bluuebunny/crossref_metadata_2025 huggingface dataset:
Accessible conformations of melanin‐concentrating hormone: A molecular dynamics approach
Authors: Paul P. K. C. , Dauber‐Osguthorpe P. , Campbell M. M. , Brown D. W. , Kinsman R. G. , Moss C. , Osguthorpe D. J.
Published: December 2004

Molecular dynamics simulations have been used to search for the accessible conformations of the melanin‐concentrationg hormone (MCH). The studies have been performed on native MCH and two of its peptide fragments, a cyclic MCH(5–14) fragment and a linear MCH(5–14) fragment. An analysis of the molecular dynamics trajectories of the three peptides indicates that two regions of the peptide have characteristic conformational properties that may be important for the biological activity. One is a region around Gly8, which is conformationally mobile, and the other is around Pro13, which shows unusual rigidity. The molecular dynamics simulation results are discussed in terms of backbone structural features like β turns, side‐chain interactions, and orientations of the disulfide bridge. The results of this analysis are used to suggest new analogues that will modify the conformational features of the peptide and further define the conformational requirements for activity. Finally, the results are related to nmr studies of the peptide and reveal agreements between the experimental nuclear Overhauser effect constraints and some of the accessible conformations obtained from the simulation.
Pressure‐induced reversible changes in secondary structure of poly(L‐lysine): An ir spectroscopic study
Authors: Carrier Danielle , Mantsch Henry H. , Wong Patrick T. T.
Published: December 2004

The effect of elevated hydrostatic pressure on the secondary structure of poly(L‐lysine) was studied using Fourier transform ir spectroscopy. According to changes observed in the amide I band, both the β‐sheet and the unordered polypeptide undergo a reversible, pressure‐induced conformational change to α‐helix. The conversion occurs at a much higher pressure from the unordered conformer (∼ 9 kbar) than from the β‐sheets (∼ 2 kbar). The structural changes were found to be slower at pH > 11, especially at the highest concentration investigated (10 wt%), reflecting the fact that extensive hydrogen‐bond networks have to reorganize. This study shows that alterations of polypeptidic conformations induced by elevated hydrostatic pressure are reversible, but that an apparent irreversibility can result from kinetic factors in the case of conformational changes involving extensive rearrangements. The present results also show that the strength of the hydrogen bonds between the backbone amide groups is not the only factor that determines the closest packing of the polypeptide molecules.
Reexamination of the polymerization of pyridoxylated hemoglobin with glutaraldehyde
Authors: Marini M. A. , Moore G. L. , Christensen S. M. , Fishman R. M. , Jessee R. G. , Medina F. , Snell S. M. , Zegna A. I.
Published: December 2004

Pyridoxylated adult human hemoglobin (HbAo) was prepared using a one molar equivalent of pyridoxal 5‐phosphate (PLP) per heme and reduced with either NaCNBH3 or NaBH4. A separate sample was pyridoxylated and passed through a mixed‐bed ion exchange column without reduction. All three preparations had a P50 of 29 ± 2 torr and a cooperativity of n = 2.4 ± 0.1. These preparations, in both the oxy and deoxy forms, were then treated with 7 equivalents of glutaraldehyde per tetramer at pH 6.8 at 4°C and at room temperature. The polymerization invariably reduced the P50 to 18 ± 2 torr with Hill coefficients of less than 2. These solutions, with or without further reduction using NaCNBH3, all retained the PLP in differing amounts (2–3 moles/tetramer). Methemoglobin concentrations were increased during the polymerization reaction. The normal pyridoxylation procedure, using sodium borohydride reduction, resulted in a number of different molecular species. Polymerization with glutaraldehyde caused a further proliferation of molecular species that could not be separated by anion exchange chromatography or by isoelectric focusing. The extent of polymerization, estimated by gel exclusion chromatography and SDS polyacrylamide gel electrophoresis, was from 40 to 50%. Analysis of the reverse phase chromatograms, which separate the heme and the α‐ and β‐chains, showed extensive polymerization and distribution of the radioactively labeled PLP on the protein for all preparations. All of the polymerized and pyridoxylated samples were unstable, and showed different chromatographic patterns after storage at 4°C for 1 month. Attempts to stabilize these preparations by further reduction with NaCNBH3 gave products with a lower P50 and lower cooperativity. When the reactions were conducted with a purified HbAo, heterogeneity was somewhat decreased compared to the normally used stroma‐free hemoglobin, but a large number of molecular species were still formed.
Computer simulation of hydrodynamic properties of semiflexible macromolecules: Randomly broken chains, wormlike chains, and analysis of properties of DNA
Authors: Molina J. J. García , Martínez M. C. López , De La Torre J. García
Published: December 2004

The translational and rotational diffusion coefficients and the intrinsic viscosity of semiflexible, randomly broken, and wormilike chains have been obtained by Monte Carlo simulation in the context of the rigid‐body treatment. Both approximate and rigorous rigid‐body hydrodynamics are used, so that the error introduced by the approximate methods can be evaluated. A randomly broken chain and a wormilike chain having the same contour length and persistence length have the same radius of gyration but different values for any of the hydrodynamic properties. The two types of chains are compared in this regard. Considering that the cross section of the chain is represented by a cylinder better than by a string of spheres, we devise a cylindrical correction to be applied to the results simulated for chains of beads. Application is made to the analysis of experimental data for the translational and rotational coefficients of DNA fragments with up to 103 base pairs, obtaining the persistence length for each model. The values for the wormlike chain agree well with model‐independent values obtained from radii of gyration and with other literature data at varying ionic strength. The randomly broken chain is equally able to reproduce the experimental length dependence of the properties, but the resulting persistence length may be too high.
Disaccharide conformational flexibility. I. An adiabatic potential energy map for sucrose
Authors: Tran V. H. , Brady J. W.
Published: December 2004

Constrained conformational energy minimizations have been used to calculate an adiabatic (ϕ, ψ) potential energy surface for the disaccharide sucrose. The inclusion of molecular flexibility in the conformational energy analysis of this disaccharide was found to have a significant effect upon the allowed conformational space of the molecule. Three low‐energy regions were identified on the adiabatic energy surface, and two of these regions were found to contain two related local minimum‐energy conformations, with similar energies, differing only in the directionality of the intra–residue hydrogen bonds of the glucose portion of the molecule. The known crystal structures of seven molecules containing the sucrose moiety all fall within the region of the primary allowed minimum and are consistent with the relaxed energy map, while these crystal conformations could not be rationalized using energy maps for rigid residue geometries. The greater flexibility of the furanoid ring relative to that of the pyranoid ring contributed significantly to the enlargement of the low‐energy region on the adiabatic map. However, in spite of the importance of limited flexibility in understanding the conformation and fluctuations of sucrose, this molecule was found to be considerably more rigid that some other disaccharides, such as maltose and cellobiose, in accord with experimental studies.
Structure of benzyloxycarbonyl‐L‐alanyl‐α‐aminoisobutyl‐α‐aminoisobutylic acid
Authors: Taga Tooru , Itoh Masato , Machida Katsunosuke , Fujita Tetsuro , Ichihara Terumi
Published: December 2004

The x‐ray diffraction study of the C‐terminally unprotected tripeptide benzyloxycarbonyl‐L‐alanyl‐α‐aminoisobutyl‐α‐aminoisobutylic acid (Z‐L‐Ala‐Aib‐Aib‐OH) has shown that the molecule adopts a consecutive type III β‐turn, which characterizes a right‐handed 310 helix. A very weak 4 → 1 intramolecular hydrogen bond with the long NO distance of 3.32 Å, and a unique “oxy analogue” of the 4 → 1 hydrogen bond with the OO distance of 2.77 Å, were observed. The stability of the observed conformation with the asymmetric Aib residues was theoretically evaluated by a conformation‐energy calculation. The stereochemical characteristics of Aib and Ala residues were made clear by a comparison of the conformations of the short peptides containing both Aib and Ala residues.
Analysis of parameter resolution from derivatives of binding isotherms
Authors: Doyle Michael L. , Simmons Joe H. , Gill Stanley J.
Published: December 2004

Examination of binding information in the form of derivative (or finite difference) measurements is explored (1) experimentally by a thin‐layer optical procedure (Dolman, D. & Gill, S. J. (1978) Anal. Biochem. 87, 127–134) and (2) theoretically by simulation in order to determine the influence of the number of data points and their standard error upon the resolvability of binding parameters in cooperative and non‐cooperative systems. The data is described by the difference in optical absorbance divided by the change in the logarithm of the ligand activity and each data point is assumed to be influenced by a random error with a given variance. It is found that increasing the number of data points, which in turn effectively reduces the magnitude of the observed absorbance changes, results in an increase in the uncertainty of the resolved parameters of the system. The effect is verified by both experimental and simulation studies. Thus one is led to suggest that fewer measurements for the change of absorbance with larger magnitudes produces the most favorable situation for parameter resolution when the data is in the form of finite difference measurements.
Excimer fluorescence of (+)‐anti‐benzo (a)pyrene diol epoxide covalently bound to poly (dG‐dC): Structural implications
Authors: Eriksson Magdalena , Eriksson Svante , Nordén Bengt , Jernström Bengt , Gräslund Astrid
Published: December 2004

Fluorescence of (+)‐anti‐benzo (a) pyrene diol epoxide [(+)‐anti‐BPDE] covalently bound to poly (dG‐dC) has been studied with steady‐state and time‐resolved techniques. Extensive formation of excimers is found, even at small (0.008) BPDE/nucleotide ratios. This indicates favored covalent binding to bases close to already modified guanines. Both fluorescence excitation spectra and lifetime measurements reveal two populations of (+)‐anti‐BPDE adducts: one that can form excimers and one that cannot. Three excimer lifetimes (4.5, 29, and 83 ns) are observed. Differently shifted monomer and excimer excitation spectra are discussed in terms of pyrene‐pyrene exciton interactions, consistent with a distance shorter than 7 Å between the excimer‐forming BPDE chromophores.
Conformational studies of nikkomycin X in aqueous solution
Authors: Krainer Eduardo , Naider Fred , Becker Jeffrey M.
Published: December 2004

Nikkomycin X is a peptidyl‐nucleoside antibiotic that inhibits chitin synthesis in fungi. Information on its conformation in aqueous solution was obtained from pH titration studies in which the nmr shifts of exchangeable and nonexchangeable protons were monitored. These studies and nuclear Overhauser effects support an unfolded or conformationally flexible structure for the antibiotic, and the syn and anti conformations of the nucleoside moiety were found to coexist. The conformation of the ribose ring was determined using a two‐state model; a slight shift from type N to type S conformers occurred as the pH was raised from 1 to 6.
The sampling properties of some distance geometry algorithms applied to unconstrained polypeptide chains: A study of 1830 independently computed conformations
Authors: Havel Timothy F.
Published: December 2004

In this paper we study the statistical geometry of ensembles of poly(L‐alanine) conformations computed by several different distance geometry algorithms. Since basic theory only permits us to predict the statistical properties of such ensembles a priori when the distance constraints have a very simple form, the only constraints used for these calculations are those necessary to obtain reasonable bond lengths and angles, together with a lack of short‐ and long‐range atomic overlaps. The geometric properties studied include the squared end‐to‐end distance and radius of gyration of the computed conformations, in addition to the usual rms coordinate and ϕ / ψ angle deviations among these conformations. The distance geometry algorithms evaluated include several variations of the well‐known embed algorithm, together with optimizations of the torsion angles using the ellipsoid and variable target function algorithms.

The conclusions may be summarized as follows: First, the distribution with which the trail distances are chosen in most implementations of the embed algorithm is not appropriate when no long‐range upper bounds on the distances are present, because it leads to unjustifiable expanded conformations. Second, chosing the trail distances independently of one another leads to a lack of variation in the degree of expansion, which in turn produces a relatively low rms square coordinate difference among the members of the ensemble. Third, when short‐range steric constraints are present, torsion angle optimizations that start from conformations obtained by choosing their ϕ / ψ angles randomly with a uniform distribution between − 180° and + 180° do not converge to conformations whose angles are uniformly distributed over the sterically allowed regions of the ϕ / ψ plane.

Finally, in an appendix we show how the sampling obtained with the embed algorithm can be substantially improved upon by the proper application of existing methodology.
Analysis of fructofuranose conformations by molecular mechanics
Authors: French Alfred D. , Tran Vinh
Published: December 2004

Energies for various envelope and twist conformers of α‐ and β‐D‐fructofuranose (FF) have been calculated with MMP2 (85). Values of low energy are found near T conformations, and, secondarily, to ranges near T shapes. α‐D‐FF has a path through the 0E form for transitions between forms, as found by other workers for β‐D‐ribose, while the slightly preferred transition for β‐D‐FF is through the 0E conformer. The majority of conformations of β‐D‐FF that have been determined by single‐crystal diffraction studies are in a fairly deep well, with energy values less than 0.5 kcal / mol above the minimum.
Depsipeptide analogues of elastin repeating sequences: Synthesis
Authors: Arad O. , Goodman M.
Published: December 2004

Depsipeptide analogues of peptide sequences can help in elucidating the role of specific hydrogen bonds in determining the conformation in peptides. The repeating pentapeptide and hexapeptide sequences of elastin have been suggested to contain a type II β‐turn with a 4 → 1 hydrogen bond. Depsipeptide analogues of the repeating sequences of elastin in which this 4 → 1 hydrogen bond cannot exist were synthesized. A fragment condensation approach was employed in which the depsipeptide ester bond was introduced early in the synthesis. This approach proved to be effective, although the increased lability of the depsipeptide ester bond resulted in side products and low yields in some reactions.
Analysis of side‐chain conformational distributions in neutrophil peptide‐5 nmr structures
Authors: Kominos Dorothea , Bassolino Donna A. , Levy Ronald M. , Pardi Arthur
Published: December 2004

The side‐chain conformations have been analyzed in the antimicrobial peptide, Neutrophil Peptide‐5(NP‐5), whose structure was independently generated from nmr‐derived distance constraints using a distance geometry algorithm. The side‐chain and peptide dihedral angle distributions in the nmr structures were compared with those constructed from a data base of high‐resolution protein crystal structures. The side‐chain conformational preferences for NP‐5 in solution are significantly different from those observed in the crystal structure data base. These results indicate that the side‐chain conformations are quite disordered for many of the residues of NP‐5. The absence of a correlation between the width of the conformational distribution and surface accessibility suggests that the disorder may be due to limitations in the structural information extracted from the nmr data rather than to molecular motion. However, it is also observed that the degree of conformational disorder is only weakly correlated with the number of nuclear Overhauser enhancements to a given side chain. Possible reasons for this are discussed. Molecular mechanics refinement of these structures did not significantly change the side‐chain populations. Anomolously wide distributions are observed for rotations about the peptide bonds and the disulfide bonds in the NP‐5 distance geometry structures, which are improved by the refinement. The very high degree of order observed for the central dihedral angle of the disulfide bond in the high‐resolution crystal data base suggests that the rotation about this bond in proteins is determined by the local potential.
Cyclic β‐alanyl‐β‐alanine containing peptides: A new molecular tool for β‐turned peptides
Authors: Pavone V. , Lombardi A. , Yang X. , Redone C. , Di Blasio B.
Published: December 2004

In the present paper we describe the synthesis, purification, and single‐crystal x‐ray analysis of the cyclic tetrapeptide cyclo‐(L‐Pro‐L‐Phe‐β‐Ala‐β‐Ala). This compound contains the β‐alanyl‐β‐alanine dipeptide as putative cyclization arm to force the remaining dipeptide‐L‐Pro‐L‐Phe‐ in a β‐turned conformation. Thepeptide was synthesized by classical methods and cyclization of the free linear tetrapeptide was accomplished in reasonable yields in diluted methylene chloride solution. The compound crystallizes in space group P21 from hot water with two independent tetrapeptide molecules and seven solvent molecules in the unit cell. This compound shows in the solid state an intramolecular hydrogen bond between the CO group of the β‐Ala4 and the NH group of the β‐Ala3 residues stabilizing a type I β‐turn conformation in which Pro1 and Phe2 occupy the relative position 2 and 3 of the turn, respectively. A rather complex network of 18 hydrogen bonds involving all the remaining CO and NH groups and the water molecules is present in the crystal.
Stereochemical behavior of acyclic peptide‐cation complexes
Authors: Grimaldi Maria , Rossi Filomena , Saviano Michele , Benedetti Ettore , Pavone Vincenzo , Pedone Carlo
Published: December 2004

The role of the β‐turns in the peptide interaction with several cations was investigated. In this work we report the solution studies of four linear peptides: Z‐Aib‐Aib‐Aib‐L‐Val‐OMe, Boc‐D‐alle‐L‐Ile‐D‐alle‐L‐Ile‐OMe, Boc‐L‐Leu‐L‐Leu‐L‐Leu‐L‐Leu‐OMe, and Boc‐L‐Phe‐B‐Phe‐L‐Phe‐D‐Phe‐OMe.

CD and 1H‐nmr spectra reveal the presence of multiple ion‐bounding equilibria. The stoichiometry and binding constant of the four peptide in the presence of Ca2+ ions in acetonitrile solution has been determined.

Variable‐temperature nmr spectra in the absence and in thepresence of a large excess of cation have shown that the complexation process is not critically dependent on the conformation of the peptide.
Theory of acoustic mode vibrations of DNA fibers
Authors: Sokoloff J. B.
Published: December 2004

A previous model for acoustic mode vibrations of a DNA molecule in water is extended to the case of an array of many DNA molecules, as occurs in the fibers studied in most experimental work on DNA. The acoustic modes of this system are found to consist of coupled modes of water sound vibrations and DNA acoustic modes. This model is used to study the electrostatic coupling of acoustic vibrations to the relaxational modes of the orientational degrees of freedom of the water molecules. It is found that the long‐range or macroscopic electric field generated by the acoustic mode vibrations of the water‐DNA system gives too small a damping and frequency shift of the acoustic modes to account for the observations on DNA fibers. Therefore, the observed damping and frequency shifts are most likely due to either friction between the surrounding water and the vibrating DNA, or coupling to the water orientation degrees of freedom resulting from the short range (i.e., screened) Coulomb interaction. The latter explanation (which is most likely the correct one) implies that the relaxation time of the hydration shell water is longer than the observed relaxation time by a factor of the static dielectric constant of the hydration water.
Thermodynamics of polymolecular duplexes between phosphate‐methylated DNA and natural DNA
Authors: Moody Maurice R. , van Genderen Marcel H. P. , Buck Henk M.
Published: December 2004

Phosphate‐methylated (P.M.) DNA possesses a very high affinity for complementary natural DNA, as a result of the absence of interstrand electrostatic repulsions. In this study, a model system phosphate‐methylated d[Cn] with natural d(Gk) (n < k)is chosen for an investigation of the thermodynamic properties that determine duplex stability. The enthalpy change of a melting transition is shown to be considerably larger than is observed for corresponding natural DNA duplexes. It is found that ΔH of GG/CC nearest neighbor pairwise interaction equals −15.6 kcal/mol, compared to −11.0 kcal/mol for the natural analog. The entropy change is strongly dependent on the length of the natural DNA strand and the number of phosphate‐methylated DNA oligomers hybridized. The results are explained by means of a model in which a cooperative effect for subsequent hybridizations of phosphate‐methylated DNA oligomers is assumed, thus giving additional stability.
Condensation of DNA by trivalent cations. 1. Effects of DNA length and topology on the size and shape of condensed particles
Authors: Arscott Patricia G. , Li An‐Zhi , Bloomfield Victor A.
Published: December 2004

In vitro condensation of DNA by multivalent cations can provide useful insights into the physical factors governing folding and packaging of DNA in vivo. We have made a detailed study of hexammine cobalt (III) induced condensation of 2700 and 1350 base pair (bp) fragments of plasmid pUCl2 DNA by electron microscopy and laser light scattering. The condensed DNA takes the form of toroids and rods. Both are present in all condensates, but the proportion of toroids is higher with the larger fragments. The intact, closed circular plasmid produces smaller particles than the linear fragments. The size of a particle is independent of DNA fragment length. Two hours after adding the condensing agent, a typical toroid is about 800 Å in diameter; the outer radius (R1) is ∼ 400 Å, and the inner radius (R2) is ∼ 140 Å for both sets of fragments. These dimensions are relatively stable, but there is sufficient change in both R1 and R2 to produce approximately 50% increase in volume from 2 to 24 h. A typical rod at 2 h is about 1800 Å long and 300 A wide. The distribution of rod lengths is similar to that of mean toroid circumferences π(R1 + R2), and the distribution of rod widths is similar to that of toroidal widths (R1 − R2). The 2700‐bp fragments show a significantly higher ratio of toroids to rods than the 1350‐bp fragments. Both types of particle are multimolecular. The average number of molecules/particle, calculated from the above dimensions, assuming hexagonally packed B‐form DNA with a center‐to‐center spacing of 27 Å, is 13 ± 4 for condensates of 2700‐bp fragments and 26 ± 11 for those of 1350‐bp fragments. Monomolecular condensates of much larger DNAs have similar dimensions, suggesting that size is governed primarily by the balance of attractive and repulsive intermolecular forces rather than by the entropic factors associated with incorporation of a number of small particles into a larger one. The similar dimensions and volumes of toroids and rods indicate that the free energy cost of continual bending in toroids, minus that gained by extra net attraction in a cyclic particle, is comparable to that of abrupt bending or kinking in rods. Although the condensed particles are multimeric, their distinct toroidal or rodlike shapes distinguish them from the random aggregates that would be generally expected from the multimolecular association of large, flexible polymers.
Dielectric study on hydration of B‐, A‐, and Z‐DNA
Authors: Umehara Toshihiro , Kuwabara Shinichi , Mashimo Satoru , Yagihara Shin
Published: December 2004

Dielectric relaxation peak due to bound water was found around 100 MHz in poly(dG‐dC) · poly(dG‐dC) and calf thymus DNA in water–ethanol mixtures with NaCl buffer. Relaxation time and strength show a transition for poly(dG‐dC) · poly(dG‐dC) at anethanol composition Cw = 0.45 (w/w) where the structural transition from B‐ to Z‐DNA takes place. It has been suggested that the transition is caused by removal of the bound water molecules preferentially from the phosphate groups. If the bound water molecules are removed equally from the phosphate groups and the grooves, the structural transition from B to A takes place. By analogy with hydration of tropocollagen, it was found that 19 water molecules per one nucleotide are at least necessary to keep B‐DNA. Thirteen molecules are bound to A‐DNA and 9 molecules to Z‐DNA. Stringlike multimers are proposed as available structures of the bound water.
Raman spectroscopic study of the effects of Ca2+, Mg2+, Zn2+, and Cd2+ ions on calf thymus DNA: Binding sites and conformational changes
Authors: Langlais Marc , Tajmir‐Riahi Heidar All , Savoie Rodrigue
Published: December 2004

The interaction of Mg2+, Ca2+, Zn2, and Cd2+ with calf thymus DNA has been investigated by Raman spectroscopy. These spectra reveal that all of these ions, and particularly Zn2+, bind to phosphate groups of DNA, causing a slight structural change in the polynucleotide at very small metal: DNA(P) concentration ratio (ca. 1 : 30). This results in increased base‐stacking interactions, with negligible change of the B conformation of DNA. Contrary to Zn2+ and Cd2+, which interact extensively with the nucleic bases (particularly at the N7 position of guanine), the alkaline‐earth metal ions are bound almost exclusively to the phosphate groups. The affinity of both the Zn2+ and Cd2+ ions for G‐C base pairs is comparable, but the Cd2+ ions interact more extensively with A · T pairs than Zn2+ ions. Interstrand cross‐linking through the N3 atom of cytosine is suggested in the presence of Zn2+, but not Cd2+.
The role of extrahelical peptides in stabilization of collagen fibrils
Authors: Wallace Donald G.
Published: December 2004

A quantitative model for fibril assembly of type I collagen was extended to include the explicit effect of extrahelical peptides. The collagen molecule was simulated by rod‐like sequences to which short, rigid tails were connected by “nondimensional” flexible joints. Three collagen structures were studied: (1) intact collagen, simulated by a rod of axial ratio 200 (The axial ratio x was taken as a segment length) with two tails of length x = 1 and x = 2, respectively, appended to each end; (2) pepsin‐digested collagen, simulated by one rigid segment of length 200 and one tail of length 1; and (3) pronase‐digested collagen, by a single rigid segment of length x = 200. Phase equilibria of such structures were calculated, using a lattice theory of Matheson and Flory, and the relation of the polymer–solvent interaction parameter χ to the equilibrium solubility was determined. The χ for each collagen species was then related to temperature (T) and ionic strength (I), based on the approximation that local (per segment) stabilization of collagen fibrils was due to hydrophobic and electrostatic forces only. Solubility vs temperature curves for all three collagen species were computed and compared to published experimental data. From the χ factors for each species, the composite χ was resolved into components representing energetic contributions of the extrahelical peptides relative to the helix, which were interpreted in terms of hydrophobic or electrostatic interactions stabilizing the collagen fibril.
Opioid peptides in micellar systems: Conformational analysis by CD and by one‐dimensional and two‐dimensional 1H‐nmr spectroscopy
Authors: Zetta Lucia , Consonni Roberto , Marco Antonio De , Longhi Renato , Manera Ernesto , Vecchio Giuseppe
Published: December 2004

β‐Endorphin has been studies iin SDS micelles by one‐ and two‐dimensional nmr spectroscopy (1D and 2D nmr), and to explore the influence of peptide length and composition on the polypeptide structure, the investigation was extended to a number of fragments. The nmr results are compared with those obtained from CD experiments and discussed in terms of a secondary structure that involves the central region of β‐endorphin.
Chiroptical labeling of folded polypeptide conformations: The thioamide probe
Authors: Hollósi M. , Kollát E. , Kajtár J. , Kajtár M. , Fasman G. D.
Published: December 2004

This paper reports the chiroptical properties of thionated N‐acyl amino acid and N‐acyl dipeptide N′‐methylamide models. It was found that the optical activity of the thioamide chromophore is dominated by the chiral contribution of perturbants attached to Cα at the N‐H side of the thioamide group. The appearance of a strong negative ππ* band near 270 nm is indicative of the semiextended conformation of this residue. The ϕ ∼ −70°, ψ ⩾ 120° set of torsion angles is compatible with a type II βt‐turn or a γt‐turn conformation with the perturbing N‐H side residue in the i + 1 position of the turn. (The subscript t or tt denotes that one or both of the H‐bonded moieties is thioamide.) Earlier data show that both βt‐ and γt‐turns may be fixed by CS ⃛H‐N(CO) intramolecular H bonds. The appearance of one or two weak nπ* bands and a positive ππ* band at about 270 nm is characteristic of type II βt‐turns containing the H‐bonded thioamide group attached to the glycine residue in position i + 2. The extended conformation (ϕ ∼ −140°, ψ ∼ 140°) of a residue after the thioamide group gives rise to a negative nπ* and a positive ππ* band of comparable magnitude. Peptid1e sequences with alternating thioamide–amide–thioamide backbone tend to adopt 1t ⇆ 4t H‐bonded βtt conformations. CD studies show that type II βtt‐turns have unique chiroptical properties: the ππ* region is dominated by an exceedingly strong negative band near 260 nm (|Δε| = 19–24) accompanied by a weaker band at higher wavelength values.
The secondary structure of turkey gizzard myosin light chain kinase and the nature of its interaction with calmodulin
Authors: Garone Louise , Albaugh Sharon , Steiner Robert F.
Published: December 2004

The enzymatic activities of native myosin light chain kinases are subject to modification by interaction with Ca2+‐calmodulin (CaM). The interaction between myosin light chain kinase isolated from turkey gizzard (tgMLCK) and calmodulin isolated from bovine testes (CaMbt) and wheat germ (CaMwg) has been examined by means of the intrinsic tryptophan fluorescence of tgMLCK and the fluorescence of extrinsic fluorescent labels located at Cys‐27 and Tyr‐139 of CaMwg and Tyr‐99 of CaMbt. Static and dynamic fluorescence measurements provide evidence for the involvement of the former two sites in the zone of contact with lesser involvement of the site marked by the probe at Tyr‐99. Complex formation protected the primary cleavage site in CaMbt (Lys‐77) from proteolysis by trypsin. These results are consistent with involvement of the N‐ and C‐terminal lobes of CaM in stabilization of the complex with tgMLCK, but cannot rule out participation of the connecting strand in the interaction. CD measurements extending to 175 nm, obtained using synchrotron radiation, indicate the following secondary structure content for tgMLCK: 17 ± 2% α‐helix, 22 ± 3% antiparailel β‐sheet, 3 ± 1% parallel β‐sheet, 24 ± 2% β‐turns, and 34 ± 2% random coil. Similar measurements of the CD spectra of CaMbt and of the 1 : 1 :: CaMbt : tgMLCK complex presently indicate that neither protein undergoes major secondary structure rearrangement during their interaction, although subtle changes in the CD spectrum of tgMLCK appear to be correlated with the interaction with CaM.
A numerical counterion condensation analysis of the B‐Z transition of DNA
Authors: Fenley Marcia O. , Manning Gerald S. , Olson Wilma K.
Published: December 2004

We examine the salt dependence of the B‐Z transition in DNA by means of the counterion condensation theory adapted to structurally realistic coordinates of the phosphate groups. The ionic contribution to the free energy difference ΔG is computed for both the ZI and ZII conformations over broad ranges of NaCl and MgCl2 concentrations and polymer lengths. For the solvent we employ both a constant‐dielectric model (dielectric constant set to 78.3) and a dielectric saturation model (distance‐dependent dielectric constant). Where comparison can be made, the results for the constant‐dielectric model are similar to those obtained by other workers for the same model but with different computational methods. The existence of a low‐salt transition, and its location when it does occur, depends strongly on the DNA length and on the dielectric model. The behavior of ZI and ZII are qualitatively similar throughout the entire salt range for the constant‐dielectric model, but qualitatively different if dielectric saturation is simulated, as we think is necessary for a realistic description. The ionic ΔG, in the presence of dielectric saturation, bears comparison with the high‐salt trend of the measured total ΔG if “Z‐DNA” is predominantly ZI, but not if it is predominantly ZII.
The molecular dimensions of G‐actin in solution as studied by dynamic light scattering
Authors: Patkowski A. , Eimer W. , Seils J. , Schneider G. , Jockusch B. M. , Dorfmüller Th.
Published: December 2004

The rotational and the translational diffusion coefficients of G‐actin in solution have been obtained by polarized and depolarized dynamic light scattering, respectively. Modeling the shape of the molecule by a biaxial ellipsoid of revolution, the hydrodynamic dimensions were calculated from the Perrin equations. In completion to previous hydrodynamic measurements, a combination of both light scattering experiments provides direct information about the anisotropic form of G‐actin in solution. The result indicates that the form of G‐actin in solution is not significantly different from the overall structure in the solid state as obtained by x‐ray crystallography.
The divalent cation‐binding sites of gramicidin A transmembrane ion‐channel
Authors: Golovanov A. P. , Barsukov I. L. , Arseniev A. S. , Bystrov V. F. , Sukhanov S. V. , Barsukov L. I.
Published: December 2004

The conductance of the gramicidin A single channels in glycerolmonooleate membranes is strongly reduced in the presence of Mn2+ cations. The nmr experiments were performed for N‐terminal to N‐terminal gramicidin A dimer formed by two right‐handed single‐stranded helixes incorporated into the sodium dodecyl sulfate micelles in the presence of Mn2+ ions. Dependence of the nonselective spin–lattice relaxation rates of the gramicidin A protons on Mn2+ concentration was analyzed to determine coordinates of the divalent cation binding sites. It is inferred that Mn2+ ions are bound at the channel mouths at distances of 6.4, 8.6, and 8.8 Å (±2 Å) from the oxygen atoms of exposed carbonyl groups of D‐Leu 12, 14, and 10, respectively. The bounded Mn2+ retains its hydrate shell, the size of which (≈ 6 Å) exceeds the inner pore diameter (≈ 4 Å). That makes the gramicidin A channel impermeable for divalent cations.
Synthetic immunogens. Part IV: Conformational studies on gastrin conjugates with the human immunoglobulin G1 hinge peptide 225‐232/225′‐232′
Authors: Moroder Luis , Bali Jean‐Pierre , Kobayashi Yuji
Published: December 2004

Hybrids of the double‐chain bis‐cystinyl fragment 225‐232/225′‐232′ of human immunoglobulin G1 (IgG1) with the human little‐gastrin sequence 2‐17 were found to induce in animals a strong antigastrin humoral immune response with antibody titers comparable to those raised with conventional gastrin/carrier‐protein conjugates. The observed gastrin receptor‐like specificity of the polyclonal antibodies led to the assumption that the gastrin component of the hybrids is still capable of folding into its preferred bioactive structure and thus to express a similar conformational epitope in the dynamic process of recognition by the B‐cell receptors. CD measurements on these hybrid compounds in aqueous and aqueous organic media confirmed the free conformational space for the antigenic gastrin moiety, which is essentially randomly coiled in aqueous solution but retains its ability to fold into the gastrin‐specific ordered structure in aqueous organic media as used to mimic the water‐limited environment of peptides while interacting with target cells at receptor level. The absence of reciprocal conformational restriction in such hybrid molecules suggests that a compact, rigid heterodetic cyclic structure as the hinge peptide is well suited for the multiple attachment of antigenic sequences in view of the preparation of fully synthetic immunogens.
Conformational analysis of bacitracin A, a naturally occurring lariat
Authors: Pons Miquel , Feliz Miguel , Molins M. Antònia , Giralt Ernest
Published: December 2004

The proton nmr spectra of bacitracin A in H2O and DMSO‐d6 have been assigned and the conformational behavior of the peptide in the two solvents has been compared. Although bacitracin A shows a conformational equilibrium between at least two conformations differing in the relative position of the cyclic and linear domains of the molecule, the spectra in water can be interpreted in terms of a preferred conformation in which the linear part is folded over the cyclic moiety and a turn is present around Ile8‐DPhe9.
Fluorescence and CD studies on the conformation of the gastrin releasing peptide in solution and in the presence of model membranes
Authors: Cavatorta P. , Sartor G. , Neyroz P. , Farruggia C. , Franzoni L. , Szabo A. G. , Spisni A.
Published: December 2004

The conformation of the heptacosapeptide hormone, gastrin releasing peptide, has been studied in buffer and in the presence of lipids, using static and dynamic fluorescence and CD. The results obtained show that, in buffer, the hormone exists in a collection of flexible, random coil type conformers, characterized by a β‐turn between residues 14‐19. On the other hand, organic solvents can induce some degree of ordered secondary structure in the peptide chain.

The marked changes, observed in CD and fluorescence spectra upon addition of lysolecitin micelles and dimyristoylphosphatidylserine vesicles, clearly show that the peptide interacts with lipids, assuming a lipid specific configuration. Interestingly, no significative spectroscopic changes are produced by exposure to dimyristoylphosphatidylcholine vesicles both in the gel and liquid‐chrystalline phases, suggesting a requirement for negatively charged lipids during the process of hormone–membrane interaction.
Conformational energy minimization by simulated annealing using molecular dynamics: Some improvements to the monitoring procedure
Authors: Lelj F. , Grimaldi P. , Cristinziano P. L.
Published: December 2004

The possibility of using molecular dynamics techniques as a tool for simulated annealing is tested in the case of the molecule of biological interest N‐acetyl, N′‐methyl amides of 3(S)‐hydroxy, 4(S)‐amino 6‐methyl heptanoic acid [(3S, 4S)‐statine] and of its (3R,4S) diastereomer. The approach is able to reach global minimum in the conformational space in the case of the mentioned molecule. A description of the method is given. The use of fractional fluctuations of the internal potential energy as an indicator able to point out transition from a given minimum region to a deeper one is investigated. The results about the lowest energy conformation of (3S,4S) diastereomer are in fairly good accordance with the results obtained in the case of search within the whole Conformational hyperspace.
Conformational and binding studies on peptides related to domains I and III of calmodulin
Authors: Foffani Maria Teresa , Battistutta Roberto , Calderan Andrea , Ruzza Paolo , Borin Gianfranco , Peggion Evaristo
Published: December 2004

The conformational and ion‐binding properties of two peptide fragments of 25 amino acid residues corresponding to the helix‐loop sequences of domains I and III of calmodulin (CaM) were investigated by CD and Tb3+‐mediated fluorescence spectroscopy. Both peptides exhibit very similar ion binding properties either in water or trifluoroethanol (TFE), and do not allow the differentiation of the two domains in the native protein in terms of their binding capacity. An aggregation phenomenon was observed in TFE with increase of the α‐helical content. We suggest that the aggregation involves an interaction between the hydrophilic surfaces of amphiphilic α‐helices in a way similar to inverse micelle formation.
Toward nonpeptidal substance P mimetic analogues: Design, synthesis, and biological activity
Authors: Chorev Michael , Roubini Eli , Gilon Chaim , Selincer Zvi
Published: December 2004

1,4‐Piperazine and 4‐hydroxy proline, two small cyclic polyfunctional systems with defined stereochemistry, were introduced as “molecular scaffolds.” We define a “bioactive topology,” which is a derived putative low‐energy conformation obtained through theoretical conformational analysis of substance P. Substitution of these molecular scaffolds by pharmacophors characteristic of the bioactive topology of the C‐terminal hexapeptide of substance P resulted in active, partially nonpeptidal substance P mimetic agonists. The study discusses the concepts arid tools used to achieve this structural transformation, and points out the need to address flexibility–rigidity issues in an attempt to maintain sufficient molecular plasticity.
Pharmacology of neurokinin receptors
Authors: Regoli D. , Nantel F.
Published: December 2004

The neurokinins are a group of naturally occurring peptides with the common C‐terminal sequence Phe‐X‐Gly‐Leu‐Met · NH2. They include substance P (SP), neurokinin A (NKA), and neurokinin B (NKB). SP and NKA are coded on the same gene, the PPT‐A, while NKB is coded on a separate gene, the PPT‐B. Neurokinins are present in the central nervous system and in peripheral organs where they exert various actions. They act on three receptors–NK‐1, NK‐2, and NK‐3–characterized through pharmacological, biochemical, and histochemical studies. Selective agonists for each neurokinin receptor were developed and evaluated on isolated smooth muscle preparations containing only one neurokinin receptor type. All three neurokinin receptors were cloned and expressed in Xenopus oocytes. Relative affinities of those receptors to neurokinins are the same as in their respective smooth muscle preparation. Finally, the mechanism of action of SP on histamine release from rat peritoneal mast cell has been studied and a direct activation of G proteins by peptides with basic amino acids is proposed as a working hypothesis.
Conformational analysis of two cyclic disulfide peptides
Authors: García‐Echeverría C. , Siligardi G. , Mascagni P. , Gibbons W. , Giralt E. , Pons M.
Published: December 2004

Complete nmr and CD studies of two cyclic tetrapeptides with disulfide bonds,
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bonds have been carried out in different solvents to investigate the formation and stabilization of β‐turn structures and to determine the stereochemistry of the disulfide linkage. Both peptides have three‐dimensional structures with a type II β‐turn, as derived from quantitative nuclear Overhauser effect data. The combined use of CD and nmr indicates that the dihedral angle of the disulfide bridge is different in the two peptides, although the chirality is maintained.
Partial intercalation with DNA of peptides containing two aromatic amino acids
Authors: Robledo‐Luiggi Cynthia , Wilson W. David , Pares Elsie , Vera Marisol , Martinez Carmen S. , Santiago Daphne
Published: December 2004

The interactions with DNA of tetrapeptide amides containing lysine at the N‐terminal position and aromatic amino acids at the second and fourth positions (Ala at position three), 1–6, have been investigated by nmr, CD, and viscometric methods. Tetrapeptides with N‐terminal lysine and a single aromatic amino acid, 7–10, were investigated as controls. Significant decreases in DNA viscosity occurred on addition of 7, with the aromatic group at the second position, but not with any of the other single aromatic amino acid peptides. All of the tetrapeptides with two aromatic groups caused DNA viscosity decreases which were two to three times larger than with 7. Peptides with p‐nitrophenylalanine (p‐NO2Phe) as the aromatic group were synthesized for nmr studies because of its simpler aromatic nmr spectrum relative to Phe. Large upfield shifts of the aromatic proton signals were obtained when the amino acid in the second position was L‐p‐NO2Phe, and the fourth position contained either p‐NO2Phe or Phe. Such peptides also caused the largest DNA viscosity decreases on complex formation. Smaller upfield shifts of the aromatic signals were obtained when the amino acid in the second position was L‐Phe or a D isomer of Phe orp‐NO2Phe. With all peptides, larger upfield nmr shifts were obtained with heat‐denatured, recooled DNA than with native DNA under the same conditions. As with nmr, CD results are quite different for the peptides with L and D amino acids at the second position. All of the results can be interpreted in terms of a model in which lysine interacts stereospecifically with the backbone in a DNA double helix and the aromatic group at the second position stacks strongly with the base pairs when the amino acid is an L isomer. The aromatic group at the fourth position can also interact with the base pairs, but primarily through a sideways stacking of the aromatic group with base pairs for either L or D isomers. Because of covalent constraints on the separation distance for the two aromatic groups in the tetrapeptides. they must stack on opposite sides of the same base pair in violation of the neighbor exclusion principle observed with classical intercalators. This stacking at the same base pair no doubt accounts for the larger viscosity decreases in DNA with the peptides containing two aromatic groups relative to those with a single aromatic group. Such protein–induced conformationai changes may be very important in protein‐DNA or RNA recognition, and in opening of DNA by single‐stranded binding proteins and enzymes such as RNA polymerase.