bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biopolymer–surfactant interaction. I. Kinetics of binding of cetyltrimethyl ammonium bromide with carboxymethyl cellulose (Na Salt)
Authors: Maulik Sudeshna , Jana Pijush Kanti , Moulik Satya Priya , Chattoraj Dipti Kumar 
Published: December 2004

AbstractThe kinetics of binding of the cationic surfactant cetyltrimethyl ammonium bromide with the Na salt of carboxymethyl cellulose was studied by the electrometric method using cetyltrimetlyl ammonium+ (CTA+) ion‐selective polyvinyl chloride membrane electrode. The binding process followed the first‐order kinetics and occurred in three stages. Its affinity increased with increasing CTA bromide concentration and decreased with ionic strength. The activation process comprised moderate E and ΔH≠ and negative ΔS≠ for all three stages with a ΔH≠ < TδS≠ trend proving it to be entropy controlled. The ΔG≠ values followed the trend ΔG < ΔG < ΔG (in accordance with k1 > k2 > k3). The enthalpies (ΔH≠) and entropies (ΔS≠) of activation followed a systematic and interdependent trend. The multiple‐stage binding kinetics is grossly comparable with the kinetics of binding of proteins to solid surfaces. © 1995 John Wiley & Sons, Inc.
Low‐frequency vibrations in α‐helices: Helicoidal analysis of polyalanine and deoxymyoglobin molecular dynamics trajectories
Authors: Furois‐Corbin S. , Smith J. C. , Lavery R. 
Published: December 2004

AbstractWe present an approach to the analysis of low‐frequency (0‐200 cm−1) α‐helix vibrations in molecular dynamics simulation. The approach employs the P‐Curves algorithm [H. Sklenar, C. Etchebest, and R. Lavery, (1989) Proteins: Structure, Function and Genetics, Vol. 6. pp. 46–60] to determine the helical axis and a set of helicoidal parameters describing the axis curvature and the position of the repealing units with respect to the axis and each other. The vibrations are analyzed in terms of time correlation functions of the fluctuations of P‐Curves parameters and their Fourier transforms. Simulations of polyalanine and myoglobin are analyzed. For polyalanine, global twisting, bending, and stretching vibrations are found at 11, 20, and 40 cm−1, respectively. In myoglobin, the spectra of the global helix vibrations are qualitatively different from those of polyalanine and considerably more complicated. Local vibrations of individual amino acid units in the helix backbones are also analyzed with P‐Curves and compared. © 1995 John Wiley & Sons, Inc.
CD and fluorescence studies of the human granulocyte‐macrophage colony‐stimulating factor and related peptide conformations in aqueous solution
Authors: Casté L. , Zandomeneghi M. , Houben J. L. , Rovero P. , Pegoraro S. , Revoltella P. R. , Brochon J. C. 
Published: December 2004

AbstractThe absorption, CD, and fluorescence emission spectra, and the fluorescence emission and depolarization lifetimes of the human granulocyte‐macrophage colony‐stimulating factor (hGM‐CSF) and related peptides previously tested for their immunological activity, were measured in water at various pHs and temperatures to obtain information on their conformation in solution. The aim was to correlate the amino acid sequences, and the chain conformations and dynamics of the peptides, with their immunological propertiesThe CD spectrum of hGM‐CSF revealed, as expected, a structure in solution similar to that in the crystalline state, but the fluorescence data suggest that the Trp 122 residue is more accessible to the solvent than the x‐ray data would lead one to expect. They also suggest that some flexibility exists between the protein's two domains, one made up of theα‐helices A and C and the other of the α‐helices B and D plus the two β‐strands. In aqueous solution, none of the tested peptide CD spectra could be linked to a recognizable ordered conformation, i.e., an α‐helix or a β‐sheet. The fluorescence of the peptide 11–24 suggests that the Trp 13 residue may appear in two types of situations: (a) in aqueous solution and (b) within a globular structure. Its CD spectra show that the tryptophan residue exists in both cases in a highly asymmetric environment independent of the pH. © 1995 John Wiley & Sons, Inc.
Design and characterization of a model αβ peptide
Authors: Butcher Daniel J. , Bruch Martha D. , Moe Gregory R. 
Published: December 2004

AbstractCD and nmr spectroscopy were used to compare the conformational properties of two related peptides. One of the peptides, Model AB, was designed to adopt a helix‐turn‐extended strand (αβ) tertiary structure in water that might be stabilized by hydrophobic interactions between two leucine residues in the amino‐terminal segment and two methionine residues in the carboxyl terminal segment. The other peptide, AB Helix, has the same amino acid sequence as Model AB except that it lacks the‐Pro‐Met‐Thr‐Met‐Thr‐Gly segment at the carboxyl‐terminus. Although the carboxyl‐terminal segment of Model AB was found to be unstructured, its presence increases the number of residues in a helical conformation, shifts the pKas of three ionizable side chains by 1 pH unit or more compared to an unstructured peptide, stabilizes the peptide as a monomer in high concentrations of ammonium sulfate, increases the conformational stability of residues at the terminal ends of the helix, and results in many slowly exchanging amide protons throughout the entire backbone of the peptide. These results suggest that interactions between adjacent segments in a small peptide can have significant structure organizing effects. Similar kinds of interactions may be important in determining the structure of early intermediates in protein folding and may be useful in the de novo design of independently folding peptides. © 1995 John Wiley & Sons, Inc.
Conformational mimicry: Synthesis and solution conformation of a cyclic somatostatin hexapeptide containing a tetrazole cis amide bond surrogate
Authors: Beusen Denise D. , Zabrocki Janusz , Slomczynska Urszula , Head Richard D. , Kao Jeff L.‐F. , Marshall Garland R. 
Published: December 2004

AbstractPotent, cyclic hexapeptide analogues of somatostatin are generally believed to adopt some common secondary structural features: a II′ β turn at one end of the cycle, and a type VI turn with a cis amide bond at the other. A proposed cis amide surrogate, the 1,5‐disubstituted tetrazole, has been placed into a cyclic hexapeptide analog of somatostatin in order to constrain the putative cis amide bond. The final cyclization was done by either chemical or enzymatic means. The product, cyclo(Ala6‐Tyr7‐D‐Trp8‐Lys9‐Val10‐Phe11‐Ψ[CN4]), was found to have 83% of the activity of somatostatin. Solution nmr analysis in DMSO/water revealed that the backbone as well as side chain χ1 and χ2 were well ordered. Relaxation matrix methods were used to extract distance restraints from the nuclear Overhauser effect spectroscopy data set, and these were used in a systematic search of torsional space to identify structures consistent with the nmr data. Restrained minimizations of these structures using a number of different force fields produced structures having the expected βII′ turn at D‐Trp8‐Lys9 and αβVIa turn in the Phe11‐Ψ[CN4]‐Ala6 portion of the molecule. The similarity of the minimized structures to those previously reported for cyclic hexapeptide analogues of somatostatin confirms the similarity of the tetrazole geometry to that of the cis amide in solution. © 1995 John Wiley & Sons, Inc.
Conformation of short DNA fragments by modulated fluorescence polarization anisotropy
Authors: Collini Maddalena , Chirico Giuseppe , Baldini Giancarlo , Bianchi Marco E. 
Published: December 2004

AbstractThe technique of fluorescence polarization anisotropy (FPA) decay of intercalated ethidium has been used to study DNA conformation and dynamics, which are being recognized as primary determinants in transcription control and other cellular processes. Frequency modulated FPA when applied to two DNA molecules, a “straight” 50 base‐pairs duplex fragment, and a bent fragment of similar length, has yielded different rotational diffusion coefficients for the two fragments. The data have been processed with an analytical model and with Brownian dynamics simulations, obtaining a good fit and a quantitative agreement between the two models. Both analyses have confirmed that one fragment can be described as a straight cylinder, while the other fragment is bent, with an angle estimated to be 45° ± 3°. FPA has proved to be very powerful in determining simple conformations of short DNA duplexes and also particularly apt to probe the dynamical features of DNA fragments where conventional methods are either too cumbersome or fail to give quantitative results. © 1995 John Wiley & Sons, Inc.
Core directed self‐assemblies in the solid state of retro aib bis‐peptide dicarboxylic acids: A design strategy for control of molecular orientation in peptides
Authors: Karle Isabella L. , Ranganathan Darshan 
Published: December 2004

AbstractSelf‐assembly patterns as a function of the central core insert in the retro bis‐peptide dicarboxylic acids HOAibXAibOH, containing oxalyl (‐COCO1), fumaryl ( OCHCH CO ;2), and adipoyl [ CO(CH2)4 CO3], have been characterized by single crystal x‐ray diffraction analyses. Extensive hydrogen bonding occurs in each crystal but there are no OH…O bonds between acid groups. Only two types of hydrogen bonds occur in all the crystals:NH…O (acid terminal),2.84‐2.98 Åand OH (acidterminal)…O (corecarbonyl),2.55–2.67 Å (exceptfor an additional intramolecular C5 type bond in the oxalyl moiety in 1). The self‐assembly patterns are a β‐network in1, separate layer assemblies (β‐networks) for two independent molecules in 2 that combine into a three‐dimensional γnetwork, and separate ribbon assembles (αnetworks) for two independent molecules in 3 that combine into an extended β‐network sheet withhydrophobic faces. © 1995 John Wiley & Sons, Inc.
Homooligopeptides composed of hydrophobic amino acid residues interact in a specific manner by taking α‐helix or β‐structure toward lipid bilayers
Authors: Lee Sannamu , Yoshitomi Hideo , Morikawa Miyuki , Ando Setzuko , Takiguchi Hideo , Inoue Tohru , Sugihar Gohsuke 
Published: December 2004

AbstractIn order to investigate the role of each amino acid residue in determining the secondary structure of the transmembrane segment of membrane proteins in a lipid bilayer, we made a conformational analysis by CD for lipid‐soluble homooligopeptides, benzyloxycarbonyl‐(Z‐) Aaan‐OEt (n = 5‐7), composed of Ala, Leu, Val, and Phe, in three media of trifluoroethanol, sodium dodecyl sulfaie micelle, and phospholipid liposomes. The lipid‐peptide interaction was also studied through the observation of bilayer phase transition by differential scanning cahrimetry (DSC). The CD studies showed that peptides except for Phe oligomers are present as a mainly random structure in trifluoroethanol, as a mixture of α‐helix, β‐sheet, β‐turn, and /or random in micelles above the critical micellization concentration and preferably as an extended structure of α‐helical or β‐structure in dipalmitoyl‐D,L‐α‐phosphatidylcholine (DPPC) liposomes of gel state. That the β‐structure content of Val oligomers in lipid bilayers is much higher than that in micelles and the oligopeptides of Leu (n = 7) and Ala (n = 6) can take an α‐helical structure with one to two turns in lipid bilayers despite their short chain lengths indicates that lipid bilayers can stabilize the extended structure of both α‐helical and β‐structures of the peptides. The DSC study for bilayer phase transition of DPPC / peptide mixtures showed that the Leu oligomer virtually affects neither the temperature nor the enthalpy of the transition, while Val and Ala oligomers slightly reduce the transition enthalpy without altering the transition temperature. In contrast, the Phe oligomer affects the phase transition in much more complicated manner. The decreasing tendency of the transition enthalpy was more pronounced for the Ala oligomer as compared with the Leu and Val oligomers, which means that the isopropyl group of the side chain has a less perturbing effect on the lipid acyl chain than the methyl group of Ala. © 1995 John Wiley & Sons, Inc.
Crystal structure and a twisted β‐sheet conformation of the tripeptide L‐leucyl‐L‐leucyl‐L‐leucine monohydrate trimethanol solvate: Conformation analysis of tripeptides
Authors: Go Kuantee , Parthasarathy R. 
Published: December 2004

AbstractIn order to test the helical preference of short oligo‐L‐leucines, we crystallized the tripeptide L‐leucyl‐L.‐leucyl‐L‐leucine (LLL) and carried out x‐ray diffraction studies of it (L‐leucyl‐L‐leucyl‐Lleucine)2. 3CH3OH. H2O, (C39H84N6O12). Crystallized in the monoclinic system, space group P21, cell parameters: a = 12.031(2), b = 15.578(3), c = 14.087(2) Å, α = 90°, β = 97.29(1)°, γ = 90°, V = 2618.6 Å3. MW = 829.1, Dc = 1.051 gcm−3. R index of 0.057 for 4213 reflections (λcukα = 1.5418 Å) > 2σ. LLL takes tip the β‐sheet rather than a helical conformation in the crystalline stale. The three methanol molecules and the water molecule that constitute the solvent of crystallization form a network of hydrogen bonds to the LLL molecules and to one another. It is rather remarkable that though A and L have stronger helical preferences than G, neither AAA nor LLL form the crystalline helix but GAL does, indicating that the helical preferences depend on the sequence context. The residue L2 in molecule A and the residues L1 and L3 of molecule B do not show the preferred conformation for forming helices. Further, very remarkably. LLL exhibits a unique super secondary feature of the protein folding topology, namely the twisted β‐sheet. Where as most short peptides show only the classical p‐sheet conformation. Thai even the tripeptide LLL is able to exhibit the twisted β‐sheet conformation, and with the correct left‐handed twist this suggests that even very short peptide segments possess the ability to assume several of the characteristic topological features exhibited by proteins. An extensive review of tripeptide conformations has been carried out and some results of this study have been included here. © 1995 John Wiley & Sons, Inc.
Conformational study of linear alternating and mixed D‐ and L‐proline oligomers using electronic and vibrational CD and fourier transform IR
Authors: Mästle Werner , Dukor Rina K. , Yoder Gorm , Keiderling Timothy A. 
Published: December 2004

AbstractVibrational CD (VCD) spectra of a series of blocked linear, alternating D‐ and L‐proline containing oligopeptides, dissolved in D2O and in CDCl3. are reported. For the Boc‐LDL‐Pro3 to Boc‐DLDLDLDL‐Pro8 oligomers. The VCD spectra in the amide I band is a positive couplet, opposite in sense to that obtained for (L‐Pro)n oligomers. While this admits the possibility of their favoring a right‐handed helical chain conformation, the amide I ir spectra for these dl oligomers in D2O indicate a mixed, apparently alternate, cis‐trans conformation that prevents a simple conclusion. Their VCD in D2O evidence no narrowing and has a progressive loss in intensity (measured as Δ /A,) with an increase in chain length. In CDCl3a similar pattern of positive VCD couplets decreasing in intensity with length was seen, but their spectra are narrower. Their electronic CD (ECD) in the uv, also indicates a loss in intensity with increasing length. Oligomers with odd or even numbers of Pro residues have different ECD patterns, indicating that those spectra are strongly influenced by local contributions arising in the N‐terminal groups. The VCD arises from dipolar and vibrational coupling of the amides in the helical structure. All the spectra are consistent with the chiral end groups leading to formation of an excess of one helical handedness. With an increase in length, the influence of this selectiveness is less and the overall CD measured decreases. © 1995 John Wiley & Sons, Inc.
Conformational studies of retro–inverso peptides: The crystal and molecular structure of the hydantoin from H‐Ala‐G‐Ala‐mGly‐OBzl
Authors: Benedetti Ettore , Pedone Emilia M , Kawahata Noriyuki H , Goodman Murray 
Published: December 2004

AbstractThe crystal structure of the hydantoin 1‐[(S)‐1′–aminoethylmalonyl benzyl ester]‐(S)‐4‐methylimidazolidin‐2.5‐dione (1) derived from the peptide H‐Ala‐gAla‐mGly‐OBzl, Having the retro‐inverso modification of the Ala‐Gly bond, has been determined by x‐ray diffraction analysis. The crystals are orthorhombic, space group P212121 with a = 6.539. b = 14.721, c = 17.101 Å, z = 4. The structure was solved by direct methods and refined with anisotropic thermal factors to a final R value of 0.067 for the 947 observed reflections.Reversal of the Ala‐Gly amide bond perturbs the folding tendency of the backbone shown by the parent peptide t‐BuCO‐Ala‐Gly‐NHiPr. The gem‐diamino residue, gAla, and the malonyl moieties are found in the helical and the extended conformations, respectively. Intramolecular hydrogen bonding is not observed. The molecules in the crystal are held together by the formation of two intermolecular hydrogen bonds of the NHOC type with NO distances of 2.86 and 3.17 Å respectively. 1995 John Wiley&Sons. Inc. © 1995 John Wiley & Sons, Inc.
Thermodynamics of melting of the circular dumbbell d〈pCGC‐TT‐GCG‐TT〉
Authors: Ippel Johannes H , Lanzotti Virginia , Galeone Aldo , Mayol Luciano , van den Boogaart Jaquelien E , Pikkemaat Jeroen A , Altonaf Cornelis 
Published: December 2004

AbstractThe conformational behavior of DNA minihairpin loops is sensitive to the directionality of the base pair that closes the loop. Especially tailored circular dumbbells, consisting of a stem of three Watson–Crick base pairs capped on each side with a minihairpin loop, serve as excellent model compounds by means of which deeper insight is gained into the relative stability and melting properties of hairpin loops that differ only in directionality of the closing pair: C‐G vs G‐C. For this reason the thermodynamic properties of the circular DNA decamers 5′‐d〈pCGC‐TT‐GCG‐TT〉‐3′(I) and reference compounds 5′‐d〈pGGC‐TT‐GCC‐TT≤‐3′(II) and 5′‐d(GCG‐TC‐CGC)‐3′(III) are studied by means of nmr spectroscopy. MoleculesIandIIadopt dumbbell structures closed on both sides by a two‐membered hairpin hop. At low temperatureIconsists of a mixture of two slowly exchanging forms, denotedL2L2andL2L4. The low‐temperatureL2L2form is the fully intact minihairpin structure with three Watson–Crick C‐G base pairs. The high‐temperature form,L2L4,contains a partially disrupted closing G‐C base pair in the 5′‐GTTC‐3′ loop, with the cytosine base placed in a syn orientation. The opposite 5′‐CTTG‐3′ loop remains stable. A study of the noncircular hairpin structureIIIshows similar conformational behavior for the 5′‐GTTC‐3′ loop as found inIa syn orientation for C(6) and two slowly exchanging imino proton signals for G(3). The melting point Tm of IIwas estimated to lie above 365 K. The Tm value of the duplex stem and the 5′‐CTTG‐3′ loop of theL2L4form ofIis 352 ± 2 K. The ΔH° is calculated as −89 ± 10 kJ/mol. The Tm value determined for the individual residues of the 5′‐GTTC‐3′ loop lies 4°–11° lower. The enthalpy ΔH° of melting the thymine residues in the 5′‐GTTC‐3′ loop is calculated to be ‐61± 7 kJ/mol. Thermodynamic data of the equilibrium between the slowly exchanging two‐ and four‐membered loop conformers of I reveal an upper limit for ΔH° of +30 kJ/mol in going from a two‐memberedto a four‐membered loop, in agreement with the enthalpy difference of +28 k.j/mol between the two loops at the Tm midpoint. For hairpin III the upper limit for ΔH° going from a two‐membered to a four‐membered loop amounts to ±21 kJ/mol. The mutual exchange rate between the L2 and L4 form in III is estimated as 13.6 s−1. Our results clearly suggest that small four‐way DNA junctions(model for immobilized Holliday junctions) can be designed that consist of a single DNA strandthat features ‐CTTG‐caps on three of the four arms of the junction. © 1995 John Wiley & Sons, Inc.
Structure of two microcystins: Refinement with nuclear overhauser effects and ensemble calculations
Authors: Mierke Dale F , Rudolph‐Böhner Sabine , Müller Gerhard , Moroder Luis 
Published: December 2004

AbstractEnsemble calculations employing restraints developed from 1H‐nmr were used to examine the conformational states of the two microcystins LR and LY. Despite the fast “flip‐flop” dynamics about the N‐methyl‐dehydroalanine residue and adjacent residues, the main conformational characteristics of the cyclic heptapeptides consist of a compact ring formed by five of the seven amino acid residues with expulsion of a dipeptide portion out of the plane and the unnatural C20 β‐amino acid (2S. 3S. 8S, 9S)‐3‐amino‐9‐methoxy‐2, 6, 8‐trimethyl‐10‐phenyldeca‐4. 6‐dienoic acid pointing upward from the ring. This structure of microcystin LR shows high degrees of similarity with the energy‐minimized structure of nodularin, a cyclic pentapeptide of identical inhibitory potency against protein phosphatases 1 and 2A. Comparison of these structures with those of the less toxic LY variant and with the structurally unrelated okadaic acid, known as potent inhibitor of the protein phosphatases 1 and 2A, allowed us to propose a rational binding mode of this structural diverse set of natural inhibitors. © 1995 John Wiley & Sons, Inc.
Structure–activity studies on magainins and other host defense peptides
Authors: Maloy W. Lee , Kari U. Prasad 
Published: December 2004

AbstractHost defense peptides are widely distributed in nature, being found in species from bacteria to humans. The structures of these peptides from insects, horseshoe crabs, frogs, and mammals are known to have the common features of a net cationic charge due to the presence of multiple Arg and Lys residues and in most cases the ability to form amphipathic structures. These properties are important for the mechanism of action that is thougln to be a nonreceptor‐mediated interaction with the anionic phospholipids of the target cell followed by incorporation into the membrane and disruption of the membrane structure. Host defense peptides have been shown to have broad spectrum antimicrobial activity, able to kill most strains of bacteria as well as some fungi, protozoa, and in addition, many types of tumor cells. Specificity for pathogenic cells over host cells is thought to be due to the composition of the cell membranes, with an increased proportion of anionic phospholipids making the pathogen more susceptible and the presence of cholesterol making the host membranes more resistant. Structure–activity relationship studies have been performed on insect cecropins and apidaecins. horseshoe crab tachyplesins and polyphemusins. and the frog magainins. CPFs (caerulein precursor fragments) and PGLa. In general, changes that increased the basicity and stabilized the amphipathic structure have increased the antimicrobial activity: however, as the peptides become more hydrophobic the degree of specificity decreases. One magainin‐2 analogue. MSI‐78. has been developed by Magainin Pharmaceuticals as a topical antiinefective and is presently in clinical trials for the treatment of infected diabetic foot ulcers. © 1994 John Wiley & Sons, Inc.
Design of metal ion binding peptides
Authors: Fattorusso R. , Morelli G. , Lombardi A. , Nastri F. , Maglio O. , D'Auria G. , Pedone C. , Pavone V. 
Published: December 2004

AbstractTwo cyclic and branched peptides (PLA and AZU) were synthesized with the aim of reproducing the active site of the blue copper proteins plastocyanin and azurin. Both peptides, designed on the basis of the x‐ray structures of Poplar plastocyanin and Alcaligenes denitrificans azurin. contain the same coordinating residues of the parent native proteins. The visible spectra of PLA in the presence of equimolar amount of Cu(II) strongly support the interaction between the peptide and copper(II) ion. The CD titration of AZU with the Hg(II) ion indicates for the formation of two species. [A ZUHg]+ and [A ZUHg2]3+ having binding constants (Keq) of 3.106 and 2–104M−1, respectively. © 1994 John Wiley & Sons, Inc.