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Luis Moroder

Publications and source records attributed to Luis Moroder.

72 records · Page 4Linked to original sources
PubMed2002

Structural properties of a collagenous heterotrimer that mimics the collagenase cleavage site of collagen type I.

Collagens contain sequence- and conformation-dependent epitopes responsible for their digestion by collagenases at specific loci. A synthetic heterotrimer construct containing the collagenase cleavage site of collagen type I was found to mimic perfectly native collagen in terms of selectivity and mode of enzymatic degradation. The NMR conformational analysis of this molecule clearly revealed the presence of two structural domains, i.e. a triple helix spanning the Gly-Pro-Hyp repeats and a less ordered portion corresponding to the collagenase cleavage site where the three chains are aligned in extended conformation with loose interchain contacts. These structural properties allow for additional insights into the very particular mechanism of collagen digestion by collagenases.

Amino Acid Sequence↗
PubMed2002

Structural plasticity and noncovalent substrate binding in the GroEL apical domain. A study using electrospay ionization mass spectrometry and fluorescence binding studies.

Advances in understanding how GroEL binds to non-native proteins are reported. Conformational flexibility in the GroEL apical domain, which could account for the variety of substrates that GroEL binds, is illustrated by comparison of several independent crystallographic structures of apical domain constructs that show conformational plasticity in helices H and I. Additionally, ESI-MS indicates that apical domain constructs have co-populated conformations at neutral pH. To assess the ability of different apical domain conformers to bind co-chaperone and substrate, model peptides corresponding to the mobile loop of GroES and to helix D from rhodanese were studied. Analysis of apical domain-peptide complexes by ESI-MS indicates that only the folded or partially folded apical domain conformations form complexes that survive gas phase conditions. Fluorescence binding studies show that the apical domain can fully bind both peptides independently. No competition for binding was observed, suggesting the peptides have distinct apical domain-binding sites. Blocking the GroES-apical domain-binding site in GroEL rendered the chaperonin inactive in binding GroES and in assisting the folding of denatured rhodanese, but still capable of binding non-native proteins, supporting the conclusion that GroES and substrate proteins have, at least partially, distinct binding sites even in the intact GroEL tetradecamer.

Binding Sites↗
PubMed2002

Ultrafast spectroscopy reveals subnanosecond peptide conformational dynamics and validates molecular dynamics simulation.

Femtosecond time-resolved spectroscopy on model peptides with built-in light switches combined with computer simulation of light-triggered motions offers an attractive integrated approach toward the understanding of peptide conformational dynamics. It was applied to monitor the light-induced relaxation dynamics occurring on subnanosecond time scales in a peptide that was backbone-cyclized with an azobenzene derivative as optical switch and spectroscopic probe. The femtosecond spectra permit the clear distinguishing and characterization of the subpicosecond photoisomerization of the chromophore, the subsequent dissipation of vibrational energy, and the subnanosecond conformational relaxation of the peptide. The photochemical cis/trans-isomerization of the chromophore and the resulting peptide relaxations have been simulated with molecular dynamics calculations. The calculated reaction kinetics, as monitored by the energy content of the peptide, were found to match the spectroscopic data. Thus we verify that all-atom molecular dynamics simulations can quantitatively describe the subnanosecond conformational dynamics of peptides, strengthening confidence in corresponding predictions for longer time scales.

Computer Simulation↗
PubMed2002

Conformational and molecular modeling studies of sulfated cholecystokinin-15.

Conformational features of the C-terminal carboxyamidated pentadecapeptide of CCK (S(19)HRISDRD[SO(4)]-YMGWMDF(33)-NH(2)) were determined by NMR spectroscopy in a zwitterionic membrane-mimetic solvent system, composed of DPC micelles. The C-terminal octapeptide consisted of a well-defined pseudohelix that was nearly identical to the structure previously reported for nonsulfated CCK-8 in the same solvent system. N-terminal amino acids of CCK-15 were highly disordered, with no clear conformational preference. Extensive NOE-restrained molecular dynamics simulations of the CCK-15/CCK(1)-R complex suggested that almost all the experimentally determined intermolecular contact points provided by NMR, site-directed mutagenesis, and photoaffinity labeling could be simultaneously satisfied, when the N-terminus of the ligand is placed in close spatial proximity to the N-terminus of the receptor.

Amino Acid Sequence↗
PubMed2002

Single-molecule optomechanical cycle.

Light-powered molecular machines are conjectured to be essential constituents of future nanoscale devices. As a model for such systems, we have synthesized a polymer of bistable photosensitive azobenzenes. Individual polymers were investigated by single-molecule force spectroscopy in combination with optical excitation in total internal reflection. We were able to optically lengthen and contract individual polymers by switching the azo groups between their trans and cis configurations. The polymer was found to contract against an external force acting along the polymer backbone, thus delivering mechanical work. As a proof of principle, the polymer was operated in a periodic mode, demonstrating for the first time optomechanical energy conversion in a single-molecule device.

Azo Compounds↗
PubMed2002

Environmental mimic of receptor interaction: conformational analysis of CCK-15 in solution.

CCK-15, a peptide derived from the 115-membered CCK preprohormone, was the object of a comparative conformational analysis by NMR spectroscopy and molecular modeling methods. NMR data in several solvents demonstrate that the propensity of the peptide to fold into a helical conformation is intrinsic, not merely a consequence of the interaction with phosphatidylcholine micelles or with a putative receptor, as suggested by a previous study on CCK-8 (Pellegrini, M.; Mierke, D. Biochemistry 1999, 38, 14775-14783.). The prevailing CCK-15 conformer in a mixture 1,1,1,3,3,3-hexafluoroacetone/water reveals that the residues common to CCK-15 and CCK-8 assume very similar conformations. Our CCK-15 structure is consistent with the model of receptor interaction proposed by Pellegrini and Mierke and discloses possible novel interactions that involve a larger area of the putative receptor. The consensus structure between CCK-15 and CCK-8 shows a good superposition of the side chains of residues 12-14 with crucial moieties of two non-peptidic CCK-A antagonists.

Acetone↗
PubMed2002

Photomodulation of conformational states. III. Water-soluble bis-cysteinyl-peptides with (4-aminomethyl) phenylazobenzoic acid as backbone constituent.

In previous studies we have shown that light-induced cis/trans isomerization of the azobenzene moiety in cyclo-[Ala-Cys-Ala-Thr-Cys-Asp-Gly-Phe-AMPB] [AMPB: (4-aminomethyl)phenylazobenzoic acid] leads both in the monocyclic and in the oxidized bicyclic form to markedly differentiated conformational states in DMSO, a fact that lends itself for photomodulation of the redox potential of such bis-cysteinyl-peptides. For this purpose water-soluble systems are required, and this was achieved by replacing three residues outside the Cys-Ala-Thr-Cys active-site motif of thioredoxin reductase with lysines. The resulting cyclo-[Lys-Cys-Ala-Thr-Cys-Asp-Lys-Lys-AMPB] fully retains its photoresponsive properties in water as well assessed by uv and CD measurements. Paralleling results of the previously investigated azobenzene-containing cyclic peptides, the trans --> cis isomerization of the water-soluble monocyclic and oxidized bicyclic peptide is accompanied by a marked transition from a well-defined conformation to an ensemble of possible conformations. However, the conformational preferences are very dissimilar from those of the DMSO-soluble peptides. In fact, hydrogen bonds as well as secondary structure elements were found that change in the mono- and bicyclic peptide upon irradiation. The photo switch between different turn types and hydrogen bonding networks offers the structural rational for the significantly differentiated redox potentials, but also the possibility of monitoring by femtosecond uv-vis and ir spectroscopy fast and ultra fast backbone rearrangement processes following the electronic trans --> cis isomerization.

Amino Acid Sequence↗
PubMed2002

Synthesis of heterotrimeric collagen peptides containing the alpha1beta1 integrin recognition site of collagen type IV.

Collagen type IV provides a biomechanically stable scaffold into which the other constituents of basement membranes are incorporated, but it also plays an important role in cell adhesion. This occurs with collagen type IV mainly via the alpha1beta1 integrin, and the proposed epitope involved in this type of collagen/integrin interaction corresponds to a non-sequential R/Xaa/D motif, where the arginine and aspartate residues are provided by the alpha2 and alpha1 chains of the collagen molecule, respectively. Since the stagger of the three alpha chains in native collagen type IV is still unknown and different alignments of the chains lead to different spatial epitopes, two heterotrimeric collagen peptides containing the natural 457-469 sequences of the cell adhesion site were synthesized in which the single chains were assembled via disulfide bonds into the two most plausible alpha1alpha2alpha1' and alpha2alpha1alpha1' registers. The differentiated triple-helical stabilities of the two heterotrimers suggest a significant structural role of the chain register in collagen, although the binding to alpha1beta1 integrin is apparently less affected as indicated by preliminary experiments.

Amino Acid Sequence↗
PubMed2002

Conformation-dependent side reactions in interstrand-disulfide bridging of trimeric collagenous peptides by regioselective cysteine chemistry.

Conversion of single-chain or disulfide-bridged dimeric collagenous peptides into Cys(Npys) derivatives as activated species for subsequent regioselective thiol/disulfide exchange reactions leads to side products whose origin and nature was determined by HPLC and ESI-MS. In both cases the high tendency of the educts to self-associate into triple-helical homotrimers, as assessed by their dichroic properties in the reaction media, is responsible for the failure of this well established cysteine chemistry. Only by optimizing the synthetic strategy or by exploiting a kinetic control of the reaction, could these conformation-dependent limitations be more or less efficiently bypassed for the regioselective assembly of heterotrimeric collagen model peptides crosslinked with artificial cystine knots.

Amino Acid Sequence↗
PubMed2002

Redox-active cyclic bis(cysteinyl)peptides as catalysts for in vitro oxidative protein folding.

The active-site hexapeptides of glutaredoxin (Grx), thioredoxin (Trx), protein disulfide isomerase (PDI), and thioredoxin-reductase (Trr) containing the common motif Cys-Xaa-Yaa-Cys were conformationally restricted by backbone cyclization, and their redox potentials were found to increase in the rank order of Trr < Grx < Trx < PDI peptide, with E'(0) values ranging between -204 mV and -130 mV. In each peptide the thiol pK(a) of one Cys residue was found to be lower than the other (e.g., 7.3 against 9.6 in the PDI peptide). Both the yield and rate of refolding of reduced RNase A in the presence of the bis(cysteinyl)peptides increased with the oxidizing character of the cyclic compounds. These results show that small peptides can function as adjuvants for the in vitro oxidative folding of proteins.

Amino Acid Sequence↗
PubMed2002

Practical aspects of the 2D 15N-[1h]-NOE experiment.

The heteronuclear 15N-NOE experiment was extensively tested with respect to statistical and systematic experimental error. The dependence of signal intensity in the NOE experiment and in the reference experiment on the saturation and relaxation time was experimentally investigated. The statistics of the experimental values were accessed by numerous repetitions of identical set-ups. As a model system a protein of typical size for NMR studies was chosen, i.e., a 120 amino acid residues containing fragment of the F-actin binding gelation factor (ABP-120). The fragment exhibits fast dynamics that are accessible with the 15N-NOE experiment with various amplitudes. The results of this study show that commonly used parameters are only adequate for accurate measurement of motions with moderate amplitude. Highly flexible parts require longer delay times and thus more experimental time than commonly used. On the other hand, a qualitative or semi-quantitative assessment of a protein's mobility on fast times scales can be obtained from rapidly recorded experiments with unusual short delay times. The findings of this study are of equal importance for highly accurate measurement of the 15N-NOE as well as for quick identification of mobile or even unstructured residues/parts of a protein.

Carrier Proteins↗
PubMed2002

Structure of cholecystokinin receptor binding sites and mechanism of activation/inactivation by agonists/antagonists.

Delineation of CCK receptor binding sites is a prerequisite for the understanding of the molecular basis for ligand recognition, partial agonism, ligand-induced traffiking of receptor signalling. In the current paper, we illustrate how, in the past 5 years, studies from our laboratory and others have provided new data on the molecular basis of the pharmacology and functioning of CCK1 and CCK2 receptors. Available data on CCK1 and CCK2R binding sites indicate that 1) homologous regions of the two receptors are involved in the binding site of CCK, however, positioning of CCK slightly differs; 2) binding sites of non-peptide agonists/antagonist are buried in the pocket formed by transmembrane helices and overlap that of CCK and 3) residues of the binding sites as well as of conserved motifs such as E/DRY, NPXXY are crucial for receptor activation.

Amino Acid Sequence↗
PubMed2001

The biologically crucial C terminus of cholecystokinin and the non-peptide agonist SR-146,131 share a common binding site in the human CCK1 receptor. Evidence for a crucial role of Met-121 in the activation process.

The cholecystokinin (CCK) receptor-1 (CCK1R) is a G protein-coupled receptor, which mediates important central and peripheral cholecystokinin actions. Our aim was to progress in mapping of the CCK1R binding site by identifying residues that interact with the methionine and phenylalanine residues of the C-terminal moiety of CCK because these are crucial for its binding and biological activity, and to determine whether CCK and the selective non-peptide agonist, SR-146,131, share a common binding site. Identification of putative amino acids of the CCK1R binding site was achieved by dynamics-based docking of the ligand CCK in a refined three-dimensional model of the CCK1R using, as constraints, previous results that identified contact points between residues of CCK and CCK1R (Kennedy, K., Gigoux, V., Escrieut, C., Maigret, B., Martinez, J., Moroder, L., Frehel, D., Gully, D., Vaysse, N., and Fourmy, D. (1997) J. Biol. Chem. 272, 2920-2926 and Gigoux, V., Escrieut, C., Fehrentz, J. A., Poirot, S., Maigret, B., Moroder, L., Gully, D., Martinez, J., Vaysse, N., and Fourmy, D. (1999) J. Biol. Chem. 274, 20457-20464). By this approach, a series of residues forming connected hydrophobic clusters were identified. Pharmacological and functional analysis of mutated receptors indicated that a network of hydrophobic residues including Cys-94, Met-121, Val-125, Phe-218, Ile-329, Phe-330, Trp-326, Ile-352, Leu-356, and Tyr-360, is involved in the binding site for CCK and in the activation process of the CCK1R. Within this hydrophobic network, the physico-chemical nature of residue 121 seems to be essential for CCK1R functioning. Finally, the biological properties of mutants together with dynamic docking of SR-146,131 in the CCK1R binding site demonstrated that SR-146,131 occupies a region of CCK1R binding site which interacts with the C-terminal amidated tripeptide of CCK, i.e. Met-Asp-Phe-NH(2). These new and important insights will serve to better understand the activation process of CCK1R and to design or optimize ligands.

Amino Acid Sequence↗
PubMedDate not supplied

(R)-3-Amidinophenylalanine-derived inhibitors of factor Xa with a novel active-site binding mode.

A putative non-substrate like binding mode of (R)-3-amidinophenylalanine derivatives to factor Xa, as derived from modeling experiments based on X-ray analysis of their complexes with trypsin, was used to design a new generation of inhibitors. However, the resulting inhibitory potencies were not at all consistent with the working assumption, although with an adamantyl-ureido derivative of (R)-3-amidinophenylalanine phenetyl amide a highly selective nanomolar inhibition of factor Xa was achieved. The X-ray analysis of the complex of this ligand with factor Xa revealed an unexpected new binding mode, of which the most important feature is the interaction of the C-terminal aryl moiety with a hydrophobic subregion of the S1 subsite, while the adamantyl group occupies the hydrophobic S3/S4 subsites of the enzyme.

Binding Sites↗