A test of the "jigsaw puzzle" model for protein folding by multiple methionine substitutions within the core of T4 lysozyme.

To test whether the structure of a protein is determined in a manner akin to the assembly of a jigsaw puzzle, up to 10 adjacent residues within the core of T4 lysozyme were replaced by methionine. Such variants are active and fold cooperatively with progressively reduced stability. The structure of a seven-methionine variant has been shown, crystallographically, to be similar to wild type and to maintain a well ordered core. The interaction between the core residues is, therefore, not strictly comparable with the precise spatial complementarity of the pieces of a jigsaw puzzle. Rather, a certain amount of give and take in forming the core structure is permitted. A simplified hydrophobic core sequence, imposed without genetic selection or computer-based design, is sufficient to retain native properties in a globular protein.

Single residue substitutions that change the gating properties of a mechanosensitive channel in Escherichia coli.

MscL is a channel that opens a large pore in the Escherichia coli cytoplasmic membrane in response to mechanical stress. Previously, we highly enriched the MscL protein by using patch clamp as a functional assay and cloned the corresponding gene. The predicted protein contains a largely hydrophobic core spanning two-thirds of the molecule and a more hydrophilic carboxyl terminal tail. Because MscL had no homology to characterized proteins, it was impossible to predict functional regions of the protein by simple inspection. Here, by mutagenesis, we have searched for functionally important regions of this molecule. We show that a short deletion from the amino terminus (3 amino acids), and a larger deletion of 27 amino acids from the carboxyl terminus of this protein, had little if any effect in channel properties. We have thus narrowed the search of the core mechanosensitive mechanism to 106 residues of this 136-amino acid protein. In contrast, single residue substitutions of a lysine in the putative first transmembrane domain or a glutamine in the periplasmic loop caused pronounced shifts in the mechano-sensitivity curves and/or large changes in the kinetics of channel gating, suggesting that the conformational structure in these regions is critical for normal mechanosensitive channel gating.

Single-amino acid substitutions eliminate lysine inhibition of maize dihydrodipicolinate synthase.

Dihydrodipicolinate synthase (DHPS; EC 4.2.1.52) catalyzes the first step in biosynthesis of lysine in plants and bacteria. DHPS in plants is highly sensitive to end-product inhibition by lysine and, therefore, has an important role in regulating metabolite flux into lysine. To better understand the feedback inhibition properties of the plant enzyme, we transformed a maize cDNA for lysine-sensitive DHPS into an Escherichia coli strain lacking DHPS activity. Cells were mutagenized with ethylmethanesulfonate, and potential DHPS mutants were selected by growth on minimal medium containing the inhibitory lysine analogue S-2-aminoethyl-L-cysteine. DHPS assays identified surviving colonies expressing lysine-insensitive DHPS activity. Ten single-base-pair mutations were identified in the maize DHPS cDNA sequence; these mutations were specific to one of three amino acid residues (amino acids 157, 162, and 166) localized within a short region of the polypeptide. No other mutations were present in the remaining DHPS cDNA sequence, indicating that altering only one of the three residues suffices to eliminate lysine inhibition of maize DHPS. Identification of these specific mutations that change the highly sensitive maize DHPS to a lysine-insensitive isoform will help resolve the lysine-binding mechanism and the resultant conformational changes involved in inhibition of DHPS activity. The plant-derived mutant DHPS genes may also be used to improve nutritional quality of maize or other cereal grains that have inadequate lysine content when fed to animals such as poultry, swine, or humans.

Codon repeats in genes associated with human diseases: fewer repeats in the genes of nonhuman primates and nucleotide substitutions concentrated at the sites of reiteration.

Five human diseases are due to an excessive number of CAG repeats in the coding regions of five different genes. We have analyzed the repeat regions in four of these genes from nonhuman primates, which are not known to suffer from the diseases. These primates have CAG repeats at the same sites as in human alleles, and there is similar polymorphism of repeat number, but this number is smaller than in the human genes. In some of the genes, the segment of poly(CAG) has expanded in nonhuman primates, but the process has advanced further in the human lineage than in other primate lineages, thereby predisposing to diseases of CAG reiteration. Adjacent to stretches of homogeneous present-day codon repeats, previously existing codons of the same kind have undergone nucleotide substitutions with high frequency. Where these lead to amino acid substitutions, the effect will be to reduce the length of the original homopolymeric stretch in the protein.

Recherches sur les substitutions, et en particulier sur les groupes transitifs.

Available on demand as hard copy or computer file from Cornell University Library.

Du projet de loi sur les successions et les substitutions, pour comparaison, quelques idées sur des institutions appropriées à l'ordre de choses qui nous régit, et qui en seraient les garanties et les appuis.

Mode of access: Internet.

De la restitution des biens des émigrés, considérée sousle triple rapport du droit public, du droit civil, et de la politique;et de la révocation de la loi des 25 octobre et 14 novembre 1792, qui a aboli les substitutions.

Mode of access: Internet.

Amino acid substitutions around the chromophore of the chromoprotein Rtms5 influence polypeptide cleavage

Extension of the conjugated pi-system of many all-protein chromophores with an acylimine bond is the basis for their red-shifted optical properties. The presence of this post-translational modification is evident in crystal structures of these proteins. Harsh denaturation of proteins containing an acylimine bond results in partial polypeptide cleavage. For the red fluorescent protein DsRed, the extent of cleavage is quantitative. However, this is not the case for the blue non-fluorescent chromoprotein Rtms5, even though all chromophores in tetrameric Rtms5 contain an acylimine bond. We have identified two positions around the chromophore of Rtms5 where substitutions can promote or suppress the extent of cleavage on harsh denaturation. We propose a model in which cleavage of Rtms5 is facilitated by a trans to cis isomerisation of the chromophore. (c) 2006 Elsevier Inc. All rights reserved.

Effects of cation substitutions on the physical properties of M2M1T2O6 pyroxenes

In this PhD study, the effects of the cation substitutions on the physical properties of pyroxenes have been discussed. The results of this work extend the knowledge on pyroxenes with different chemical compositions. These properties might be used in the development of ceramic pigments, advanced materials and for the mineralogical phase identification. First of all, the crystallographic differences between Ge and Si pyroxenes have been examined. The structure of C2/c Ca rich Ge clinopyroxenes is very close to the low pressure C2/c structural configuration found in Ca-rich Si-pyroxenes. The shear of the unit cell is very similar, and the difference between a Ge end member and the corresponding Si-rich one is less than 1°. Instead, a remarkable difference exists between Ca-poor Si and Ge clinopyroxenes. First, Ca-poor Ge pyroxenes do not display a P21/c symmetry, but retain the C2/c symmetry; second, the observed C2/c structure shows, at room pressure, the configuration with highly kinked tetrahedral chains characteristic of the high pressure C2/c symmetry of Si Ca-poor pyroxenes. In orthopyroxenes, with Pbca symmetry, Ge-pyroxenes have volume larger than Si-pyroxenes. Samples along the system CaCoGe2O6 - CoCoGe2O6 have been synthesized at three different temperatures: 1050 °C, 1200 °C and 1250 °C. The aim of these solid state syntheses was to obtain a solid solution at ambient pressure, since the analogues Si-system needs high pressure. Unfortunately, very limited solution occurs because the structure forms of the two end member (high temperature for CaCoGe2O6 and high pressure CoCoGe2O6) are incompatible. The phase diagram of this system has been sketched and compared to that of Si. The cobalt end member (CoCoGe2O6) is stable at ambient pressure in two symmetries: at 1050 °C C2/c and 1200 °C Pbca. The impurity phase formed during these experiments is cobalt spinel. Raman spectroscopy has been used to investigate the vibrational properties of Ca-pyroxenes CaCoGe2O6, CaMgGe2O6, CaMgSi2O6 and CaCoSi2O6. A comparison between silicate and germanate pyroxenes shows significant changes in peak positions of the corresponding modes caused mainly by the difference of the Ge-Si atomic weight along with the distortion and compression of the coordination polyhedra. Red shift in Raman spectra of germanates has been calculated by a rough scale factor calculated by a simple harmonic oscillator model, considering the different bond lengths for 4-coordinated Si ~ 1.60- 1.65 Å vs Ge–O distance ~1.70 - 1.80 Å. The Raman spectra of CaMgGe2O6 and CaCoGe2O6 have been classified, in analogy with silicate (Wang et al., 2001) counterparts, in different ranges: - R1 (880-640 cm-1): strong T-O stretching modes of Ge and non-bridging O1 and O2 atoms within the GeO4 tetrahedron; - R2 (640-480 cm-1): stretching/bending modes of Ge-Obr-Ge bonds (chain stretching and chain bending); - R4 (480-360 cm-1): O-Ge-O vibrations; - R3 (360-240 cm-1): motions of the cations in M2 and M1 sites correlated with tetrahedral chain motion and tilting tetrahedra; - R5 (below 240 cm-1): lattice modes. The largest shift with respect to CaMgSi2O6 - CaCoSi2O6 is shown by the T-O stretching and chain modes. High-pressure Raman spectroscopy (up to about 8 GPa) on the same samples of Ca-pyroxenes using an ETH-type diamond anvil cell shows no phase transition within the P-ranges investigated, as all the peak positions vary linearly as a function of pressure. Our data confirm previous experimental findings on Si-diopside (Chopelas and Serghiou, 2000). In the investigated samples, all the Raman peaks shift upon compression, but the major changes in wavenumber with pressure are attributed to the chain bending (Ge-Obr-Ge bonds) and tetrahedra stretching modes (Ge-Onbr). Upon compression, the kinking angle, the bond lengths and T-T distances between tetrahedra decrease and consequently the wavenumber of the bending chain mode and tetrahedra stretching mode increases. Ge-pyroxenes show the higher P-induced peak-position shifts, being more compressible than corresponding silicates. The vibrational properties of CaM2+Ge2O6 (M2+ =Mg, Mn, Fe, Co, Ni, Zn) are reported for the first time. The wavenumber of Ge-Obr-Ge bending modes decreases linearly with increasing ionic radius of the M1 cation. No simple correlation has been found with M1 atomic mass or size or crystallographic parameters for the peak at ~850 cm-1 and in the low wavenumber regions. The magnetic properties of the system CaCoSi2O6 - CoCoSi2O6 have been investigated by magnetometry. The join is always characterized by 1 a.p.f.u. of cobalt in M1 site and this causes a pure collinear antiferromagnetic behaviour of the intra-chain superexchange interaction involving Co ions detected in all the measurements, while the magnetic order developed by the cobalt ions in M2 site (intra-chain) is affected by weak ferromagnetism, due to the non-collinearity of their antiferromagnetic interaction. In magnetically ordered systems, this non-collinearity effect promotes a spin canting of anti-parallel aligned magnetic moments and thus is a source of weak ferromagnetic behaviour in an antiferromagnetic. The weak ferromagnetism can be observed only for the samples with Co content higher than 0.5 a.p.f.u. in M2, when the concentration is sufficiently high to create a long range order along the M2 chain which is magnetically independent of M1 chain. The ferromagnetism was detected both in the M(T) at 10 Oe and M(H).

Organic reactions in ionic liquids: a simple highly regioselective or regiospecific substitutions of benzotriazole

In the absence of any added base in ionic liquids [Bmim][BF4], benzotriazole replaces the halogen atom of an a-halogenated ketone or a-halogenated carboxylic ester to give the corresponding N-1-substituted benzotriazole as the only isomer, and 1-chloro-2,4-dinitrobenzene reacted similarly with benzotriazole to afford the N-1-substituted benzotriazole in a good yield. Alkyl halides reacted regioselectively to afford the N-1-alkylbenzotriazole in ratios of more than 15 to 1 over the N-2-isomer.

Differential impact of amino acid substitutions on critical residues of the human glucagon-like peptide-1 receptor involved in peptide activity and small-molecule allosterys

The glucagon-like peptide-1 receptor (GLP-1R) is a class B G protein-coupled receptor that has a critical role in the regulation of glucose homeostasis, principally through the regulation of insulin secretion. The receptor systemis highly complex, able to be activated by both endogenous [GLP-1(1-36)NH2, GLP-1(1-37), GLP-1(7-36)NH2, GLP-1(7-37), oxyntomodulin], and exogenous (exendin-4) peptides in addition to small-molecule allosteric agonists (compound 2 [6,7-dichloro-2-methylsulfonyl-3-tertbutylaminoquinoxaline], BETP [4-(3-benzyloxy)phenyl)-2-ethylsulfinyl-6-(trifluoromethyl)pyrimidine]). Furthermore, the GLP-1R is subject to single-nucleotide polymorphic variance, resulting in amino acid changes in the receptor protein. In this study, we investigated two polymorphic variants previously reported to impact peptidemediated receptor activity (M149) and small-molecule allostery (C333). These residues were mutated to a series of alternate amino acids, and their functionality was monitored across physiologically significant signaling pathways, including cAMP, extracellular signal-regulated kinase 1 and 2 phosphorylation, and intracellular Ca2+ mobilization, in addition to peptide binding and cell-surface expression. We observed that residue 149 is highly sensitive to mutation, with almost all peptide responses significantly attenuated at mutated receptors. However, most reductions in activity were able to be restored by the small-molecule allosteric agonist compound 2. Conversely, mutation of residue 333 had little impact on peptide-mediated receptor activation, but this activity could not be modulated by compound 2 to the same extent as that observed at the wild-type receptor. These results provide insight into the importance of residues 149 and 333 in peptide function and highlight the complexities of allosteric modulation within this receptor system.

Admissible Substitutions in Sequent Calculi

For first-order classical logic a new notion of admissible substitution is defined. This notion allows optimizing the procedure of the application of quantifier rules when logical inference search is made in sequent calculi. Our objective is to show that such a computer-oriented sequent technique may be created that does not require a preliminary skolemization of initial formulas and that is efficiently comparable with methods exploiting the skolemization. Some results on its soundness and completeness are given.

Comparing Entire Prototypes at Semigroup Homomorphisms and Specifically at Regular Languages Substitutions

The following statements are proven: A correspondence of a semigroup in another one is a homomorphism if and only if when the entire prototype of the product of images contains (always) the product of their entire prototypes. The Kleene closure of the maximal rewriting of a regular language at a regular language substitution contains in the maximal rewriting of the Kleene closure of the initial regular language at the same substitution. Let the image of the maximal rewriting of a regular language at a regular language substitution covers the entire given regular language. Then the image of any word from the maximal rewriting of the Kleene closure of the initial regular language covers by the image of a set of some words from the Kleene closure of the maximal rewriting of this given regular language everything at the same given regular language substitution. The purposefulness of the ¯rst statement is substantiated philosophically and epistemologically connected with the spirit of previous mathematical results of the author. A corollary of its is indicated about the membership problem at a regular substitution.

Substitutions in the glycogenin-1 gene are associated with the evolution of endothermy in sharks and tunas

We thank Sean Tracey and Jaime McAllister for supplying albacore and southern bluefin tuna samples, Eva Giacomello for collecting the skipjack tuna sample, Elena Sarropoulou for providing the Atlantic bonito assembly, Helen Hipperson for assistance in the lab, Barbara Block and Ziheng Yang for advice, the editors and reviewers for comments, and the Leverhulme Trust and BBSRC for funding

Ordo ab chaos: Organisation des substitutions dans 'Un mot pour un autre' de Jean Tardieu

info:eu-repo/semantics/published