bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accommodation of a D‐Phe residue into a right‐handed 310‐helix: Structure of Boc‐D‐Phe‐(Aib)4‐Gly‐L‐Leu‐(Aib)2‐Ome, an analogue of the amino terminal segment of antiamoebins and emerimicins
Authors: Karle I. L. , Flippen‐Anderson J. L , Uma K. , Balaram P. 
Published: December 2004

AbstractThe crystal structure of the nonapeptide Boc‐D‐Phe‐Aib‐Aib‐Aib‐Aib‐Gly‐Leu‐Aib‐AibOMe (I), which is an analogue of the N‐terminal sequence of antiamoebins and emerimicins, establishes a completely 310‐helical conformation with seven successive intramolecular 4 → 1 hydrogen bonds. The average, ϕ, ψ values for residues 1–8 are −59° and −32°, respectively. Crystal parameters are C47H77N9O12, space group P1, a = 10.636(4) Å, b = 11.239(4) Å, c = 12.227(6) Å, α = 101.17(4)°, β = 97.22(4)°, γ = 89.80(3)°, Z = 1, R = 5.95% for 3018 data with |F0| > 3α(F), resolution 0.93 Å. The use of the torsion angle κ = C(i − 1)N(i)Cα(i)Cβ(i), where κ = 68° for D‐Phe and κ = 164° for L‐Leu, confirms the opposite configurations of these residues. The ϕ, ψ values of −62° and −32° at D‐Phe are unusual, since this region is characteristic of residues with L configurations. Peptide I possesses only two chiral residues of opposing configuration. The observed right‐handed 310‐helical structure suggests that helix sense has probably been determined by the stereo‐chemical preferences of the Leu residue. © 1993 John Wiley & Sons, Inc.
Synthesis, conformation, and activity of HCO‐Met‐ΔZ Leu‐Phe‐Ome, an active analogue of chemotactic N‐formyltripeptides
Authors: Pagani Zecchini G. , Paradisi M. Paglialunga , Torrini I. , Lucente G. , Gavuzzo E. , Mazza F. , Pochetti G. , Paci M. , Sette M. , Di Nola A. , Veglia G. , Traniello S. , Spisani S. 
Published: December 2004

AbstractIn order to induce a β‐turn conformation into the chemotactic linear tripeptide N‐formyl‐L‐methionyl‐L‐leucyl‐L‐phenylalanine (fMLP), the new analogue N‐formyl‐L‐methionyl‐ΔZleucyl‐L‐phenylalanine methyl ester [ ΔZLeu]2f MLP‐OMe (1) has been synthesized. The conformational and biochemical consequences of this chemical modification have been determined. Analogue 1 has been synthesized by using N‐carboxy‐(Z)‐α,β‐didehydroleucine anhydride as key compound to introduce the unsaturated residue at the central position of the tripeptide 1. The x‐ray analysis shows that 1 adopts in the crystal a type II β‐turn conformation in which the new residue occupies the (i + 2) position, and an intramolecular H bond is formed between the formylic oxygen and the Phe NH. 1H‐nmr analysis based on nuclear Overhauser effect measurements suggests that the same folded conformation is preferred in CDCl3 solution; this finding is also supported by molecular dynamics simulation. The biological activity of 1 has been determined on human neutrophils (polymorphonuclear leukocytes) and compared to that shown by f MLP‐OMe. Chemotactic activity, granule enzyme release, and superoxide anion production have been determined. Analogue 1 is practically inactive as chemoattractant, highly active in the superoxide generation, and similar to the parent in the lysozyme release. The conformational restriction imposed on the backbone by the presence of the unsaturated residue is discussed in relation with the observed bioselectivity. © 1993 John Wiley & Sons, Inc.
The preparation and characterization of a twin‐tailed, lipid‐linked polysialic acid
Authors: Matthews Ian , Petrak Karel 
Published: December 2004

AbstractReactions between water‐insoluble and water‐soluble components are often slow, giving low yields. In order to prepare glycolipids composed of polysialic acid and N‐(4‐(p‐maleimidylphenyl)butyryl)dipalmitoyl‐L‐α‐phosphatidylethanol amine triethylammonium salt, we used liposomes to enhance the interfacial reaction between the reagents. Thus, thiolreactive liposomes were reacted with polysialic acid cysteamine. A 70% yield was achieved with this addition reaction, and the product was isolated by dialysis and centrifugation © 1993 John Wiley & Sons, Inc.
Looking into the grooves of DNA
Authors: Boutonnet Nathalie , Hui Xiaowen , Zakrzewska Krystyna 
Published: December 2004

AbstractThe present study is aimed at understanding the effects of DNA sequence, local conformation, and curvature on groove geometry. Energy‐optimized structures are obtained by Jumna methodology; groove geometry is analyzed by a recently developed technique that allows an accurate and continuous measurement of width and depth. The mechanics of groove deformations is also studied and analyzed in terms of helicoidal parameters. © 1993 John Wiley & Sons, Inc.
Helix promotion in polypeptides by polyols
Authors: Bello Jake 
Published: December 2004

AbstractThe helix content of [L‐Lys(Me3)]n · ClO4, and [L‐Lys(Me3)50, L‐Ala50]n · ClO4 in water is markedly increased by the presence of sucrose and glycerol. For [L‐Lys(Me3)]n · ClO4 the ellipticity at 222 nm changes from +2 × 103 deg cm2 dmole−1 in water to −44 × 103 in 50% glycerol. Sucrose does not promote helix formation in melittin at pH 7.2, but glycerol does. At pH 5.5 sucrose and, more so, glycerol, induce helix in melittin. Glycerol induces some helix in methylated melittin, but less than in melittin. The results are discussed in relation to excluded volume effects, ΔG of transfer of peptide and hydrophobic groups from water to mixed solvents, electrostatic effects, and preferential hydration. © 1993 John Wiley & Sons, Inc.
β‐Alanine containing peptides: γ‐Turns in cyclotetrapeptides
Authors: Di Blasio B. , Lombardi A. , D'Auria G. , Saviano M. , Isernia C. , Maglio O. , Paolillo L. , Pedone C. , Pavone V. 
Published: December 2004

AbstractIn the present paper we describe the synthesis, purification, single‐crystal x‐ray analysis, solution conformational characterization, and conformational energy calculations of the cyclic tetrapeptide cyclo‐ (β‐Ala‐L‐Pro‐β‐Ala‐L‐Val). The peptide was synthesized by classical solution methods and the cyclization of the free tetrapeptide was accomplished in good yields in diluted methylene chloride solution using N,N‐dicyclohexyl‐carbodiimide. The compound crystallizes in the monoclinic space group P21 from ethanol with two independent molecules in the unit cell. All peptide bonds are trans. The nmr molecular conformation in the acetonitrile solution as well as that derived from the molecular dynamic simulation in vacuo is quite different from those observed in the solid state and is very similar to that previously observed for the parent compound cyclo‐(β‐Ala‐L‐Pro‐β‐Ala‐L‐Pro). © 1993 John Wiley & Sons, Inc.
Nmr and computer‐aided studies of the three interchanging stereoisomers of the cyclic hexapeptide cyclo[‐Pro1‐Gly2‐Glu3(OBzl)‐Pro4‐Phe5‐Leu6‐]: Unexpected observation of a cis isomer of a secondary amide peptide bond in the presence of two trans proline peptide bonds
Authors: Ewen Ian Mc 
Published: December 2004

AbstractThe cyclic hexapeptide cyclo[‐Pro1‐Gly2‐Glu3(OBzl)‐Pro4‐Phe5‐Leu6‐] (1; OBzl: benzyl ester) was modeled and synthesized to be used as a chiral site for the separation of enantiomers. Total correlation spectroscopy and nuclear Ovehauser effect spectroscopy spectra of the peptide in CDCl3 showed the presence of three stereoisomers. The two dominant stereoisomers 1a and 1b exchanged chemically with each other, while the minor stereoisomer 1c exchanged exclusively with the stereoisomer 1b. Stereoisomer 1a had two cis proline peptide bonds while stereoisomer 1b had all‐trans peptide bonds. The stereoisomer 1c had, for nonstrained peptides, an unusual cis phenylalanine peptide bond while both proline peptide bonds were trans. © 1993 John Wiley & Sons, Inc.
Solid state and solution structure of Boc‐L‐Ala‐ΔPhe‐ΔPhe‐NHMe: A dehydropeptide showing propensity for 310‐helices of both screw senses
Authors: Tuzi Angela , Ciajolo M. Rosaria , Guarino Gennaro , Temussi Pier Andrea , Fissi Adriano , Pieroni Osvaldo 
Published: December 2004

AbstractThe crystal and molecular structure of the peptide Boc‐L‐Ala‐Δphe‐Δphe‐NHMe, containing two consecutive dehydro‐phenylalanine (Δphe) residues, has been solved by x‐ray diffraction. Two independent molecules, X and Y, are present in the crystallographic unit. Their conformation corresponds approximately to an incipient 310‐helix stabilized by two intramolecular hydrogen bonds. The (ϕ, ψ) torsion angles, however, have negative and positive signs in the two molecules X and Y, respectively. Therefore, in spite of the presence of an amino acid residue of the L configuration, the two helical molecules have opposite screw senses, even though the right‐handed helix is less distorted than the left‐handed one in correspondence of the L‐Ala residue.The CD spectra in various solvents exhibit exciton bands originating from dipole–dipole interaction between the Δphe side chains. Addition of DMSO to the chloroform solution produces, as a first step, a strong increasing of the CD bands, which are then progressively canceled by increasing DMSO concentration. The nmr data parallel the behavior observed in the CD spectra. In CDCl3 solution, the temperature coefficients of the NH resonances are consistent with the involvement of the last two amide protons of the sequence in intramolecular hydrogen bonds, but only negligibly small nuclear Overhauser effects (NOE) are observed. Addition of 5% DMSO‐d6 allows the observation of diagnostic NOEs. CD and nmr data indicate that the solid state structure is retained in solution, and are consistent with the presence of right‐handed and left‐handed conformers, with a prevalence of the more stable right‐handed one. © 1993 John Wiley & Sons, Inc.
DNA orientation in shear flow
Authors: Simonson Tomas , Kubista Mikael 
Published: December 2004

AbstractThe linear dichroism (LD) has been measured for DNA molecules 239–164,000 base pairs long oriented in shear flow over a large range of velocity gradients (30–3,000 s −1) and ionic strengths (2–250 mM). At very low gradients, the degree of DNA orientation increases quadratically with the applied shear as predicted by the Zimm theory [J. Zimm, (1956) Chemical Physics, Vol. 24, p. 269]. At higher gradients, the orientation of fragments ≥ 7 kilobase pairs (kbp) increases linearly with increasing shear, whereas the orientation of fragments ≥ 15 kbp shows a more complicated dependence. In general, the orientation decreases with increasing ionic strength throughout the studied ionic strength interval, owing to a decrease in the persistence length of the DNA. The effect is most dramatic at ionic strengths below 10 mM, and is more pronounced for longer DNA fragments. For fragments ≥ 15 kbp and velocity gradients ≥ 100 s−1, the orientation can be adequately described by the empirical relation: LDr= –(k1‐G)/(k2 + G), where k1is a linear function of the square root of the ionic strength and k2 depends on the DNA contour length. Since the DNA persistence length can be represented as a linear function of the reciprocal square root of the ionic strength [D. Porschke, (1991) Biophysical Chemistry, Vol. 40, p. 169], extrapolation of the empirical relation provides information about the stiffness of the DNA fibers. © 1993 John Wiley & Sons, Inc.
Proton magnetic resonance studies of bradykinin antagonists
Authors: Liu Xiaohong , Stewart John M. , Gera Lajos , Kotovych George 
Published: December 2004

AbstractBradykinin (BK) is a peptide hormone with sequence Arg1‐Pro2‐Pro3‐Gly4‐Phe5‐Ser6‐Pro7‐Phe8‐Arg9 and has been implicated in a multitude of pathophysiological processes such as the ability to lower systemic blood pressure and stimulate pain. BK analogues having bulky, β‐branched D‐aliphatic residues at position 7 combined with bulky L‐aliphatic residues at position 8 have now been observed to be strong antagonists. Conformational studies based on two‐dimensional nmr experiments in methanol/water (80/20 v/v) were carried out on several such active antagonists in a polar solvent. Included in this study were the very active antagonists, [D‐Arg0, Hyp3, Thi5, D‐Cpg7, Cpg8]‐BK [Cpg: α‐cyclo‐pentyl‐glycine; Hyp: trans‐4‐hydroxy‐L‐proline; Thi: β‐(2‐thienyl)‐L‐alanine] (I), [D‐Arg0, Hyp3, D‐Cpg7, Cpg8] ‐BK (II), as well as its variant with D‐Cpg7 replaced by Cpg7, namely [D‐Arg0, Hyp3, Cpg7, Cpg8]‐BK (III). A turn‐like structure, which coexists with the extended conformation, was observed between residues 2 and 5 for the most active antagonists I and II, in direct correlation with the peptide activities. No turn‐like structure was found for residues 6–9. In peptide III, a turn‐like structure was not identified. The existence of a turn at the C‐terminal end of bradykinin and its analogues has been predicted by empirical calculations and supported by nmr measurements. But the present nmr study on the most active antagonists (I, II) does not support this hypothesis. Instead, the data suggest that a turn‐like structure between residues 2 and 5 could be important for antagonist activity. Finally, one weak inhibitor [D‐Cpg7]‐BK (IV) showed no defined secondary structure. © 1993 John Wiley & Sons, Inc.
Computer simulations of the flexibility of a series of synthetic cyclic peptide analogues
Authors: Thomas Aline , Roux Benoit , Smith Jeremy C. 
Published: December 2004

AbstractThe flexibility of a series of cyclic peptides derived from the epitope of a snake toxin is investigated using computer simulation techniques. Molecular dynamics (MD) simulations and vibrational analyses are performed on chemically constrained peptides modeled on the parent protein loop. In the 50 ps MD simulations, large variations in the atomic fluctuations are seen between the peptides, and can be related to the nature of the chemical constraints present in the molecules. Normal mode analyses are performed on energy‐minimized configurations derived from the dynamics trajectories. The atomic fluctuations calculated from the normal modes are about 30% of those of the molecular dynamics for the more flexible peptides and 70% for the more constrained molecules. The calculated differences in flexibility between the molecules are much less significant in the harmonic approximation. © 1993 John Wiley & Sons, Inc.
On the interaction of polypeptides with bile salts or bilirubin‐IXα
Authors: D'Alagni Maria , D'Archivio Angelo A. , Giglio Edoardo 
Published: December 2004

AbstractAqueous solutions formed by polypeptides, simple models of proteins, and bile salts (sodium cholate and deoxycholate, NaC and NaDC, respectively) or bilirubin‐IXα (BR) have been studied by CD measurements. They could mimic more complicated biliary systems, thus supplying a possible interpretation of the behavior of some amino acid residues in the biliary proteins. The aggregation of NaDC and NaC in water can be monitored by CD measurements. Bile salts, in submicellar and micellar form, stabilize poly (L‐Lys) (PLL) in α‐helical conformation. The α‐helix content increases with increasing bile salt concentration and ionic strength. NaDC seems to be a slightly better stabilizing agent of the α‐helix conformation than NaC. Models characterized by hydrogen bonds between bile salts and PLL are proposed, also resorting to previous data available on the systems formed by NaDC and poly(L‐Leu‐L‐Leu‐L‐Lys) (PLLL) or poly(L‐Leu‐L‐Leu‐L‐Asp) (PLLA). Binding of BR to PLL, poly(D‐Lys), poly(L‐Glu), PLLL, and PLLA in water has been investigated by CD spectra in order to clarify the nature of the association complexes and the mechanism of the BR enantioselective complexation. Potential energy calculations provide binding models capable of explaining the enantioselective ability of the PLL and PLLL α‐helices toward the left‐ and right‐handed enantiomer of BR, respectively. BR is bound to ‐NH2 groups of PLL and PLLL lying on a right‐ and left‐handed spiral, respectively. These results, together with those formerly obtained for some bile salts–BR systems, indicate that the selectivity originates from a binding that involves large regions of the BR molecule and gives rise, very probably, to moderate conformational changes from the “ridge tile” structure observed in the crystals. In some cases van der Waals forces can play a crucial role in the chiral recognition of bilirubin. Moreover, possible interaction models of BR with human serum albumin are proposed on the basis of a recent x‐ray crystal structure of the protein. © 1993 John Wiley & Sons, Inc.
Single‐residue substitution in homopolypeptides: Perturbative helix–coil theory at a single site
Authors: Qian Hong 
Published: December 2004

AbstractBased on Lifson–Roig's helix–coil transition theory, substitution of a single heteroresidue into a homopolymer host is studied. This study models recent experiments that substitute a single amino acid into a small peptide in water [A. Chakrabartty, J. A. Schellman, and R. L. Baldwin (1991), Nature, Vol. 351, pp. 586–688]. Our formalism, which is based on a perturbation method, differs from the existing theory for sequenced polymers and is naturally analogous, hence likely to be useful, to substitution experiments in the laboratory. It is shown that the intrinsic helix propensity w is directly proportional to the equilibrium constant for the helix–coil equilibrium of a single residue in a host peptide. This intuitive new result will simplify experimental data interpretations for measurements of the helical conformation on the single amino acid level. It is also shown that substitution affects the total helicity of the host peptide according to two considerations: the helicity of the replaced residue prior to the substitution, and the sensitivity of the site, a measure of neighboring interactions. The relationship between substitution stability and thermal stability is explored. © 1993 John Wiley & Sons, Inc.
Identification of the adenine binding site in the ricin toxin A‐chain by fluorescence, CD, and electron spin resonance spectroscopy
Authors: Ramalingam T. S. , Das Puspendu K. , Podder Sunil K. 
Published: December 2004

AbstractCD, electron spin resonance, and fluorescence spectroscopy have been utilized to study the adenine binding site of ricin and its toxic A‐subunit. At acidic (4.5) and physiological (7.3) pH, adenine or a spin‐labeled analogue of adenine, N6‐(2,2,6,6‐tetramethyl‐1‐oxypiperidin‐4‐yl) adenine, alters the near uv CD spectra of the ricin A‐chain as well as intact ricin, whereas the far uv CD spectra of all proteins remain unchanged. Electron spin resonance data show that the adenine spin‐labeled analogue interacts strongly with the A‐chain both at pH 4.5 and 7.3, but no or very weak binding is observed for the intact ricin or the isolated B‐chain. The adenine spin label gets highly immobilized (2AII = 65.5G) by the A‐chain. The apparent dissociation constant Kd for the toxic A‐chain ligand complex is 1.55 × 10−4 M and 5.6 × 10−5 M at pH 7.3 and 4.5, respectively. Fluorescence intensity of ricin A‐chain bound 1,8‐anilinonaphthalenesulfonic acid (ANS) decreases by ∼55% at pH 4.5 with the addition of the spin‐labeled analogue of adenine, implying that both the ANS and adenine spin label (ADSL) bind to the hydrophobic domain of the A‐chain. Fluorescence of the only intrinsic tryptophan probe of the A‐chain is also efficiently quenched by ADSL, indicating that the tryptophan residue and the hydrophobic adenine binding site are closely located. All spectroscopic measurements indicate that adenine or its spin‐labeled analogue has a single binding site adjacent to the TRP211 residue in the A‐chain. Expansion of the A‐chain globule and subsequent exposure of the hydrophobic binding site seem to be responsible for the increased binding of adenine at pH 4.5. © 1993 John Wiley & Sons, Inc.
Dynamics and structures of DNA: Long‐range effects of a 16 base‐pair (CG)8 sequence on secondary structure
Authors: Kim Ug‐Sung , Fujimoto Bryant S. , Furlong Clement E. , Sundstrom Joseph A. , Humbert Richard , Teller David C. , Schurr J. Michael 
Published: December 2004

AbstractThe effects of inserting 16 base pair (bp) of alternating CG[(CG)8] near the middle of a much longer restriction fragment (1097 bp) are investigated by measuring various properties that are sensitive to secondary and tertiary structure. Results for this fragment are compared with those for a control fragment (1089 bp) with the identical sequence except at the insert. Another fragment (1382 bp), which contains a 296‐bp extension at the 5′‐end of the 1089‐bp control fragment, is also used as a secondary control in some experiments. When the 1097‐bp (CG)8 insert fragment is compared with the control fragments in 0.1M NaCl buffer, the (CG)8 insert is found to induce disproportionately large relative changes in the molar ellipticity at 273 nm ([θ)273], the torsion constant (α) measured by fluorescence polarization anisotropy, the optical melting profile, and the susceptibility to S1 nuclease. Estimates of the minimum distance over which the (CG)8 insert alters the secondary structure range from 330 to 550 bp. With increasing NaCl concentration, the 1097‐bp insert fragment undergoes a structural transition between 2.0 and 2.5M that is manifested in the apparent diffusion coefficient (Dplat) from dynamic light scattering at large scattering vector. This transition, which is not exhibited by the control DNAs, is presumed to involve formation of Z‐helix at the insert. However, the observed decrease in (Dplat) is attributed to an increase in bending rigidity, which perforce must be globally distributed far beyond the (CG)8 insert per se. In 4.25M NaCl (but not in 0.1M NaCl), the addition of 1 ethidium dye per 300 bp induces an extensive structural transition in the 1097 bp (CG)8 insert fragment. This transition, which also is not exhibited by the control DNAs, significantly decreases the bending rigidity, doubles [θ]273, and takes place on a time scale of a few days. Removal of ethidium and salt by dialysis vs 0.1M NaCl buffer restores the original properties of the 1097‐bp (CG)8 insert fragment. The present results are consistent with a (fluctuating, long‐range) description of the secondary structure in which a given short sequence transiently fluctuates among two or more distinct secondary structures that extend over much larger domains of variable position and size, and whose relative stabilities depend on distant as well as close‐lying base pairs. © 1993 John Wiley & Sons, Inc.
A conformational study of the dehydroalanine: Dipeptide and homopolypeptide
Authors: Alemán Carlos , Perez Juan J. 
Published: December 2004

AbstractA molecular mechanics study of polydehydroalanine [poly‐(Δ Ala)] is presented. For this purpose the AMBER 3a program has been used to perform the calculations. With exception of the point charges, the parameters for the terminal groups were taken from AMBER 3a libraries, whereas those for the Δ Ala residue from Alagona et al. [J. Comp. Chem. (1991) Vol. 12, pp. 934–942]. Charges for the residue and terminal groups have been fitted from the MNDO electrostatic potential and scaled to achieve an ab initio 6‐31G* quality. Calculations have been carried out using the continuous solvent approximation with three different dielectrics ε = 1, 1r, and 4r. The results show that, despite the preferred structure for the isolated residue is an extended conformation, a 310‐helix is the preferred conformation in the solid state (ε = 1 and 1r), whereas a peculiar structure with ψ = 0° is preferred with ε = 4r. © 1993 John Wiley & Sons, Inc.
Molecular dynamics in sodium poly (L‐glutamate) aqueous solutions analyzed by means of the stretched exponential decay of the williams–watts function
Authors: Bordi F. , Cametti C. , Paradossi G. 
Published: December 2004

AbstractThe high‐frequency dielectric dispersions of the sodium salt of poly(L‐glutamic acid) aqueous solutions in the frequency range from 1 to 1000 MHz have been analyzed by means of the Cole–Davidson relaxation function in the frequency domain and by means of the Williams‐Watts relaxation function in the time domain. The analogies between the two descriptions are discussed on the basis of the analysis carried out by Lindsey and Patterson and the connections between the dipole–dipole correlation function based on the kinetic model for polyion dynamics proposed by Skinner and the Williams–Watts nonexponential decay function are briefly discussed. © 1995 John Wiley & Sons, Inc.