Medicine by design

This review describes studies of particular enzymatically catalyzed reactions to investigate the possibility that catalysis is mediated by protein dynamics. That is, evolution has crafted the protein backbone of the enzyme to direct vibrations in such a fashion to speed reaction. The review presents the theoretical approach we have used to investigate this problem, but it is designed for the nonspecialist.

10p system191 01-06-2013 37 4   Download

In this study, we isolated a 25-kDa novel snake venom protein, designated ablomin, from the venom of the Japanese Mamushi snake (Agkistrodon blomhoffi). The amino-acid sequence of this protein was determined by peptide sequencing and cDNA cloning. The deduced sequence showed high similarity to helothermine from the Mexican beaded lizard (Heloderma horridum horridum), which blocks voltage-gated calcium and potassium channels, and ryanodine receptors. Ablomin blocked contraction of rat tail arterial smooth muscle elicited by high K+-induced depolarization in the 0.

8p system191 01-06-2013 26 3   Download

We report the cloning and functional charaterization of the full-length cDNA and gene encoding a Toxoplasma gondii DNA repair enzyme designated TgDRE. The gene is composed of three exons separated by two introns of 780 and 630 bp, and encodes a protein with a predicted molecular mass of 49.6 kDa. The native TgDRE protein, with a molecular mass of 60 kDa, is only detected in the virulent tachyzoite stage of T. gondii. However, the transcript is present in both asexual parasite stages, virulent tachyzoite and avirulent encysted bradyzoite. ...

9p research12 01-06-2013 33 5   Download

In an effort to explore the role of glycine clusters on the cold adaptation of enzymes, we designed point mutations aiming to alter the distribution of glycine residues close to the active site of the psychrophilic alkaline phosphatase from the Antarctic strain TAB5. The mutagenesis targets were residues Gly261 and Gly262. The replacement of Gly262 by Ala resulted in an inactive enzyme. Substitution of Gly261 by Ala resulted to an enzyme with lower stability and increased energy of activation.

6p research12 01-06-2013 37 5   Download

A technique has been developed to search a proteome database for new members of a functional class of membrane protein. It takes advantage of the highly conserved secondary structure of functionally related membrane proteins. Such proteins typically have the same number of transmembrane domains located at similar relative positions in their polypeptide sequence. This gives rise to a characteristic pattern of peaks in their hydropathy profiles.

7p research12 01-06-2013 32 4   Download

The aim of this study was to increase the stability of the thermolabile (ba)8-barrel enzyme indoleglycerol phosphate synthase from Escherichia coli by the introduction of disulfide bridges. For the design of such variants, we selected two out of 12 candidates, in which newly introduced cysteines potentially form optimal disulfide bonds. These variants avoid short-range connections, substitutions near catalytic residues, and crosslinks between the new and the three parental cysteines.

9p research12 01-06-2013 38 4   Download

Insulin-like growth factor (IGF) binding to the type 1 IGF receptor (IGF1R) elicits mitogenic e€ects, promotion of di€erentiation and protection from apoptosis. This study has systematically measured IGF1R binding anities of IGF-I, IGF-II and 14 IGF analogues to a recombinant high-anity form of the IGF1R using BIAcore technology. The analogues assessed could be divided into two groups: (a) those designed to investigate binding of IGF-binding protein, which exhibited IGF1R-binding anities similar to those of IGF-I or IGF-II;...

8p research12 01-06-2013 40 4   Download

Two novel pore-forming peptides have been isolated from the venom of the South-African scorpion Opistophtalmus carinatus. These peptides,designated opistoporin 1 and 2, differ by only one amino acid and belong to a group of a-helical,cationic peptides. For the first time,a comparison of the primary structures ofa-helical pore-forming peptides from scorpion venom was undertaken.

12p research12 29-04-2013 43 3   Download

TheDrosophila melanogasterprotein sprouty is induced uponfibroblast growth factor (FGF)- andepidermal growth factor (EGF)-receptor tyrosine kinase activation and acts as an inhibitor of the ras/MAP kinase pathway downstreamof these receptors. By differential displayRT-PCRof activated vs. resting umbilical artery smooth muscle cells (SMCs) we detected a new human sprouty gene, which we designated human sprouty 4 (hspry4) based on its homology with murine sprouty 4.

11p research12 29-04-2013 45 2   Download

This studywas designed to yield data on the supramolecular organization of the phycobilisome apparatus from Synechocystis, and the possible effects of environmental stress on this arrangement. Phycobilisomes were dissociated ina low ionic strength solutionandaquantitative estimation of the protein components present in each subcomplex was obtained using liquid chromatography coupled on-line with a mass spectrometer equipped with an electrospray ion source (ESI-MS).

9p research12 29-04-2013 50 3   Download

A new human/rat CRH analogue has been synthesized using the Fmoc/tBu solid-phase synthetic protocol. The sequence ofthe new peptide differs from the original in two positions, 12 and 15, at which the native amino acids L-phenylalanine 12 and L-leucine 15 have been replaced by the nonprotein amino acids D-phenylalanine and a-aminoisobutyric acid (Aib), respectively. The high resolution three-dimensional solution structure of [D-Phe12, Aib15]CRH has been determined by 688 dis-tance constraints (656 meaningful NOE and 32 H-bonds distance limits) and 21 angle constraints. ...

11p tumor12 22-04-2013 34 3   Download

The present study was conducted on human Jurkat T-cell lines in order to elucidate the role of phospholipase A2in capacitative calcium entry. We have employed thapsigar-gin (TG)that induces increases in [Ca 2+ ] i by emptying the calcium pool of endoplasmic reticulum, followed by capacitative calcium entry. We designed a Ca 2+ free/Ca 2+ reintroduction (CFCR)protocol for the experiments, conducted in Ca 2+ -free medium.

7p tumor12 22-04-2013 30 2   Download

Theb-amyloid peptide (Ab) is a major component of toxic amyloid plaques found in the brains of patients with Alzheimer’s disease.Abis liberated by sequential cleavage of amyloid precursor protein (APP) byb-andc-secre-tases.The level of Abdepends directly on the hydrolytic activity ofb-secretase.Therefore, b-secretase is an excel-lent target for drug design.An approach based on RNA-cleaving ribozymes was developed to control expression ofb-secretase.

9p tumor12 20-04-2013 37 4   Download

A histone heterodimer, designated as p28, which contains an N e (c-glutamyl)lysine cross-link between Gln9 of histone H2B and Lys5 or Lys12 of histone H4, is present in starfish (Asterina pectinifera) sperm. Treatment of spermnuclei with micrococcal nuclease produced soluble chromatin, which was size-fractionated by sucrose-gradient centrifugation to give p28-containing oligonucleosome and p28-free mono-nucleosome fractions, indicating that the cross-link is inter-nucleosomal.

10p tumor12 20-04-2013 39 4   Download

Novel chromogenic substrates for endo-b-galactosidase were designed on the basis of the structural features of keratan sulfate. Galb1-4GlcNAcb1-3Galb1-4GlcNAcb-pNP (2),which consists of two repeating units ofN-acetyl-lactosamine,was synthesized enzymatically by consecutive additions of GlcNAc and Gal residues top-nitrophenyl b-N-acetyllactosaminide. In a similar manner,Glc-NAcb1-3Galb1-4GlcNAcb-pNP (1),GlcNAcb1-3Galb1-4Glcb-pNP (3),Galb1-4GlcNAcb1-3Galb1-4Glcb-pNP (4), Galb1-3GlcNAcb1-3Galb1-4Glcb-pNP (5),and Galb1-6GlcNAcb1-3Galb1-4Glcb-pNP (6) were synthesized as analogues of2.

11p tumor12 20-04-2013 28 2   Download

Different pathways of bilayer disruption by the structurally related antimicrobial peptides cecropin B, B1 and B3, revealed by surface plasma resonance analysis of immobi-lized liposomes, differential scanning calorimetryof peptide– large unilamellar vesicle interactions, and light microscopic analysis of peptide-treated giant unilamellar vesicles, have been identified inthis study.

10p tumor12 20-04-2013 39 3   Download

In the case of oxidized plastocyanin fromSynechocystissp. PCC6803, an NMR approach based on classical two and three dimensional experiments for sequential assignment leaves unobserved 14 out of 98 amino acids. A protocol which simply makes use of tailored versions of 2D HSQC and 3D CBCA(CO)NH and CBCANH leads to the identi-fication of nine of the above 14 residues.

10p tumor12 20-04-2013 35 4   Download

Amathematicalmodel hasbeendevelopedtostudy theeffect of external tryptophan on the trp operon. The model accounts for the effect of feedback repression by tryptophan through the Hill equation. We demonstrate that the trp operonmaintains an intracellular steady-state concentration in a fivefold range irrespective of extracellular conditions. Dynamic behavior of thetrp operon corresponding to varying levels of extracellular tryptophan illustrates the adaptive nature of regulation.

8p fptmusic 16-04-2013 49 4   Download

We report experiments to investigate the role of the physio-logically relevant protein tyrosine kinase Lck in the ordered phosphorylation of the T-cell receptorfchain. Six synthetic peptides were designed based on the sequences of the immunoreceptor tyrosine-based activation motifs (ITAMs) of thefchain. Preliminary 1 H-NMRstudies of recombinant f chain suggested that it is essentially unstructured and therefore that peptide mimics would serve as useful models for investigating individual ITAM tyrosines....

8p fptmusic 16-04-2013 26 1   Download

The cysteine-rich peptide hepcidin is known to be an antimicrobial peptide and iron transport regulator that has been found in both fish and mam-mals. Recently, we found two different types (designated Hep-JF1 and Hep-JF2) of hepcidin cDNA in the Japanese flounder,Paralichthys oliva-ceus, by expressed sequence tag analysis. The identity of amino acid sequences between Hep-JF1 and Hep-JF2 was 51%. The Hep-JF1 and Hep-JF2 genes both consist of three exons and two introns, and both exist as single copies in the genome. ...

8p fptmusic 12-04-2013 41 2   Download