bluuebunny/crossref_metadata_2025 huggingface dataset:
Calorimetric study of 2U:1A three‐stranded complexes formed between poly(U) and adenine dinucleotides: ApA and diastereoisomers of nonionic adenine dideoxyribonucleoside methyl phosphonate
Authors: Wierzchowski Kazimierz L. , Zielenkiewicz Anna , Miller Paul S.
Published: December 2004

Melting parameters of 2U:1A complexes formed by polyuridylic acid [poly(U)] and three adenine dinucleotides, diribonucleoside monophosphonate ApA and diastereoisomers of dideoxyribonucleoside methyl phosphonate [(dApA)1 and (dApA)2], in 1M NaCl and at a number of dinucleotide concentrations were obtained from differential scanning microcalorimetric data and interpreted in terms of the theory of helix–coil equilibrium in oligonucleotide–polynucleotide systems. The apparent binding constant, 1/cm, at 39°C and melting temperatures, Tm, at 1 × 10−3 M dinucleotide concentration indicate the following order of thermodynamic stability of the complexes: 2 poly(U) · (dApA)2 (2.27 × 103M−1, 44.2°C) > 2 poly(U) · (dApA)1 (9.9 × 102M1, 39.2°C) > 2 poly(U) · (ApA) (5.9 × 102M−1, 35.8°C). Corresponding calorimetric enthalpies of melting, ΔHm: 13.5, 12.7, and 12.8 kcal/mol (UUA base triplets) were found to be considerably lower than the van't Hoff enthalpies, ΔHapp: 29.4, 16.2, and 16.2 kcal/mol, respectively, evaluated from the dependence of the melting temperatures on dinucleotide concentration. Self‐association of dinucleotides and their simultaneous binding as monomers, dimers, and higher‐order associated species is suggested as the most probable cause of the differences between ΔHm and ΔHapp values. The differences in thermodynamic properties of the complexes formed by (dApA)1 and (dApA)2 diastereoisomers are discussed in connection with their known conformational properties. The higher and essentially enthalpic stability of the 2 poly(U) · (dApA)2 complex correlates with a lower degree of intramolecular stacking of the (dApA)2 isomer. The hydrophobically enhanced strong self‐association of the latter greatly influences the thermodynamics of its complex formation with poly(U) and results in ΔHapp/ΔHm = 2.3.
Molecular‐Mechanical studies of the mismatched base analogs of d(CGCGAATTCGCG)2:d(CGTGAATTCGCG)2, d(CGAGAATTCGCG)2, d(CGCGAATTCACG)2, d(CGCGAATTCTCG)2, and d(CGCAGAATTCGCG)·d(CGCGAATTCGCG)
Authors: Keepers Joe W. , Schmidt Paul , James Thomas L. , Kollman Peter A.
Published: December 2004

Molecular‐mechanical simulations have been carried out on “mismatched base” analogs of the DNA double‐helical structure d(CGCGAATTCGCG)2, in which the base pairs CG at the 3 and 10 positions have been replaced by CA, AG, TC, and TG base pairs, as well as an insertion analog in which an extra adenine has been incorporated into one strand of the above structure between bases 3 and 4. The results of these simulations (calculated relative stabilities, structures, and nmr ring‐current shifts) have been compared with calorimetric and nmr data. The calculated relative stabilities of the double‐helical parent dodecamer and the various “wobble” base pairs qualitatively correlate with the experimental melting temperatures. The base‐pairing structure for the GT wobble pair is in agreement with that previously determined from nmr experiments. For the GA base pair, the structure with both bases anti has a slightly more favorable energy from base pairing and stacking than a structure with non‐Watson‐Crick H‐bonding with adenine syn, in agreement with nmr experiments. The CA wobble base is calculated to favor an adenine 6NH2 …︁ cytosine N3 H‐bond over cytosine 4NH2 …︁ adenine N1, again, in agreement with nmr experiments. There is no definitive experimental data on the TC base pair, but the existence of (somewhat long and weak) H‐bonds involving cytosine 4NH2 …︁ thymine 4CO and cytosine N3 …︁ thymine HN3 seems reasonable. We find a structure in which the extra adenine base of the insertion analogs sits “inside” the double helix.
Differential scattering of circularly polarized light by chromatin modeled as a helical array of dielectric ellipsoids within the born approximation
Authors: Belmont Andrew S. , Zietz Stanley , Nicolini Claudio
Published: December 2004

Theoretical predictions within the Born approximation of the expected differential light scattering of circularly polarized light (CIDS) were made for the 300‐Å chromatin fiber, modeled as a helical array of dielectric ellipsoids. Computed CIDS values were strongly dependent on the exact geometry of the solenoid model, depending particularly on parameters relaed to the chiral nature of the fiber and the orientation of the nucleosomes within the helix, in contrast to the values of the total light scattering, which mainly probed size and shape. In particular, both a superbead model and a strict linear 110‐Å nucleosome filament would be predicted as giving rise to zero CIDS (in disagreement with the finite values observed). At the same time, helical models in which the normal vectors to the nucleosome faces were exactly parallel to the helical axis also yielded zero CIDS. Confirming earlier expectations, CIDS values were significantly less dependent on helical length than total light scattering. Finally, comparison of these calculated results from those extrapolated from available experimental data indicates that predicted CIDS values, based on currently accepted models of solenoid structure, are within an order of magnitude of those experimentally observed. Together, these results indicate the potential of differential light scattering measurements as a probe of chromatin higher‐order structure, complementary to existing scattering measurements.
Effect of the electric field on the apparent mobility of large DNA fragments in agarose gels
Authors: Stellwagen Nancy C.
Published: December 2004

The electrophoresis of a series of DNA fragments ranging in size from 0.5 to 12 kilobase pairs, has been studied as a function of agarose gel concentration and electric field strength. The apparent mobility of all fragments decreased with decreasing electric field strength and with increasing gel concentration. When extrapolated to zero electric field strength and zero agarose concentration, the apparent mobility of all DNA fragments extrapolated to a common value (2.0 ± 0.1) × 10−4 cm2/V s. The square roots of the retardation coefficients of the various fragments were found to be linearly related to the root‐mean‐square radii of gyration of the fragments, as predicted by pore‐size distribution theory. As predicted by reptation theory, the molecular weights of the various fragments were found to be linearly related to the reciprocal of the apparent mobilities. An equation is given for estimating the apparent pore size of agarose gels between 0.25 and 1.5% in concentration.
Phase‐structure transitions of the elastin polypentapeptide–water system within the framework of composition–temperature studies
Authors: Urry D. W. , Trapane T. L. , Prasad K. U.
Published: December 2004

The temperature dependence of the composition of coacervate and equilibrium phases is examined for the polypentapeptide of elastin (L‐Val1‐L‐Pro2‐Gly3‐L‐Val4‐Gly5)n in water. This provides for the development of a phase diagram. CD data is presented that provides information on associated polypeptide structure changes that, when added to previous CD, nmr, and dielectric relaxation data at lower water composition, allow construction of a phase‐structure diagram of the polypentapeptide–water system. The molecular‐weight dependence of phase change (coacervation) is included. The volume–composition studies as a function of temperature also provide temperature coefficients of expansion and of composition important in analyzing the mechanism of elasticity.
Spermine–nucleic acid interactions: A theoretical study
Authors: Zakrzewska Krystyna , Pullman Bernard
Published: December 2004

The interaction of spermine with nucleic acids is simulated theoretically using refined semi‐empirical energy formulae and an advanced minimization procedure. Various nucleic acids are considered: model homopolymeric DNA's, a dodecamer (CGCGAATTCGCG) of type B‐DNA, as well as a transfer RNA, tRNAPhe. The dominant role of electrostatic potential in determining the preferential binding sites of spermine is demonstrated in each of these cases and the role of counterions, nucleic acid structure, and base‐pair sequence is analyzed.
Structural variation of native cellulose related to its source
Authors: Okano Takeshi , Koyanagi Akio
Published: December 2004

X‐ray diffraction diagrams of 80 specimens, mainly from woody plants, were recorded and resolved into characteristic reflections of cellulose I. Significant differences were observed in d‐spacings and integrated intensity ratios between softwoods and hardwoods. Of the lattice parameters, the monoclinic angle was found to be correlated with plant taxonomy and tended towards the right angle in the more advanced taxonomic groups. We have therefore demonstrated that the crystal structure of natural cellulose shows some variations related to the source of the cellulose.
Peptide‐bond distortions and the curvature of α‐helices
Authors: Chakrabarti P. , Bernard M. , Rees D. C.
Published: December 2004

Solvent accessible peptide bonds in proteins exhibit a 1–3° compression of the OCN bond angle and a corresponding expansion of the NCCa bond angle, relative to buried peptide bonds. These changes are consistent with an increase in hydrogen bonding to the carbonyl oxygen accompanying solvent exposure (J. D. Dunitz and F. K. Winkler, (1975) Acta Cryst. B31, 251–263). For amphiphilic structures such as α‐helices, systematic differences in peptide‐bond geometry between solvent‐exposed and buried residues will generate significant curvature. A decrease of 4° in the OCN bond angle between hydrophilic and hydrophobic sides of an amphiphilic helix will lead to smooth bending, with a radius of curvature of about 70 Å. This curvature is in the range observed for α‐helices in proteins. Helix curvature is estimated to have only a small effect on the magnitude and direction of the helical dipole moment.
Conformation of mucous glycoproteins in aqueous solvents
Authors: Shogren R. L. , Jamieson A. M. , Blackwell J. , Jentoft N.
Published: December 2004

Light‐scattering techniques have been used to measure the z‐average radius of gyration Rg z‐average translational diffusion coefficient Dt and weight–average molecular weight Mw of porcine submaxillary mucin (PSM) in solution. PSM isolated at low shear in the presence of protease inhibitors has a Mw about twice as large as a sample prepared without these precautions. The former sample has a Mw of 17 × 106 in 0.1M NaCl, which decreases to 8 × 106 in 6M guanidine hydrochloride (GdnHCl) and then to 2 × 106 on addition of 0.1M mercaptoethanol to the 6M GdnHCl solution. The Rg or D values obtained for PSM in this work superimpose with those of other authors for different mucin glycoproteins, leading to linear log–log relationships to the molecular weight of the protein core. Comparison of these results with those in the literature for denatured proteins suggest that mucins are linear random coils in which the protein core is stiffened by the presence of the oligosaccharide side chains. The length of the oligosaccharides and the nature of the solvent have little effect on the extension of the protein core. This suggests that the stiffness of the protein core is maintained by steric repulsion of the residues at the beginning of the oligosaccharide chains.
Prediction of protein structural class from the amino acid sequence
Authors: Klein Petr , Delisi Charles
Published: December 2004

The multidimensional statistical technique of discriminant analysis is used to allocate amino acid sequences to one of four secondary structural classes: high α content, high β content, mixed α and β, low content of ordered structure. Discrimination is based on four attributes: estimates of percentages of α and β structures, and regular variations in the hydrophobic values of residues along the sequence, occurring with periods of 2 and 3.6 residues. The reliability of the method, estimated by classifying 138 sequences from the Brookhaven Protein Data Bank, is 80%, with no misallocations between α‐rich and β‐rich classes. The reliability can be increased to 84% by making no allocation for proteins classified with odds close to 1. Classification using previously developed secondary structural prediction methods is considerably less reliable, the best result being 64% obtained using predictions based on the Delphi method.
The distribution of charged groups in proteins
Authors: Barlow D. J. , Thornton J. M.
Published: December 2004

The distributions of charged groups in 32 proteins of known three‐dimensional structure have been analyzed to determine how regularly the groups are spread over the molecule's surfaces, and to identify and to study those proteins where charge asymmetry would seem important for their function. The distributions have been analyzed in terms of charge “polarity,” surface “charge density,” and electric dipole moments. More detailed studies of the distributions for individual proteins are made using map projections specifically developed for this purpose. In the light of the results obtained we discuss the role of charged groups in relation to protein function.
Conformational properties of somatostatin. VI. In a methanol solution
Authors: van den Berg E. M. M. , Jans A. W. H. , van Binst G.
Published: December 2004

The peptide hormone, somatostatin, has been studied by nmr at 500 MHz in a methanol solution and at low temperature (263 K) in order to investigate a possible similarity with conformationally restricted biologically active analogs. The more pronounced predominancy of one conformer already present in a water solution is demonstrated. No evidence has been shown for interactions between Phe11 and other Phes in the molecule.
Thermodynamics of water–biopolymer interactions: Irreversible sorption by a single, uniform sorbent phase
Authors: Bryan William P.
Published: December 2004

Sorption isotherms of water vapor by solid biopolymers are necessary for the determination of thermodynamic quantities for water–biopolymer interactions. Such isotherms are generally irreversible, so equilibrium thermodynamics may not be applicable. General relationships are derived for thermodynamic quantities of sorption when the sorbent is a single uniform phase. In general, use of the Clausius–Clapeyron equation allows correct determination of differential entropies of sorption. However, calorimetric data are also necessary for the correct determination of other thermodynamic quantities. The single uniform phase model appears more useful than a domain model in explaining the hysteresis seen in water–biopolymer sorption isotherms.
Cytochrome c chimerae from natural and synthetic fragments: Significance of the biological properties
Authors: Wallace Carmichael J. A. , Corradin Giampietro , Marchiori Fernando , Borin Gianfranco
Published: December 2004

Analogs of natural proteins have application in basic research, in medicine, and increasingly, in industry. Of the many methods developed for the fabrication of modified proteins, semisynthesis has so far been the most productive [R. E. Offord (1983) Proc. Eur. Peptide Symp., 17 31–42]. The technique of fragment‐condensation semisynthesis takes as its basic raw material the native protein; fragments derived from it are manipulated by sequential degradation and resynthesis before recombination. While gene manipulation may overtake protein manipulation in general usefulness, certain types of analogs will remain accessible only by semisynthesis. Fragment condensation semisynthesis, as described above, has been used in preparing cytochrome c analogs [C. J. A. Wallace (1979) Proc. Am. Peptide Symp. 6, 609–612]. To overcome the difficulty of replacing amino acids far from convenient cleavage sites, a number of variants of the method have also been used. These include fragment‐specific chemical modification [C. J. A. Wallace & K. Rose (1983) Biochem. J. 215, 651–658] and solid‐phase synthesis of small [P. J. Boon, G. I. Tesser, H. H. K. Brinkhof & R. J. F. Nivard (1981) Proc. Eur. Peptide Symp. 16, 127–130] or large fragments [L. E. Barstow, R. S. Young, E. Yakali, J. J. Sharp, J. C. O'Brien, P. W. Berman & H. A. Harbury (1977) Proc. Natl. Acad. Sci. USA 74, 4148–4250]. The latter study gave low final recoveries, so we have prepared large peptides (38–42 residues) by classical solution methods. We have examined both their use in the reformation of the complete protein, and the physical and biochemical properties of the product analogs compared with those of the native proteins.
Sol–sol structural transition of aqueous agarose systems
Authors: Biagio P. L. San , Madonia F. , Newman J. , Palma M. U.
Published: December 2004

A structural transition is reported to occur in aqueous sols of agarose, an electrically uncharged biostructural polysaccharide. The transition has no measurable effect on size dispersity on the shape of the solute polysaccharide as observed by precision photon correlation spectroscopy. It originates a low‐angle pattern of scattered light similar to that which monitors phase separations in polymer blends. Thus, it must be due to some extent to spatially modulated polymer clustering, typical of spinodal decomposition. In the interval of temperatures studied, it precedes very distinctly in time the thermoreversible sol–gel transition, which is known to be promoted at higher concentrations. It also anticipates to an appreciable extent the spatial density modulation observed in the gel. Although reported here for the first time, a spinodal decomposition of the sol that precedes and possibly triggers the processes leading to gelation does not come unexpectedly in terms of site‐bond correlated‐percolation theory. In general, this occurrence raises the question as to whether the spontaneous onset of regions of higher and lower polymer concentration (spinodal separation) may be regarded as a novel path for biomolecular interactions and the self‐assembly of order in biomolecular systems.
Evidence for a folded structure of met‐enkephalin in membrane mimetic systems: 1H‐nmr studies in sodiumdodecylsulfate, lyso‐phosphatidylcholine, and mixed lyso‐phosphatidylcholine/sulfatide micelles
Authors: Zetta Lucia , De Marco Antonio , Zannoni Giulio , Cestaro Benvenuto
Published: December 2004

1H‐nmr spectra of Met‐enkephalin dissolved in aqueous solution of sodiumdodecylsulfate (SDS) micelles are reported as a function of pH and temperature. The temperature behavior of the amide protons is compared with that observed for the same peptide dissolved in aqueous solution of lyso‐phosphatidylcholine (LPC) and lyso‐phosphatidylcholine‐sulfatide (LPC‐SH) micelles. The temperature coefficients are affected by the micelle polarity, which suggests that the peptide backbone is not remote from the micelle surface. pH titration performed in the presence of SDS micelles gives a number of intrinsic and extrinsic pKa values, indicative of a folded structure of the opioid molecule. This conformation is characterized by the existence of an intramolecular hydrogen bond involving the Met‐5 amide proton and an interaction of the N‐terminal residue with the aliphatic side chains of both Phe‐4 and Met‐5.
Lateral packing of protofibrils in fibrin fibers and fibrinogen polymers
Authors: Voter William A. , Lucaveche Carmen , Blaurock Allen E. , Erickson Harold P.
Published: December 2004

The distinctive transverse banding pattern of fibrin fibers clearly indicates ordering of molecules in the longitudinal direction. In this study we examined the fibers of fibrin clots, as well as two types of fibrinogen polymers, by thin‐section electron microscopy. The fibrinogen polymers have a transverse banding pattern identical to that of fibrin fibers—clearly indicating a regular longitudinal repeat—but they are larger in diameter, and show little or no branching. We therefore expected their overall ordering to be better than that of fibrin fibers. Several different fixation protocols were used. We readily observed the typical transverse banding seen previously by negative stain and metal replication techniques. However, only very rarely was any regular lateral lattice seen in any of the samples. X‐ray diffraction was used to examine unfixed specimens of the two fibrinogen polymers and, once again, although a longitudinal repeat was evident, only rarely was evidence for lateral crystallinity seen. The electron‐microscope and x‐ray results showed that the needles and pellet fibers of fibrinogen have essentially the same internal architecture as thick fibrin fibers, and that all three types of polymer, although clearly transversely banded, have almost no crystallinity in their lateral protofibril packing.
The influence of calcium ions on fibrin polymerization
Authors: Häberli A. , Straub P. W. , Dietler G. , Känzig W.
Published: December 2004

The influence of calcium ions on the polymerization induced in fibrinogen solutions by thrombin and by Reptilase has been investigated by meansof static and dynamic light scattering in combination with measurements of the release of the fibrinopeptide A. The calcium concentration was varied in the range between 0.3 and 103 calcium ions per fibrinogen molecule. The enzyme concentration was chosen sufficiently low so that it was possible to make quantitative observations as a function of time, in particular, beforethe onset of gelation. Likewise, the influence of calcium ions on the enzymatically induced polymerization of fragment X was studied. The results indicate that there are at least three mechanisms by which calcium can influence the evolution of the polymer system on the path to gelation and clotting. Which mechanism dominates depends upon the calcium concentration.
Crystal structure and molecular conformation of the tripeptide, N‐Boc‐L‐Phe‐Dehydro‐Phe‐L‐Val‐OCH3
Authors: Singh T. P. , Haridas M. , Chauhan V. S. , Kumar A. , Viterbo D.
Published: December 2004

The tripeptide, N‐Boc‐L‐Phe‐dehydro‐Phe‐L‐Val‐methyl ester (C29H37N3O6) was synthesized as a model peptide to produce a specific β‐turn with the help of dehydro‐Phe. This peptide crystallizes in the triclinic space group Pl with a = 6.085(2) Å, b = 9.515(4) Å, c = 13.243(5) Å, α = 105.16(3)°, β = 92.69(3)°, γ = 104.9(3)°, and Z = 1. The structure was solved by direct methods using MULTAN 80. The structure was refined by the block‐diagonal least‐squares method to an R value of 0.075 for 2438 observed reflections. The bond lengths and angles, in general, are in good agreement with the standard values. The peptide backbone adopts the β‐conformation as a result of deprotonation at the Cα and Cβ atoms in the dehydro‐Phe residue. The backbone conformations around the Cα atoms are cis, and the corresponding moieties are nonplanar. The backbone segments between the Cα atoms have extended trans conformations with highly planar configurations. The chain conformation angles—ϕ1, ψ1, ω1, ϕ2, ψ2, ω2, ϕ3, and ψ—are −45.4(11)°, −45.6(6)°, − 179.3(4)°, −46.5(5)°, −38.0(6)°, 165.3(9)°, 51.7(5)°, and 43.0(6)°, respectively. The phenyl rings of Phe and dehydro‐Phe are essentially planar and their planes are inclined with respect to each other at 69.7(5)°. The CβCγ bonds in Phe and dehydro‐Phe are trans with respect to the NCα bonds, with a X1 torsion angle (about CαCβ) of −176.3(1)° and −179.4(5)°, respectively. The C′Cα bonds are cis and trans with respect to the CβCγ bonds, with torsion angles of −56.8(7)° and −170.0(16)° in Phe and dehydro‐Phe, respectively. The β‐turn conformation is stabilized by an intramolecular hydrogen bond, N3H3 …︁ O2, of a distance of 3.116(6) Å. The molecules are held in the crystal structure by a network of hydrogen bonds and the van der Waals forces.
Cystine peptides: The intramolecular antiparallel β‐sheet conformation of a 20‐membered cyclic peptide disulfide
Authors: Kishore R. , Raghothama S. , Balaram P.
Published: December 2004

A 20‐membered cyclic peptide disulfide magnified image has been synthesized as a conformational model for disulfide loops of limited ring size. 1H‐nmr studies at 270 MHz establish the presence of three intramolecular hydrogen bonds involving the Leu, Val, and methylamide NH groups in CDCl3. Evidence for peptide aggregation in CDCl3 is also presented. A structural transition involving loosening of the hydrogen bond formed by the Val NH group is observed upon the measured addition of (CD3)2SO to CDCl3. Hydrogen‐bonding studies, together with unusually low field positions of the Cys(1) and Cys(6) CαH resonances and high J values provide support for an intramolecular antiparallel β‐sheet conformation, facilitated by a chain reversal at the Aib‐Ala segment. Extensive nuclear Overhauser effect studies provide compelling evidence for the proposed conformation and also establish a type I′ β‐turn at the Aib‐Ala residues, the site of the chain reversal.
Raman spectroscopic study on low‐frequency collective modes in self‐associates of guanosine monophosphates
Authors: Urabe Hisako , Sugawara Yoko , Tsukakoshi Motowo , Ikegami Akira , Iwasaki Hitoshi , Kasuya Takahiro
Published: December 2004

Low‐frequency Raman spectra of the self‐associates of guanosine monophosphates (GMPs) Na2 · 5′GMP, K2 · 5′GMP, Na2 · 3′GMP, and K2 · 3′GMP, and polyribonucleic acid K · poly(rG), were obtained. In acidic gels and dried fibers, GMP molecules are known to form helical stacks of hydrogen‐bonded tetramers. Some low‐frequency collective modes specific to the helically stacked structures were observed. We examined the dependence of these modes on counterions and water content. The lowest frequency mode at ca. 20 cm−1 is sensitive to the water content of the sample and is clearly visible in solid‐state samples, so it works as a marker band of the environmental condition of the helices. The intensity and the peak frequency of this mode in solid‐state samples depend on the helical structure and counterions. The broad peaks in the vicinity of 100 cm−1 are influenced by cations and are independent of water content.
Molecular mechanics studies of parallel and antiparallel phosphate‐methylated DNA
Authors: Van Genderen Marcel H. P. , Koole Leo H. , Aagaard Olav M. , Van Lare Coert E. J. , Buck Henk M.
Published: December 2004

Methylation of phosphate groups in oligo‐dT strands leads to a parallel duplex with T · T base pairs. Molecular mechanics calculations on parallel d(TTTTTT)2 show it to be a symmetric right‐handed helix with B‐DNA conformational characteristics. Phosphate methylation stabilizes the duplex by ca. 41 kcal/mol, due to removal of the interstrand phosphate electrostatic repulsions. The chirality introduced with phosphate methylation is important for the molecular geometry, since RP methylation predominantly influences the conformation around the ζ bond (PO3′), while SP methylation mostly changes the α conformation (PO5′). This is also true in antiparallel helices with methylated phosphates, as is shown by molecular mechanics calculations on d(GCGCGC)2. These results may be of relevance to protein–DNA interactions, where phosphate charges are also shielded. As the pro‐SP oxygen is most available in a right‐handed helix, we suggest changes around the α bond to occur upon protein complexation, leading to a widening of the major groove in the d(GCGCGC)2 duplex (from 12 to 13 Å) and reduced minor groove (from 6 to 5 Å).
The melting behavior of a DNA junction structure: A calorimetric and spectroscopic study
Authors: Marky Luis A. , Kallenbach Neville R. , McDonough Kathleen A. , Seeman Nadrian C. , Breslauer Kenneth J.
Published: December 2004

We present an investigation of the helix–coil transition in a stable branched oligomer of DNA, known as an immobile DNA junction. This junction is composed of four 16‐mer strands, which yield four double‐helical arms, each containing 8 nucleotide pairs. Properties of the individual arms of this complex are modeled by four octameric duplexes. We have performed experiments using calorimetry, uv absorbance, and CD spectroscopy to characterize the melting transitions of the junction and each arm. By comparing our spectroscopic and calorimetric results on the junction and its component arms, we are able to conclude the following: (1) The calorimetric transition enthalpy for the overall junction complex is equal to the sum of the calorimetric transition enthalpies of the four constituent duplex arms. (2) The optical and the calorimetric measurements yield qualitatively similar, but not identical thermodynamic data. (3) The melting temperature of the junction is less dependent on concentration than the melting temperatures of the individual arms. We attribute this observation to the tetrameric nature of the junction. (4) The ratio of the calorimetric transition enthalpy of the junction and its corresponding van't Hoff value is close to unity. (5) The CD spectrum of the junction is equal quantitatively to the sum of the B‐like CD spectra of the four constituent duplex arms.
Application of the augmented theory of α‐helix‐to‐random‐coil transitions of two‐chain, coiled coils to extant data on synthetic, tropomyosin‐analog peptides
Authors: Holtzer Alfred , Skolnick Jeffrey
Published: December 2004

The statistical mechanical theory for the helix‐to‐random‐coil transition in two‐chain coiled coils is applied to extant data for two synthetic coiled‐coil polypeptides. These peptides have the primary structure K(LEALEGK)n, in which n = 4, 5. This repeating heptet sequence mimics the pattern of hydrophobic, acidic, and basic residues characteristic of the 284‐residue tropomyosin molecule, the prototypical coiled‐coil protein. Theoretical calculations for single chains show that such model peptides cannot be directly compared to proteins like tropomyosin because of differences in chain length (29 and 36 residues vs 284) and in intrachain interactions, the latter caused by the differences in amino acid composition and seqeunce between protein and model. Application of the theory to extant data on the two synthetic peptides provides a semiquantitative fit and results in an assessment of the interhelix interaction in the model peptides. The value obtained, ∼ 2000 cal · (mol of turn pairs)–1, is four to five times larger than has been obtained for tropomyosin. This probably is a result of greater regularity in the structure of the synthetics and of the exclusive presence of leucine in the hydrophobic interface. The theory employed here insists that this powerful interhelix interaction in the synthetic is the principal reason that such short chains can be so highly helical at moderate and low temperatures. Theory predicts, indeed, that a tropomyosin‐length chain with a sequence homologous to these synthetics would be completely thermally stable in the entire temperature range accessible in aqueous solutions. Theory also predicts a much more pronounced effect of concentration on the 29‐ and 36‐residue synthetic polymers than is predicted or observed in the case of tropomyosin, and it also predicts a pronounced stabilizing effect of pH‐reduction on the thermal curves. On the last two points, sufficient data are not yet available with which to test the theory.
The structure of agarose gels, and the accommodation within them of irregularly shaped particles
Authors: West Roger
Published: December 2004

This paper shows how the number of cross‐linkage points (nodes) in a random reticulum, such as an ideal polysaccharide gel, may be calculated in accordance with mathematical principles. The influence of nodal configurations upon the statistical geometry of the reticulum is discussed, and it is shown from experimental evidence that the nodal configurations in agarose gel are nonrandom. A method is given for calculating the accommodation probability of an irregularly shaped particle in a reticulum, which is relevant to the theory of gel chromatography and to the distribution of cells in tissues permeating a network of capillaries or veins.
Determination of thermodynamic functions from scanning calorimetry data. II. For the system that includes self‐dissociation / association process
Authors: Kidokoro Shun‐Ichi , Uedaira Hatsuho , Wada Akiyoshi
Published: December 2004

The basic relations between the molar fractions and the scanning calorimetry data for the system that includes self‐dissociation/association process such as

are presented, where mi is the stoichiometric coefficient of the ith state Ai. The relations are described for each state j as

where fj(T) is the molar fraction function of state j and ΔHj(T) is the difference enthalpy function of the system referred to the state j, which can be obtained by scanning calorimetry; R is the gas constant; and T is the absolute temperature. By these relations, scanning calorimetry data can be deconvoluted in order to determine the thermodynamic functions by means of single and double deconvolution. The concentration dependence of the data is analyzed by a method presented in this paper. The nonlinear least squares fitting method for the determination of the functions is discussed. For an example of the application of this method to the actual scanning calorimetry data, thermodynamic data of multistate thermal transition of Vibrio parahaemolyticus hemolysin are analyzed.
Distance distributions in native and random‐coil troponin I from frequency‐domain measurements of fluorescence energy transfer
Authors: Lakowicz Joseph R. , Gryczynski Ignacy , Cheung Herbert C. , Wang Chien‐Kao , Johnson Michael L.
Published: December 2004

We used time‐dependent fluorescence energy transfer to determine the distribution of donor‐to‐acceptor distances in native and denatured troponin I(TnI). The single tryptophan residue (Trp 158) of TnI served as the donor (D), and the acceptor (A) was a labeled cysteine residue (Cys 133). The time‐dependent intensity decays of the donor were measured by the frequency‐domain method from 10 to 320 MHz. The frequency response of the donor emission, in the absence and presence of acceptor, was used to recover the distribution of D to A distances, using an algorithm that accounts for the intrinsic multiexponential decay of the donor. In the native state the D–A distribution is characterized by an average distance of 23 Å and a half‐width of 12 Å. Denaturation results in a modest increase in the average distance to 27 Å, and a dramatic increase in half‐width to 47 Å. We believe the ability to recover distance distributions will have numerous applications in the characterization of biological macromolecules.
Study of the bisintercalation of the antitumor drug ditercalinium by 31P‐nmr
Authors: Delepierre Muriel , Igolen Jean , Roques B. P.
Published: December 2004

Bisintercalation of ditercalinium, a potent antitumoral 7H‐pyriodo[4,3‐c]carbazole rigid dimer, into the self‐complementary tetranucleotides d(CpGpCpG)2, d(m5CpGpm5CpG) and the self‐complementary hexanucleotide d(CpGpApTpCpG)2 was investigated by 162‐MHz 31P‐nmr. The slow exchange, on the nmr time scale, observed between the free and complexed nucleotides allows identification of the phosphorus signals in the complexes through two‐dimensional chemical exchange spectroscopy. Differences in 31P chemical shifts upon intercalation are discussed in relation to the complex geometry and nature of the drug.
Conformational studies of N‐acetyl‐N′‐methylamide derivatives of α‐aminobutyric acid, norvaline, and valine. I. Preferred conformations in solution as studied by 1H‐nmr spectroscopy
Authors: Yamazaki Toshimasa , Abe Akihiro
Published: December 2004

The 1H‐nmr studies were extensively carried out to elucidate preferred conformations of dipeptides CH3C*O—X—NHCH3, with X = Abu, nVal, and Val in various solvents. The vicinal 1H—1H coupling constants for the NH—CαH moiety and those around the Cα—Cβ bond in the articulated side chain provided the information regarding the average conformation of these molecules. The results indicate that transformation of skeletal conformations takes place in solution among conformers having similar dihedral angles, θ, in the Karplus expression.
Frictional models for stochastic simulations of proteins
Authors: Venable Richard M. , Pastor Richard W.
Published: December 2004

As a first step toward a systematic parametrization of friction constants of atoms in proteins, a model in which frictional resistance is placed explicitly on each atom accessible to solvent is used to calculate overall translational and rotational diffusion constants. It is found that these quantities are relatively insensitive to the precise value of the atomic friction constant, as long as the effective hydrodynamic radius of the surface atoms is approximately 1 Å. However, if only protein atoms are included in the calculation, no reasonable range atomic of radii can reproduce the experimental translational diffusion constant to better than 20% for lysozyme and 5% for ribonuclease. When a hydration shell of approximately 70% coverage for lysozyme and 20% for ribonuclease is included, there is quantitative agreement with experimental results. The sensitivity of peptide diffusion to levels of hydration is also investigated; it is found that for glycine, two bound waters are required to provide agreement with experiment. These findings imply that the effects of solvent damping will be underestimated in stochastic simulations of proteins and peptides unless bound waters are taken into account.
13C‐nmr spectroscopic investigation of two yeast cell wall β‐D‐glucans
Authors: Kogan Grigorij , Alföldi Juraj , Masler Ladislav
Published: December 2004

By means of alkaline extraction of the cell walsl of the yeasts Saccharomyces cerevisiae and Canadida albicans, water‐insoluble glucans were obtained. Methylation analysis and 13C‐nmr investigation in dimethyl sulfoxide solution revealed the similar chemical structure of these glucans, being composed of β(1 → 3) glycosidically linked D‐glucopyranosyl units with a small amount of β(1 → 6) linkages. More detailed study in dilute alkaline solutions and in the gel state at neutral pH, however, showed that an ordered helical conformation of the glucan chain is less stable in the case of the S. cerevisiae glucan in comparison with that of C. albicans. Measurements of the shift of the absorption maximum of the glucan complexes with Congo Red also demonstrated such difference. The S. cerevisiae glucan was also inable to form a gel at neutral pH. The difference in stability of helical conformation of the glucans is explained on the basis of the methylation analysis, so that the S. cerevisiae glucan possesses longer side chains, which hinder its adoption of a stable helical conformation.
Effects of pH and temperature on cardioactive polypeptides from sea anemones: A 1H‐nmr study
Authors: Gooley Paul R. , Blunt John W. , Beress Laszlo , Norton Raymond S.
Published: December 2004

The effects of pH and temperature on the 300‐MHz 1H‐nmr spectra of three cardioactive polypeptides from sea anemones, anthopleurin‐A from Anthopleura xanthogrammica (AP‐A) and Anemonia sulcata toxins I and II (ATX I and II), are described. AP‐A and ATX II exhibit major spectral heterogeneity. Evidence from the pH and temperature studies and from high performance liquid chromatography indicates that this heterogeneity is conformational rather than chemical in origin. By contrast, purified isotoxins of ATX I show no evidence of conformational heterogeneity. The pKa values of most of the ionizable groups in these polypeptides are not strongly perturbed by interactions in the tertiary structure, with the exception of one of the Asp carboxylates, which has a pKa of ≲ 2 in AP‐A and ATX II and 3.0 in ATX I. Protonation of this carboxylate, suggested to be Asp‐9, leads to a conformational change in all three molecules. All three polypeptides are thermally stable, showing some conformational changes but not major unfolding at elevated temperatures.
Crystal structure and molecular conformation of N‐boc‐L‐pro‐dehydro‐leu‐OCH3
Authors: Narula Punit , Patel H. C. , Singh T. P. , Chauhan V. S. , Sharma Ashwani K.
Published: December 2004

The peptide N‐Boc‐L‐Pro‐dehydro‐Leu‐OCH3 was synthesized by coupling dehydroleucine methyl ester with Boc‐Pro‐OH. It was crystallized from its solution in a methanol–water mixture at 4°C and the crystals belong to the orthorhombic space group P212121 with a = 10.239(1) Å, b = 19.276(4) Å, c = 20.319(3) Å, V = 4010(1) Å3, and Z = 8. The structure was solved by direct methods using MULTAN 80. The structure was refined to an R value of 0.095 for 1871 observed reflections. There are two crystallographically independent molecules in the unit cell. The molecular dimensions of the two molecules are very similar. The backbone conformation angles of these molecules are as follows: θ1 = −176(1)°, ω0 = −2(2)°, ϕ1 = −72(1)°, ψ1 = 141(1)°, ω1 = 169(1)°, ϕ2 = −98(1)°, ψ2 = −179(1)°, θT = 179(1)°, θ = 174(1)°, ω10 = −3cm−1, ϕ11 = −64(1)°, ψ11 = 148(1)°, ω11 = 167(1)°, ϕ12 = −67(1)°, ψ12 = 175(1)°, and θ1T = 172(1)°, respectively. Other torsion angles such as θ = 86(1)°, χ2 = −5(2)°, = 131(1)°, and χ12 = −16(2)° are interesting to define the backbone conformation together with the dehydro‐Leu side chain as a conformation similar to that of the β‐bend type II. The central amide bond of Pro‐dehydro‐Leu segment is deviated from the planarity. The Boc group adopts a trans–cis conformation. The side‐chain torsion angles χ1, χ2, χ3, χ4, and χ0 for Pro‐residue in the two molecules are 11(2)°, −11(2)°, 6(2)°, 2(1)°, −9(1)° and −18(1)°, 31(1)°, −31(1)°, 21(1)°, and −1(1)° respectively. The side chain of the Pro residue of molecule A is in the flattened Cγ‐endo conformation while the pyrrolidine ring in miolecule B adopts the well‐known Cγ‐exo conformation. The side‐chain torsion angles χ, χ2,1, and χ2,2 in the leucyl residues of molecules A and B are −5(2)°, −111(2)°, 126(2)° and −16(2)°, −110(2)°, and 133(2)°, respectively. The molecular packing is stabilized by intermolecular hydrogen bonds and van der Waals interactions.
Nmr studies on the presence of domain structures in polysaccharides. II. 1H spin‐‐lattice relaxation time dispersion
Authors: Lacelle Serge , Gerstein Bernard C.
Published: December 2004

The behavior of 1H‐nmr spin–lattice relaxation times as a function of frequency is examined for powders of α‐ and β‐cyclodextrins, dextran B512F, and their “deuterated” analogues, where deuterium replaces exchangeable protons. A crossover from two‐ to one‐component relaxation decays is observed with increasing frequency (ν). By considering the effect of spin diffusion in spin–lattice relaxation measurements as a function of the frequency, estimates of domain sizes (∼ 7–10 Å) consistent with the lower limit of spatial resolution of the Goldman–Shen experiments are obtained.
Dynamic coupling between DNA and its primary hydration shell studied by brillouin scattering
Authors: Tao N. J. , Lindsay S. M. , Rupprecht A.
Published: December 2004

We have measured the dispersion of phonon line widths between frequencies of about 2 and 10 GHz in DNA films at relative humidities between 0 and 95%. The results show that the relaxation mode of the primary hydration shell retains its basic characteristics even in samples with very high water content. A modified mode coupling model is used to include both the collective nature of the sound wave and to describe the change in hydration explicitly. It enables us to describe the coupling between the phonons and the water relaxation mode at various water contents, and allows us to extract values for the primary shell relaxation time and coupling constants over the range of hydration studied. The primary shell relaxation time (∼ 40 ps) and coupling parameters remain nearly constant over the entire range of hydration. We have reanalyzed our earlier Brillouin data (taken as a function of temperature) in terms of two relaxation processes (primary plus a secondary shell contribution of about 2 ps at room temperature). This new analysis indicates that both processes follow a simple Arrhenius behavior with activation energies of 5 kcal mole−1 for the primary relaxation and 7 kcal mole−1 for the secondary relaxation. We also observe a rather broad central mode that can be fitted by a Lorentzian, and that may arise from direct (as opposed to coupled‐mode) scattering from the primary relaxation mode.
Conformational behavior of α,α‐dialkylated peptides: Ab initio and empirical results for cyclopropylglycine
Authors: Barone Vincenzo , Fraternali Franca , Cristinziano Pier Luigi , Lelj Francesco , Rosa Angela
Published: December 2004

The preferred conformations of model cyclopropylglycine peptides have been investigated by means of ab initio and empirical methods. Empirical computations performed with fixed bond lengths and valence angles using two well‐known force fields show that only values of ϕ in the ranges ±70° ± 20° are sterically allowed, and that the C7‐conformation corresponds to the absolute energy minimum irrespective of the terminal groups used. Also, ab initio computations give similar results, but suggest greater stabilities for bridge and, especially, extended structures. These discrepancies can be removed, adding to the empirical force field a twofold torsional potential on ψ and using softer steric repulsive potentials. Complete geometry optimization using both ab initio and empirical methods does not affect the relative stabilities of folded conformations, but leads to a further significant stabilization of the fully extended structure via large modifications of some valence angles.
Dielectric relaxation studies on bovine ligamentum nuchae
Authors: Luan Chi‐Hao , Harris R. Dean , Urry Dan W.
Published: December 2004

Dielectric relaxation studies of bovine ligamentum nuchae are reported over the frequency range of 1 MHz to 1 GHz and over the temperature range of 23–48°C. A temperature‐dependent relaxation process was observed at low megahertz‐frequency with the correlation time of around 40 ns. The result is quite similar to that of a synthetic polypentapeptide (VPGVG) and of α‐elastin. The relaxation is proposed to arise in part from the peptide libration within the polypentapeptide of bovine ligamentum nuchae.
Molecular structure of L‐lysyl‐L‐alanyl‐L‐alanine: A tripeptide found in histone H1
Authors: Verdaguer N. , Urpí L. , Fita I. , Subirana J. A.
Published: December 2004

The crystal structure of L‐lysyl‐L‐alanyl‐L‐alanine hydrochloride has been determined by x‐ray diffraction. The peptide is in zwitterionic form with the carboxylic group deprotonated, and with positive charges both in the amino terminal and ϵ‐amino groups of lysine. Crystals are monoclinic, space group P21 and Z = 4, with two peptide molecules in the asymmetric unit, which show different conformations. While one molecule has torsional angles for the Lys‐Ala peptide bond (φ2, φ2) in the β‐pleated sheet region, the values for the other molecule are close to those for the α‐helix. This molecular flexibility is of interest for the study of H1 histone, which contains this sequence repeated several times. The two lysine residues show fully extended side chains. Two methanol molecules and two acetonitrile molecules are also present in the unit cell. An extensive network of hydrogen bonds and ionic interactions stabilize the crystal structure.
Secondary structure of the human growth hormone releasing factor (GRF 1–29) by two‐dimensional 1H‐nmr spectroscopy
Authors: Theriault Y. , Boulanger Y. , Saunders J. K.
Published: December 2004

The secondary structure of the human growth hormone releasing factor (GRF 1‐29) in a solution mixture of 60% aqueous phosphate buffer:40% 2,2,2‐trifluoroethanol‐d3 has been investigated by two‐dimensional 1H‐nmr spectroscopy. Sequential resonance assignments and elements of secondary structure were obtained from phase‐sensitive correlation spectroscopy, relayed coherence spectroscopy, and nuclear Overhauser spectroscopy experiments. The observation of a large number of α‐amide and amide‐amide interresidual nuclear Overhauser effect connectivities as well as the existence of 11 slowly exchanging amide protons indicates that the peptide adopts a well‐defined secondary structure most likely constituted of a single long helix. This conclusion is consistent with the CD measurements.