bluuebunny/crossref_metadata_2025 huggingface dataset:
Quasielastic light scattering by biopolymers. V. Interparticle interactions between polynucleosomes
Authors: Schmitz Kenneth S. , Parthasarathy Nambi , Kent Jacqueline C. , Gauntt Jennifer
Published: December 2004

Quasielastic light scattering and electrophoretic light scattering experiments were performed on chicken erythrocyte polynucleosome solutions at various temperatures and ionic strengths. The apparent diffusion coefficient, Dapp, was found to depend on the scattering vector K. In general, Dapp can be described as a damped oscillatory function of K in the ionic strength range of 10 to 60 mM and over the temperature range of 10 to 40°C. Electrophoretic light scattering studies on total digest chromatin samples indicate the apparent charge on the polynucleosomes increases as the ionic strength is lowered from 10 to 1 mM. These data are interpreted in terms of fluctuations in the surface charge distribution of the polyion and subsequent inducement of an asymmetric distribution of small ions about the polyion. These fluctuation components lead to the formation of “clusters” of polyions.
Dissociation of bovine and bacterial catalases by sodium n‐dodecyl sulfate
Authors: Jones M. N. , Manley P. , Midgley P. J. W. , Wilkinson A. E.
Published: December 2004

The dissociation of beef liver and bacterial (Micrococcus lysodeikticus) catalases by the action of sodium n‐dodecyl sulfate (SDS) has been investigated as a function of SDS concetration and time by ultracentrifugation. The rate of dissociation of beef liver catalase is found to be much faster than that for bacterial catalase in 25 mM SDS at pH 7.0. Beef liver catalase is dissociated into its four subunits after 24 h, whereas bacterial catalase is not completely dissociated after 36 days of incubation. The binding of SDS to beef liver catalase obeys a Hill equation with a cooperativity exponent of 2.0 and a binding constant of 440. The initial interaction of SDS with beef liver catalase can be detected by microcalorimetry, whereas the mixing of SDS with bacterial catalase is athermal. Bacterial catalase retains enzymic activity in the presence of SDS, whereas beef liver catalase is completely deactivated at SDS concentrations above 5 mM. Beef liver catalase is more sensitive to acid denaturation than bacterial catalase, and the rate of dissociation for both catalases is sixth‐order in proton concentration. Comparison of the amino acid analysis of the two catalases shows that bacterial catalase has a smaller number of lysyl residues and a larger number of glutamyl residues than beef liver catalase. Taken together these structural differences could lead to a reduced affinity of bacterial catalase for the binding of SDS as observed.
Light‐scattering spectroscopic study of polysaccharide protein conjugate
Authors: Patkowski A. , Bujalowski W. , Chu B. , Schneerson R. , Robbins J. B.
Published: December 2004

By combining gel permeation chromatography (GPC) and light‐scattering spectroscopy, including photon correlation and angular distribution of absolute scattered intensity, we were able to characterize immunologically active Haemophilus influenzae type b polysaccharide (HIB Ps) bovine serum albumin (BSA) conjugates in terms of equivalent hydrodynamic radius rh ∼ (6.2 ± 0.6) × 102 Å, apparent radius of gyration rg ∼ (5.4 ± 0.3) × 102 Å, apparent molecular weight Mw ∼ (3.5 ± 0.4) × 106 g/mol, and a second virial coefficient A2 ∼ (1.9 ± 0.3) × 10−4 cm3 mol/g2. We could study the effects of each of the processes in the conjugate formation according to the following procedure: BSA (dialysis, modification, fractionation) + HIB Ps → HIB Ps/BSA conjugate (conjugate formation, fractionation). Narrow distributions of HIB Ps BSA conjugate formation can be achieved using fractionated BSA.
Cooperative effects in α‐helices: An ab initio molecular‐orbital study
Authors: Van Duijnen P. T. , Thole B. T.
Published: December 2004

Some properties of α‐helices of polyclycine and polyalanine, up to the decapeptide, were investigated by ab initio molecular‐orbital calculations. These helices were found to be unstable relative to the corresponding “fully extended chain” conformation. The electric field of helices of 8–10 residues is about 20% stronger than that of models built from noninteracting monomers, for example. This is a result of cooperativity, which is essentially governed by the intramolecular hydrogen bonds. The cooperativity is manifest in all properties of the helices: relative stability, dipole moment, proton affinity, electrical potential. The electric potential of helices of three and four residues is such that their instability can be compensated for by a single charged group acting as an “initiator.” The computed proton affinity of the (Ala)8 α‐helix is about 45 kcal/mol larger than that of formamide, which confirms that long helices may be protonated at the carboxyl end in solution.
Theoretical study of the fraction of a long‐chain DNA that can be incorporated in a recombinant DNA partial‐digest library
Authors: Seed Brian
Published: December 2004

Experimental evidence indicates that the cleavage sites for site‐specific DNA cleavage enzymes are randomly distributed throughout the DNA polymer [Botchan et al. (1973) Cold Spring Harbor Symp. Quantum Biol. 38, 383–395; Hamer and Thomas (1973) Chromosoma 49, 243–267]. Using this information we derive equations for the probability that a DNA base pair chosen at random can be found within the population of enzymatically generated partial cleavage products whose lengths fall between L + 1 and L + r base pairs. The results describe the fraction of a long‐chain DNA that can be incorporated in a recombinant DNA partial digest library. The weight‐fraction distribution of Kuhn (1930) is a special case of the distribution derived here.
Study of agarose gels by electron microscopy of freeze‐fractured surfaces
Authors: Waki Seichi , Harvey J. D. , Bellamy A. R.
Published: December 2004

The distribution of fibers in agarose gels has been studied by electron‐microscopic examination of replicas formed from freeze‐fracture surfaces. For gels set in water, the results obtained support the model proposed for the gel structure by Arnott et al. (1974) of a random array of long, straight, connected fibers, with each fiber having a diameter equivalent to that of an aggregate of approximately 10–30 agarose helixes, depending on the initial agarose concentration. The density of these fibers, their water content, and the total length of fibers per unit volume have been derived from the measured distribution of intersections per unit area of freeze‐fracture surfaces. For gels set in the presence of salt, the distribution of fibers becomes distinctly non‐Poissonian, leading to larger interfiber spaces and a gel of greater effective pore size. The larger pore size of gels set in the presence of salt also has been revealed by electrophoretic measurements in which the relative migration rates of plasmid DNA molecules of varying conformations have been determined.
Monte carlo simulations of peptide solvation
Authors: Madison Vincent , Osguthorpe David J. , Dauber Pnina , Hagler Arnold T.
Published: December 2004

To increase our understanding of peptide–water interactions, we are simulating the behavior of water molecules in the intermolecular channels of [Phe4Val6]antamanide dododecahydrate crystals. There is good overall agreement between the positions predicted using two alternative potential functions and those that have been observed by x‐ray diffraction. Detailed differences between the predictions for the two potential functions are discussed.
Coupling between the helix–coil transition and nematic–isotropic transitions in polypeptide solutions
Authors: Matheson Robert R.
Published: December 2004

The lattice model of Flory has been extended in order to consider equilibrium between isotropic and nematic phases containing helix–coil type chains. Nearly complete exclusion of coil sequences from the lyotropic nematic phase produces an enhanced cooperativity in the helix–coil transition. In poor solvents this enhancement begins to occur at concentrations typical of some experiments.
Domain characteristics of the carboxyl‐terminal fragment 206–316 of thermolysin
Authors: Fontana Angelo , Vita Claudio , Chaiken Irwin M.
Published: December 2004

The existence, location, and characteristics of protein domains have been investigated by studying the structural properties of the carboxyl‐terminal cyanogen bromide fragment 206–316 of thermolysin. As judged by far‐uv CD measurements in aqueous solution under neutral conditions, the fragment attains a substantial degree of α‐helical structure comparable to that exhibited by the corresponding region in native thermolysin. By radioimmunoassay techniques, a considerable degree of nativeness of fragment conformation has been deduced from comparison of the relative affinities of thermolysin and fragment 206–316 for antibodies specific for the 206–316 region in the intact protein. The fragment shows noteworthy stability to protein denaturants. The overall spectroscopic and immunochemical data suggest that fragment 206–316 is able to refold into a stable, nativelike structure independently from the rest of the molecule, thus providing support for the view that this fragment may contain a substantial part, if not all, of a protein domain structure.
The unfolding mechanism of thermolysin
Authors: Corbett R. J. T. , Roche Rodney S.
Published: December 2004

The ligand‐modulated kinetics of the autoproteolysis of thermolysin and the high‐molecular‐weight products of the reaction provide evidence for the conclusion that separation of the two structural domains is most probably the first step on the unfolding pathway of the protein under native conditions.
The optical activity of polypeptides
Authors: Schellman John A. , Becktel Wayne J.
Published: December 2004

The present status of the theory of the optical properties of polypeptides is discussed in a general way. Arguments are presented that indicate that the interaction of exciton bands in helices will occur in a tensorial way with the parallel polarized bands normally having stronger interactions than the perpendicular polarized bands, with only small cross‐interactions. The net result is an anisotropy of the hyperchromism of the ππ* band and an imbalance of the rotatory strengths of the parallel and perpendicular components. According to the evidence of Mandel and Holzwarth [(1973) Biopolymers 13, 655–674], this is, in fact, the origin of the strongly nonconservative CD bands of polyproline II and related structures. The implications of anisotropic hyperchromicity on the interpretation of the linear dichroism of crystals is discussed.
1H‐NMR studies on substance P hexapeptide analogs
Authors: Ribeiro Anthony , Jardetzky Oleg , Gilon Chaim , Teitelbaum Dina , Chorev Michael
Published: December 2004

1H‐nmr studies of [pGlu6]SP6–11, [gpGlu6,mPhe7]SP6–11, and [pGlu6,N‐CH3Phe7]SP6–11 in DMSO‐d6 reveal characteristic chemical shifts, 3JNH‐αCH, temperature dependence, as well as deuterium exchange half‐times. Marked similarities are revealed for the two first analogs, whereas the N‐methylated analog is clearly different. Possible conformations are considered.
Sequential hydration of a dry globular protein
Authors: Poole P. L. , Finney J. L.
Published: December 2004

Using direct difference ir and laser Raman spectroscopy, the sequential hydration of hen egg‐white lysozyme was monitored. The ir data allowed us to identify some specific molecular hydration events that occur as water is added, whereas the Raman is interpreted in terms of conformational changes. The largest of these solvent‐induced changes occurs below the hydration level at which activity commences.
Functional significance of flexibility in proteins
Authors: Huber Robert , Bennett William S.
Published: December 2004

The structural basis and the functional implications of large‐scale flexibility are discussed for three systems: trypsin–trypsinogen, immunoglobulins, and citrate synthase. The trypsin–trypsinogen system provides an example in which an order–disorder transition is used as a means to regulate enzymatic activity. Immunoglobulins demonstrate how flexibly linked domains may be used to allow the binding of ligands with diverse arrangements. In citrate synthase, domain motion forms an active site that is shielded from solvent. Analogous large‐scale flexibility has been observed in a number of other systems.
Conformational flexibility in a small globular hormone: X‐ray analysis of avian pancreatic polypeptide at 0.98‐Å resolution
Authors: Glover Ian , Haneef Illyas , Pitts Jim , Wood Steve , Moss David , Tickle Ian , Blundell Tom
Published: December 2004

The 36‐amino acid avian pancreatic polypeptide has been studied by x‐ray analysis at 0.98‐Å resolution and refined using a restrained least‐squares technique to an agreement factor of 15.6%. The polypeptide, which has a compact globular structure with a hydrophobic core, comprises a polyproline–like helix (residues 2–8) and an α‐helix (residues 14–32). The molecule forms symmetrical dimers linked through zinc atoms in the crystal lattice. The high‐resolution analysis defines sequence‐dependent distortions in the α‐helical parameters due to hydrogen bonding of water molecules and side chains. The thermal parameters indicate an increased flexibility of the main chain at the turn between the helices and in the C‐terminal residues. For the first time, six‐parameter anisotropic thermal ellipsoids have been refined for each atom; these define the directions of the molecular motions in the polypeptide, indicating concerted vibrations. The physiological roles of conformation, flexibility, and dynamics of this polypeptide hormone are discussed.
Multiple intermediates in the reaction of bovine β‐trypsin with bovine pancreatic trypsin inhibitor (kunitz)
Authors: Antonini Eraldo , Ascenzi Paolo , Menegatti Enea , Guarneri Mario
Published: December 2004

The kinetics of the formation of the complex between bovine β‐trypsin and the bovine basic pancreatic trypsin inhibitor (BPTI) was investigated using three different signals: the displacement of proflavine, the optical density changes in the UV region, and the loss of the enzymatic activity. For the three different signals, with inhibitor in excess over bovine β‐trypsin ([BPTI] ≥ 5 × [bovine β‐trypsin]), the time course of the reaction corresponds to a pseudo‐first‐order process. The concentration dependence of the rate is second order at low BPTI concentrations and tends to first order at high inhibitor concentrations. This behavior may be explained by relatively rapid preequilibria followed by limiting first‐order processes according to

The values of Ki, k+i, and k(on)i ( = k+i/Ki) have been determined for the different reactions at three pH values: 6.80, 4.80, and 3.50. The kinetic parameters differ widely for the processes reflected by the various signals; the difference increases upon lowering pH. The results indicate that the formation of the bovine β‐trypsin–BPTI complex is not an all‐or‐nothing process, but involves several intermediates corresponding to discrete reaction steps, which are differently affected by ionization processes.
Gramicidin a adopts distinctly different conformations in membranes and in organic solvents
Authors: Wallace B. A.
Published: December 2004

Gramicidin A exists in distinctly different conformations in phospholipid vesicles and in organic solvents. These different folding motifs are also reflected in crystals of gramicidin formed in the presence and absence of lipid molecules.
How antigenic are antigenic peptides?
Authors: Leach S. J.
Published: December 2004

Most of a protein surface is potentially antigenic, consisting of numerous overlapping domains each complementary to antibody‐combining sites. These domains may include peptide sequences that are demonstrably antigenic but only when antibodies from the appropriate host individuals and species are used. Methods for locating antigenic peptide sequences are described in which hydrophilic polyamide supports are used for peptide synthesis, then solid‐phase radioimmunoassay with antisera and protein A. Most antigenic domains, however, comprise amino acid side chains contributed by two or more nearby polypeptide chains. Such domains can be identified by comparing the cross‐reactivities of groups of very closely related proteins towards monoclonal antibodies raised to one of them. Such studies, using myoglobins, have identified a number of residues not previously shown to be antigenic and have provided a guide for the choice of synthetic peptides which are likely to carry several immunodominant side chains. One such peptide corresponding to residues (72–89) of beef myoglobin has been shown, using CD and antibodies to the parent protein, to have interesting conformational and antigenic properties. The peptide (25–55) is also antigenic.
Antigenic reactivity: Molecular delineation of monohaptenic anaphylactogens
Authors: Schneider C. H. , Guenin R.
Published: December 2004

Anaphylactogenic, monohaptenic conjugates carrying a 2,4‐dinitro‐5‐carboxyphenyl substituent as haptenic group and either one of two types of auxiliary groups essential for their anaphylactogenicity were studied. The “hydrocarbon auxiliary groups” require the presence of a hydrocarbon structure such as aliphatic chains of discrete length or planar rings such as provided by phenyl‐ or nicotinoyl residues and become particularly effective in conjunction with a carboxylate group. The benzylpenicilloyl group is an effective auxiliary structure, but the thiazolidine ring as such is not. It appears that the distance between haptenic and hydrocarbon auxiliary groups can be quite large. The “carbohydrate auxiliary group” becomes effective via a different mechanism. It requires disaccharide residues or two closely connected monosaccharides. Single monosaccharides are ineffective. A concept of interest with regard to drug allergy is the possibility that attachment of a single haptenic molecule to a glycoprotein constitutes an anaphylactogen.
Controlled release of macromolecules and pharmaceuticals from synthetic polypeptides based on glutamic acid
Authors: Sidman Kenneth R. , Steber William D. , Schwope Arthur D. , Schnaper Gayle R.
Published: December 2004

Biocompatible, biodegradable copolymers of glutamic acid and ethyl glutamate were evaluated for their permeability to proteins ranging in molecular weight from 12,300 to 69,000. The results showed that the copolymers were sufficiently permeable that they could be used for the preparation of implantable, controlled‐release systems capable of releasing therapeutic amounts of high‐molecular‐weight drugs.
Crystal structure and conformation of a cyclic tetrapeptide cyclo(L‐Pro‐Sar)2 containing all‐cis peptide units
Authors: Ueno Katsuhiko , Shimizu Toshimi
Published: December 2004

The crystal structure and conformation of the synthetic cyclic tetrapeptide, cyclo(L‐Pro‐Sar)2, was determined by x‐ray analysis. The peptide crystallizes in the orthorhombic space group P212121 with cell parameters a = 9.277(1), b = 12.884(1), and c = 15.581(2) Å. The crystal structure was solved by the symbolic addition procedure for direct phase determination and least‐squares refinement using 1796 reflections, which led to the final R value of 0.043. This structure provides the first example observed in a crystal of a cyclic tetrapeptide in which all four peptide units have been found in the cis conformation with ω angles deviating slightly by 2°–10° from the ideal value of 0°. It was also found that the two Pro Cα‐CO single bonds assumed a trans′ (ψ = 159.6° and 158.4°) conformation. Adjoining average planes of the peptide groups fall at nearly right angles to each other. The pyrrolidine ring conformations of the two prolyl residues are in the envelope form, with Cγ carbon out of the least‐squares planes for the remaining four atoms.
High‐resolution nmr studies of A‐ and G‐containing oligonucleotides
Authors: Shum Betty Wai‐King , Crothers Donald M.
Published: December 2004

We report the temperature dependence of the H2 and H8 purine ring proton resonances of oligoriboadenylates up to chain length 11, with or without a single guanosine residue at the 5′‐end, second position, or 3′‐end. The results suggest the following generalizations: (1) Stacking of the bases in a right‐handed single‐stranded helix is more extensive in the interior of the chain than at the chain ends. (2) The tendency of the terminal base to unstack is greater at the 5′‐end than at the 3′‐terminus. (3) G stacks more weakly than A, as evidenced by weak stacking of 3′‐terminal G. Anomalies were also observed in the unstacking profile of G at the second position in the chain, indicating a conformational anomaly such as looping out of G, thereby allowing adjacent A's to stack together, or adoption by G of some other alternative structure. (4) The results imply that the environment at a given base is influenced by effects of longer range than nearest‐ or next‐nearest‐neighbor. Increasing ion condensation as chain length increases may be responsible for the slow approach of oligomer behavior to the properties of the high polymer.
Improved methods of analysis for CD data applied to single‐strand stacking
Authors: Causley Gary C. , Staskus Paul W. , Johnson W. Curtis
Published: December 2004

CD spectra of ApA, Poly(A), CpC, and poly(C), measured as a function of tempeature, are used to demonstrate improved methods of analysis for this type of data. Each of the four sets of temperature‐dependent CD spectra are decomposed using singular value deocmposition. This method demonstrates that there are only two independnet parameters in each set of data. The two basis curves in the wavelength domain for each set of data are use to average the CD curves even though they are taken at different temperatures. Each of the four sets of temperature‐dependent data, smoothed in this way, is decomposed in the Taylor series to separate degenerate interactions due to stacking from the intrinsic CD of the chromophores and nondegenerate interactions. Such a decomposition allow the comparison of corresponding interactions whose relative magnitudes are not obvious in the data. The CD due to degenrate interactions fits the van't Hoff equation well in all four cases and thermodynamic parameters are determined. A simplex routine is used to search the space before performing the least‐squares fit of the data of the van't Hoff equation. This guarantees a global solution rather than a local solution. The first of the two basis curves in the temperature domain derived by singular value decomposition also fits the van't Hoff equation well and gives comparable thermodynamic parameters, although the basis curves derived in this manner have no a priori physical significance. Rather than comparing room temperature CD curves, we compare CD curves of the various compounds at their melting temperature where the populations of the stacked conformation are equivalent. We use the Cantor‐Tinoco equation, which relates the CD of a polymer to the CD of the corresponding dimer, to show that the secondary structure of ApA is not the same as poly(A), and the secondary structure of CpC is not the same as poly(C). However, the two dimers have similar degenerate stacking interactions as do the two polymers. A sound theoretical basis is provided for the semiempirical Cantor‐Tonoco equation.
Behavior of amphipathic helices on analysis via matrix methods, with application to glucagon, secretin, and vasoactive intestinal peptide
Authors: Hamed Maher M. , Robinson Randall M. , Mattice Wayne L.
Published: December 2004

A configuration partition function, which incorporates concepts embodied in the amphipathic helix hypothesis, has been formulated for a polypeptide in the presence of zwitterionic phospholipid. An enhanced probability is assigned to helix formation in any region of the polypeptide chain where side chains bearing charges of opposite sign will be situated on the same side of the α‐helix but displaced from one another by one turn. This situation will arise when residues i − 4 (or i − 3) and i bear charges of opposite sign and residue i − 4 (or i − 3) through i are in a helical state. Illustrative calculations are performed for polypeptide chains in which the generalized nonionic amino acid residue serving as host has Zimm‐Bragg parameters of σ = 10−4, s = 1. These calculations define conditions under which two interacting charged pairs can cooperate in a synergistic helix augmentation even when the two pairs are separated by significantly more than four generalized nonionic amino acid residues. Furthermore, the two interacting charged pairs, as well as the intervening amino acid residues, may become helical as one unit. Significant augmentation in helicity is observed with plausible values for the enhanced probablity assigned to helix formation for an interacting pair. This model predicts correctly that glucagon and secretin, but not vasoactive intestinal peptide, undergo a coil‐to‐helix trnsition in the presence of zwitterionic phospholipid. This prediction is made with plausible values for the parameter used to express the helicity enhancement. The experimental observation with zwitterionic phospholipids is the direct opposite of that seen for these three peptides in the presence of anionic lipids and detergents. In anionic lipids the amount of induced helicity is in the following order: glucagon < secretin < vasoactive intestinal peptide. Results obtained with these three peptides demonstrate that the nature of the head group of the lipid is important for lipid–protein interaction and that the resulting conformational changes can be rationalized by matrix methods.
Nuclear magnetic resonance study of ring conformations of cyclic tetradepsipeptide AM‐toxins and related peptides
Authors: Higashijima Tsutomu , Shimohigashi Yasuyuki , Kato Tetsuo , Izumiya Nobuo , Ueno Tamio , Miyazawa Tatsuo
Published: December 2004

Cyclic tetradepsipeptides, AM‐toxin I and II, are the host‐specific phytotoxins of Alternaria mali. In order to elucidate conformation‐toxicity relationships, we analyzed the 270‐MHz proton nmr spectra of AM‐toxins and hydrogenated analogs, (D‐Ala2)AM‐toxin I (toxic) and (L‐Ala2)AM‐toxin I (not toxic), in (C2H3)2SO. These cyclic tetradepsipeptides do not contain N‐substituted amino acid residues, and all the peptide and ester groups have been found to be transoid. Two conformers with very unequal populations have been found for AM‐toxin I and II; the CβCαCO conformations of the Dha2 residues are nonplanar S‐trans in the major conformer and nonplanar S‐cis in the minor conformer. Only one ring conformation has been found for each of (L‐Ala2) and (D‐Ala2)AM‐toxin I. (L‐Ala2)AM‐toxin I takes a C4‐type ring conformation; all the CO groups and Cα‐H bonds are oriented to the same side of the ring. (D‐Ala2)AM‐toxin I takes a new ring conformation; the side chain and CO group of the L‐Amp1 residue are oriented to the same side of the ring. This new conformation is also found for the major conformers of AM‐toxin I and II and thus appears to be required for the toxicity. The ring conformations of Tyr(OCH3)1‐bearing analog tetradepsipeptides have been found to be much the same as those of Amp1‐bearing depsipeptides. Furthermore, on the basis of the two distinct conformations of (D‐Ala2) and (L‐Ala2)AM‐toxin I, an empirical rule is proposed for the stable ring conformations of cyclic tetra‐D,L‐peptides, not containing N‐substituted amino acid residues.
Temperature dependence of the dynamic light scattering of linear ϕ29 DNA: Implications for spontaneous opening of the double‐helix
Authors: Wilcoxon Jess , Schurr J. Michael
Published: December 2004

The apparent diffusion coefficient Dapp(K) of a single sample of linear ϕ29 DNA (Mr = 11.5 × 106) has been measured as a function of K2 from 0.21 × 1010 to 20 × 1010 cm−2 at a variety of temperatures from −0.5 to +70°C. Dapp(K) scales closely as T/η at every value of K2. All of these data are simulated by a particular Rouse‐Zimm model comprised of a constant number of subchains with constant rms subchain extension b = 1057 Å and an apparent subchain diffusion coefficient Dplat that scales at T/η from −0.5 to +70°C. It is inferred from these results that any temperature dependence of the flexural and torsional rigidities of DNA must be rather weak. A less firm inference is that these rigidities actually increase slightly with temperature, possibly in proportion to T, which is weak T dependence in this context. These findings eliminate the possibility that spontaneous transient opening of the DNA structure has any significant effect on the flexural and torsional rigidities of the DNA filament. A review of the most pertinent available data from other experiments concerning spontaneous transient opening of the DNA is presented. The formaldehyde kinetics data do not unequivocally implicate an open base‐pair intermediate and provide only an upper limit to the fraction of open base pairs. An alternative nonopening model with a protonated doorway state is proposed to accommodate the hydrogen‐exchange data. It is concluded that there is presently no incontrovertible evidence for a fraction of unstacked open base pairs greater than about 10−4.
Interaction of calcium ions with peptide hormones of the gastrin family
Authors: Peggion E. , Mammi S. , Palumbo M. , Moroder L. , Wünsch E.
Published: December 2004

The interactions of Des‐Trp1‐Nle12‐minigastrin I (Nle11‐HG‐13) and Nle15‐little gastrin I (Nle15‐HG‐17) with calcium ions have been investigated in water and in trifluoroethanol solution using uv and CD absorption techniques. Both hormones strongly interact with Ca2+ in the organic medium. In the case of Nle11‐HG‐13, the near‐uv chiroptical properties (dominated by the transitions of the Trp residue in the C‐terminal tetrapeptide sequence) indicate that three metal ions per mole of hormone are involved in the binding process. From the different response of near‐uv and far‐uv CD properties to the addition of calcium and from the change of the CD spectra in the aromatic absorption region, it is concluded that the biologically important C‐terminal sequence is directly involved in the interaction with calcium. Elongation of the peptide chain from Nle11‐HG‐13 to Nle15‐HG‐17 (Nle15‐little gastrin I) does not provide any additional binding site for calcium ions. The change of the CD properties in the near‐ and far‐uv indicates that three metal ions per mole of hormone are involved in the binding process. The dichroic absorption in the aromatic region indicates that only one of the two Trp residues of the little gastrin analog is sensitive to the presence of calcium. On the assumption that the variation of the CD properties is proportional to the extent of calcium binding, the binding constants K1, K2, and K3 have been estimated roughly. Two similar sets of binding constants have been found, with K1 ≥ 106M−1 and K3 of the order of 105M−1, indicating similar binding sites in the two hormones with high affinity for calcium ions.
Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features
Authors: Kabsch Wolfgang , Sander Christian
Published: December 2004

For a successful analysis of the relation between amino acid sequence and protein structure, an unambiguous and physically meaningful definition of secondary structure is essential. We have developed a set of simple and physically motivated criteria for secondary structure, programmed as a pattern‐recognition process of hydrogen‐bonded and geometrical features extracted from x‐ray coordinates. Cooperative secondary structure is recognized as repeats of the elementary hydrogen‐bonding patterns “turn” and “bridge.” Repeating turns are “helices,” repeating bridges are “ladders,” connected ladders are “sheets.” Geometric structure is defined in terms of the concepts torsion and curvature of differential geometry. Local chain “chirality” is the torsional handedness of four consecutive Cα positions and is positive for right‐handed helices and negative for ideal twisted β‐sheets. Curved pieces are defined as “bends.” Solvent “exposure” is given as the number of water molecules in possible contact with a residue. The end result is a compilation of the primary structure, including SS bonds, secondary structure, and solvent exposure of 62 different globular proteins. The presentation is in linear form: strip graphs for an overall view and strip tables for the details of each of 10.925 residues. The dictionary is also available in computer‐readable form for protein structure prediction work.
Matrix‐method calculation of linear and circular dichroism spectra of nucleic acids and polynucleotides
Authors: Rizzo Vincenzo , Schellman John A.
Published: December 2004

Calculations of the optical properties (absorption, linear dichroism, circular dichroism, and anisotropic components of the CD) are presented for polynucleotides of random or regular sequence within the formalism of the matrix method using a set of parameters that includes only the ππ* transitions of the aromatic bases. Experimental solution spectra agree favorably with calculated CD spectra for A‐RNA, A‐DNA, and B‐DNA, when coordinates derived from x‐ray studies on fibers are used. Excessive hypochromicity is predicted when parameters intended to reproduce the vacuum‐uv absorption of the chromophores are included in the calculations, but total elimination of these parameters leads to an insufficient hypochromicity for the long‐wavelength absorption band. Using alternative conformations for DNA in low‐salt aqueous solution did not improve the agreement between experimental and calculated spectra, but some features of the optical properties predicted for these variant structures suggest that the tilt of the bases with respect to the helical axis may be larger than that of the fiber B‐form.

In the case of polynucleotides with regular structure, which have been traditionally less easy to understand in terms of the standard nucleic acid conformations, a series of alternative structures has been examined. Unexpectedly, the calculated spectrum for the Z‐DNA structure compares almost quantitatively with the experimental spectrum of poly(dGC·dGC) in low salt. This result, which confirms a recent report [Vasmel, H. & Greve, J. (1981) Biopolymers 20, 1329–1332], is in contrast with the current identification of Z‐DNA with the high‐salt form of poly(dGC·dGC). Finally, the optical properties of single‐stranded polyribonucleotides appear to be better explained when alternative structures [91‐helix for poly(rA) and 61‐helix for poly(rC)] are introduced instead of the A‐RNA form.
A monte‐carlo estimate of DNA loop formation
Authors: Post Carol Beth
Published: December 2004

The ends of rather short double‐helical DNA segments (approximately two persistence lengths) can be enzymatically joined to form closed circles. Such covalent closure into circles is a measure of the likelihood of the two ends of the DNA coming into close contact. There is a length of DNA for which loop formation is most likely to occur. We have determined the chain‐length dependence of loop formation for stiff chains using computer‐generated chains of cylinders. The distribution from which the values for the angles between cylinders were chosen relates the chain parameters to a given chain persistence. Our results are compared with those of other theories, including a statistical wormlike chain model, and with the experimental measurements for ring closure of DNA restriction fragments.
Mean‐square helical hydrophobic moments in partially ordered proteins
Authors: Hamed Maher M. , Mattice Wayne L.
Published: December 2004

Helical hydrophobic moment ratios, 〈h2〉/〈H2〉, have been evaluated for 34 polypeptides under conditions where the helix content is dictated solely by the short‐range interactions operative in aqueous media. The mean‐square helical hydrophobic moment is denoted by 〈h2〉, and 〈H2〉 is the averaged of the squared hydrophobicites. This ratio would be one in absence of any correlation in the hydrophobicities of amino acid residues in helices. The 〈h2〉/〈H2〉 tend to be substantially larger than values of the analogous ratio formulated for the mean‐square dipole moments of typical synthetic polymers. For 24 of the 34 polypeptide chains considered, 〈h2〉/〈H2〉 is found to be greater than one, indicating a tendency to form helices with amphiphilic character. The ratio is exceptionally large in the case of the δ‐hemolysins. It is also large for two other surface‐active peptides, for two of the four apolipoproteins examined, and for myohemerythrin. A much smaller 〈h2〉/〈H2〉 is found for melittins. If melittins is to form helices with large 〈h2〉/〈H2〉, the configurational statistics must be governed by effects in addition to those short‐range interactions that occur when water is the solvent.
Synthesis and properties of L‐cysteinyl‐L‐cysteine disulfides
Authors: Capasso Sante , Mazzarella Lelio , Tancredi Teodorico , Zagari Adriana
Published: December 2004

Oligomeric cyclic disulfides, obtained by mild oxidation of the fully protected dipeptide L‐cysteinyl‐L‐cysteine, have been isolated by gel and thin‐layer chromatography. Polymeric material was recycled by a thiol–disulfide exchange‐reaction performed at basic pH. Spectroscopic investigations of the monomer and the two dimers indicate that conformers characterized by dihedral angles about the SS bond close to ±90° are preferred. Moreover, chiroptical and 1H‐nmr data for these compounds suggest higher mobility for the two dimers. The antiparallel dimeric disulfide can be considered a model compound for the hinge region formed at the subunit interface of the bovine seminal ribonuclease, a dimeric enzyme showing a complex kinetic behavior.
β‐Bend conformation of CH3CO‐Pro‐Pro‐Gly‐Pro‐NHCH3: Implications for posttranslational proline hydroxylation in collagen
Authors: Lee Eok , Némethy George , Scheraga Harold A. , Ananthanarayanan V. S.
Published: December 2004

Conformational‐energy computations have been carried out for the N‐acetyl‐N′‐methylamides of the Pro‐Pro, Pro‐Gly, and Gly‐Pro dipeptides and of the Pro‐Pro‐Gly‐Pro tetrapeptide, serving as models for the conformational analysis of single‐stranded poly(Gly‐Pro‐Pro). The probability of β‐bend formation for the Pro‐Gly sequence is very high, viz., 0.72 for the terminally blocked Pro‐Gly dipeptide, and rises to 0.86 in the tetrapeptide. The β‐bend conformations of the Pro‐Gly sequence are of low energy in single‐chain poly(Gly‐Pro‐Pro) as well. The β‐bend structure had been postulated earlier to be a requirement for post‐translational proline hydroxylation during the biosynthesis of collagen. The present results lend strong support to this proposal by demonstrating that the β‐bend structure is energetically favorable and hence can be accommodated easily in single‐stranded poly(Gly‐Pro‐Pro).
Conversion from a virtual‐bond chain to a complete polypeptide backbone chain
Authors: Purisima Enrico O. , Scheraga Harold A.
Published: December 2004

A method for generating a complete polypeptide backbone structure from a set of Cα coordinates is presented. Initial trial values of ϕ and ψ for a selected residue are chosen (essentially from an identification of the conformational region of the virtual‐bond backbone, e.g., and α‐helical region), and values of ϕ and ψ for the remaining residues (both towards the N‐ and C‐terminus) are then computed, subject to the constraint that the chain have the same virtual‐bond angles and virtual‐bond dihedral angles as the given set of Cα coordinates. The conversion from Cα coordinates to full backbone dihedral angles (ϕ,ψ) involves the solution of a set of algebraic equations relating the virtual‐bond angles and virtual‐bond dihedral angles to standard peptide geometry and backbone dihedral angles. The procedure has been tested successfully on Cα coordinates taken from standard‐geometry full‐atom structures of bovine pancreatic trypsin inhibitor (BPTI). Some difficulty was encountered with error‐sensitive residues, but on the whole the backbone generation was successful. Application of the method to Cα coordinates for BPTI derived from simplified model calculations (involving nonstandard geometry) showed that such coordinates may be inconsistent with the requirement that ϕPro be near −75°. In such a case, i.e., for residues for which the algebraic method failed, a leastsquares minimizer was then used in conjunction with the algebraic method; the mean‐square deviation of the calculated Cα coordinates from the given ones was minimized by varying the backbone dihedral angles. Thus, these inconsistencies were circumvented and a full backbone structure whose Cα coordinates had an rms deviation of 0.26 Å from the given set of Cα coordinates was obtained.
Rigidity of myosin and myosin rod by electric birefringence
Authors: Hvidt Søren , Chang Taihyun , Yu Hyuk
Published: December 2004

The rotational relaxation times of rabbit myosin and myosin rod have been determined by electric birefringence measurement. The relaxation time of myosin measured in 10 mM pyrophosphate buffers in a pH range of 7.6–9.5 was found to have substantial concentration and pH dependences. The infinite‐dilution limit of the relaxation time, τ°, was determined as 38 ± 2 μs, and it was found to be independent of pH. For myosin rod, a possible thermally induced conformational change was investigated in a temperature range of 1–43°C. The rotational relaxation time of myosin rod shows no clear indication of conformational change in this temperature range, and the radius of gyration measurement by light scattering was shown to be consistent with this observation. The steady‐state birefringence, however, decreases substantially above around 40°C. This, the myosin rod appears to be only slightly flexible even at physiological temperature, but the possibility of a “melting” or “hinging” of the myosin rod cannot completely be ruled out on the basis of these experiments.
Effect of cationic surfactants on the conformation and aggregation of poly(L‐glutamic acid)
Authors: Maeda Hiroshi , Kato Hiroshi , Ikeda Shoichi
Published: December 2004

The effects of three cationic surfactants, dodecylammonium chloride (DAC), dodecyldimethylammonium chloride (DDAC), and dodecyldimethylammonium chloride (DTDAC), on the conformation of poly(L‐glutamic acid) and at neutral pH were examined by CD. The maximum extent of the α‐helix induction occurs for each surfactant when the mixing ration is about unity. Different effects specific to each surfactant, as described below, appear in the range of mixing ratios larger than that required for the maximum induction. In the case of DTAC, the α‐helices disintegrate into random coils. In the case of DDAC, the aggregation of α‐helices takes place eventually leading to precipitation. Solubilization of the precipitates occurs at high mixing ratios. The most complex behavior is seen in the case of DAC; aggregation of α‐helices occurs only to a small extent and the formation of a small complex predominates over aggregation takes place again as DAC concentration increases further. Induction of the α‐helix is favored by dilution at a constant mixing ratio but is suppressed by the addition of NaCl.
Conformation of oligopeptides with L‐leucyl‐L‐leucyl‐L‐alanyl and L‐methionyl‐L‐methionyl‐L‐leucyl repeating units
Authors: Katakai Ryoichi , Iizuka Yasuko
Published: December 2004

The conformation of oligopeptides with hydrophobic side chains, Nps‐(L‐Leu‐L‐Leu‐L‐Ala)n‐OEt and Nps‐(L‐Met‐L‐Met‐L‐Leu)n‐OEt(n = 1–6), in the solid state, obtained either by evaporation of the solvent or by precipitation with diethyl ether from a 1,1,1,3,3,3‐hexafluoropropan‐2‐ol (HFIP) solution, has been studied with ir spectroscopy and x‐ray powder‐diffraction measurements. The conformation of these peptides in the HFIP solution has been studied by CD spectroscopy. Due to a strong preference of the amino acids to form an α helix, the peptides begin forming α helices at the dodecapeptide in the HFIP solution, and in the solid state by evaporation. In the solid state, with precipitation, the α‐helical conformation is first observed at the octadecapeptide and the lower peptides assume a β structure. The conformational change, from the α helix to the β structure of the peptides with 12 to 15 amino acid residues, during the precipitation process, is due to a strong tendency of the amino acids to form the β‐structure in rather short peptide lengths.
Helix formation by hydroxyamyl‐L‐glutaminyl residues in water and aqueous sodium dodecyl sulfate
Authors: Overgaard Trina , Erie Dorothy , Darsey J. A. , Mattice Wayne L.
Published: December 2004

Conformational properties of the hydroxyamyl‐L‐glutaminyl residue have been deduced from a CD study of two copolypeptides containing hydroxypropyl‐L‐glutaminyl residues. Mole fractions of hydroxyamyl‐L‐glutaminyl residues were 0.17 and 0.45. Zimm–Bragg statistical weights for the hydroxyamyl‐L‐glutaminyl residue in water are found to be similar to those determined by P.H. von Dreele, N. Lotan, V.S. Ananthan‐arayanan, R.H. andreatta, D. Poland, and H.A. Scheraga [(1971) Macromolecules 4, 408–417] for the hydroxybutyl‐L‐glutaminyl residue. Sodium dodecyl sulfate has only a marginal effect on the helix‐forming tendency of hydroxyamyl‐L‐glutaminyl residues in water.
Temperature‐dependent reversible transition of poly(dCdG) · poly(DcdG) in ethanolic and methanolic solutions
Authors: Hall K. B. , Maestre M. F.
Published: December 2004

Using CD we investigated the transitions of poly(dCdG) · poly(dGdC) from B‐to‐Z form and from Z‐to‐Z′ form. We have found experimental conditions that allow the cooperative transition to occur as a function of temperature in ethanolic solutions. The transition is reversible and can be repeated as often as desired. There is no evidence of strand separation during the cooperative transition as monitored by absorbance. For purposes of calculation, we have assumed a two‐state model for the B‐to‐Z transition, although the data indicate that such a model is too simplistic. The calculations allow the estimation of the change in enthalpy per mole of cooperative unit for the transition as a function of ethanol concentration. The values range from ±140 to ±200 kcal/mol for ethanol concentrations between 10 and 20%. Investigations of the noncooperative Z‐to‐Z′ transition show that it is a reversible two‐state transition. The different forms of poly(dCdG) · poly(dGdC) give no scattering contributions to the CD as shown by fluorescent‐detected CD or fluorscat techniques. This indicates that the CD spectra are true spectra, and contain no contributions from differential scattering of the polynucleotide. This is particularly significant in the case of the Z′ form, since it exists at high ethanol concentrations (80%) where condensation of polynucleotides can provide large contributions to the CD spectra. Analogous investigations using methanol show that the two transitions also occur, but the final Z′ form in methanol is qualitatively different from the ethanol form.