Effect of proline and glycine residues on dynamics and barriers of loop formation in polypeptide chains

Glycine and proline residues are frequently found in turn and loop structures of proteins and are believed to play an important role during chain compaction early in folding. We investigated their effect on the dynamics of intrachain loop formation in various unstructured polypeptide chains. Loop formation is significantly slower around trans prolyl peptide bonds and faster around glycine residues compared to any other amino acid. However, short loops are formed fastest around cis prolyl bonds with a time constant of 6 ns for end-to-end contact formation in a four-residue loop. Formation of short loops encounters activation energies in the range of 15 to 30 kJ/mol. The altered dynamics around glycine and trans prolyl bonds can be mainly ascribed to their effects on the activation energy. The fast dynamics around cis prolyl bonds, in contrast, originate in a higher Arrhenius pre-exponential factor, which compensates for an increased activation energy for loop formation compared to trans isomers. All-atom simulations of proline-containing peptides indicate that the conformational space for cis prolyl isomers is largely restricted compared to trans isomers. This leads to decreased average end-to-end distances and to a smaller loss in conformational entropy upon loop formation in cis isomers. The results further show that glycine and proline residues only influence formation of short loops containing between 2 and 10 residues, which is the typical loop size in native proteins. Formation of larger loops is not affected by the presence of a single glycine or proline residue.     

Preparation,Structure, and Reactivity of Thioxo and Imino Derivatives of the Triolide (and Pentolide) from (R)-3-Hydroxybutanoic Acid

Reaction of the triolide 1 from (R)-3-hydroxybutanoic acid with Lawesson's reagent 5 leads to the mono-, di-, and trithio derivatives 6–8 which can be isolated in pure form (20–40% yields), and which have crystal structures very similar to the parent triolide 1 (Fig. 1). Similarly, pentolide 3 is converted to mixtures of various thio derivatives, three of which are separated ( 10–12 ) by HPLC and fully characterized. The X-ray structures of the mono- and of one of the dithiopentolides ( 10, 12 ) differ remarkably from each other (Fig. 3). Reduction of the thiotriolides 6–8 (NaBH₄, R₃SnH, Cl₃SiH, Raney-Ni) gives 12-membered rings containing up to three ether groups (chiral crown ethers, 15, 17–19 ) in poor yields. The thiotriolides react spontaneously and in yields of up to 96% with ammonia, certain primary amines, and hydroxylamine to give imine and oxime derivatives with intact 12-membered-ring backbones ( 20, 22–24, 30 , see crystal structures in Figs. 4–7). The rigid structure of all the derivatives of triolide 1 puts the C?O, C?S, and C?NR O-, S-, and N-atoms in juxtaposition (a feature reminiscent of the side chains in the iron-binder enterobactin, Fig. 6). Imines containing PPh₂ groups are prepared ( 30, 33, 35 ) from the thiotriolides and tested as chiral ligands for Pd^II-catalyzed 1,3-diphenyallylations (→ 37 , enantiomer ratio up to 77:23). The reactions described demonstrate that multiple reactions of the triolide 1 from (R)-3-hydroxybutanoic acid which proceed through tetrahedral intermediates are possible without ring opening – the skeleton is remarkably stable, and this might be exploited as a template for bringing up to three pendent substituents into close proximity to allow a study of their interactions and cooperative properties. Also, the di- and trithio derivatives 7 and 8 could be used for cross-linking in molecules containing primary NH₂ groups.     

Heck reactions of aryl bromides with alk-1-en-3-ol derivatives catalysed by a tetraphosphine/palladium complex

cis,cis,cis-1,2,3,4-Tetrakis(diphenylphosphinomethyl)cyclopentane/[PdCl(C₃H₅)]₂ efficiently catalyses the Heck reaction of alk-1-en-3-ol with a variety of aryl bromides. In the presence of hex-1-en-3-ol or oct-1-en-3-ol, the β-arylated carbonyl compounds were selectively obtained. Linalool and 2-methylbut-3-en-2-ol led to the corresponding 1-arylalk-1-en-3-ol derivatives. Turnover numbers up to 69,000 can be obtained for this reaction. A minor electronic effect of the substituents of the aryl bromide was observed. Similar reaction rates were observed in the presence of activated aryl bromides such as bromoacetophenone and deactivated aryl bromides such as bromoanisole.     

Rovibrational product state distribution for inelastic H+D2 collisions

Experimental measurements of rovibrational product state distributions for the inelastic scattering process H + D2(nu=0,j)-->H + D2(nu' = 1,2,j') are presented and compared with the results of quasiclassical and quantum mechanical calculations. Agreement between theory and experiment is almost quantitative. Two subtle trends are found: the relative amount of energy in product rotational excitation decreases slightly with increasing collision energy and increases slightly with increasing product vibrational excitation. These trends are the reverse of what has been found for reactive scattering in which the opposite trends are much more pronounced.     

Shear-induced morphology transition and microphase separation in a lamellar phase doped with clay particles

We report on the influence of shear on a nonionic lamellar phase of tetraethyleneglycol monododecyl ether (C12E4) in D2O containing clay particles (Laponite RD). The system was studied by means of small-angle light scattering (SALS) and small-angle neutron scattering (SANS) under shear. The SANS experiments were conducted using a H2O/D2O mixture of the respective scattering length density to selectively match the clay scattering. The rheological properties show the familiar shear thickening regime associated with the formation of multilamellar vesicles (MLVs) and a shear thinning regime at higher stresses. The variation of viscosity is less pronounced as commonly observed. In the shear thinning regime, depolarized SALS reveals an unexpectedly strong variation of the MLV size. SANS experiments using the samples with lamellar contrast reveal a change in interlamellar spacing of up to 30% at stresses that lead to MLV formation. This change is much more pronounced than the change observed, when shear suppresses thermal bilayer undulations. Microphase separation occurs, and as a consequence, the lamellar spacing decreases drastically. The coincidence of the change in lamellar spacing and the onset of MLV formation is a strong indication for a morphology-driven microphase separation.     

Binuclear rhodium(II) complexes with leucine and proline

The dimeric rhodium(II) complexes [Rh₂(leu)₄(H₂O)₂]- (ClO₄)₄ and [Rh₂(pro)₄(H₂O)₂](ClO₄)₄ have been prepared and characterized by elemental analyses, i.r., u.v.–vis. and ¹H-n.m.r. spectroscopy. The amino acid molecules are coordinated as bridging ligands via their carboxylato groups. Cyclic voltammetry in DMF has shown that the complexes undergo a quasi-reversible reduction to yield dimers containing a Rh ₂ ³⁺ core. Oxidation processes within the 0–1.5V range were not observed.     

Correlation between Dynamic Heterogeneity and Local Structure in a Room‐Temperature Ionic Liquid: A Molecular Dynamics Study of [bmim][PF6]

The complex dynamics of a room‐temperature ionic liquid, 1‐n‐butyl‐3‐methylimidazolium hexafluorophosphate ([bmim][PF₆]), is studied using equilibrium classical molecular dynamics simulations in the temperature range of 250–450 K. The activation energies for the self‐diffusion of ions are around 30–34 kJ mol^?1, with that of the anion a little higher than that for the cation. The electrical conductivity of the liquid is calculated and good agreement with experiments is obtained. Structural relaxation is studied through the decay of coherent (total density–density correlation) and incoherent (self part of density–density correlation) intermediate scattering functions over a range of temperatures and wave vectors relevant to the system. The relaxation data are used to identify and characterize two processes, α and β. The dependence of the two relaxation times on temperature and wave vector is obtained. The dynamical heterogeneity of the ions determined through the non‐Gaussian parameter indicates the motion of the cation to be more heterogeneous than that of the anion. The faster ones among the cations are coordinated to faster anions, while slower cations are surrounded predominantly by slower anions. Thus, the dynamical heterogeneity in this ionic liquid is shown to have structural signatures.