bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparative fluorescence studies of native and crosslinked glucose oxidase
Authors: Solomon Beca , Shinitzky Meir
Published: December 2004

The binding characteristics of flavin adenine dinucleotide (FAD) to apoenzyme preparations obtained from native and intramolecularly crosslinked glucose oxidase were determined and compared. The dissociation constants Kdiss as well as rates of recombination of FAD with the two apoenzyme preparations, were independently evaluated from fluorescence quenching of either the tryptophans of FAD. The Kdiss values thus obtained were <10−19M for native glucose oxidase and 4 ± 1 × 10−7M for the crosslinked enzyme. The recombination of apo glucose oxidase with FAD, which is presumably diffusion controlled, is followed by an apparent first order decrease in fluorescence intensity of both the protein tryptophans and FAD, with a rate constant around 0.2 min−1. This could be related to conformational changes which occur immediately after binding of FAD to the apoenzyme, an interpretation which is supported by the markedly different results obtained in the analogous experiments with the crosslinked enzyme. A model for the conformational characteristics of glucose oxidase, based on this study, is proposed.
The temperature‐induced conformational transition of immobilized chymotrypsinogen
Authors: Brynda E. , Bleha M.
Published: December 2004

A method has been suggested for obtaining kinetic thermodynamic data on conformational transitions of insoluble proteins by fluorescence measurements. The method was used for treatment of the temperature‐induced conformational transition of chymotrypsinogen bonded to the hydroxyethyl methacrylate Spheron matrix. The bonding to Spheron causes destabilization of the native conformation of chymotrypsinogen. Two types of transition of immobilized chymotrypsinogen have been found which are controlled by first‐order kinetics with different rate constants. The entropy and enthalpy changes were smaller than for free chymotrypsinogen in solution. The data obtained are interpreted as an effect of the physical interaction of the protein in the activated and denatured states with the polymeric matrix.
Influence of temperature and ionic strength on the low‐frequency dielectric dispersion of DNA solutions
Authors: Tung Ming Sung , Molinari Robert J. , Cole Robert H. , Gibbs Julian H.
Published: December 2004

The dielectric properties of DNA solutions at low frequencies (5 Hz to 2 kHz) have been measured by means of a four‐terminal bridge method utilized to minimize electrode polarization errors. At 24°C native salt‐free DNA has a very large specific dielectric increment, Δε/c = 9.8 × 106 l/mol and a very low frequency relaxation centered at 18 Hz. Both the dielectric increment and the relaxation time are greatly decreased by partial heat denaturation at temperatures above 60°C or by addition of salt, the effects being much larger for divalent anions. These results are shown to be in qualitative agreement with theoretical treatments of counterion fluctuation polarization by McTague and Gibbs for the equilibrium case and by Mandel for relaxation. The ratio of the relaxation time for the low‐frequency process to that previously observed at much higher frequencies suggests that these relaxations result from counterion fluctuations along the longitudinal and transverse axes of the molecule, respectively.
Block oligopeptides (L‐lysyl)m‐(L‐alanyl)L‐tyrosyl‐(L‐alanyl)n‐ (L‐lysyl)m. I. Synthesis through fragment condensation and characterization
Authors: Mayer R. , Caille A. , Spach G.
Published: December 2004

Model peptides containing one aromatic residue were synthesized and characterized in order to investigate their interactions with polynucleotides. Chromatographically pure block oligopeptides (L‐alysyl)m‐(L‐alanyl)n‐ L‐tyrosyl‐ (L‐alanyl)n, with n = 3 and m=3 or 6, were prepared by fragments condensation using the mixed anhydride method. The protected fragments were prepared by stepwise addition of amino acid residues through the dicyclohexylcarbodiimide method. The purity of the intermediate coupling product was analyzed by gradient elution chromotography on carboxylmethylcellulose. Both block oligopeptides were isolated by preparative chromatography on carboxymethylcellulose. The different features of these syntheses are discussed.
Measurement of the expected DNA lengthening caused by mono‐ and bisintercalating drugs using electron microscopy
Authors: Butour J. L. , Delain E. , Coulaud D. , Le Pecq J. B. , Barbet J. , Roques B. P.
Published: December 2004

PM2 DNA molecules were treated with intercalating reagents (ethidium bromide, ethidium dimer, acridine dimer) and observed by electron microscopy. The adaptation of different electron microscopy techniques has enabled the determination of DNA lengthening upon drug intercalation. A 50% length increase was generally obtained for DNA saturated with the drugs. This result is in agreement with the intercalation model proposed by Lerman. In some cases (ethidium dimer), an increase of length larger than 50% can be obtained. Experimental conditions of DNA spreading strongly interfere with the DNA–drug interaction. In some cases it was possible to estimate the apparent binding constants and also to distinguish the mono‐ from the bisintercalating derivatives in their reaction with DNA.
Nucleic acid derivatives studied by preresonance and resonance Raman spectroscopy in the ultraviolet region
Authors: Chinsky L. , Turpin P. Y. , Duquesne M. , Brahms J.
Published: December 2004

Raman spectra of AMP, UTP, GMP, and CMP, and of their bromo‐derivatives (8 Br‐ATP, 8‐bromo‐adenosine, 8‐bromo‐guanosine, 5‐bromo‐deoxyuridine, 5‐bromo‐cytidine), are reported. They are obtained using excitation wavelengths of 457.9 nm (ionized continuous argon laser) and of 300 nm (tunable pulsed dye laser). Comparison of spectra leads to the following observations: (1) preresonances Raman effects on nucleotides spectra at 300 nm; (2) resonance Raman effects on bromoderivatives spectra at 300 nm; (3) in dilute solution (10−4M), shifts and enhancements of Raman lines of the bromo‐derivatives with respect to the corresponding lines of nucleoctides. On the basis of these comparisons, the assignments of the Raman lines are discussed, This provide the necessary background for the understanding of the properties of selected groups in DNA in dilute solution. The new experimental set‐up for measurements of Raman spectra using excitation in the uv regions is described. It is specially designed to incorporate the pulsed feature of the excitation laser and for correcting of the instabilities of the sourse.
Self‐association phenomenon specific to the copper complexes with ADP, dADP, and IDP
Authors: Gabriel Marc , Larcher Dominique , Thirion Christian , Torreilles Jean , De Paulet André Crastes
Published: December 2004

Circular dichroism spectra between 200 and 800 nm are presented for solutions of nucleotides with pyrophosphate group derived from adenine and inosine in the presence of the Cu2+ cation. A study as a function of the pH, temperature, and concentration has shown the existence of a self‐association, which implies a strong interaction between the bases of the two nucleotides. The interpretation of the dichroic spectra allows us to show that two oligomer species are formed successively in low concentrations in the presence of the Cu2+ cation. The first, constituted by Cu(ADP)− molecules, appears at pH 5.3 and gives rise to a nonconservative excitonic term. The second, responsible for a conservative excitonic term, is a heterooligomer formed at pH 7.3 by the assembling of a Cu(ADP)− and a Cu(ADP)(OH)2− molecule. Furthermore, this self‐association is destabilized if the nucleotide derived from adenine is replaced by the corresponding deoxyribonucleotide or by IDP.
Conformational studies of sequential polypeptides containing lysine and tyrosine
Authors: St. Pierre S. , Ingwall R. T. , Verlander M. S. , Goodman M.
Published: December 2004

The conformation of three sequential copolypeptides, poly(L‐tyrosyl‐L‐lysine), poly(L‐tyrosyl‐L‐lysyl‐L‐lysine), and poly[L‐tyrosyl‐(L‐lysyl)2‐L‐lysine] have been studied by a variety of techniques, including CD, ir spectroscopy, analytical ultracentrifugation, and x‐ray diffraction. Depending upon the pH and sovent composition, poly(L‐tyrosyl‐Llysyl‐L‐lysine) and poly [L‐tyrosyl‐(Llysyl)2‐L‐lysine] can adopt either the α‐helical or random‐coil conformation, while poly(L‐tyrosyl‐L‐lysine) forms either inter‐ or intramolecular β‐structures.
Influence of local interactions on protein structure. II. Conformational energy studies of N‐acetyl‐N′‐methylamides of Ala‐X and X‐Ala dipeptides
Authors: Zimmerman S. Scott , Scheraga Harold A.
Published: December 2004

Conformational energy calculations using an empirical conformational energy program for peptides (ECEPP) were carried out on 17 N‐acetyl‐N′‐methylamides of Ala‐X and X‐Ala dipeptides, Where X = Ala, Asn, Asp, Gly, Phe, Ser, Tyr, Val, and Pro. Each dipeptide was found to have many low‐energly minima, some of which corresponded to bend structures. The stability of bends was found to depend on the amino acid composition and sequence, with the Ala‐X dipeptide generally favoring bends more than the X‐Ala dipeptide for a particular X. In bends and nonbends alike, intraresidue interactions dominate over interresidue interactions in determining conformational propeties. The calcutions were shown to be in good agreement with available experimental data.
A circular dichroic investigation of the secondary structure of lectins
Authors: Herrmann M. S. , Richardson C. E. , Setzler L. M. , Behnke W. D. , Thompson R. E.
Published: December 2004

The far‐uv CD spectra of eight lectins are presented. These eight lectins, as well as others previously studied, are grouped into three classes according to their particular CD spectra. The eight lectins studied appeared to have secondary structure dominated by β‐pleated sheet, which so far has been true of all lectins. An attempt was made to quantitate the three structural components (α‐helix, β‐pleated sheet, and aperiodic) in the lectins using the data for reference proteins given by Chen et al. [Biochemistry 13,3350 (1974)]. For lectins in two of the classes, this method proved excellent and values for the three components are given. However, for the third class of lectins, which includes most of the lectins as well as Concanavalin A, this method of analysis proved to be unsatisfactory. This inadequacy was due to two factors: (1) the reference proteins used by Chen and (2) the unusual CD spectra of these lectins manifested by considerable ellipticity above 225 nm in a region where there are no known peptide electronic transitions.
A solvent effect on the side‐chain conformation of phenylalanine derivatives and phenylalanine residuces in dipeptides
Authors: Kobayashi Jun'Ichi , Nagai Ukon
Published: December 2004

Three phenylalanine derivatives, Ac‐Phe‐NHMe, H‐Phe‐NHMe, and Ac‐Phe‐OH, were selected as models of Phe residues situated at the internal, the N‐terminal, and the C‐terminal positions of peptide chains, respctively. The side‐chain conformations of the three compounds were analyzed from the vicnal coupling constants 3JαβR and 3JαβS, of their 1H‐ nmr spectra measured in various organic sovlent. The two β‐protons were unambiguously assined by use of sterospecifically β‐monodeuterated phenylalanines. The pro‐S β‐proton was always situated at lower field than the pro‐R one when they were observed separately. The results of a solvent effect on the conformation of the tree compounds demonstrated that the rotamer populations are remarkable sensitive of the three compounds demonstrated that the rotamer populations are remarkably sensitive to solvent polarity and that the tendencies of the solvent effects are quite different from each other. Ac‐Phe‐OH Showed a trend similar to that of Ac‐Phe‐OEt reported by early workers. The rotamer populations of other derivatives (Ac‐Phe‐NMe2, Ac‐Phe‐NH2, Ac‐Phe‐OBut, and Ac‐Phe‐OBzl) and of Phe residues in some N‐acetyl dipeptde esters (Ac‐Phe‐Gly‐OMe, Ac‐Phe‐Val‐OMe, and Ac‐Gly‐Phe‐OMe) were also examined in several sovent, and it was found that substituents of the Phe carboxyl group—amides or esters—determine the tendency of the solvent effect. These results are interesting in the side‐chain conformations of Phe residues in peptides and proteins in an environment of low polarity can be disscussed on this experimental basis. Factors responsible for the solvent effect are discussed from (1) a structural comparison of the compunds with various carboxylic substituents, (2) an expriment with cyclohexylalanine derivatives, and (3) the measurement in mixed solvents wiht similar polarity.
Synthesis and circular dichroism characterization of L‐azetidine‐2‐carboxylic acid cyclic peptides
Authors: Boni R. , Verdini A. S. , Deber C. M. , Blout E. R.
Published: December 2004

Several cyclic hemopeptides containing L‐azetidine‐2‐carboxylix acid (Aze)—an imino acid homologous with proline but containing one less methylene group in its cyclic side chain—have been prepared. The peptides reported include (Aze)2, cyclo(Aze)3, and cyclo(Aze)6. The synthesis and spectral characterization of these cyclic peptides are described, and the results discussed in terms of the rigidity and steric constraints attributable to Aze‐containing peptides. CD spectra of these materials in several solvents are reported and compared with those of proline analogs; the similarity between the CD spectra of cyclo(Aze)3 and cyclo (Pro)3, is noted.
An analysis of the amide I mode in the vibrational spectra of unordered polypeptides and proteins
Authors: Painter P. C. , Coleman M. M.
Published: December 2004

The difference in the observed frequency of the amide I mode between the Raman and ir spectra of many unordered polypeptides is interpreted in terms of a model in which sequences of amide groups have similar ϕ, ψ angles. The splittings due to intramolecular interactions for the infinite helices generated by all ϕ, ψ angles are calculated by assuming transition dipole coupling. The effect of finite sequence length and distortions are then considered. This hypothesis accounts for the general features of the amide I mode of unordered polypeptides.
13C Nuclear magnetic resonance study of salt induced conformational change of basic polypeptides: Poly (L‐lysine), poly (L‐arginine), and poly (L‐ornithine)
Authors: Saitô Hazime , Ohki Toyokazu , Kodama Masahiko , Nagata Chikayoshi
Published: December 2004

A 13C‐nmr study of the salt‐induced helix–coil transition of the basic polypeptides poly(L‐lysine) [(Lys)n], poly(L‐arginine) [(Arg)n], and poly (L‐ornithine) [(Orn)n] was performed to serve as a reference of the helical portion of histones and other proteins. As is the case with pH‐induced helix–coil transition, the downfield displacement of the Cα and carbonyl carbon signals are observed in the helical state. The upfield shift of the Cβ signals, on the other hand, is noted in the salt‐induced transition. Regardless of the differences in the side chains and also the salts used, very similar helix‐induced chemical shifts are obtained for (Lys)n and (Arg)n. However, the displacement of the Cα, Cβ, and carbonyl carbons of (Orn)n in the presence of 4M NaClO4 is found to be almost 50% of that of (Lys)n and (Arg)n. This is explained by the fact that the maximum helical content is about 50%, consistent with the ORD result. Further, the motion of the backbone and side chains of the helical from was estimated by measuring the spin‐lattice relaxation time (T1), nuclear Overhauser enhancement (NOE), and line width. In the case of (Lys)n, the motion of the side chains is charged very little in comparison with that of the random coil. Indicating that the aggregation of the salt‐induced helix is small in contrast to that of the pH‐induced helix. For (Arg)n, however, the precipitate of the helical polymers is mainly due to aggregation.
Conformational energy analysis of retro‐all‐Dmethionine enkephalin
Authors: Momany F. A. , Aubuchon J. R.
Published: December 2004

Empirical conformational energy calculations have been carried out on the molecule retro‐all‐D‐methionine enkephalin. Low‐energy conformers were found by energy minimization and conformational search procedures. The lowest energy conformers wee found toi have some stereochemical relationship to the calculated normal met‐enkephalin conformers, but they were not retro‐all‐D‐equivalent to the Met‐enkephalin structures. The retro‐all‐D‐equivalent conformations were ∼10 kcal/mol higher energy than the low‐energy conformers found here. A structural comparison between the retro‐all‐D‐conformers and the met‐enkephalin conformers shows hat one cannot rely solely on topochemical analysis to predict biological activity for linear retro‐all‐D‐peptides.
A new method for determining sulfoxides in peptide molecules using x‐ray photoelectron spectroscopy
Authors: Jones Derek , Disteffano Giuseppe , Toniolo Claudio , Bonora Gian Maria
Published: December 2004

The problem of the quantitative determination of sulfoxide groups in peptide molecules has been re‐examined. The approaches currently available for the estimation of δ‐sulfoxide amino acids are limited in number and characterized by serious shortcomings; in addition, the choice of methods for the estimation of γ‐sulfoxide amino acids is even more restricted. A new, rapid, and nondestructive direct method for determining quantitatively all types of sulfoxides in peptide molecules by using x‐ray photoelectron spectroscopy is described.
Dielectric properties of hydrated collagen
Authors: Grigera J. Raul , Vericat Fernando , Hallenga Klaas , Berendsen Herman J. C.
Published: December 2004

Dielectric measurements have been carried out on partially hydrated collagen in the frequency ranges 100 kHz–5 MHz, 100 MHz–1 GHz, and 8–23 GHz. In the low‐frequency range, a dispersion was observed around 100 kHz which results from inhomogeneous conductivity of the samples. A dielectric relaxation was observed aroud 0.3 GHz using time‐domain‐spectroscopy techniques. This relaxation can be considered to originate from mobile side chains. Microwave measurements indicate that the water relaxation may extend into the 10‐GHz region. An apparent discrepancy between the main water relaxation time and the average rotational correlation time of water as measured by nmr line widths was resolved by the assumption that a fraction of the water molecules is bound to the collagen with residence times on the order of 10−6 sec, whereas the remainder of the water is only weakly bound and exhibits rotational rates on the order of 10−10 sec.
The effect of counter‐ion substitution on the transport properties of polyelectrolyte solutions
Authors: Magdelénat H. , Turr P. , Tivant P. , Chemla M. , Menez R. , Drifford M.
Published: December 2004

The effects of counter‐ion substitution in aqueous polyelectrolyte solutions (chondroitin sulfate) on the two main transport phenomena of the ionic species, self‐diffusion and electrical mobility, were studied experimentally by tracer methods and dynamic light scattering. The data were analyzed with respect to counter‐ion condensation and stoichiometric substitution of low‐ionic counterions by high‐ionic charge ones and compared to Manning's theory. Substitution effects on the apparent charge of the macro‐ion were derived from the transport data using an extended Nernst‐Einstein relationship and discussed in the light of the condensation effect in polyelectrolyte solutions. The effective charge of the polyion (i.e., its residual charge after condensation of counter‐ions) and the charge difference between the substituting counter‐ions appear determinant in the mechanism of substitution.
The influence of asymmetric carbon atoms of the side chains on the conformational properties of polypeptides: Comparison of diastereomeric homooligopeptides of L‐isoleucine and D‐alloisoleucine
Authors: Widmer Urs , Lorenzi Gian Paolo , Pino Piero
Published: December 2004

The conventionally protected oligopeptides of the two homologous series Boc‐(L‐Ile)n‐OMe and Boc‐(D‐aIle)n‐OMe (n = 2–6) were synthesized in a standard stepwise fashion and their uv and CD spectra in 2,2,2‐trifluoroethanol, and solid‐state ir spectra were investigated. In addition, two oligomeric products derived from the NCAs of L‐isoleucine and of D‐allo‐isoleucine and having a DP of 20 and 12, respectively, were studied in the solid state by x‐ray and ir. No substantial differences between the properties of the diastereomeric oligomers in the solid state were noticed, a β‐structure being very likely at least for the Boc‐protected hexapeptides and the higher oligomers. In contrast, differences were observed between the spectroscopic properties of the diastereomeric oligopeptides, and especially of the hexapeptides, in trifluoroethanol solution. The different properties of the hexapeptides in solution were related to the existence, in the case of Boc‐(L‐Ile)6‐OMe, of soluble molecular aggregates in which the peptide chains assume the β‐conformation. These results provide an additional example of the influence of the configuration of asymmetric carbon atoms of the side chains on the conformational properties of peptide molecules in solution.
Structure and conformation of peptides: N‐benzyloxycarboyl‐(γ‐ethyl)‐L‐glutamyl‐(γ‐ethyl)‐L‐glutamic acid ethyl ester
Authors: Benedetti Ettore , Blasio Benedetto Di , Pavone Vincenzo , Pedone Carlo , Germain Gabriel , Goodman Murray
Published: December 2004

C24H34N2O9, orthorhombic, P212121; a = 39.432 (10), b = 14.061 (5), c = 4.850 (2) Å, M = 494 a.m.u., Z = 4, Dm = 1.22 g cm−3, Dx = 1.22 g cm−3, R = 0.13 for 1205 observed reflections after refinement with isotropic thermal factors. The urethane and amide bonds are in the trans configuration, as well as all the ester groups. The φ and ψ angles of the L‐glutamyl residues fall in the β‐structure region of the Ramachandran's plot; the molecule is rather flat with the amide plane almost parallel to the c axis along which two hydrogen bonds hold the molecules together to form long rows in a “parallel pleated‐sheet” fashion.
Helix–coil transition of the dG‐dC‐dG‐dC self‐complementary duplex and complex formation with daunomycin in solution
Authors: Patel Dinshaw J.
Published: December 2004

The duplex‐to‐strand transition of the self‐complementary sequence dG‐dC‐dG‐dC has been probed at the exchangeable and nonexchangeable protons and backbone phosphates by high‐resolution nmr spectroscopy. The Watson‐Crick imino and amino hydrogen‐bonded protons, as well as the exposed amino protons, could be followed through the duplex‐to‐strand transition and provide information on base‐pair stability at the tetranucleotide duplex level. The magnitudes of the experimental upfield nonexchangeable base‐proton chemical shifts on duplex formation are consistent with calculations based on base‐pair overlap geometries of the B‐DNA type. The variation of the 31P chemical shifts in dG‐dC‐dG‐dC with temperature appear to monitor changes in the ω,ω′ rotation angles about the OP bonds in the postmelting transition temperature region. The complex formed between the antitumor anthracycline antibiotic daunomycin and the dG‐dC‐dG‐dC duplex was probed at the nucleic acid and the antibiotic resonances as a function of temperature. The experimental complexation shifts of the observable daunomycin resonances have put constraints on possible overlap geometries between the intercalating anthracycline ring and adjacent base pairs.
Theoretical studies on peptidoglycans. II. Conformations of the disaccharide–peptide subunit and the three‐dimensional structure of peptidoglycan
Authors: Virudachalam R. , Rao V. S. R.
Published: December 2004

Possible conformations of the disaccharide–peptide subunit of peptidoglycan (of Staphylococcus aureus or Micrococcus luteus) have been studied by an energy‐minimization procedure. The favored conformation of the disaccharide N‐acetyl‐glucosaminyl‐β(1–4)‐N‐acetylmuramic acid (NAG‐NAM) is different from that of cellulose or chitin; this disagrees with the assumption of earlier workers. The disaccharide–peptide subunit favors three types of conformations, among which two are compact and the third is extended. All these conformations are stabilized by intramolecular hydrogen bonds. Based on these conformations of the subunit, two different models are proposed for the three‐dimensional arrangement of peptidoglycan in the bacterial cell wall.
Circular dichroism of helices formed by purine monomers with pyrimidine polynucleotides
Authors: Mathelier Hansie Dorcal , Howard F. B. , Miles H. Todd
Published: December 2004

The CD spectra of a number of helical complexes formed by purine monomers and complementary pyrimidine polyribonucleotides have been observed over the range 200–400 nm. Each of these spectra is quite similar to that of the corresponding polymer–polymer helix. The spectra are evidently determined by the geometry of the asymmetric array of bases, largely unperturbed by the ribose–phosphate backbone. The helix structure (A‐form), on the other hand, is determined by the backbone of the pyrimidine homopolymer. Data on the monomer–polymer complexes support the conclusion that the CD spectra of ribohomopolymer helices depend primarily on interastrand interactions of the same transition within a given base and are relatively unaffected by transitions of the complementary base.
Specificity of DNA–basic polypeptide interactions. III. Sequential and random copolymers of lysine and aromatic amino acids
Authors: Seipke Gerhard , Arfmann Hans‐Adolf , Wagner Karl G.
Published: December 2004

Sequential and random lysine copolymers containing various amounts of different aromatic amino acids were synthesized. The sequential copolypeptides exhibited strong dependence of yield and degree of polymerization on the amino acid sequence of the repeating unit. To elucidate the specific contributions of aromatic side chains to the interaction of these copolymers with DNA, direct‐mixed complexes were studied by thermal denaturation and CD. The melting behaviour of peptide‐bound DNA was found to be strongly affected by amino acid composition and sequence. The contribution of the different aromatic amino acids to thermal stability decreased in the order: polylysine > [Lys, Tyr]n > [Lys,Phe]n > [Lys,(OMe)Tyr]n. The CD spectrum of DNA was altered by random copolymers, whereas sequential copolymers exhibited no changes. The influence of the random copolymers on the CD spectrum of DNA decreased in the series: polylysine > [Lys,Phe]n > [Lys,(OMe)Tyr]n > [Lys,Tyr]n. The contribution of the different aromatic amino acids to thermal stability is interpreted as stacking tendencies toward denatured and, in the case of Tyr, H‐bond formation with native DNA. The differences found for the random and the sequential polypeptides can best be explained by assuming a cooperative action of rather small peptide segments.
Conformational changes of poly(L‐histidyl‐L‐alanyl‐α‐L‐glutamic acid) in solution. Transition pathways and conformational intermediates
Authors: Goren H. Joseph , Fridkin Mati , Katchalskikatzir Ephraim , Lotan Noah
Published: December 2004

The conformation and conformational transitions of poly(His‐Ala‐Glu) have been investigated by ir, nmr, and CD measurements. The results obtained—as well as the results of our previous investigations by potentiometric titration and hydrodynamic techniques [Goren et al., Biopolymers (1977) 16, 1541–1555]—indicate that when dissolved in water, the co‐polymer assumes a disordered conformation. On changing the pH of the solution, the states of ionization of the side‐chain imidazole and carboxyl groups change in the same manner as in low‐molecular‐weight model compounds. Concomitantly, the overall shape of the macromolecule is altered, while the conformation of the polypeptide backbone changes from one disordered state to another but never assumes a regular form. In water/methanol and water/trifluoroethanol mixtures, transitions from a disordered state to the α‐helix conformation were observed on increasing the alcohol content of the system. The conformational transitions followed pathways which differ from one another according to the experimental conditions employed. Conformational landmarks (intermediates) have been identified along these pathways.
The flexible DNA double helix. I. Average dimensions and distribution functions
Authors: Olson Wilma K.
Published: December 2004

A scheme has been developed to treat the spatial arrangements and properties of double‐helical DNA in terms of the constituent atoms and bonds of the system. Heretofore the behavior of DNA in solution has been interpreted in terms of various artificial theoretical models. In this work the flexibility of the DNA double helix is taken to arise from minor perturbations of the rotation angles along the polynucleotide backbone. The rotational motions of the chain are limited to conformations within the B‐DNA family of helices that permit base stacking. The disruptions of hydrogen bonding associated with these angular fluctuations are offered as a plausible description of the well‐known breathing of double‐stranded DNA. Radii of gyration 〈s2〉0 computed on the basis of this model are found to agree with experimental measurements on B‐DNA helices spanning a wide range of molecular weights. Moreover, the three‐dimensional spatial distribution functions Wa(ρ) generated by these limited internal rotations are compatible with various macroscopic descriptions (i.e., rigid rod, wormlike coil, ideal Gaussian) previously ascribed to DNA of different chain lengths. It is further evident from the Wa(ρ) that the “rigid” B‐DNA backbone modeled here, if long enough, can bend into compact conformations. Thus it does not appear necessary to invoke the occurrence of sharp bends or links to account for the condensed forms of DNA in naturally occurring systems.
Fluorescent 2‐aza‐ε‐adenosine derivatives of polyadenylic acid, polyuridylic acid, and polyinosinic acid
Authors: Yip K. F. , Tsou K. C.
Published: December 2004

A new fluorescent analog of adenosine, 1,N6‐etheno‐2‐aza‐adenosine, has been incorporated into polynucleotides by polynucleotide phosphorylase polymerization of 1,N6‐etheno‐2‐aza‐adenosine‐5′‐diphosphate and adenosine‐5′‐diphosphate, uridine‐5′‐diphosphate, or inosine‐5′‐diphosphate. These new oligonucletides possess high fluorescence when excited at 358 nm and emit at 495 nm. The ratio of the fluorescent and nonfluorescent portions of the copolymer can be controlled by the initial composition of the 2‐aza‐ε‐adenosine‐diphosphate and the corresponding nucleoside diphosphate. Fluorescent copolymers with a ratio varying from 1.6 to 35 have thus been synthesized. The physicochemical study of copolymers containing less than 10% of the 1,N6‐etheno‐2‐aza‐adenosine moiety showed that they are similar to poly(A), poly(U), or poly(I). Therefore, fluorescence and polarization study of the 1,N6‐etheno‐2‐aza‐adenosine residues that have been incorporated into the copolymer provides a sensitive indicator for the structure of the copolymer. Potentially these new copolymers may provide unique roles in probing the structure of poly(C) and poly(A) in cellular mRNA.
Model for the conformational analysis of hydrated peptides. Effect of hydration on the conformational stability of the terminally blocked residues of the 20 naturally occurring amino acids
Authors: Hodes Zachary I. , Némethy George , Scheraga Harold A.
Published: December 2004

The effects of hydration are included in empirical conformational energy computations on oligopeptides by means of a modified hydration‐shell model. Free energy terms are introduced to account for “specific hydration” due to water–solute hydrogen bonding and for “nonspecific hydration” describing the interaction of the solute with water molecules in a first‐neighbor shell. The dielectric constant has been doubled (over the value used for calculations in the absence of water) to take into account the presence of solvent. Computations were carried out for the N‐acetyl‐N′‐methylamides of the 20 naturally occurring amino acids. Conformational energy maps are compared with similar maps calculated in the absence of hydration. Minimum‐energy conformations are located and compared with the corresponding minima for unhydrated peptides in terms of ordering with respect to potential energy, the dihedral angles at the minima, and the presence of intramolecular hydrogen bonds. The Boltzmann factors for various conformational regions are altered significantly on hydration in some cases. These changes can be explained in terms of differences in the hydration free energy terms for various conformations.
Catastrophic variation of twist and writhing of circular DNAs with constraint?
Authors: Le Bret Marc
Published: December 2004

The number of constraint turns is defined as the number of bound unwinding ligands converted in turns necessary to relax the energy stored in a supercoiled DNA. It is equal to the sum of the twist and of the writhing and is interpreted geometrically. The twist is shown to be related to the derivative of the energy of superhelix formation with respect to the constraint turns. This leads to a semiempirical evaluation of the variation of the conformational energy with the writhing and of the writhing number. The bending contribution to the conformational energy is estimated independently using first‐order elasticity. The variation of the twist and of the writhing with the constraint is, in this model, catastrophic. In particular, the writhing number jumps between intervals of allowed values.
Conformational dependence of vicinal 13C′NCαH coupling constants in peptides: A dirac vector model investigation
Authors: Mohanakrishnan P. , Easwaran K. R. K.
Published: December 2004

Theoretical calculations of the heteronuclear vicinal coupling constant 3J(13C′NCαH) in peptides have been carried out using the Dirac vector model. The results showed an angular dependence for this coupling constant, which can be expressed in the form 3J(13C′NCαH) = A cos2 θ + B cos θ + C, where A, B, and C are constants and θ is related to the torsional angle ϕ of the peptide backbone. The results of the present calculations are in very good agreement with those obtained using finite perturbation theory at the INDO level of approximation.
Titration and fluorometric studies of the tyrosine side chain of angiotensin II and related peptides
Authors: Juliano Luiz , Laluce Cecilia , Oliveira Maria C. F. , Paiva Antonio C. M.
Published: December 2004

The effect of charged side chains on the ionization and fluorescence of the Tyr4 phenolic group in angiotensin (Asp‐Arg‐Val‐Tyr‐Ile‐His‐Pro‐Phe) was investigated. Several synthetic peptides related to angiotensin were titrated spectrophotometrically and quantum yields of tyrosine fluorescence were also determined. The electrostatic interactions were interpreted according to the Kirkwood‐Tanford theory, and the results were related to a recently proposed model [J. L. De Coen and E. Ralston (1977) Biopolymers 16, 1929] for angiotensin conformation in solution. The titration and fluorescence results are in good agreement with the folded conformations of this model, with the exception that the data indicate a weaker interaction between the histidine side chain and the C‐terminal carboxyl groups than that proposed in the model.
Raman spectra of polypeptides containing L‐histidine residues and tautomerism of imidazole side chain
Authors: Ashikawa Ikuo , Itoh Koichi
Published: December 2004

Raman spectra were measured for poly(L‐histidine) in H2O, poly(L‐histidine‐d2 and ‐d3) in D2O, L‐histidine in H2O, L‐histidine‐d3 (and d4) in D2O, and 4‐methylimidazole in H2O with various pH (or pD) values. The Raman scattering peaks observed for these samples were ascribed to the neutral and positively charged imidazole groups on the basis of the spectral changes due to the pH variation and to the deuterium substitution of the imino protons. The vibrational modes of these peaks were deduced from the normal coordinate analysis made on the positively charged and neutral 4‐ethylimidazoles. The Raman scattering peaks from the imidazole groups in the neutral form clearly indicate that these imidazole groups exist in the equilibrium between the two tautomeric forms, the 1‐N protonated from (tautomer I) and the 3‐N protonated one (tautomer II). For example, the breathing vibration of the 1‐N protonated form is observed at 1282 cm−1 for L‐histidine and at 1304 cm−1 for 4‐methylimidazole, while the breathing vibration of the 3‐N protonated form is observed at 1260 cm−1 for L‐histidine and 4‐methylimidazole. From the temperature dependence of the relative intensities of the tautomer I peak to that of the tautomer II, it was concluded that the tautomer I is energetically more stable than the tautomer II, and the ΔH value is 1.0 ± 0.3 kcal/mol for L‐histidine and 0.4 ± 0.1 kcal/mol for 4‐methylimidazole. Poly(L‐histidine) with the neutral imidazole side chains shows the amide I peak at 1672 cm−1, indicating that the sample assumes the antiparallel pleated‐sheet structure. Poly(L‐Ala75L‐His25) and poly(L‐Ala50L‐His50) were found to take the α‐helical and β‐form conformations, respectively.
Affinity of glycogen synthetase to crosslinked glycogen
Authors: Zemek J. , Bauer Š. , Kuniak Ľ.
Published: December 2004

The affinity of yeast glycogen synthetase to glycogen modified by crosslinking has been studied under various experimental conditions. It was found that the higher the degree of crosslinking, the lower the affinity of glycogen synthetase to glycogen. The amount of glycogen synthetase adsorbed from the solution depends on the amount of crosslinked glycogen added and is inversely proportional to the concentration of the soluble glycogen. The stability of the complex formed between yeast glycogen synthetase and the crosslinked glycogen was found to be maximal at neutral pH range. The presence of glucose 6‐phosphate, uridine 5′‐di‐phosphate, and uridine 5′‐diphosphate glucose enhanced the stability of the complex.
Electron diffraction study of single crystals of amylose complexed with n‐butanol
Authors: Booy F. P. , Chanzy H. , Sarko A.
Published: December 2004

Electron diffraction patterns obtained from single crystals of amylose complexed with n‐butanol are reported. The crystals were examined in the frozen state, after quench‐freezing in liquid nitrogen in order to maintain the complexed state in the electron microscope. The patterns may be indexed in the base plane with an orthorhombic unit cell of dimensions a = 27.0 ± 0.2 Å and b = 26.4 ± 0.2 Å, and the symmetry of the patterns is consistent with the P212121 space group. The relationship between the orthorhombic patterns and the pseudohexagonal patterns obtained by previous workers from dried crystals is discussed.
Potentiometric Studies on Interactions of α‐L‐glutamic Acid Oligomers with Cu(II) in aqueous Solutions
Authors: Mosoni L. , Petit‐Ramel M. M. , Domard A. , Rinaudo M.
Published: December 2004

Four oligomers of α‐L‐glutamic acid with ends blocked by nonionizable protecting groups were studied in 0.1M NaClO4 solution using potentiometric measurements. The titrations were analyzed using a pit‐mapping method. The results are compared with those obtained with the corresponding polymer. The successive dissociation constants of the carboxylic side chains are obtained for oligomers with degrees of polymerization varying from 1 to 6. Then the successive stability constants corresponding to the association Cu2+–oligomer are given, and the MpHqLr distribution is calculated for each oligomer introducing MHqL complexes.
Effects of metal ions on the hydrolysis of p‐nitrophenyl caproate by modified poly(ethylenimine)s
Authors: Takagishi Toru , Klotz Irving M.
Published: December 2004

Hydrolysis of nitrophenyl caproate by modified poly(ethylenimine)s containing imidazole moieties is markedly enhanced in the presence of divalent metal ions. The order of effectiveness is Cu(II) > Co(II) > Zn(II) > Ni(II) > Mn(II), with Cu increasing the rate about 20‐fold. The acceleration by the metal ion is much greater in the presence of CH3COO− or Cl− as counterions than in the presence of ClO4−. Turnover experiments, in which moles of substrate cleaved were in substantial excess of moles of metal present, established the catalytic nature of the effects of the metals. The extent of binding of Cu(II) by the polymers was measured. Maximum accentuation in rate of hydrolysis of nitrophenyl ester was observed for the imidazole‐containing polymer when the ratio of imidazole:Cu(II) was 2.75. Some possible mechanisms for the rate enhancement by metal ions are described.
Conformational energy studies of linear dipeptides H‐X‐L‐Pro‐OH
Authors: Hetzel Robert , Wüthrich Kurt
Published: December 2004

Empirical conformational energy calculations with the use of ECEPP energy functions have been carried out for linear dipeptides H‐X‐L‐Pro‐OH, with X = Gly, L‐Ala, D‐Ala, L‐Leu, D‐Leu, L‐Phe, and D‐Phe, in different states of protonation of the end groups. The results of these calculations are compared with the previously reported experimental equilibrium populations for the cis and trans isomers of the X‐Pro bond in the different species. For all the protonation states of the seven dipeptides, the calculated nonbonded interactions and the conformational entropy term lead to a preference of the trans forms over the cis isomers by at least 1 kcal/mol. The electrostatic interactions stabilize the cis conformations in all species except the cationic forms of the D,L‐peptides, and it could further be shown that only the carbonyl group of X and the two end groups contribute significantly to the total electrostatic energy. One of the principal results of the experimental studies, i.e., the occurrence of 5–15% cis‐proline in all the peptides with an uncharged C‐terminus, was corroborated by our investigation of the cationic species. A detailed assessment of the electrostatic contribution to the total energy of the different conformations of H‐Gly‐L‐Pro‐OH indicates that the standard ECEPP parameters tend to overestimate the electrostatic interactions in aqueous solutions of the X‐Pro dipeptides.
Effect of O(2′)‐methylation on the stability of polynucleotide helices
Authors: Yathindra N. , Sundaralingam M.
Published: December 2004

The effect of ribose(O2′)‐methylation on the stability of (O2′)‐methylated polyribonucleotide helices has been studied by conformational energy calculations. The preferred orientation of the methyl group is found to further stabilize the helical phosphodiester conformation (g−,g−) due to the enhanced short‐range interactions arising between the methyl groups and the adjacent ribose moieties. The experimentally observed increase in melting temperature of (O2′)‐alkylated polyribonucleotides is thus attributable to the enhanced stability of the helical backbone conformation.
Energetic and structural aspects of ethidium cation intercalation into DNA minihelices
Authors: Ornstein Rick L. , Rein Robert
Published: December 2004

The enthalpy ΔH for the intercalation of the ethidium cation (EC) into DNA minihelices can be decomposed into (1) an energy of conformational adjustment (i.e., the energy of minihelix extension and unwinding from the B‐form to the intercalated form) and (2) EC minihelix intermolecular interactions. In the present study, we have focused our attention mainly on a decomposition of the energetic factors of the EC minihelix intermolecular interactions, while the essential features of the energy of conformational adjustment have been discussed in detail elsewhere by us. The structural features of the various resulting energy‐minimized EC‐intercalated complexes are compared with each other and the initial x‐ray model structure. ΔH is estimated to be in the range of −12.3 to −24.0 kcal/mol. This theoretical estimate is qualitatively and quantitatively in agreement with a variety of available experimental data.

The energy of conformational adjustment is an energetically unfavorable step, while the energetically favorable contribution of the EC minihelix intermolecular interactions is responsible for the overall favorable nature of the intercalation process involving the EC. On the other hand, the observed preference for intercalation into Pyr(3′–5′)Pur DNA sequences over their isomeric Pur(3′–5′)Pyr sequences is controlled by the energy of conformational adjustment and not by the EC minihelix intermolecular interaction contribution. No base‐composition effect is expected at EC concentrations normally found at cellular conditions. Moreover, the structural features of the various EC‐intercalated complexes are very similar regardless of minihelix base sequence or composition. These results compare favorably with available evidence. The nature of biologically preferred sites of EC binding with the minihelices is discussed.
Study of the rotational diffusion properties of peptides in solution
Authors: Bleich H. E. , Glasel J. A. , Latina M. , Visintainer J.
Published: December 2004

In this paper we examine the theory and method for obtaining rotational diffusion coefficients for peptides in dilute solution from 13C‐nmr spin‐lattice relaxation data. We show that even for the case of nearly equal observed relaxation times of chemically and magnetically nonequivalent alpha‐carbons marked rotational anisotropy will be the usual case. We describe two interactive, minicomputer programs which are of general use in this type of work. The implications of this study on spectral density‐based conformational determinations of peptides is discussed.
Structural characterization of ordered domains in a hydrophobic membrane protein
Authors: Macchi E. M. , Barrantes F. J.
Published: December 2004

A delipidized proteolipid protein fraction was purified from organic solvent extracts of bovine cerebral cortex and studied by means of diffraction, electron microscopic, and ir techniques. Special use was made of an electron diffraction procedure which minimized the electron damage to the biological specimens. The ir spectroscopy of the apoprotein fraction indicated the presence of polypeptides in extended β‐conformation, possibly in the antiparallel mode of packing. Electron microscopy of the fraction, negatively stained in organic media, made apparent the presence of both ordered and amorphous material. Only the former, characterized by repeating units of about 40–45 Å in diameter and varying length, produced diffraction patterns in the selected area mode exhibiting a highly undistorted lattice. The two‐dimensional cell parameters of the protein fraction were a = 4.79 Å, b = 7.20 Å, and γ = 90°. The plane group symmetry, corresponding to the systematic absences, was p 2gg, consistent with the β‐pleated sheet structure of simple polypeptides.
Physical association of two simple alkylators to some DNA sequences
Authors: Pearlstein R. A. , Tripathy S. K. , Potenzone R. , Malhotra D. , Hopfinger A. J. , Klopman G. , Max N.
Published: December 2004

Molecular mechanics calculations have been used to determine the preferred physical association sites of the known alkylating agent dimethyl aziridinium ion (Az+) and a CH prototype test probe with B‐form, tetrameric DNA sequences. Electrostatic interactions are most important in determining these preferential physical association sites. In turn, the intermolecular energy minima depend on the charge distribution assigned to the DNA sequence. However, for three reported DNA charge distributions, only two distinct sets of energy minima were obtained for the CH‐like ion interacting with (G‐C)4, (A‐T)4, and [(G‐C)·(A‐T)]2 deoxyribonucleic acids. These minima correspond to physical association geometries in which the CH‐like ion is near known alkylation sites. The results of the Az+ … [(G‐C)·(A‐T)]2 interaction are virtually identical to those found for the CH‐like ion. Aqueous solvation energetics have little effect on the physical association of Az+ with [(G‐C)·(A‐T)]2.