Showing papers in "Biopolymers in 1982"

Structure of methylene blue-DNA complexes studied by linear and circular dichroism spectroscopy.

Abstract: Bradley et al. [(1972) Biopolymers11, 645–652] used electro-optical measurements to show that methylene blue (MB), like acridine orange, in its DNA complex is oriented more or less perpendicular to the helix axis as expected if intercalated. High-precision flow linear dichroism (LD) here confirms that MB is coplanar with the DNA bases at low dye/DNA binding ratios and low ionic strengths. CD shows two origins of induced optical activity for the transition of lowest energy (polarized parallel to the long-axis of the dye molecule): at low binding ratios (r 300 mM Na+ or >0.4 mM Mg2+). Nondegenerate coupled-oscillator theory can explain the CD in terms of interactions of transition moments of the dye and the nearest nucleotide bases and indicates a change between two intercalation geometries: a Lerman type of mode, denoted γ−, and an orthogonal mode, denoted γ+. This rotation of MB in the base-pair pocket is accomplished at Na+ and Mg2+ concentrations when the phosphates are effectively screened and the result suggests a more localized bonding of Mg2+ than is expected from simple polyelectrolyte models. The exciton effect at high binding ratios, observed both in CD and in LD, can be interpreted in terms of an interaction between an intercalated and a nonintercalated MB. The geometry of this “accidental” dimer is consistent with a location of the nonintercalated MB in the minor groove, bridging the strands by the positively charged amino groups directed towards phosphate groups. The dihedral angle of the MB pairs, corresponding to a left-handed helix, is opposite to that with acridine orange and proflavine on DNA, indicating that the latter ligands bind to DNA in a different way.

Equilibrium dialysis studies of polyamine binding to DNA.

Abstract: Binding constants and binding site sizes for the interactions of the polyamines spermine (+4), spermidine (+3), and putrecine (+2) with helical DNA have been determined as a function of ionic conditions and temperature by equilibrium dialysis using 14C-labeled polyamines. In addition, competition equilibrium dialysis has been used to determine binding parameters for the divalent cations putrescine and Mg2+ from the competitive effect of these ions on the binding of spermine or spermidine. In all cases, the logarithm of the binding constant (log Kobs) varies linearly with the logarithm of the monovalent salt concentration; the slopes d log Kobs/d log[NaCl] are proportional to the valence of the ligand, and values of the extrapolated binding constants at 1M NaCl obtained from the intercepts are small (of order 1–10M−1). In those cases examined, Kobs is insensitive to temperature; the free energy of binding is predominantly entropic. Consequently, polymines as DNA-binding ligands behave analogously to the oligolysines investigated previously [cf. Record, Lohman & de Haseth (1976) J. Mol. Biol.107, 145–158; Lohman, de Haseth & Record (1980) Biochemistry19, 3522–3530]. The interactions of these oligocations with DNA are predominantly electrostatic and are driven by the release of thermodynamically bound electrolyte ions from the vicinity of the DNA. The extent to which these oligocations are localized at individual phosphate binding sites or delocalized on the DNA molecule is currently not known.

Solution properties and chain flexibility of pullulan in aqueous solution

Abstract: Molecular characteristics for pullulan, a polysaccharide produced by a fungus Aureobasidium pullulans, were measured by light scattering, viscometry, and gel-permeation chromatography. From the experimental data the Mark-Houwink-Sakurada viscosity equation in water at 25°C was determined for samples having the molecular weight M ranging from 48 × 103 to 2.18 × 106 g mol−1 as [η] = (1.91 ± 0.02) × 10−2Mw0.67±0.01 (in cm3 g−1); and as molecular weight decreased, the slope of the viscosity equation decreased, although the molecular weight values below 30 × 103 g mol−1 evaluated by gel-permeation chromatography were somewhat unreliable. The unperturbed dimensions 〈R2〉01/2 of pullulan were estimated by determining the expansion factor αs, from the theoretical combination of theories for the interpenetration function Ψ and those for αs. The 〈R2〉0/M value estimated from this procedure in 6.7 × 10−17 cm2 mol g−1. We concluded that the polysaccharide chain that is linked by the α-1,6-glucosidic linkage behaves like a flexible chain in aqueous solution.

Theory of DNA condensation: collapse versus aggregation.

Abstract: In an unfavorable solvent environment, DNA (and other polymers) undergo a conformational transition to a collapsed form, accompanied by a dramatic reduction in the effective volume of the molecule. Solvent conditions leading to the collapse are the same as those that cause aggregation. We give here a thermodynamic description of the collapse and its relations to aggregation (or precipitation). This is formulated in terms of the Flory-Huggins theory of the thermodynamics of polymer solutions. The results show that it is possible for three different states of DNA to be stable under different conditions: (1) the extended random coil, (2) the collapsed coil, and (3) a concentrated phase of aggregated random coils. The collapsed coil is predicted to be stable against aggregation only at high dilutions, of the order of parts per million. For DNA the transition between the extended coil and the collapsed coil is predicted to be discontinuous, in the sense that intermediate states are not present, because of the relatively high stiffness of the chain. The transition should appear diffuse because of the small size of the single molecule in comparison to macroscopic systems.

Study of agarose gels by electron microscopy of freeze-fractured surfaces

Abstract: The distribution of fibers in agarose gels has been studied by electron-microscopic examination of replicas formed from freeze-fracture surfaces. For gels set in water, the results obtained support the model proposed for the gel structure by Arnott et al. (1974) of a random array of long, straight, connected fibers, with each fiber having a diameter equivalent to that of an aggregate of approximately 10–30 agarose helixes, depending on the initial agarose concentration. The density of these fibers, their water content, and the total length of fibers per unit volume have been derived from the measured distribution of intersections per unit area of freeze-fracture surfaces. For gels set in the presence of salt, the distribution of fibers becomes distinctly non-Poissonian, leading to larger interfiber spaces and a gel of greater effective pore size. The larger pore size of gels set in the presence of salt also has been revealed by electrophoretic measurements in which the relative migration rates of plasmid DNA molecules of varying conformations have been determined.

The C-terminal extrahelical peptide of type I collagen and its role in fibrillogenesis in vitro

Abstract: The formation in vitro of fibrils from type I acid-soluble calf skin collagen has been studied before and after removal of the extrahelical peptides with carboxypeptidase and with pepsin. Turbidimetric studies show that the mechanism of fibril growth in undigested collagen is similar to that in pepsin-digested collagen; following carboxypeptidase digestion, however, a different growth mechanism was apparent. The two mechanisms have been further characterized by electron microscopy. In the course of formation of fibrils from undigested collagen, “early fibrils” (short D-periodic fibrils that have both ends visible) occurred in the lag phase under the precipitating conditions employed here. After pepsin or carboxypeptidase digestion of the collagen no “early fibrils” were seen. In carboxypeptidase-digested collagen, lateral assembly was inhibited; after pepsin digestion, linear assembly was inhibited. Complete removal of the extrahelical peptides prevented fibril formation under the conditions used here. Electron-optical examination of segment-long-spacing (SLS) dimers established a more complete removal of the C-terminal peptide after carboxypeptidase digestion than after pepsin digestion. Analyses of staining patterns of SLS dimers and fibrils from undigested and digested samples showed that the C-terminal peptide in SLS crystallites and fibrils formed from undigested collagen is in a condensed conformation. A proposed conformation, in which condensation occurs predominantly in a hydrophobic region at the proximal end of the C-terminal peptide, is discussed in terms of a dual role for the C-terminal peptide in fibrillogenesis. One role, shared with the N-terminal peptide, is to participate in interactions between the 4D-staggered molecules leading to the formation of linear aggregates; the other is to participate in interactions between these linear aggregates giving rise to D-periodic aggregates and lateral (as well as linear) growth.

Cyclodextrin–adamantanecarboxylate inclusion complexes: A model system for the hydrophobic effect

Abstract: Thermodynamic studies of the binding of adamantanecarboxylate to cyclodextrins have been made as a function of temperature and added organic cosolvent (methanol) using flow microcalorimetry. The negative heat capacity change associated with the adamantanecar-boxylate/β-cyclodextrin interaction and the fact that the interaction is weakened by the addition of methanol implicate the binding process as being a hydrophobically driven one. The negative enthalpy change (ΔH0 = −5.5 kcal/mol) and near-zero entropy change (ΔS0 = 1.5 cal/mol deg) are quite different from the values normally expected for a hydrophobic bond, indicating that other bonding forces are important in addition to the hydrophobic effect. The relative contribution of the hydrophobic effect and other bonding forces (most likely van der Waals forces) to the overall binding was judged from an analysis of the dependence of the thermodynamics of the association process on the surface tension of the water–methanol mixtures following a model for “solvophobic” bonding described by Sinanoglu [Molecular Associations in Biology (1968) Academic Press, New York, pp. 427–445]. From this analysis, adamantane–carboxylate/cyclodextrin complex formation is found to be driven to the extent of −1.9 kcal/mol by the hydrophobic effect. Furthermore, the hydrophobic driving force is found to be characterized by a positive ΔS0 of 10 cal/mol deg. The remaining free energy of binding (and the ΔH0 of binding of ∼−6 kcal/mol) is then due to the intrinsic (surface-tension-independent) van der Waals interaction between the ligand and cyclodextrin cavity.

Calorimetric determination of base‐stacking enthalpies in double‐helical DNA molecules

Abstract: Differential scanning calorimetry was used to directly determine the transition enthalpies accompanying the duplex-to-single-strand transition of poly[d(AT)], poly(dA)·poly(dT), poly[d(AC)]·poly[d(TG)], and d(GCGCGC). The calorimetric data allow us to define the following average base-stacking enthalpies: Interaction ΔH (kcal/stack) AC/TG, TG/AC 5.6 AT/TA, TA/AT 7.1 AA/TT 8.6 GC/CG, CG/GC 11.9 Comparison with published data on the corresponding RNA interactions reveals remarkably good agreement. By assuming transition enthalpies to result from the pairwise disruption of nearest-neighbor stacking interactions, we used the enthalpy data listed above to predict the transition enthalpies for three oligomeric DNA duplexes. Excellent agreement was found between the predicted and the calorimetrically determined values.

Physicochemical properties of pectic acid. I. Thermodynamic evidence of a pH‐induced conformational transition in aqueous solution

Abstract: On the basis of measurements of enthalpy of dissociation and of dilution, an interamolecular conformational transition induced by pH change is shown for pectic acid in aqueous solution. Additional evidence is given by potentiometic, viscometric, and chiroptical results. The transition from a more rigid, probably H-bonded, structure prevailing at low pH to a more extended one at around neutrality is accompanied by a ΔH value of about 500 cal/equiv and a ΔS value of 1.6 cal/equiv K in water at 25°C. The addition of salts increases the stability of the rigid conformation without changing the general features of the phenomenon. Dilatometric measurements suggest that the transition is accompanied by practically no change in the overall solvation of the polymer chain.

Light scattering of bovine serum albumin solutions: Extension of the hard particle model to allow for electrostatic repulsion

Abstract: The light scattering of bovine serum albumin (BSA) has been measured at protein concentration up to 90 g/L and at pH values between 4.4 and 7.6. The dependence of scattering on both protein concentration and pH may be quantitatively accounted for by a simple extension of the hard-sphere model for protein solutions [Ross, P. D. & Minton, A. P. (1977) J. Mol. Biol.112, 437–452] allowing for electrostatic repulsions between molecules. According to the extended model, the radius of the effective hard spherical particle representing BSA varies with the net electrical charge of the BSA molecule in a manner which may be calculated from electrostatic theory.

Structure of the deoxytetranucleotide d-pApTpApT and a sequence-dependent model for poly(dA-dT)

Abstract: Synopsis The x-ray structure of the hydrated ammonium salt of the deoxytetranucleotide dpApTpApT was determined by Patterson and direct methods at a resolution of 1 A. The crystal structure contains right-handed double-helical segments formed by complementary Watson-Crick-type hydrogen bonding between the adenine and thymine bases of neighboring molecules. The minihelix contains two base pairs. The chains are antiparallel. The A-T and T-A sequences have different phosphodiester conformations. The deoxyribose-pucker and the sugar-base orientation alternate along the chain depending on the nature of the base (3’-endo for purine and 2’-endo for pyrimidine). The extended structure is stabilized by base-base, base-sugar, and hydrogen-bond interactions. The minihelix of two base pairs provides starting coordinates for model-building studies of the dA-dT polymer. A B-DNAtype polymer structure is described, which has sequence-dependent alternations of both the deoxyribose pucker and the phosphate diester bridge conformation. Such sequence-dependent DNA structures, if present locally in regions such as operator sequences, could facilitate sequence-specific interactions. The crystal study also suggests possible geometrical parameters for the replication fork.

Light-scattering study of DNA condensation: Competition between collapse and aggregation

Abstract: Light-scattering studies were done to investigate the DNA collapse transition, a large and discontinuous reduction in the radius of gyration. Of particular concern was differentiating the compaction of a single DNA molecule from aggregation. Solutions of RK2 plasmid DNA (Mr = 37 × 106) or bacteriophage T7 DNA (Mr = 25 × 106) were titrated with the condensing reagents spermidine in aqueous solvent or magnesium ion in ethanol–water solvent. The transition was followed by the change in scattering at a single angle or by the change in the angular dependence of scattering. At concentrations below 1 μg/mL, only aggregation could be detected by observation at a single angle; therefore, to study the collapse transition, it was necessary to measure the angular dependence of scattering. The intensities measured between the angles 30° and 60° were fit to known scattering functions. At low concentrations of the condensing reagent, the data were consistent with the scattering function of a random coil. On the other hand, during the transition at higher reagent concentrations, the curve that fit the data required two components—the scattering function for a random coil with a large radius of gyration, plus that for a sphere with a radius about one-fifth of that of the coil. The fractional concentration of the sphere increased with increasing condensing-reagent concentration. This two-component behavior is in apparent contrast to the situation with a more flexible polymer such as polystyrene, in accord with theoretical predictions. At still higher reagent concentrations, aggregation was apparent. Condensation to a collapsed state was reversible without hysteresis, while dissolution of the aggregated state nearly always occurred with hysteresis. Qualitative agreement between the observed DNA collapse transition and the theoretical phase diagram presented in the preceding paper was found, although the light-scattering results did not show quantitative agreement with the simple theoretical model.

Aggregation of apolar peptides in organic solvents. Concentration dependence of 1H-nmr parameters for peptide NH groups in 310 helical decapeptide fragment of suzukacillin

Abstract: Peptide NH chemical shifts and their temperature dependences have been monitored as a function of concentration for the decapeptide, Boc-Aib-Pro-Val-Aib-Val-Ala-Aib-Ala-Aib-Aib-OMe in CDCl3 (0.001-0.06M) and (CD3)2SO (0.001-0.03M). The chemical shifts and temperature coefficients for all nine NH groups show no significant concentration dependence in (CD3)2SO. Seven NH groups yield low values of temperature coefficients over the entire range, while one yields an intermediate value. In CDCl3, the Aib(1) NH group shows a large concentration dependence of both chemical shift and temperature coefficient, in contrast to the other eight NH groups. The data suggest that in (CD3)2SO, the peptide adopts a 310 helical conformation and is monomeric over the entire concentration range. In CDCl3, the 310 helical peptide associates at a concentration of 0.01M, with the Aib(1) NH involved in an intermolecular hydrogen bond. Association does not disrupt the intramolecular hydrogen-bonding pattern in the decapeptide.

Thermodynamic functions of biopolymer hydration. I. Their determination by vapor pressure studies, discussed in an analysis of the primary hydration process

Abstract: The primary hydration process of native biopolymers is analyzed in a brief review of the literature, pertaining to various aspects of biopolymer–water systems. Based on this analysis, a hydration model is proposed that implies that the solution conformation of native biopolymers is stable at and above a critical degree of hydration (hp′ = 0.06–0.1 g H2O/g polymer). This water content corresponds to the fraction of strongly bound water, and amounts to ∼20% of the primary hydration sphere. In order to test this model, detailed sorption–desorption scanning experiments were performed on a globular protein (α-chymotrypsin). The results obtained are consistent with the proposed hydration model. They show that under certain experimental conditions, sorption isotherms can be obtained that do not exhibit hysteresis. These data represent equilibrium conditions and are thus accessible to thermodynamic treatment. Valid thermodynamic functions, pertinent to the interaction of water with biopolymers in their solution state, can be obtained from these sorption experiments.

Conformational dependence of the vicinal proton coupling constant for the CαCβ bond in peptides

Abstract: We use the nmr data concerning the CαHCβH fragment in eight peptides with rigid side chains to parametrize a Karplus correlation between the vicinal proton Jαβ coupling constant and the dihedral angle θ. When considering molecules containing the fragment CαHαCβHβHβ′, the three-dimensional structure of the model peptides does not need to be known with accurate precision, since each set of Jαβ and Jαβ′ coupling constants is then related to the coefficients of the Karplus equation. A good correlation is observed with the Karplus equation, which is in substantial agreement with the Jαβ coupling constants reported for rigid as well as rotating CαCβ bonds in peptides.

Lipid‐induced conformational changes in glucagon, secretin, and vasoactive intestinal peptide

Abstract: The CD of glucagon, secretin, and vasoactive intestinal peptide has been studied as a function of temperature in water and in aqueous solutions of dodecyl sulfate, phosphatidyl glycerol, and L-α-phosphatidic acid (dipalmitoyl). The anionic detergent and lipids induce helix formation in all three peptides, with the amount of induced helical content increasing in the order glucagon < secretin < vasoactive intestinal peptide. These observations are subject to quantitative rationalization using a matrix formulation for the configuration partition function. In this formulation the major conformational consequences of the interaction with anionic lipids or detergents is an increase in the probability for helix formation by arginyl, histidyl, and lysyl residues. The region in which helix formation is maximal is found to be at amino acid residues 13–20 in all three peptides. Other studies have implicated this portion of the polypeptide chain in receptor binding. Thus, the helical segment induced by interaction with anionic lipids may play an important physiological role.

Vibrational circular dichroism in amino acids and peptides. 7. Amide stretching vibrations in polypeptides

Abstract: Vibrational circular dichroism (VCD) spectra for the principal amide stretching vibrations, amide A (NH stretch) and amide I (predominantly CO stretch), are presented and analyzed for a variety of polypeptides dissolved in chloroform, as well as for two examples in D2O. Our results for poly(γ-benzyl-L-glutamate) confirm the first and only previous report of VCD in polypeptides carried out by Singh and Keiderling [(1981) Biopolymers20, 237–240]. Collectively, our spectra show that the sense of the bisignate VCD in these two regions depends on the sense of α-helicity and not on the absolute configuration of the constituent amino acids. This conclusion is established by obtaining VCD for the two polypeptides, poly(β-benzyl-L-asparate) and poly(im-benzyl-L-histidine), that form left-handed as opposed to right-handed α-helices. A new amide band having significant VCD intensity owing to its Fermi resonance interaction with the NH stretching mode has been identified as a weak shoulder on the low-frequency side of the amide A band near 3200 cm−1 and is assigned as a combination band of the amide I and amide II vibrations. VCD spectra of polypeptides in D2O solution, although weak, have been successfully measured in the amide I region, where spectra appear to be more complicated due to the presence of solvated and internally hydrogen-bonded amide groups. Strong monosignate contributions to the VCD in the amide A and amide I regions for some of the polypeptides indicate coupling of an electronic nature between these two regions and is deduced by an application of the concept of local sum rules of rotational strength. It appears that a detailed understanding of the VCD obtained for polypeptides will not only be diagnostic of secondary structure, but also of more subtle structural and vibrational effects that give rise to local, intrinsic chirality in the amide vibrations.

Crystallization behavior of glucomannan

Abstract: Five different glucomannan samples were recrystallized from dilute solution. Depending on the experimental conditions, the crystals obtained could be identified as corresponding to the mannan I (anhydrous precipitate of more or less regular lozenge-shaped crystals) or mannan II (hydrated gel-forming pseudo-fibrillar precipitate). High-molecular-weight material, low temperature of crystallization, or a polar crystallization medium favored the mannan II polymorph, whereas a low-molecular weight, a high temperature of crystallization, and a crystallization medium of low polarity yielded the mannan I polymorph. Since the base-plane unit-cell dimensions are fairly constant with respect to variation of glucose, it is likely that isomorphous replacement of mannose by glucose occurs in glucomannan crystallization; the data also indicate that perfection of the glucomannan crystals was reduced in specimens having a high glucose:mannose ratio. The oriented crystallization of glucomannan on cellulose microfibrils was also studied under conditions where the mannan I polymorph was obtained. This gave shish-kebab structures that were characterized.

Interactions of DNA with divalent metal ions. I. 31P‐nmr studies

Abstract: 31P-nmr has been used to investigate the specific interaction of three divalent metal ions, Mg2+, Mn2+, and Co+2, with the phosphate groups of DNA. Mg2+ is found to have no significant effect on any of the 31P-nmr parameters (chemical shift, line-width, T1, T2, and NOE) over a concentration range extending from 20 to 160 mM. The two paramagnetic ions, Mn2+ and Co2+, on the other hand, significantly change the 31P relaxation rates even at very low levels. From an analysis of the paramagnetic contributions to the spin–lattice and spin–spin relaxation rates, the effective internuclear metal–phosphorus distances are found to be 4.5 ± 0.5 and 4.1 ± 0.5 A for Mn2+ and Co2+, respectively, corresponding to only 15 ± 5% of the total bound Mn2+ and Co2+ being directly coordinated to the phosphate groups (inner-sphere complexes). This result is independent of any assumptions regarding the location of the remaining metal ions which may be bound either as outer-sphere complexes relative to the phosphate groups or elsewhere on the DNA, possibly to the bases. Studies of the temperature effects on the 31P relaxation rates of DNA in the absence and presence of Mn2+ and Co2+ yielded kinetic and thermodynamic parameters which characterize the association and dissociation of the metal ions from the phosphate groups. A two-step model was used in the analysis of the kinetic data. The lifetimes of the inner-sphere complexes are 3 × 10−7 and 1.4 × 10−5 s for Mn2+ and Co2+, respectively. The rates of formation of the inner-sphere complexes with the phosphate are found to be about two orders of magnitude slower than the rate of the exchange of the water of hydration of the metal ions, suggesting that expulsion of water is not the rate-determining step in the formation of the inner-sphere complexes. Competition experiments demonstrate that the binding of Mg2+ ions is 3–4 times weaker than the binding of either Mn2+ or Co2+. Since the contribution from direct phosphate coordination to the total binding strength of these metal ion complexes is small (∼15%), the higher binding strength of Mn2+ and Co2+ may be attributed either to base binding or to formation of stronger outer-sphere metal–phosphate complexes. At high levels of divalent metal ions, and when the metal ion concentration exceeds the DNA–phosphate concentration, the fraction of inner-sphere phosphate binding increases. In the presence of very high levels of Mg2+ (e.g., 3.1M), the inner-sphere ⇄ outer-sphere equilibrium is shifted toward ∼100% inner-sphere binding. A comparison of our DNA results and previous results obtained with tRNA indicates that tRNA and DNA have very similar divalent metal ion binding properties. A comparison of the present results with the predictions of polyelectrolyte theories is presented.

Linear dichroism studies of nucleic acids. II. Calculation of reduced dichroism curves of A-and B-form DNA†

Abstract: We have calculated the uv linear dichroism for the A- and B-forms of DNA using π-π* transition moments and band components determined from the free DNA bases. The reduced dichroism (LDR) as a function of wavelength is estimated is in the 220–300-nm region, for both the oriented-gas model and a simple exciton model. For B-form DNA, LDR is obtained to −1.48S (S being the orientation factor) over the whole wavelenth region by both models. For A-form DNA, LDR is not constant, but changes monotonically from about −1.15S at 220 nm to about −1.35S to −1.45S at 300 nm, depending on base combination and degree of interaction (−1.35S for the oriented gas). It is emphasized that a common assumption of a single “effective” transition moment of the principal band at 260 nm may not generally be made because of the extensive overlap of differently polarized bands. The possibility of using the reduced dichroism curve for characterizing the secondary structure of DNA is discussed.

Effect of water on piezoelectric, dielectric, and elastic properties of bone

Abstract: The complex piezoelectric constant (d = d′ − id″), elastic constant (c = c′ + ic″), and dielectric constant (e = e′ − ie″) were measured at a frequency of 10 Hz over the temperature range from −150 to 50°C and for a range of hydration up to 0.26 g/g for decalcified bone and up to 0.084 g/g for bone. For decalcified bone, e′ and e″ increased with increasing hydration with a deflection at the critical hydration hc = 0.08 g/g;d′ at −150°C increased below hc but decreased above hc with increasing hydration; c′ increased below −60°C but decreased above −60°C with increasing hydration; and the peak temperatures of e″, d″, and c″ below −50°C agree with each other and decreased with increasing hydration with a deflection at hc. For bone, similar hydration and temperature dependences were observed for e and c. However, the dependence of d on hydration and temperature was different from that of decalcified bone, reflecting a two-phase structure consisting of collagen fibers and mineral hydroxyapatite. The critical hydration for bone was 0.04 g/g.

Simulations of the solvent structure for macromolecules. III. Determination of the Na+ counter ion structure.

Abstract: We report on a computer experiment in which, using Monte Carlo techniques, we considered a three-turn (30-base-pairs) B-DNA fragment as a solute and a set of 1200 water molecules and 60 sodium counterions (at a temperature of 300 K) as a solvent. From a statistical analysis of the Monte Carlo simulation (applied to the water molecules and counterions in the B-DNA field), we determined that the counterions themselves conform to two helical structures intertwined with the two strands. The strutures of the water molecules solvating both counterion helices and the two B-DNA strands are fully analyzed and described in detail. A model for base-pair recognition based on the above findings is proposed. Aspects of the unwinding mechanism are discussed.

Molecular‐mechanics studies on d(CGCGAATTCGCG)2 and dA12·dT12: An illustration of the coupling between sugar repuckering and DNA twisting

Abstract: Molecular-mechanics calculations have been carried out on the base-paired deoxy dodecanucleoside undecaphosphates d(CGCGAATTCGCG)2 and d(A12)·d(T12). These refinements were carried out using the model-built Arnott B-DNA geometry as initial coordinates (with a helix repaeat of 10.0 residues/turn), as well as helix repeats ranging from 9 to 12 residues/turn. There was some variation in the optimum calculated helix repeat, depending on the dielectric model, the presence or absence of counterions, and the method used for inclusion for nonbonded interactions; the most interesting general result of these calculations was the coupling between furanose sugar puckering and twist. This coupling was observed for all models. With a helix repeat of 9.0 residues/turn, all sugars remain C(2′)endo after refinement; as the helix repear increases to 12.0 residues/turn, the number of sugars repuckering to O(1′)endo and C(3′)endo increases also. With our most rigorous model (i.e., a model with no cutoff distance for nonbonded interactions) and a helix repeat of 10.0 residues/turn, we find a greater tendency for pyrimidine than purine repuckering in d(CGCGAATTCGCG)2, in agreement with the x-ray structural data of Drew et al. [(1981) Proc. Natl. Acad. Sci. USA78, 2179–2185]. We also carried out a number of calculations in which we “forced” one of two deoxy sugars to repucker or one of the C3′-O3′-P-O5′ (ω) torsion angles to change from gauche− to trans using dihedral angle constraints. After the constraints were removed, some of these structures “reverted” to the sugar pucker of the initial structures, while others remained repuckered. In all cases, the energies for repuckered structures after refinement were very similar to energies of the initial structure. Experiments and theory suggest that local conformational fluctuations play an essential role in nmr relaxation of 31P and 13C atoms in double-helical DNA. The results of our previous calculations on hexanucleoside phosphates and the calculations presented there are consistent with an important contribution to nmr relaxation processes of conformational changes in the torsion angle ω′ from gauche− to trans and deoxy sugar repuckering from C(2′)endo to C(3′)endo. Specifically, the calculations presented here indicate a very flexible phosphate backbone in helixes having an intermediate helix repeat of 10 to 11 residues/turn. These helixes may accommodate sugars of variable pucker without significantly disrupting base–base hydrogen-bonding and stacking interactions. All of the variant structures are similar in energy, suggesting that conversion between them can occur on a nanosecond time scale, as observed in nmr relaxation experiments.

On the theory of Ψ‐condensation

Abstract: We suggest a theory of Ψ-condensation, based on the assumption that a compact DNA particle is a globule, and specifically that a polymer solution is a strongly fluctuating system and that double-stranded DNA is a stiff homopolymer single-stranded chain. We show the DNA globule as it appears in a dilute poly(ethylene oxide) (PEO) solution. The corresponding phase transition is investigated in detail. Growth of the PEO concentration should lead to a decrease in the size of the compact particle and to an increase in its optical rotatory power. Conditions are defined at which drastic compaction of DNA takes place, accompanied by the loss of its optic rotatory power, in regions of high PEO concentrations.

Effects of salts on the nonequivalent stability of the α-helices of isomeric block copolypeptides

Abstract: The stability of the α-helices of isomeric block copolypeptides is nonequivalent, as reported previously. In order to explore the origin of the nonequivalence, the stability of α-helix of two block copolypeptides, (L-Ala)20-(L-Glu)20-(L-Phe) (designated as AEF) and (L-Glu)20-(L-Ala)20-(L-Phe) (EAF), in aqueous solution was investigated as a function of pH, temperature, and salt concentration by the measurement of the α-helical content using CD at 223 nm. The transition temperature, Tm, as a measure of the stability of the α-helix, decreased with increasing the salt concentration for EAF, while Tm increased for AEF. The results indicate that electrostatic interactions affect the nonequivalence of such helical stability. Thermodynamic quantities, ΔG, ΔH, and ΔS, of the thermal transition from random coil to α-helix were obtained by applying the curve-fitting method to the data. The major contribution to the effects of salts seems to be the entropic term, not the enthalpy term. This is unexpected, since the salt ions would weaken electrostatic interactions between ionized groups and the dipole along the helical axis, which affect the enthalpy term. In addition, the dependence of the electrostatic effect on the salt concentration is different for EAF and AEF. There fore, the nonequivalence cannot be accounted for by only the electrostatic effect, suggesting that it originates from some intrinsic property of the α-helix.