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Conformational Equilibrium (conformational + equilibrium)
Selected AbstractsMultiple polypeptide forms observed in two-dimensional gels of Methylococcus capsulatus (Bath) polypeptides are generated during the separation procedureELECTROPHORESIS, Issue 4 2003Frode S. Berven Abstract We have examined two-dimensional electrophoresis (2-DE) gel maps of polypeptides from the Gram-negative bacterium Methylococcus capsulatus (Bath) and found the same widespread trains of spots as often reported in 2-DE gels of polypeptides of other Gram-negative bacteria. Some of the trains of polypeptides, both from the outer membrane and soluble protein fraction, were shown to be generated during the separation procedure of 2-DE, and not by covalent post-translational modifications. The trains were found to be regenerated when rerunning individual polypeptide spots. The polypeptides analysed giving this type of trains were all found to be classified as stable polypeptides according to the instability index of Guruprasad et al. (Protein Eng. 1990, 4, 155,161). The phenomenon most likely reflects conformational equilibria of polypeptides arising from the experimental conditions used, and is a clear drawback of the standard 2-DE procedure, making the gel picture unnecessarily complex to analyse. [source] Synthesis and Conformational Analysis of Tetrahydroisoquinoline-Fused 1,3,2-Oxazaphospholidines and 1,2,3-OxathiazolidinesEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 8 2008Ildikó Schuster Abstract The cyclizations of tetrahydroisoquinoline 1,2-amino alcohols with phenylphosphonic dichloride, bis(2-chloroethyl)phosphoramidic dichloride, thionyl chloride and sulfuryl chloride were utilized to synthesize 1,5,6,10b-tetrahydro-1,3,2-oxazaphospholo[4,3- a]isoquinolines (2, 3), 1,5,10,10a-tetrahydro-1,3,2-oxazaphospholo[3,4- b]isoquinolines (8, 9), 1,5,6,10b-tetrahydro-1,2,3-oxathiazolo[4,3- a]isoquinolines (4,6) anda 1,5,10,10a-tetrahydro-1,2,3-oxathiazolo[3,4- b]isoquinoline (11), which are the first representatives of these ring systems. NMR spectroscopic analysis revealed the existence of conformational equilibria that are fast on the NMR timescale. Theoretical DFT calculations pointed to the participation of generally two preferred conformers in the conformational equilibria; the positions of the equilibria were indicated by the experimental NMR spectroscopic parameters, and they are in good agreement with the theoretically calculated energy differences of the participating conformers. For two compounds, which could be not isolated (10, 12), both the preferred conformers and the stereochemistry could be concluded from the DFT calculation results. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008) [source] Inhibitors of the Large Ribosomal Subunit from Haloarcula marismortuiISRAEL JOURNAL OF CHEMISTRY, Issue 1 2010Peter Abstract The crystal structures that have been obtained for 23 different inhibitors bound to the large ribosomal subunit from Haloarcula marismortui are reviewed here. These structures provide important insights into how anti-ribosomal antibiotics inhibit protein synthesis, how species specificity arises, and the relationship between ribosomal mutations and antibiotic resistance. These structural studies also provide compelling evidence that the conformation of the peptidyl transferase center of the large ribosomal subunit is intrinsically variable, and that conformational equilibria play a role in determining its functional properties. [source] A generalized exo -anomeric effect.ISRAEL JOURNAL OF CHEMISTRY, Issue 3-4 2000Substituent, solvent effects on the conformational equilibria of 2-(arylseleno)cyclohexanones The effects of substitution and solvent on the conformational equilibria of 2-[(4-R-substituted-phenyl)seleno]cyclohexanones are described. The conformational equilibria were determined by comparison of the linewidths of the H-2 resonances in the 1H NMR spectra of the conformationally averaged systems with those of the anancomeric (highly biased) 4-isopropyl-2-substituted cyclohexanones. The substituent (R = NMe2, OMe, Me, H, F, Cl, CF3, NO2) and solvent ((CD3)2CO, CD3CN, CD2Cl2, CDCl3) effects are discussed in terms of electrostatic effects and the possible stabilizing orbital interactions. The values of Keq (axial-equatorial) increase as the substituent becomes more electron withdrawing, in agreement with the dominance of nSe , ,*C=O or ,C-Se , ,*C=O orbital interactions in the axial conformers. The increase in the proportion of the equatorial isomers in more polar solvents for a given substituent suggests a damping of the dipolar interactions in the equatorial isomers. However, the proportion of the equatorial isomers in a given solvent increases as the substituent becomes more electron withdrawing, indicating that electrostatic interactions do not dominate in controlling the conformational equilibria. Analysis of the equilibrium data by means of a dual substituent parameter approach indicates the best correlation with ,I and ,+R substituent constants in CD2Cl2 and with ,I and ,°R substituent constants in CD3CN, with similar sensitivities to the resonance and polar effects. The correlations are interpreted in terms of accommodation of effective positive charge on the selenium atom in the axial isomers in CD2Cl2, and a lesser sensitivity to the buildup of positive charge in the more polar solvent CD3CN. Comparison of the IR ,CO -stretching frequencies for the axial and equatorial ArSe-substituted anancomeric systems (R = NO2, NMe2) indicates a higher stretching frequency for the NO2 -substituted isomers. In the case of the NMe2 -substituted compounds, ,CO appears at a higher frequency in the equatorial isomer, whereas in the case of the NO2 -substituted compounds, ,CO is less sensitive to the axial or equatorial orientation of the substituent. The results are consistent with the operation of nse , ,*c=0 or ,C-Se , ,*C=O orbital interactions in the axial isomers. The JC2-H2 values in the axially-substituted anancomeric isomers are of greater magnitude than those in the equatorially-substituted isomers, which is also consistent with the operation of the orbital interactions described above. There is, however, no marked substituent effect on the JC2,H2 values within the series of axial or equatorial isomers. We argue that this does not support the dominance of ,C-Se , ,*C=O orbital interactions. Examination of crystal structures reported in the literature for related compounds indicates a particular gauche orientation about the C2,Se bond, which lends further support to the operation of an nSe , ,*C=O orbital interaction. We suggest that the latter interaction is a manifestation of a generalized exo -anomeric effect. [source] ABSINTH: A new continuum solvation model for simulations of polypeptides in aqueous solutionsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 5 2009Andreas Vitalis Abstract A new implicit solvation model for use in Monte Carlo simulations of polypeptides is introduced. The model is termed ABSINTH for self- Assembly of Biomolecules Studied by an Implicit, Novel, and Tunable Hamiltonian. It is designed primarily for simulating conformational equilibria and oligomerization reactions of intrinsically disordered proteins in aqueous solutions. The paradigm for ABSINTH is conceptually similar to the EEF1 model of Lazaridis and Karplus (Proteins 1999, 35, 133). In ABSINTH, the transfer of a polypeptide solute from the gas phase into a continuum solvent is the sum of a direct mean field interaction (DMFI), and a term to model the screening of polar interactions. Polypeptide solutes are decomposed into a set of distinct solvation groups. The DMFI is a sum of contributions from each of the solvation groups, which are analogs of model compounds. Continuum-mediated screening of electrostatic interactions is achieved using a framework similar to the one used for the DMFI. Promising results are shown for a set of test cases. These include the calculation of NMR coupling constants for short peptides, the assessment of the thermal stability of two small proteins, reversible folding of both an ,-helix and a ,-hairpin forming peptide, and the polymeric properties of intrinsically disordered polyglutamine peptides of varying lengths. The tests reveal that the computational expense for simulations with the ABSINTH implicit solvation model increase by a factor that is in the range of 2.5,5.0 with respect to gas-phase calculations. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009 [source] Conformational studies of novel estrogen receptor ligands by 1D and 2D NMR spectroscopy and computational methodsMAGNETIC RESONANCE IN CHEMISTRY, Issue 4 2003Albert B. Sebag Abstract The solution conformations of the novel estrogen receptor ligands (17,,20E)-(p -trifluoromethylphenyl)vinylestradiol (1) and (17,,20E)-(o -trifluoromethylphenyl)vinylestradiol (2) were investigated in 2D and 1D NOESY studies and by comparison of 13C NMR chemical shifts with theoretical shieldings. The 1H and 13C assignments of 1 and 2 were determined by DEPT, COSY and HMQC experiments. The conformations of the 17,-phenylvinyl substituents of 1 and 2 are of interest because of their differing receptor binding affinities and effects in in vivo uterotrophic growth assays. A statistical method of evaluating contributing conformers of 1 and 2 from predicted 13C shifts of possible structures correlated fairly well with conformational conclusions derived from the NOE data. The 17, substituents of 1 and 2 apparently exist in similar conformational equilibria, suggesting that while 1 and 2 would occupy a similar receptor volume, interactions with the protein may shift the equilibrium and thereby influence the expression of the ligand. Copyright © 2003 John Wiley & Sons, Ltd. [source] Synthesis and conformational study of P -heterocyclic androst-5-ene derivativesHETEROATOM CHEMISTRY, Issue 1 2008Éva Frank The reactions of (20R)-3,-acetoxy-21-hydroxymethylpregn-5-en-20-ol (2) and (20R)-3,-acetoxypregn-5-ene-20,21-diol (11) with phenylphosphonic dichloride 3 and aryl dichlorophosphates 4,6 afforded novel types of P -heterocyclic androst-5-ene derivatives 7,10 and 12 as epimeric pairs. The diastereomers were separated by column chromatography and were characterized by NMR spectroscopy. Estimation of the stereostructures of the corresponding epimers by B3LYP/631G(d) DFT ab initio calculations suggested that the six-membered hetero ring in compounds 7b and 8a,10a adopts predominantly a chair conformation, with the P -substituents in their preferred orientation. The cyclic phosphonate moiety in 7a or 8b,10b, however, seems to exist as an equilibrium mixture of chair,distorted- boat or chair,chair forms. The theoretical calculations indicate that the conformational equilibrium is shifted toward the distorted- boat conformer for 7a, with a pseudoequatorial P -phenyl substituent, whereas for 8b,10b the chair conformer with an equatorial P -phenoxy group predominates. © 2008 Wiley Periodicals, Inc. Heteroatom Chem 19:7,14, 2008; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/hc.20372 [source] Influence of the C,H· · ·N intramolecular interaction on the spatial structures and 1H and 13C NMR parameters of heteroaryl vinyl ethers and sulfidesMAGNETIC RESONANCE IN CHEMISTRY, Issue 8 2003Andrei V. Afonin Abstract A complete analysis of the 1H and 13C spectra of the representative series of heteroaryl vinyl ethers and sulfides and heteroaryl styryl sulfides was carried out. The electronic and spatial structures of these compounds are discussed. It was shown that the C,H· · ·N intramolecular interactions in the investigated molecules influence significantly the spectral parameters and the conformational equilibrium. Copyright © 2003 John Wiley & Sons, Ltd. [source] Coupling of Protonation Switches During Rhodopsin Activation,PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 2 2007Reiner Vogel Recent studies of the activation mechanism of rhodopsin involving Fourier-transform infrared spectroscopy and a combination of chromophore modifications and site-directed mutagenesis reveal an allosteric coupling between two protonation switches. In particular, the ring and the 9-methyl group of the all- trans retinal chromophore serve to couple two proton-dependent activation steps: proton uptake by a cytoplasmic network between transmembrane (TM) helices 3 and 6 around the conserved ERY (Glu-Arg-Tyr) motif and disruption of a salt bridge between the retinal protonated Schiff base (PSB) and a protein counterion in the TM core of the receptor. Retinal analogs lacking the ring or 9-methyl group are only partial agonists,the conformational equilibrium between inactive Meta I and active Meta II photoproduct states is shifted to Meta I. An artificial pigment was engineered, in which the ring of retinal was removed and the PSB salt bridge was weakened by fluorination of C14 of the retinal polyene. These modifications abolished allosteric coupling of the proton switches and resulted in a stabilized Meta I state with a deprotonated Schiff base (Meta ISB). This state had a partial Meta II-like conformation due to disruption of the PSB salt bridge, but still lacked the cytoplasmic proton uptake reaction characteristic of the final transition to Meta II. As activation of native rhodopsin is known to involve deprotonation of the retinal Schiff base prior to formation of Meta II, this Meta ISB state may serve as a model for the structural characterization of a key transient species in the activation pathway of a prototypical G protein-coupled receptor. [source] Integrin ,IIb,3:ligand interactions are linked to binding-site remodelingPROTEIN SCIENCE, Issue 8 2006Roy R. Hantgan Abstract This study tested the hypothesis that high-affinity binding of macromolecular ligands to the ,IIb,3 integrin is tightly coupled to binding-site remodeling, an induced-fit process that shifts a conformational equilibrium from a resting toward an open receptor. Interactions between ,IIb,3 and two model ligands,echistatin, a 6-kDa recombinant protein with an RGD integrin-targeting sequence, and fibrinogen's ,-module, a 30-kDa recombinant protein with a KQAGDV integrin binding site,were measured by sedimentation velocity, fluorescence anisotropy, and a solid-phase binding assay, and modeled by molecular graphics. Studying echistatin variants (R24A, R24K, D26A, D26E, D27W, D27F), we found that electrostatic contacts with charged residues at the ,IIb/,3 interface, rather than nonpolar contacts, perturb the conformation of the resting integrin. Aspartate 26, which interacts with the nearby MIDAS cation, was essential for binding, as D26A and D26E were inactive. In contrast, R24K was fully and R24A partly active, indicating that the positively charged arginine 24 contributes to, but is not required for, integrin recognition. Moreover, we demonstrated that priming,i.e., ectodomain conformational changes and oligomerization induced by incubation at 35°C with the ligand-mimetic peptide cHarGD,promotes complex formation with fibrinogen's ,-module. We also observed that the ,-module's flexible carboxy terminus was not required for ,IIb,3 integrin binding. Our studies differentiate priming ligands, which bind to the resting receptor and perturb its conformation, from regulated ligands, where binding-site remodeling must first occur. Echistatin's binding energy is sufficient to rearrange the subunit interface, but regulated ligands like fibrinogen must rely on priming to overcome conformational barriers. [source] Molecular dynamics simulations of HPr under hydrostatic pressureBIOPOLYMERS, Issue 5 2004Muriel Canalia Abstract The histidine-containing protein (HPr) plays an important role in the phosphotransferase system (PTS). The deformations induced on the protein structure at high hydrostatic pressure values (4, 50, 100, 150, and 200 MPa) were previously (H. Kalbitzer, A. Görler, H. Li, P. Dubovskii, A. Hengstenberg, C. Kowolik, H. Yamada, and K. Akasaka, Protein Science 2000, Vol. 9, pp. 693,703) analyzed by NMR experiments: the nonlinear variations of the amide chemical shifts at high pressure values were supposed to arise from induced shifts in the protein conformational equilibrium. Molecular dynamics (MD) simulations are here performed, to analyze the protein internal mobility at 0.1 MPa, and to relate the nonlinear variations of chemical shifts observed at high pressure, to variations in conformational equilibrium. The global features of the protein structure are only slightly modified along the pressure. Nevertheless, the values of the Voronoi residues volumes show that the residues of ,-helices are more compressed that those belonging to the ,-sheet. The ,-helices are also displaying the largest internal mobility and deformation in the simulations. The nonlinearity of the 1H chemical shifts, computed from the MD simulation snapshots, is in qualitative agreement with the nonlinearity of the experimentally observed chemical shifts. © 2004 Wiley Periodicals, Inc. Biopolymers 2004 [source] Interpreting Experimental Data by Using Molecular Simulation Instead of Model BuildingCHEMISTRY - A EUROPEAN JOURNAL, Issue 26 2009Zrinka Gattin Abstract A proper description of the conformational equilibrium of polypeptides or proteins is essential for a correct description of their function. The conformational ensembles from 16 molecular dynamic simulations of two ,- heptapeptides were used to interpret the primary NMR data, which were also compared to a set of NMR model structures (see graphic). One of the most used spectroscopic techniques for resolving the structure of a biomolecule, such as a protein or peptide, is NMR spectroscopy. Because only NMR signal intensities and frequencies are measured in the experiment, a conformational interpretation of the primary data, that is, measured data, is not straightforward, especially for flexible molecules. It is hampered by the occurrence of conformational and/or time-averaging, by insufficient number of experimental data and by insufficient accuracy of experimental data. All three problematic aspects of structure refinement based on NMR nuclear Overhauser effect (NOE) intensities and 3J coupling data are illustrated by using two ,-heptapeptides in methanol as an example. We have performed 16 molecular dynamics (MD) simulations between 20 to 100,ns in length of unrestrained and NOE distance-restrained cases (instantaneous and time-averaged) of two ,-heptapeptides with a central ,-HAla(,-OH) amino acid in methanol at two different temperatures using two different GROMOS force-field parameter sets, 45,A3 and 53,A6. The created conformational ensembles were used to interpret the primary NMR data on these molecules. They also were compared to a set of NMR model structures derived by single-structure refinement in vacuo by using standard techniques. It is shown that the conformational interpretation of measured experimental data can be significantly improved by using unrestrained, instantaneous and time-averaged restrained MD simulations of the peptides by using a thermodynamically calibrated force field and by explicitly including solvent degrees of freedom. [source] Synthesis and Structural Model of an ,(2,6)-Sialyl-T Glycosylated MUC1 Eicosapeptide under Physiological ConditionsCHEMISTRY - A EUROPEAN JOURNAL, Issue 19 2006Sebastian Dziadek Dr. Abstract To study the effect of O-glycosylation on the conformational propensities of a peptide backbone, a 20-residue peptide (GSTAPPAHGVTSAPDTRPAP) representing the full length tandem repeat sequence of the human mucin MUC1 and its analogue glycosylated with the (2,6)-sialyl-T antigen on Thr11, were prepared and investigated by NMR and molecular modeling. The peptides contain both the GVTSAP sequence, which is an effective substrate for GalNAc transferases, and the PDTRP fragment, a known epitope recognized by several anti-MUC1 monoclonal antibodies. It has been shown that glycosylation of threonine in the GVTSAP sequence is a prerequisite for subsequent glycosylation of the serine at GVTSAP. Furthermore, carbohydrates serve as additional epitopes for MUC1 antibodies. Investigation of the solution structure of the sialyl-T glycoeicosapeptide in a H2O/D2O mixture (9:1) under physiological conditions (25,°C and pH 6.5) revealed that the attachment of the saccharide side-chain affects the conformational equilibrium of the peptide backbone near the glycosylated Thr11 residue. For the GVTSA region, an extended, rod-like secondary structure was found by restrained molecular dynamics simulation. The APDTR region formed a turn structure which is more flexibly organized. Taken together, the joined sequence GVTSAPDTR represents the largest structural model of MUC1 derived glycopeptides analyzed so far. [source] | |||||||||||||||||||||||||