bluuebunny/crossref_metadata_2025 huggingface dataset:
Conformational and functional properties of hemoglobin in perturbed solvent: Kinetics of O2 release
Authors: Cordone Lorenzo , Cupane Antonio , Fornili Sandro L.
Published: May 2005

We studied the kinetics of O2 release by oxyhemoglobin caused by sodium dithionite, in the presence and in the absence of organic cosolvents (monohydric alcohols and formamide) at 10°C. This study was performed by using standard stopped‐flow techniques coupled with microprocessor‐based data acquisition. We have fitted the experimental data to a mathematical expression obtained on the basis of a two‐state model that takes into account the kinetic heterogeneity between α‐ and β‐chains and the presence of αβ‐dimers in oxyhemoglobin solutions. Results indicate that the cosolvents mainly affect the allosteric parameter L, i.e., the T ⇄ R conformational equilibrium of hemoglobin, leaving the intrinsic deoxygenation rates of both R and T states almost unaltered. The L values obtained in the present work are in excellent agreement with analogous values previously estimated from oxygen equilibrium measurements.
Flexibility of collagen determined from dilute solution viscoelastic measurements
Authors: Nestler F. Henry M. , Hvidt Søren , Ferry John D. , Veis Arthur
Published: May 2005

The frequency dependences of the storage and loss shear moduli, G′ and G″, of pronase‐treated collagen dissolved in acetate buffer at pH 4.0 were measured at 17.0°C by use of the Birnboim‐Schrag multiple lumped resonator apparatus. Some of the solutions contained 70% glycerol. The infinite‐dilution moduli were determined and compared with theoretical models for a rigid cylinder and a semiflexible rod. Only the latter could fit the data. A rotational time of 144 μs and a slowest flexural relaxation time of 21 μs, both reduced to water at 20°C, were determined from the fit. The intrinsic viscosity and rotational relaxation time correspond to a semiflexible rod with persistence length of about 170 nm and a Young's modulus of 4 × 1010 dyn/cm2.
Modeling biological macromolecules in solution. II. The general tri‐axial ellipsoid
Authors: Harding Stephen E. , Rowe Arthur J.
Published: May 2005

The use of the general (tri‐axial) ellipsoid as a model for the conformation of biological macromolecules in solution is discussed. The recent derivation of an expression for the viscosity increment of dispersions of tri‐axial ellipsoids [S. E. Harding et al. (1979) IRCS Med. Sci. 7, 33; and (1981) J. Colloid Interface Sci. 79, 7–13] makes the fitting of such a model possible by the derivation of appropriate volume‐independent functions. We now derive these volume‐independent functions for tri‐axial ellipsoids and investigate by exhaustive computer simulation the possibility of deriving the two axial ratios (a/b, b/c) from data of various types, in every case containing plausible experimental error. It is shown that transport properties alone cannot be used to yield estimates for the axial ratios, given current experimental precision. However, a combination of transport and rotational diffusion properties is more promising, and an algorithm is developed and tested that will reliably yield estimates from simulated data obtained by the methods of sedimentation, viscosity, and electric birefringence.
Effect of finite ionic size on the solution of the Poisson‐Boltzmann equation: Application to the binding of divalent metal ions to DNA
Authors: Granot Joseph
Published: May 2005

The nonlinear Poisson‐Boltzmann equation is solved for a cylindrical polyelectrolyte solution containing mono‐ and divalent counterions and monovalent coions. The finite size of the ions is taken into account by the introduction of the distances of closest approach between the ionic charges and the surface of the polyelectrolyte. The choice of these distances is based on the physicochemical properties of the polyelectrolyte and ions in solution. The effects of the finite ionic size on the distribution of the counterions around the polyelectrolyte and on the local ion concentration and the integrated charge fraction of the divalent cations in the vicinity of the polyelectrolyte are discussed. Theoretical predictions regarding the overall extent of binding and the extent of inner‐sphere binding of divalent counterions to rodlike polyions are compared with the results of nmr studies of the binding of divalent metal ions to DNA.
Proton NMR studies of partially modified retro–inverso peptides
Authors: Ribeiro Anthony , Chorev Michael , Goodman Murray
Published: May 2005

High‐resolution 1H‐nmr analyses are presented for partially modified retro‐inverso derivatives of peptides with emphasis on enkephalins. Studies in DMSO‐d6 reveal the unique as well as common characteristics of the non‐amino acid residues incorporated into these modified peptides. The complete assignment of 1,1‐diaminoalkyl and malonyl, as well as of amino acid, residues provides the basis for the exploration of the conformational features induced in peptides by such topochemical modifications.
Reversing‐pulse electric birefringence of poly(γ‐benzyl‐L‐glutamate). I. Transient behavior of fractionated samples in the low electric field region
Authors: Ueda Kazuyoshi , Nomura Minoru , Yamaoka Kiwamu
Published: May 2005

Reversing‐pulse electric birefringence (RPEB) was measured for the first time for four fractionated poly(γ‐benzyl‐L‐glutamate), [Glu(OBzl)]n, samples in N,N‐dimethylformamide (DMF) at 20°C and at 535 nm. The RPEB signal showed a deep minimum for each sample on reversal of an applied electric field. The profiles of the reverse‐transient signal were analyzed by taking into account the polydispersity for the continuous distribution of molecular lengths. The best set of three quantities (lw, lw/ln, (βw)2/2γw), which determine a signal profile, was evaluated for each sample. By combining the experimental data of intrinsic viscosity and RPEB, the diameter of a cylinder, which is assumed for the [Glu(OBzl)]n helix, was found to be 17 Å. The value (βw)2/2γw, which is related to the ratio of weight‐average permanent dipole moment μw, and electric polarizability anisotropy Δαw, was found to be in the range of 20–45. This indicates that the former contributes predominantly to electric field orientation, but the latter also should not be ignored. With the three parameters from the reverse portion, the rise and decay curves were regenerated theoretically in excellent agreement with experimental signals.
Infrared spectroscopic study of C7 intramolecular hydrogen bonds in peptides
Authors: Rao Ch. Pulla , Balaram P. , Rao C. N. R.
Published: May 2005

The ir‐spectra in the NH stretching region of Piv‐Pro‐NHMe and Boc‐Pro‐NHMe have been studied in carbon tetrachloride and chloroform solutions over a wide range of concentrations. Based on the concentration dependence of the NH stretching bands, it has been shown that the characteristic NH stretching band due to the C7 intramolecular hydrogen bond is around 3335 cm−1. Intermolecular hydrogen bonding also occurs to a small extent in these peptides, giving rise to a slight concentration dependence of the NH stretching bands. The band around 3335 cm−1 need not necessarily be due to C7 hydrogen bonds alone as proposed by Tsuboi et al. or to intermolecular hydrogen bonding alone as proposed by Maxfield et al.; this conclusion is supported by studies on Boc‐Leu‐NHMe, which undergoes only intermolecular hydrogen bonding. We have shown that Z‐Aib‐Aib‐OMe and Z‐Aib‐Ala‐OMe form C7 intramolecular hydrogen bonds in addition to C5 intramolecular hydrogen bonds. The present studies also show that all the peptides studied exist in more than one conformation in solution.
Computer building of β‐helical polypeptide models
Authors: Koeppe Roger E. , Kimura Michio
Published: May 2005

A general method is presented for computing the atomic coordinates of helices in which a dipeptide is the repeating unit. The method will generate both single‐ and double‐stranded model helices having idealized bond lengths and angles, and any arbitrary, user‐specified, pitch and number of residues per turn. The variation of inter‐ and intrastrand hydrogen bonds with pitch and number of residues per turn can thus be examined. An application of the method is the construction of a β‐helix having pitch of 6.3 Å per turn and 4.85 residues per turn, a model which can pack nicely into the unit cell of crystals of cation‐bound gramicidin A.
Conformational change in yeast tRNAAsp
Authors: Huong P. V. , Audry E. , Giege R. , Moras D. , Thierry J. C. , Comarmond M. B.
Published: May 2005

The structure of yeast tRNAAsp in aqueous solutions has been analyzed in the light of results obtained from Raman spectra recorded at from 5 to 82°C and compared to those of tRNAPhe. Firm evidence is given of a reversible conformation transition for tRNAAsp at 20°C. This transition is observed for the first time in the tRNA series. The low‐temperature conformation appears to have a more regular ribose–phosphate backbone and a more effective G base‐stacking. This conformational change, which occurs essentially in the D loop, could be connected to the existence of two (A and B) crystal forms obtained depending on crystallization conditions. The melting temperatures, which are different for each base stacking in tRNAAsp, lie in a range of about 70°C, much higher than for tRNAPhe. This fact is interpreted by a higher ratio of G‐C base pairs in tRNAAsp.
Structure of a cellulose I–ethylenediamine complex
Authors: Lee David M. , Burnfield Keith E. , Blackwell John
Published: May 2005

The structure of a crystalline cellulose I–ethylenediamine complex has been determined by x‐ray diffraction methods as part of an investigation of cellulose–solvent interaction. The complex studied is that formed when native ramie fibers are swollen in ethylenediamine and then vacuum‐dried. The unit cell is monoclinic with dimensions a = 12.87 Å, b = 9.52 Å, c = 10.35 Å, and γ = 118.8°, and it contains disaccharide segments of two chains, with one ethylenediamine per glucose residue. The refined model contains parallel cellulose chains that are linked by hydrogen‐bonded ethylenediamine molecules. The chains along the b‐axis are packed in register, leading to stacks of chains analogous to those in chitin. All the hydroxyl groups are satisfactorily hydrogen‐bonded and each ethylenediamine forms four donor and two acceptor hydrogen bonds. From this work it can be seen that the interaction of cellulose I with ethylenediamine involves scission of the intermolecular hydrogen bonds followed by disruption of the stacks of quarter‐staggered chains.
Interactions of molecules with nucleic acids. VII. Intercalation and T·A specificity of daunomycin in DNA
Authors: Newlin Donald D. , Miller Kenneth J. , Pilch Daniel F.
Published: May 2005

Intercalation complexes of daunomicin(+1) with tetramer duplexes in DNA are studied with the theoretically determined intercalation sites (I, −0.4), (II, −0.4), and (III, −1.4). These sites occur with base pairs separated by 6.76 Å for helical angles of 26°, 22°, and 8° about the intercalation site. Site I is preferred, and this is in agreement with experimental unwinding angles. Optimum binding positions and conformations are established, and these are in agreement with experimental results from crystal structures. A systematic procedure is devised to study base‐pair and base‐sequence specificity, which results in the demonstration that the most stable sequences are mainly ↑BP1, T·A, DAUN, A·T, BP4↓ and ↑BP1, T·A, DAUN, G·C, BP4↓, i.e., with the TpA and CpG (pyrimidine)p(purine) sequences about the intercalation site. These 32 possible sequences are found among the 40 most stable complexes. These theoretical calculations of intercalation complexes with daunomicin(+1) provide the first example in which a drug specifically selects the base pair T·A and prefers it in a particular sequence about the intercalation site. This specificity is in agreement with some experimental results. Problems associated with the interpretation of specificity are discussed in terms of the base, base‐pair, and base‐sequence resulting from the DNA site and the DNA–drug interactions. T·A specificity is rationalized by noting that the 2′deoxyribo‐5′‐monophosphate backbone attached to A is slightly more negative than that on the other nucleotides. Hence, a preference exists for binding to the protonated daunosamine (+1) groups. Stereographic projections of daunomycinone and daunomycin(+1) in a bond model and in a space‐filling model with steric contours illustrate the results.
Transport properties of rigid and flexible macromolecules by brownian dynamics simulation
Authors: Allison S. A. , McCammon J. A.
Published: May 2005

The method of Ermak and McCammon [Ermak, D. L. & McCammon, J. A. (1978) J. Chem. Phys. 69, 1352–1360] is used to simulate the Brownian dynamics of a system of identical, interacting beads. In the present study, we use the method to obtain transport coefficients for a variety of rigid and flexible structures modeled as arrays of spherical subunits. Constraints are enforced using the SHAKE algorithm or a modification, SHAKE‐HI, that is described for the first time. In SHAKE‐HI, hydrodynamic interactions between subunits are taken into account when the constraints are enforced. Use of SHAKE‐HI yields transport coefficients that are in perfect agreement with those obtained by other methods. The primary advantage of the present method is its generality. We also propose that multistep Brownian dynamics may be important in simulating actual experiments (such as fluorescence depolarization) on well‐defined model systems that possess an arbitrary degree of internal flexibility.
Conformation of LiDNA in solutions of LiCl
Authors: Borochov Nina , Eisenberg Henryk
Published: May 2005

We have derived radii of gyratin, Rg, from the absolute intensity of the scattered light of mondisperse linear Col E1 LiDNA in solution at various LiCl concentrations up to 5M. The second virial coefficients, A2, decrease strongly with increasing LiCl concentration, and vanish between 3 and 5M LiCl. It was thus possible to calculate a limiting value at a high salt concentration of 28.5 nm for the persistence length, a0, of LiDNA, without the necessity of applying excluded‐volume corrections. The value obtained is in good agreement with the value previously obtained for NaDNA at high NaCl concentrations, and can be identified with the high salt limit of DNA flexibility, with long‐range electrostatic interactions effectively screened. Sedimentation coefficients in the ultracentrifuge and apparent and translational diffusion coefficients (at finite and vanishing scattering vectors, respectively) from dynamic laser‐light scattering have also been obtained up to 5M LiCl. From the sedimentation and apparent diffusion, D(90), (at 90° scattering angle only) above 5M, and up to 9M LiCl, it could be shown that the solutions are stable for reasonable periods of time, and the molecular parameters vary smoothly and moderately at high salt. Conformational transitions were not observed and precipitation occurs between 9 and 10M LiCl.
Theoretical π‐π* absorption, circular dichroic, and linear dichroic spectra of collagen triple helices
Authors: Caldwell James W. , Applequist Jon
Published: May 2005

Absorption, CD, and LD spectra of the π‐π* transition near 200 nm are calculated for poly(Gly‐X‐Y) (X,Y = Gly, Ala, Pro) in four conformations proposed for collagen like triple helices in the recent literature. A dipole interaction model is used with the same optical paramenters as in previous studies of polypeptide spectra. The CD spectra are sensitive to backbone structure and amino acid composition, although the experimentally observed negative peak near 200 nm is a general feature of most the calculated spectra. Interchain interactions significantly affect the CD spectra in most cases. Calculations for (Gly‐Pro‐Ala)3 and (Gly‐Ala‐Pro)3 in the triple helical structure of Fraser, MacRae, and Suzuki [(1979) J. Mol. Biol. 129, 463–481] show absorption, CD, and LD spectra in fairly good agreement with experiment. The characteristics of the π‐π* normal modes responsible for the calculated spectra are compared with those of the component bands resolved from the experimental spectra of collagen by Mandel and Holzwarth [(1973) Biopolymers 12, 655–674].
Kinetic studies of the complex formation in the ternary system of amylose, SDS, and iodine
Authors: Yamamoto Masako , Harada Shoji , Sano Takayuki , Yasunaga Tatsuya , Tatsumoto Nobuhide
Published: May 2005

Complex formation in the ternary system of amylose (degree of polymerization,DP, 1100), SDS, and iodine was studied statically by spectrophotometry and amperometric titration and kinetically by the pressure‐jump method. It was clarified that (1) iodine (I3−) to some extent binds to amylose saturated with SDS to form an inclusion complex (ASI system); (2) the binding of SDS apparently transforms amylose ofDP1100 to that of much lowerDP(less than 60) from the viewpoint of iodine binding; and (3) iodine binds to sites unoccupied by SDS in the center of the helical segment of amylose. Pressure‐jump relaxation phenomenon was not observed in solutions in which iodine was dissolved prior to SDS (AIS system), but it was observed in the ASI system; it is ascribed to the association and dissociation of three molecules of iodine in the center of the amylose helix. Comparison of the rate constants in the ASI system with those in the amylose (DP32) and iodine system indicates that iodine runs to and from the helical segment of amylose perpendicularly to the axial plane in the former, while it runs horizontally in the latter. We discuss the order of ligand mixing on the resulting structure of the ternary complexes of amylose, SDS, and iodine.
Molecular model for the complex between Concanavalin A and a biantennary‐complex class glycopeptide
Authors: Carver J. P. , MacKenzie A. E. , Hardman K. D.
Published: May 2005

A molecular model for the complex formed between the jack bean lectin concanavalin A (Con A) and glycopeptides of the complex biantennary class is described. The model was derived using coordinates for Con A determined by x‐ray crystalographic refinement techniques, with 1.75‐Å resolution data, and coordinates for the glycopeptides obtained from 1H‐nmr measurements, using the nuclear Overhauser effect. Previous solution and crystallographic studies provided several constraints on the possible mode of interaction of the lectin and the glycopeptide. Examination of the model suggests that the glycopeptide binding site is defined by four loops on the protein surface made up by amino acid residues: 12–18, 98–102, 205–208, and 226–229. Within these loops, it favorable interactions with high‐affinity ligands and tose responsible for the unfavourable interactions with poor ligands.
Membrane proteins as light‐energy transducers
Authors: Ovchinnikov Yu. A.
Published: May 2005

Monoclonal antibodies to different parts of bacteriorhodopsin were raised to define its topography in the membrane. It is shown that the amino acid residue Glu 194 is a part of an antigenic determinant and should be located on the membrane surface. We found that the removal of the C‐terminal 17 amino acid sequence does not affect the efficiency of the proton transport in bacteriorhodopsin. From a combination of proteolysis and secondary structure prediction methods an experimentally testable structural model for bovine rhodopsin is presented. The complete amino acid sequence of the transducin γ‐subunit consisting of 69 residues was determined.
Studies on proline‐containing tetrapeptide models of β‐turns
Authors: Hollośi M. , Kawai M. , Fasman G. D.
Published: May 2005

The synthesis of a series of protected tetrapeptides of the general formula Cbz‐Gly‐X2‐Y3‐Gly‐OR (R = stearyl or methyl, X and/or Y = proline) is described. Detailed CD studies have been performed to evaluate the contribution of proline‐containing β‐turns to the CD spectra of proteins. The CD spectra of all the models are dominated by the chiral contribution of the proline residue. In polar, proton‐donating solvents, a poly‐proline II‐like spectrum was observed in almost all cases. The tetrapeptide model Cbz‐Gly‐Gly‐Pro‐Gly‐OStearyl, in acetonitrile shows a type C spectrum that has not been previously reported for linear peptides. The ir and nmr data on this model support the assumption of that of a type III β‐turn, exhibiting a type C spectrum, participate in the conformational equilibrium. The most interesting finding of the CD studies is the observation of a type D spectrum (according to the classification of Woody [Woody, R. W. (1974) in Peptides, Polypeptides and Proteins, Blout, E. R. Bovey, F. A. Lotan, N. & Goodman, M. (Eds.), Wiley, New York]) for models Cbz‐Gly‐Pro‐Asp(OBut)‐Gly‐OStearyl and Cbz‐Gly‐Pro‐Ser(OBut)‐Gly‐OStearyl in cyclohexane. The results of the CD measurements ae discussed in correlation with ir and nmr data and with recent literature.
The octamers d(CGCGCGCG) and d(CGCATGCG) both crystallize as Z‐DNA in the same hexagonal lattice
Authors: Fujii Satoshi , Wang Andrew H.‐J. , Quigley Gary J. , Westerink Henk , Van Der Marel Gijs , Van Boom Jacques H. , Rich Alexander
Published: May 2005

Both (dC‐dG)4 and d(CGCATGCG) crystallize in hexagonal lattices and their three‐dimensional structure has been solved by x‐ray diffraction analysis. Both molecules are found to form Z‐DNA, although the fine details of the structure cannot be visualized due to the statistical disordering of the molecules along the c‐axis, which is brought about by the symmetry constraints of the space group. This represents the first time in which the unmodified dinucleotide sequences CpAp and TpGp have been found to form Z‐DNA in a crystalline lattice.
Determinations of atomic partial charges for nucleic acid constituents from x‐ray diffraction data. I. 2′‐Deoxycytidine‐5′‐monophosphate
Authors: Pearlman David A. , Kim Sung‐Hou
Published: May 2005

The first experimentally derived set of partial charges for a nucleotide has been determined. A high‐resolution x‐ray data set (5122 independent observed reflections to sin(θ)/λ = 0.995 Å−1) has been collected at T = −150°C for 2′‐deoxycytidine‐5′‐monophosphate monohydrate in the zwitterionic form. Radial refinement was carried out on the data, a refinement method that allows variation of atomic valence sphere radii and populations and hence directly yields the partial charges of atoms in a structure [Coppens, P., Guru Row, T. N., Leung, P., Stevens, E. D., Becker, P. J. & Yang, Y. W. (1979) Acta Crystallogr., Sect. A 35, 63–72]. The atomic partial charges thus determined are in general qualitative agreement with theoretical values, but significant differences exist, indicating a reassessment of the applicability of the theoretical sets currently in use is necessary. The ab initio charges determined by Nuss and Kollman [(1979) J. Med. Chem. 22, 1517–1524] are closest to experiment in the sugar and base regions, while the Del Re charges of Renugopalakrishnan et al. [(1971) Biopolymers 10, 1159–1167] match best in the phosphate region. The presence of an additional hydrogen on N3 appears to have a small effect on the charge densities of all base atoms, rather than a large localized effect on adjacent atoms. Inspection of deformation density maps for the hydrogen bonds in this crystal suggests possible differences between those bonds that include a nitrogen atom as part of the bond and those that do not.
Thermodynamics of the daunomycin–DNA interaction: Ionic strength dependence of the enthalpy and entropy
Authors: Chaires Jonathan B.
Published: May 2005

Fluorescence and absorbance methods were used to study the interaction of daunomycin with calf‐thymus DNA over a wide range of temperatures and NaCl concentrations. van't Hoff analysis provided estimates for the enthalpy of the binding reaction over the NaCl range of 0.05–1.0 M. Daunomycin binding is exothermic over this entire range, and the favorable binding free energy arises primarily from the large, negative enthalpy. Both the enthalpy change and entropy change are strong functions of ionic strength. Possible molecular contributions to the enthalpy and entropy are discussed, leading to the tentative conclusion that hydrogen‐bonding interactions at the interacalation site are the primary contributors to the observed thermodynamic parameters. The dependence of the enthalpy on the ionic strength is well beyond the predictions of current polyelectrolyte theory and cannot be fully accounted for. The enthalpy and entropy changes observed compensate one another to produce relatively small free‐energy changes over the range of solution conditions studied.
Dielectric effects in biopolymers: The theory of ionic saturation revisited
Authors: Hingerty B. E. , Ritchie R. H. , Ferrell T. L. , Turner J. E.
Published: May 2005

Electrostatic effects are believed to determine the molecular structure and function of macromolecules in many ways. In metallo‐based enzymes and in metal–macromolecule interactions in solution, these effects may predominate. In order to tackle metal ion–nucleic acid interactions theoretically, we propose a modification of Debye's distance‐dependent dielectric function first proposed more than 50 years ago. This function more closely approximates physical reality at small interatomic separations. Our theory yields a dielectric function that gives reasonable agreement with experimental data in preliminary calculations.
Conformation of double‐stranded polydeoxynucleotides in solution by proton two‐dimensional nuclear overhauser enhancement spectroscopy
Authors: Borah Babul , Cohen Jack S. , Bax Ad
Published: May 2005

Proton 2D‐NOE spectroscopy has been used to investigate the three‐dimensional conformations of several sonicated polydeoxynucleotides in solution. The observed pattern of cross peaks indicate that poly(dA‐dT) · poly(dA‐dT) in all salt concentrations studied (up to 6.6M CsF), and poly(dG‐m5dC) · poly(dG‐m5dC) in low salt (0.1M NaCl) are righthanded B‐structures. Poly(dG‐m5dC) · poly(dG‐m5dC) in Mg2+ (3 mM) solution exhibits a pattern characteristic of the left‐handed Z‐form. These results for poly(dA‐dT) · poly(dA‐dT) are in contrast to suggestions that this copolymer exists as a left‐handed form, either in low or high salt. We present pure absorption‐mode 2D‐NOE spectra that enable us to compare several distances and define the conformations of these polydeoxynucleotides in solution.
The physical origin of the low solubility of nonpolar solutes in water
Authors: Lee B.
Published: May 2005

Elementary but general statistical‐mechanical relations are derived that relate the thermodynamic properties of the dissolution process to those of the pure solvent. A number of conclusions are drawn from qualitative arguments that these relations suggest. These include the following: (1) The low solubility of nonpolar solutes in water arises not from the fact that water molecules can form hydrogen bonds, but rather from the fact that they are small in size. (2) The large entropy decrease attending the transfer of an inert solute from a nonaqueous solvent to water is largely due to the decrease in entropy of the nonaqueous solvent as the solvent–solvent interaction is restored on removal of the solute from it. (3) It is improper to use values of thermodynamic quantities obtained from small‐molecule transfer studies for those that involve macromolecular folding and interaction.
Base tilt of poly[d(A)]–poly[d(T)] and poly[d(AT)]–poly[d(AT)] in solution determined by linear dichroism
Authors: Edmondson Stephen P. , Johnson W. Curtis
Published: May 2005

We have measured the CD, isotropic absorption, and LD of poly[d(A)]–poly[d(T)] and poly[d(AT)]–poly[d(AT)] in the vacuum‐uv spectral region. The reduced dichroism (LD divided by isotropic absorption) varied as a function of wavelength and was independent of shear gradient. Thus, the bases are not perpendicular to the helix axis in solution. Since the directions of the transition dipoles are known, the orientations of the bases in the polymers can be calculated from the reduced dichroism spectra. The results show that the base normals are tilted at angles greater than 25°, with respect to the helix axis, and thymine is tilted more than adenine for both polymers. The tilt axes of adenine and thymine are not parallel, indicating a large propeller twist. Space‐filling models of poly[d(A)]–poly[d(T)] and poly[(AT)]–poly[d(AT)] are built based on our results, and the conformations of the two (A + T) polymers in solution are discussed.
Conformation of cyclic analogs of enkephalin. III. Effect of varying ring size
Authors: Hall David , Pavitt Nicola
Published: May 2005

A comparative study has been made using molecular mechanics of the ring entity of the active enkephalin analogs, Tyr‐cyclo(‐Nω‐D‐XXX‐Gly‐Phe‐Leu‐), where XXX is variously A2pr, A2bu, and Orn. Several conformations are favored for all three, and the lower‐energy models are compatible with a Gly3‐Phe4 bend in the active form of enkephalin. Some difficulties in assuming standard geometries in conformational surveys are illustrated.
Crystal structure of the α‐helical undecapeptide Boc‐L‐Ala‐Aib‐Ala‐Aib‐Ala‐Glu(OBzl)‐Ala‐Aib‐Ala‐Aib‐Ala‐OMe
Authors: Bosch R. , Jung G. , Schmitt H. , Winter W.
Published: May 2005

The x‐ray structure of Boc‐L‐Ala‐Aib‐Ala‐Aib‐Ala‐Glu(OBzl)‐Ala‐Aib‐Ala‐Aib‐Ala‐OMe(I) represents the first α‐helix determined by direct methods. This undecapeptide is a model of the N‐terminus of alamethicin, and it exhibits voltage‐dependent pores in bilayer membranes at a higher voltage and concentration than alamethicin. The molecule crystallizes in the monoclinic space group P21 with a = 10.602(1), b = 23.884(3), c = 13.622(1) Å, β = 95.61(6)°, and Z = 2. It adopts a right‐handed α‐helical conformation in the solid state with intramolecular 5 → 1 hydrogen bonds. An additional intramolecular hydrogen bond is bifurcated, forming a stronger 4 → 1 interaction (i.e., a β‐turn III) and a weaker 5 → 1 interaction, thus prolonging the α‐helical part up to 9 residues. The α‐helix radius of 2.1 Å, the height per residue (distance Ni … Ni + 4) of 1.53 Å, the resulting length of the α‐helical part of 13.8 Å (9 residues) resp. 15.3 Å (10 residues), the van der Waals radius (4.7 Å), and the minimal diameter of pores formed by aggregation of 3–10 α‐helices were calculated omitting the Glu(OBzl) side chain. In the crystal, the α‐helices are linked head to tail via two hydrogen bridges forming continuous chains. Adjacent helices are oriented in antiparallel with their helix axes and have only van der Waals contacts.
Crystal structure of Boc‐Leu‐Aib‐Pro‐Val‐Aib‐Aib‐Glu(OBzl)‐Gln‐Phl × H2O, the C‐terminal nonapeptide of the voltage‐dependent ionophore alamethicin
Authors: Bosch R. , Jung G. , Schmitt H. , Winter W.
Published: May 2005

Boc‐L‐Leu‐Aib‐Pro‐Val‐Aib‐Aib‐Glu(OBzl)‐Gln‐Phl (Boc = t‐butyloxycarbonyl, Aib = α‐aminoisobutyric acid, Bzl = benzyl, Phl = phenylalaninol), C59H90N10O14, the protected C‐terminal nonapeptide with the sequence 12–20 of alamethicin, crystallizes in the orthorhombic space group P212121 with a = 15.666, b = 16.192, c = 26.876 Å, and Z = 4. The molecular conformation is right‐handed helical with three α‐(5 → 1 hydrogen bonds) and three β‐turns (4 → 1 hydrogen bonds). All but two of the hydrogen bonds are significantly longer than the usual value and show bifurcation to some extent. The α/3‐helical nonapeptide molecules are arranged head‐to‐tail along the a direction. The resulting linear antiparallel chains are linked by a weak intermolecular hydrogen bridge, thus forming a two‐dimensional layer structure in the ab plane. The conformation of this nonapeptide is almost identical with that of the corresponding C‐terminal part found by x‐ray crystallography of the eicosapeptide alamethicin.
Influence of supercoiling on DNA structure: Laser Raman spectroscopy of the plasmid pBR322
Authors: Vasmel Henk
Published: May 2005

We report high‐resolution Raman spectra obtained from the circularly closed double stranded DNA (Form I) of the plasmid pBR322 and from its corresponding linear form (Form III). Comparison of the Raman spectra of the two forms demonstrates that, at a superhelical density (σ) of −0.069, which is of the same order as those found for most naturally occurring circularly closed DNAs, no major structural transitions occur under the influence of supercoiling. It is shown that at least 98% of all bases are fully basepaired, and that the conformation of the sugar–phosphate backbone is essentially identical to that of linear DNA. Thus, the structural influence of supercoiling, under these conditions, is confined to minor stretches of the plasmid DNA.
Torsional dynamics and rigidity of fractionated poly(dGdC)
Authors: Fujimoto Bryant S. , Shibata John H. , Schurr Rebecca L. , Schurr J. Michael
Published: May 2005

Time‐resolved fluorescence polarization anisotropy measurements were performed on two fractionated samples of duplex poly(dGdC) containing 230 (+40, −30) base pairs (bp) and 590 ± 40 bp. Deconvolution using the intermediate zone formula for the twisting correlation functions (which is not valid for such short DNAs) yields apparent torsion constants for these two samples that are disparate and, in any case, too low. By similarly deconvoluting simulated data constructed from the correct twisting correlation functions, it can be inferred that these two samples actually exhibit the same torsion constant, α = (4.0 ± 0.4) × 10−12 dyn cm. Within the experimental uncertainties, this value is the same as that reported previously from this laboratory for linear ϕ29 and linearized M13mp7 DNAs. The 590‐bp sample exhibited a peculiar evolution of its apparent torsional rigidity from a very high initial value, \documentclass{article}\pagestyle{empty}\begin{document}$ \hat \alpha $\end{document} = (11 ± 1) × 10−12 dyn cm, to a normal value over a period of several months, during which time many very small fragments appeared to be dissociated from, or annealed out, of the predominant high‐molecular‐weight species. Possible interpretations of these observations are discussed.
Guanine residue: A normal‐coordinate analysis of the vibrational spectra
Authors: Majoube Michel
Published: May 2005

The force field established for guanine is applied here to guanine‐containing biopolymers by considering the model compound 9‐methylguanine, in which the methyl group is taken as a dynamic unit whose mass is concentrated on the carbon. In‐plane normal‐mode frequencies for this model compound and its N‐deuterated analog are calculated. Band frequencies observed for guanine residue in Raman biopolymer spectra, such as those for DNA, RNA, or poly(G), are associated with calculated modes having similar wavelengths. They are discussed by taking into account observed and calculated D, 15N, and 18O isotopic shifts. The atomic displacements for the normal modes corresponding to the principal bands are illustrated and a number of assignments proposed.
Raman spectroscopic elucidation of DNA backbone conformations for poly(dG‐dT) · poly(dA‐dC) and poly(dA‐dT) · poly(dA‐dT) in CsF solution
Authors: Fodor Stephen P. A. , Starr Philip A. , Spiro Thomas G.
Published: May 2005

Raman spectra have been recorded for poly(dG‐dT) · poly(dA‐dC) and poly(dA‐dT) · poly(dA‐dT) in low salt and at high concentrations of CsF. Poly(dG‐dT) · poly(dA‐dC) shows no change in the 682‐cm−1 guanine mode, demonstrating the absence of the Z‐structure at high salt. The 790‐cm−1 phosphodiester symmetric stretch, however, shifts up 5 cm−1 in 4.3M CsF, suggesting a slight conformational change, associated with ion binding or hydration changes. Poly(dA‐dT) · poly(dA‐dT) shows an additional broad band at 816 cm−1, attributed to the phosphodiester modes associated with the C3′‐endo deoxyribose units in the alternating B‐structure. In this case, both the 841‐ and the 816‐cm−1 asymmetric phosphodiester stretches, associated with the C2′‐ and C3′‐endo units, shift down on addition of CsF in a sequential manner. Correlation of this sequence with that previously observed for the two 31P‐nmr resonances, establishes that the phosphodiester stretching frequencies depend on the conformation of the 5′‐sugar, and not on the 3′‐sugar.
Theory of gel electrophoresis of DNA
Authors: Lumpkin Oscar J. , Déjardin Philippe , Zimm Bruno H.
Published: May 2005

A theory of the electrophoresis of DNA through gels with large interfiber spacing, such as dilute agarose, is presented. We assume that the DNA molecule moves along its axis through a “tube” in a neutral gel under the influence of the electric field. The tube is random except for possible bias due to the effects of the field. When the field is small, we easily recover the inverse‐length dependence of the mobility found previously by de Gennes and by Doi and Edwards. At higher fields, a new effect appears; the tube becomes oriented because the field biases the direction of the leading end of the chain as it moves to form an extension of the tube. This leads to an increase of the mobility with increasing field by adding a field‐dependent but length‐independent term to the mobility expression. In agreement with experiment, we find that the field effect can be important at fields as low as 1 V/cm and that the effect can seriously decrease the sensitivity of the mobility to chain length. We also examine the fluctuation of the migration distance, the degree of orientation induced by the field, and the transient effects occurring when the feld direction is rotated by a right angle.
Segmental flexibility in pig immunoglobulin G studied by neutron spin‐echo technique
Authors: Alpert Yolande , Cser László , Faragó Béla , Franěk František , Mezei Ferenc , Ostanevich Yuriy M.
Published: May 2005

The dynamic behavior of pig immunoglobulin G in deuterium oxide solutions was investigated by the neutron spin‐echo technique. This novel technique makes it possible to study intramolecular motion without introducing probes into the macromolecule. Using neutron spin‐echo, the effective diffusion coefficient, Deff, was obtained as a function of the transferred momentum, κ. For interpretation of the experimental data, two models were designed, and computed Deff values were compared with experimental data. The rigid T‐shape model was compatible with the experimental data only by assuming an unrealistically high rotational diffusion coefficient, and it was therefore unacceptable. Reasonable agreement with all available experimental data was obtained with a flexible model of immunoglobulin G molecule, which the Fab arms are assumed to wobble around the hinge region within an angle of 50°.
Thermodynamics of the helix–coil transition in polypeptides in mixed organic solvents: The influence of inert solvent and side chain
Authors: Jeremic K. , Karasz F. E.
Published: May 2005

The thermally induced coil–helix transition of poly(γ‐benzyl‐L‐glutamate) (PBLG) and poly(γ‐methyl‐L‐glutamate) (PMLG) in binary solvent mixtures was investigated by calorimetric and optical rotatory dispersion (ORD) measurements. Dichloroacetic acid was the common active solvent, and the inert solvent was one of the chlorinated hydrocarbons, such as chloroform, 1,3‐dichloropropane, 1‐chlorobutane, or 1‐chlorooctane.

The thermodynamic parameters characterizing the intramolecular polypeptide and polypeptide–solvent interactions were calculated using the Karasz and Gajnos theoretical model [(1973) J. Phys. Chem. 77, 1139–1145]. It was found that the enthalpy (ΔH1) and entropy (ΔS1) of helix stabilization in the absence of the active solvent depend on the inert solvent, but only in the case of PBLG. This is explained by the additional helix stabilization achieved by the stacking of the benzyl groups. The stacking is more pronounced in less polar chlorinated hydrocarbons with longer aliphatic chains. The results obtained indicate that the maximum helix stability is reached in chlorinated hydrocarbons with 12 C atoms. In the case PMLG, with an aliphatic ester side group, ΔH1 and ΔS1 are independent of the inert solvent.

The ORD measurements were used to determine the maximum fraction of helicity attained at constant solvent composition and the transition temperature, Tc, at the point where fH = 0.5. It was found that, for the same solvent composition, Tc was higher than the temperature of the midpoint of the calorimetric peak. This is explained by the fact that the maximum fraction of helicity is less than unity. The finite transition width was taken into account by calculating the phase boundaries for different fractions of helicity using the value of σ estimated from the calorimetric and van't Hoff enthalpies in the usual manner.
Analysis of the ring‐closure probabilities of isotropic wormlike chains: Application to duplex DNA
Authors: Hagerman Paul J.
Published: May 2005

The configurational properties of an isotropically bendable wormlike chain have been investigated using a Monte Carlo approach. In particular, radial distributions for end‐to‐end separation, ring closure probabilities, and the angular correlation of the two ends of the chain have all been determined as a function of the contour length of the chain. The results of this analysis, when applied to the data of Shore et al. [(1981) Proc. Natl. Acad. Sci. USA 78, 4833–4837] for the length dependence of ring closure for doublehelical DNA, yields a value for the persistence length of DNA in remarkable agreement with earlier hydrodynamic studies.
DNA Motions in the nucleosome core particle: A reanalysis
Authors: Schurr J. Michael , Schurr Rebecca L.
Published: May 2005

Transient photodichroism (TPD) data of Wang, Hogan and Austin [(1982) Proc. Natl. Acad. Sci. USA 79, 5896–5900] for methylene blue intercalated in nucleosomal DNA are reanalyzed using correct expressions for the twisting correlation functions of short DNAs. The data are found to rule out several models, including one in which the helix axis is constrained to girdle the equator of the sphere (representing a core particle) but the DNA is everywhere able to undergo twisting deformations and/or spinning around its local helix axis. However, when the ends of the DNA are rigidly clamped (against twisting/spinning) to the sphere, the same model gives an excellent fit to the data with suitable choices of parameters. From these and other observations, it is concluded that nucleosomal DNA must be rigidly clamped to the core particle at one or more points, although it is free to twist at most sites of binding of the dye. Moreover, if the dye is actually bound between two clamped points, then the torsional rigidity of DNA in the nucleosome is at least 2.5 times smaller than that of an ordinary linear DNA.
Adsorption of polypeptides on a solid surface. IV. Adsorption and β‐structure–coil transition
Authors: Birshtein T. M. , Borisov O. V. , Karaev A. K. , Zhulina E. B.
Published: May 2005

A theory of adsorption of a polypetide chain capable of undergoing the coil–β‐structure transition on a solid planar surface has been developed. The mutual influence of two order–disorder phase transitions, a conformational and an adsorption transition, was investigated. Various types of adsorption transitions are possible, depending on the initial conformational state (partly or completely β‐structured) and the selectivity of adsorption: (a) the second‐order phase transition, in which the chain is partly structured, both in adsorbed and desorbed states; and (b) the first‐order phase transition, in which the chain exhibits a regular β‐structure, at least on one side of the adsorption transition boundary. The chain bonding to the surface alters the degree of β‐structure, both in the case of selective and nonselective adsorption (similar to the adsorption of the chains with other types of secondary structure). We show that the slope of the adsorption curves for partly β‐structural chains increases as a result of an increase in the degree of β‐structuring, and this effect is even stronger than the analogous effect of β‐structuring.
Secondary structure of peptides. 18. 15N‐nmr and 13C‐nmr CP/MAS investigation of the primary and secondary structure of (Ala/Val) copolypeptides
Authors: Kricheldorf Hans R. , Müller Detlef , Hull William E.
Published: May 2005

Various copolypeptides were prepared by benzylamine or tertiary amine‐initiated copolymerizations of alanine–N‐carboxyanhydride (Ala‐NCA) and valine–N‐carboxyanhydride (Val‐NCA). The number‐average molecular weights of these copolypeptides were detemined by 1H‐nmr spectroscopic end‐group analyses and viscosity measurements. The sequences were characterized by 15N‐nmr spectra in solution, and the average lengths of the homogeneous blocks were determined from the signal intensities. The 50.3‐and 75.4‐MHz 13C‐nmr CP/MAS spectra of the solid copolypeptides are not sensitive to sequence effects, but allow qualitative and quantitative analyses of the secondary structures. In contrast to other methods, the 13C‐nmr spectra allow determination of the extent to which individual amino acids are incorporated into β‐sheet or α‐helix phases. Depending on primary structure and molecular weight, the secondary structure of (Ala/Val) copolypeptides may vary significantly. Both monomer units may be predominantly helical or predominantly β‐sheet structure, or the Val units may prefer the β‐sheet structure with most Ala‐units forming β‐helices. However, these secondary structures are more or less thermodynamically unstable and revert to the stable conformations on reprecipitation from trifluoroacetic acid/water.
Vibrational circular dichroism of polypeptides. VI. polytyrosine α‐helical and random‐coil results
Authors: Yasui S. C. , Keiderling T. A.
Published: May 2005

We have measured the VCD of polytyrosine in the amide I and II regions in dimethyl sulfoxide (DMSO) and in 80:20 mixtures of DMSO with trifluoroethanol, trifluoroacetic acid (TFA), and dichloroacetic acid and in 50:50 mixtures of DMSO and trimethyl phosphate (TMP). Additionally, VCD was obtained for deuterated polytyrosine in DMSO and DMSO:D2O, DMSO:TFA(d1), and DMSO:TMP mixtures as before. Amide A VCD was obtained in DMSO and DMSO:TMP mixtures. In the pure solvent, VCD of an opposite sign was seen as compared with that seen in the mixtures. The latter were characteristic in sign pattern and shape of right‐handed α‐helices for poly(L‐tyrosine). The pure polytyrosine:DMSO results are similar to those of polylysine:D2O at neutral pH and poly(β‐benzyl‐aspartate) in DMSO and may be characteristic of random‐coil VCD.
Vibrational circular dichroism of polypeptides, V. A study of 310‐helical‐octapeptides
Authors: Yasui Sritana C. , Keiderling Timothy A. , Bonora Gian Maria , Toniolo Claudio
Published: May 2005

We have measured vibrational CD spectra in the 3600–1250 cm−1 region of two monodisperse, protected octapeptides, which form right‐handed 310‐helices in CDC13 solution. The spectra are similar in sign pattern to those obtained for right‐handed α‐helices in solution but are smaller in magnitude and, additionally, provide evidence of some line‐shape differences. The delineation of this type of ordered conformation was accomplished by means of 1H‐nmr. Such a solution structure is consistent with the x‐ray crystal structure of one of these molecules.