Spectral representation of reduced protein models

We consider a spectrum-like two-dimensional graphical representation of proteins based on a reduced protein model in which 20 amino acids are grouped into five classes. This particular grouping of amino acids was suggested by Riddle and co-workers in 1997. The graphical representation is based on depicting sequentially the amino acids on five horizontal lines at equal separations. One-letter codes, B, O, U, X and Y, to which numerical values 1 to 5 have been assigned, are suggested as labels for the fictional amino acids that represent all the amino acids within each group. The approach is illustrated on ND6 proteins of eight species having from 168 to 175 amino acids. While visual inspection of the novel spectral graphical representations of proteins may reveal local similarities and dissimilarities of protein sequences, arithmetic manipulations of spectra offer an elegant route to graphic visualization of the degree of similarity for selected pairs of proteins.     

Geranylgeranyl diphosphate synthases from Scoparia dulcis and Croton sublyratus. cDNA cloning, functional expression, and conversion to a farnesyl diphosphate synthase

cDNAs encoding geranylgeranyl diphosphate synthase (GGPPS) of two diterpene producing plants, Scoparia dulcis and Croton sublyratus, were isolated using the homology-based polymerase chain reaction method. Both cloned genes showed high amino acid sequence homology (60-70%) to other plant GGPPSs and contained highly conserved aspartate-rich motifs. The obtained clones were functionally expressed in Escherichia coli and showed sufficient GGPPS activity to catalyze the condensation of farnesyl diphosphate (FPP) and isopentenyl diphosphate to form geranylgeranyl diphosphate. To investigate the factor determining the product chain length of plant GGPPSs, S. dulcis GGPPS mutants in which either the small amino acids at the fourth and fifth positions before the first aspartate-rich motif (FARM) were replaced with aromatic amino acids or in which two additional amino acids in FARM were deleted were constructed. Both mutants behaved like FPPS-like enzymes and almost exclusively produced FPP when dimethylallyl diphosphate was used as a primer substrate, and failed to accept FPP as a primer substrate. These results indicate that both small amino acids at the fourth and fifth positions before FARM and the amino acid insertion in FARM play essential roles in product length determination in plant GGPPSs.     

Representation of proteins as walks in 20-D space

A novel representation of proteins was introduced. It is independent of arbitrary decisions with respect to the choice of labels to be assigned to the 20 natural amino acids. The approach is based on an assignment of 20 unit vectors in 20-dimensional vector space to the 20 natural amino acids. Proteins are then represented by a walk, that is, a sequence of steps in the 20-dimensional space analogous to a walk in the (x, y) plane in the case of binary strings. A straightforward numerical characterization of proteins is obtained from the distance matrix associated with the walk representing the protein in 20-dimensional space combining the information on the Euclidean distance between various amino acids in protein sequence. The Line Distance matrix offers additional numerical characterization of proteins, while the lengths of steps of the walk in 20-D space allow construction of a "protein profile," which represents distribution of average lengths of the steps and their powers.     

PhAST: pharmacophore alignment search tool

We present a ligand-based virtual screening technique (PhAST) for rapid hit and lead structure searching in large compound databases. Molecules are represented as strings encoding the distribution of pharmacophoric features on the molecular graph. In contrast to other text-based methods using SMILES strings, we introduce a new form of text representation that describes the pharmacophore of molecules. This string representation opens the opportunity for revealing functional similarity between molecules by sequence alignment techniques in analogy to homology searching in protein or nucleic acid sequence databases. We favorably compared PhAST with other current ligand-based virtual screening methods in a retrospective analysis using the BEDROC metric. In a prospective application, PhAST identified two novel inhibitors of 5-lipoxygenase product formation with minimal experimental effort. This outcome demonstrates the applicability of PhAST to drug discovery projects and provides an innovative concept of sequence-based compound screening with substantial scaffold hopping potential.     

Engineered bacterially expressed polypeptides: assembly into polymer particles with tailored degradation profiles

In nature, the sequence of amino acids in a protein is determined by the genetic code. Biosynthesis of polypeptides by bacteria can be used to exploit this natural process to afford exact control over properties such as molecular weight, chemical functionality, and structure. It is demonstrated how control over the positioning of functional groups can be used to tune the degradation of assembled polypeptide particles (see scheme).     

Detection of Asp371, Phe375, and Tyr376 Influence on GD-95-10 Lipase Using Alanine Scanning Mutagenesis

GD-95-10 and GD-95-20 lipases are modified GD-95 lipase variants, which lack 10 and 20 C-terminal amino acids, respectively. Previous analysis showed that GD-95-10 lipase has higher activity than GD-95 lipase, while GD-95-20 lipase almost completely loses its activity. Analysis in silico suggested three conservative amino acids at region between 369 and 378 amino acids which can be relevant to the activity of GD-95-10 lipase. These amino acids have direct contacts with residues involved in substrate binding, stabilization of the serine loop or form oxyanion hole. In this work, the role of Asp371, Phe375, and Tyr376 on activity, functionality, and structure of GD-95-10 lipase was analyzed by Ala scanning mutagenesis. We showed that even a single mutation can impact the main structure and activity of Geobacillus lipases. Our experiments provide new knowledge about lipases from thermophilic Geobacillus bacteria and are important for protein engineering and synthetic biology. These enzymes and their engineering can be basis for future biocatalysts applied in production of biofuel or other industrial esters.     

Cloning and Characterization of the Gene Encoding Alpha-Pinene Oxide Lyase Enzyme (Prα-POL) from <Emphasis Type="Italic">Pseudomonas rhodesiae</Emphasis> CIP 107491 and Production of the Recombinant Protein in <Emphasis Type="Italic">Escherichia coli</Emphasis>

The alpha-pinene oxide lyase (Prα-POL) from Pseudomonas rhodesiae CIP107491 belongs to catabolic alpha-pinene degradation pathway. In this study, the gene encoding Prα-POL has been identified using mapping approach combined to inverse PCR (iPCR) strategy. The Prα-POL gene included a 609-bp open reading frame encoding 202 amino acids and giving rise to a 23.7 kDa protein, with a theoretical isoelectric point (pI) of 5.23. The amino acids sequence analysis showed homologies with those of proteins with unknown function from GammaProteobacteria group. Identification of a conserved domain in amino acid in positions 18 to 190 permitted to classify Prα-POL among the nuclear transport factor 2 (NTF2) protein superfamily. Heterologous expression of Prα-POL, both under its native form and with a histidin tag, was successfully performed in Escherichia coli, and enzymatic kinetics were analyzed. Bioconversion assay using recombinant E. coli strain allowed to reach a rate of isonovalal production per gramme of biomass about 40-fold higher than the rate obtained with P. rhodesiae.     

Design and synthesis of 2(5H)-furanone liquid-crystal compounds based on natural molecules and biphenyl derivatives

Starting from natural molecules, for example l-menthol and amino acids, a series of 2(5H)-furanone liquid-crystal compounds were designed, and synthesized by esterification of N-[5-menthoxy-2(5H)-furanonyl] amino acids with biphenyl-4-ol or biphenyl-4,4′-diol in the presence of dehydrating agents. The structures of all the novel compounds were confirmed by FTIR, ¹H NMR, and mass spectroscopy, and by elemental analysis. The liquid-crystal properties of the target compounds were characterized by differential scanning calorimetry (DSC), X-ray diffraction (XRD), and polarization optical microscopy (POM). The DSC and XRD results showed that some compounds containing short alkyl chains or with the phenyl far from the amino in the amino acid unit formed a mesomorphic phase. Products obtained from biphenyl-4,4′-diol were more likely to form a mesomorphic phase. However, POM revealed no optical texture. These investigations provide, for the first time, a basis for application of 2(5H)-furanones in liquid crystals by combination of different functional units, including biphenyl, l-menthol, and amino acids.     

Stoichiometric inhibition of amyloid beta-protein aggregation with peptides containing alternating alpha,alpha-disubstituted amino acids

We have prepared two peptides based on the hydrophobic core (Lys-Leu-Val-Phe-Phe) of amyloid beta-protein (Abeta) that contain alpha,alpha-disubstituted amino acids at alternating positions, but differ in the positioning of the oligolysine chain (AMY-1, C-terminus; AMY-2, N-terminus). We have studied the effects of AMY-1 and AMY-2 on the aggregation of Abeta and find that, at stoichiometric concentrations, both peptides completely stop Abeta fibril growth. Equimolar mixtures of AMY-1 and Abeta form only globular aggregates as imaged by scanning force microscopy and transmission electron microscopy. These samples show no signs of protofibrillar or fibrillar material even after prolonged periods of time (4.5 months). Also, 10 mol % of AMY-1 prevents Abeta self-assembly for long periods of time; aged samples (4.5 months) show only a few protofibrillar or fibrillar aggregates. Circular dichroism spectroscopy of equimolar mixtures of AMY-1 and Abeta show that the secondary structure of the mixture changes over time and progresses to a predominantly beta-sheet structure, which is consistent with the design of these inhibitors preferring a sheet-like conformation. Changing the position of the charged tail on the peptide, AMY-2 interacts with Abeta differently in that equimolar mixtures form large ( approximately 1 mum) globular aggregates which do not progress to fibrils, but precipitate out of solution. The differences in the aggregation mediated by the two peptides is discussed in terms of a model where the inhibitors act as cosurfactants that interfere with the native ability of Abeta to self-assemble by disrupting hydrophobic interactions either at the C-terminus or N-terminus of Abeta.     

PROGEN: An automated modelling algorithm for the generation of complete protein structures from the α-carbon atomic coordinates

Summary A modelling algorithm (PROGEN) for the generation of complete protein atomic coordinates from only the -carbon coordinates is described. PROGEN utilizes an optimal geometry parameter (OGP) database for the positioning of atoms for each amino acid of the polypeptide model. The OGP database was established by examining the statistical correlations between 23 different intra-peptide and inter-peptide geometric parameters relative to the -carbon distances for each amino acid in a library of 19 known proteins from the Brookhaven Protein Database (BPDB). The OGP files for specific amino acids and peptides were used to generate the atomic positions, with respect to -carbons, for main-chain and side-chain atoms in the modelled structure. Refinement of the initial model was accomplished using energy minimization (EM) and molecular dynamics techniques. PROGEN was tested using 60 known proteins in the BPDB, representing a wide spectrum of primary and secondary structures. Comparison between PROGEN models and BPDB crystal reference structures gave r.m.s.d. values for peptide main-chain atoms between 0.29 and 0.76 Å, with a grand average of 0.53 Å for all 60 models. The r.m.s.d. for all non-hydrogen atoms ranged between 1.44 and 1.93 Å for the 60 polypeptide models. PROGEN was also able to make the correct assignment of cis- or trans-proline configurations in the protein structures examined. PROGEN offers a fully automatic building and refinement procedure and requires no special or specific structural considerations for the protein to be modelled.     

Evaluating the ability of polyhydroxyalkanoate synthase mutants to produce P(3HB-co-3HA) from soybean oil

Polyhydroxyalkanoate (PHA) synthase from Pseudomonas sp 61-3 (PhaC1(Ps)) is able to synthesize P(3HB-co-3HA), consisting of a 3HB unit and medium-chain-length 3HA units of 6-12 carbon atoms. Expression vectors encoding 76 PhaC1(Ps) mutants with an amino acid replacement at position 130, 325, 477 or 481 were individually introduced into Ralstonia eutropha. The mutant enzyme genes were evaluated in terms of their abilities to synthesize P(3HB-co-3HA) using soybean oil as a carbon source. 20 mutants showed significantly high accumulation levels of PHA exceeding 30 wt.-% and as high as 57 wt.-%. It was found that hydrophobic amino acids at the positions are more likely to enhance accumulation of PHA in R. eutropha.     

Transition metal ion directed supramolecular assembly of one- and two-dimensional polyrotaxanes incorporating cucurbituril

This paper reports a synthetic strategy to construct one- and two-dimensional (1D and 2D) polyrotaxanes, in which a number of rings are threaded onto a coordination polymer, by the combination of self-assembly and coordination chemistry. Our approach to construct polyrotaxanes with high structural regularity involves threading a cucurbituril (CB) "bead" with a short "string" to form a stable pseudorotaxane, followed by linking the pseudorotaxanes with metal ions as "linkers" to organize into a 1D or 2D polyrotaxane. A 4- or 3-pyridylmethyl group is attached to each end of 1,4-diaminobutane or 1,5-diaminopentane to produce the short "strings", which then react with the cucurbituril "bead" to form stable pseudorotaxanes. The reaction of the pseudorotaxanes with various transition metal ions including CuII, CoII, NiII, AgI, and CdII produces 1D or 2D polyrotaxanes, in which many molecular "beads" are threaded onto 1D or 2D coordination polymers as confirmed by X-ray crystallography. The overall structure of a polyrotaxane is the result of interplay among various factors that include the coordination preferences of the metal ion, spatial disposition of the donor atoms with respect to the CB beads in the pseudorotaxane, and the size and coordination ability of the counteranion.     

1-(d-Glucopyranosyl-2′-deoxy-2′-iminomethyl)-2-hydroxybenzene as chemosensor for aromatic amino acids by switch-on fluorescence

A glucose based C2-glyco-conjugate, that is, 1-(d-glucopyranosyl-2′-deoxy-2′-iminomethyl)-2-hydroxybenzene (L), has been synthesized in a high yield and characterized. Titration of L with all the 20 naturally occurring amino acids resulted in a large fluorescence intensity enhancement only in case of aromatic amino acids, that is, Phe, Trp, His, and Tyr and not with the others. This has been attributed to the initial formation of 1:1 hydrogen bonded complex followed by π-π interactions present between the aromatic moieties of such complexes as demonstrated by absorption and computational methods. Thus L has been able to recognize aromatic amino acids down to 1.5-3 ppm through switch-on fluorescence behavior.     

In situ encapsulating silver nanocrystals into hydrogels. A "green" signaling platform for thiol-containing amino acids or small peptides

We found that Ag(I) could serve as a "bridging agent" for triggering sodium carboxymethylcellulose (NaCMC) solution to form a hydrogel which enabled Ag nanocrystals to be in situ produced and encapsulated into the stable gel matrix by means of photoreduction; the conceptual system could act as a novel signaling platform for thiol-containing amino acids or small peptides, operating in a "self-assembly and disassembly" model.     

Expression of a partial synthetic human TNF cDNA in E. coli.

A recombinant human tumour necrosis factor (rhTNF) cDNA was constructed. The TNF gene was isolated from a human genomic gene library. There are four exons in the TNF gene. The fourth exon codes for 140 amino acids of the TNF matured protein which is composed of 157 amino acids. A major portion of the fourth exon was isolated and then ligated to a synthesized DNA fragment coding for the remaining amino acids. The partial synthetic hTNF (rhTNF) cDNA thus generated was subcloned into a vector and successfully expressed in E. coli. 5-1 fermentator was used to produce rhTNF. About 20 g (wet weight) of bacterial pellet per liter medium and 10(6)-10(7) units of cytotoxicity to L929 cells per milliliter medium were obtained. rhTNF was purified by HPLC and dried with a freeze dryer. rhTNF with a purity of about 95% in the form of white powder was obtained. The sequence of ten amino acids at the amino terminus of the rhTNF was determined. The result showed that it was identical with that of the natural human TNF.     

5-Trifluoromethylfuryl derivatives of phosphocarboxylic acids

Methods of synthesis of trifluoromethylfuryl derivatives of phosphonocarboxylic acids are studied. By addition of diethyl hydrogen phosphite to alkyl 3-(5-trifluoromethylfur-2-yl)acrylate under the conditions of the Pudovik reaction the corresponding derivative of 3-phosphonopropionic acid was prepared. Diethyl (5-trifluoromethylfur-2-yl)methanephosphonate in presence of potassium tert-butylate reacts with ethyl acrylate to form trifluoromethylfuryl derivative of 4-phosphonobutyric or 4-phosphonopimelic acid depending on the reaction conditions. In the products of reaction of the alkyl 3-(5-trifluoromethylfur-2-yl)-3-(diethoxyphosphoryl) propionate with ethyl acrylate in the presence of potassium tert-butylate formation of trifluoromethylfuryl derivative of the 3-phosphonoadipic acid is detected. 3-(5-Trifluoromethylfur-2-yl)-3-(diethoxyphosphoryl) propionic acid and its acid chloride are synthesized. The latter compound is used for acylation of glycine to form the corresponding N-acyl derivative. It is suggested that such compounds may be transported in the cell using usual channels of transportation of the amino acids and short peptides.     

Efficient construction of a large collection of phage-displayed combinatorial peptide libraries

Selections from phage-displayed combinatorial peptide libraries are an effective strategy for identifying peptide ligands to target proteins. Existing protocols for constructing phage-displayed libraries utilize either ligation into double-stranded phage DNA or Kunkel mutagenesis with single-stranded phagemid DNA. Although the Kunkel approach rapidly provides library sizes of up to 10(11), as many as 20% of the phagemids may be non-recombinant. With several modifications to current Kunkel protocols, we have generated peptide libraries with sizes of up to 10(11) clones and recombination frequencies approaching 100%. The production of phage libraries, as opposed to phagemid libraries, simplifies selection experiments by eliminating the need for helper phage. Our approach relies upon the presence of an amber stop codon in the coding region of gene III of bacteriophage M13. Oligonucleotides containing randomized stretches of DNA are annealed to the phage genome such that the randomized region forms a heteroduplex with the stop codon. The oligonucleotide is then enzymatically extended to generate covalently-closed, circular DNA, which is electroporated into a non-suppressor strain of Escherichia coli. If the amber stop codon is present in the DNA molecule, protein III is not synthesized and the phage cannot propagate itself. This method is customizable for the display of either random or focused peptide libraries. To date, we have constructed 22 different libraries ranging from 8-20 amino acids in length, utilizing complete or reduced codon sets.     

Synthesis of (2<Emphasis Type="Italic">R</Emphasis>,4<Emphasis Type="Italic">R</Emphasis>)-2-alkyl-3-(2-mercaptobenzoyl)thiazolidine-4-carboxylic acids

Basing on natural amino acid L-cysteine, commercially available aliphatic aldehydes, 2-acetylsulfanylbenzoyl chloride and 2,2′-disulfandiyldibenzoyl dichloride a synthesis was developed of (2R,4R)-2-alkyl-3-(2-mercaptobenzoyl)thiazolidine-4-carboxylic acids, potential antihypertensive compounds, inhibitors of angiotensin transforming enzyme.     

Particle dynamics and the development of string-like motion in a simulated monoatomic supercooled liquid

The microscopic details of local particle dynamics is studied in a glass-forming one component supercooled liquid modeled by a Dzugutov potential developed for simple metallic glass formers. Our main goal is to investigate particle motion in the supercooled liquid state, and to ascertain the extent to which this motion is cooperative and occurring in quasi-one-dimesional, string-like paths. To this end we investigate in detail the mechanism by which particles move along these paths. In particular, we show that the degree of coherence--that is, simultaneous motion by consecutive particles along a string--depends on the length of the string. For short strings, the motion is highly coherent. For longer strings, the motion is highly coherent only within shorter segments of the string, which we call "microstrings." Very large strings may contain several microstrings within which particles move simultaneously, but individual microstrings within a given string are temporally uncorrelated with each other. We discuss possible underlying mechanism for this complex dynamical behavior, and examine our results in the context of recent work by Garrahan and Chandler [Phys. Rev. Lett. 89, 035704 (2002)] in which dynamic facilitation plays a central role in the glass transition.