of 12 A. Denaturation results in a modest increase in the average distance to 27 A, and a dramatic increase in half-width to 47 A. We believe the ability to recover distance distributions will have numerous applications in the characterization of biological macromolecules.
TL;DR: A modification of the Zimm–Bragg two‐state model for the helix–coil transition in polypeptides, which considers the effect of charge–dipole, charge–charge, and other specific interactions on helix stability, is presented.
Abstract: A modification of the Zimm–Bragg two-state model for the helix–coil transition in polypeptides, which considers the effect of charge–dipole, charge–charge, and other specific interactions on helix stability, is presented. The new model introduces a series of adjustable parameters whose values are estimated by fitting to recent spectroscopic results on medium-sized peptides. This formalism, based on traditional two-state helix–coil transition models, provides a framework in which data on the helix contents of peptides of specific sequence can be rationalized by a statistical mechanical theory.
TL;DR: Reduced‐denatured ribonuclease A has residual structure that limits segmental Brownian motion in the N‐terminal segment, indicating that large‐scale segmental motions do not take place in the denatured protein within the excited‐state lifetime of the donor.
Abstract: Time-dependent fluorescence measurements have been used to determine the distribution of distances between probes attached to residues 1 and (49 + 53) of bovine pancreatic ribonuclease A in the native, denatured, and reduced-denatured states. Measurements were made on donor and on doubly labeled (donor + acceptor) protein in 50% aqueous glycerol solutions at −30°C and at room temperature. The fluorescence-decay curves were used to compute distribution functions for the interprobe distances. The native protein has a narrow distribution of interprobe distances at −30°C (high-viscosity medium); this distribution is narrower at room temperature (low-viscosity medium), due primarily to the dynamic flexibility of the probes. Denaturation by 6M guanidine hydrochloride leads to a wider distribution of distances at −30°C, with a shift of the distribution curve to larger distances, because of the increased disorder of the protein. Reduction of the disulfide bonds by dithiothreitol leads to further decreases in transfer efficiency (a unique distribution curve for the reduced protein was not obtained because of the low transfer efficiency). Both the denatured and reduced-denatured species have average interprobe distances of about 60 A, compared to 36 A for the native protein. Reduction of the solvent viscosity leads to nearly monoexponential decay of the donor fluorescence in the doubly labeled derivative. This is interpreted as a manifestation of fast local Brownian motions. It appears that large-scale segmental motions do not take place in the denatured protein within the excited-state lifetime of the donor (ca. 8 ns). The above results indicate that reduced-denatured ribonuclease A has residual structure that limits segmental Brownian motion in the N-terminal segment.
TL;DR: Emphasis is placed on theoretical methodology and the practical relevance of the calculated chain moments to observed physical properties, including the average unperturbed moments of the end‐to‐end vector r and the mean angular orientation of terminal chain residues.
Abstract: Matrix generator techniques have been adapted to account for precise structural features of the nucleotide repeating unit and to translate the primary sequence of DNA base pairs into three-dimensional structures. Chains have been constructed to reflect the local sequence-dependent differences of bending and twisting of adjacent residues and various overall chain properties, including the average unperturbed moments of the end-to-end vector r and the mean angular orientation (〈γ〉 between base pair normals, 〈ϕ1〉 between long axes, and 〈ϕ2〉 between short axes) of terminal chain residues, have been computed. The chain backbone is treated implicitly in terms of the spatial fluctuations of successive base pairs. Motions are limited to low-energy perturbations of the standard B-DNA helix. Approximate potential energy schemes are used to represent the rules governing the patterns of local base–base morphology and flexibility. Theoretical predictions are compared with experimental observations at both the local and the macro-molecular level. Initial applications are limited to the rodlike poly(dA) · poly(dT) and poly(dG) · poly(dC) helices. The former duplex is found to be more compressed and the latter more extended than random-sequence DNA of the same chain length. The flexibility of the duplexes as a whole is described in terms of the average higher moments of the displacement vector ρ = r - 〈r〉 and the likelihood of chain cyclization is estimated from the three-dimensional Hermite series expansions of the displacement tensors. Emphasis is placed on theoretical methodology and the practical relevance of the calculated chain moments to observed physical properties.
TL;DR: The results show that the relaxation mode of the primary hydration shell retains its basic characteristics even in samples with very high water content, and a modified mode coupling model is used to include both the collective nature of the sound wave and to describe the change in hydration explicitly.
Abstract: We have measured the dispersion of phonon line widths between frequencies of about 2 and 10 GHz in DNA films at relative humidities between 0 and 95%. The results show that the relaxation mode of the primary hydration shell retains its basic characteristics even in samples with very high water content. A modified mode coupling model is used to include both the collective nature of the sound wave and to describe the change in hydration explicitly. It enables us to describe the coupling between the phonons and the water relaxation mode at various water contents, and allows us to extract values for the primary shell relaxation time and coupling constants over the range of hydration studied. The primary shell relaxation time (∼ 40 ps) and coupling parameters remain nearly constant over the entire range of hydration. We have reanalyzed our earlier Brillouin data (taken as a function of temperature) in terms of two relaxation processes (primary plus a secondary shell contribution of about 2 ps at room temperature). This new analysis indicates that both processes follow a simple Arrhenius behavior with activation energies of 5 kcal mole−1 for the primary relaxation and 7 kcal mole−1 for the secondary relaxation. We also observe a rather broad central mode that can be fitted by a Lorentzian, and that may arise from direct (as opposed to coupled-mode) scattering from the primary relaxation mode.
TL;DR: The optical absorption spectra of sperm whale deoxy‐, oxy‐, and carbonmonoxymyoglobin in the temperature range 300–20 K and in 65% glycerol or ethylene glycol–water mixtures are reported.
Abstract: Synopsis We report the optical absorption spectra of sperm whale deoxy-, oxy-, and carbonmonoxymyoglobin in the temperature range 300-20 K and in &5'% glycerol or ethylene glycol-water mixtures. By lowering the temperature, all bands exhibit half-width narrowing and peak frequency shift; moreover, the near-ir bands of deoxymyoglobin show a marked increase of the integrated intensities. Opposed to what has already been reported for human hemoglobin, the temperature dependence of the first moment of the investigated bands does not follow the behavior predicted by the harmonic Franck-Condon approximation and is sizably affected by the solvent composition; this solvent effect is larger in liganded than in nonligmded myoglobin. However, for all the observed bands the behavior of the second moment can be quite well rationalized in terms of the harmonic Ranck-Condon approximation and is not dependent on solvent composition. On the basis of these data we put forward some suggestions concerning the structural and dynamic properties of the heme pocket in myoglobin and their dependence upon solvent composition. We also discuss the different behaviok of myoglobin and hemoglobin in terms of the different heme pocket structures and deformabilities of the two proteins.
TL;DR: In this paper, the preferred conformations of model cyclopropylglycine peptides have been investigated by means of ab initio and empirical methods, showing that the C7-conformation corresponds to the absolute energy minimum.
Abstract: The preferred conformations of model cyclopropylglycine peptides have been investigated by means of ab initio and empirical methods. Empirical computations performed with fixed bond lengths and valence angles using two well-known force fields show that only values of ϕ in the ranges ±70° ± 20° are sterically allowed, and that the C7-conformation corresponds to the absolute energy minimum irrespective of the terminal groups used. Also, ab initio computations give similar results, but suggest greater stabilities for bridge and, especially, extended structures. These discrepancies can be removed, adding to the empirical force field a twofold torsional potential on ψ and using softer steric repulsive potentials. Complete geometry optimization using both ab initio and empirical methods does not affect the relative stabilities of folded conformations, but leads to a further significant stabilization of the fully extended structure via large modifications of some valence angles.