Home About us Contact
|
Home About us Contact | ||
|
|
||
Backbone Conformation (backbone + conformation)
Selected AbstractsEfficient Synthesis of Structurally Diverse Diazabicycloalkanes: Scaffolds for Modular Dipeptide Mimetics with Tunable Backbone ConformationsEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 7 2004Wolfgang Maison Abstract A stereoselective synthesis of new dipeptide mimetics based on a diazabicycloalkane scaffold is reported. The route starts from enantiomerically pure azabicycloalkenes 1 that are bis(hydroxylated) and coupled N -terminally to a second amino acid. The key step of the reaction sequence is an oxidative cleavage of the resulting dipeptides 5 to give highly functionalised diazabicycloalkanes 6, which can be easily converted into a number of dipeptide mimetics with defined and variable stereochemistry and a number of different amino acid side chains. The backbone dihedral angles within these dipeptide mimetics can be tuned by varying the stereochemistry and the ring sizes of the diazabicycloalkane scaffold. The syntheses of conformationally constrained dipeptide analogues in four to five steps are presented. With the syntheses of dipeptide mimetics 19a,c, suitable linker moieties for conjugation of diazabicycloalkanes to other functional molecules like markers or solid phases are introduced, making these compounds modular dipeptide mimetics that might find applications as modular ligands or as solid-phase-attached scaffolds in combinatorial chemistry. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004) [source] Deamidation of labile asparagine residues in the autoregulatory sequence of human phenylalanine hydroxylaseFEBS JOURNAL, Issue 5 2003Structural, functional implications Two dimensional electrophoresis has revealed a microheterogeneity in the recombinant human phenylalanine hydroxylase (hPAH) protomer, that is the result of spontaneous nonenzymatic deamidations of labile asparagine (Asn) residues [Solstad, T. and Flatmark, T. (2000) Eur. J. Biochem.267, 6302,6310]. Using of a computer algorithm, the relative deamidation rates of all Asn residues in hPAH have been predicted, and we here verify that Asn32, followed by a glycine residue, as well as Asn28 and Asn30 in a loop region of the N-terminal autoregulatory sequence (residues 19,33) of wt-hPAH, are among the susceptible residues. First, on MALDI-TOF mass spectrometry of the 24 h expressed enzyme, the E. coli 28-residue peptide, L15,K42 (containing three Asn residues), was recovered with four monoisotopic mass numbers (i.e., m/z of 3106.455, 3107.470, 3108.474 and 3109.476, of decreasing intensity) that differed by 1 Da. Secondly, by reverse-phase chromatography, isoaspartyl (isoAsp) was demonstrated in this 28-residue peptide by its methylation by protein- l -isoaspartic acid O -methyltransferase (PIMT; EC 2.1.1.77). Thirdly, on incubation at pH 7.0 and 37 °C of the phosphorylated form (at Ser16) of this 28-residue peptide, a time-dependent mobility shift from tR,,34 min to ,,31 min (i.e., to a more hydrophilic position) was observed on reverse-phase chromatography, and the recovery of the tR,,34 min species decreased with a biphasic time-course with t0.5 -values of 1.9 and 6.2 days. The fastest rate is compatible with the rate determined for the sequence-controlled deamidation of Asn32 (in a pentapeptide without 3D structural interference), i.e., a deamidation half-time of ,,1.5 days in 150 mm Tris/HCl, pH 7.0 at 37 °C. Asn32 is located in a cluster of three Asn residues (Asn28, Asn30 and Asn32) of a loop structure stabilized by a hydrogen-bond network. Deamidation of Asn32 introduces a negative charge and a partial ,-isomerization (isoAsp), which is predicted to result in a change in the backbone conformation of the loop structure and a repositioning of the autoregulatory sequence and thus affect its regulatory properties. The functional implications of this deamidation was further studied by site-directed mutagenesis, and the mutant form (Asn32,Asp) revealed a 1.7-fold increase in the catalytic efficiency, an increased affinity and positive cooperativity of L-Phe binding as well as substrate inhibition. [source] High resolution X-ray analysis of two mutants of a curaremimetic snake toxinFEBS JOURNAL, Issue 5 2000Jean-François Gaucher A previous mutational analysis of erabutoxin a (Ea), a curaremimetic toxin from sea snake venom, showed that the substitutions S8G and S8T caused, respectively, 176-fold and 780-fold affinity decreases for the nicotinic acetylcholine receptor (AchR). In view of the fact that the side-chain of Ser8 is buried in the wild-type toxin, we wondered whether these affinity changes reflect a direct binding contribution of S8 to the receptor and/or conformational changes that could have occurred in Ea as a result of the introduced mutations. To approach this question, we solved X-ray structures of the two mutants S8G and S8T at high resolution (0.18 nm and 0.17 nm, with R factors of 18.0% and 17.9%, respectively). The data show that none of the mutations significantly modified the toxin structure. Even within the site where the toxin binds to the receptor the backbone conformation remained unchanged. Therefore, the low affinities of the mutants S8T and S8G cannot be explained by a large conformational change of the toxin structure. Although we cannot exclude the possibility that undetectable structural changes have occurred in the toxin mutants, our data support the view that, although buried between loop I and II, S8 is part of the functional epitope of the toxin. [source] Solution, solid phase and computational structures of apicidin and its backbone-reduced analogsJOURNAL OF PEPTIDE SCIENCE, Issue 6 2006Michael Kranz Abstract The recently isolated broad-spectrum antiparasitic apicidin (1) is one of the few naturally occurring cyclic tetrapeptides (CTP). Depending on the solvent, the backbone of 1 exhibits two ,-turns (in CH2Cl2) or a ,-turn (in DMSO), differing solely in the rotation of the plane of one of the amide bonds. In the X-ray crystal structure, the peptidic COs and NHs are on opposite sides of the backbone plane, giving rise to infinite stacks of cyclotetrapeptides connected by three intermolecular hydrogen bonds between the backbones. Conformational searches (Amber force field) on a truncated model system of 1 confirm all three backbone conformations to be low-energy states. The previously synthesized analogs of 1 containing a reduced amide bond exhibit the same backbone conformation as 1 in DMSO, which is confirmed further by the X-ray crystal structure of a model system of the desoxy analogs of 1. This similarity helps in explaining why the desoxy analogs retain some of the antiprotozoal activities of apicidin. The backbone-reduction approach designed to facilitate the cyclization step of the acyclic precursors of the CTPs seems to retain the conformational preferences of the parent peptide backbone. Copyright © 2005 European Peptide Society and John Wiley & Sons, Ltd. [source] Raman microspectroscopic study on low-pH-induced DNA structural transitions in the presence of magnesium ionsJOURNAL OF RAMAN SPECTROSCOPY, Issue 10 2002C. M. Muntean Low-pH-induced DNA structural changes were investigated in the pH range 6.8,2.10 by Raman microspectroscopy. Measurements were carried out on calf thymus DNA in the presence of low concentrations of Mg2+ ions. Vibrational spectra are presented in the wavenumber region 500,1650 cm,1. Large changes in the Raman spectra of calf-thymus DNA were observed on lowering the pH value. These are due to protonation and unstacking of the DNA bases during DNA melting and also to changes in the DNA backbone conformation. The intensities of the Raman bands of guanine (681 cm,1), adenine (728 cm,1), thymine (752 cm,1) and cytosine (785 cm,1), typical of the C2,- endo - anti conformation of B-DNA, are discussed. The B-form marker near 835 cm,1 and the base vibrations in the higher wavenumber region (1200,1680 cm,1) are analysed. Effects of low pH value upon the protonation mechanism of opening AT and changing the protonation of GC base pairs in DNA are discussed. Copyright © 2002 John Wiley & Sons, Ltd. [source] Conformational constraints in solid-state NMR of uniformly labeled polypeptides from double single-quantum-filtered rotational echo double resonance,MAGNETIC RESONANCE IN CHEMISTRY, Issue S1 2007Nathan A. Oyler Abstract A solid-state nuclear magnetic resonance (NMR) technique is described for obtaining constraints on the backbone conformation of a protein or peptide that is prepared with uniform 15N,13C labeling of consecutive pairs of amino acids or of longer segments. The technique, called double single-quantum-filtered rotational echo double resonance (DSQ-REDOR), uses frequency-selective REDOR to prepare DSQ coherences involving directly bonded backbone 13CO and 15NH sites, to dephase these coherences under longer-range 15NH13CO dipole-dipole couplings in a conformationally dependent manner, and to convert the remaining DSQ coherences to detectable transverse 13C-spin polarization. The efficacy of DSQ-REDOR is demonstrated in experiments on two isotopically labeled samples, the helical peptide MB(i + 4)EK and the amyloid-forming peptide A,11,25. Published in 2007 John Wiley & Sons, Ltd. [source] Photophysics of organic emissive semiconductors under hydrostatic pressurePHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 14 2004S. Guha Abstract The impact of hydrostatic pressure on conjugated organic semiconductors has been studied using optical spectroscopic techniques. This work focuses on three blue emitters with distinct backbone conformations: planar methylated ladder-type poly para phenylene, semi-planar polyfluorene (PF), and nonplanar para hexaphenyl. The effect of pressure on the backbone emission and defect related emission allows an understanding of the localized, delocalized electronic states and energy transfer mechanisms of the singlet excitons into defect states. The Raman spectrum of the organic emitters under pressure demonstrates changes in the backbone conformation and mesomorphic phases. The Raman peaks in PF exhibit asymmetric Fano-type line shapes beyond 40 kbar, where the defect emission is enhanced. (© 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Cleavage of the iron-methionine bond in c-type cytochromes: Crystal structure of oxidized and reduced cytochrome c2 from Rhodopseudomonas palustris and its ammonia complexPROTEIN SCIENCE, Issue 1 2002Silvano Geremia Abstract The three-dimensional structures of the native cytochrome c2 from Rhodopseudomonas palustris and of its ammonia complex have been obtained at pH 4.4 and pH 8.5, respectively. The structure of the native form has been refined in the oxidized state at 1.70 Å and in the reduced state at 1.95 Å resolution. These are the first high-resolution crystal structures in both oxidation states of a cytochrome c2 with relatively high redox potential (+350 mV). The differences between the two oxidation states of the native form, including the position of internal water molecules, are small. The unusual six-residue insertion Gly82-Ala87, which precedes the heme binding Met93, forms an isolated 310 -helix secondary structural element not previously observed in other c-type cytochromes. Furthermore, this cytochrome shows an external methionine residue involved in a strained folding near the exposed edge of the heme. The structural comparison of the present cytochrome c2 with other c-type cytochromes has revealed that the presence of such a residue, with torsion angles , and , of approximately ,140 and ,130°, respectively, is a typical feature of this family of proteins. The refined crystal structure of the ammonia complex, obtained at 1.15 Å resolution, shows that the sulphur atom of the Met93 axial ligand does not coordinate the heme iron atom, but is replaced by an exogenous ammonia molecule. This is the only example so far reported of an X-ray structure with the heme iron coordinated by an ammonia molecule. The detachment of Met93 is accompanied by a very localized change in backbone conformation, involving mainly the residues Lys92, Met93, and Thr94. Previous studies under typical denaturing conditions, including high-pH values and the presence of exogenous ligands, have shown that the detachment of the Met axial ligand is a basic step in the folding/unfolding process of c-type cytochromes. The ammonia adduct represents a structural model for this important step of the unfolding pathway. Factors proposed to be important for the methionine dissociation are the strength of the H-bond between the Met93 and Tyr66 residues that stabilizes the native form, and the presence in this bacterial cytochrome c2 of the rare six-residue insertion in the helix 310 conformation that increases Met loop flexibility. [source] Antimicrobial peptide RP-1 structure and interactions with anionic versus zwitterionic micellesBIOPOLYMERS, Issue 1 2009Sarah Bourbigot Abstract Topologically, platelet factor-4 kinocidins consist of distinct N-terminal extended, C-terminal helical, and interposing ,-core structural domains. The C-terminal ,-helices autonomously confer direct microbicidal activity, and the synthetic antimicrobial peptide RP-1 is modeled upon these domains. In this study, the structure of RP-1 was assessed using several complementary techniques. The high-resolution structure of RP-1 was determined by NMR in anionic sodium dodecyl sulfate (SDS) and zwitterionic dodecylphosphocholine (DPC) micelles, which approximate prokaryotic and eukaryotic membranes, respectively. NMR data indicate the peptide assumes an amphipathic ,-helical backbone conformation in both micelle environments. However, small differences were observed in the side-chain orientations of lysine, tyrosine, and phenylalanine residues in SDS versus DPC environments. NMR experiments with a paramagnetic probe indicated differences in positioning of the peptide within the two micelle types. Molecular dynamics (MD) simulations of the peptide in both micelle types were also performed to add insight into the peptide/micelle interactions and to assess the validity of this technique to predict the structure of peptides in complex with micelles. MD independently predicted RP-1 to interact only peripherally with the DPC micelle, leaving its spherical shape intact. In contrast, RP-1 entered deeply into and significantly distorted the SDS micelle. Overall, the experimental and MD results support a preferential specificity of RP-1 for anionic membranes over zwitterionic membranes. This specificity likely derives from differences in RP-1 interaction with distinct lipid systems, including subtle differences in side chain orientations, rather than gross changes in RP-1 structure in the two lipid environments. © 2008 Wiley Periodicals, Inc. Biopolymers 91: 1,13, 2009. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Fourier transform vibrational circular dichroism as a decisive tool for conformational studies of peptides containing tyrosyl residuesBIOPOLYMERS, Issue 1 2003Attila Borics Abstract Previous UV,circular dichroism (UV,CD) and NMR studies showed that Ac-AAAAAAAEAAKA-NH2 has an ,-helical structure in 50% (v/v) aqueous trifluoroethanol. Replacement of Ala1 to Ala6 with Tyr results in spectra that show an apparent loss of helicity in the same solvent. This apparent loss of helicity could be attributed to the coupling of the tyrosyl side chain chromophore with the backbone amide. However, such electronic coupling does not affect the vibrational CD (VCD) spectra. The VCD spectra of the peptides with tyrosyl residues were identical to that of the peptide containing no Tyr, which shows the same ,-helical structure. Because it is now clear that Tyr replacement does not change the backbone conformation of peptides, UV,CD measurements should be complemented by VCD to determine the secondary structure when electronic effects can disturb the UV,CD spectrum of the inherent structure. © 2002 Wiley Periodicals, Inc. Biopolymers (Biospectroscopy) 72: 21,24, 2003 [source] Probing multiple effects on 15N, 13C,, 13C,, and 13C, chemical shifts in peptides using density functional theoryBIOPOLYMERS, Issue 6 2002Xiao-Ping Xu Abstract We have used density functional calculations on model peptides to study conformational effects on 15N, 13C,, 13C,, and 13C, chemical shifts, associated with hydrogen bonding, backbone conformation, and side-chain orientation. The results show a significant dependence on the backbone torsion angles of the nearest three residues. Contributions to 15N chemical shifts from hydrogen bonding (up to 8 ppm), backbone conformation (up to 13 ppm), side-chain orientation and neighborhood residue effects (up to 22 ppm) are significant, and a unified theory will be required to account for their behavior in proteins. In contrast to this, the dependence on sequence and hydrogen bonding is much less for 13C, and 13C, chemical shifts (<0.5 ppm), and moderate for carbonyl carbon shifts (<2 ppm). The effects of side-chain orientation are mainly limited to the residue itself for both nitrogen and carbon, but the ,1 effect is also significant for the nitrogen shift of the following residue and for the 13C, shift of the preceding residue. The calculated results are used, in conjunction with an additive model of chemical shift contributions, to create an algorithm for prediction of 15N and 13C shifts in proteins from their structure; this includes a model to extrapolate results to regions of torsion angle space that have not been explicitly studied by density functional theory (DFT) calculations. Crystal structures of 20 proteins with measured shifts have been used to test the prediction scheme. Root mean square deviations between calculated and experimental shifts 2.71, 1.22, 1.31, and 1.28 ppm for N, C,, C,, and C,, respectively. This prediction algorithm should be helpful in NMR assignment, crystal and solution structure comparison, and structure refinement. © 2002 Wiley Periodicals, Inc. Biopolymers 65: 408,423, 2002 [source] The ribbon of hydrogen bonds and the pseudomolecule in the three-dimensional structure of globular proteins.BIOPOLYMERS, Issue 5 2002Abstract The model of the three-dimensional structure of globular proteins, which is based on a ribbon of hydrogen bonds along the whole of the backbone, is now applied to the comparison between monomeric bovine pancreatic ribonuclease A and dimeric bovine seminal ribonuclease. Some waters are involved in the hydrogen bonding of the ribbon, and the protein molecule plus these waters forms a pseudomolecule. The conformations of the three backbones are essentially identical and the three ribbons of hydrogen bonds are conserved with greater than 90% accuracy. We suggest that the conservation of the backbone conformations of the two molecules is a consequence of the conservation of the ribbons of hydrogen bonds. There are 16 simple mutations between the two molecules, of which 15 involve only side-chain groups with no more than one hydrogen bond to the backbone. Such mutations are not sufficient to change the ribbon of hydrogen bonds and hence there is no change in the backbone conformation. Generalizing this result, we suggest that the conservation of the ribbon is the reason why single point mutations rarely change the conformation of the backbone of the globular proteins. © 2002 Wiley Periodicals, Inc. Biopolymers 65: 347,353, 2002 [source] Nuclear magnetic resonance studies of CXC chemokine receptor 4 allosteric peptide agonists in solutionCHEMICAL BIOLOGY & DRUG DESIGN, Issue 2005O.K. Baryshnikova Abstract:, CXC chemokine receptor 4 (CXCR4) is an important pharmacological target due to its involvement in HIV-1 pathogenesis and cancer metastasis. Two recently discovered allosteric agonists that bind and activate CXCR4, the ASLW and RSVM peptides, were analyzed using solution nuclear magnetic resonance spectroscopy. Both peptides assumed an extended backbone conformation with several well-defined local motifs in the regions from residues 5 to 8 and 9 to 12. The local structures in the region of residues 5,8 were different for agonists studied here and natural ligands. The local structure in the region 9,12 was adopted by the entire ensemble of the ASLW peptide structures and by the subset of conformations for the RSVM peptide. The same turn was found in full-length stromal derived factor (SDF)-1 and in the small family of the SDF-1 N-terminal 17-mer. Similar examples in literature suggest the relevance of nascent structures in peptides to their biologically relevant conformations. The significance of found local structures and implications for further drug design are discussed. [source] Incorporation of vinylogous scaffolds in the C-terminal tripeptide of substance PCHEMICAL BIOLOGY & DRUG DESIGN, Issue 5 2004S. Claudel Abstract:, Glycine-9 and leucine-10 of substance P (SP) are critical for (NK)-1 receptor recognition and agonist activity. Pro,(Z)-CH=CH(CH3)-CONH)Leu (or Met) and Pro,((E) -CH=CH(CH3)-CONH)Leu (or Met) have been introduced in the sequence of SP, in order to restrict the conformational flexibility of the C-terminal tripeptide, Gly-Leu-Met-NH2, of SP. Pro,((Z) -CH=C(CH2CH(CH3)2)-CONH)Met-NH2, with an isobutyl substituent to mimic the Leu side-chain, was also incorporated in place of the C-terminal tripeptide. The substituted-SP analogs were tested for their affinity to human NK-1 receptor specific binding sites (NK-1M and NK-1m) and their potency to stimulate adenylate cyclase and phospholipase C in Chinese Hamster ovary (CHO) cells transfected with the human NK-1 receptor. The most potent SP analogs [Pro9,((Z)CH=C(CH3)CONH)Leu10]SP and [Pro9, ((E)CH=C(CH3)CONH)Leu10]SP, are about 100-fold less potent than SP on both binding sites and second messenger pathways. These vinylogous (Z) - or (E) -CH=C(CH3)- or (Z) -CH=C(CH2CH(CH3)2) moieties hamper the correct positioning of the C-terminal tripeptide of SP within both the NK-1M- and NK-1m-specific binding sites. The origin of these lower potencies is related either to an incorrect peptidic backbone conformation and/or an unfavorable receptor interaction of the methyl or isobutyl group. [source] NMR solution structure of a potent cyclic nonapeptide inhibitor of ICAM-1-mediated leukocyte adhesion produced by homologous amino acid substitutionCHEMICAL BIOLOGY & DRUG DESIGN, Issue 4 2004L.O. Sillerud Abstract:, We have previously described a disulfide-linked cyclic nonapeptide (inhibitory peptide-01, IP01), with the sequence CLLRMRSIC, which binds to intercellular adhesion molecule-1 (ICAM-1), and blocks binding to its counter-structure, the integrin ,L,2 (leukocyte functional antigen-1, LFA-1) (Sillerud et al., J. Peptide Res. 62, 2003: 97). We now report the optimization of this peptide by means of single homologous amino acid substitutions to yield a new peptide (IP02-K6; CLLRMKSAC) which shows an approximately sixfold improvement in inhibitory activity of multivalent leukocyte binding (inhibition constant for 50% inhibition, IC50 = 90 ,m) compared with IP01 (IC50 = 580 ,m). This improvement in activity gives IP02-K6 potent in vivo activity in a murine model of ischemia reperfusion injury (Merchant et al., Am. J. Physiol. Heart Circ. 284, 2003: H1260). In order to determine the structural features relevant to ICAM-1-binding, we have determined the structure of IP02-K6 using proton nuclear magnetic resonance (NMR) spectroscopy and restrained molecular modeling. In our previously reported study of solution models of IP01, we observed three interconverting conformations during low-temperature molecular dynamics simulation. In the present study, we find a single conformation of IP02-K6 similar to one of the previously found conformations of IP01 (family C). In particular, an R4-S7 , -turn is present in similar proportions in both conformation C of IP01 and in IP02-K6; this motif is important in binding to ICAM-1 because this turn enables the IP02-K6 backbone to drape over proline-36 on ICAM-1. The NMR-derived solution model of IP02-K6 was found to dock at the ,L,2 -binding site on ICAM-1 with no changes in peptide backbone conformation. This docking model displaced five of the 15 ,L,2 residues at the ICAM-1-binding site and provided a rationale for understanding the quantitative relationship between IP02-K6 structure and biologic activity. [source] Synthesis, Structure, and Nonlinear Optical Properties of Cross-Conjugated Perphenylated iso -PolydiacetylenesCHEMISTRY - A EUROPEAN JOURNAL, Issue 1 2005Yuming Zhao Prof. Abstract Monodisperse, cross-conjugated perphenylated iso- polydiacetylene (iso- PDA) oligomers, ranging from monomer 15 to pentadecamer 25, have been synthesized by using a palladium-catalyzed cross-coupling protocol. Structural characteristics elucidated by X-ray crystallographic analysis demonstrate a non-planar backbone conformation for the oligomers due to the steric interactions between alkylidene phenyl groups. The electronic absorption spectra of the oligomers show a slight red-shift of the maximum absorption wavelength as the chain length increases from dimer 17,b to pentadecamer 25, a trend that has saturated by the stage of nonamer 22. Fluorescence spectroscopy confirms that the pendent phenyl groups present on the oligomer framework enhance emission, and the relative emission intensity consistently increases as a function of chain length n. The molecular third-order nonlinearities, ,, for this oligomer series have been measured via differential optical Kerr effect (DOKE) detection and show a superlinear increase as a function of the oligomer chain length n. Molecular modeling and spectroscopic studies suggest that iso- PDA oligomers (n>7) adopt a coiled, helical conformation in solution. [source] Solution, solid phase and computational structures of apicidin and its backbone-reduced analogsJOURNAL OF PEPTIDE SCIENCE, Issue 6 2006Michael Kranz Abstract The recently isolated broad-spectrum antiparasitic apicidin (1) is one of the few naturally occurring cyclic tetrapeptides (CTP). Depending on the solvent, the backbone of 1 exhibits two ,-turns (in CH2Cl2) or a ,-turn (in DMSO), differing solely in the rotation of the plane of one of the amide bonds. In the X-ray crystal structure, the peptidic COs and NHs are on opposite sides of the backbone plane, giving rise to infinite stacks of cyclotetrapeptides connected by three intermolecular hydrogen bonds between the backbones. Conformational searches (Amber force field) on a truncated model system of 1 confirm all three backbone conformations to be low-energy states. The previously synthesized analogs of 1 containing a reduced amide bond exhibit the same backbone conformation as 1 in DMSO, which is confirmed further by the X-ray crystal structure of a model system of the desoxy analogs of 1. This similarity helps in explaining why the desoxy analogs retain some of the antiprotozoal activities of apicidin. The backbone-reduction approach designed to facilitate the cyclization step of the acyclic precursors of the CTPs seems to retain the conformational preferences of the parent peptide backbone. Copyright © 2005 European Peptide Society and John Wiley & Sons, Ltd. [source] Photophysics of organic emissive semiconductors under hydrostatic pressurePHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 14 2004S. Guha Abstract The impact of hydrostatic pressure on conjugated organic semiconductors has been studied using optical spectroscopic techniques. This work focuses on three blue emitters with distinct backbone conformations: planar methylated ladder-type poly para phenylene, semi-planar polyfluorene (PF), and nonplanar para hexaphenyl. The effect of pressure on the backbone emission and defect related emission allows an understanding of the localized, delocalized electronic states and energy transfer mechanisms of the singlet excitons into defect states. The Raman spectrum of the organic emitters under pressure demonstrates changes in the backbone conformation and mesomorphic phases. The Raman peaks in PF exhibit asymmetric Fano-type line shapes beyond 40 kbar, where the defect emission is enhanced. (© 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Physical-chemical determinants of turn conformations in globular proteinsPROTEIN SCIENCE, Issue 8 2007Timothy O. Street Abstract Globular proteins are assemblies of ,-helices and ,-strands, interconnected by reverse turns and longer loops. Most short turns can be classified readily into a limited repertoire of discrete backbone conformations, but the physical,chemical determinants of these distinct conformational basins remain an open question. We investigated this question by exhaustive analysis of all backbone conformations accessible to short chain segments bracketed by either an ,-helix or a ,-strand (i.e., ,-segment-,, ,-segment-,, ,-segment-,, and ,-segment-,) in a nine-state model. We find that each of these four secondary structure environments imposes its own unique steric and hydrogen-bonding constraints on the intervening segment, resulting in a limited repertoire of conformations. In greater detail, an exhaustive set of conformations was generated for short backbone segments having reverse-turn chain topology and bracketed between elements of secondary structure. This set was filtered, and only clash-free, hydrogen-bond,satisfied conformers having reverse-turn topology were retained. The filtered set includes authentic turn conformations, observed in proteins of known structure, but little else. In particular, over 99% of the alternative conformations failed to satisfy at least one criterion and were excluded from the filtered set. Furthermore, almost all of the remaining alternative conformations have close tolerances that would be too tight to accommodate side chains longer than a single ,-carbon. These results provide a molecular explanation for the observation that reverse turns between elements of regular secondary can be classified into a small number of discrete conformations. [source] The ribbon of hydrogen bonds and the pseudomolecule in the three-dimensional structure of globular proteins.BIOPOLYMERS, Issue 5 2002Abstract The model of the three-dimensional structure of globular proteins, which is based on a ribbon of hydrogen bonds along the whole of the backbone, is now applied to the comparison between monomeric bovine pancreatic ribonuclease A and dimeric bovine seminal ribonuclease. Some waters are involved in the hydrogen bonding of the ribbon, and the protein molecule plus these waters forms a pseudomolecule. The conformations of the three backbones are essentially identical and the three ribbons of hydrogen bonds are conserved with greater than 90% accuracy. We suggest that the conservation of the backbone conformations of the two molecules is a consequence of the conservation of the ribbons of hydrogen bonds. There are 16 simple mutations between the two molecules, of which 15 involve only side-chain groups with no more than one hydrogen bond to the backbone. Such mutations are not sufficient to change the ribbon of hydrogen bonds and hence there is no change in the backbone conformation. Generalizing this result, we suggest that the conservation of the ribbon is the reason why single point mutations rarely change the conformation of the backbone of the globular proteins. © 2002 Wiley Periodicals, Inc. Biopolymers 65: 347,353, 2002 [source] Cross-reactive and species-specific immunoglobulin E epitopes of plant profilins: an experimental and structure-based analysisCLINICAL & EXPERIMENTAL ALLERGY, Issue 7 2006C. Radauer Summary Background Profilins are cross-reactive plant allergens responsible for multiple pollen sensitization and pollen-associated food allergy. While it is assumed that profilins from different species are immunologically equivalent, some studies suggest partial or even lacking IgE cross-reactivity between certain profilins. Objective We aimed to obtain a semi-quantitative assessment of the contributions of conserved and species-specific epitopes to IgE binding of plant profilins. Methods We compared model structures of profilins from timothy, mugwort, celery and bell pepper with crystal structures of birch and latex profilins. We predicted potential conformational epitopes that consisted of contiguous patches of at least 20% surface-exposed residues. Celery and timothy profilins were purified from their natural sources, and profilins from birch, mugwort, bell pepper and latex were expressed in Escherichia coli. The structural integrity of all purified proteins was confirmed by circular dichroism spectroscopy. IgE ELISAs and ELISA inhibitions using sera from 22 profilin-sensitized allergic patients were carried out. Results Peptide backbone conformations of all six profilins were highly similar. Nine variable epitopes and two containing high proportions of conserved residues were predicted. IgE from all sera bound to all tested profilins and the amounts were highly correlated. However, IgE inhibition experiments revealed that up to 60% of total IgE binding was mediated by species-specific epitopes. The extent of cross-reactivity among profilins from timothy, birch, latex and celery was greater than cross-reactivity to mugwort and bell pepper profilins. This pattern was mirrored by sequence similarities among one of the predicted variable epitopes. Patients with IgE to cross-reactive epitopes displayed allergic reactions to a greater number of plant foods than patients having IgE directed to species-specific epitopes. Conclusion The large extent of cross-reactivity among plant profilins justifies using a single profilin for diagnosis. However, the fine specificity of IgE directed to variable epitopes may influence the clinical manifestation of profilin sensitization. [source] | ||||||||||