bluuebunny/crossref_metadata_2025 huggingface dataset:
CD of gels and suspensions: Apparent CD in the soret region of sickle hemoglobin gels
Authors: Hjelm Rex P. , Thiyagarajan Pappannan , Johnson Michael E.
Published: December 2004

CD spectra in the soret region of sickle‐cell deoxyhemoglobin (deoxy‐HbS) fiber gels are radically different from the CD of deoxy‐HbS in solution. An explanation is found using the Stokes–Mueller representation of the interaction of a polarized beam with the instrument optical train and sample to derive expressions for the apparent CD of gels and suspensions of optically active molecules that consist of randomly oriented domains or particles that are linearly dichroic and linearly birefringent. These theoretical considerations show that the apparent CD spectra from such systems have contributions from the LD and birefringence of each domain even if no net linear birefringence and dichroism is apparent in the sample. Thus, the interpretation of the CD from gels and suspensions is problematic, unless it can be demonstrated that each domain or particle has extremely small absorbance or that the LD and birefringence of each is a very small fraction of the total absorbance. As a result, we conclude that the spectra of HbS gels are not due to the CD of the heme per se; rather, they also reflect the randomly oriented domain structure of the gels and the LD and linear birefringence associated with each domain.
Helix breakers in block copolypeptides
Authors: Mattice Wayne L.
Published: December 2004

The ability of residues of type Y to disrupt the helix formed by residues of type X has been studied in X‐Y‐X‐block copolypeptides. The degree of polymerization of each X‐block is so large that it can be considered to be infinite. Matrix methods are used to obtain a general expression for the helix content of the central residue in the Y‐block. The resulting expression is specialized to the case where the statistical‐weight matrix is of dimensions 2 × 2, with elements, 1, 1, σs, and s. The behavior is evaluated for physically realistic values of σ and s. Two useful generalizations emerge: (1) The ability of the Y‐block to disrupt the helix is determined primarily by the value of s for residues of type Y. Helix disruption does not correlate well with the helix content of a Y‐homopolymer of infinite degree of polymerization. (2) In contrast, the ability of the X‐block to resist the influence of the Y‐block is determined primarily by the helix content of the X‐block. It does not correlate well with s for residues of type X. A random‐coil region in a Y‐block that continues into the following X‐block is more stable if residues of type X have a large value of σ because there is helix initiation in the X‐block. It is this influence of σ that prevents a correlation between s and the ability of the X‐block to resist the disruptive influence of the Y‐block.
Nucleic acid–metal interactions: V. The effect of silver(I) on the structures of A‐ and B‐DNA forms
Authors: Nordén Bengt , Matsuoka Yukio , Kurucsev Tomas
Published: December 2004

The interaction of silver(I) with DNA has been studied with uv LD in aqueous solution and in a humid anisotropic poly(vinyl alcohol) host (B‐DNA) and also in 80% ethanolic solution (A‐DNA). Addition of silver ions has a pronounced effect on the dichroic spectra of DNA, indicating that the DNA structure is significantly altered. By correlation with calculated reduced LD spectra, using intensities and moments of the corresponding electronic transitions of the DNA bases, the experimental spectra of DNA at high silver content may be interpreted in terms of tilt and roll angles of the bases in the double helix. In ethanolic A‐DNA solution there is a pronounced decrease in the orientation by flow of DNA, suggesting that the complexation of DNA to silver may be accompanied by the formation of compact tertiary structures.
Chemical synthesis of polysaccharides. 7. Enzymatic hydrolysis of (1 → 6)‐α‐DL‐glucopyranan (DL‐dextran)
Authors: Okada Masahiko , Sumitomo Hiroshi , Hirasawa Takahito
Published: December 2004

Hydrolysis of (1 → 6)‐α‐DL‐glucopyranan (synthetic DL‐dextran) by an endo‐dextranase from a Penicillium species was examined in an acetate buffer solution (pH 5.3) at 37°C. Three samples of different tacticities (isotactic dyad content, 55, 63, and 72%) were employed with a clinical dextran for comparison. Colorimetric determination of the reducing end units of the saccharides produced during hydrolysis showed that the maximum degrees of hydrolysis based on the D‐glucose units, (D.H.)D, for the DL‐dextrans were 21.4, 27.8, and 33.0% in the order of increasing isotacitic dyad content, whereas the (D.H.)D value for the clinical dextran was 51.9%. A statistical treatment of the enzymatic hydrolysis is proposed to interpret the experimental results.
Molecular orbital calculations on the oligopeptides netropsin, distamycin and related compounds
Authors: Manning Mark C. , Woody Robert W.
Published: December 2004

The electronic structure of the antibiotics netropsin, distamycin A, and related compounds has been examined by various theoretical models. Calculations of both the Pariser‐Parr‐Pople (PPP) and the semiempirical CNDO/S types can account for the absorption spectrum of netropsin and distamycin A. The CD spectrum has been calculated for the conformation of netropsin found in the crystal structure of a netropsin/DNA dodecamer. Not all the CD spectral features can be attributed entirely to the chiral conformation of netropsin, indicating that there are significant interactions between netropsin and DNA. A CD calculation was also performed for distamycin A in a similar conformation. An examination of the charge‐density maps of the excited states suggests that there is substantial charge transfer from the pyrrole ring to either of the adjacent peptide linkages in these systems. At higher energies, even longer distance charge transfer can be observed. Similar behavior was seen in the monomers pyrrole‐2‐carboxamide and 3‐(formylamino)pyrrole.
The role of the solvent on the binding of ethidium bromide to DNA in alcohol–water mixtures
Authors: Baldini Giancarlo , Varani Gabriele
Published: December 2004

The binding of ethidium bromide to calf thymus DNA is investigated over a wide range of temperatures and alcohol concentrations by means of fluorescence techniques. The presence of alcohol is found to lower the association constant, as isopropanol and n‐propanol are more effective than ethanol and methanol. It is also found that the data from different alcohols fall very close on the same straight line when plotted vs the solution dielectric constant ϵ. It is shown that the dependence of the binding constant on ϵ is beyond the prediction of current polyelectrolyte theories; rather, it appears that the binding is greatly controlled by the activity coefficient of the dye. The thermodynamic functions of the reaction have been estimated by means of Van't Hoff analysis: a large, negative enthalpy contributes to the binding, whereas the entropy, also favorable, is only slightly responsible for the overall free energy. Both enthalpy and entropy are strong functions of temperature and alcohol concentration. We show that the dependence of the thermodynamic quantities on the temperature is removed by considering “isodielectric” binding. This can be accomplished by a proper choice of the alcohol concentration, so that the thermal dependence of ϵ is compensated. It is found that the isodielectric free energy, enthalpy, and entropy are the same for different alcohols when plotted vs ϵ. When looking at the isodielectric quantities, it appears that the binding is now opposed by a positive enthalpy, whereas the observed favorable free energy results mainly from a large and positive entropy. The relevance of hydrophobic effects emerges from the behavior of the isodielectric thermodynamic quantities, as well as from the similarities observed when other interacting systems are compared.
Stereochemistry of α‐aminoisobutyric acid peptides in solution: Conformations of decapeptides with a central triplet of contiguous L‐amino acids
Authors: Balaram Hemalatha , Sukumar M. , Balaram P.
Published: December 2004

The decapeptides Boc‐Aib‐L‐Val‐Aib‐Aib‐(L‐Val)3‐Aib‐L‐Val‐Aib‐OMe and Boc‐Aib‐L‐Leu‐Aib‐Aib‐(L‐Leu)3‐Aib‐L‐Leu‐Aib‐OMe have been studied in CDCl3 and (CD3)2SO solutions by 270‐MHz1 H‐nmr. In CDCl3, the presence of eight intramolecularly hydrogen‐bonded NH groups has been established, consistent with a 310‐helical conformation, for both decapeptides. In (CD3)2SO, only seven solvent‐shielded NH groups are observed, supporting either an α‐helical conformation or a partially unfolded 310‐helix. Ir studies provided supporting evidence for intramolecularly hydrogen‐bonded structures in CHCl3, while CD studies suggest helical conformation in both decapeptides in various solvents. CD studies also support helical folding in the C‐terminal hexapeptides. The central triplet of L‐amino acids appears to destabilize 310‐helical conformations in polar solvents like (CD3)2SO.
A Raman spectroscopic study of the interaction between nucleotides and the DNA binding protein gp32 of bacteriophage T4
Authors: Otto C. , De Mul F. F. M. , Greve J.
Published: December 2004

Raman spectra of the bacteriophage T4 denaturing protein gp32, its complex with the polynucleotides poly(rA), poly(dA), poly(dT), poly(rU), and poly(rC), and with the oligonucleotides (dA)8 and (dA)2, were recorded and interpreted. According to an analysis of the gp32 spectra with the reference intensity profiles of Alix and co‐workers [M. Berjot, L. Marx, and A. J. P. Alix (1985) J. Ramanspectrosc., submitted; A. J. P. Alix, M. Berjot, and J. Marx (1985) in Spectroscopy of Biological Molecules, A. J. P. Alix, L. Bernard, and M. Manfait, Eds., pp. 149–154], 1 gp32 contains ≈ 45% helix, ≈ 40% β‐sheet, and 15% undefined structure. Aggregation of gp32 at concentrations higher than 40 mg/mL leads to a coordination of the phenolic OH groups of 4–6 tyrosines and of all the sulfhydryl (SH) groups present in the protein with the COO− groups of protein. The latter coordination persists even at concentrations as low as 1 mg/mL. In polynucleotide–protein complexes the nucleotide shields the 4–6 tyrosine residues from coordination by the COO− groups even at high protein concentration. The presence of the nucleotide causes no shielding of the SH groups. With Raman difference spectroscopy it is shown that binding of the protein to a single‐stranded nucleotide involves both tyrosine and trytophan residues. A change in the secondary structure of the protein upon binding is observed. In the complex, gp32 contains more β‐sheet structure than when uncomplexed. A comparison of the spectra of complexed poly(rA) and poly(dA) with the spectra of their solution conformations at 15°C reveals that in both polynucleotides the phosphodiester vibration changes upon complex formation in the same way as upon a transition from a regular to a more disordered conformation. Distortion of the phosphate–sugar–base conformation occurs upon complex formation, so that the spectra of poly(rA) and poly(dA) are more alike in the complex than they are in the free polynucleotides. The decrease in intensity of the Raman bands at 1304 cm−1 in poly(rA), at 1230 cm−1 in poly(rU), and at 1240 and 1378 cm−1 of poly(dT) may be indicative of increased stacking interactions in the complex. No influence of the nucleotide chain length upon the Raman spectrum of gp322 in the complex was detected. Both the nucleotide lines and the protein lines in the spectrum of a complex are identical in poly(dA) and (dA)8.
Conformation‐Determining role for the N‐acetyl group in the O‐glycosidic linkage, α‐GalNAc‐Thr
Authors: Maeji N. J. , Inoue Yoshio , Chûjô Riichirô
Published: December 2004

An 1H‐nmr study of 2‐acetamido‐2‐deoxy‐3,4,6‐tri‐O‐acetyl‐D‐galactopyranose (AcGalNAc) glycosylated Thr‐containing tripeptides in Me2SO‐d6 solution reveals two mutually exclusive intramolecular hydrogen bonds. In Z‐Thr(AcGalNAc)‐Ala‐Ala‐OMe, there is an intramolecular hydrogen bond between the Thr amide proton and the sugar N‐acetyl carbonyl oxygen. The strength of this hydrogen bond will be dependent on the amino acid residues on the Thr C terminal side to some undetermined distance. In Ac‐Thr(AcGalNAc)‐Ala‐Ala‐OMe, a different intramolecular hydrogen bond between the sugar N‐acetyl amide proton and the Thr carbonyl oxygen exists. The choice of hydrogen bonds seems dependent on the bulkiness of the residues on the Thr N terminal side. The consequence of such strong hydrogen bonds is a clearly defined orientation of the sugar moiety with respect to the peptide backbone. In the former, the plane of the sugar pyranose ring is roughly oriented perpendicularly to the peptide backbone. The latter orientation is where the plane of the sugar ring is roughly in line with the peptide backbone. In both orientations, the sugar moiety can increase the shielding of the neighboring amino acid residues from the solvent. The idea that the amino acid residues near the glycosylated Thr influence orientation of the sugar moiety with respect to the peptide backbone and in turn possibly hinder peptide backbone flexibility has interesting implications in the conformational as well as the biological role of O‐glycoproteins.
A predictive model of enzymatic cleavage of nucleic acids
Authors: Hough Christopher J.
Published: December 2004

A new static model of enzymatic cleavage of polymeric substrates such as nucleic acids has been derived. The model is compared to that elaborated by Tanford and to experimental data. In predicting the fragment distribution for a restriction enzyme digestion of a circular substrate, the model is superior to that of Tanford.
Normal‐Mode calculation for methylated Z‐DNA poly(dG‐m5dC) · (dG‐m5dC)
Authors: Hua X. M. , Prohofsky E. W.
Published: December 2004

Normal modes of methylated Z‐DNA poly(dG‐m5dC) · (dG‐m5dC) are computed by helix‐lattice dynamics. Good agreement with Raman spectral data is obtained. We discuss improvements in the formulation of the problem that allow us to greatly reduce the size of the matrix used. This leads to greatly reduced calculation times. The improvements come from using knowledge of the C2 and time‐reversal symmetries.
A 2H‐nmr study of the A‐DNA conformation in films of oriented Na‐DNA: Evidence of a disordered B‐DNA contribution
Authors: Brandes Rolf , Vold Regitze R. , Kearns David R. , Rupprecht Allan
Published: December 2004

Solid‐state 2H‐nmr spectra have been obtained from folded films of oriented Li‐ and Na‐DNA molecules with the purine bases selectively deuterium labeled at the 8 position. From line shape simulations, we find that the Na‐DNA sample at 75% relative humidity (rh) contains both A‐DNA and surprisingly large amounts of B‐DNA

Here, B‐DNA refers to “B‐DNA family” (i.e. B‐ or C‐DNA).

(57%). For the A‐DNA component the average base tilt is 23°, and the total distribution width of tilt angles and helix axis orientations is ∼ 4° (standard deviation). In the B‐DNA component the base tilt is ∼ 0° and the total distribution width is ∼ 20°. In contrast, films of Li‐DNA only exhibit the B‐form line shape, consistent with a base tilt of ∼ 0° and a total distribution width of base tilt angles and helix axis orientations of 9°. The nmr results that demonstrate the presence of large amounts of B‐DNA in the Na‐DNA sample contrast with the x‐ray diffraction measurements that indicated mainly A‐form. The nmr spectra are used to monitor the B‐DNA content in the Na‐films and to evaluate procedures for increasing the A‐DNA fraction.
α‐Helix‐to‐random‐coil transitions of two‐chain coiled coils: Experiments on the thermal denaturation of ββ tropomyosin cross‐linked selectively at C‐190
Authors: Bracken William Clay , Carey John , Holtzer Marilyn Emerson , Holtzer Alfred
Published: December 2004

A method is described for preparation of a species of β tropomyosin that is sulfhydryl‐blocked at C36 and disulfide‐cross‐linked at C190. Five steps are involved: (1) Rabbit skeletal muscle tropomyosin, comprising αα and αβ species, is oxidized with ferricyanide, disulfide‐cross‐linking both species at C190. (2) The product is treated with iodoacetamide, blocking the only remaining free sulfhydryl, i.e., C36 of the β‐chains. (3) The C36‐blocked, C190‐cross‐linked product is reduced with dithiothreitol (DTT), unfolded in urea, and α and β chains separated by ion‐exchange chromatography. (4) The C36‐blocked β chains are refolded by dialysis. (5) The refolded, C36‐blocked ββ species are cross‐linked at C190 by ferricyanide oxidation. The resulting C36‐blocked, C190‐cross‐linked ββ product is separated from contaminating species—mostly completely blocked β‐chains and multichain cross‐linked molecules—by size‐exclusion chromatography in denaturing (guanidinium chloride) solvent. The five‐step process and the final product were monitored by titration of free sulfhydryls and by NaDodSO4/polyacrylamide gel electrophoresis (PAGE). Thermal unfolding curves from CD are reported for the resulting pure, C36‐blocked, C190‐cross‐linked ββ species and for its DTT‐reduction product, the noncross‐linked C36‐blocked species. The latter shows almost the same thermal unfolding transition as intact, noncross‐linked ββ species. The former shows a pretransition similar to, but larger in extent than, the one well known to occur in the analogous case of C190‐cross‐linked αα tropomyosin. These unfolding transitions are compared with one another and with that previously reported for doubly cross‐linked (at C36 and C190) ββ species. These comparisons are made in the light of current physical models for coiled‐coil unfolding equilibria. It is concluded that although no extent model is demonstrably satisfactory, any successful model must include strain at the cross‐link, loop entropy, and regional nonuniformities as essential parts of the physics.
Microcalorimetric studies of solvent‐induced conformational change of sodium and cesium salts of poly(L‐glutamic acid) in aqueous media
Authors: Daoust Hubert , St‐Cyr Daniel
Published: December 2004

Organic solvent‐induced coil → helix conformational change of poly(sodium) L‐glutamate (NaPLG) and poly(cesium L‐glutamate) (CsPLG) in solution in aqueous mixed solvents have been studied at 25°C. Heats of dilution of NaPLG in the water–dioxane pair have been measured as a function of polymer concentration and solvent composition. The results indicate that the overall chain conformation in the disordered form is not too different from that in the α‐helical form. Heat capacity measurements by flow microcalorimetry have also been done. The apparent monomolar heat capacity at constant pressure of the polymer, Cp, ϕ, decreases with dilution similarly to other strong polyelectrolytes in aqueous media. In the water–dioxane pair, Cp, ϕ increases with the dioxane content due to partial desolvation of ionic species resulting from increasing ionic association. In the case of the water‐2‐chloroethanol (CE) pair, the transition takes place at low CE content and results show a fast decrease in Cp, ϕ when the α‐helical conformation predominates. It is believed carboxylate groups and CE molecules associate themselves into a complex formation responsible for the transition. The size of the cation plays a significant role in the thermodynamic properties of these polyelectrolytes in solution since sodium ions are more strongly bound to the chain than cesium ions.
Helix–coil dynamics of a Z‐helix hairpin
Authors: Antosiewicz J. , German M. W. , Van De Sande J. H. , Porschke D.
Published: December 2004

The helix–coil transition of a Z‐helix hairpin formed from d(C‐G)5T4(C‐G)5 has been characterized by equilibrium melting and temperature jump experiments in 5M NaClO4 and 10 mM Na2HPO4, pH 7.0. The melting curve can be represented by a simple all‐or‐none transition with a midpoint at 81.6 ± 0.4°C and an enthalpy change of 287 ± 15 kJ/mole. The temperature jump relaxation can be described by single exponentials at a reasonable accuracy. Amplitudes measured as a function of temperature provide equilibrium parameters consistent with those derived from equilibrium melting curves. The rate constants of Z‐helix formation are found in the range from 1800 s−1 at 70°C to 800 s−1 at 90°C and are associated with an activation enthalpy of −(50 ± 10) kJ/mole, whereas the rate constants of helix dissociation are found in the range from 200 s−1 at 70°C to 4500 s−1 at 90°C with an activation enthalpy +235 kJ/mole. These parameters are consistent with a requirement of 3–4 base pairs for helix nucleation. Apparently nucleation occurs in the Z‐helix conformation, because a separate slow step corresponding to a B to Z transition has not been observed. In summary, the dynamics of the Z‐helix–coil transition is very similar to that of previously investigated right‐handed double helices.
Thermodynamics of the B to Z transition in poly(dGdC)
Authors: Chaires Jonathan B. , Sturtevant Julian M.
Published: December 2004

The thermodynamics of the B to Z transition in poly(dGdC) was examined by differential scanning calorimetry, temperature‐dependent absorbance spectroscopy, and CD spectroscopy. In a buffer containing 1 mM Na cacodylate, 1 mM MgCl2, pH 6.3, the B to Z transition is centered at 76.4°C, and is characterized by ΔHcal = 2.02 kcal (mol base pair)−1 and a cooperative unit of 150 base pairs (bp). The tm of this transition is independent of both polynucleotide and Mg2+ concentrations. A second transition, with ΔHcal = 2.90 cal (mol bp)−1, follows the B to Z conversion, the tm of which is dependent upon both the polynucleotide and the Mg2+ concentrations. Turbidity changes are concomitant with the second transition, indicative of DNA aggregation. CD spectra recorded at a temperature above the second transition are similar to those reported for ψ(–)‐DNA. Both the B to Z transition and the aggregation reaction are fully and rapidly reversible in calorimetric experiments. The helix to coil transition under these solution conditions is centered at 126°C, and is characterized by ΔHcal = 12.4 kcal (mol bp)−1 and a cooperative unit of 290 bp. In 5 mM MgCl2, a single transition is seen centered at 75.5°C, characterized by ΔHcal = 2.82 kcal (mol bp)−1 and a cooperative unit of 430 bp. This transition is not readily reversible in calorimetric experiments. Changes in turbidity are coincident with the transition, and CD spectra at a temperature just above the transition are characteristic of ψ(–)‐DNA. A transition at 124.9°C is seen under these solution conditions, with ΔHcal = 10.0 kcal (mol bp)−1 and which requires a complex three‐step reaction mechanism to approximate the experimental excess heat capacity curve. Our results provide a direct measure of the thermodynamics of the B to Z transition, and indicate that Z‐DNA is an intermediate in the formation of the ψ‐(–) aggregate under these solution conditions.
Pulsed field electrophoresis
Authors: Dee Gregory T.
Published: December 2004

Pulsed field electrophoresis, or PFE, provides good separation between large molecules that under constant field electrophoresis are hard to isolate. This is due to the weak dependence of the constant field mobility on the molecular weight for these large molecules. If a spectrum of relaxation times exists that describes the recovery of the mobility to its constant field value after a reversal of the field, then we show that molecules with differing molecular weights are separated into two groups. Those with short relaxation times are unaffected by the cycling of the field and those with long relaxation times exhibit reduced mobilities. If the molecules adopt conformations that decrease their mobility initially, after a field reversal we demonstrate that a minimum develops in the mobility as a junction of the relaxation time. Using the model we demonstrate that effects of varying the switching times as a function of time. We predict that exponential rather than linear dependencies of the switching times on time increase the range of molecular weights over which enhanced separation can occur.
The influence of glycerol on hydrogen isotope exchange in lysozyme
Authors: Gregory Roger B.
Published: December 2004

Hydrogen isotope exchange rates for lysozyme in glycerol cosolvent mixtures [D. G. Knox and A. Rosenberg (1980) Biopolymers 19, 1049–1068] have been analyzed as functions of solvent viscosity and glycerol activity in an attempt to determine which solvent properties influence protein internal dynamics. The effect of glycerol on the fast‐ and slow‐exchanging protons is different. Slow‐exchanging protons [H(t) < 20] are slowed by ever‐increasing amounts as H(t) decreases. However, comparison with data for the effect of glycerol on the thermal unfolding of lysozyme [K. Gekko (1982) J. Biochem. 19, 1197–1204] indicates that the large decrease in exchange rates for the slow protons is not consistent with a local unfolding mechanism of exchange. These effects are also too large to be easily rationalized in terms of solvent viscosity. Instead, we suggest that the large effect of glycerol on exchange of the slow protons is due to a “compression” of the protein, as a result of thermodynamically unfavorable interactions of glycerol with the protein surface. This reduces the protein void volume, which in turn decreases the probability of conformational transitions required for exchange of the slowest protons. Present data do not allow a distinction to be made between thermodynamic (glycerol activity) and dynamic (solvent viscosity) influences on exchange rates for the fast‐exchanging protons, although the effect of glycerol on these protons is also probably too large to be consistent with a local unfolding mechanism. In this case, glycerol decreases the rate of catalyst diffusion within the protein matrix, either by decreasing the probabilities or amplitudes of “gating” reactions that allow passage of the catalyst from the solvent to the exchange site, or by increasing the relaxation times for these conformational rearrangements.
Cluster analysis of protein fourier transform infrared spectra
Authors: Lipkus Alan H. , Lenk Thomas J. , Chittur Krishnan K. , Gendreau R. Michael
Published: December 2004

Cluster analysis techniques were used to examine a set of Fourier transform infrared (FT‐IR) spectra of bovine serum albumin (BSA) in the adsorbed and nonadsorbed states. The region from 1480 to 1600 cm−1, comprising the amide II band, was used. Spectra were preprocessed to compensate for linear baseline variation, and the single linkage method of cluster analysis was applied. As expected, the spectra of adsorbed and nonadsorbed BSA fell into two distinct clusters. However, no further clustering was observed among the adsorbed BSA spectra on the basis of surface type, suggesting that surface specificity of the spectral changes induced in BSA by adsorption is not detectable above experimental variation. This work illustrates the value of using cluster analysis in the FT‐IR study of proteins as a complement to other data analysis methods.
Pseudopeptides and β folding: X‐ray structures compared with structures in solution
Authors: Aubry André , Marraud Michel
Published: December 2004

In order to restrain the flexibility of the peptide molecules and reduce their biodegradation, modifications of the main chain are now introduced in pseudopeptide analogues. Surprisingly, there is very little data on the conformational properties of these derivatives. We have examined pseudopeptide analogues of RCO‐X‐Y‐NHR′ model dipeptides in the depsi, N‐methylated, reduced, retro, α, β‐dehydro, β‐amino acid, and hydrazino series, in the solid state by x‐ray diffraction, and in solution by ir and 1H‐nmr spectroscopy. This study provides us with accurate dimensions of the peptide surrogates, and gives some information on the conformational tendencies induced by these substitutions, with reference to those of the related dipeptide sequences.
Structural versatility of peptides from Cα,αdialkylated glycines: Linear Ac3c homo‐oligopeptides
Authors: Benedetti E. , Di Blasio B. , Pavone V. , Pedone C. , Santini A. , Crisma M. , Valle G. , Toniolo C.
Published: December 2004

The crystal‐state molecular structures of five linear Ac3c homo‐oligopeptides to the tetramer were determined by x‐ray diffraction. The oligomers are H‐(Ac3c)2‐OMe, Fmoc‐(Ac3c)2‐OMe MeOH, Ac‐(Ac3c)2‐OMe, pBrBz‐(Ac3c)3‐OMe · H2O, and t‐Boc‐(Ac3c)4‐OMe · 2H2O. The results indicate the propensity of the tri‐ and tetrapeptides to fold into type I β‐bends and distorted 310‐helices, respectively, in partial contrast to Aib, Ac5c, and Ac6c homo‐peptides of comparable main‐chain length, where regular type III β‐bends and 310‐helical structures were found. When the influence of the constraints produced by the intramolecular H bonds of the C10‐type is absent, other less common structural features may be observed. The average geometry of the cyclopropyl group of the Ac3c residue is found to be asymmetric and the NCαC′ bond angle significantly expanded from the regular tetrahedral value.
1H‐nmr studies of synthetic polypeptide models of Plasmodium falciparum circumsporozoite protein tandemly repeated sequence
Authors: Esposito G. , Pessi A. , Verdini A. S.
Published: December 2004

The major immunodominant region of the coating protein of Plasmodium falciparum sporozoites contains multiple tandem copies of the sequence Asn‐Ala‐Asn‐Pro (NANP). Current efforts for the development of an antisporozoite vaccine are focused on the synthesis of polypeptides reproducing part of the circumsporozoite protein repeat sequence and, in an attempt to relate conformational properties and biological response, 1H‐nmr one‐ and two‐dimensional studies of the synthetic models (NANP)2NA and (NANP)6 were carried out in water and water/methanol mixtures, at 400 and 500 MHz. In water, (NANP)6 undergoes fast conformational averaging. At variance, in water/methanol, the molecule appears to adopt an extensive structure, but detailed analysis is impaired by high spectral degeneracy. Based on the results obtained with (NANP)2NA and from preliminary expermints in water/trifluoroethanol, an interpretation is suggested for the (NANP)6 data in water/methanol in terms of a mixed sequence of βI‐turns and half‐turns (or/and γI‐turns) around the positions Ni−1‐Pi‐Ni+1.
Conformation and ion binding properties of peptides related to calcium binding domain III of bovine brain calmodulin
Authors: Borin Gianfranco , Ruzza Paolo , Rossi Maura , Calderan Andrea , Marchiori Fernando , Peggion Evaristo
Published: December 2004

The conformational and ion binding properties of the sequences 93–104, 96–104, and 93–98 of domain III of bovine brain calmodulin (CaM) have been studied by CD and Tb3+‐mediated fluorescence. In aqueous solution the interaction of all fragments with Ca2+ and Mg2+ ions is very weak and without any effect on the peptide conformation, which remains always random. In trifluoroethanol the interaction is very strong and the different fragments exhibit very distinct binding properties. In particular, the dodecapeptide fragment 93–104, and its N‐terminal hexapeptide 98–104, bind calcium and magnesium with a very high binding constant (Kb > 105M−1), undergoing a substantial conformational change. The structural rearrangement is particularly evident in the hexapeptide fragment, which tend to form a β‐bend. The C‐terminal nonapeptide fragment 96–104 interacts with calcium and magnesium more weakly, and the binding process causes a decrease of ordered structure. These results suggest that, even in the entire dodecapeptide sequence corresponding to the loop of domain III of CaM, the calcium binding site is shifted toward the N‐terminal hexapeptide segment. This interpretation is consistent with the results of crystallographic studies of CaM, which show that the calcium ions are located toward the amino terminal portion of the loop.
The crystal and molecular structure of the α‐helical nonapeptide antibiotic leucinostatin A
Authors: Cerrini S. , Lamba D. , Scatturin A. , Rossi C. , Ughetto G.
Published: December 2004

The crystal and molecular structure of the nonapeptide antibiotic leucinostatin A, containing some uncommon amino acids and three Aib residues, has been determined by x‐ray diffraction analysis. The molecule crystallizes in the orthorhombic space group P212121, a = 10.924, b = 17.810, c = 40.50 Å, C62H111N11O13, HCl · H2O, Z = 4. The peptide backbone folds in a regular right‐handed α‐helix conformation, with six intramolecular i ← (i + 4) hydrogen bonds, forming C13 rings. The nonapeptide chain includes at the C end an unusual β‐Ala residue, which also adopts the helical structure of the other eight residues. In the crystal the helices are linked head to tail by electrostatic and hydrogen‐bond interactions, forming continuous helical rods. The crystal packing is formed by adjacent parallel and antiparallel helical rods. Between adjacent parallel helical columns there are only van der Waals contacts, while between adjacent antiparallel helical columns hydrogen‐bond interactions are formed.
Conformations of dehydrophenylalanine containing peptides: nmr studies of an acyclic hexapeptide with two Δz‐Phe residues
Authors: Chauhan V. S. , Uma K. , Kaur Paramjeet , Balaram P.
Published: December 2004

The conformation of an acyclic dehydrophenylalanine (Δz‐Phe) containing hexapeptide, Boc‐Phe‐Δz‐Phe‐Val‐Phe‐Δz‐Phe‐Val‐OMe, has been investigated in CDCl3 and (CD3)2SO by 270‐MHz 1H‐nmr. Studies of NH group solvent accessibility and observation of interresidue nuclear Overhauser effects (NOEs) suggest a significant solvent‐dependent conformational variability. In CDCl3, a population of folded helical conformations is supported by the inaccessibility to solvent of the NH groups of residues 3–6 and the detection of several NiH ⟷ Ni+1H NOEs. Evidence is also obtained for conformational heterogeneity from the detection of some CH ⟷ Ni+1H NOEs characteristic of extended strands. In (CD3)2SO, the peptide largely favors an extended conformation, characterized by five solvent‐exposed NH groups and successive CH ⟷ Ni+1 H NOEs for the L‐residues and CH ⟷ Ni+1H NOEs for the Δz‐Phe residues. The results suggest that Δz‐Phe residues do not provide compelling conformational constraints.
Effect of the mitogenic lectin concanavalin A on the thermotropic behavior of glycosyl‐free cationic lipids and their mixtures with zwitterionic lipids
Authors: Lüscher‐Mattli Madeleine
Published: December 2004

The effect of concanavalin A (Con A) on the thermotropic behavior of positively charged, glycosyl‐free lipids and their mixtures with zwitterionic lipids was investigated by differential scanning calorimetry.

The gel to liquid‐crystal phase transition enthalpy of pure dipalmitoylcholine (DPC) was found to be significantly increased in the presence of Con A (ΔH = 31.2 and 42.5 KJ mol−1 lipid in the presence and in absence of Con A, respectively). Addition of the lectin to DPC liposomes, furthermore, induces the appearance of a new phase transition centered at 320 K. These results are interpretable by a partial hydrophobic interdigitation of the lectin molecule into the liposomal bilayer.

The effect of Con A on the phase behavior of three 2:1 mixtures of zwitterionic and of positively charged lipids was also investigated. Phase diagrams of the systems dipalmitoylphosphatidylcholine‐dihydrosphingosine (DPPC‐DHS), sphingomyelin‐dipalmitoylcholine (SPM‐DPC), and dimyristoylphosphatidylcholine‐dipalmitoylcholine (DMPC‐DPC) are presented. In lipid mixtures of limited miscibility (DPPC‐DHS and SPM‐DPC), Con A induces pronounced phase‐separation effects. These effects are attributable to a direct hydrophobic interaction of the lectin with the liposomal bilayer and do not require the presence of specific receptor groups.

The possible relationship between lectin‐induced phase separations in the lipid matrix of biomembranes, and the observed changes in membrane permeability, membranal enzymatic activities, etc., is briefly discussed.
Adduct‐induced base‐shifts: A mechanism by which the adducts of bulky carcinogens might induce mutations
Authors: Loechler Edward L.
Published: December 2004

Most carcinogens have been shown to be mutagens, and DNA adducts are formed when mutagenic/carcinogenic substances react with DNA. It is generally believed these adduclts (or their derivatives) induce misreplication events that result in mutations. Many of the more potently mutagenic substances are bulky and three‐dimensionally complex, such as the polycyclic aromatic hydrocarbons, aromatic amines, and aflatoxins; little is known about the mechanisms by which they induce mutations. Several theories exist and herein an additional mechanism is proposed by which bulky adducts might induce mutations at GC base pairs. Molecular modeling in conjunction with molecular mechanical calculation is used to assess if the mutagen/carcinogen moiety of the adduct might be able to shift the position of the base moiety of the adduct in such a way that misreplication events might be facilitated. This mechanism is referred to as adduct‐induced base‐shift, and two classes appeared possible; adduct‐induced base‐wobble and adduct‐induced base‐rotation. The latter has been proposed previously. By addut‐induced, base‐wobble, the mutagen/carcinogen moiety of the adduct induces a shift in the position of the base moiety of the adduct with respect to the helix axis, which might facilitate mispairing events that are reminisent of non‐Watson/Crick pairing that occurs at the wobble base of tRNA during translation. For example, in some guanine adducts, the guanine appears more thymine‐like, which might facilitate G. A mispairing and thereby ultimately GC to TA transversion mutations. Adduct‐induced base‐rotation involves the rotation of the adducted base from the anti to the syn conformation and a variety of mispairing events might result.
The acceleration of linear DNA during pulsed‐field gel electrophoresis
Authors: Holzwarth G. , Platt Kevin J. , McKee Chad B. , Whitcomb Richard W. , Crater Glenn D.
Published: December 2004

The velocity and orientation of T4 and λ DNA have been measured for the first 20 s during pulsed‐field gel electrophoresis in order to clarify the DNA motions that occur. For a square pulse with field strength E = 10 V/cm, the velocity of λ DNA increases gradually to 10.5 μm/s in 1.0 s, declines to 8.6 μm/s, and then rises to a plateau value of 9.3 μm/s after 4 s. T4 DNA behaves similarly, but more slowly. Parallel measurements of fluorescence‐detected linear dichroism show that the DNA becomes substantially aligned with its chain axis parallel to the electrophoretic field E after the pulse is applied. The alignment also shows an overshoot, an undershoot, and a plateau comparable to those seen for velocity. When the field strength increases, both the velocity and the alignment reach their peaks more quickly. For all field strengths and both molecular weights, the velocity peak occurs when the molecular center of mass has moved 0.3 to 0.5 L, where L is the chain contour length. A qualitative model is provided.
Two‐dimensional 1H‐NMR study of the 1–34 fragment of human parathyroid hormone
Authors: Lee Susannie C. , Russell Anne F.
Published: December 2004

The complete assignment of resonances in the proton nmr spectrum of the 1–34 amino acid fragment of human parathyroid hormone [hPTH(1–34)], determined using a combination of one‐ and two‐dimensional nmr techniques at 500 MHz, is described. In particular, homonuclear Hartmann–Hahn experiments, recorded in H2O and D2O, are used to resolve ambiguities in the connectivities between the highly overlapped resonances in the aliphatic region of the spectrum. One‐dimensional multiple quantum filtering experiments are used to identify serine and phenylalanine spin systems. Analyses of the through‐bond and through‐space connectivities in the αH‐NH fingerprint regions of the correlated spectroscopy (COSY) and nuclear Overhauser effect spectroscopy (NOESY) spectra lead to the assignment of resonances to specific amino acid residues in the polypeptide. Examination of the observed NOE cross peaks indicates that hPTH(1–34) has no detectable secondary structural elements in aqueous solution.
Light scattering studies of bovine skin proteodermatan sulfate
Authors: Zangrando David , Gupta Rekha , Jamieson Alex M. , Blackwell John , Scott Paul G.
Published: December 2004

The proteodermatan sulfate (PDS) of bovine skin is a low molecular weight proteoglycan with a molecular structure consisting of a protein chain and a sulfated polysaccharide chain covalently linked at the 4‐serine of the protein. Static and dynamic laser light scattering methods have been used to determine the weight‐average molecular weight, Mw, z‐average radius of gyration, R′, and z‐average translational diffusion coefficient, Dt,z°, of bovine skin PDS. We have also characterized the two components of PDS, i.e., the protein core and the dermatan sulfate (DS) chain. (The latter contained an N‐terminal‐linked penta‐ or tetrapeptide.) Interpretation of the PDS data is complicated by the block copolymer nature of its structure. When appropriate corrections are made, our results indicate that Mw for PDS monomer is 62,000 when dissolved in 4M guanidine hydrochloride (GdnHCl), and increases to 610,000 in 0.15M NaCl. Mw for the core protein in 4M GdnHCl is 39,000, and this also increases substantially to 650,000 in 0.15M NaCl. In contrast, Mw for the DS chain is 24,000 in 0.15M NaCl, indicating that there is minimal self‐association of DS in 0.15M NaCl. Thus we conclude that the self‐association of PDS involves the protein core. Comparison of R and Rh, the average hydrodynamic radius, suggests that trace amounts of aggregation persist for the PDS and its core protein even in 4M GdnHCl. This conclusion is supported by evaluation of the second moments of the dynamic light scattering correlation function. Comparisons of the observed Dt,z° for PDS with predicted values using hydrodynamic theory are consistent with a “lollipop” conformation for the molecule.
The osmotic coefficients of the sodium form of some biopolymers
Authors: Jang Larry K. , Quintero Ernesto J. , Gordon Grisel , Röhricht Markus , Geesey Gill G.
Published: December 2004

The osmotic coefficients ϕp,Na of dilute solutions of the sodium form of some weakly acidic polymers are theoretically predicted in this work. Based on the measured value 0.73 of γNa, the activity coefficient of free Na+, of the completely ionized humic acid (sodium salt) in a salt‐free solution, the effective interligand distance b is calculated to be 11.34 Å by using Manning's counterion condensation theory [Manning, G. S. (1969) J. Chem. Phys. 51(3), 924]. The corresponding values of γNa (measured experimentally) and b for the completely ionized exopolymer of Pseudomonas atlantica are 0.624 and 7.57 Å when cultivated at a dilution rate D = 0.015 h−1, 0.647 and 8.19 Å at D = 0.025 h−1, and 0.613 and 7.29 Åat D = 0.06 h−1. For alginic acid (in the completely ionized sodium form), γNa = 0.40 and b = 4.71 Å. The osmotic coefficients ϕp,Na for the partially and the completely ionized polymers are then predicted with Manning's theory as well.
Time‐resolved synchrotron radiation x‐ray solution scattering study of DNA melting
Authors: Puigdomenech J. , Perez‐Grau L. , Porta J. , Vega M. C. , Sicre P. , Koch M. H. J.
Published: December 2004

Time resolved x‐ray solution scattering measurements were made during thermal denaturation of DNA from various sources in the temperature range of 20–90°C. Preliminary results on the influence of fragement length, ionic strength, and origin of the DNA on the time course of the scattering are described. Interpretation is based on model calculations of the scattering patterns. The resluts indicate that, for long DNA fragments at very low ionic strength, the melting process is a continuous phenomenon over the whole temperature range. It is accompanied by a progressive decrease of the radius of gyration of the cross section and of the mass per unit length. For short fragments of 146 base pair nucleosomal core DNA, stiffening of the DNA appears to precede a sharp melting transition.
Glycosaminoglycan conformations and changes on periodate oxidation
Authors: Ueno Norio , Chakrabarti Bireswar
Published: December 2004

The progressive periodate oxidation of glycosaminoglycans (GAG), including hyaluronate (HA), chondroitins (CH) (chondroitin, chondroitin 4‐ and 6‐sulfate), dermatan sulfate (DS), and keratan sulfate (KS), were monitored by CD and high performance liquid chromatography (HPLC) using a size‐exclusion column. The rate of oxidation also was measured and calculated using first‐ and second‐order kinetics, and the data appear to fit better with first‐order kinetics. In both HA and CH, the n – π* amide band at 208 nm decreases in intensity upon oxidation, but in HA it becomes positive after 16 h of periodate treatment. In CH, the band disappears, and the π – π* amide band below 200 nm becomes optically active. Concomitantly, a second negative band near 290 nm appears for these two oxidized GAG. Oxidation causes a slight change in the CD of DS. It ordinarily displays a very weak n – π* band at 210 nm, but instead shows an intense π – π* amide band near 190 nm. CD of KS remains unaffected by periodate. Kinetic studies, however, show a higher oxidation rate for DS than HA and CH. With the exception of KS, all other oxidized polymers shown an apparent decrease in molecular weight (higher peak retention time) in HPLC analysis. Both CD and HPLC results have been attributed to a major conformational cahange of HA and CH, and a minor one for DS. The ease and extent of periodate oxidation as well as the changes in molecular properties following periodate treatmenat are critically dependent on the changes in molecular properties following periodate treatment are critically dependent on the configuration of the individual GAG rather than the oxidation rate. There is a distinct difference in the conformational change between HA and CH, as manifested by their dichroic behavior, that was attributed to the equatorial disposition of C‐4 hydroxyl group in HA and axial disposition CH.
Secondary structure of a core protein from pig skin proteodermatan sulfate: Cd and fourier transform ir spectroscopic studies in solution
Authors: Renugopalakrishnan V. , Damle Shridhar P. , Horowitz Paul M. , Moore Sheri , Hutson Timothy B. , Gregory John D.
Published: December 2004

The secondary structure of a 38 kDa core protein from pig skin proteodermatan sulfate (PDS), was investigated in solution using CD and Fourier transform (FT) ir spectroscopy. Both techniques generally have provided complementary data on the secondary structures of proteins. CD spectral analysis has shown that the core protein contains 60% β‐turn and α‐helical structures, the rest being “unordered” structure. FT ir data do not permit calculation of quantitative contributions of substructures, at the present time, to the overall secondary structure of the core protein. CD spectrum of the intact PDS is similar to the core protein CD spectrum.
Conformational characteristics of polyglutamic acid esters: Persistence of orientational correlation along the side chain flanking the α‐helical backbone
Authors: Yamazaki Toshimasa , Abe Akihiro , Ono Hirobumi , Toriumi Hirokazu
Published: December 2004

The side chain conformations of α‐helical poly(L‐glutamic acid) esters \documentclass{article}\pagestyle{empty}\begin{document}$ \rlap{--}[NHCH(CH_2 CH_2 COOR)CO\rlap{--}]_x $\end{document}, carrying a homologous series of ester residues such as R = (CH2)nϕ with n = 1–3, have been studied in the lyotropic liquid crystalline state (chloroform 20 v/v%) by the deuterium nmr method. In order to study the surface chirality of the molecule, the phenyl groups situated at the terminal of the side chain have been deuterated. From the observed deuterium quadrupolar splittings, the average inclination θp of the para‐axis of the phenyl group with respect to the α‐helical backbone was elucidated. A distinct odd–even oscillation in the quantity such as 〈 cos2 θp〉 was observed with the number of methylene units n. A rotational isomeric state analysis has indicated that the observed orientational correlation arises from the interdependence of the neighboring bond rotation along the side chain. Preference of the “extended” conformations is also enhanced by the mutual conformational exclusion of neighboring side chains.