Institut de Chimie

New protein parameters are reported for the all-atom empirical energy function in the CHARMM program. The parameter evaluation was based on a self-consistent approach designed to achieve a balance between the internal (bonding) and interaction (nonbonding) terms of the force field and among the solvent-solvent, solvent-solute, and solute-solute interactions. Optimization of the internal parameters used experimental gas-phase geometries, vibrational spectra, and torsional energy surfaces supplemented with ab initio results. The peptide backbone bonding parameters were optimized with respect to data for N-methylacetamide and the alanine dipeptide. The interaction parameters, particularly the atomic charges, were determined by fitting ab initio interaction energies and geometries of complexes between water and model compounds that represented the backbone and the various side chains. In addition, dipole moments, experimental heats and free energies of vaporization, solvation and sublimation, molecular volumes, and crystal pressures and structures were used in the optimization. The resulting protein parameters were tested by applying them to noncyclic tripeptide crystals, cyclic peptide crystals, and the proteins crambin, bovine pancreatic trypsin inhibitor, and carbonmonoxy myoglobin in vacuo and in crystals. A detailed analysis of the relationship between the alanine dipeptide potential energy surface and calculated protein φ, χ angles was made and used in optimizing the peptide group torsional parameters. The results demonstrate that use of ab initio structural and energetic data by themselves are not sufficient to obtain an adequate backbone representation for peptides and proteins in solution and in crystals. Extensive comparisons between molecular dynamics simulations and experimental data for polypeptides and proteins were performed for both structural and dynamic properties. Energy minimization and dynamics simulations for crystals demonstrate that the latter are needed to obtain meaningful comparisons with experimental crystal structures. The presented parameters, in combination with the previously published CHARMM all-atom parameters for nucleic acids and lipids, provide a consistent set for condensed-phase simulations of a wide variety of molecules of biological interest.

Despite the imminent commercial introduction of Li-ion batteries in electric drive vehicles and their proposed use as enablers of smart grids based on renewable energy technologies, an intensive quest for new electrode materials that bring about improvements in energy density, cycle life, cost, and safety is still underway. This Progress Report highlights the recent developments and the future prospects of the use of phases that react through conversion reactions as both positive and negative electrode materials in Li-ion batteries. By moving beyond classical intercalation reactions, a variety of low cost compounds with gravimetric specific capacities that are two-to-five times larger than those attained with currently used materials, such as graphite and LiCoO(2), can be achieved. Nonetheless, several factors currently handicap the applicability of electrode materials entailing conversion reactions. These factors, together with the scientific breakthroughs that are necessary to fully assess the practicality of this concept, are reviewed in this report.

Aluminum 1,4-benzenedicarboxylate Al(OH)[O(2)C-C(6)H(4)-CO(2)]. [HO(2)C-C(6)H(4)-CO(2)H](0.70) or MIL-53 as (Al) has been hydrothermally synthesized by heating a mixture of aluminum nitrate, 1,4-benzenedicarboxylic acid, and water, for three days at 220 degrees C. Its 3 D framework is built up of infinite trans chains of corner-sharing AlO(4)(OH)(2) octahedra. The chains are interconnected by the 1,4-benzenedicarboxylate groups, creating 1 D rhombic-shaped tunnels. Disordered 1,4-benzenedicarboxylic acid molecules are trapped inside these tunnels. Their evacuation upon heating, between 275 and 420 degrees C, leads to a nanoporous open-framework (MIL-53 ht (Al) or Al(OH)[O(2)C-C(6)H(4)-CO(2)]) with empty pores of diameter 8.5 A. This solid exhibits a Langmuir surface area of 1590(1) m(2)g(-1) together with a remarkable thermal stability, since it starts to decompose only at 500 degrees C. At room temperature, the solid reversibly absorbs water in its tunnels, causing a very large breathing effect and shrinkage of the pores. Analysis of the hydration process by solid-state NMR ((1)H, (13)C, (27)Al) has clearly indicated that the trapped water molecules interact with the carboxylate groups through hydrogen bonds, but do not affect the hydroxyl species bridging the aluminum atoms. The hydrogen bonds between water and the oxygen atoms of the framework are responsible for the contraction of the rhombic channels. The structures of the three forms have been determined by means of powder X-ray diffraction analysis. Crystal data for MIL-53 as (Al) are as follows: orthorhombic system, Pnma (no. 62), a = 17.129(2), b = 6.628(1), c = 12.182(1) A; for MIL-53 ht (Al), orthorhombic system, Imma (no. 74), a = 6.608(1), b = 16.675(3), c = 12.813(2) A; for MIL-53 lt (Al), monoclinic system, Cc (no. 9), a = 19.513(2), b = 7.612(1), c = 6.576(1) A, beta = 104.24(1) degrees.

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReduced Transition Metal Colloids: A Novel Family of Reusable Catalysts?Alain Roucoux, Jürgen Schulz, and Henri PatinView Author Information Ecole Nationale Supérieure de Chimie de Rennes, UMR CNRS 6052 "Synthèses et Activations de Biomolécules", Institut de Chimie de Rennes, Avenue du Gal Leclerc − 35700 Rennes, France Cite this: Chem. Rev. 2002, 102, 10, 3757–3778Publication Date (Web):September 10, 2002Publication History Received30 January 2002Published online10 September 2002Published inissue 1 October 2002https://pubs.acs.org/doi/10.1021/cr010350jhttps://doi.org/10.1021/cr010350jresearch-articleACS PublicationsCopyright © 2002 American Chemical SocietyRequest reuse permissionsArticle Views13864Altmetric-Citations1699LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Colloidal particles,Colloids,Metal nanoparticles,Metals,Nanoparticles Get e-Alerts

A preparative method for isolating high‐molecular‐weight DNA from animal cells is described. This method is based on the use of proteinase K, a powerful proteolytic enzyme with a broad action spectrum, which is very active in the presence of sodium dodecylsulfate and ethylene‐diamine tetraacetate. The DNA preparation is free of RNA, protein and degrading enzymes. The number‐average molecular weight of the native DNA is 190 × 10 6 , whereas it is 90 × 10 6 for single‐stranded DNA, indicating that the DNA molecules do not contain single‐stranded nicks. The native DNA molecules range in molecular weight from 40 × 10 6 to more than 500 × 10 6 .

The fragile X syndrome, a common cause of inherited mental retardation, is characterized by an unusual mode of inheritance. Phenotypic expression has been linked to abnormal cytosine methylation of a single CpG island, at or very near the fragile site. Probes adjacent to this island detected very localized DNA rearrangements that constituted the fragile X mutations, and whose target was a 550-base pair GC-rich fragment. Normal transmitting males had a 150- to 400-base pair insertion that was inherited by their daughters either unchanged, or with small differences in size. Fragile X-positive individuals in the next generation had much larger fragments that differed among siblings and showed a generally heterogeneous pattern indicating somatic mutation. The mutated allele appeared unmethylated in normal transmitting males, methylated only on the inactive X chromosome in their daughters, and totally methylated in most fragile X males. However, some males had a mosaic pattern. Expression of the fragile X syndrome thus appears to result from a two-step mutation as well as a highly localized methylation. Carriers of the fragile X mutation can easily be detected regardless of sex or phenotypic expression, and rare apparent false negatives may result from genetic heterogeneity or misdiagnosis.

The efficiency of the successive dichotomy method for powder diffraction pattern indexing [Louër & Louër (1972). J. Appl. Cryst . 5 , 271–275] has been proved over more than 30 years of usage. Features implemented in the new version of the computer program DICVOL 04 include (i) a tolerance to the presence of impurity (or inaccurately measured) diffraction lines, (ii) a refinement of the `zero-point' position, (iii) a reviewing of all input lines from the solution found from, generally, the first 20 lines, (iv) a cell analysis, based on the concept of the reduced cell, to identify equivalent monoclinic and triclinic solutions, and (v) an optional analysis of input powder data to detect the presence of a significant `zero-point' offset. New search strategies have also been introduced, e.g. each crystal system is scanned separately, within the input volume limits, to limit the risk of missing a solution characterized by a metric lattice singularity. The default values in the input file have been extended to 25 Å for the linear parameters and 2500 Å 3 for the cell volume. The search is carried out exhaustively within the input parameter limits and the absolute error on peak position measurements. Many tests with data from the literature and from powder data of pharmaceutical materials, collected with the capillary technique and laboratory monochromatic X-rays, have been performed with a high success rate, covering all crystal symmetries from cubic to triclinic. Some examples reported as `difficult' cases are also discussed. Additionally, a few recommendations for the correct practice of powder pattern indexing are reported.

A method is presented for determining activation free energies in complex molecular systems. The method relies on knowledge of the minimum energy path and bases the activation free energy calculation on moving along this path from a minimum to a saddle point. Use is made of a local reaction coordinate which describes the advance of the reaction in each segment of the minimum energy path. The activation free energy is formulated as a sum of two terms. The first is due to the change in the local reaction coordinate between the endpoints of each segment of the path. The second is due to the change in direction of the minimum energy path between consecutive segments. Both contributions can be obtained by molecular dynamics simulations with a constraint on the local reaction coordinate. The method is illustrated by applying it to a model potential and to the C7eq to C7ax transition in the alanine dipeptide. It is found that the term due to the change of direction in the reaction path can make a substantial contribution to the activation free energy.

Abstract A unified scale is recommended for reporting the NMR chemical shifts of all nuclei relative to the 1 H resonance of tetramethylsilane (TMS). The unified scale is designed to provide a precise ratio, Ξ , of the resonance frequency of a given nuclide to that of the primary reference, the 1H resonance of TMS in dilute solution (volume fraction, φ < 1%) in chloroform. Referencing procedures are discussed, including matters of practical application of the unified scale. Special attention is paid to recommended reference samples, and values of Ξ for secondary references on the unified scale are listed, many of which are the results of new measurements. Some earlier recommendations relating to the reporting of chemical shifts are endorsed. The chemical shift, δ , is redefined to avoid previous ambiguities but to leave practical usage unchanged. Relations between the unified scale and recently published recommendations for referencing in aqueous solutions (for specific use in biochemical work) are discussed, as well as the special effects of working in the solid state with magic-angle spinning. In all, nine new recommendations relating to chemical shifts are made. Standardized nuclear spin data are also presented in tabular form for the stable (and some unstable) isotopes of all elements with nonzero quantum numbers. The information given includes quantum numbers, isotopic abundances, magnetic moments, magnetogyric ratios and receptivities, together with quadrupole moments and line-width factors where appropriate.

capture as well as utilization were systematically discussed and compared. With our great effort, this review would be of significant importance for academic researchers for obtaining an overall understanding of the current developments and future trends of CCU. This work is bound to benefit researchers in fields relating to CCU and facilitate the progress of significant breakthroughs in both fundamental research and commercial applications to deliver perspective views for future scientific and industrial advances in CCU.

Penicillin-binding proteins (PBPs) have been scrutinized for over 40 years. Recent structural information on PBPs together with the ongoing long-term biochemical experimental investigations, and results from more recent techniques such as protein localization by green fluorescent protein-fusion immunofluorescence or double-hybrid assay, have brought our understanding of the last stages of the peptidoglycan biosynthesis to an outstanding level that allows a broad outlook on the properties of these enzymes. Details are emerging regarding the interaction between the peptidoglycan-synthesizing PBPs and the peptidoglycan, their mesh net-like product that surrounds and protects bacteria. This review focuses on the detailed structure of PBPs and their implication in peptidoglycan synthesis, maturation and recycling. An overview of the content in PBPs of some bacteria is provided with an emphasis on comparing the biochemical properties of homologous PBPs (orthologues) belonging to different bacteria.

A Gaussian solvent-exclusion model for the solvation free energy is developed. It is based on theoretical considerations and parametrized with experimental data. When combined with the CHARMM 19 polar hydrogen energy function, it provides an effective energy function (EEF1) for proteins in solution. The solvation model assumes that the solvation free energy of a protein molecule is a sum of group contributions, which are determined from values for small model compounds. For charged groups, the self-energy contribution is accounted for primarily by the exclusion model. Ionic side-chains are neutralized, and a distance-dependent dielectric constant is used to approximate the charge-charge interactions in solution. The resulting EEF1 is subjected to a number of tests. Molecular dynamics simulations at room temperature of several proteins in their native conformation are performed, and stable trajectories are obtained. The deviations from the experimental structures are similar to those observed in explicit water simulations. The calculated enthalpy of unfolding of a polyalanine helix is found to be in good agreement with experimental data. Results reported elsewhere show that EEF1 clearly distinguishes correctly from incorrectly folded proteins, both in static energy evaluations and in molecular dynamics simulations and that unfolding pathways obtained by high-temperature molecular dynamics simulations agree with those obtained by explicit water simulations. Thus, this energy function appears to provide a realistic first approximation to the effective energy hypersurface of proteins.

Advances in transition state theory and computer simulations are providing new insights into the sources of enzyme catalysis. Both lowering of the activation free energy and changes in the generalized transmission coefficient (recrossing of the transition state, tunneling, and nonequilibrium contributions) can play a role. A framework for understanding these effects is presented, and the contributions of the different factors, as illustrated by specific enzymes, are identified and quantified by computer simulations. The resulting understanding of enzyme catalysis is used to comment on alternative proposals of how enzymes work.

Selected regions of cloned EcoRI fragments of the chicken ovalbumin gene have been sequenced. The positions where the sequences coding for ovalbumin mRNA (ov-mRNA) are interrupted in the genome have been determined, and a previously unreported interruption in the DNA sequences coding for the 5' nontranslated region of the messenger has been discovered. Because directly repeated sequences are found at exon-intron boundaries, the nucleotide sequence alone cannot define unique excision-ligation points for the processing of a possible ov-mRNA precursor. However, the sequences in these boundary regions share common features; this leads to the proposal that there are, in fact, unique excision-ligation points common to all boundaries.

Continuation of mammalian species requires the formation and development of the sexually dimorphic germ cells. Cultured embryonic stem cells are generally considered pluripotent rather than totipotent because of the failure to detect germline cells under differentiating conditions. Here we show that mouse embryonic stem cells in culture can develop into oogonia that enter meiosis, recruit adjacent cells to form follicle-like structures, and later develop into blastocysts. Oogenesis in culture should contribute to various areas, including nuclear transfer and manipulation of the germ line, and advance studies on fertility treatment and germ and somatic cell interaction and differentiation.

Compound null mutations of retinoic acid receptor (RAR) genes lead to lethality in utero or shortly after birth and to numerous developmental abnormalities. In the accompanying paper (Lohnes, D., Mark., M., Mendelsohn, C., Dollé, P., Dierich, A., Gorry, Ph., Gansmuller, A. and Chambon, P. (1994). Development 120, 2723-2748), we describe malformations of the head, vertebrae and limbs which, with the notable exception of the eye defects, were not observed in the offspring of vitamin A-deficient (VAD) dams. We report here abnormalities in the neck, trunk and abdominal regions of RAR double mutant mice, which include: (i) the entire respiratory tract, (ii) the heart, its outlow tract and the great vessels located near the heart, (iii) the thymus, thyroid and parathyroid glands, (iv) the diaphragm, (v) the genito-urinary system, and (vi) the lower digestive tract. A majority of these abnormalities recapitulate those observed in the fetal VAD syndrome described by Joseph Warkany's group more than fourty years ago [Wilson, J. G., Roth, C. B. and Warkany, J. (1953) Am. J. Anat., 92, 189-217; and refs therein]. Our results clearly demonstrate that RARs are essential for vertebrate ontogenesis and therefore that retinoic acid is the active retinoid, which is required at several stages of the development of numerous tissues and organs. We discuss several possibilities that may account for the apparent functional redundancy observed amongst retinoic acid receptors during embryogenesis.

We present the sequence of regions of the chicken ovalbumin gene believed to be important in the control of initiation of transcription, splicing, and transcription termination or polyadenylation. Comparison with corresponding areas of other genes reveals some homologous regions which might play a role in these processes.

In vitro genetic techniques were used to study the sequence requirements for the initiation of specific transcription. Deletion mutants were constructed around the putative promoter of the adenovirus-2 major late and chicken conalbumin genes. Specific transcription in vitro by RNA polymerase B together with a HeLa cell cytoplasmic extract was used as the test for promoter function. With this approach sequences which are essential for the initiation of specific transcription in vitro, were shown to be located between 12 and 32 base pairs upstream from the 5' end of these genes.

In recent years, N-heterocyclic carbenes (NHC) have proved to be a versatile class of spectator ligands in homogeneous catalysis. Being robust anchoring functions for late transition metals, their ligand donor capacity and their molecular shape is readily modified by variation of the substituents at the N-atoms and the structure of the cyclic backbone. After the first attempts to use chiral NHC ligands in asymmetric catalysis in the late 1990's, which initially met with limited success, several novel structural concepts have emerged during the past two years which have led literally to an explosion of the field. With a significant number of highly selective chiral catalysts based on chiral NHCs having been reported very recently, several general trends in the design of new NHC-containing molecular catalysts for stereoselective transformations in organic synthesis emerge.

Interest in the Ets proteins has grown enormously over the last decade. The v-ets oncogene was originally discovered as part of a fusion protein expressed by a transforming retrovirus (avian E26), and later shown to be transduced from a cellular gene. About 30 related proteins have now been found in species ranging from flies to humans, that resemble the vEts protein in the so-called 'ets domain'. The ets domain has been shown to be a DNA-binding domain, that specifically interacts with sequences containing the common core trinucleotide GGA. Furthermore, it is involved in protein-protein interactions with co-factors that help determine its biological activity. Many of the Ets-related proteins have been shown to be transcription activators, like other nuclear oncoproteins and anti-oncoproteins (Jun, Fos, Myb, Myc, Rel, p53, etc.). However, Ets-like proteins may have other functions, such as in DNA replication and a general role in transcription activation. Ets proteins have been implicated in regulation of gene expression during a variety of biological processes, including growth control, transformation, T-cell activation, and developmental programs in many organisms. Signals regulating cell growth are transmitted from outside the cell to the nucleus by growth factors and their receptors. G-proteins, kinases and transcription factors. We will discuss how several Ets-related proteins fit into this scheme, and how their activity is regulated both post- and pre-translationally. Loss of normal control is often associated with conversion to an oncoprotein. vEts has been shown to have different properties from its progenitor, which might explain how it has become oncogenic. Oncogene-related products have been implicated in the control of various developmental processes. Evidence is accumulating for a role for Ets family members in Drosophila development, Xenopus oocyte maturation, lymphocyte differentiation, and viral infectious cycles. An ultimate hope in studying transformation by oncoproteins is to understand how cells become cancerous in humans, which would lead to more effective treatments. vEts induces erythroblastosis in chicken. Cellular Ets-family proteins can be activated by proviral insertion in mice and, most interestingly, by chromosome translocation in humans. We are at the beginning of understanding the multiple facets of regulation of Ets activity. Future work on the Ets family promises to provide important insights into both normal control of growth and differentiation, and deregulation in illness.