bluuebunny/crossref_metadata_2025 huggingface dataset:
Prediction of fluorine chemical shifts in proteins
Authors: Gregory D. H. , Gerig J. T.
Published: December 2004

Molecular dynamics calculations have been used in an effort to estimate the change in fluorine nmr shielding when a fluorine nucleus enters the tertiary structure of a protein. Considerations of the possible interactions that can define the shift parameter change suggest that van der Waals interactions are the leading determinant of fluorine shifts in proteins, although aromatic ring currents, other magnetic anisotropies, and electrostatic field effects could result in shift distinctions of 1 ppm or smaller. Results of our studies of a fluorine‐containing analogue of the ribonuclease A S‐protein/S‐peptide complex indicate that static structures such as those implied by crystallographic data lead to overestimates of the magnitude of the van der Waals shielding term; molecular dynamics simulations provide indications of the effects of conformational averaging in defining this term. The treatment used predicts the correct direction of the shift change when the fluorine enters this protein environment from aqueous solution and, with an experimentally supported choice of adjustable parameters, gives agreement with the magnitude of the shift.
An antigenic determinant common to human chorionic somatomammotropin and human growth hormone revealed by limited proteolysis of immune complexes
Authors: Santucci Annalisa , Rustici Mauro , Bracci Luisa , Neri Paolo
Published: December 2004

An epitope of human chorionic somatomammotropin for one of the monoclonal antibodies raised against the whole antigen has been identified. We compared the release of peptides from limited proteolysis of the antigen in the presence and absence of the related antibody. Using enzymes of different specificity, we could determine the amino acid sequence that can be considered at least inclusive of the epitope. The monoclonal antibody selected is 100% cross‐reactive with human growth hormone, so the antigenic determinant identified is shared by the two protein hormones.
Differential behavior of the two free sulfhydryl groups of human plasma fibronectin: Effects of environmental factors
Authors: Narasimhan C. , Lai Ching San
Published: December 2004

We report here a novel approach to label specifically one of the two cryptic, free sulfhydryl groups per subunit of human plasma fibronectin with either an 15N, 2H‐maleimide spin label or a coumarinylphenyl maleimide fluorescent label. This permits the use of electron spin resonance (ESR) or fluorescence techniques to study molecular dynamics of fibronectin with the label attached to a single site per chain on the protein molecule. The method is based on our observation that upon adsorption of fibronectin to a gelatin‐coated surface, the SH1 site, located between the DNA‐binding and the cell‐binding domains, is partially exposed, while the SH2 site, located within the carboxyl‐terminal fibrin‐binding domain, remains buried and unreactive. The procedures for the preparation of the selectively labeled fibronectins are described in detail. The physicochemical properties of these single‐site labeled fibronectins, particularly as affected by high salt, heparin, surface binding, and temperature, were characterized by ESR spin‐label and steady‐state fluorescence techniques. The steady‐state fluorescence measurement indicates that both local environments of SH1 and SH2 sites are relatively hydrophobic, and that the SH2 site is more hydrophobic than the SH1 site. The ESR results show that heparin or high salt induces an increase in the domainal flexibility in both SH1 and SH2 regions, perhaps through the disruption of domain–domain interactions in the fibronectin molecule, and that the former is more effective than the latter in producing such an effect. The observed heparin effect is reversible by addition of calcium ions in the SH2 regions but not in the SH1 regions. In addition, at temperatures above 44°C, both type III homologous regions containing the free sulfhydryl groups are shown to undergo denaturation and aggregation processes. The data presented here suggest that the newly developed method for differential labeling of the free sulfhydryl groups in fibronectin should be useful for mapping the spatial arrangement of structural domains in the protein molecule using spin‐label–spin‐probe and fluorescence energy transfer techniques.
Conformational studies on bombesin antagonists: CD and NMR characterization of [Thr6, Leu13ψ(CH2NH) Met14] bombesin (6–14)
Authors: Di Bello Carlo , Scatturin Angelo , Vertuani Gianni , D'Auria Gabriella , Gargiulo Mario , Paolillo Livio , Trivellone Enrico , Gozzini Luigia , De Castiglione Roberto
Published: December 2004

The conformational flexibility of the [Thr6, Leu13ψ(CH2NH) Met14]bombesin (6‐14) nonapeptide has been studied by CD and one‐ and two‐dimensional (1D and 2D) nmr techniques. The CD and nmr parameters in different solvents and in a micellar environment (SDS) are compared with the data collected for the parent bombesin (BN) and [D–Phe12, Leu14]BN. A preliminary investigation on spantide is also reported. In particular, the results obtained from CD measurements indicate that there is a shift from random coil structures, in aqueous solutions, toward folded structures in apolar media (2,2,2‐trifluoroethanol) and in a membrane–mimetic environment (40 mM SDS) for all three peptides, namely BN, [D‐Phe12, Leu14]BN, and [Thr6, Leu13ψ(CH2NH)Met14]BN (6‐14). Spantide, which also possesses some inhibitory activity against BN but very little sequence similarity, even in water, shows an ordered conformation. Nuclear magnetic resonance parameters such as backbone NH‐αCH coupling constant values, amidic temperature coefficients, and the presence of only sequential nuclear Overhauser effects have not provided, so far, any clear evidence for a preferential ordered structure in the peptides studied, and this may be due to rapid exchange among different conformers in the nmr time scale.
A general approach for determining scalar coupling constants in polypeptides and proteins
Authors: Montelione Gaetano T. , Emerson S. Donald , Lyons Barbara A.
Published: December 2004

A general approach is described for measuring homo‐ and heteronuclear spin coupling constants in polypeptides and small proteins. This method uses selective magnetization transfer to generate cross peaks similar to exclusive correlated spectroscopy (E.COSY) and a large direct spin coupling (1J) in one dimension to “pull apart” cross‐peak components by frequencies much larger than the resonance line width. A general description of this method is presented, along with a brief discussion of spin topology and relaxation effects that must be considered in designing multidimensional nmr pulse sequences for measuring vicinal coupling constants. The principles are demonstrated in designs of several two‐dimensional nmr experiments for determining coupling constants in polypeptides and proteins. These include experiments for measuring 3J(HN‐Hα), 3J(H‐15Ni), 3J(15N‐Hβ), and 3J(Hα‐Hβ) coupling constants, which depend on the polypeptide dihedral angles ϕ, ψ and χ1. Multidimensional nmr experiments developed with this approach will allow measurements of many vicinal coupling constants in peptides, proteins, and other molecules. Coupling constants measured in these spectra can be used to determine backbone and side‐chain conformations, to obtain stereospecific resonance assignments of prochiral atoms, and to characterize conformational distributions of dihedral angles. Combined with information obtained from nuclear Overhauser effect measurements, these data will provide more precise determinations of protein solution structures by nmr spectroscopy.
Fixation of aldehydic dextrans onto human deoxyhemoglobin
Authors: Klett D. , Grandgeorge M. , Dellacherie E.
Published: December 2004

A procedure commonly used to transform native adult human hemoglobin (Hb) into a physiological oxygen carrier consists of a pyridoxylation of the protein to lower its oxygen affinity, followed by its polymerization in the presence of glutaraldehyde, with or without further reduction, to increase its circulating half‐life. This series of reactions yields derivatives presenting a great molecular heterogeneity that have to be fractionated for use in vivo. Hemoglobin derivatives with low oxygen affinity and a narrow distribution of molecular weights were obtained by linking a dextran polyaldehydic derivative to deoxyhemoglobin at pH 8. From oxygen‐binding measurements carried out in the presence of inositolhexaphosphate, a strong effector of hemoglobin, it appeared that the allosteric site of hemoglobin was blocked, probably by crosslinking bonds, which stabilizes its deoxy structure. On the other hand, when the reaction was performed in the presence of inositolhexaphosphate, the resulting conjugates exhibited an oxygen affinity identical to that of unmodified hemoglobin. After treatment with NaBH4, the polymer–hemoglobin derivatives were stable and possessed a reversible oxygen‐carrying capacity similar to that of blood. The conjugates prepared from oxyhemoglobin all possessed a lower P50 than native hemoglobin whatever the reaction conditions.
Partial molar volumes of the amino acid side‐chains of proteins in aqueous solution: Some comments on their estimation using partial molar volumes of amino acids and small peptides
Authors: Hedwig Gavin R.
Published: December 2004

The partial molar volumes of some amino acid side‐chains were determined in two recent studies [Makhatadzes, G. I., et al. (1990) Biopolymers 30, 1001, and Reading, J. F. & Hedwig, G. R. (1990) J. Chem. Soc. Faraday Trans. 86, 3117] using partial molar volume data, V, in aqueous solution at 25°C for some peptides of sequence Gly‐X‐Gly, where X is an amino acid. These side‐chain partial molar volumes are critically compared with those obtained using V data for amino acids. It is concluded that side‐chain partial molar volumes calculated using V data for the tripeptides are better estimates of side‐chain partial molar volumes in proteins than are those determined using V data for amino acids.
Crystal and molecular structure of the doubly unsaturated dehydropeptide Ac‐ΔPhe‐Ala‐ΔPhe‐NH‐Me
Authors: Ciajolo M. Rosaria , Tuzi Angela , Pratesi Claudio R. , Fissi Adriano , Pieroni Osvaldo
Published: December 2004

The dehydropeptide Ac‐ΔPhe‐L‐Ala‐ΔPhe‐NH‐Me, containing two dehydro‐phenylalanine (ΔPhe) residues, crystallizes from methanol/water in space group P212121, with a = 12.508 (2), b = 12.746(1) and c = 15.465(9).

In the crystalline state, the peptide chain assumes a right‐handed 310‐helical conformation stabilized by two intramolecular hydrogen bonds, between the N‐terminal acetyl group and the NH of ΔPhe3, and between the CO of ΔPhe1 and the NH of the C‐terminal methylamide group, respectively. The two consecutive 10‐membered rings formed by the hydrogen bonds have torsion angles quite close to the standard values for type III β‐bends. ΔPhe1 is located in the (i + 1) position of the first β‐bend, while ΔPhe2 is located in the (i + 2) position of the other β‐bend.

In the crystal, the molecules are linked head to tail by intermolecular hydrogen bonds to form long helical chains. The axes of the helices are parallel to the c axis, but neighboring helices run in antiparallel directions. This crystal packing is similar to the packing motifs frequently observed in Aib‐containing peptides.
Studies of DNA dumbbells. III. Theoretical analysis of optical melting curves of dumbbells with a 16 base‐pair duplex stem and Tn end loops (n = 2, 3, 4, 6, 8, 10, 14)
Authors: Paner Teodoro M. , Amaratunga Mohan , Benight Albert S.
Published: December 2004

Optical melting curves of seven DNA dumbbells with the 16 base‐pair duplex sequence 5′G‐C‐A‐T‐A‐G‐A‐T‐G‐A‐G‐A‐A‐T‐G‐C3′ linked on both ends by Tn (n = 2, 3, 4, 6, 8, 10, and 14) loops measured in 30, 70, and 120 mM Na+ are analyzed in terms of the numerically exact statistical thermodynamic model of DNA melting. The construction and characterization of these molecules were described in the previous paper (Amaratunga et al., 1992). As was recently reported for hairpins (T. M. Paner, M. Amaratunga, M. J. Doktycz, and A. S. Benight, 1990, Biopolymers, Vol. 29, pp. 1715‐1734) theoretically calculated melting curves were fitted to experimental curves by simultaneously adjusting the parameters representing loop and circle formation to optimize the fits. The systematically determined empirical parameters provide evaluations of the free energies of hairpin loop formation ΔGloop(n) and single‐strand circles ΔGcircle(N), as a function of end loop size, n = 2–14, and circle size, N = 32 + 2n. The dependence of these quantities on solvent ionic strength over the range from 30 to 120 mM Na+ was evaluated. An approximately analytical expression for the partition function Q(T) of the dumbbells was formulated that allowed a means for determining the transition enthalpy ΔH° and entropy ΔS° for every dumbbell, revealing the dependence of these quantities on loop size. In this multistate approach a manifold of partially melted intermediate microstates are considered and therefore no assumptions regarding the nature of the melting transitions (that they are two‐state) are required. The transition thermodynamic parameters were also determined from a van't Hoff analysis of the melting curves. Comparisons between the results of the multistate analysis and the two‐state van't Hoff analysis revealed significant differences for the dumbbells with larger end loops, indicating that the melting transitions of the larger looped dumbbells deviate considerably from two‐state behavior. Results are then compared with published melting studies of much larger DNA dumbbells (D. B. Naritsin and Y. L. Lyubchenko, 1990, Journal of Biomolecular Structure and Dynamics, Vol. 8, pp. 1–13), of small hairpins (Paner et al., 1990; M. J. Doktycz, T. M. Paner, M. Amaratunga and A. S. Benight, 1990, Biopolymers, Vol. 30, pp. 829–845) and another dumbbell (A. S. Benight, J. M. Schurr, P. F. Flynn, B. R. Reid, and D. E. Wemmer, 1988) Journal of Molecular Biology, Vol. 200, (pp. 377–399). ΔGloop (n = 4) and ΔGcircle (40) were also evaluated from analysis of the melting curves of the 15 DNA dumbbells with 16 base‐pair stems presented in the first paper (Doktycz et al., 1992). With the exception of the dumbbell with the central sequence 5′‐T‐T‐A‐A‐3′, these quantities were found to be virtually independent of the sequence identity of the central 4 base pairs of the stem.
Vibrational studies of the disulfide group in proteins. VI. General correlations of SS and CS stretch frequencies with disulfide bridge geometry
Authors: Qian Weili , Krimm Samuel
Published: December 2004

Normal mode calculations have been done on a range of disulfide bridge conformations in order to determine how the SS stretch and CS stretch frequencies depend on structure. In addition to varying the CαCβSS and NCαCβS dihedral angles, we have varied the ϕ,Ψ of the adjoining peptide groups since we have shown that these also influence the above frequencies. In order to obtain structural information from the observed frequencies, we have done a study of the conformational states found in 92 disulfide bridges in 25 known protein structures. This permits making a statistically based correlation between CS stretch frequencies and the possible contributing conformers. © 1992 John Wiley & Sons, Inc.
Conformation of diastereomeric peptide sequences: Structural analysis of Z‐D‐Val‐Ac6c‐Gly‐L‐Phe‐OMe
Authors: Di Blasio B. , Lombardi A. , Nastri F. , Saviano M. , Pedone C. , Yamada T. , Nakao M. , Kuwata S. , Pavone V.
Published: December 2004

We have recently undertaken a systematic structural analysis of fully protected tetrapeptides containing at the N‐ and C‐terminus either homo‐ or heterochiral amino acids, spaced by an achiral dipeptide segment. The interest for this class of peptides derives from the observation that, on reverse‐phase (HPLC), the homo‐ and heterochiral sequences have a markedly different retention times. The diastereomeric sequences, namely Z‐(L/D)‐Val‐X‐Y‐L‐Phe‐OMe (X = Sar, Gly, Ac3c, Aib, Ac5c, Ac6c, Deg, Dpg, Dbu, Dip, Dph; Y = Sar, Gly, Ac3c, Aib, Ac6c, Ac6c) show different overall hydrophobicity attributed to a different three‐dimensional structure that also depends on the X‐Y segment. Therefore, following preliminary studies in solution, we report here the detailed x‐ray analysis of the tetrapeptide Z‐D‐Val‐Ac6c‐Gly‐L‐Phe‐OMe in order to understand the structural features governing the overall hydrophobicity of linear fully protected tetrapeptides. © 1992 John Wiley & Sons, Inc.
Determination of the aromatic lignin content in oak wood by quantitative solid state 13C‐NMR
Authors: Love G. D. , Snape C. E. , Jarvis M. C.
Published: December 2004

The problems concerning quantification with cross polarization (CP) and high‐field 13C‐nmr measurements has meant that, for ligno‐cellulosic plant materials, aromatic carbons in lignins are often discriminated against. In this study, the aromatic lignin content of an American red oak sample has been determined at the relatively low field strength of 25 MHz to obviate problems with spinning side bands using both CP and Bloch decay or single pulse excitation (SPE), a more time‐consuming acquisition technique but that is, in many cases, considerably more quantitative than CP. The value of 14 mole % carbon from SPE is in close agreement with that of 15% derived from elemental analysis and the Klason lignin content. Although virtually all of the carbon was observed by both SPE and CP, the latter significantly underestimated the aromatic content at contact times less than 1.5 ms and thus longer times should be used for reliable quantification. The quaternary carbon content was estimated as 11 mole % carbon by combining dipolar dephasing with SPE and CP. © 1992 John Wiley & Sons, Inc.
Design of peptides: Synthesis, crystal structure, molecular conformation, and conformational calculations of N‐Boc‐L‐Phe‐Dehydro‐Ala‐OCH3
Authors: Padmanabhan B. , Dey S. , Khandelwal B. , Rao G. Subba , Singh T. P.
Published: December 2004

It is noteworthy that the dehydro‐Ala residue adopts an extended conformation that is different than those observed in dehydro‐Phe, dehydro‐Leu, and dehydro‐Abu. The peptide N‐Boc‐L ‐Phe‐dehydro‐Ala‐OCH3 (C18H24N2O5) was synthesized by the usual workup procedure and finally by converting N‐Boc‐L‐Phe‐L‐Ser‐OCH3 to N‐Boc‐L‐Phe‐dehydro‐Ala‐OCH3. It was crystallized from its solution in a methanol–water mixture at room temperature. The crystals belong to the monoclinic space group P21 with a = 9.577(1) Å, b = 5.195 (3) Å, c = 19.563 (3) Å, β = 94.67 (5)°, V = 970.1(6) Å3, Z = 2, dm = 1.201(5) Mg m−3, dc = 1.197 (5) Mg m−3. The structure was determined using direct method procedures. It was refined by a full‐matrix least‐squares procedure to an R value of 0.048 for 1370 observed reflections. The C‐C distance is 1.327 (8) Å, while the bond angles N2‐C‐C and C‐N2‐C are 109.8 (5)° and 127.8 (5)°, respectively. The backbone adopts a nonspecific conformation with dehydro‐Ala in a fully extended conformation with the following torsion angles: θl = 175.2 (4)°, ω, 0 = 170.2 (4)°, ø1 = 135.8 (5)°, ψ 1 = ‐22.6(6)°, ω1 = 168.5 (5)°, ψ2,= ‐170.3(5)°, ψ = –178.6(5)°', θT = 178.4(7)°. The rigid planar and trans conformation of dehydro‐Ala forces Phe to adopt a strained conformation. The Boc group has a trans‐trans conformation. The side‐chain torsion angles of the Phe residue are χ1 = 63.3(6)°, χ = −92.1(6)°, χ12,2 = 89.5 (6)°. The observed conformation is stabilized by three nonlinear intramolecular C—H‐‐‐O type of interactions. The crystal structure is stabilized by an intermolecular hydrogen bond N1—H1‐‐‐O2 of distance 2.938(7) Å along the b axis while the van der Waals forces are the stabilizing interactions in the ac plane. The low‐energy conformation found by calculations corresponds to the solid state conformation established by the crystal structure analysis. © 1992 John Wiley & Sons, Inc.
Dipeptide backbone conformation and antibody recognition of a viral octapeptide epitope
Authors: Feller David C. , Collett Marc S.
Published: December 2004

The peptide YKGTMDSG (Tyr‐Lys‐Gly‐Thr‐Met‐Asp‐Ser‐Gly) represents an important antigenic determinant from the glycoprotein G2 of the pathogenic Rift Valley fever virus. By preparing a series of single‐residue substitution peptides, the importance to antigenicity of individual residues within this octapeptide has been determined. Here, we investigated a simple and rapid computational analysis to test for correlations between the observed antigenicity of the substitution analogue peptides and the calculated conformational preferences in local regions of the peptides. Conformational energy analyses were carried out on all dipeptide combinations represented in the wild‐type octapeptide and in the singleresidue substitution analogue peptides. Conformational similarities and differences between wild‐type and substitution dipeptide pairs were determined. The results of these computational analyses were then compared with the data on the relative antigenicity of the wild‐type octapeptide and the substitution analogues. This comparison revealed a positive correlation. Substitution peptides showing changes in antigenicity possessed significant changes in the calculated backbone conformation relative to wild type in the dipeptides encompassing the residue substitution. Substitution peptides showing no change in antigenicity similarly showed no significant changes in dipeptide conformation. The potential utility of dipeptide conformational energy analyses and this preliminary structure‐activity correlation are discussed. © 1992 John Wiley & Sons, Inc.
Measurement of restricted rotational diffusion of fluorescent lipids in supported planar phospholipid monolayers using angle‐dependent polarized fluorescence photobleaching recovery
Authors: Timbs Melanie M. , Thompson Nancy L
Published: December 2004

A theory describing the shapes of polarized fluorescence photobleaching recovery (PFPR) curves for a population of fluorophores undergoing restricted rotational diffusion in two‐dimensional systems such as planar membranes has been developed. In this model, restricted rotational diffusion of the fluorophores is described by using reflective boundary conditions, in which the fluorophores are assumed to diffuse freely but only within an angular space of width 2ω. The magnitude and apparent rate of the PFPR postbleach fluorescence curves are a function of both ω and the angle between the bleaching and observation beam polarizations ψ. It is shown that estimates of the degree of rotational restriction ω may be obtained from changes in the ψ‐dependent postbleach fluorescence intensities.

Using angle‐dependent PFPR, slow rotational reorientations of the fluorescent lipid analogue 1,1′‐dioctadecyl‐3,3,3′,3′‐tetramethylindocarbocyanine in distearoylphosphatidylcholine Langmuir–Blodgett monolayers deposited on octadecyltrichlorosilane‐treated fused quartz were measured. As theoretically predicted for a rotationally restricted fluorophore population, both the initial Fψ(0) and final Fψ(∞) postbleach fluorescence intensities varied as a function of ψ, and no measurable change in the postbleach fluorescence intensities was observed for ψ = 45°. Using the theory for restricted rotational motion, the ψ‐dependent variations of the final fluorescence intensities Fψ(∞) obtained at two bleaching intensities gave an average apparent ω ≈︁ 52°. However, to adequately fit the Fψ(0) data, inclusion of the theoretical effects of rapid (faster than the duration of the photobleaching pulse) fluorophore dynamics was also required. Best fits of the Fψ(0) and Fψ(∞) data were obtained when the fluorophores were assumed to rapidly wobble within a cone of semiangle δ ≈︁ 30°–50° while slowly rotating within an angular space defined by semiangle ω ≈︁ 35°–60°. Subsequent analysis of the time‐ and ψ‐dependent changes in the postbleach fluorescence curves Fψ(t) gave apparent diffusion coefficients ranging from D ≈︁ 10−3 s−1 to 4 × 10−2 s−1. © 1993 John Wiley & Sons, Inc.
Calculation and measurement of the dipole moment of small proteins: Use of protein data base
Authors: Takashima Shiro , Asami Koji
Published: December 2004

The dipole moments of small protein molecules were determined experimentally in order to validate the calculated dipole moments by previous investigators. We found that the agreements are satisfactory for some proteins. There are, however, many proteins for which the agreement is less than satisfactory. In order to find the cause of the disagreement, the dipole moments of these proteins were recalculated using the Brookhaven Protein Data Bank. We calculated the dipole moment due to fixed surface charges and the bond moments of all the carbonyl groups in main chain and side chains. The calculation consists of the mean moments and their mean square fluctuations. In addition, we investigated the effect of electrostatic interactions between charged sites for several proteins. These results show that incorporation of the interactions does not affect substantially the calculated dipole moments. The rms fluctuation of the dipole moment is found to be small but not negligible. In conclusion, recalculated dipole moments are in good agreement with the observed values. © 1993 John Wiley & Sons, Inc.
Linear dichroism demonstrates that the bases in poly[d(AC)] · poly[d(GT)] and poly[d(AG)] · poly[d(CT)] are inclined from perpendicular to the helix axis
Authors: Kang Hunseung , Curtis W. Johnson
Published: December 2004

Flow linear dichroism is used to measure specific inclinations for each of the four bases in poly[d(AC)]·;poly[d(GT)] and poly[d(AG)]·poly[d(CT)] in both the B and A forms. For the B form in solution the bases are found to have a sizable inclination. Inclination is increased in the A form, as expected. In all cases the pyrimidines are more inclined than the purines. © 1993 John Wiley & Sons, Inc.
Permethylation alters the conformational transitions and the complexing ability of melittin: A model for methylated proteins
Authors: Ramalingam Kalaiyarasi , Bello Jake , Aimoto Saburo
Published: December 2004

Melittin exhibits a transition from random‐coil monomer to helical tetramer as a function of peptide concentration [ J. Bello, H. R. Bello, and E. Granados (1982) Biochemistry, Vol. 21, pp. 461–465]. When permethylated on each of the four amino groups (Gly‐1 Nα and Lys‐7, 21, and 23 Nε) to yield trimethylammonium groups, melittin exists as a random coil and does not show any concentration‐dependent conformational transition (up to 290 μM). Acylation of the amino groups of melittin with glycine or 5‐aminopentanoic acid followed by permethylation increases helix formation, but to a lesser extent than for the unmethylated aminoacylmelittin derivatives. The results are discussed in relation to hydrophobicity, charge repulsions, and ion binding. Melittin, and more weakly, permethylated melittin (MLT‐Me) form helical hybrids with an anionic random‐coil melittin analogue (E‐MLT), in which all the lysine and arginine residues of melittin were replaced by glutamate residues. The hybrid between MLT‐Me and E‐MLT shows a concentration‐dependent increase in helicity. E‐MLT, when succinylated at the N‐terminal glycine (E‐MLT‐suc), forms a stronger hybrid with MLT‐Me, possibly as a result of increased electrostatic interaction between equal but opposite charges in E‐MLT‐suc (net charge –6) and MLT‐Me (net charge +6). The hybrids exhibit both cold‐ and heat‐induced denaturation, similar to the phenomenon exhibited by proteins. The hybrids also exhibit significant residual structures in the temperature range of 80–100°C, which may be similar to the molten globular states that have been suggested for proteins. © 1993 John Wiley & Sons, Inc.
The structure of the left‐handed antiparallel amylose double helix: Theoretical studies
Authors: Schulz Wolfgang , Sklenar Heinz , Hinrichs Winfried , Saenger Wolfram
Published: December 2004

The atomic coordinates from the crystal structure of a hexasaccharide complex accommodating a zigzag polyiodide [ W. Hinrichs, G. Büttner, M. Steifa, Ch. Betzel, V. Zabel, B. Pfannemüller, and W. Saenger (1987) Science Vol. 238, pp. 205–208; W. Hinrichs and W. Saenger (1990) Journal of the American Chemical Society, Vol. 112, pp. 2789–2796 ] served to construct an antiparallel‐stranded amylose double helix with a 5 Å wide central cavity. Using our methodology for the energetic optimization of polymer structures in the internal/ helical variable space [ H. Sklenar, R. Lavery, and B. Pullman (1986) Journal of Biomolecular Structure Dynamics, Vol. 3, pp. 967–987, 989–1014; 1015–1031], we have calculated a theoretical counterpart of this idealized double helix by constraining the helical twist and rise to their experimental values (−45° and 2.33 Å, respectively). Applying the same constraints to the parallel‐stranded duplex, this also leads to a low‐energy structure with wide central cavity. It is considered as an alternative model to accommodate iodine as observed in the starch–iodine complex.

Release of the helical constraints leads to left‐handed antiparallel‐ and parallel‐stranded double helices, respectively, with narrow central cavities. Both structures have very similar helix parameters and correspond, in their main characteristics, to the experimentally derived parallel‐stranded structure of amylose in starch (6 residues per turn and a pitch height of about 21 Å). The intramolecular energy calculated for the optimized antiparallel‐stranded amylose double helix is comparable to that of the parallel‐stranded structure. This result raises the question why parallel‐stranded amylose seems to be favored in nature. © 1993 John Wiley & Sons, Inc.
Molecular dynamics simulations of B‐DNA: An analysis of the role of initial molecular configuration, randomly assigned velocity distribution, long integration times, and nonconstrained termini
Authors: Falsafi Sassan , Reich Norbert O.
Published: December 2004

Molecular dynamics simulations of three DNA sequences using the AMBER 3.0 force field were performed with implicit inclusion of water through a distance‐dependent dielectric constant and solvated counterions. Simulations of the self‐complementary DNA dodecamer d(CGCGAATTCGCG) were started from a regular B‐DNA structure and the x‐ray single crystal B‐DNA structure. Although mean convergence during the 89‐ps calculation was confirmed, localized differences in backbone torsionals and base‐pair helicoidals were observed. A nanosecond simulation of the nonself‐complementary 14 base‐pair DNA d(GGCGGAATTGGCGG) indicates that most structural parameters stabilize within the first 100–200 ps, while isolated features show low‐frequency oscillations throughout the calculation. The lack of harmonic constraints on the ends of the molecules was shown not to perturb the structural dynamics of the internal oligonucleotide beyond the external 2 base pairs. Comparison of three simulations of the nonself‐complementary 14 base‐pair DNA d(GGCGAAATTCGCGG), identical in all respects other than the assignment of initial Maxwellian atomic velocity distributions, revealed the inherent systematic variability. The three calculations result in nearly superimposable global structures, with localized variations in torsionals and helicoidals. Our results provide a basis for performing a comparative analysis of the effect of DNA sequence on localized structure. © 1993 John Wiley & Sons, Inc.
Heat capacities of solid poly(amino acid)s. II. The remaining polymers
Authors: Roles K. A. , Xenopoulos A. , Wunderlich Bernhard
Published: December 2004

In the first paper heat capacities Cp, of polyglycine, poly(L‐alanine), and poly (L‐valine) were analyzed using approximate group vibrations and fitting the Cp contributions of the skeletal vibrations to a two‐parameter Tarasov function. In this second paper all other poly (amino acid) s are similarly analyzed. Heat capacities were measured by differential scanning calorimetry in the temperature range of 230–390 K for poly(L‐leucine), poly(L‐serine), poly (sodium‐L‐aspartate), poly(sodium‐L‐glutamate), poly(L‐asparagine), poly(L‐phenylalanine), poly(L‐tyrosine), poly(L‐methionine), poly (L‐tryptophane), poly(L‐proline), poly(L‐lysine · HBr), poly(L‐histidine), poly(L‐histidine‐ HCl), and poly(L‐arginine · HCl). Good agreement exists between experiment and calculation. Predictions of heat capacities were made for all not‐measured poly (amino acid) s. Enthalpies, entropies, and Gibbs functions for the solid state have been derived. © 1993 John Wiley & Sons, Inc.
1H‐ and 13C‐nmr investigations on cis–trans isomerization of proline peptide bonds and conformation of aromatic side chains in H‐Trp‐(Pro)n‐Tyr‐OH peptides
Authors: Poznański J. , Ejchart A. , Wierzchowski K. L. , Ciurak M.
Published: December 2004

1H and 13C high‐resolution nmr spectra of cationic, zwitterionic, and anionic forms of the peptides: H‐Trp‐(Pro)n‐Tyr‐OH, n = 0‐5, and H‐Trp‐Pro‐OCH3 were obtained in D2O solution. Analysis of Hα(Pro1), Hα(Trp), Cγ(Pro), Hε(Tyr), and Hδ(Trp) resonances provided evidence for the presence of two predominant backbone isomers: the all‐trans one and another with the Trp‐Pro peptide bond in cis conformation; the latter constituted about 0.8 molar fraction of the total peptide (n > 1) concentration. Relative content of these isomers varied in a characteristic way with the number of Pro residues and the ionization state of the peptides. The highest content of the cis (Trp‐Pro) isomer, 0.74, was found in the anionic form of H‐Trp‐Pro‐Tyr‐OH; it decreased in the order of: anion ≫ zwitterion ≈ cation, and with the number of Pro residues to reach the value of 0.42 in the cationic form of H‐Trp‐ (Pro)5‐Tyr‐OH. Isomerization equilibria about Pro‐Pro bond(s) were found to be shifted far (⩾0.9) in favor of the trans conformation. Interpretation of the measured vicinal coupling constants Jα−β′ and Jα−β″ for CαH‐CβH2 proton systems of Trp and Tyr side chains in terms of relative populations of g+, g−, and t staggered rotamers around the χ1 dihedral angle indicated that in all the peptides studied (a) rotation of Trp indole ring in cis (Trp‐Pro) isomers is strongly restricted, and (b) rotation of Tyr phenol ring is relatively free. The most preferred χ1 rotamer of Trp (0.8‐0.9 molar fraction) was assigned as the t one on the basis of a large value of the vicinal coupling constant between the high‐field Hβ and carbonyl carbon atoms of Trp, estimated for the cis (Pro1) form of H‐Trp‐Pro‐Tyr‐OH from a 1H, 13C correlated spectroscopy 1H detected multiple quantum experiment. This indicates that cis ↔ trans equilibrium in the Trp‐Pro fragment is governed by nonbonding interactions between the pyrrolidine (Pro) and indole (Trp) rings. A molecular model of the terminal cis Trp‐Pro dipeptide fragment is proposed, based on the presented nmr data and the results of our molecular mechanics modeling of low‐energy conformers of the peptides, reported elsewhere. © 1993 John Wiley & Sons, Inc.
A method for studying the structure of uniaxially aligned biopolymers using solid state 15N‐nmr: Application to Bombyx mori silk fibroin fibers
Authors: Nicholson Linda K. , Asakura Tetsuo , Demura Makoto , Cross Timothy A.
Published: December 2004

Recent advances in the application of solid state nmr spectroscopy to uniformly aligned biopolymers have opened a window through which to view the detailed structure of biological macromolecules that are unable to be seen with standard techniques for structure determination such as x‐ray diffraction. Atomic resolution structural details are obtained from solid state nmr data in the form of bond orientations, which yield the relative positions of specific atoms within the molecule. For static aligned systems such as fibers, in which rapid reorientation about the axis of alignment does not occur, it has generally been necessary to perform trial and error line‐shape simulations to extract structural details from nmr spectra arising from a single type of nuclear spin interaction. In the present work, a new method is developed in which solid state 15N‐nmr spectra obtained from uniaxially aligned molecules placed with the axis of alignment both parallel and perpendicular to the magnetic field are analyzed to yield the orientations of specific molecular bonds. Analytical expressions are derived that utilize spectral features read from 15N chemical shift anisotropy line shapes to calculate a discrete number of possible orientations for a specific site. The 15N‐1H dipolar interaction is employed to further narrow the number of unique orientations possible for a given site. With this method, a neighborhood of possible orientations is quickly determined, and full line‐shape simulations within this region of allowed space can be performed to refine the limits of orientation. This technique demonstrates the use of a single type of isotopic label to determine the orientation of a specific molecular group such as a peptide plane within a protein. Results from the application of this method to the Bombyx mori silk fibroin protein provide structural detail that is consistent with currently accepted structural models based on fiber diffraction studies. © 1993 John Wiley & Sons, Inc.
Improved molecular dynamics simulations for the determination of peptide structures
Authors: Mierke Dale F. , Kessler Horst
Published: December 2004

In this article a few methods or modifications proven to be useful in the conformational examination of peptides and related molecules by molecular dynamics are illustrated. The first is the explicit use of organic solvents in the simulations. For many cases such solvents are appropriate since the nmr measurements (or other experimental observations) were carried out in the same solvent. Here, the use of dimethylsulfoxide and chloroform in molecular dynamics is described, with some advantages of the use of these solvents highlighted.

A constant allowing for the scaling of the nonbonded interactions of the force field, an idea previously employed in distance geometry and simulated annealing, has been implemented. The usefulness of this method is that when the nonbonded term is turned to zero, atoms can pass through each other, while the connectivity of the molecule is maintained. It will be shown that such simulations, if a sufficient driving force is present (i.e., nuclear Overhauser effects restraints), can produce the correct stereoconfiguration (i.e., chiral center) as well as configurational isomer (i.e., cis/trans isomers).

Lastly, a penalty term for coupling constants directly related to the Karplus curve has been plemented into the potential energy force field. The advantages of this method over the commonly used dihedral angle restraining are discussed. In particular, it is shown that with more than one coupling constant about a dihedral angle a great reduction of the allowed conformational space is obtained. © 1993 John Wiley & Sons, Inc.
Effect of counterion concentration on the dielectric behavior of a polypeptidic chain in the helix–coil transition
Authors: Bordi F. , Cametti C. , Paradossi G.
Published: December 2004

On the basis of the two‐state model of a polyelectrolyte solution, the ion concentration in the polymer domain has been calculated by using the spherical Poisson–Boltzmann equation. The ion accumulation in the neighboring of the polyion influences, on different time scales, various electrical properties of the solution, in particular the low‐frequency electrical conductivity and the high‐frequency dielectric dispersion. These predictions have been compared with recent dielectric measurements on poly (L‐glutamic acid) aqueous solutions during the conformational transition from the α‐helix to random coil, and a satisfactory agreement has been found. This finding suggests that counterion distribution plays a different role in determining the electrical properties of charged polymer solutions, causing a electrophoretic contribution of the polymer domain to the electrical conductivity and influencing the high‐frequency dielectric dispersion. © 1993 John Wiley & Sons, Inc.
Z → B transition in poly[d(G‐m5C)2] induced by interaction with 4′,6‐diamidino‐2‐phenylindole
Authors: Kim Seog K. , Eriksson Svante , Nordén Bengt
Published: December 2004

The Z form of poly[d(G‐m5C)2], in presence of Mg2+ ion, is found to be transformed into B form upon interaction with 4′,6‐diamidino‐2‐phenylindole (DAPI). The Z → B transformation is complete at a mixing ratio of about 0.07 DAPI per DNA base pairs, i.e., each DAPI molecule may be related to the conversion of 6–7 base pairs. An interaction between DAPI and poly[d(G‐m5C)2] in its Z form at low drug: DNA ratios is suggested from optical dichroism and time‐resolved luminescence anisotropy results. The spectroscopic behaviour of DAPI indicates that the Z conformation of DNA does not provide normal binding sites for DAPI, such as groove or intercalation sites, but that the initial association may be of external nature. © 1993 John Wiley & Sons, Inc.
Depolarization of Raman scattering from some nucleotides of RNA and DNA
Authors: Ueda Toyotoshi , Ushizawa Koichi , Tsuboi Masamichi
Published: December 2004

Depolarization ratios of Raman bands, excited at 488.0 nm, of guanosine‐5′‐monophosphoric 4 acid, cytidine‐5′‐monophosphoric acid, adenosine‐5′‐monophosphoric acid, thymidine‐5′‐monophosphoric acid, and uridine‐5′‐monophosphoric acid have been measured in their H2O and D2O solutions in the spectral region from 300 to 1800 cm−1. For comparison, the disodium salt of 2′‐deoxyadenosine‐5′‐monophosphoric acid was also subjected to the depolarization measurement in its H2O solution. The results have been correlated with possible orientations of the principal axes of the Raman scattering tensors as well as with the relative magnitudes of the tensor components. Results should be useful for future polarized Raman studies of synthetic and natural DNA. © 1993 John Wiley & Sons, Inc.
Bioactive peptides: Solid state, solution and molecular dynamics studies of a cyclolinopeptide A‐related cystinyl cyclopentapeptide
Authors: Rossi Filomena , Saviano Michele , Di Blasio Benedetto , Zanotti Giancarlo , Maione Anna Maria , Tancredi Teodorico , Pedone Carlo
Published: December 2004

The conformational analysis of
magnified image
the disulphide cyclopeptide‐related cyclolinopeptide A, has been carried out by solid state methods using x‐ray diffraction techniques, in solution by nmr, CD, ir spectroscopies, and by molecular dynamics (MD) analysis. The structure of the monoclinic form, obtained from ethanol (a = 11.303(2) Å, b = 14.467(8) Å, c = 12.355(2) Å, β(°) = 109.40(1), space group P21, Z = 2) presents two transannular H bonds with the formation of one type VIa β‐turn involving the C  O of the urethane moiety and the Phe3 NH, and an intramolecular H bond between the C  O of urethane group and the Phe4 NH.

In the solid state all the peptide bonds are in the trans configuration with the exception of a cis peptide bond occurring between the Cys1 and Pro2 residues; the linkage S—S assumes right‐handed chirality. The conformational study in solution by nmr spectroscopy indicates that the peptide is very flexible and that some conformer families are present at room temperature both in polar and apolar solvents.

CD studies confirm that this cyclic system tends to give rise to a complex mixture of quasi‐isoenergetic conformations, favored by the flexibility of the disulphide bridge and by the isomerism of the Xxx‐Pro bond.

MD studies carried out in vacuo and in solution shows that the structure determined by solid state represents a energy minimum. All hydrogen conds found in the crystalline state are correctly reproduced in vacuo and in solution simulations. © 1994 John Wiley & Sons, Inc.
The amplitude of local angular motion of purines in DNA in solution
Authors: Nuutero Sirkku , Fujimoto Bryant S. , Flynn Peter F. , Reid B. R. , Ribeiro N. S. , Schurr J. Michael
Published: December 2004

Nuclear magnetic resonance and optical experiments are combined to determine the rms amplitude of local angular motion of purines in DNA in solution. A 12 base‐pair duplex DNA with the sequence d (CGCGAATTCGCG)2 is deuterated at the H8 positions of adenine and guanine by exchange with solvent dklstwxzat 55°C. The deuterium nmr spectrum of this DNA is measured at 30 mg/mL at 30°C in an 11.76 Tesla magnet (76.75 MHz). The time‐resolved fluorescence polarization anisotropies (FPA) of this same sample and also a greatly diluted sample (0.215 mg/mL) were measured after addition of ethidium. FPA measurements of the dilute sample yield the hydrodynamic radius, RH = 9.94 ± 0.2 Å, while those at the nmr concentration are employed to characterize the collective motions in terms of either an enhanced viscosity or dimer formation. The rms amplitude of local angular motion was determined by analyzing the 2H‐nmr spectrum, in particular the line width, using recently developed theory for the transverse relaxation rate (R) together with essential information about the collective motions from these and other optical studies. When the principal‐axis frame of the electric field gradient tensor is assumed to undergo overdamped libration around each of its three body‐fixed axes in an isotropic deflection potential, then the rms amplitude of local angular motion around any single axis is found to lie in the range 10°–11°, provided the high DNA concentration acts to enhance the viscosity, and is about 9°–11°, if it acts to produce end‐to‐end dimers. The proton nmr relaxation data of Eimer et al. are reanalyzed and shown to yield an rms amplitude of angular motion of the cytosme H5–H6 internuclear vector of 9°–10°, depending upon its orientation with respect to the helix axis. In all of these analyses, full account is taken of the collective twisting and bending deformations, which have a small but significant effect on the results. It is shown that the rms amplitudes of local angular motion do not depend strongly on the model (potential), provided that isotropic rotation around the same number of axes is allowed and that one compares rms angles of the same dimensionality. The rms amplitudes of local angular motion in solution are comparable to those observed for the same sequence at low levels of hydration in the solid state. © 1994 John Wiley & Sons, Inc.
The interaction of ellipticine derivatives with nucleic acids studied by optical and 1H‐nmr spectroscopy: Effect of size of the heterocyclic ring system
Authors: Behravan G. , Leijon M. , Sehlstedt U. , Nordén B. , Vallberg H. , Bergman J. , Gräuslund A.
Published: December 2004

The DNA interaction of derivatives of ellipticine with heterocyclic ring systems with three, four, or five rings and a dimethylaminoethyl side chain was studied. Optical spectroscopy of drug complexes with calf thymus DNA, poly [(dA‐dT) · (dA‐dT)], or poly [(dG‐dC) · (dG‐dC)] showed a 10 nm bathochromic shift of the light absorption bands of the pentacyclic and tetracyclic compounds upon binding to the nucleic acids, which indicates binding by intercalation. For the tricyclic compound a smaller shift of 1–3 nm was observed upon binding to the nucleic acids.

Flow linear dichroism studies show that the geometry of all complexes is consistent with intercalation of the ring system, except for the DNA and poly [(dG‐dC) · (dG‐dC)] complexes of the tricyclic compound, where the average angle between the drug molecular plane and the DNA helix axis was found to be 65°.

One‐dimensional 1H‐nmr spectroscopy was used to study complexes between d(CGCGATCGCG)2 and the tricyclic and pentacyclic compounds. The results on the pentacyclic compound show nonselective broadening due to intermediate chemical exchange of most oligonucleotide resonances upon drug binding. The imino proton resonances are in slow chemical exchange, and new resonances with upfield shifts approaching 1 ppm appear upon drug binding, which supports intercalative binding of the pentacyclic compound. The results on the tricyclic compound show more rapid binding kinetics and very selective broadening of resonances. The data suggest that the tricyclic compound is in an equilibrium between intercalation and minor groove binding, with a preference to bind close to the AT base pairs with the side chain residing in the minor groove. © 1994 John Wiley & Sons, Inc.