bluuebunny/crossref_metadata_2025 huggingface dataset:
Role of proline …︁ proline interactions in the packing of collagenlike poly(tripeptide) triple helices
Authors: Némethy George , Scheraga Harold A.
Published: December 2004

Conformational energy computations were carried out on the packing of two identical collagenlike poly(tripeptide) triple helices in order to determine the energetics of favorable packing arrangements as a function of composition and chain length. The triple helices considered were [CH3CO‐(Gly‐Pro‐Pro)nt‐NHCH3]3 and [CH3CO‐(Gly‐Pro‐Ala)nt‐NHCH3]3, with nt = 3, 4, and 5. The packing arrangements were characterized in terms of their intermolecular energies and orientation angles Ω0 of the axes of the two triple helices. For short triple helices (nt = 3 or 4), many low‐energy orientations, with a wide range of values of Ω0, can occur. When the triple helices are longer (nt = 5), the only low‐energy packing arrangements of two poly(Gly‐Pro‐Pro) triple helices are those with a nearly parallel orientation of the two helix axes, with Ω0 ≈ −10°. This result accounts for the observed parallel (rather than antiparallel) arrangement of collagen molecules in microfibril assembly and stands in contrast to the preferred antiparallel arrangement of a pair of α‐helices. Since the preference for a parallel arrangement of these collagenlike triple helices is less pronounced in the case of poly(Gly‐Pro‐Ala), it appears that this preference is a consequence of the frequent presence of imino acids in position Y of the Gly‐X‐Y repeating triplet. In poly(Gly‐Pro‐Ala), most of the low‐energy packing arrangements are parallel, but a few arrangements with low energies and high values of |Ω0| occur. These packing arrangements have a high energy, however, when Pro is substituted for Ala, and thus they are not accessible for collagen with natural amino (imino) acid sequences. The computations reported here account for some of the characteristic features of collagen packing in terms of the local interaction energies of a pair of triple helices.
Absorption and circular dichroism spectra of CuCl2 complexed with poly(S‐carboxymethyl‐L‐cysteine) and poly(S‐carboxyethyl‐L‐cysteine)
Authors: Maeda Hiroshi , Oka Kazuki , Ikeda Shoichi
Published: December 2004

The interaction of CuCl2 with poly(S‐carboxymethyl‐L‐cysteine) (poly[Cys(CH2COOH)]) and poly(S‐carboxyethyl‐L‐cysteine) (poly[Cys(C2H4COOH)]) were studied by absorption spectra and circular dichroism (CD). On mixing CuCl2 with polypeptide solutions, absorption bands appeared at 320–325 nm in both polypeptides, and at 255–260 nm in the case of poly[Cys(CH2COOH)]. A stable bound species was formed in the case of poly[Cys(CH2COOH)], since the apparent molar absorption coefficient of the bound species did not depend on the mixing ratio. From the absorption data, it was inferred that Cu2+ ions were complexed with the side chains, most probably with sulfur atoms and carboxyl groups. Induced optical activities were observed for the two polypeptides. The CD spectra of poly[Cys(CH2COOH)] + CuCl2 gave simpler aspects than those of poly[Cys(C2H4COOH)] + CuCl2.
Determination of NOE “silent” dipolar interactions between magnetically equivalent nuclei: Application to poly(dA) · poly(dT)
Authors: Behling Ronald W. , Kearns David R.
Published: December 2004

The ratio of the spin–spin relaxation rate, R2, to the selective spin–lattice relaxation rate, R, can be used to detect and determine the magnitude of dipolar interactions between magnetically equivalent unclei in macromolecules. We use this method to show that there is strong interaction between adjacent AH2 protons in poly(dA) · poly(dT). The largest possible AH2–AH2 distance that will account for the observed magnitude of the interaction is ∼3.5 Å, provided the AH2 protons are located close (within 0.6 Å) to the helix axis. Structures with shorter AH2–AH2 separations could account for the nmr data, but they are rejected because they would reduce the interbase separation to unacceptably small values. A comparison of rates measured at 360 and 500 MHz shows that the chemical‐shift anisotropy makes a negligible contribution to the observed relaxation rates.
Quasielastic laser light scattering and electron microscopy studies of the conformational transitions and condensation of poly(dA‐dT) · poly(dA‐dT)
Authors: Thomas T. J. , Bloomfield V. A.
Published: December 2004

Poly(dA‐dT) · poly(dA‐dT) undergoes a reversible conformational transition in the presence of Co(NH3) or spermidine in low salt (10 mM NaCl + 1 mM Na cacodylate). This transition is similar, as judged by changes in the CD spectrum, to the B‐to‐X transition of the polymer provoked by alcohol and Cs+ [Vorlickova et al. (1983) J. Mol. Biol. 166, 85–92; (1982) Nucleic Acids Res. 10, 6969–6979] and by meso‐substituted porphyrin ligands [Carvlin et al. (1983) Nucleic Acids Res. 11, 6141–6154]. Under the salt conditions indicated, the CD transition begins with Co(NH3) at about 70 μM and is complete by 150 μM; with spermidine, it begins at about 300 μM and is complete by 600 μM. Total intensity light scattering shows a marked increase at trivalent cation concentrations somewhat below those at which the CD transition begins. Quasielastic laser light scattering (QLS) measurement of the translational diffusion coefficient, DT, shows that, in the presence of Co(NH3), the hydrodynamic radius, Rh, increases from 260 to 1450 Å over the concentration range of 25 to 200 μM. With spermidine, Rh is 550±50 Å up to 200 μM, then increases rapidly. Values of Rh in this range are generally found for toroidal or other compact condensed forms of DNA. Such forms—toroidal, spheroidal, and rodlike structures—are observed in electron micrographs of poly(dA‐dT) · poly(dA‐dT) when the trivalent cation concentration is in the transition range. Above that range, extensive aggregation of the polymer chains is seen. Taken together, these results suggest a sequenc of related secondary and tertiary structure changes as trivalent cations are added to a low‐salt solution of poly(dA‐dT) · poly(dA‐dT). At very low Co(NH3) or spermidine, condensation of the polymer takes place while it is still in the B‐form. Further additions of trivalent cation provoke a transition from B‐ to X‐form, finally resulting in extensively aggregated polymer. These results are different from those generally observed with native DNA, where condensation with polyamines or Co(NH3) in aqueous solution is not accompanied by secondary structural change. They are also different from those we have seen with poly(dG‐me5dC) · poly(dG‐me5dC), where condensation and the B–Z transition occur at the same ionic conditions. These distinctions are another entry in the growing catalog of sequence‐dependent structural effects that may be important in the regulation of the biological activity of DNA.
Molecular organization of glycophorin A: Implications for membrane interactions
Authors: Welsh E. J. , Thom D. , Morris E. R. , Rees D. A.
Published: December 2004

Physical studies and conformational analysis of human glycophorin A suggest a revised model for its molecular organization, self‐association, and interactions with the erythrocyte membrane. Intrinsic viscosity has been used to study, under more physiological conditions, the monomer–dimer equilibrium demonstrated previously by polyacrylamide–SDS gel electrophoresis. The results show that the equilibrium persists in the absence of detergent and support earlier indications that the dimer is probably the physiologically relevant form and that it is promoted by salt, inhibited by conventional denaturants, and abolished by carboxymethylation.

Combined application of CD, fitted to the poly‐(L‐lysine) model spectra of Greenfield and Fasman, and conformational prediction, by the statistical method of Chou and Fasman and the stereochemical approach of Lim, suggests five helical sequences in glycophorin A: Arg‐39 to Tyr‐52 (A); Gln‐63 to Glu‐70 (B); Glu‐72 to Leu‐89 (C); Ile‐95 to Lys‐101 (D); and Leu‐118 to Asn‐125 (E). Sequence A occurs only at low pH and may be stabilized by favorable noncovalent interactions of O‐linked tetrasaccharide side chains. The other four helices all occur in the dimeric form of glycophorin A at physiological pH and ionic strength. Sequence D is destroyed by trypsin, and is also lost on conversion to the monomeric form of the glycoprotein at low ionic strength. Sequence E is denatured by 6M guanidine hydrochloride/4M urea. Sequences B and C, which are separated by a single proline residue, are stable under all these conditions.

Dimerization of the major, hydrophobic helical sequence, (C) may be promoted and directed by an adjacent short sequence of intermolecular parallel β‐sheet (Leu‐90 to Tyr‐93). It is proposed that these two structures span the lipid bilayer in vivo, and that helices B and D lie, respectively, along the outer and inner surfaces of the membrane. Molecular organization in the N‐ and C‐terminal regions of the molecule is discussed in terms of evidence from the present work and from other recent investigations.
Sequence‐specific assignment of the backbone 1H‐ and 31P‐nmr lines in a short DNA duplex with homo‐ and heteronuclear correlated spectroscopy
Authors: Frey M. H. , Leupin W. , Sørensen O. W. , Denny W. A. , Ernst R. R. , Wüthrich K.
Published: December 2004

We report the assignment of the backbone 1H‐ and 31P‐nmr lines in the synthetic hexadeoxyribonucleotide pentaphosphate duplex d(GCATGC)2, using double quantum filtered 1H‐1H correlation spectroscopy, 1H observed 1H‐31P heteronuclear correlation spectroscopy, and 31P relayed 1H‐1H correlation spectroscopy. The strategy used enables one to make sequence‐specific resonance assignments without reference to a known or assumed conformation of the DNA fragment.
Rapid estimation of length distributions of microtubule preparations by quasi‐elastic light scattering
Authors: Hallett F. R. , Keates R.
Published: December 2004

A new method for determining the length distribution of microtubule preparations, using quasi‐elastic light scattering (QELS) is described. The experimental electric field autocorrelation functions are analyzed using a closed‐form expression recently described by Hallett, Craig, and Nickel [(1985) Biopolymers 24, 947–960], which is incorporated into an exponential sampling procedure. The resulting length distributions are compared with those obtained for the same samples with electron microscopy (EM). If standard grid‐preparation procedures were used, the EM results yielded shorter length distributions than QELS. When grids were prepared at lower microtubule number densities, less grid washing was required. In these cases, excellent agreement between the EM and QELS techniques were achieved.
Chain association of pectic molecules during calcium‐induced gelation
Authors: Thibault J. F. , Rinaudo M.
Published: December 2004

The chain association of pectic molecules with different levels and patterns of esterification during calcium‐induced gelation was studied by methods such as light scattering, viscometry, and determination of calcium activity coefficient and of calcium transport parameter. A gel point can be determined, assuming a power law including a critical ratio (equivalent concentration of calcium ions/pectin carboxylic groups) and quasi‐critical exponents varying in the range 0.50–1.26. The values of these critical parameters were discussed as a function of polymer concentration, of level and pattern of esterification, and of the nature of the divalent counterion. The lower these values are, the better, apparently, the gel‐forming ability of the pectins is.
DNA orientation during gel electrophoresis and its relation to electrophoretic mobility
Authors: Hurley Ian
Published: December 2004

Intensities of polarized fluorescence from ethidium bound to phage λ DNA undergoing agarose gel electrophoresis were measured. The intensities were strongly field dependent at voltage gradients of 8 V/cm, consistent with a partial orientation of DNA helices in the direction of electrophoresis about 500 times larger than seen in the same field in solution. Such an orientation was predicted by a reptation model of gel electrophoresis advanced by Lumpkin et al. [(1985) Biopolymers, 24, 1573–1593]. The present results can be fit successfully to this theory with a single adjustable parameter, the gel–DNA contact distance. Also, λ DNA electrophoretic mobilities in the same concentration gel were determined using the same buffer system. Both orientation and mobility measurements can be fit to the reptation theory within a factor of two using the same values of two parameters, the gel–DNA contact distance and the ratio of DNA charge to frictional coefficient.
Halogenated nucleic acids: Effects of 5‐fluorouracil on the conformation and properties of a polyribonucleotide and its constituents
Authors: Loomis Ronald E. , Alderfer James L.
Published: December 2004

The conformational properties of 5‐fluorouracil derivatives are compared to uracil derivatives. FUrd, 5′‐FUMP, and poly(FU) are studied as a function of pH and temperature by 19F‐ and 1H‐nmr spectroscopy, and the corresponding uracil derivatives by 1H‐nmr spectroscopy. FUrd exhibits no significant conformational changes with solution pH (5–10). In contrast, at low pH (6–7) 5′‐FUMP and 5′‐UMP show similar conformational features, while at high pH (9) 5′‐FUMP shows significant conformational alterations. Also, poly(U) and poly(FU) are conformationally similar at low pH, but increasing pH induces changes in poly(FU). These changes are observed in the backbone [γ(C4′‐C5′)], furanose, and furanose‐base conformations. The apparent pKa of N3‐H ionization of the FUra base is determined by 1H‐ and 19F‐nmr to range from 7.5 to 8.2 [FUrd < 5′‐FUMP < 5′‐FUDP < poly(FU)]. These observations are interpreted as a result of electrostatic interactions generated between the ionized phosphate group and the negatively charged base moiety as the pH is raised. The interaction properties of poly(FU) with ApA are studied by 1H‐ and 19F‐nmr spectroscopy, and these properties compared to those published for poly(U). Poly(FU) forms a complex with ApA inducing upfield 1H‐shifts in both components, and downfield 19F‐ shifts in poly(FU). The base stoichiometry of the complex for poly(U)·ApA is 2U:1A at various U/A ratios. In contrast, the base stoichiometry of the poly(FU)·ApA complex appears to be dependent on the FU/A ratio. At high FU/A ratio, the complex is 2FU:1A, and as the FU/A ratio approaches unity the complex becomes 1FU:1A.
Sequential polypeptides containing arginine as histone models: Synthesis and conformational studies
Authors: Panoy‐Pomonis Eugenia , Sakarellos Constantinos , Sakarellos‐Daitsiotis Maria
Published: December 2004

The sequential polypeptides (L‐Arg‐X‐Gly)n, where X represents amino acid residues Ala, Val, and Leu, were prepared as models of arginine‐rich histones to be used in studying their structure and their interactions with DNA. The polymerization was carried out on the pentachlorophenyl active esters of the appropriate tripeptides, while the toluene‐4‐sulfonyl group was used for protecting the arginine guanido group. CD was employed to investigate the conformation of (L‐Arg‐X‐Gly)n polymers in aqueous solutions, at different pH, as well as in trifluoroenthanol and hexafluoroisopropyl alcohol solutions. In aqueous solutions (at pH 7 and 12) the prepared sequential polymers behaved as a random coil. The CD spectra in various trifluoroethanol–water or hexafluoroisopropyl alcohol–water mixtures indicated that the degree of helical conformation of the studied polytripeptides increased in the order of Ala → Val → Leu. The opposite was true for the β‐structure. Characteristics of β‐turn are excluded from the poly(L‐Arg‐L‐Leu‐Gly), which assumed the most pronounced helical conformation. The poly(L‐Arg‐L‐Val‐Gly) exerts a significant preference to the β‐turn structure compared to that of poly(L‐Arg‐L‐Ala‐Gly). Thus the probability for helical, β‐structure or β‐turn conformations of the polymers was analyzed in relation to the bulkiness and length, and to the special features of the X‐residue side chain (β‐branching). We concluded that the prepared sequential arginine‐containing polypeptides are plausible models for histone fractions, f3 and f2α1.
Picosecond relaxations in model substances for proteins: A millimeter‐wave investigation on crystalline alkyl amides
Authors: Häseler S. , Poglitsch A. , Genzel L. , Kremer F.
Published: December 2004

The dielectric absorption at millimeter‐wave (mm‐wave) frequencies (50–150 GHz) of N‐methylacetamide (NMA), N,N‐dimethylacetamide (DiNMA), and N,N‐dimethylacrylamide (DiNMAcry) is measured. Measurements are performed using the oversized‐cavity technique in the temperature range from liquid helium to room temperature. Additionally, a mm‐wave interferometeric measurement at room temperature is made. NMA and DiNMAcry exhibit monotonic increases of the absorption coefficient with temperature as well as with frequency. For DiNMA a monotonic increase of the absorption coefficient with frequency is also found, while the absorption coefficient as a function of temperature shows a pronounced maximum at approximately 30 K. At this maximum the absorption coefficient of DiNMA exceeds those of NMA and DiNMAcry by about two orders of magnitude. The dielectric behavior of the three substances can be described by relaxation processes in asymmetric double‐well potentials. For the low‐temperature relaxation in DiNMA the double well could be established by two possible positions of the molecule in the crystal that are separated by a rotational movement. Hydrogen bonds and long side chains may hinder these relaxational movements in NMA and DiNMAcry, respectively, and thereby account for their comparatively lower absorption. The results are compared with similar results recently obtained on proteins and synthetic biopolymers.
Conformation of dioxopiperazines, II. CNDO/2 quantum mechanical calculations on conformational preferences in cyclo (glycyl‐L‐alanyl), cyclo(glycyl‐L‐valyl), and both epimers of cyclo‐di‐(alanyl)
Authors: Bielinski Henryk , Ciarkowski Jerzy
Published: December 2004

Conformational energy calculations, aimed at verification of the suitability of the semiempirical molecular orbital CNDO/2 method for conformational elucidations in cyclic dipeptides formed from amino acids with aliphatic side chains, have been carried out. The results obtained for four dioxopiperazines [DOP; cyclo(Glycyl‐L‐Alanyl), cyclo(Glycyl‐L‐Valyl), and both epimers of cyclo‐di‐(Alanyl)] point out very good agreement with experimental premises. The latter include (1) the preference of the cis‐peptide bonds for being nonplanar, which results in twisted‐boat conformations of the DOP ring; (2) greater stability of conformers with a side chain oriented axially over those with a side chain oriented equatorially; (3) the preference of cyclo(Gly‐Val) for assuming a folded conformation with one of the side chain γ‐methyl groups sticking over the DOP ring.
Experimental tests of a geometrical abstraction of fibrin polymerization
Authors: Dietler G. , Känzig W. , Häberli A. , Straub P. W.
Published: December 2004

By combining measurements of the enzymatic release of fibrinopeptide A (FPA) with measurements of intensity and linewidth of Rayleigh scattering from fibrin polymer solutions prior to gelation, we have systematically tested a variety of predictions that can be made on the basis of a simple geometrical abstraction of fibrin polymerization. The experimental investigations include FPA content of fibrin polymers, aggregation of fibrin with fibrinogen, enzyme kinetics, shift of the chemical equilibrium by adding Gly‐Pro‐Arg‐Pro or fibrinogen to the polymer solution, evolution of the polymerization, and influence of fibrinopeptide B release. Among the considered geometrical abstractions there is only one that survives the experimental tests and at the same time is compatible with the electron micrographs by other authors. The main conclusions that can be drawn are (1) the location of binding sites A must be taken from the structure of the fibrinogen molecule proposed by Hoeprich and Doolittle [Biochemistry (1983) 22, 2049–2055], (2) The fibrinogen monomer is basically centrosymmetric, (3) the state of polymerization is reversible and corresponds to a chemical equilibrium, and (4) Michaelis–Menten enzyme kinetics can be applied.
Structure of native proteoglycan aggregates from chick limb‐bud chondrocytes
Authors: Ohno Hiroyuki , Blackwell John , Jamieson Alexander M. , Pechak David G. , Carrino David A. , Caplan Arnold I.
Published: December 2004

Laser light‐scattering has been used to investigate the size of native proteoglycan aggregates (PGA‐aA1) from day‐8 chick limb‐bud chondrocyte cultures isolated under associative extraction and purification conditions in 0.4M guanidinium chloride (GdnHCl) solution. Dynamic light‐scattering measurements yielded a hydrodynamic radius, Rs, of 244 ± 10 nm for PGA‐aA1 in 0.4M GdnHCl, and a weight‐average molecular weight (Mw) of 150 ± 50 × 106 was obtained from a Zimm plot. Disaggregation in 4.0M GdnHCl aqueous solution yielded proteoglycan subunits (PGS) with Rs = 39 ± 2 nm, Mw = 1.6 ± 0.3 × 106, which reassembled in 0.4M GdnHCl to form “reconstituted native” aggregates (PGA‐raA1) with Rs = 121 ± 6 nm, Mw = 17 ± 3 × 106. A second specimen of PGA‐aA1 had Rs = 192 ± 10 nm, Mw = 100 ± 10 × 106. The latter value was estimated from an empirical relationship between Mw and Rs. After dissociation, this specimen reassembled to form PGA‐raA1 with Rs = 85 ± 5 nm, Mw = 12 ± 1 × 106. These data are compared with those for a specimen of reconstituted aggregate (PGA‐A1) that had been extracted under dissociative conditions and then reaggregated by dialysis to 0.4M GdnHCl aqueous solution, for which Rs = 138 ± 9 nm, Mw = 45 ± 8 × 106. From these values, we have calculated the weight‐average number of subunits per aggregate Nw: 111 for PGA‐aA1 and 12 for raA1 (70 and 7 for the second PGA‐aA1 and PGA‐raA1 specimen, respectively) as compared to 32 for PGA‐A1. The numbers of subunits per aggregate were also determined from electron micrographs of spread specimens. The latter results show the same trends as those obtained by light scattering, but lead in each case to lower numbers of subunits per aggregate. These data demonstrate conclusively that PGA samples exhibit a higher degree of aggregation in solution than visualized in typical electron microscopy (EM) preparations, probably due to disaggregation during EM specimen preparation. Since Nw determined both by light scattering (LS) and by EM are larger for native versus reconstituted aggregate samples, our data point to a more compact aggregation of subunits along the hyaluronic acid (HA) chains in the former.
Kinetics of nonspecific binding reactions of proteins with DNA flexible coils: Site‐based and molecule‐based association reactions
Authors: Mazur Sharlyn J. , Record M. Thomas
Published: December 2004

Domain effects on the pseudo‐first‐order kinetics of the reversible and irreversible association of proteins or other ligands with nucleic acids containing multiple binding sites are treated using the classical reaction‐diffusion equation applied to a spherical cell model of the nucleic acid solution and a diffuse‐sphere model for the nucleic acid chain molecule. Both uniform and Gaussian distributions of chain segments are analyzed. In general, the details of the segment distribution do not have a major effect on the kinetics of association. Domain effects are best examined experimentally by determining the effect of the molecular weight of the nucleic acid on the kinetics of the association reaction. A theoretical framework is presented that permits such data to be analyzed simply. Kinetic studies over a wide range of nucleic acid molecular weights are required in order to separate the contributions of diffusion and reaction to the observed kinetics, and to determine the contributions of site‐based and molecule‐based elements to the rate constants.
Thermodynamic parameters for the helix–coil thermal transition of ribonuclease‐S‐peptide and derivatives from 1H‐nmr data
Authors: Rico M. , Santoro J. , Bermejo F. J. , Herranz J. , Nieto J. L. , Gallego E. , Jiménez M. A.
Published: December 2004

Values for the thermodynamic quantities, ΔH° = 11.8 ± 2.0 Kcal/mole and ΔS° = 43.6 ± 6.0 e.u., of the 3‐13 helix–coil equilibrium of isolated S‐peptide (19 residue N‐terminal fragment of ribonuclease A) in aqueous solution (3 m M, 1M NaCl, pD 5.4) have been determined from a joint analysis of the Thr 3γ, Ala 6β, Phe 8meta, and Phe 8para 1H chemical shift vs temperature curves (−7 to 80°C) in several aqueous–trifluorethanol mixtures. Chemical shifts in the coil and in the helix have been determined for up to 16 protons belonging to the 3‐13 fragment. Thermodynamic parameters have also been determined for C‐peptide (13 residue fragment) and a number of S‐peptide derivatives. From the variation of the values of the thermodynamic parameters at pD 2.5, 5.4, and 8.0, a quantitation of the two helix‐stabilizing side‐chain interactions can be made: (1) Δ(ΔH°) ≃ 5 Kcal/mole and Δ(ΔS°) ≃ 18 e.u. for the salt bridge Glu 2− … Arg 10+ and (2) Δ(ΔH°) ≃ 3 Kcal/mole and Δ(ΔS°) = 9 e.u. for the one in which the His 12+ imidazolium group is involved, presumably a partial stacking with the Phe 8 side chain.
Enantioselective interactions of inversion‐labile trigonal iron(II) complexes upon binding to DNA
Authors: Härd Torleif , Nordén Bengt
Published: December 2004

We studied the interactions of the substitution‐inert inversion‐labile complexes Fe(bipy) and Fe(phen) [and the inversion‐stable complex Ru(bipy)] with DNA. The association of these complexes to DNA is mainly electrostatic, and Fe(phen) shows a more effective binding to DNA than the two bipyridyl complexes, possibly owing to a different binding mode. The interactions are enantioselective, leading to a Pfeiffer shift in the diastereomeric inversion equilibria and an excess of the Δ‐enantiomer of Fe(phen) and Fe(bipy), which is directly monitorable through CD. The partition constants for the inversion equilibrium range from 1.3 to 2.0 for Fe(bipy) and Fe(phen), depending on ionic conditions. From flow LD information about the orientation of the complexes on DNA was obtained: it is consistent with a fit of the Δ‐enantiomer in the major groove of the right‐handed DNA helix. The mechanisms of interaction are discussed against equilibrium, spectroscopic, and kinetic data.
Analysis of the interaction of membrane‐active peptides with membranes: The case of melittin in surfactant assemblies
Authors: Chandani Bina , Balasubramanian D.
Published: December 2004

Some of the factors that govern the interaction between membrane‐active peptides and membranes were analyzed using melittin as an example. The structural properties of melittin were studied in a variety of micellar and reverse micellar assemblies of varying sizes, shapes, and net charges. The roles of the polarity, packing, and the charge carried by the host assembly on the structural features of the incorporated melittin are delineated. Such an analysis is expected to be of relevance to other membrane‐active peptides as well.
Kinetics of ethidium's intercalation in packaged bacteriophage T7 DNA: Effects of DNA packing density
Authors: Griess Gary A. , Serwer Philip , Kaushal Varsha , Horowitz Paul M.
Published: December 2004

The kinetics of ethidium's intercalative binding to DNA packaged in bacteriophage T7 and two T7 deletion mutants have been determined, using enhancement of fluorescence to quantitate binding. At a constant ethidium concentration, the results can be described as first‐order binding with two different rate constants,k(=k1+k−1) andk(=k2+k−2). The larger rate constant (k) was at least four orders of magnitude smaller than the comparable first‐order forward rate constant for binding to DNA released from its capsid. At 25°C values ofkdecreased as the amount of DNA packaged per internal volume increased. This latter observation indicates that the rate of ethidium's binding to packaged T7 DNA is limited by an event that occurs inside of the DNA‐containing region of T7, not by the crossing of T7 capsid's outer shell. Arrhenius plots ofkMare biphasic, indicating a transition for packaged DNA at a temperature of 20°C. The data indicate thatks are limited by either sieving of ethidium during its passage through the packaged DNA or subsequent hindered intercalation.
Calculations on the effect of methylation on the electrostatic stability of the B‐ and Z‐conformers of DNA
Authors: Pack George R. , Prasad C. V. , Salafsky Joshua S. , Wong Linda
Published: December 2004

The three‐dimensional Poisson–Boltzmann equation for the distribution of counterion charge density around double‐helical DNA has been solved for solutions of .01M, .10M, and .20M monovalent salt. The polymers, poly[d(CpGp)] and poly[d(m5CpGp)], were studied in the B‐ and the Z‐conformations. The effect of methylation on the relative stabilities of these conformers in solutions of different ionic strengths is known to favor the Z‐form. Accumulation of charge density around the B‐ and the Z‐conformers is compared in detail. The relative electrostatic stabilities of the B‐ and Z‐conformers in .01M, .10M, and .20M solutions are compared and discussed in terms of the ion–DNA interactions and the self‐energy of the structured ionic environment. The ion–DNA interaction energies, termed “phosphate screening,” monotonically decrease with ionic strength and are consistent with a B‐to‐Z conformation change induced in either polymer by increased electrolyte concentration. However, these calculated energies alone do not account for the fact that the ionic strength at the midpoint of the transition of the methylated polymer is substantially lower than that of its unmethylated analogues. The phosphate screening effect is counterbalanced by changes in the self‐energy required for the creation of the structured counterion environment. This self‐energy of the electrolyte environment monotonically increases with ionic strength. Methylation‐induced shifts in the overall conformational equilibria depend on the relative changes of these competing effects. Increasing salt concentration is calcualted to favor the Z‐conformer. The effect of methylation, lowering the ionic strength of the transition midpoint, is proposed to originate in minor structural changes in the Z‐form of the polymer, making the groove more accessible to counterions in the G(3′ – 5′)C region. This allows a redistribution of counterion density and a lowering of the self‐energy of the ionic environment, conferring added stability to the Z‐conformation, as indicated by calculations of relative entropies. The experimentally observed temperature dependence of the B‐to‐Z transition, however, cannot be explained without assuming the release of bound water. Maps of the calculated three‐dimensional structure at the counterion distribution near the surface of these molecules in both the B‐ and the Z‐forms are also presented.
Sequence‐dependence of the CD of synthetic double‐stranded RNAs containing inosinate instead of guanylate subunits
Authors: Ratliff Robert L. , Liu Jung‐Jen , Vaughan Marilyn R. , Gray Donald M.
Published: December 2004

The CD spectra and melting profiles have been measured for nine synthetic double‐stranded RNAs containing I · C instead of G · C base pairs: poly[r(I) · r(C)], poly[r(I‐C) · r(I‐C)], poly[r(A‐I‐C) · r(I‐C‐U)], poly[r(A‐C) · r(I‐U)], poly[r(A‐I) · r(C‐U)], poly[r(A‐C‐C) · r(I‐I‐U)], poly[r(A‐A‐C) · r(I‐U‐U)], poly[r(A‐C‐U) · r(A‐I‐U)], and poly[r(A‐U‐C) · r(I‐A‐U)]. CD spectra have not previously been reported for the latter six of these polymers. The substitution of inosinate for guanylate led to recognizable CD differences, with all but two of the polymers having two resolved positive bands above 230 nm. Also, the I‐containing RNAs differed from their G‐containing counterparts in the almost complete absence of negative CD bands at long wavelengths and in the reduction of negative CD bands near 210 nm. First‐neighbor comparisons showed that the CD spectra of the I‐containing RNAs were consistent with the nearest‐neighbor sequences of the polymers, as previously shown for G‐containing RNAs (D. M. Gray, J.‐J. Liu, R. L. Ratliff, and F. S. Allen, Biopolymers (1981) 20, 1337–1382). Moreover, two of the first‐neighbor comparisons involved spectra of poly[r(A) · r(U)] and poly[r(I) · r(C)], polymers known to be in the A family of conformations in fibers (S. Arnott, D. W. L. Hukins, S. D. Dover, W. Fuller, and A. Hodgson, (1973) J. Mol. Biol. 81, 107–122). Thus, differences in the CD spectra of I‐ and G‐containing RNAs could be simply explained as resulting from differences in the hypoxanthine and guanine chromophores, without invoking differences in conformation. Finally, melting temperatures of the I‐containing RNAs were found to vary much less with base composition than do the melting temperatures of G‐containing RNAs, since A · U base pairs are closer to I · C than to G · C base pairs in stability.
The hinge‐bending mode of a lysozyme–inhibitor complex
Authors: Bruccoleri Robert E. , Karplus Martin , McCammon J. Andrew
Published: December 2004

The hinge‐bending mode of hen egg white lysozyme is studied by a constrained minimization technique. Results with and without a bound inhibitor, tri‐N‐acetyl‐glucosamine, are obtained. The frequency of the mode with the inhibitor is found to be 4.3 cm−1, in contrast to 3.0 cm−1 for the free enzyme. Also, the hinge‐bending angle with the lowest energy is shifted 10° towards a more closed cleft in the bound species. The main contribution to these differences arise from interactions with the residues lining the cleft and those on the back side of it. Structural details that account for the energetics are presented. The method of calculation is somewhat different from a previous study [J. A. McCammon, B. R. Gelin, M. Karplus & P. G. Wolynes, (1976) Nature 262, 325–326] to reduce the likelihood of artifacts in the results.
Comparison of the effects of cationic porphyrins on DNA properties: Influence of GC content of native and synthetic polymers
Authors: Banville Debra L. , Marzilli Luigi G. , Strickland James A. , Wilson W. David
Published: December 2004

Interactions of meso‐tetra(4‐N‐methylpyridyl)porphyrin [TMpyP(4)], meso‐tetra(2‐N‐methylpyridyl)porphyrin [TMpyP(2)], and meso‐tetra(para‐N‐trimethylanilinium)porphyrin (TMAP) with several native and synthetic DNAs were studied by a variety of physical techniques: nmr (31P and 1H), absorption spectroscopy, viscosity, and flow dichroism (FD). Of the three porphyrins studied, only the interaction of TMpyP(4) with poly [d(G‐C)2] was fully consistent with intercalation. In particular, a large increase in viscosity, a downfield 31P‐nmr signal (ca. ‐1 ppm), and upfield imino proton signals (11 to 12 ppm range) were observed. Comparison of the effects of TMpyP(4) on DNAs of different GC contents revealed larger changes in solution viscosity with increased GC content. However, the characteristic changes in 31P‐ and 1H‐nmr spectra were not observed. The viscosity increases observed in studies with poly[d(A‐C)(G‐T)] and C. Perf. DNA were much lower than with poly[d(G‐C)2], M. Lys. DNA, and calf thymus DNA. Thus, GC sequence and content are clearly important. The principal change in the 31P‐nmr signal of native DNA is the appearance of a very broad shoulder centered at ca. ‐2.0 ppm, which is larger in M. Lys. DNA than in C. Perf. DNA. FD studies indicate highly ordered TMpyP(4) cations arranged perpendicular to the DNA axis of calf thymus DNA. Together, these results suggest the major effects of TMpyP(4) on DNA properties are due to strong GC‐binding interactions that influence DNA structure. The data are consistent with combined intercalative and outside binding interactions of TMpyP(4) with GC regions of DNA. In contrast, similar studies with TMAP suggest that it influences AT regions of DNA by an outside binding mode. On the other hand, TMpyP(2) effects on DNA properties are consistent with nonselective outside binding.
Multiple denaturational transitions in fibrillar collagen
Authors: Wallace Donald G. , Condell Richard A. , Donovan John W. , Paivinen Amy , Rhee Woonza M. , Wade Susan B.
Published: December 2004

The heat denaturation of pepsinized bovine nonfibrillar and fibrillar collagen was studied by differential scanning calorimetry. For fibrillar preparations that had been rapidly precipitated with stirring at low ionic strength, then resuspended at physiological ionic strength, multiple denaturational transitions were observed. At heating rates of 10°C/min, melting endotherms occurred at about 44, 50, 53, and 57°C. Fibrillar collagen that was slowly gelled without stirring at physiological ionic strength exhibited a similar series of endotherms, but the lower melting transitions were less conspicuous. In contrast, nonfibrillar bovine collagen in acidic solution showed only a single denaturational transition at 40°C. Nonfibrillar solutions at pH 7, to which inhibitors of fibrillogenesis were added, showed a major endotherm as high as 46°C. These results suggest that reconstituted fibrillar collagen contains a heterogeneous fibril population, possibly including molecules in a nonfibrillar state. It was proposed that the multiple melting endotherms of such preparations were due to sequential melting of molecular and fibril classes, each with a distinct melting temperature. The fibrillar classes may represent three or more types of banded and nonbanded species that differ from each other in packing order, collagen concentration, and possibly also in fibril width and level of cross‐linking.
Elastic model of highly supercoiled DNA
Authors: Tsuru Hideo , Wadati Miki
Published: December 2004

The equilibrium shapes of supercoiled DNA are investigated by employing an elastic model. First, a set of Euler equations is derived to determine the equilibrium shapes under ring‐closure conditions. Two exact solutions that describe circular and figure‐8 shapes are obtained. Using these and their topological properties, the configuration change from the circular to the figure‐8 form is discussed. Second, more intricate structures of supercoiling DNA are studied by a numerical analysis. Among a class of configurations, the shape that has the minimum elastic energy is explicitly determined. Poisson's ratio, the ratio of the self‐avoiding radius to the total length, and the deficit (or excess) of the linking number ΔLk are found to be the important parameters. We conclude that the topology and the elastic theory of looped DNA explain the essential features of the supercoiling phenomena.
The dielectric constant of a folded protein
Authors: Gilson Michael K. , Honig Barry H.
Published: December 2004

The goal of this paper is to obtain a theoretical estimate of the dielectric constant of a folded protein. To this end, we develop a form of the Kirkwood–Fröhlich dielectric theory that applies to polar solids and folded proteins. The resulting theory incorporates a factor expressing the degree to which dipolar groups are constrained within the material's structure, as well as a generalized form of Kirkwood's correlation factor. The theory is applied to a hypothetical isotropic protein composed of randomly oriented α‐helices and having a number density of dipolar groups equal to that found in actual proteins. The factor of constraint and the generalized dipole correlation factor are calculated using normal mode analysis. Temperature factors are also computed by normal mode analysis and are in reasonable agreement with those found experimentally. The computed dielectric constant is low; the best estimate is that it falls between 2.5 and 4.
A novel peptide conformation: First unequivocal observation of the oxy‐analog of a β‐bend
Authors: Toniolo Claudio , Valle Giovanni , Bonora Gian Maria , Crisma Marco , Formaggio Fernando , Bavoso Alfonso , Benedetti Ettore , Di Blasio Benedetto , Pavone Vincenzo , Pedone Carlo
Published: December 2004

The x‐ray diffraction analysis of the N‐benzyloxycarbonyl homo‐tripeptide from α‐amino‐isobutyric acid has shown the occurrence of an incipient 310‐helix characterized by one type‐III (or type‐III′) β‐bend followed by one oxy‐analog of the same type of β‐bend. This represents the first unequivocal observation of the latter conformation, where the O—H group of the COOH moiety present at the C‐terminus of the peptide main chain plays the role of the hydrogen‐bonding donor. These results have been compared with those of the same peptide in its monohydrate form and of its methyl ester derivative, the x‐ray diffraction structures of which are also described here.
Synthesis of fragments by classical solution methods for use in cytochrome c semisynthesis
Authors: Borin Gianfranco , Marchiori Fernando , Calderan Andrea , Corradin Giampietro , Wallace Carmichael J. A.
Published: December 2004

We report details of the chemical synthesis of two fragments reproducing the C‐terminal sequences 71‐108 and 70‐108 of Saccharomices cerevisiae cytochrome c. Preparation of the fragments employed classical solution methods and a fragment‐condensation strategy; they have been used, together with a third fragment (sequence 67‐108) [L. Moroder, B. Filippi, G. Borin & F. Marchiori (1975) Biopolymers 14, 2061–2074], in the semisynthesis of chimeric cytochromes [C. J. A. Wallace, G. Corradin, F. Marchiori & G. Borin (1986) Biopolymers 25, 2121–2132].
DNA polymorphism: Spectroscopic and electro‐optic characterizations of Z‐DNA and other types of left‐handed helical structures induced by Ni2+
Authors: Hacques Marie‐Françoise , Marion Christian
Published: December 2004

CD and uv spectroscopy reveal that the synthetic polynucleotides poly(dG–dC) · poly(dG–dC) and poly(dG–m5dC) · poly(dG–m5dC) undergo a transition induced by small amounts of Ni++ cation from a right‐handed B‐form to left‐handed Z‐type conformations. We describe the application of steady‐state and transient electric birefringence to the characterization of the transition observed at very low ionic strength (10 mM Tris HCl, pH 7.4). Dialysis experiments show that the changes in spectroscopic and electro‐optic properties upon addition of Ni++ are completely reversible. The differences in shape of the inverted CD spectra suggest the existence of a family of left‐handed conformations, depending on the polymer used and on the amounts of cation added. The stoichiometry required for inducing the Z‐conformation of poly(dG–m5dC) is 1 cation/4 nucleotide phosphates. The transition is accompanied by a decrease in birefringence, an increase in length, and the more important contribution of a permanent or slowly induced dipole moment to the orientation mechanism. High concentrations of Ni++ promote the Z → Z* transition. Upon increasing the Ni++ concentration, poly(dG–dC) undergoes a biphasic transition, first to one intermediate conformation that is neither B‐ nor Z‐like and then to a left‐handed form that is probably different from Z*. These conversions are accompanied by regular decreases both in birefringence and in chain length, but no transient appears in the field‐reversal experiments.
Energy transfer in polynucleotide homopolymers and copolymers
Authors: Burns Victor W.
Published: December 2004

Using the fluorophore Tb3+ as a reporter, the effect of thallium (Tl+1) on the transfer of energy in polyribonucleotides and polydeoxynucleotides at room temperature has been studied. In p(G), p(G, I), and pd(G)6 thallium greatly increases the transfer of uv energy absorbed by the bases to Tb3+. In DNA, p(G, U), p(G, A), p(A, U), p(X), p(A), p(U), p(I), pd(G, A)6, and pd(G, T)5 thallium has little or no effect. Thallium increases intersystem crossing to the triplet states only in p(G), p(G, I), and pd(G)6, and the triplets overlap the excited singlet state in Tb3+. In those G‐ and X‐containing polymers showing little thallium effect, the evidence suggests that intersystem crossing is comparatively high to begin with. These polymers, including DNA, appear to transfer absorbed energy to triplet states efficiently at room temperature.
Effect of cosolvents on solubility of protein in equilibrium between different states
Authors: Arakawa Tsutomu
Published: December 2004

This paper describes a theoretical work on the solubility of a protein in equilibrium between different forms such as isomerization (A ⇌ B) and dimerization (2A ⇌ B). Under the assumptions that A and B have different solubilities and form their own solid phases (in the form of either precipitation or crystal), it was shownthat only either A or B precipitates at a given condition, another form being in equilibrium in solution with the precipitating form, provided that the solubility ratio of A to B is not identical to their equilibrium composition in the solution phase determined by the equilibrium constant. It follows, then, that the total concentration of the protein in the solution phase can be calculated by summing the solubility of the precipitating form and the concentration in solution of another form in equilibrium with the precipitating form. Assuming various preferential protein‐solvent interactions for the two forms in solution as well as solid phases, dependences of the total protein solubility on the additive concentration were examined. It was shown that this dependence may be complex, showing maximum, minimum, or inflection point, depending on the preferential protein interactions with solvent components.
Proton polarizability and proton transfer in histidine‐phosphate hydrogen bonds as a function of cations present: Ir investigations
Authors: Burget Ulrike , Zundel Georg
Published: December 2004

(L‐His)n‐ dihydrogen phosphate systems are studied by ir spectroscopy in the presence of various cations and as a function of the degree of hydration. Ir continua indicate that (I) OH … N ⇌ O−…H+N (IIR) hydrogen bonds are formed and that these bonds show high proton polarizability, which increases from the Li+ to the K+ system. In the K+−system, His‐Pi‐Pi chains are formed, showing particularly high proton polarizability due to collective proton motion within both hydrogen bonds. The OH N ⇌ O−…H−N equilibria are determined from ir bands. With the Li+ system, 55% of the protons are present at the histidine residues; this percentage is smaller with the Na+ system (41%), and amounts to only 32% with the K+ system. With the increasing degree of hydration the removal of the degeneracy of νas−PO2−3 vanishes, indicating loosening of the cations from the phosphates. Nevertheless, the hydrogen bond acceptor O atom becomes more negative; a shift of the equilibrium to the right is observed in the OH… N ⇌ O−…H+N bond. This is explained by the strong interaction of the dipole of the hydrogen bonds with the water molecules. All these results show that protons can be shifted easily in these hydrogen bonds due to their high proton polarizability. The transfer equilibria can be controlled easily by local electrical fields. In addition, these results may be of significance when phosphates interact with proteins.
Site specificity of binding of antitumor antibiotics to DNA
Authors: Jones Martin B. , Hollstein Ulrich , Allen Fritz S.
Published: December 2004

The site specificities for intercalation of steffimycin B, adriamycin, echinomycin, and ethidium bromide with DNA have been determined by CD first‐neighbor analysis. The first three, which are antineoplastic antibiotics, all exhibit preferential binding to sites comprised of guanine and cytosine (GpC, CpG, and CpC or its complement GpG). Ethidium bromide displays nonspecific intercalation. The results are compared with findings from “footprinting” studies.