摘要:

AbstractReversed‐phase high performance liquid chromatography (RP HPLC) has been found to be a convenient and powerful tool for the study of the secondary structure of peptides. Here, the ability of proline to perturb the secondary structures of peptides induced at aqueous‐lipid interfaces and the induced conformation of polyproline peptides were investigated by means of RP HPLC. For these studies, four different complete sets of substitution analogues of model peptides expected to have specific induced conformations were used. In the first two studies, a single lysine was “walked” through two 18‐residue polyproline sequences (one N‐acetylated, the other not). In the remaining two studies, a proline was “walked” through two different sequences that had been found earlier to be induced into an α‐helical conformation during RP HPLC (an 18‐residue polyalanine sequence and the amphipathic 14‐residue sequence Ac‐LLKLLKKLLKKLKK‐NH2). Sixty‐eight individual analogues were synthesized for this study and the effect of the respective substitutions on retention times was determined. The results are consistent with the concept that, upon interaction with the C‐18 of the stationary phase during RP HPLC, polyproline is induced into a type II helical conformation, polyalanine into an α‐helical conformation, and Ac‐LLKLLKKLLKKLKK‐NH2into an amphipathic α‐helical array. In an extension of this study, the antimicrobial activities of Ac‐LLKLLKKLLKKLKK‐NH2and its 18 proline substitution analogues were found to be inversely c

ISSN:0006-3525    

DOI:10.1002/bip.360320602

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1992

数据来源: WILEY

摘要:

AbstractAs model compounds for Ni(II)‐binding heparin‐like compounds isolated from human kidneys (Templeton, D. M.&Sarkar, B. (1985)Biochem. J.23035–42.), we investigated two disaccharides—4‐O‐(2‐O‐sulfo‐α‐L‐idopyranosyluronic acid)‐2,5‐anhydro‐D‐mannitol, disodium salt (1a), and 4‐O‐(2‐O‐sulfo‐α‐L‐idopyranosyluronic acid)‐6‐O‐sulfo‐2,5‐an‐hydro‐D‐mannitol, trisodium salt (1b)—that were isolated from heparin after nitrous acid hydrolysis and reduction. The monosulfate (1a) was active whereas the disulfate (1b) was inactive in a high‐performance liquid chromatography (HPLC) binding assay with the tracer ions63Ni(II)54Mn(II),65Zn(II), and109Cd(II). This result is in accord with the isolation of two67Cu(II) and63Ni(II) binding fractions from a complete pool of nitrous‐acid‐derived heparin disaccharides using sulfate gradients and a MonoQ anion exchange column on an FPLC system. One was identified as compound (1a) and the other as a tetrasulfated trisaccharide by high resolution FAB‐MS, NMR and HPLC‐PAD. Similarly, two synthetic disaccharides—methyl, 2‐O‐sulfo‐4‐O‐(α‐L‐idopyranosyluronic acid)‐2‐deoxy‐2‐sulfamido‐α‐D‐glucosamine, trisodium salt [IdopA2S(α1,4)GlcNSαMe,2a], and 2‐O‐sulfo‐4‐O‐ (α‐L‐idopyranosyluronic acid)‐2‐deoxy‐2‐sulfamide‐6‐O‐sulfo‐α‐D‐glucosamine, tetrasodium salt [IdopA2S(α1,4) GlcNS6SαMe,2b]—were shown to bind tracer amounts of63Ni and67Cu using chromatographic assays. Subsequently,1H NMR titrations of1a,1b,2a, and2bwith Zn(OAc)2were analyzed to yield 1:1 Zn(II)‐binding constants of 472 ± 59, 698 ± 120, 8,758 ± 2,237 and 20,100 ± 5,598M−1, respectively. The values for2aand2bsuggest chelation. It is suggested that the idopyranosiduronic acid residue is the major metal binding site. N

ISSN:0006-3525    

DOI:10.1002/bip.360320603

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1992

数据来源: WILEY

摘要:

AbstractTo map out the heavy metal binding sites of iduronic acid containing oligosaccharides isolated from human kidneys, we studied Zn (II) binding by nuclear magnetic resonance (NMR) and molecular modeling to two disaccharides isolated after nitrous acid depolymerization of heparin and two synthetic disaccharides representative of the heparin structure, namely, IdopA2S(α1,4) AnManOH,1a, IdopA2S(α1,4)AnManOH6S,1b, IdopA2S‐(α1,4) GlcNSαMe,2a, and IdopA2S(α1,4)GlcNS6SαMe,2b(see previous article in this series). A conformational analysis of the metal free and metal bound solutions was made by comparing calculated 〈(NOE)〉s, 〈T1〉s, and 〈J〉s to experimental values. The1C4,4C1, and2S0conformations of theL‐idopyranosiduronate ring and the4E and4T3of the anhydro‐D‐mannitol ring are evaluated as are rotations about the C5–C6 hydroxymethylene of the AnManOH (6S) or GlcNS(6S) residues. The NOE between IdopA2S H1 and H3 and the known NOE between H2 and H5, as well as theT1of IdopA2S H3, are introduced as NMR observables sensitive to the IdopA2S ring conformation. Similarly, a NOE between IdopA2S H5 and AnManOH (6S) or GlcNS (6S) H3 was observed that directly restricts the allowed interglycosidic conformational space. For all disaccharides, the Zn(II) bound spectral data are consistent with models in which these motions are partially “frozen” such that the1C4conformation of the IdopA2S is stabilized along with the4T3conformation of the AnManOH (6S) ring. The interglycosidic conformation is also stabilized in one of two minima. Electrostatic potential energy calculations gave the best overall agreement with experiment and suggest metal binding conformations with the carboxylate and ring oxygen of the IdopA2S residues (1C4conformation) and either O3 of the GlcNS (6S) residues or the sulfate oxygens of the 6‐sulphate for2bproviding additional chelating sites. These chelation models concur with the observation of marked13C and1H NMR chemical shifts for the IdopA2S resonances and of GlcNS H3 for2aand GlcNS6S C6 for2b.This study of model compounds implicates the IdopA2S(α1,4) GlcNS6S group as part of the heavy metal binding site in biologically important acidi

ISSN:0006-3525    

DOI:10.1002/bip.360320604

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1992

数据来源: WILEY

摘要:

AbstractA molecular mechanical study has been carried out to determine the most favorable conformation of poly(Aib) both in solution and in the solid state. An energetic approach to the packing has been carried out by studying the stability of pairs of poly(Aib) chains. The study reveals a higher stability of a 310‐helix when forming part of a dimer whereas in isolated molecules the α‐helix structure seems to be more stable depending on the length of the chain and dielectric constant of the environ

ISSN:0006-3525    

DOI:10.1002/bip.360320605

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1992

数据来源: WILEY

摘要:

AbstractA new constraint potential is proposed for the refinement of the three‐dimensional structure of biomolecules in solution from nmr data. It is based on the nuclear Overhauser effect (NOE) intensity calculations, taking into account the spin diffusion phenomenon. For restrained energy minimization or molecular dynamics techniques, a constraint potential term expressed as a function of the negative inverse of the sixth power of the NOE intensities (NOE−1/6) is added to the classical potential energy function. The properties of this new NOE constraint potential are discussed and compared to those of a harmonic NOE intensity potential.The method integrated in the molecular modeling program GROMOS is tested on the regular α‐helical structure of a decaglycylp

ISSN:0006-3525    

DOI:10.1002/bip.360320606

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1992

数据来源: WILEY

摘要:

AbstractWe synthesized and solved the crystalline structure of the oligopeptide acetyl‐ (glycyl‐β‐alanyl)2‐NH propyl. The crystal is formed by layers of helical molecules with the same chirality; however, right‐handed layers alternate with left‐handed ones. Inside every layer, the packing of helices is pseudohexagonal with hydrogen bonds between neighbor molecules. The structure found affords direct support for the model proposed by Crick and Rich for polyglycine II and also provides an interpretation for the structure of a newly found family of polyamides that do not form sheets as observed in most nylo

ISSN:0006-3525    

DOI:10.1002/bip.360320607

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1992

数据来源: WILEY

摘要:

AbstractSolution structures were determined for a linear analogue of growth hormone releasing factor (GRF), and cyclic and dicyclic analogues in which the side chains of aspartyl and lysyl residues spaced at positionsi‐(i+ 4) were joined to form a lactam. The four analogues were [Ala15]‐GRF‐(1–29)‐NH2and its cyclo8–12, cyclo21–25, and dicyclo8–12;21–25derivatives. The peptides were studied in two solvent systems: 75% methanol/25% water at pH 6.0; and 100% water at pH 3.0. CD spectroscopy was used to assess the overall α‐helical content. Nuclear magnetic resonance spectroscopy was used to determine the structures in more detail. Nearly complete proton resonance assignments were made for each of the peptides, in both solvents. Nuclear Overhauser effects were converted into distance constraints and applied in the molecular dynamics program CHARMM to evaluate the range of low‐energy structures that satisfied the nmr data. In 75% methanol, all of the peptides are comprised of a single α‐helical segment with fraying of one to three residues at each end. The linear analogue has a tendency to kink. In water, the analogues have two helical segments with flexible regions between them and at the termini of the peptides. The linear analogue is helical at residues 7–14 and 21–28. In the cyclo8–12analogue, the N‐terminal helical region extends to include residues 7–19, while the other helical region is slightly shortened. In the cyclo21–25analogue, the C‐terminal helical region is extended to include residues 19–28, while the N‐terminal helical region is destabilized. The dicyclic analogue has the largest N‐terminal helix, spanning residues 7–20, but its helical segment at residues 21–28 is not well ordered. All of the analogues exhibit substantial biological activity. The cyclic and dicyclic analogues show dramatically increased resistance to degradation during incubation with human plasma. Thei−(i+ 4) lactam, therefore, appears to be a synthetic means of stabilizing a local α‐helical conformation, which may be o

ISSN:0006-3525    

DOI:10.1002/bip.360320608

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1992

数据来源: WILEY

摘要:

AbstractLow singlet transition energies and line strengths were calculated for the cytosine : in‐dole : guanine complex by the INDO/1S‐CI method. The chromophores were arranged in three sets of 270 intercalating geometries. Calculations were executed in the supermolecule model with single excited configurations. Errors due to basis set extension and incomplete configuration representation were assessed, for all chromophore pairs, by full BSSE correction calculations and inclusion of double‐excited configurations. The intercalation‐induced perturbations of the principal transitions are characterized by but not limited to (a) a decrease in strength of {π*,π} transitions, (b) increase in strength in {π*,n} transitions, (c) splitting of {π*,π} transitions into components of unequal strength, and (d) energy and strength dependence in mixed transitions on rise and shift movements of the nucleic acid bases. These predictions are in accord with absorption, fluorescence emission, and scattering, and resonance Raman spectroscopic data on oligonucleotides and analogous aromatic complexes. The calculations suggest that major differences in intercalating coordinations are discernible in the near‐uv spectroscopic domain of proteins and

ISSN:0006-3525    

DOI:10.1002/bip.360320609

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1992

数据来源: WILEY

摘要:

AbstractWe suggest, using dynamical simulations of a simple heteropolymer modelling the α‐carbon sequence in a protein, that genetically the folded states of globular proteins correspond to statistically well‐defined metastable states. This hypothesis, called the metastability hypothesis, states that there are several free energy minima separated by barriers of various heights such that the folded conformations of a polypeptide chain in each of the minima have similar structural characteristics but have different energies from one another. The calculated structural characteristics, such as bond angle and dihedral angle distribution functions, are assumed to arise from only those configurations belonging to a given minimum. The validity of this hypothesis is illustrated by simulations of a continuum model of a heteropolymer whose low temperature state is a well‐defined β‐barrel structure. The simulations were done using a molecular dynamics algorithm (referred to as the “noisy” molecular dynamics method) containing both friction and noise terms. It is shown that for this model there are several distinct metastable minima in which the structural features are similar.Several new methods of analyzing fluctuations in structures belonging to two distinct minima are introduced. The most notable one is a dynamic measure of compactness that can in principle provide the time required for maximal compactness to be achieved. The analysis shows that for a given metastable state in which the protein has a well‐defined folded structure the transition to a state of higher compactness occurs very slowly, lending credence to the notion that the system encounters a late barrier in the process of folding to the most compact structure. The examination of the fluctuations in the structures near the unfolding → folding transition temperature indicates that the transition state for the unfolding to folding process occurs closer to

ISSN:0006-3525    

DOI:10.1002/bip.360320610

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1992

数据来源: WILEY

摘要:

AbstractSolute partitioning data for dilute solutions have almost invariably been interpreted by equating experimental values of –RTInKx(whereinKxis the mole fraction partition coefficient) to Δμ∞, the standard Gibbs energy change for solute transfer from one solvent to another. Recently, it has been alleged that this relation is insufficiently general. Instead, the statistical mechanical Flory‐Huggins (FH) theory has been recommended for use, because it is designed to account for disparities in molecular size between solute and solvent. Our examination of the thermodynamics of partitioning shows that: (1) The customary interpretation is not only entirely correct (providing only that the solute is dilute), but is model‐independent. (2) The dilute limit of the FH theory is seen to agree entirely with the usual interpretation of –RTInKx, once certain misnomers are cleared away. (3) The use of FH theory being urged upon us in fact serves only to extract from Δμ∞;(the latter quite correctly determined as –RTInKx) thecontact partof Δμ∞in order to obtain information on hydrophobic interactions. Some caveats are cited concerning such use of the FH statist

ISSN:0006-3525    

DOI:10.1002/bip.360320611

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1992

数据来源: WILEY