Normal mode analysis of oligomeric proteins: Reduction of the memory requirement by consideration of rigid geometry and molecular symmetry

A method is presented to reduce the memory requirement of normal mode analysis applied to systems containing two or more large proteins when these systems exhibit symmetry properties. We use a rigid geometry model (i.e., only the dihedral angles of the polypeptide chain are considered as variables). This model allows a reduction by a factor of 8 on average of the number of variables with a concomitant freezing of the high-frequency modes. The symmetry properties of the system are used to reduce further the number of variables that must be considered in the computation. Application of group theory leads to a factorization of the matrices of interest (the coefficient and the Hessian matrices) into independent blocks along the diagonal. The initial, reducible representation is thus transformed into a number of irreducible representations of smaller dimensions. In the case of the C₂ symmetry group, the method leads to a reduction of the size of the matrices that must be manipulated during the computation (coefficient matrix, Hessian matrix, and eigenvectors matrix) by a factor of 256 compared with the usual normal mode analysis in Cartesian coordinate space. The method is particularly well adapted to the study of the dynamics of oligomeric proteins because these proteins often display symmetry properties (e.g., virus coat proteins, immunoglobulins, hemoglobin, etc.). In favorable cases, in conjunction with X-ray diffuse scattering data, the study of systems showing allosteric properties might be considered. © 1994 by John Wiley & Sons, Inc.     

Etude des petits cycles—XXX : Extension de cycle generale de cyclopropanols: Halomethyl-1, hydroxymethyl-1, vinyl-1, acyl-1, cyclopropanols,et des oxaspiropentanes en cyclobutanones

Cyclopropanols 5, 6 and 2 with substituent groups (-CH₂OH, -CH₂OTs, -CH₂Br) in the 1-position, and oxaspiropentane 8, have been prepared from methylenecyclopropane. Cyclopropanols with vinyl groups in the 1-position (1-vinyl 12, 1-cyclopentenyl 13 and 1-cyclohexenyl 14) and 1-cyclopropylcyclopropanol 20 have been prepared from 1, 3-dichloroacetone.Each of the compounds readily undergoes ring expansion to the corresponding cyclobutanones. The reaction provides a simple route to cyclobutanones, the parent ketone itself being easily obtained from oxaspiropentane 8.     

Stéréochimie des réactions de substitution des alcoxygermanes par les organolithiens et par les réactifs de Grignard

The reactions of organolithium reagents and Grignard reagents with optically active alkoxygermanes R₃GeOR′ have been studied [R₃GeOR′ = ()-i-PrPhNpGeOCH₃, ()-i-PrPhNPGeOMen and ()-MePhNpGeOMen]. Saturated reagents (e.g. butyllithium) give retention of configuration at germanium whilst unsaturated reagents (e.g. allyl- or benzyllithium) lead to inversion.     

Efficient method for visualization and isolation of proteins resolved in polyacrylamide gels

Polyacrylamide gel electrophoresis is a popular method used to purify proteins for reconstitution experiments, amino acid composition and sequence determinations. In this report we describe methods that will be of general use in the isolation and characterization of proteins and the benefits of substituting boric acid for glycine in the electrophoresis tray buffers. We also describe how proteins resolved in a variety of gel systems (including those containing sodium dodecyl sulfate) may be rapidly visualized with 8-anilino-1-naphthalene sulfonic acid and efficiently transferred to a second gel for two-dimensional gel analysis, or isolated by electroelution for subsequent characterization.     

Nouvelles voies d'accès aux diaryl-3,6 hydroxy-5 triazines-1,2,4 à partir des nitriles α-thioéthers

Ar-C(CN)=NN=C(CN)-Ar and Ar-C(CN)=NNHCO-Ar′, easily prepared from the bromoderivatives Ar-CBr(SEt)-CN, afford in good yields, by heating in a basic medium, 3,6-diaryl-5 hydroxy-1,2,4-triazines.     

A new protecting group for the exocyclic amino groups of nucleosides

A new protecting group has been developed for the exocyclic amino groups of nucleosides that occur in DNA. 3-Phenyl-[{N-(2-trimethylsilyl-ethoxycarbonyl)-2-amino}]-propanoic acid used as the protective agent.     

Probing the glycosidic linkage: UV and IR ion-dip spectroscopy of a lactoside

The beta(1-->4) glycosidic linkage found in lactose is a prevalent structural motif in many carbohydrates and glycoconjugates. Using UV and IR ion-dip spectroscopies to probe benzyl lactoside isolated in the gas phase, we find that the disaccharide unit adopts only a single, rigid structure. Its fully resolved infrared ion-dip spectrum is in excellent agreement with that of the global minimum structure computed ab initio. This has glycosidic torsion angles of phi(H) (H1-C1-O-C4') approximately 180 degrees and psi(H) (C1-O-C4'-H4') approximately 0 degrees which correspond to a rotation of approximately 150 degrees about the glycosidic bond compared to the accepted solution-phase conformation. We discuss the biological implications of this discovery and the generality of the strategies employed in making it.     

Phenylselenolactonisation des acides homogeranique et homonerique

The reaction of PhSeCl and N-PSP with homogeranic acid ($\text{1}$) or homoneric acid ($\text{2}$) affords butanolides in a stereospecific way. Despite the large number of cyclic cases studied in the literature such acyclic systems were remained largely unexplored. PhSe⁺ was unable to realize polycyclization.     

Kinetics of poly(ethylene terephthalate) glycolysis by diethylene glycol. I. Evolution of liquid and solid phases

The kinetics of uncatalysed glycolysis, at 220 °C, of poly(ethylene terephthalate) (PET) by diethylene glycol (DEG) in high excess has been studied. An experimental device allowing good separation, at reaction temperature, of the solid and liquid phases was set up.The results suggest that PET is initially depolymerized in the slightly swollen solid phase, by glycolysis of the amorphous interlamellar chains. This mechanism continues until a solid phase of highly crystallized polyester is obtained.The internal tensions engendered by this chemical modification cause cracks, delamination and mechanical disintegration of the polymer. The transfer towards the liquid phase is then strongly accelerated and the solvolysis of the depolymerization products continues in the liquid phase, up to equilibrium.