Prediction of protein structure using a knowledge-based off-lattice united-residue force field and global optimization methods

A united-residue model of polypeptide chains developed in our laboratories with united side-chains and united peptide groups as interaction sites is presented. The model is designed to work in continuous space; hence efficient global-optimization methods can be applied. In this work, we adopted the distance-scaling method that is based on continuous deformation of the original rugged energy hypersurface to obtain a smoothed surface. The method has been applied successfully to predict the structures of simple motifs, such as the three-helix bundle structure of the 10-58 fragment of staphylococcal protein A in de novo folding simulations and more complicated motifs in inverse-folding simulations. Received: 24 April 1998 / Accepted: 4 August 1998 / Published online: 2 November 1998     

Polymorphism of Acrylic and Methacrylic Acid Esters Containing Long Fluorocarbon Chains and Their Polymerizability

The molecular aggregation of acrylic and methacrylic acid esters containing long-fluorocarbon chains: 2-(perfluoroalkyl)ethyl acrylate (FF_nEA) and 2-(perfluoroalkyl)ethyl methacrylate (FF_nEMA) (F(CF₂)_nCH₂CH₂OCOC(X)=CH₂, where X=H, CH₃ and n=6, 8, 10) was investigated by differential scanning calorimetry (DSC) and temperature controlled X-ray powder diffraction measurement. These compounds exhibited some characteristic polymorphic behaviors depending on the length of fluorocarbon chain and the -position methyl group. The solid-state polymerization by -ray irradiation was studied for these compounds in the various crystal forms. In the solid-state polymerization, highest polymerizability was observed in the crystal form that exists in the highest temperature region for each compound.This revised version was published online in November 2005 with corrections to the Cover Date.     

Analyzing patterns between regular secondary structures using short structural building blocks defined by a hidden Markov model

Hidden Markov models were used to identify recurrent short 3D structural building blocks (SSBBs) describing protein backbones. Polypeptide chains were broken down into successive short segments defined by their inter-alpha-carbon distances. Fitting the model to a database of nonredundant proteins identified 12 distinct SSBBs and described the preferred pathways by which SSBBs were assembled to form the 3D structure of the proteins. Protein backbones were labelled in terms of these SSBBs. The observed SSBB preferences for fragments located between regular secondary structures suggested that they depended more on the following regular structure than on the preceding one. Extraction of repeated series of SSBBs between regular secondary structures showed some structural specificity within different connection types. These results confirm that SSBBs can be used as building blocks for analyzing protein structures, and can yield new information on the structures of the coils flanking secondary structures. Received: 14 May 1998 / Accepted: 4 August 1998 / Published online: 16 November 1998     

Biaxial ordering of terminal diene groups in lipid membranes: an infrared linear dichroism study

The molecular order within the hydrophobic core of membranes of the diene lipid di-tetradecadienoylphosphatidylcholine was studied by means of infrared spectroscopy on multibilayer assemblies which orient macroscopically on the surface of an attenuated total reflection crystal. The relative humidity and temperature were used as variable parameters to demonstrate that there were profound differences in the melting transition of lipids possessing predominantly cis and trans diene groups. The cis isomer undergoes the phase transition at a vapor pressure which is increased by 0.15 GPa when compared with that of the trans isomer. The methylene wagging band progression gives no indication of differences between the acyl chain conformation of the cis and trans forms in the gel state. The frequencies of a number of absorption bands of the diene groups reveal that these moieties are predominantly in the s-trans conformation to accommodate a favorable packing within the bilayer. The linear dichroism of selected in-plane and out-of-plane vibrations of the diene groups gives indications of the biaxial ordering of these moieties. We present the basic equations for the quantitative analysis of IR dichroism data of lamellar structures in terms of transverse and longitudinal molecular order parameters. It turns out that the planes of the rigid diene groups orient preferentially in a perpendicular direction with respect to the bilayer surface and parallel to each other forming in this way a layer of well-aligned diene groups in the bilayer center. This finding is confirmed by the results of X-ray measurements. We suggest that the partial interdigitation of the diene groups of the sn-1 acyl chains promotes the formation of the inverse H_II phase and/or enables the formation of covalent bonds between both the monolayers upon polymerization of diene lipids.     

Nd（i－PrO）_2Cl－AlEt_3均相二元催化剂异戊二烯聚合动力学──Ⅲ．AlEt_3的链转移作用

Ｎｄ（ｉ－ＰｒＯ）_２Ｃｌ－ＡｌＥｔ_３均相二元催化剂异戊二烯聚合动力学──Ⅲ．ＡｌＥｔ_３的链转移作用蔡小平，龚志，王佛松朱行洁，李秀华（中国科学院长春应用化学研究所长春１３００２２）（吉林化工集团公司研究院吉林）关键词异戊二烯，聚合动力学，均相催化...     

A series of azo-type side-chain liquid crystalline polysiloxane–palladium complexes

A series of azo-type side-chain liquid crystalline polysiloxanes (AZLCPs) were synthesized, starting from organic polysiloxane and azo-type mesogenic compounds having an end allyl group. The AZLCPs were further used to coordinate with palladium dichloride and potassium chloride, by which a series of palladium complexes of AZLCPs (Pd–AZLCPs) were prepared. The mesogenic properties of all of the liquid crystalline polymers were characterized by using differential scanning calorimetry, polarized microscope and wide-angle X-ray diffraction. It was found that all of the polymer ligands and their palladium complexes showed thermotropic liquid crystallinity and that the incorporation of the palladium ions gave positive effects to the mesogenic properties of their polymer ligand counterpart. Compared with the corresponding AZLCPs, the Pd–AZLCPs have higher isotropization temperatures and a broader mesophase temperature range. The mesogenic properties of the liquid crystalline polymer ligands and their palladium complexes were also varied gradually by changing the length of the alkoxy groups on the side chain. The polymers that have a color emissive group and a highly flexible polysiloxane main chain may potentially be used as nonlinear optical materials.     

Intrachain and Interchain Interactions in Polystyrene: Dilute and Semidilutc Solutions

Thestudiesofpolymersolutionpropertiesfromdilatetoconcentratedsolutionbyfluorescencetechniquehaveattractedmoreattentionsinrecentdecadesl'2.InordertoinvestigateintrachainandinterchainilltCractionsindilutesolutionregion,pyrenewasusedaslabelsattachedtopolystyrene,whichwasintenselyfluorescentwithalongfluorescentlifetime3.Inthepresentwork,thepolystyreneattachedwithpyrenylgroupshadanunfavourablestrUcturetothenearestneighborexcimerformationwiththepyrenylgroupsseparatedbymorethanthreeatomsalongthechain…     

Nutritional requirements of a strain of bacillus thuringiensis subsp. kurstaki and use of gruel hydrolysate for the formulation of a new medium for δ-endotoxin production

Nutritional requirements of a strain ofBacillus thuringiensis (Bt) subsp.kurstaki were elucidated for δ-endotoxin production. The effect of some principal nutrients was deeply investigated, showing several nutritional and metabolite limitations in Bt growth and δ-endotoxin synthesis. This led us to formulate a new medium based on the hydrolysate of gruel, a cheap and abundant byproduct of semolina factories, supporting growth and δ-endotoxin synthesis. After hydrolysis of gruel by α-amylase, followed by proteolysis using alcalase, the resultant soluble material substituted glucose very well for Bt δ-endotoxin production. Indeed, 15 g/L total sugars coming from that hydrolysate, supplemented by 5.4 g/L ammonium sulfate as nitrogen source and either 5 g/L yeast extract or 3 g/L peptone from casein or 3 g/L casaminoacids or 0.25 g/L cysteine or aspartic acid, were the principal components of this new medium in which almost 1 g/L of δ-endotoxin in 4.5 g/L total dry biomass was produced.     

Homolytic cyclization of 1,3-propanedithiol to 1,2-dithiolane in the presence of 2,5-dimethyl-2,4-hexadiene

2,2-Diethyl-1,3-propanedithiol undergoes cyclization to 4,4-diethyl-1,2-dithiolane upon interaction with 2,5-dimethyl-2,4-hexadiene in benzene in the presence of azodiisolbutyronitrile. The reaction proceeds according to the radical chain mechanism. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 10, pp. 2078–2080, October, 1998.     

Variable metric optimization of molecular geometry in electronically excited states

The variable metric (VM) method is used to optimize molecular geometry in electronically excited states. A general expression for the first derivative of energy in the particular excited state is derived, considering configuration interaction of all singly excited configurations. A special expression for the excited states energy derivative is given for calculations with semiempirical methods of CNDO type. The geometry optimizations of a set of molecules in various excited states have been carried out by the CNDO/2 method. The results of computations have been discussed and compared with the available experimental data. A good agreement of the calculated geometries with the experimental ones has been shown in the first excited states and a relatively good agreement in the higher states, with some exceptions. Some special features of the proposed method are discussed.