bluuebunny/crossref_metadata_2025 huggingface dataset:
Interaction of water‐soluble porphyrins with single‐ and double‐stranded polyribonucleotides
Authors: Bustamante Carlos , Gurrieri Sergio , Pasternack Robert F. , Purrello Roberto , Rizzarelli Enrico
Published: December 2004

CD and uv‐visible absorption studies with several tetracationic water‐soluble porphyrin derivatives show that some of these species can serve as probes to discriminate between A‐ and B‐conformational forms of single‐stranded polynucleotides. It is also observed that these porphyrins can participate in the formation of double helices by forming transient intermediate complexes enroute to duplex formation. © 1994 John Wiley & Sons, Inc.
Flow linear dichroism and fourier transform IR spectra reveal geometry for X‐form DNA
Authors: Riazance‐Lawrence Jeannine H. , Kang Hunseung , Chou Ping‐Jung , Johnson W. Curtis , Vorlíc̆ková Michaela
Published: December 2004

Flow linear dichroism measurements extended into the vacuum uv region yield inclinations for the base normal from the helix axis of 21° for dA and 40° for dT in the X‐form of poly (dAdT) · poly (dAdT). These inclination angles are similar to the B form of the synthetic polymer, but the axes around which the bases incline are different. Hydrogen‐bonded base pairs are consistent with the geometry for the standard B, C, D, and Z forms of natural DNA, but will not fit into the A form. Fourier transform ir spectra indicate that the X form has sugar pucker and phosphate geometry similar to B‐form DNA, and supports the dinucleotide repeat with two kinds of phosphates seen in earlier work, in analogy to Z‐form DNA. Clearly, X‐form DNA has a unique geometry. © 1994 John Wiley & Sons, Inc.
Nuclear overhauser effect spectroscopy (NOESY) detection of the specific interaction between substituents in cellulose and amylose triacetates
Authors: Tezuka Yasuyuki
Published: December 2004

Nuclear Overhauser effect spectroscopy measurements on cellulose triacetate and on amylose triacetate with a mixing time of 500 ms, on the order of T1, of acetyl protons, were performed to detect the specific through‐space interaction between acetyl groups arising from their helix structures in solution. For cellulose triacetate, cross peaks were detected in CDCl3 between acetyl proton signals at 3 and 6 positions on an anhydroglucose unit. In DMSO‐d6, on the other hand, correlation peaks were observed not only between the 3 and 6 positions but also the 2 and 6 positions. For amylose triacetate, cross peaks were detected in CDCl3 between the acetyl proton signals at the 2 and 6 positions. The through‐space interaction of acetyl groups in cellulose triacetate and in amylose triacetate in solution was then interpreted based on their three‐dimensional structures in solid state determined by x‐ray crystallography. © 1994 John Wiley & Sons, Inc.
Redox‐active bis‐cysteinyl peptides. II. Comparative study on the sequence‐dependent tendency for disulfide loop formation
Authors: Siedler Frank , Quarzago Daniela , Rudolph‐Böhner Sabine , Moroder Luis
Published: December 2004

Bis (cysteinyl) octapeptides related to the active sites of the oxidoreductases protein disulfide isomerase (PDI), thioredoxin reductase (trr), glutaredoxin (grx), and thioredoxin (trx) were analyzed for their propensity to form the intramolecular 14‐membered disulfide ring in oxidation experiments. The rank order of percentage of cyclic monomer formed in aqueous buffer (pH 7.0) at 10−3 M concentration was found to be very similar, but opposite to that of the Kox and, correspondingly, of the redox potentials of the native enzymes. Attempts to induce intrinsic conformational preferences of the peptides by addition of trifluoroethanol led to enhancements of β‐turn structures as reflected by the CD and Fourier transform ir spectra. The induced secondary structure, instead of aligning the tendencies of the excised fragments for loop formation with those of the intact proteins, was found to suppress the differences by significantly increasing the preference for cyclic monomers (≈ 90%). Similarly, operating under denaturing conditions, i.e., in 6M guanidinium hydrochloride, only for the trx peptide was the statistical product distribution obtained. For the remaining peptides, again a strong increase of cyclic monomer contents was observed that could not be correlated with dissolution of β‐sheet type aggregates. The CD spectra are more consistent with the presence of ordered structure to some extent, possibly resulting from an hydrophobic collapse of the sparingly soluble peptides. The results of the oxidation experiments further support previous findings from thiol disulfide interchange equilibria, which clearly revealed a decisive role of the characteristic thioredoxin structural motif in dictating the redox properties of the enzymes. Point mutations in the active sites of the oxidoreductases allowed us to affect their redox potentials strongly, but apparently only in the constraint form of the three‐dimensional structure as similar exchanges in the excised fragments did not produce the expected effect. This observation contrasts with numerous reports that the conformation of short disulfide loops is mainly dictated by the amino acid sequence. © 1994 John Wiley & Sons, Inc. © 1994 John Wiley & Sons, Inc.
Peptide libraries: Determination of relative reaction rates of protected amino acids in competitive couplings
Authors: Ostresh John M. , Winkle James H. , Hamashin Vince T. , Houghten Richard A.
Published: December 2004

In the solid phase preparation of synthetic peptide libraries, equimolarity of the resultant peptides in the mixture simplifies the identification of active compounds. Two primary methods for the preparation of combinatorial peptide mixtures are currently used. In the first method, the starting resin is divided into equal aliquots, individual amino acids are coupled to each aliquot, and the resin is then recombined. This process is repeated for each position. However, due to the physical process, each resin bead contains only one peptide sequence. Statistically, for mixtures of longer sequences, an ever‐increasing amount of resin is necessary to ensure complete representation of each peptide in the library. Thus, each peptide will be represented in the library if a sufficient number of resin beads are used. In addition, the concentration of each peptide in the library depends on both the number of mixture positions in the library and the amount of resin used. In the second method, mixtures of amino acids are coupled simultaneously at each addition step. The proportion of each amino acid in the reaction mixture is varied inversely to its reaction rate such that, ideally, an equimolar mixture of each peptide is synthesized. An advantage of this method over the previous method is that each peptide is ensured to be represented in the library, although not necessarily in equimolar amounts. It is known that not only do the coupling rates of each amino acid vary, but the coupling rates of individual amino acids also change when coupled to different amino acid resins. Consequently, in order to obtain equimolar peptide mixtures through the use of mixtures of protected amino acids, the ratio of reaction rates of one amino acid over another must be constant irrespective of the resin‐bound amino acid. If this premise is true, this method of synthesis offers a significant advantage over the previous method since, theoretically, equimolar peptide libraries could be synthesized. The influence of the resin‐bound amino acid on the relative reaction rates of incoming amino acids was investigated in the current study. © 1994 John Wiley & Sons, Inc.
The use of the AMBER force field in conformational analysis of carbohydrate molecules: Determination of the solution conformation of methyl α‐lactoside by NMR spectroscopy, assisted by molecular mechanics and dynamics calculations
Authors: Asensio Juan Luis , Jimenez‐Barbero Jesus
Published: December 2004

The solution conformation of methyl α‐lactoside has been studied through nmr spectroscopy and molecular mechanics calculations using the assisted model building with energy refinement (AMBER) force field. The nmr data have included nuclear Overhauser effect (NOE) measurements hot It in the laboratory and rotating frames, longitudinal relaxation times, and homonuclear and heteronuclear coupling constants. The steady‐state and transient NOEs have been interpreted in terms of an ensemble average distribution of conformers, making use of the complete relaxation matrix approach. The molecular mechanics calculations have been performed at two dielectric constants [ε = 1 * r and 80 Debyes (D)] in an exhaustive way, and have been complemented with specific calculations at intermediate ε values. Relaxed energy maps and adiabatic surfaces have been generated for the different dielectric constants. The probability distribution of conformers has been estimated from these steric energy maps. Molecular dynamics simulations in vacuo have also been performed. The experimental results indicate that the β(1 → 4)‐glycosidic linkage shows some fluctuations among three low energy regions, although spends ca. 85% of its lime in the region close to the global minimum. It is shown that the over estimation of the electrostatic contributions in AMBER is responsible for the failure of this force field to explain the experimental results when Used at low dielectric constant (ε < 20 D). The matching between the expected and observed facts increases for ε > 40 D. Different conditions have been tested to perform temperature constant molecular dynamics simulations in vacuo, which have indicated that, when used without explicit solvent, this force field should only be employed in a qualitatively way when analyzing dynamical properties of oligosaccharides. © 1995 John Wiley & Sons, Inc.
Synthesis, and crystal and molecular structure of the 310‐helical α,β‐dehydro pentapeptide Boc‐Leu‐Phe‐Ala‐ΔPhe‐Leu‐Ome
Authors: Rajashankar K. R. , Ramakumar S. , Mal T. K. , Jain R. M. , Chauhan V. S.
Published: December 2004

α,β‐Dehydro amino acid residues are known to constrain the peptide backbone to the β‐bend conformation. A pentapeptide containing only one α,β dehydrophenylalanine (ΔPhe) residue has been synthesized and crystallized, and its solid state conformation has been determined. The pentapeptide Boc‐Leu‐Phe‐Ala‐ΔPhe‐Leu‐OMe (C39H55N5O8, Mw = 721.9) was crystallized from aqueous methanol. Monoclinic space group was P21, a = 10.290(2)°, b = 17.149(2)°, c = 12.179(2) Å, β = 96.64(1)° with two molecules in the unit cell. The x‐ray (Mo Kα, λ = 0.7107A) intensity data were collected using a CAD4 diffractometer. The crystal structure was determined by direct methods and refined using least‐squares technique. R = 4.4% and Rw = 5.4% for 4403 reflections having |F0| ≥ 3σ(|F0|). All the peptide links are trans and the pentapeptide molecule assumes 310‐helical conformation. The mean ϕ,ψ values, averaged over the first four residues, are −64.4°, −22.4° respectively. There are three 4 → 1 intramolecular hydrogen bonds, characteristic of 310,‐helix. In the crystal, the peptide helices interact through two head‐to‐tail. NHO intermolecular hydrogen bonds. The peptide molecules related by 21, screw symmetry form a skewed assembly of helices. © 1995 John Wiley & Sons, Inc.
Viscoelastic properties of human tracheobronchial mucin in aqueous solution
Authors: McCullagh C. M. , Jamieson A. M. , Blackwell J. , Gupta R.
Published: December 2004

Human tracheobronchial mucin isolated from cystic fibrosis patients (CF HTBM) was purified using a combination of gel filtration and density gradient centrifugation. The resulting mucin was fractionated to reduce polydispersity and to facilitate studies of the molecular weight dependence of mucin viscoelasticity in concentrated solution. The viscoelastic properties of CF HTBM were examined in distilled water, 0.1M salt solutions and chaotropic solvents. In controlled strain experiments (strain ≥ 5%) with increasing mucin concentration, a crossover from sol to gel behavior is observed. The gel strength, as measured by the magnitude of the storage modulus at comparable mucin concentrations, is greatest for distilled water, intermediate for 0.1M NaCl, and lowest far 6M GdnHCl. In distilled water, high molecular weight mucin undergoes a sol‐gel transition at ∼ 12 mg/mL, and shows evidence of a plateau modulus at higher concentrations. The storage and loss moduli of concentrated high molecular weight fractions in 6M GdnHCl exhibit a power law dependence on frequency typical of weak gels near the sol–gel transition at 20 mg/mL. Similar rheology is observed in 0.1M NaCl and 0.091M NaCl/3 mM CaCl2, but with evidence for additional weak associations at low frequency. The power law exponent in these systems is 0.70 ± 0.02, in good agreement with prediction for networks formed by a percolation mechanism. Low molecular weight fractions in these solvents exhibit a fluid‐like viscoelastic response. However, low molecular weight mucin in distilled water shows a strain‐dependent increase in elasticity at low frequency indicative of weak intermolecular associations. Comparison of the rheological behavior of CF HTBM with our earlier studies of ovine submaxillary mucin lends support to the idea that carbohydrate side‐chain interactions are important in the gelation mechanism of mucins. © 1995 John Wiley & Sons, Inc.
Kinetic and thermodynamic characterization of DNA duplex–hairpin interconversion for two DNA decamers: d(CAACGGGTTG) and d(CAACCCGTTG)
Authors: Avizonis Daina Z. , Kearns David R.
Published: December 2004

The duplex–hairpin interconversion of two DNA decamers, d(CAACGGGTTG) and d(CAACCCGTTG), has been characterized thermodynamically and kinetically by using uv‐melting and nmr relaxation methods. Separately, each decamer shows slow exchange between hairpin and duplex conformations. The hairpin conformations have melting points of 47 and 50°C, respectively, and exhibit similar thermodynamic stabilities. The enthalpies of duplex formation, measured by nmr, were found to be very similar (ΔHDH = 26 ± 3 kcal/mole) for both decanters at low salt concentrations (< 50 mM NaCl). However, as the salt concentration was increased the behavior of ΔHDH, and kinetics is significantly different for each decamer. The d(CAACGGGTTG) decamer forms a duplex containing two central G·G mismatches at high salt and DNA concentration. Based upon the measurement of high interconversion activation energies and a decrease in hairpin formation rate with increasing salt, the interconversion between hairpin and duplex was concluded to proceed by complete strand dissociation. In contrast, the d(CAAC‐CCGTTG) decamer was determined to form a duplex with two centrally located C·C mismatches at pH values less than 6.2, consistent with the formation of a hemiprotonated C+·C mismatch. At pH values greater than 6.4, the hairpin–duplex equilibrium is almost completely shifted toward the hairpin conformation at DNA concentrations of 0.5–7.0 mM and salt concentrations of 10–100 mM. The interconversion of duplex and hairpin conformations was ascertained by means of both kinetic and thermodynamic measurements to proceed by a slightly different mechanism than its complementary decamer. Although the interconversion proceeds by complete strand separation as suggested by high duplex‐hairpin interconversion activation enthalpies, the increasing hairpin formation rate with increasing ionic strength as well as the ΔHDH, dependence on sail indicate that an intermediate internally bulged duplex (no C+·C formation) is stabilized by increasing ionic strength. These data support an interconversion mechanism where an intermediate internally bulged duplex may be the rate limiting step before strand separation. © 1995 John Wiley & Sons, Inc.
Pressure dependence of the helix–coil transition temperature of poly[d(G‐C)]
Authors: Wu John Q. , Macgregor Robert B.
Published: December 2004

The Pressure Dependence of the Helix‐Coil Transition Temperature (Tm) of Poly[d(G‐C)] was studied as a function of sodium ion concentration in phosphate buffer. The molar volume change of the transition (ΔV) was calculated using the Clapeyron equation and calorimetrically determined enthalpies. The ΔV of the transition increased from +4.80 (±0.56) to +6.03 (±0.76) mL mol−1 as the sodium ion concentration changed from 0.052 to 1.0M. The van't Hoff enthalpy of the transition calculated from the half‐width of the differentiated transition displayed negligible pressure dependence: however, the value of this parameter decreased with increasing sodium ion concentration, indicating a decrease in the size of the cooperative unit. The volume change of the transition exhibits the largest magnitude of any double‐stranded DNA polymer measured using this technique. For poly[d(G‐C)] the magnitude of the change in ΔV with sodium ion concentration (0.94 ± 0.05 mL mol−1) is approximately one‐half that observed for either poly[d(A‐T)] or poly (dA)·poly(dT). The ΔV values are interpreted as arising from changes in the hydration of the polymer due to the release of counterions and changes in the stacking of the bases of the coil form. As a consequence of solvent electrostriction, the release of counterions makes a net negative contribution to the total ΔV, implying that disruption of the slacking interactions contributes a positive volume change to the total ΔV. The larger magnitude of the ΔV compared with that of other double‐stranded polymers may be due in part to the high helix‐coil transition temperature of poly[d(G‐C)], which will attenuate the contribution of electrostriction to the total volume change. The data in addition show that in the absence of other cellular components, the covalent structure of DNA is stabile under conditions of temperature and pressure more extreme than those experienced by any known organism. © 1995 John Wiley & Sons, Inc.
A dynamic laser light‐scattering study of chitosan in aqueous solution
Authors: Wu Chi , Zhou Shuiqin , Wang Wei
Published: December 2004

The solution behavior of four chitosans (91% deacetylated chitin) with different molecular weights in 0.2M CH3COOH/0.1M CH3COONa aqueous solution was investigated at 25°C by dynamic laser light scattering (LLS). The Laplace inversion of the precisely measured intensity‐intensity lime correlation function leads us to an estimate of the line‐width distribution G(Γ), which could be further reduced too translational diffusion coefficient distributions G(D). By using a combination of static and dynamic LLS results, i.e., Mw and G (D), we were able to establish a calibration of D = kDM with kD = (3.14 ± 0.20) × 10−4 and αD = 0.655 ± 0.015. By using this calibration, we successfully converted G(D) into a molecular weight distribution fw(M). The larger αD value confirms that the chitosan chain is slightly extended in aqueous solution even in the presence of salts. This is mainly due to its backbone and polyelectrolytes nature. As a very sensitive technique, our dynamic LLS results also revealed that even in dilute solution chitosan still forms a small amount of larger sized aggregates that have been overlooked in previous studies. The calibration obtained in this study will provide another way to characterize the molecular weight distribution of chitosan in aqueous solution at room temperature. © 1995 John Wiley & Sons, Inc.
Fluctuations in molecular size, entanglement complexity, and anisometry along molecular dynamics trajectories of short α‐helices
Authors: Arteca Gustavo A.
Published: December 2004

We present a detailed study of the intrinsic shape stability of short flexible polypeptide chains by using a number of distinct descriptors. Some large‐scale structural features found in macromolecular folding—unfolding dynamics can be monitored in terms of molecular size and compactness. Similarly, one could employ descriptors of anisometry to that purpose. In addition, we have recently proposed a new family of global, absolute shape descriptors to quantify the complexity of the self‐entanglements in a polymer, or, loosely, its “degree of folding.” This latter aspect of the molecular shape is characterized by combining simple geometrical and topological properties of the α‐carbon backbone. The resulting descriptor, the probability of observing a rigid backbone as a projected curve exhibiting N overcrossings, has been employed already for the analysis of molecular dynamics of linear hydrocarbons and aliphatic carboxylic acids. In this work, three distinct properties of a molecular chain are monitored simultaneously, for the first lime, along computer‐simulated dynamic trajectories: size, anisotropy, and entanglements. The systems studied are a series of 3 polypeptide helices: 10‐polyalanine, 10‐polyvaline, and 10‐polyglycine. Constant temperature trajectories have been computed for these helices, at thermal equilibrium with a simulated external bath, with temperatures ranging from 300 to 700 K. The differential structural stability of the helices is assessed from the various viewpoints. Even though the systems are simple, they contain some of the essential features expected in polypeptides of relevance to structural biology. The results show that the, descriptors of anisometry and entanglements are rather independent. For instance, it is found that, contrary to intuition the unfolding of helices may involve nonhelical “coil” configurations that are both self‐entangled and prolate. The simultaneous study of independent shape descriptors provides a new picture of the nature of conformations found during dynamics trajectories. The resulting description characterizes a polymer conformation in a absolute terms, and not relative to an ad hoc reference structure. The proposed approach gives some insights into the stability of secondary structural motifs in proteins and the mechanisms involved into their formation or unfolding. © 1995 John Wiley & Sons, Inc.
The interaction of methylene blue, azure B, and thionine with DNA: Formation of complexes with polynucleotides and mononucleotides as model systems
Authors: Tuite Eimer , Kelly John M.
Published: December 2004

The interactions of methylene blue, azure B, and thionine with calf thymus DNA, [poly (dG‐dC)]2, [poly(dA‐dT)]2, and the constituent mononucleotides 2′‐deoxyguanosine‐5′‐monophosphate(dGMP), 2′‐deoxyadenosine‐5′‐monophosphate(dAMP), 2′‐deoxycytidine‐5′‐monophosphate(dCMP), and thymidine‐5′‐monophosphate(dTMP) have been studied by steady‐state absorption spectroscopy and with equilibrium dialysis. Scatchard plots for binding of the dyes to the nucleic acid polymers were convex downward at low binding ratios, characteristic of intercalation, and binding constants for this mode were calculated under conditions of varying ionic strength. For each of the dyes, binding constants with [poly(dG‐dC)]2 and [poly(dA‐dT)]2 were of the same order of magnitude, so that previously reported (G‐C) preferentially is not very marked. At high binding ratios, the Scatchard plots did not return to the abscissa but curved upward, indicative of a weaker cooperative binding mode, occurring under conditions where the dye is in excess, which is suggested to be external stacking of the dye molecules promoted by the polyanion. The dependence of the absorption spectra on added salt demonstrated a shift in the strong binding mode for the three dyes with [poly(dA‐dT)]2 with increasing ionic strength, while with [poly(dG‐dC)]2 this does not occur. The dyes were found to bind to purine but not pyrimidine mononucleotides with dGMP and dAMP, 1:1 complexes were formed initially and also 1:2 dye/nucleotide complexes with increasing nucleotide concentrations. Under low salt conditions, binding to dAMP was slightly stronger than to dGMP for the three dyes studied, while at high ionic strength, when the binding constants are significantly lower, all binding constants become very similar. Binding to mononucleotides is suggested to be primarily stabilised by π‐π stacking interactions between the planar dyes and the nucleobases: for thionine and azure B there also appears to be H‐bonds between the exocyclic amines and the sugar–phosphates conferring extra stability. Neither increasing the number of phosphate groups on the nucleotides nor changing from deoxyribose to ribose sugars had any significant effect on the binding constants. © 1995 John Wiley & Sons, Inc.
Anisotropic behavior of the pH dependence part of Young's modulus in a lysozyme triclinic crystal
Authors: Alexov E. , Atanasov B. , Ueki T.
Published: December 2004

A numerical simulation of the Young's modulus pH dependence in a triclinic crystal of hen egg white lysozyme is performed. On the basis of calculation of electrostatic interactions between the molecules in the crystal at different pH values, we obtain the Young's modulus quantity as a function of pH. The analysis is carried out along the main crystal axes as well as along the [011] direction. In the last case, a good agreement between our calculations of Young's modulus pH dependence and the experimental data [V. N. Morosov and T. Ya. Morozova (1981) Biopolymers, Vol. 20, pp. 451–467] is obtained.

The calculations show a strong anisotropy of both the absolute value of the electrostatic part of Young's modulus and its pH dependence along different directions. A detailed analysis of the electrostatic potential inside the crystal, as well as the charged group distribution in the contact areas, permit us to find the reason for the anisotropy. It is caused by a nonuniform distribution of the charged residues in the lysozyme molecule and especially by the titration behavior of certain acidic groups. It is also shown that Young's modulus depends on the ionic strength, being anisotropic. The reason is that the cavities are not uniformly distributed within the crystal. They are located predominantly along the c axis. © 1995 John Wiley & Sons, Inc.
Design of B‐DNA cross‐linking and sequence‐reading molecules
Authors: Walker Wynn L. , Kopka Mary L. , Filipowsky Mark E. , Dickerson Richard E. , Goodsell David S.
Published: December 2004

We report the design of hybrid molecules to bind in the minor groove of B‐DNA, which combine DNA alkylating and cross‐linking ability for increased chemotherapeutic efficacy, with sequence specificity, to minimize side effects. Optimal linkage geometries have been determined for the synthesis of bis‐anthramycin and anthramycin‐netropsin hybrid molecules. Earlier studies on linked drugs have typically been based on molecular mechanics calculations. This work, in contrast, uses the observed crystal structures of a netropsin/DNA complex and a new anthramycin/DNA complex to determine the exact spacing between two individual drugs when bound in the minor groove of B‐DNA. Molecular linkers then are designed and tested between these two experimental positions, to form a chimeric or bis‐linked compound molecule. A linked anthramycin‐netropsin molecule has been designed specifically to target the polypurine tract second‐strand primer site of the reverse transcriptase of HIV‐1. © 1995 John Wiley & Sons, Inc.
Predictions of protein backbone bond distances and angles from first principles
Authors: Scháfer Lothar , Cao Ming , Meadows Mary Jane
Published: December 2004

A procedure is described, based on a spline‐function representation of ab initio peptide conformational geometry maps, that allows one to predict backbone bond distances and angles of proteins as functions of the peptide ϕ(N‐Cα)/Ψ(Cα‐C′) torsions with an accuracy comparable to that of high‐resolution protein crystallography. For example, for the more than 40 residues of crambin, the rms deviation between predicted and crystallographic values of N‐Cα‐C′ is 1.9° for the 1.5 Å resolution structure and 1.9° for the 0.83 Å resolution structure, compared with angle variations of < 10°. Accurate information on protein backbone geometries is important for establishing dictionaries of flexible geometry functions for use in empirical peptide and protein modeling. © 1995 John Wiley & Sons, Inc.
Atypical gly‐X‐Y sequences surround interruptions in the repeating tripeptide pattern of basement membrane collagen
Authors: Long Cynthia Gwynne , Thomas Michael , Brodsky Barbara
Published: December 2004

The triple‐helical domains of type IV collagen chains have more than 20 sites at which the repeating (Gly‐X‐Y)n pattern is interrupted. Analysis of α1 (IV) and α2 (IV) chains indicates the residues in the three Gly‐X‐Y triplets preceding or following interruptions differ statistically from the rest of the chain. Unusually high frequencies of charged residues are seen at a number of X and Y sites, with the charge density being particularly high C‐terminal to the interruption site. Analyses were carried out on individual categories of interruptions, classified as insertions or deletions in the Y position. All of the residues in the X and Y positions of the triplets flanking insertion sites are atypical, with a high concentration of charged residues. Triplets flanking sites where there has been a deletion in the Y position show unusually high frequencies of charged residues at some sites, hydrophobic residues at other sites, and an invariant imino acid N‐terminal to the interruption. The presence of atypical sequences surrounding interruptions could be important at a molecular level, related to triple‐helix stability, or at a supramolecular level, related to the association of molecules to form networks in basement membranes. © 1995 John Wiley & Sons, Inc.
Synthesis and interfacial behavior of poly(Lys‐Tyr‐Tyr‐Lys)
Authors: Maget‐Dana Régine , Bolbach Gérard , Trudelle Yves
Published: December 2004

Poly(Lys‐Tyr‐Tyr‐Lys) was synthesized by polycondensation of the tetrapeptide unit using paranitrophenyl esters. The conformation of poly (Lys‐Tyr‐Tyr‐Lys) is very dependent on its environment. CD spectra in bulk are difficult to interpret owing to the contribution of Tyr residues, but from ir spectra it seems that poly(Lys‐Tyr‐Tyr‐Lys) adopts preferentially an unordered conformation in water. Addition of salts induces a partial transition to a β structure. The behavior is different at interfaces. When poly(Lys‐Tyr‐Tyr‐Lys) is spread as a film on a water subphase, the shape of the compression isotherm curves is compatible with a stacking of two β‐sheets. On a KCl subphase, the polymer film is more expanded and more compressible, and the isotherm curve resembles that of a polymer in a random conformation. The analysis by CD and ir spectroscopy of transferred monolayers using the Langmuir–Blodgett technique allowed us to confirm and make these data more precise: on a water subphase the spectra are those of an antiparallel β structure. At the interface of a saline solution the spectra are compatible with a mixture of random coil (largely) and a small content of β structures. © 1995 John Wiley & Sons, Inc.
Energetics of protein–DNA interactions: An exact calculation for binding of ligands to a lattice of overlapping sites
Authors: Saroff Harry A.
Published: December 2004

Exact equal ions are developed for analyzing the binding of ligands to a linear lattice of overlapping sites in which occupied–unoccupied as well as occupied–occupied interactions are included for the analysis of the binding isotherms. We demonstrate that positive cooperativity on the binding of ligands to multiple sites may derive from either occupied–unoccupied or occupied–occupied interactions. When the binding of proteins to linear polynucleotides and DNA has exhibited positive cooperativity protein–protein (occupied–occupied), interactions have heretofore been invoked as the sole energetic source in determining the cooperative effect. Models and equations developed previously for the analysis of these binding isotherms have included only the protein–protein interactions (usually characterized with the symbol ω). The exact equations of this paper are capable of analyzing binding data in a manner to evaluate the relative importance of both occupied–unoccupied and occupied–occupied interactions

Relations derived here are employed to analyze some existing data, and the resulting parameter values are compared to those developed with equations employing only the protein–protein (occupied–occupied) interactions. The resulting parameter values are qualitatively different. Values of the binding constants differ by about three orders of magnitude. When only protein–protein interactions are taken into account, the resulting free energy of interaction is negative, indicating attractive forces between bound protein molecules; when both occupied–unoccupied and occupied–occupied interactions are applied, the resulting free energies of interaction are positive, indicating destabilizing forces acting primarily on the polynucleotide lattice. © 1995 John Wiley & Sons, Inc.
Conformational states governing the rates of spontaneous transition mutations
Authors: Mitra Rahul , Pettitt B. Montgomery , Blake R. D.
Published: December 2004

We report the results of a theoretical study, combining the results of sequence analysis and integral equation structural methods for nucleic acids in aqueous solutions, on the effects of nearest neighbors on the (T.G) mispair in solution, for 12 nearest neighbor contexts. Attempts have been made to classify the structural and energetic effects of the 5′ and 3′ neighbors with respect to the observed spontaneous mutation rates in vertebrates. It is found that 5′ nearest neighbor is probably the most critical structural factor in facilitating or discouraging mutations. Local conformational states correlate with discrimination of bases to be excised in mispairs. Our study confirms the role of the flexibility of the DNA molecule in governing the rates of spontaneous mutations. © 1995 John Wiley & Sons, Inc.
Symmetry and structure of RNA and DNA triple helices
Authors: Raghunathan G. , Miles H. Todd , Sasisekharan V.
Published: December 2004

Despite wide interest in nucleic acid triple helices, there has beenno stereochemically satisfactory structure of an RNA triple helixin atomic detail. An RNA triplex structure has previously been proposed based on fiber diffraction and molecular modeling [S. Arnott and P. J. Bond (1973) Nature New Biology, Vol. 244. pp. 99–101; S. Arnott. P. J. Bond. E. Seising, and P. J. C. Smith (1976) Nucleic Acids Research, Vol. 3. pp.2459–2470], but it has nonallowed close contacts at every triplet and is therefore not stereochemically acceptable. We propose here a new modelfor an RNA triple helix in which the three chains have identical backbone conformations and are symmetry related. There are no short contacts. The modeling employs a novel geometrical approach using the linked atom least squares [P. J. C. Smith and S. Arnott (1978) Acta Crystallographica, Vol. A34, pp. 3–11] program and is not based on energy minimization. In general, the method leads to a range of possible structures rather than a unique structure. In the present case, however, the constraints resulting from theintroduction of a third strand limit the possible structures to a very small range of conformation space. This method was used previously to obtain a model for DNA triple helices [G. Raghunathan, H. T. Miles, and V. Sasisekharan (1993) Biochemistry, Vol. 32, pp. 455–462], subsequently confirmed by fiber‐type x‐ray diffraction of oligomeric crystals [K. Liu. H. T. Miles. K. D. Parris, and V. Sasisekharan (1994) Nature Structural Biology, Vol. 1. pp. 11–12]. The above triple helices have Watson–Crick–Hoogsteen [K. Hoogsteen (1963) Acta Crystallographica, Vol. 16. pp. 907–916] pairing of the three bases.

The same modeling method was used to investigate the feasibility of three‐dimensional structures based on the three possible alternative hydrogen‐bonding schemes: Watson–Crick–reverse Hoogsteen, Donogue [J. Donohue (1953) Proceeding of the national Academy of Science USA, Vol. 39, pp. 470–475] (reverse Watson–Crick)–Hoogsteen, and Donohue–reverse Hoogsteen. We found that none of these can occur in either RNA or DNA helices because they give rise only to structures with prohibitively short contacts between backbone and base atoms in the same chain. © 1995 John Wiley & Sons, Inc.
Structural properties and thermal stability of human liver and heart fatty acid binding proteins: A fourier transform IR spectroscopy study
Authors: Tanfani Fabio , Kochan Zdzislaw , Swierezynski Julian , Zydwo Mariusz M , Bertoli Enrico
Published: December 2004

The secondary structure and the thermal stability of human liver (L‐FARP) and heart (77‐FAUP) fatty acid‐binding proteins were analyzed, in the absence and in the presence of oleic acid, by Fourier transform ir spectroscopv. The study was done in order to gain information on the secondary us well three‐dimensional structure of L.‐FARP and to check the possible H‐FABP self‐association that has been found to occur in rat and pig H‐FABP. Comparison of human L‐FABP and H‐FABP ir spectra reveals that, in spite of the low sequencehomology, the two proteins have similar secondary and probably tertiary structures. The air data indicates that a larger amount of β‐strands are exposed to the solvent in H‐FABP as compared to L‐FABP, suggesting mi nordifferences in the three‐dimensional structures of these proteins. The binding of oleic acid to L‐FABP and H‐FABP stabilizes their structures and does not modify their secondary structure. Their spectra neither confirm nor exclude self‐association of human H‐FABP. © 1995 John Wiley & Sons, Inc.
Effect of locust bean gum and konjac glucomannan oh the conformation and rheology of agarose and κ‐carrageenan
Authors: Goycoolea F. M. , Richardson R. K. , Morris E. R. , Gidley M. J.
Published: December 2004

Mixing with locust bean gum (LBG) induces obvious gel‐like character in very dilute solutions of K+κ‐carrageenan (< 0.01% w/w in 100 mM KCl). At higher concentration (0.085%), addition of LBG (0.036%) gives a shoulder on the high‐temperature side of the DSC (differential scanning calorimetry) exotherm associated with the carrageenan disorder‐order transition, with an accompanying increase in gelation temperature and enhancement in gel strength (storage modulus, G′). On substitution of LBG by konjac glucomannan (KM) the shoulder in DSC cornverts to a discernable peak. Van't Hoff analysis of optical rotation data indicates that the high‐temperature thermal processes could arise from association of LBG or KM chains to the carrageenan double helix as it forms, with the main transition at lower temperature corresponding to ordering of surplus carrageenan. WithK‐carrageenan in the nongelling tetra‐methylaminonium salt form, addition of LBG causes no delectable change in DSC; rheological enhancement at high concentration (1% w/w) is limited to development of a very tenuous network, and in dilute solution a decrease in viscosity is observed. Agarose shows only a very slight increase in the disorder‐order transition temperature on addition of KM, and it shows no detectable change with LBG. These observations are interpreted as showing that efficient binding of mannan or glucomannan chains requires some aggregation of the algal polysaccharide helices, but that extensive aggregation restricts synergistic interaction by competition with heterotypic association. © 1995 John Wiley & Sons, Inc.
Incorporation of diacids into the polyglycine II structure: Model studies
Authors: Navarro Eloísa , Tereshko Valya , Subirana Juan A , Puiggalí Jordi
Published: December 2004

Aliphatic diacids Eare often incorporated into polypeptide structures in order to obtain model compounds for hormones, protein turns, etc. They are also fundamental components of many commercial polyamides. On the other hand glycine, the simplest amino acid, shows unique conformational features. In order to better understand the structure of such compounds, we have synthetized and determined the molecular structure of three models represented by the general formula CH3‐CH2CH2‐NH‐CO‐CH2NH‐CO‐(CH2)n‐2‐CO‐NH‐CH2CO‐NH‐CH2CH2CH3, with n = 3, 4, or 6. Conformational differences have been found in the dicarboxylic moiety, whereas glycine always has the polyglycine II conformation. The ‐CO‐(CH2)n‐2‐CO‐ segment adopts a folded conjformation: SS, TGT, and SḠTGS̄ for n = 3, 4, and 6, respectively. Molecular packing is always pseiidohexagonal and a network of hydrogen bonds oriented in three directions at 120° is formed. The results are of interest in order to provide information about polyamides in which gljrine residues are incorporated. Our results confirm the tendency of glycine residues to adopt the polyglycine II conformation in its copolymers with aliphatic compounds. © 1995 John Wiley & Sons, Inc.
Influence of sample pH on the conformational backbone dynamics of a pseudotripeptide (H‐Tyr‐TicΨ[CH2‐NH] Phe‐OH) incorporating a reduced peptide bond: An NMR investigation
Authors: Carpenter K. A. , Wilkes B. C. , Schiller P. W.
Published: December 2004

In the present paper we investigate the influence of sample pH on the conformational and dynamical properties of the pseudotripeptide H‐Tyr‐TicΨ[CH2NH]Phe‐OH(TIP[Ψ]:Tic: l, 2, 3, 4,‐tetrahydroisoquinoline‐3‐carboxylic acid) using various one‐ and two‐dimensional nmt techniques in conjunction with molecular modeling. Studies were conducted at three different pH levels‐corresponding to the zwitterionic peptide containing a formal positive charge(pH 3. 1).the deprotonated molecule(pH 9. 1), and a situation at neutral pH(pH 7. 2) involving both protonated and deprotonated states of the reduced peptide bond. Analysis of the one‐dimensional1H‐nmr spectra reveals that in solution TIP[Ψ]is in slow dynamic exchange between conformations containing cis and trans configurations of the Tyr‐Tic bond. An nmr pH dependence study of the cis:trans ratio indicated that the exchange process was governed by the protonation state of the reduced bond amine. From the nmr data, reduced peptide bond pKavalues of 6. 5 and 7. 5 were determined for the cis and trans conformers, respectively. It was concluded that conformations containing a trans Tyr‐Tic bond are stabilized at law pH by an intramolecular hydrogen bond between the Tyr carbonyl and the reduced peptide bond protonated amine. This observation was corroborated by molecular mechanics investigations that revealed low energy trans structures compatible with nmr structural data, and furthermore, were consistently characterized by the existence of a strong N+ HO C interaction closing a seven‐membered cycle. The dynamics of cis‐trans isomerization about the Tyr‐Tic peptide bond were probed by nmr exchange experiments. The selective presaturation of exchanging resonances carried out at several temperatures between 50 and 70°C allowed the determination of isomerization rate constants as well as thermodynamic activation parameters. ΔG≠ values were in close agreement with the cis → trans energy barrier found in X‐Pro peptide fragments (∼83 kJ/mol).A large entropic barrier determined for the trans → cis conversion of TIP[Ψ](5. 7 JK−1 mol−1 at pH 3. 1; 6. 5 JK−1 mol−1 at pH 9. 1) is discussed in terms of decreased solvent molecular ordering around the conformers possessing a trans Tyr‐Tic bond. Evidence that the neutral form of the reduced peptide bond gains rigidity upon protonation was obtained from relaxation measurements in the rotating frame. TJp measurements of several protons in the vicinity of the reduced peptide bond were made as a function of spin‐lock field. Quantitative analysis of the relaxation data indicated that chemical shift fluctuations in the 10−4‐10−5s range were more pronounced in the case of deprotonated TIP[Ψ]. Results of molecular dynamics simulations in addition to 3Jαβ coupling constant measurements support the experimentally observed greater flexibility in the C‐terminal region of TIP[Ψ]. © 1995 John Wiley & Sons, Inc.
The conformation of an alamethicin in methanol by multinuclear NMR spetroscopy and distance geometry/simulated annealing
Authors: Yee Adelinda A , Babiuk Randal , O'Neil Joe D. J
Published: December 2004

The solution conformation of the antibiotic peptide alamethicin was investigated using multi‐nuclear spectroscopy and the distance geometry/simulated annealing algorithms from the program DSPACE. 1H‐, 13C‐, and 15N‐nmr chemical shifts and homonuclear 1H coupling constants suggest that the molecule is flexible in the vicinity of Gly‐11 and Leu‐12. The temperature dependence of the amide proton chemical shifts indicates that there is flexibility in the middle of the 20 residue peptide and provides evidence that, at the very N‐terminus, the molecule adopts a 310‐helical conformation. The large differences in the 13C chemical shifts of the pro‐R and pro‐S methyls of the α‐aminoisobutyric acid residues were used to constrain those residues to the right‐handed helical conformation in the distance geometry/simulated annealing algorithms. A family of 24 structures was generated but did not converge to a common conformation when superimposed over the entire polypeptide sequence. The molecules did converge to a helical conformation over residues 1–10 and residues 13–18. The lack of convergence when the entire lengths of the molecules are superimposed is explained by the flexibility of the peptide near Gly‐11/Leu‐12. The results suggest that the protein consists of two helices connected by a flexible “hinge.” The flexibility of the molecule is discussed with respect to the macrodipole model of voltage gating. © 1995 John Wiley & Sons, Inc.
The use of light‐directed combinatorial peptide synthesis in epitope mapping
Authors: Holmes Christopher P. , Adams Cynthia L. , Kochersperger Lynn M. , Mortensen Richard B. , Aldwin Lois A.
Published: December 2004

The application of light‐directed combinatorial peptide synthesis to epitope mapping is described. Photolithography and solid phase peptide synthesis were combined in an automated fashion to assemble arrays containing 1024 peptide sequences on a glass support in ten steps with the precise location of each peptide known. The simultaneous synthesis of two slides containing three arrays of peptidtes each allowed for the independent screening of both a monoclonal antibody (mAb) and its Fab fragment at two different concentrations. A binary synthesis strategy was used to assemble the arrays, resulting in all deletions and truncations possible within the FLRRQFKVVT sequence being present and available for screening. The relative binding interactions of each peptide was determined by incubating the arrays with either mAb D32.39 and goat antimouse immunoglobulin G–FITC or mAb D32.39 Fab‐FITC conjugate, followed by scanning the surface for fluorescence with an epifluorescence microscope. The fragment RQFKVVT was found to bind lightly to both the mAb and Fab fragment while tethered to the surface, and was measured to have 0.49 n M affinity in solution. The frame‐shifted RRQFKVV sequence was found to have lower affinity both in solution (1.3 m M) and on the surface. The fragment RQFKVV was determined to be responsible for antibody recognition and was found to bind tightly when tethered to the surface, yet exhibited no binding in solution as the free acid, suggesting the requirement of an amidated C‐terminus or an additional flunking residue. A deletion analysis revealed that the novel RQFKVT sequence exhibited higher affinity than the RQFKVV sequence while tethered to the surface. © 1994 John Wiley & Sons, Inc.
Exploring the peptide 310‐helix ⇆ α–helix equilibrium with double label electron spin resonance
Authors: Fiori Wayne R. , Millhauser Glenn L.
Published: December 2004

Over the last several years we have used spin labeling as a means for exploring the structure of helical peptides. Two nitroxide labels are engineered into a peptide sequence and distances are ranked with electron spin resonance (ESR). We have found that there is a significant amount of 310–helix in 16–residue model peptides containing only L–amino acids. This review covers several facets of the methodology including spin labeling strategy, interpretation of ESR spectra and the influence of molecular dynamics on the spectral line shapes. Also covered are recent findings of a length–dependent 3l0‐helix → α‐helix transition and the role of Arg+ in the stabilization of specific helix structures. © 1994 John Wiley & Sons, Inc.