Publications

2011

• The deinococcal DdrB protein is involved in an early step of DNA double strand break repair and in plasmid transformation through its single-strand annealing activity.
  
  • Bouthier de La Tour C.
  • Boisnard S.
  • Norais Cedric A.
  • Toueille M.
  • Bentchikou E.
  • Vannier F.
  • Cox M.M.
  • Sommer S.
  • Servant P.
  DNA Repair, Elsevier, 2011, 10 (12), pp.1223-31. The Deinococcus radiodurans bacterium exhibits an extreme resistance to ionizing radiation. Here, we investigated the in vivo role of DdrB, a radiation-induced Deinococcus specific protein that was previously shown to exhibit some in vitro properties akin to those of SSB protein from Escherichia coli but also to promote annealing of single stranded DNA. First we report that the deletion of the C-terminal motif of the DdrB protein, which is similar to the SSB C-terminal motif involved in recruitment to DNA of repair proteins, did neither affect cell radioresistance nor DNA binding properties of purified DdrB protein. We show that, in spite of their different quaternary structure, DdrB and SSB occlude the same amount of ssDNA in vitro. We also show that DdrB is recruited early and transiently after irradiation into the nucleoid to form discrete foci. Absence of DdrB increased the lag phase of the extended synthesis-dependent strand annealing (ESDSA) process, affecting neither the rate of DNA synthesis nor the efficiency of fragment reassembly, as indicated by monitoring DNA synthesis and genome reconstitution in cells exposed to a sub-lethal ionizing radiation dose. Moreover, cells devoid of DdrB were affected in the establishment of plasmid DNA during natural transformation, a process that requires pairing of internalized plasmid single stranded DNA fragments, whereas they were proficient in transformation by a chromosomal DNA marker that integrates into the host chromosome through homologous recombination. Our data are consistent with a model in which DdrB participates in an early step of DNA double strand break repair in cells exposed to very high radiation doses. DdrB might facilitate the accurate assembly of the myriad of small fragments generated by extreme radiation exposure through a single strand annealing (SSA) process to generate suitable substrates for subsequent ESDSA-promoted genome reconstitution. (10.1016/j.dnarep.2011.09.010)
  DOI : 10.1016/j.dnarep.2011.09.010
• Computational protein design with a generalized Born solvent model: application to Asparaginyl-tRNA synthetase.
  
  • Polydorides S.
  • Amara Najette
  • Aubard Caroline
  • Plateau Pierre
  • Simonson T.
  • Archontis G.
  Proteins - Structure, Function and Bioinformatics, Wiley, 2011, 79 (12), pp.3448-68. Computational Protein Design (CPD) is a promising method for high throughput protein and ligand mutagenesis. Recently, we developed a CPD method that used a polar-hydrogen energy function for protein interactions and a Coulomb/Accessible Surface Area (CASA) model for solvent effects. We applied this method to engineer aspartyl-adenylate (AspAMP) specificity into Asparaginyl-tRNA synthetase (AsnRS), whose substrate is asparaginyl-adenylate (AsnAMP). Here, we implement a more accurate function, with an all-atom energy for protein interactions and a residue-pairwise generalized Born model for solvent effects. As a first test, we compute aminoacid affinities for several point mutants of Aspartyl-tRNA synthetase (AspRS) and Tyrosyl-tRNA synthetase and stability changes for three helical peptides and compare with experiment. As a second test, we readdress the problem of AsnRS aminoacid engineering. We compare three design criteria, which optimize the folding free-energy, the absolute AspAMP affinity, and the relative (AspAMP-AsnAMP) affinity. The sequences and conformations are improved with respect to our previous, polar-hydrogen/CASA study: For several designed complexes, the AspAMP carboxylate forms three interactions with a conserved arginine and a designed lysine, as in the active site of the AspRS:AspAMP complex. The conformations and interactions are well maintained in molecular dynamics simulations and the sequences have an inverted specificity, favoring AspAMP over AsnAMP. The method is not fully successful, since experimental measurements with the seven most promising sequences show that they do not catalyze at a detectable level the adenylation of Asp (or Asn) with ATP. This may be due to weak AspAMP binding and/or disruption of transition-state stabilization. (10.1002/prot.23042)
  DOI : 10.1002/prot.23042
• RNA-binding site of Escherichia coli peptidyl-tRNA hydrolase.
  
  • Giorgi Laurent
  • Bontems François
  • Fromant Michel
  • Aubard Caroline
  • Blanquet Sylvain
  • Plateau Pierre
  Journal of Biological Chemistry, American Society for Biochemistry and Molecular Biology, 2011, 286 (45), pp.39585-39594. In a cell, peptidyl-tRNA molecules that have prematurely dissociated from ribosomes need to be recycled. This work is achieved by an enzyme called peptidyl-tRNA hydrolase. To characterize the RNA-binding site of Escherichia coli peptidyl-tRNA hydrolase, minimalist substrates inspired from tRNA(His) have been designed and produced. Two minisubstrates consist of an N-blocked histidylated RNA minihelix or a small RNA duplex mimicking the acceptor and TψC stem regions of tRNA(His). Catalytic efficiency of the hydrolase toward these two substrates is reduced by factors of 2 and 6, respectively, if compared with N-acetyl-histidyl-tRNA(His). In contrast, with an N-blocked histidylated microhelix or a tetraloop missing the TψC arm, efficiency of the hydrolase is reduced 20-fold. NMR mapping of complex formation between the hydrolase and the small RNA duplex indicates amino acid residues sensitive to RNA binding in the following: (i) the enzyme active site region; (ii) the helix-loop covering the active site; (iii) the region including Leu-95 and the bordering residues 111-117, supposed to form the boundary between the tRNA core and the peptidyl-CCA moiety-binding sites; (iv) the region including Lys-105 and Arg-133, two residues that are considered able to clamp the 5'-phosphate of tRNA, and (v) the positively charged C-terminal helix (residues 180-193). Functional value of these interactions is assessed taking into account the catalytic properties of various engineered protein variants, including one in which the C-terminal helix was simply subtracted. A strong role of Lys-182 in helix binding to the substrate is indicated. (10.1074/jbc.M111.281840)
  DOI : 10.1074/jbc.M111.281840
• Selenodiglutathione uptake by the Saccharomyces cerevisiae vacuolar ATP-binding cassette transporter Ycf1p.
  
  • Lazard Myriam
  • Ha-Duong Nguyet-Thanh
  • Mounier Stephanie
  • Perrin Romary
  • Plateau Pierre
  • Blanquet Sylvain
  FEBS Journal, Wiley, 2011, 278 (21), pp.4112-21. The Saccharomyces cerevisiae vacuolar ATP-binding cassette transporter Ycf1p is involved in heavy metal detoxification by mediating the ATP-dependent transport of glutathione-metal conjugates to the vacuole. In the case of selenite toxicity, deletion of YCF1 was shown to confer increased resistance, rather than sensitivity, to selenite exposure [Pinson B, Sagot I & Daignan-Fornier B (2000) Mol Microbiol36, 679-687]. Here, we show that when Ycf1p is expressed from a multicopy plasmid, the toxicity of selenite is exacerbated. Using secretory vesicles isolated from a sec6-4 mutant transformed either with the plasmid harbouring YCF1 or the control plasmid, we establish that the glutathione-conjugate selenodigluthatione is a high-affinity substrate of this ATP-binding cassette transporter and that oxidized glutathione is also efficiently transported. Finally, we show that the presence of Ycf1p impairs the glutathione/oxidized glutathione ratio of cells subjected to a selenite stress. Possible mechanisms by which Ycf1p-mediated vacuolar uptake of selenodiglutathione and oxidized glutathione enhances selenite toxicity are discussed. (10.1111/j.1742-4658.2011.08318.x)
  DOI : 10.1111/j.1742-4658.2011.08318.x
• Evaluation of DNA Force Fields in Implicit Solvation.
  
  • Gaillard T.
  • Case D.A.
  Journal of Chemical Theory and Computation, American Chemical Society, 2011, 7 (10), pp.3181-3198. DNA structural deformations and dynamics are crucial to its interactions in the cell. Theoretical simulations are essential tools to explore the structure, dynamics, and thermodynamics of biomolecules in a systematic way. Molecular mechanics force fields for DNA have benefited from constant improvements during the last decades. Several studies have evaluated and compared available force fields when the solvent is modeled by explicit molecules. On the other hand, few systematic studies have assessed the quality of duplex DNA models when implicit solvation is employed. The interest of an implicit modeling of the solvent consists in the important gain in the simulation performance and conformational sampling speed. In this study, respective influences of the force field and the implicit solvation model choice on DNA simulation quality are evaluated. To this end, extensive implicit solvent duplex DNA simulations are performed, attempting to reach both conformational and sequence diversity convergence. Structural parameters are extracted from simulations and statistically compared to available experimental and explicit solvation simulation data. Our results quantitatively expose the respective strengths and weaknesses of the different DNA force fields and implicit solvation models studied. This work can lead to the suggestion of improvements to current DNA theoretical models. (10.1021/ct200384r)
  DOI : 10.1021/ct200384r
• NMR-based substrate analog docking to Escherichia coli peptidyl-tRNA hydrolase.
  
  • Giorgi Laurent
  • Plateau Pierre
  • O'Mahony Gavin
  • Aubard Caroline
  • Fromant Michel
  • Thureau Aurélien
  • Grøtli Morten
  • Blanquet Sylvain
  • Bontems François
  Journal of Molecular Biology, Elsevier, 2011, 412 (4), pp.619-33. Escherichia coli peptidyl-tRNA hydrolase activity is inhibited by 3'-(L-[N,N-diacetyl-lysinyl)amino-3'-deoxyadenosine, a stable mimic of the minimalist substrate 2'(3')-O-(L-[N,N-diacetyl-lysinyl)adenosine. The complex of this mimic with the enzyme has been analyzed by NMR spectroscopy, enabling experimental mapping of the catalytic center for the first time. Chemical shift variations point out the sensitivity of residues Asn10, Met67, Asn68, Gly111, Asn114, Leu116, Lys117, Gly147, Phe148, and Val149 to complex formation. Docking simulations based on ambiguous interaction restraints involving these residues show bondings of the peptide moiety of 3'-(l-[N,N-diacetyl-lysinyl)amino-3'-deoxyadenosine with Asn10, Asn68, and Asn114. A stacking interaction of Phe66 with the purine is also indicated. Drawn is a model of enzyme-bound peptidyl-tRNA substrate, in which: (i) the Asn114 δ(2) NH(2) group holds the water molecule that participates in the hydrolysis of the substrate, while Tyr15 binds the phosphate in the 5'-position of the 3'-terminal tRNA adenosine; (ii) the δ(2) NH(2) group of Asn68 holds the main-chain carbonyl of the C-terminal residue of the peptide esterified to tRNA; and (iii) the δ(2) NH(2) group of Asn10 holds the main-chain carbonyl of the penultimate C-residue. Functional value is given to this model by (i) showing that the enzyme becomes confusable with an aminoacyl-tRNA hydrolase upon mutagenesis of Asn10 and (ii) reinterpreting already obtained site-directed mutagenesis data. (10.1016/j.jmb.2011.06.025)
  DOI : 10.1016/j.jmb.2011.06.025
• Modélisation de l'évolution dirigée de la tyrosyl-ARNt synthétase in silico. Introduction d'acides aminés non naturels dans les protéines.
  
  • Amara Najette
  , 2011. Les protéines sont synthétisées essentiellement à partir d'acides aminés L. Cependant, les acides aminés D sont naturellement présents dans notre organisme. Il existe plusieurs mécanismes de régulation pour limiter leur présence. Il peut y avoir un intérêt bio-technologique à introduire des acides aminés D dans les protéines pour leur conférer des fonctions chimiques nouvelles. Les protéases, chargées de dégrader les peptides, reconnaissent moins bien les protéines possédant de tels acides aminés. Dans notre cas, présenter la tyrosine sous son énantiomère D donnerait un avantage par rapport aux protéases. En effet, un peptide qui aurait des acides aminés D, resterait plus longtemps actif dans un organisme. La tyrosyl-ARNt synthétase (TyrRS) a déjà été utilisée pour l'incorporation de plus d'une trentaine d'analogues de la tyrosine dans les protéines. Cette enzyme possède déjà une activité naturelle pour la D-tyr, mais celle ci est très faible. L'objectif du présent travail est de l'améliorer par une méthode d'évolution dirigée iin silico. Cette méthode consiste à muter aléatoirement une protéine puis à sélectionner les mutants qui ont les propriétés désirées, mimant les mécanismes de l'évolution naturelle. L'évolution dirigée textit{in silico} a déjà été utilisée pour l'ingénierie d'un grand nombre de protéines. On utilise pour cette étude le programme d'évolution dirigée développé au laboratoire qui procède à une optimisation itérative de la séquence et de la structure. Des mutations ont été retenues par cette méthode et proposées aux expérimentalistes du laboratoire de biochimie pour des validations expérimentales. Ils ont conclut que plusieurs mutants présentent une activité faible mais mesurable pour la D-Tyrosine. L'étude a été étendue à d'autres résidus proches de l'ammonium de la L-Tyr. Nous avons identifié d'autres positions qui pourraient être intéressantes à muter. L'étude, faite dans un premier temps avec le ligand tyrosine, a été ensuite améliorée en considérant le ligand Tyrosyl adénylate (tyrAMP). C'est l'intermédiaire qui va interagir avec l'ARNt pour former l'ARNt-Tyr . Le L-TyrAMP et le D-TyrAMP ont tous deux été modélisés avec la TyrRS d'Escherichia coli. Toutes ces modélisations ont conduit à une liste de séquences mutantes qui ont été prédites comme favorables à la liaison du D-TyrAMP. Chacune des séquences obtenues pour les deux synthétases a ensuite fait l'objet d'une étude plus approfondie visant à déterminer la spécificité pour le ligand D-TyrAMP. Suite à cela, nous avons sélectionné une dizaine de séquences de TyrRS mutantes d'Escherichia coli afin de réaliser des calculs de dynamique moléculaire. Nous avons utilisé les ressources du super calculateur du CINES (Centre Informatique Nationale de l'Education Supérieur) pour faire des études de dynamique moléculaire. Une meilleure estimation de l'affinité de ces différents mutants pour le D-TyrAMP a été atteinte. Un autre but de la thèse était d'améliorer notre protocole de Protein Design en adoptant un champ de force tout atome et un modèle de solvant plus sophistiqué. Pour le solvant, le modèle de Born généralisé que nous avons implémenté dans le protocole est basé sur la théorie de Poisson-Boltzmann, avec un continuum diélectrique qui entoure la protéine. Les validations sur des peptides tests ont été concluantes. L'évolution dirigée de la TyrRS de Bacillus Stearothermophilus sert de validation à ce protocole car des mesures expérimentales pour une quinzaine de mutants sont disponibles.
• Efficient solvent boundary potential for hybrid potential simulations.
  
  • Aleksandrov Alexey
  • Field Martin J
  Physical Chemistry Chemical Physics, Royal Society of Chemistry, 2011, 13 (22), pp.10503-9. A common challenge in computational biophysics is to obtain statistical properties similar to those of an infinite bulk system from simulations of a system of finite size. In this work we describe a computationally efficient algorithm for performing hybrid quantum chemical/molecular mechanical (QC/MM) calculations with a solvent boundary potential. The system is partitioned into a QC region within which catalytic reactions occur, a spherical region with explicit solvent that envelops the quantum region and is treated with a MM model, and the surrounding bulk solvent that is treated implicitly by the boundary potential. The latter is constructed to reproduce the solvation free energy of a finite number of atoms embedded inside a low-dielectric sphere with variable radius, and takes into account electrostatic and van der Waals interactions between the implicit solvent and the QC and MM atoms in the central region. The method was implemented in the simulation program pDynamo and tested by examining elementary steps in the reaction mechanisms of two enzymes, citrate synthase and lactate dehydrogenase. Good agreement is found for the energies and geometries of the species along the reaction profiles calculated with the method and those obtained by previous experimental and computational studies. Directions in which the utility of the method can be further improved are discussed. (10.1039/c0cp02828b)
  DOI : 10.1039/c0cp02828b
• Free energy simulations of a GTPase: GTP and GDP binding to archaeal initiation factor 2.
  
  • Satpati Priyadarshi
  • Clavaguera Carine
  • Ohanessian Gilles
  • Simonson Thomas
  Journal of Physical Chemistry B, American Chemical Society, 2011, 115 (20), pp.6749-63. Archaeal initiation factor 2 (aIF2) is a protein involved in the initiation of protein biosynthesis. In its GTP-bound, "ON" conformation, aIF2 binds an initiator tRNA and carries it to the ribosome. In its GDP-bound, "OFF" conformation, it dissociates from tRNA. To understand the specific binding of GTP and GDP and its dependence on the ON or OFF conformational state of aIF2, molecular dynamics free energy simulations (MDFE) are a tool of choice. However, the validity of the computed free energies depends on the simulation model, including the force field and the boundary conditions, and on the extent of conformational sampling in the simulations. aIF2 and other GTPases present specific difficulties; in particular, the nucleotide ligand coordinates a divalent Mg(2+) ion, which can polarize the electronic distribution of its environment. Thus, a force field with an explicit treatment of electronic polarizability could be necessary, rather than a simpler, fixed charge force field. Here, we begin by comparing a fixed charge force field to quantum chemical calculations and experiment for Mg(2+):phosphate binding in solution, with the force field giving large errors. Next, we consider GTP and GDP bound to aIF2 and we compare two fixed charge force fields to the recent, polarizable, AMOEBA force field, extended here in a simple, approximate manner to include GTP. We focus on a quantity that approximates the free energy to change GTP into GDP. Despite the errors seen for Mg(2+):phosphate binding in solution, we observe a substantial cancellation of errors when we compare the free energy change in the protein to that in solution, or when we compare the protein ON and OFF states. Finally, we have used the fixed charge force field to perform MDFE simulations and alchemically transform GTP into GDP in the protein and in solution. With a total of about 200 ns of molecular dynamics, we obtain good convergence and a reasonable statistical uncertainty, comparable to the force field uncertainty, and somewhat lower than the predicted GTP/GDP binding free energy differences. The sign and magnitudes of the differences can thus be interpreted at a semiquantitative level, and are found to be consistent with the experimental binding preferences of ON- and OFF-aIF2. (10.1021/jp201934p)
  DOI : 10.1021/jp201934p
• Optimal viral strategies for bypassing RNA silencing.
  
  • Rodrigo G.
  • Carrera J.
  • Jaramillo A.
  • Elena S.F.
  Interface, Mitchell Publ., 2011, 8 (55), pp.257-68. The RNA silencing pathway constitutes a defence mechanism highly conserved in eukaryotes, especially in plants, where the underlying working principle relies on the repressive action triggered by the intracellular presence of double-stranded RNAs. This immune system performs a post-transcriptional suppression of aberrant mRNAs or viral RNAs by small interfering RNAs (siRNAs) that are directed towards their target in a sequence-specific manner. However, viruses have evolved strategies to escape from silencing surveillance while promoting their own replication. Several viruses encode suppressor proteins that interact with different elements of the RNA silencing pathway and block it. The different suppressors are not phylogenetically nor structurally related and also differ in their mechanism of action. Here, we adopt a model-driven forward-engineering approach to understand the evolution of suppressor proteins and, in particular, why viral suppressors preferentially target some components of the silencing pathway. We analysed three strategies characterized by different design principles: replication in the absence of a suppressor, suppressors targeting the first protein component of the pathway and suppressors targeting the siRNAs. Our results shed light on the question of whether a virus must opt for devoting more time into transcription or into translation and on which would be the optimal step of the silencing pathway to be targeted by suppressors. In addition, we discussed the evolutionary implications of such designing principles. (10.1098/rsif.2010.0264)
  DOI : 10.1098/rsif.2010.0264
• Intrinsic resistance to aminoglycosides in Enterococcus faecium is conferred by the 16S rRNA m5C1404-specific methyltransferase EfmM.
  
  • Galimand Marc
  • Schmitt Emmanuelle
  • Panvert Michel
  • Desmolaize Benoit
  • Douthwaite Stephen
  • Mechulam Yves
  • Courvalin Patrice
  RNA, Cold Spring Harbor Laboratory Press, 2011, 17 (2), pp.251-62. Aminoglycosides are ribosome-targeting antibiotics and a major drug group of choice in the treatment of serious enterococcal infections. Here we show that aminoglycoside resistance in Enterococcus faecium strain CIP 54-32 is conferred by the chromosomal gene efmM, encoding the E. faecium methyltransferase, as well as by the previously characterized aac(6')-Ii that encodes a 6'-N-aminoglycoside acetyltransferase. Inactivation of efmM in E. faecium increases susceptibility to the aminoglycosides kanamycin and tobramycin, and, conversely, expression of a recombinant version of efmM in Escherichia coli confers resistance to these drugs. The EfmM protein shows significant sequence similarity to E. coli RsmF (previously called YebU), which is a 5-methylcytidine (m⁵C) methyltransferase modifying 16S rRNA nucleotide C1407. The target for EfmM is shown by mass spectrometry to be a neighboring 16S rRNA nucleotide at C1404. EfmM uses the methyl group donor S-adenosyl-L-methionine to catalyze formation of m⁵C1404 on the 30S ribosomal subunit, whereas naked 16S rRNA and the 70S ribosome are not substrates. Addition of the 5-methyl to C1404 sterically hinders aminoglycoside binding. Crystallographic structure determination of EfmM at 2.28 Å resolution reveals an N-terminal domain connected to a central methyltransferase domain that is linked by a flexible lysine-rich region to two C-terminal subdomains. Mutagenesis of the methyltransferase domain established that two cysteines at specific tertiary locations are required for catalysis. The tertiary structure of EfmM is highly similar to that of RsmF, consistent with m⁵C formation at adjacent sites on the 30S subunit, while distinctive structural features account for the enzymes' respective specificities for nucleotides C1404 and C1407. (10.1261/rna.2233511)
  DOI : 10.1261/rna.2233511
• A large decoy set of protein-protein complexes produced by flexible docking.
  
  • Launay G.
  • Simonson T.
  Journal of Computational Chemistry, Wiley, 2011, 32 (1), pp.106-20. Computational methods are needed to help characterize the structure and function of protein-protein complexes. To develop and improve such methods, standard test problems are essential. One important test is to identify experimental structures from among large sets of decoys. Here, a flexible docking procedure was used to produce such a large ensemble of decoy complexes. In addition to their use for structure prediction, they can serve as a proxy for the nonspecific, protein-protein complexes that occur transiently in the cell, which are hard to characterize experimentally, yet biochemically important. For 202 homodimers and 41 heterodimers with known X-ray structures, we produced an average of 1217 decoys each. The structures were characterized in detail. The decoys have rather large protein-protein interfaces, with at least 45 residue-residue contacts for every 100 contacts found in the experimental complex. They have limited intramonomer deformation and limited intermonomer steric conflicts. The decoys thoroughly sample each monomer's surface, with all the surface amino acids being part of at least one decoy interface. The decoys with the lowest intramonomer deformation were analyzed separately, as proxies for nonspecific protein-protein complexes. Their interfaces are less hydrophobic than the experimental ones, with an amino acid composition similar to the overall surface composition. They have a poorer shape complementarity and a weaker association energy, but are no more fragmented than the experimental interfaces, with 2.1 distinct patches of interacting residues on average, compared to 2.6 for the experimental interfaces. The decoys should be useful for testing and parameterizing docking methods and scoring functions; they are freely available as PDB files at http://biology.polytechnique.fr/decoys. (10.1002/jcc.21604)
  DOI : 10.1002/jcc.21604
• Computational modelling elucidates the mechanism of ciliary regulation in health and disease.
  
  • Kotov Nikolay V.
  • Bates Declan G.
  • Gizatullina Antonina N.
  • Gilaziev Bulat
  • Khairullin Rustem N.
  • Chen Michael Z. Q.
  • Drozdov Ignat
  • Umezawa Yoshinori
  • Hundhausen Christian
  • Aleksandrov Alexey
  • Yan Xing-Gang
  • Spurgeon Sarah K.
  • Smales C. Mark
  • Valeyev Najl V.
  BMC Systems Biology, BioMed Central, 2011, 5 (NC), pp.143. BACKGROUND: Ciliary dysfunction leads to a number of human pathologies, including primary ciliary dyskinesia, nephronophthisis, situs inversus pathology or infertility. The mechanism of cilia beating regulation is complex and despite extensive experimental characterization remains poorly understood. We develop a detailed systems model for calcium, membrane potential and cyclic nucleotide-dependent ciliary motility regulation. RESULTS: The model describes the intimate relationship between calcium and potassium ionic concentrations inside and outside of cilia with membrane voltage and, for the first time, describes a novel type of ciliary excitability which plays the major role in ciliary movement regulation. Our model describes a mechanism that allows ciliary excitation to be robust over a wide physiological range of extracellular ionic concentrations. The model predicts the existence of several dynamic modes of ciliary regulation, such as the generation of intraciliary Ca2+ spike with amplitude proportional to the degree of membrane depolarization, the ability to maintain stable oscillations, monostable multivibrator regimes, all of which are initiated by variability in ionic concentrations that translate into altered membrane voltage. CONCLUSIONS: Computational investigation of the model offers several new insights into the underlying molecular mechanisms of ciliary pathologies. According to our analysis, the reported dynamic regulatory modes can be a physiological reaction to alterations in the extracellular environment. However, modification of the dynamic modes, as a result of genetic mutations or environmental conditions, can cause a life threatening pathology. (10.1186/1752-0509-5-143)
  DOI : 10.1186/1752-0509-5-143
• The mechanical resonances of electrostatically coupled nanocantilevers
  
  • Perisanu S.
  • Barois Thomas
  • Poncharal P.
  • Gaillard T.
  • Ayari A.
  • Purcell S. T.
  • Vincent P.
  Applied Physics Letters, American Institute of Physics, 2011, 98 (6), pp.063110. We present here an experimental study of the electrostatic coupling between the mechanical resonances of two nanowires or two nanotubes. This coupling occurs when the eigenfrequencies of the two resonators are matched by electrostatic tuning and it changes from a weak coupling to a strong coupling regime as the distance between the cantilevers is decreased. Linear coupling theory is shown to be in excellent agreement with the experimental data. (10.1063/1.3553779)
  DOI : 10.1063/1.3553779
• Translation Initiation
  
  • Mechulam Yves
  • Blanquet Sylvain
  • Schmitt Emmanuelle
  , 2011, pp.Chapter 4.2.2. Selection of correct start codons on mRNAs is a key step required for faithful translation of the genetic message. Such a selection occurs in a complex process, during which a translation-competent ribosome assembles, eventually having in its P site a specialized tRNAMet base paired with the start codon on the mRNA. This chapter summarizes recent advances describing, at the molecular level, the successive steps involved in the process. In particular, structural analyses concerning complexes containing ribosomal subunits, as well as detailed kinetic studies, have shed new light on the sequence of events leading to initiation of protein synthesis in Bacteria
• An atomistic model for simulations of nilotinib and nilotinib/kinase binding
  
  • Valeyev N.V.
  • Aleksandrov Alexey
  Theoretical Chemistry Accounts: Theory, Computation, and Modeling, Springer Verlag, 2011, 129 (6), pp.747. Nilotinib is a novel anticancer drug, which specifically binds to the Abl kinase and blocks its signaling activity. In order to model the nilotinib/protein interactions, we have developed a molecular mechanics force field for nilotinib, consistent with the CHARMM force field for proteins and nucleic acids. Atomic charges were derived by utilizing a supermolecule ab initio approach. We considered the ab initio energies and geometries of a probe water molecule that interacts with nilotinib fragments at six different positions. We investigated both neutral and protonated states of nilotinib. The final rms deviation between the ab initio and the force field energies, averaged over both forms, was equal 0.2 kcal/mol. The model reproduces the ab initio geometry and flexibility of nilotinib. To apply the force field to nilotinib/Abl simulations, it is also necessary to determine the most likely protein and nilotinib protonation state when it binds to Abl. This task was carried out using molecular dynamics free energy simulations. The simulations indicate that nilotinib can interact with Abl in protonated and deprotonated forms, with the protonated form more favoured for the interaction. In the course of our calculations, we established that the His361, a titratable amino acid residue that mediates the interaction, prefers to be neutral. These insights and models should be of interest for drug design. © 2011 Springer-Verlag. (10.1007/s00214-011-0931-y)
  DOI : 10.1007/s00214-011-0931-y
• Possibility of proton passage through all metal aromatic Al 42- ring in HAl4
  
  • Satpati Priyadarshi
  International Journal of Quantum Chemistry, Wiley, 2011, 111 (14), pp.3816. We report theoretical investigations on HAl 4- in which the proton can move through the Al 42- ring similar to umbrella inversion. The potential energy for the motion is a double well, with an activation barrier of 4.45 kcal/mol. We find that excitation to v = 6 vibrational levels should lead to easy passage of H+ through the ring. After considering the tunnelling effect, inversion rate at 298 K is calculated using transition state theory and is found to be 1.3 × 1010/s-1. © 2010 Wiley Periodicals, Inc. (10.1002/qua.22932)
  DOI : 10.1002/qua.22932