Publications by authors named "Juliette Martin"

51 Publications

The Det.Belt Server: A Tool to Visualize and Estimate Amphipathic Solvent Belts around Membrane Proteins.

Membranes (Basel) 2021 Jun 22;11(7). Epub 2021 Jun 22.

Molecular Microbiology and Structural Biochemistry Laboratory (CNRS UMR 5086), University of Lyon, IBCP, 7 Passage du Vercors, 69367 Lyon, France.

Detergents wrap around membrane proteins to form a belt covering the hydrophobic part of the protein serving for membrane insertion and interaction with lipids. The number of detergent monomers forming this belt is usually unknown to investigators, unless dedicated detergent quantification is undertaken, which for many projects is difficult to setup. Yet, having an approximate knowledge of the amount of detergent forming the belt is extremely useful, to better grasp the protein of interest in interaction with its direct environment rather than picturing the membrane protein "naked". We created the Det.Belt server to dress up membrane proteins and represent in 3D the bulk made by detergent molecules wrapping in a belt. Many detergents are included in a database, allowing investigators to screen in silico the effect of different detergents around their membrane protein. The input number of detergents is changeable with fast recomputation of the belt for interactive usage. Metrics representing the belt are readily available together with scripts to render quality 3D images for publication. The Det.Belt server is a tool for biochemists to better grasp their sample.
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http://dx.doi.org/10.3390/membranes11070459DOI Listing
June 2021

Rhizosphere Bacterial Networks, but Not Diversity, Are Impacted by Pea-Wheat Intercropping.

Front Microbiol 2021 28;12:674556. Epub 2021 May 28.

Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne - Université de Bourgogne Franche-Comté, Dijon, France.

Plant-plant associations, notably cereal-legume intercropping, have been proposed in agroecology to better value resources and thus reduce the use of chemical inputs in agriculture. Wheat-pea intercropping allows to decreasing the use of nitrogen fertilization through ecological processes such as niche complementarity and facilitation. Rhizosphere microbial communities may account for these processes, since they play a major role in biogeochemical cycles and impact plant nutrition. Still, knowledge on the effect of intecropping on the rhizosphere microbiota remains scarce. Especially, it is an open question whether rhizosphere microbial communities in cereal-legume intercropping are the sum or not of the microbiota of each plant species cultivated in sole cropping. In the present study, we assessed the impact of wheat and pea in IC on the diversity and structure of their respective rhizosphere microbiota. For this purpose, several cultivars of wheat and pea were cultivated in sole and intercropping. Roots of wheat and pea were collected separately in intercropping for microbiota analyses to allow deciphering the effect of IC on the bacterial community of each plant species/cultivar tested. Our data confirmed the well-known specificity of the rhizosphere effect and further stress the differentiation of bacterial communities between pea genotypes (Hr and hr). As regards the intercropping effect, diversity and structure of the rhizosphere microbiota were comparable to sole cropping. However, a specific co-occurrence pattern in each crop rhizosphere due to intercropping was revealed through network analysis. Bacterial co-occurrence network of wheat rhizosphere in IC was dominated by OTUs belonging to Alphaproteobacteria, Bacteroidetes and Gammaproteobacteria. We also evidenced a common network found in both rhizosphere under IC, indicating the interaction between the plant species; this common network was dominated by Acidobacteria, Alphaproteobacteria, and Bacteroidetes, with three OTUs belonging to Acidobacteria, Betaproteobacteria and Chloroflexi that were identified as keystone taxa. These findings indicate more complex rhizosphere bacterial networks in intercropping. Possible implications of these conclusions are discussed in relation with the functioning of rhizosphere microbiota in intercropping accounting for its beneficial effects.
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http://dx.doi.org/10.3389/fmicb.2021.674556DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8195745PMC
May 2021

Using normal mode analysis on protein structural models. How far can we go on our predictions?

Proteins 2021 May 6;89(5):531-543. Epub 2021 Jan 6.

CNRS, UMR 5086 Molecular Microbiology and Structural Biochemistry, Université de Lyon, Lyon, France.

Normal mode analysis (NMA) is a fast and inexpensive approach that is largely used to gain insight into functional protein motions, and more recently to create conformations for further computational studies. However, when the protein structure is unknown, the use of computational models is necessary. Here, we analyze the capacity of NMA in internal coordinate space to predict protein motion, its intrinsic flexibility, and atomic displacements, using protein models instead of native structures, and the possibility to use it for model refinement. Our results show that NMA is quite insensitive to modeling errors, but that calculations are strictly reliable only for very accurate models. Our study also suggests that internal NMA is a more suitable tool for the improvement of structural models, and for integrating them with experimental data or in other computational techniques, such as protein docking or more refined molecular dynamics simulations.
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http://dx.doi.org/10.1002/prot.26037DOI Listing
May 2021

Evaluation of CONSRANK-Like Scoring Functions for Rescoring Ensembles of Protein-Protein Docking Poses.

Front Mol Biosci 2020 21;7:559005. Epub 2020 Oct 21.

CNRS, UMR 5086 Molecular Microbiology and Structural Biochemistry, University of Lyon, Lyon, France.

Scoring is a challenging step in protein-protein docking, where typically thousands of solutions are generated. In this study, we ought to investigate the contribution of consensus-rescoring, as introduced by Oliva et al. (2013) with the CONSRANK method, where the set of solutions is used to build statistics in order to identify recurrent solutions. We explore several ways to perform consensus-based rescoring on the ZDOCK decoy set for Benchmark 4. We show that the information of the interface size is critical for successful rescoring in this context, but that consensus rescoring in itself performs less well than traditional physics-based evaluation. The results of physics-based and consensus-based rescoring are partially overlapping, supporting the use of a combination of these approaches.
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http://dx.doi.org/10.3389/fmolb.2020.559005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7641601PMC
October 2020

Allosteric Inhibition of Adenylyl Cyclase Type 5 by G-Protein: A Molecular Dynamics Study.

Biomolecules 2020 09 17;10(9). Epub 2020 Sep 17.

CNRS, UMR 5086 Molecular Microbiology and Structural Biochemistry, University of Lyon, F-69367 Lyon, France.

Adenylyl cyclases (ACs) have a crucial role in many signal transduction pathways, in particular in the intricate control of cyclic AMP (cAMP) generation from adenosine triphosphate (ATP). Using homology models developed from existing structural data and docking experiments, we have carried out all-atom, microsecond-scale molecular dynamics simulations on the AC5 isoform of adenylyl cyclase bound to the inhibitory G-protein subunit Gαi in the presence and in the absence of ATP. The results show that Gαi has significant effects on the structure and flexibility of adenylyl cyclase, as observed earlier for the binding of ATP and Gsα. New data on Gαi bound to the C1 domain of AC5 help explain how Gαi inhibits enzyme activity and obtain insight on its regulation. Simulations also suggest a crucial role of ATP in the regulation of the stimulation and inhibition of AC5.
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http://dx.doi.org/10.3390/biom10091330DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7563791PMC
September 2020

Cover Crop Management Practices Rather Than Composition of Cover Crop Mixtures Affect Bacterial Communities in No-Till Agroecosystems.

Front Microbiol 2019 9;10:1618. Epub 2019 Jul 9.

Université Bourgogne Franche-Comté, INRA, AgroSup Dijon, Agroécologie, Dijon, France.

Cover cropping plays a key role in the maintenance of arable soil health and the enhancement of agroecosystem services. However, our understanding of how cover crop management impacts soil microbial communities and how these interactions might affect soil nutrient cycling is still limited. Here, we studied the impact of four cover crop mixtures varying in species richness and functional diversity, three cover crop termination strategies (i.e., frost, rolling, and glyphosate) and two levels of irrigation at the cover crop sowing on soil nitrogen and carbon dynamics, soil microbial diversity, and structure as well as the abundance of total bacteria, archaea, and -cycling microbial guilds. We found that total nitrogen and soil organic carbon were higher when cover crops were killed by frost compared to rolling and glyphosate termination treatments, while cover crop biomass was positively correlated to soil carbon and C:N ratio. Modifications of soil properties due to cover crop management rather than the composition of cover crop mixtures were related to changes in the abundance of ammonia oxidizers and denitrifiers, while there was no effect on the total bacterial abundance. Unraveling the underlying processes by which cover crop management shapes soil physico-chemical properties and bacterial communities is of importance to help selecting optimized agricultural practices for sustainable farming systems.
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http://dx.doi.org/10.3389/fmicb.2019.01618DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6629898PMC
July 2019

computation of the PDB to audit diffraction anisotropy of soluble and membrane proteins.

Data Brief 2018 Aug 19;19:753-757. Epub 2018 May 19.

Molecular Microbiology and Structural Biochemistry institute, UMR5086 CNRS Univ-Lyon, F-69367 Cedex 7, Lyon, France.

This data article makes available the informed computation of the whole Protein Data Bank (PDB) to investigate diffraction anisotropy on a large scale and to perform statistics. This data has been investigated in detail in "X-ray diffraction reveals the intrinsic difference in the physical properties of membrane and soluble proteins" [1]. Diffraction anisotropy is traditionally associated with absence of contacts in-between macromolecules within the crystals in a given direction of space. There are however many case that do not follow this empirical rule. To investigate and sort out this discrepancy, we computed diffraction anisotropy for every entry of the PDB, and put them in context of relevant metrics to compare X-ray diffraction in reciprocal space to the crystal packing in real space. These metrics were either extracted from PDB files when available (resolution, space groups, cell parameters, solvent content), or calculated using standard procedures (anisotropy, crystal contacts, presence of ligands). More specifically, we separated entries to compare soluble membrane proteins, and further separated the later in subcategories according to their insertion in the membrane, function, or type of crystallization (Type I Type II crystal packing). This informed database is being made available to investigators in the raw and curated formats that can be re-used for further downstream studies. This dataset is useful to test ideas and to ascertain hypothesis based on statistical analysis.
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http://dx.doi.org/10.1016/j.dib.2018.05.072DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6139481PMC
August 2018

Identification and visualization of protein binding regions with the ArDock server.

Nucleic Acids Res 2018 07;46(W1):W417-W422

Molecular Microbiology and Structural Biochemistry, Unité Mixte de Recherche, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, 69367 Lyon Cedex 07, France.

ArDock (ardock.ibcp.fr) is a structural bioinformatics web server for the prediction and the visualization of potential interaction regions at protein surfaces. ArDock ranks the surface residues of a protein according to their tendency to form interfaces in a set of predefined docking experiments between the query protein and a set of arbitrary protein probes. The ArDock methodology is derived from large scale cross-docking studies where it was observed that randomly chosen proteins tend to dock in a non-random way at protein surfaces. The method predicts interaction site of the protein, or alternate interfaces in the case of proteins with multiple interaction modes. The server takes a protein structure as input and computes a score for each surface residue. Its output focuses on the interactive visualization of results and on interoperability with other services.
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http://dx.doi.org/10.1093/nar/gky472DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6031020PMC
July 2018

A molecular dynamics study of adenylyl cyclase: The impact of ATP and G-protein binding.

PLoS One 2018 25;13(4):e0196207. Epub 2018 Apr 25.

MMSB, Univ. Lyon I / CNRS UMR 5086, Institut de Biologie et Chimie des Protéines, Lyon, France.

Adenylyl cyclases (ACs) catalyze the biosynthesis of cyclic adenosine monophosphate (cAMP) from adenosine triphosphate (ATP) and play an important role in many signal transduction pathways. The enzymatic activity of ACs is carefully controlled by a variety of molecules, including G-protein subunits that can both stimulate and inhibit cAMP production. Using homology models developed from existing structural data, we have carried out all-atom, microsecond-scale molecular dynamics simulations on the AC5 isoform of adenylyl cyclase and on its complexes with ATP and with the stimulatory G-protein subunit Gsα. The results show that both ATP and Gsα binding have significant effects on the structure and flexibility of adenylyl cyclase. New data on ATP bound to AC5 in the absence of Gsα notably help to explain how Gsα binding enhances enzyme activity and could aid product release. Simulations also suggest a possible coupling between ATP binding and interactions with the inhibitory G-protein subunit Gαi.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0196207PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5918993PMC
July 2018

X-ray diffraction reveals the intrinsic difference in the physical properties of membrane and soluble proteins.

Sci Rep 2017 12 5;7(1):17013. Epub 2017 Dec 5.

Molecular Microbiology and Structural Biochemistry institute, UMR5086 CNRS Univ-Lyon, F-69367, Cedex 7, Lyon, France.

Membrane proteins are distinguished from soluble proteins by their insertion into biological membranes. This insertion is achieved via a noticeable arrangement of hydrophobic amino acids that are exposed at the surface of the protein, and renders the interaction with the aliphatic tails of lipids more energetically favorable. This important difference between these two categories of proteins is the source of the need for a specific handling of membrane proteins, which transpired in the creation of new tools for their recombinant expression, purification and even crystallization. Following this line, we show here that crystals of membrane proteins display systematically higher diffraction anisotropy than those of soluble proteins. This phenomenon dramatically hampers structure solution and refinement, and has a strong impact on the quality of electron-density maps. A farther search for origins of this phenomenon showed that the type of crystallization, and thus the crystal packing, has no impact on anisotropy, nor does the nature or function of the membrane protein. Membrane proteins fully embedded within the membrane display equal anisotropy compared to the ones with extra membranous domains or fusions with soluble proteins. Overall, these results overturn common beliefs and call for a specific handling of their diffraction data.
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http://dx.doi.org/10.1038/s41598-017-17216-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5717104PMC
December 2017

Decomposing protein-DNA binding and recognition using simplified protein models.

Nucleic Acids Res 2017 Sep;45(17):10270-10283

MMSB UMR 5086 CNRS / Univ. Lyon I, Institut de Biologie et Chimie des Protéines, 7 passage du Vercors, Lyon 69367, France.

We analyze the role of different physicochemical factors in protein/DNA binding and recognition by comparing the results from all-atom molecular dynamics simulations with simulations using simplified protein models. These models enable us to separate the role of specific amino acid side chains, formal amino acid charges and hydrogen bonding from the effects of the low-dielectric volume occupied by the protein. Comparisons are made on the basis of the conformation of DNA after protein binding, the ionic distribution around the complex and the sequence specificity. The results for four transcription factors, binding in either the minor or major grooves of DNA, show that the protein volume and formal charges, with one exception, play a predominant role in binding. Adding hydrogen bonding and a very small number of key amino acid side chains at the all-atom level yields results in DNA conformations and sequence recognition close to those seen in the reference all-atom simulations.
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http://dx.doi.org/10.1093/nar/gkx627DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5622342PMC
September 2017

Expanding the Kinome World: A New Protein Kinase Family Widely Conserved in Bacteria.

J Mol Biol 2017 10 7;429(20):3056-3074. Epub 2017 Sep 7.

University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry," 7 Passage du Vercors, F-69367 Lyon, France. Electronic address:

Fine tuning of signaling pathways is essential for cells to cope with sudden environmental variations. This delicate balance is maintained in particular by protein kinases that control the activity of target proteins by reversible phosphorylation. In addition to homologous eukaryotic enzymes, bacteria have evolved some specific Ser/Thr/Tyr protein kinases without any structural resemblance to their eukaryotic counterparts. Here, we show that a previously identified family of ATPases, broadly conserved among bacteria, is in fact a new family of protein kinases with a Ser/Thr/Tyr kinase activity. A prototypic member of this family, YdiB from Bacillus subtilis, is able to autophosphorylate and to phosphorylate a surrogate substrate, the myelin basic protein. Two crystal structures of YdiB were solved (1.8 and 2.0Å) that display a unique ATP-binding fold unrelated to known protein kinases, although a conserved HxD motif is reminiscent of that found in Hanks-type protein kinases. The effect of mutations of conserved residues further highlights the unique nature of this new protein kinase family that we name ubiquitous bacterial kinase. We investigated the cellular role of YdiB and showed that a ∆ydiB mutant was more sensitive to paraquat treatment than the wild type, with ~13% of cells with an aberrant morphology. In addition, YdiE, which is known to participate with both YdiC and YdiB in an essential chemical modification of some specific tRNAs, is phosphorylated in vitro by YdiB. These results expand the boundaries of the bacterial kinome and support the involvement of YdiB in protein translation and resistance to oxidative stress in B. subtilis.
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http://dx.doi.org/10.1016/j.jmb.2017.08.016DOI Listing
October 2017

Non-interacting proteins may resemble interacting proteins: prevalence and implications.

Sci Rep 2017 01 13;7:40419. Epub 2017 Jan 13.

Univ Lyon, CNRS, UMR 5086 MMSB, 7 passage du Vercors F-69367, Lyon, France.

The vast majority of proteins do not form functional interactions in physiological conditions. We have considered several sets of protein pairs from S. cerevisiae with no functional interaction reported, denoted as non-interacting pairs, and compared their 3D structures to available experimental complexes. We identified some non-interacting pairs with significant structural similarity with experimental complexes, indicating that, even though they do not form functional interactions, they have compatible structures. We estimate that up to 8.7% of non-interacting protein pairs could have compatible structures. This number of interactions exceeds the number of functional interactions (around 0.2% of the total interactions) by a factor 40. Network analysis suggests that the interactions formed by non-interacting pairs with compatible structures could be particularly hazardous to the protein-protein interaction network. From a structural point of view, these interactions display no aberrant structural characteristics, and are even predicted as relatively stable and enriched in potential physical interactors, suggesting a major role of regulation to prevent them.
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http://dx.doi.org/10.1038/srep40419DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5289270PMC
January 2017

The C-terminal Domains of Apoptotic BH3-only Proteins Mediate Their Insertion into Distinct Biological Membranes.

J Biol Chem 2016 Nov 7;291(48):25207-25216. Epub 2016 Oct 7.

From the Departament de Bioquímica i Biologia Molecular, ERI BioTecMed, Universitat de València, E-46100 Burjassot, Spain,

Changes in the equilibrium of pro- and anti-apoptotic members of the B-cell lymphoma-2 (Bcl-2) protein family in the mitochondrial outer membrane (MOM) induce structural changes that commit cells to apoptosis. Bcl-2 homology-3 (BH3)-only proteins participate in this process by either activating pro-apoptotic effectors or inhibiting anti-apoptotic components and by promoting MOM permeabilization. The association of BH3-only proteins with MOMs is necessary for the activation and amplification of death signals; however, the nature of this association remains controversial, as these proteins lack a canonical transmembrane sequence. Here we used an in vitro expression system to study the insertion capacity of hydrophobic C-terminal regions of the BH3-only proteins Bik, Bim, Noxa, Bmf, and Puma into microsomal membranes. An Escherichia coli complementation assay was used to validate the results in a cellular context, and peptide insertions were modeled using molecular dynamics simulations. We also found that some of the C-terminal domains were sufficient to direct green fluorescent protein fusion proteins to specific membranes in human cells, but the domains did not activate apoptosis. Thus, the hydrophobic regions in the C termini of BH3-only members associated in distinct ways with various biological membranes, suggesting that a detailed investigation of the entire process of apoptosis should include studying the membranes as a setting for protein-protein and protein-membrane interactions.
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http://dx.doi.org/10.1074/jbc.M116.733634DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5122786PMC
November 2016

Protein-DNA interfaces: a molecular dynamics analysis of time-dependent recognition processes for three transcription factors.

Nucleic Acids Res 2016 Nov 21;44(20):9990-10002. Epub 2016 Sep 21.

MMSB UMR 5086 CNRS/University of Lyon I, Institut de Biologie et Chimie des Protéines, 7 passage du Vercors, Lyon 69367, France

We have studied the dynamics of three transcription factor-DNA complexes using all-atom, microsecond-scale MD simulations. In each case, the salt bridges and hydrogen bond interactions formed at the protein-DNA interface are found to be dynamic, with lifetimes typically in the range of tens to hundreds of picoseconds, although some interactions, notably those involving specific binding to DNA bases, can be a hundred times longer lived. Depending on the complex studied, this dynamics may or may not lead to the existence of distinct conformational substates. Using a sequence threading technique, it has been possible to determine whether DNA sequence recognition is sensitive or not to such conformational changes, and, in one case, to show that recognition appears to be locally dependent on protein-mediated cation distributions.
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http://dx.doi.org/10.1093/nar/gkw841DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5175364PMC
November 2016

Implication of Terminal Residues at Protein-Protein and Protein-DNA Interfaces.

PLoS One 2016 9;11(9):e0162143. Epub 2016 Sep 9.

Univ Lyon, CNRS, UMR 5086 MMSB, 7 passage du Vercors F-69367, Lyon, France.

Terminal residues of protein chains are charged and more flexible than other residues since they are constrained only on one side. Do they play a particular role in protein-protein and protein-DNA interfaces? To answer this question, we considered large sets of non-redundant protein-protein and protein-DNA complexes and analyzed the status of terminal residues and their involvement in interfaces. In protein-protein complexes, we found that more than half of terminal residues (62%) are either modified by attachment of a tag peptide (10%) or have missing coordinates in the analyzed structures (52%). Terminal residues are almost exclusively located at the surface of proteins (94%). Contrary to charged residues, they are not over or under-represented in protein-protein interfaces, but strongly prefer the peripheral region of interfaces when present at the interface (83% of terminal residues). The almost exclusive location of terminal residues at the surface of the proteins or in the rim regions of interfaces explains that experimental methods relying on tail hybridization can be successfully applied without disrupting the complexes under study. Concerning conformational rearrangement in protein-protein complexes, despite their expected flexibility, terminal residues adopt similar locations between the free and bound forms of the docking benchmark. In protein-DNA complexes, N-terminal residues are twice more frequent than C-terminal residues at interfaces. Both N-terminal and C-terminal residues are under-represented in interfaces, in contrast to positively charged residues, which are strongly favored. When located in protein-DNA interfaces, terminal residues prefer the periphery. N-terminal and C-terminal residues thus have particular properties with regard to interfaces, which cannot be reduced to their charged nature.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0162143PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5017611PMC
August 2017

Nutritional stress exacerbates hepatic steatosis induced by deletion of the histidine nucleotide-binding (Hint2) mitochondrial protein.

Am J Physiol Gastrointest Liver Physiol 2016 04 14;310(7):G497-509. Epub 2016 Jan 14.

Department of Clinical Research, University of Bern, Bern, Switzerland; and Department of Hepatology, Gastroenterology; and.

The histidine nucleotide-binding protein, Hint2, is a mitochondrial phosphoramidase expressed in liver, brown fat, pancreas, and muscle. The livers of Hint2 knockout (Hint2(-/-)) mice accumulate triglycerides and show a pattern of mitochondrial protein lysine hyperacetylation. The extent and nature of the lysine acetylation changes and the response of Hint2(-/-) mice to nutritional challenges that elicit a modification of protein acetylation have not been investigated. To compare the adaptation of Hint2(-/-) and control (Hint2(+/+)) mice with episodes of fasting and high-fat diet (HFD), we subjected animals to either feeding ad libitum or fasting for 24 h, and to either a HFD or control diet for 8 wk. Triglyceride content was higher in Hint2(-/-) than in Hint2(+/+) livers, whereas plasma triglycerides were fourfold lower. Malonyl-CoA levels were increased twofold in Hint2(-/-) livers. After 24 h fasting, Hint2(-/-) displayed a decrease in body temperature, commensurate with a decrease in mass of brown fat and downregulation of uncoupling protein 1. HFD-treated Hint2(-/-) livers showed more steatosis, and plasma insulin and cholesterol were higher than in Hint(+/+) mice. Several proteins identified as substrates of sirtuin 3 and 5 and active in intermediary and ketone metabolism were hyperacetylated in liver and brown fat mitochondria after both HFD and fasting regimens. Glutamate dehydrogenase activity was downregulated in fed and fasted livers, and this was attributed to an increase in acetylation and ADP-ribosylation. The absence of Hint2 deregulates the posttranslational modification of several mitochondrial proteins, which impedes the adaptation to episodes of nutritional stress.
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http://dx.doi.org/10.1152/ajpgi.00178.2015DOI Listing
April 2016

Dynamics and recognition within a protein-DNA complex: a molecular dynamics study of the SKN-1/DNA interaction.

Nucleic Acids Res 2016 Feb 31;44(3):1440-8. Epub 2015 Dec 31.

BMSSI UMR 5086 CNRS/Univ. Lyon I, Institut de Biologie et Chimie des Protéines, 7 passage du Vercors, Lyon 69367, France

Molecular dynamics simulations of the Caenorhabditis elegans transcription factor SKN-1 bound to its cognate DNA site show that the protein-DNA interface undergoes significant dynamics on the microsecond timescale. A detailed analysis of the simulation shows that movements of two key arginine side chains between the major groove and the backbone of DNA generate distinct conformational sub-states that each recognize only part of the consensus binding sequence of SKN-1, while the experimentally observed binding specificity results from a time-averaged view of the dynamic recognition occurring within this complex.
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http://dx.doi.org/10.1093/nar/gkv1511DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4756839PMC
February 2016

CLAP: a web-server for automatic classification of proteins with special reference to multi-domain proteins.

BMC Bioinformatics 2014 Oct 4;15:343. Epub 2014 Oct 4.

Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.

Background: The function of a protein can be deciphered with higher accuracy from its structure than from its amino acid sequence. Due to the huge gap in the available protein sequence and structural space, tools that can generate functionally homogeneous clusters using only the sequence information, hold great importance. For this, traditional alignment-based tools work well in most cases and clustering is performed on the basis of sequence similarity. But, in the case of multi-domain proteins, the alignment quality might be poor due to varied lengths of the proteins, domain shuffling or circular permutations. Multi-domain proteins are ubiquitous in nature, hence alignment-free tools, which overcome the shortcomings of alignment-based protein comparison methods, are required. Further, existing tools classify proteins using only domain-level information and hence miss out on the information encoded in the tethered regions or accessory domains. Our method, on the other hand, takes into account the full-length sequence of a protein, consolidating the complete sequence information to understand a given protein better.

Results: Our web-server, CLAP (Classification of Proteins), is one such alignment-free software for automatic classification of protein sequences. It utilizes a pattern-matching algorithm that assigns local matching scores (LMS) to residues that are a part of the matched patterns between two sequences being compared. CLAP works on full-length sequences and does not require prior domain definitions.Pilot studies undertaken previously on protein kinases and immunoglobulins have shown that CLAP yields clusters, which have high functional and domain architectural similarity. Moreover, parsing at a statistically determined cut-off resulted in clusters that corroborated with the sub-family level classification of that particular domain family.

Conclusions: CLAP is a useful protein-clustering tool, independent of domain assignment, domain order, sequence length and domain diversity. Our method can be used for any set of protein sequences, yielding functionally relevant clusters with high domain architectural homogeneity. The CLAP web server is freely available for academic use at http://nslab.mbu.iisc.ernet.in/clap/.
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http://dx.doi.org/10.1186/1471-2105-15-343DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4287353PMC
October 2014

Disruption of tumor suppressor gene Hint1 leads to remodeling of the lipid metabolic phenotype of mouse liver.

J Lipid Res 2014 Nov 5;55(11):2309-19. Epub 2014 Sep 5.

Hepatology Research Group, Department of Clinical Research, University of Bern, Switzerland Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD.

A lipidomic and metabolomic investigation of serum and liver from mice was performed to gain insight into the tumor suppressor gene Hint1. A major reprogramming of lipid homeostasis was found in both serum and liver of Hint1-null (Hint(-/-)) mice, with significant changes in the levels of many lipid molecules, as compared with gender-, age-, and strain-matched WT mice. In the Hint1(-/-) mice, serum total and esterified cholesterol were reduced 2.5-fold, and lysophosphatidylcholines (LPCs) and lysophosphatidic acids were 10-fold elevated in serum, with a corresponding fall in phosphatidylcholines (PCs). In the liver, MUFAs and PUFAs, including arachidonic acid (AA) and its metabolic precursors, were also raised, as was mRNA encoding enzymes involved in AA de novo synthesis. There was also a significant 50% increase in hepatic macrophages in the Hint1(-/-) mice. Several hepatic ceramides and acylcarnitines were decreased in the livers of Hint1(-/-) mice. The changes in serum LPCs and PCs were neither related to hepatic phospholipase A2 activity nor to mRNAs encoding lysophosphatidylcholine acetyltransferases 1-4. The lipidomic phenotype of the Hint1(-/-) mouse revealed decreased inflammatory eicosanoids with elevated proliferative mediators that, combined with decreased ceramide apoptosis signaling molecules, may contribute to the tumor suppressor activity of Hint1.
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http://dx.doi.org/10.1194/jlr.M050682DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4617133PMC
November 2014

The relationship between classification of multi-domain proteins using an alignment-free approach and their functions: a case study with immunoglobulins.

Mol Biosyst 2014 May;10(5):1082-93

Molecular Biophysics Unit, Indian Institute of Science Mathematics Initiative, Indian Institute of Science, Bangalore 560012, India.

Establishing functional relationships between multi-domain protein sequences is a non-trivial task. Traditionally, delineating functional assignment and relationships of proteins requires domain assignments as a prerequisite. This process is sensitive to alignment quality and domain definitions. In multi-domain proteins due to multiple reasons, the quality of alignments is poor. We report the correspondence between the classification of proteins represented as full-length gene products and their functions. Our approach differs fundamentally from traditional methods in not performing the classification at the level of domains. Our method is based on an alignment free local matching scores (LMS) computation at the amino-acid sequence level followed by hierarchical clustering. As there are no gold standards for full-length protein sequence classification, we resorted to Gene Ontology and domain-architecture based similarity measures to assess our classification. The final clusters obtained using LMS show high functional and domain architectural similarities. Comparison of the current method with alignment based approaches at both domain and full-length protein showed superiority of the LMS scores. Using this method we have recreated objective relationships among different protein kinase sub-families and also classified immunoglobulin containing proteins where sub-family definitions do not exist currently. This method can be applied to any set of protein sequences and hence will be instrumental in analysis of large numbers of full-length protein sequences.
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http://dx.doi.org/10.1039/c3mb70443bDOI Listing
May 2014

Benchmarking protein-protein interface predictions: why you should care about protein size.

Authors:
Juliette Martin

Proteins 2014 Jul 12;82(7):1444-52. Epub 2014 Feb 12.

Bases Moléculaires et Structurales des Systèmes Infectieux, CNRS, UMR 5086; Université Lyon 1, IBCP, 7 passage du Vercors F-69367, France.

A number of predictive methods have been developed to predict protein-protein binding sites. Each new method is traditionally benchmarked using sets of protein structures of various sizes, and global statistics are used to assess the quality of the prediction. Little attention has been paid to the potential bias due to protein size on these statistics. Indeed, small proteins involve proportionally more residues at interfaces than large ones. If a predictive method is biased toward small proteins, this can lead to an over-estimation of its performance. Here, we investigate the bias due to the size effect when benchmarking protein-protein interface prediction on the widely used docking benchmark 4.0. First, we simulate random scores that favor small proteins over large ones. Instead of the 0.5 AUC (Area Under the Curve) value expected by chance, these biased scores result in an AUC equal to 0.6 using hypergeometric distributions, and up to 0.65 using constant scores. We then use real prediction results to illustrate how to detect the size bias by shuffling, and subsequently correct it using a simple conversion of the scores into normalized ranks. In addition, we investigate the scores produced by eight published methods and show that they are all affected by the size effect, which can change their relative ranking. The size effect also has an impact on linear combination scores by modifying the relative contributions of each method. In the future, systematic corrections should be applied when benchmarking predictive methods using data sets with mixed protein sizes.
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http://dx.doi.org/10.1002/prot.24512DOI Listing
July 2014

Replacing tin in lactide polymerization: design of highly active germanium-based catalysts.

Angew Chem Int Ed Engl 2013 Dec 26;52(51):13584-7. Epub 2013 Nov 26.

Chimie ParisTech, UMR CNRS 7223, 11 rue P. et M. Curie, 75005 Paris (France) http://www.thomasgroup.legtux.org/

Most germane: Hexacoordinate germanium(IV) species exhibit unprecedented activities, yet controlled behavior, as initiators for the ring-opening polymerization of rac-lactide to form polylactide polymers.
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http://dx.doi.org/10.1002/anie.201306623DOI Listing
December 2013

Phenotypic and genotypic convergences are influenced by historical contingency and environment in yeast.

Evolution 2014 Mar 25;68(3):772-790. Epub 2013 Nov 25.

Univ Paris-Sud, UMR de Génétique Végétale, INRA / Univ Paris-Sud / CNRS, Ferme du Moulon, Gif-sur-Yvette, F-91190, France.

Different organisms have independently and recurrently evolved similar phenotypic traits at different points throughout history. This phenotypic convergence may be caused by genotypic convergence and in addition, constrained by historical contingency. To investigate how convergence may be driven by selection in a particular environment and constrained by history, we analyzed nine life-history traits and four metabolic traits during an experimental evolution of six yeast strains in four different environments. In each of the environments, the population converged toward a different multivariate phenotype. However, the evolution of most traits, including fitness components, was constrained by history. Phenotypic convergence was partly associated with the selection of mutations in genes involved in the same pathway. By further investigating the convergence in one gene, BMH1, mutated in 20% of the evolved populations, we show that both the history and the environment influenced the types of mutations (missense/nonsense), their location within the gene itself, as well as their effects on multiple traits. However, these effects could not be easily predicted from ancestors' phylogeny or past selection. Combined, our data highlight the role of pleiotropy and epistasis in shaping a rugged fitness landscape.
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http://dx.doi.org/10.1111/evo.12302DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4439200PMC
March 2014

Characterization of the effect of the mitochondrial protein Hint2 on intracellular Ca(2+) dynamics.

Biophys J 2013 Sep;105(5):1268-75

Institut National de la Santé et de la Recherche Médicale, Orsay, France.

Hint2, one of the five members of the superfamily of the histidine triad AMP-lysine hydrolase proteins, is expressed in mitochondria of various cell types. In human adrenocarcinoma cells, Hint2 modulates Ca(2+) handling by mitochondria. As Hint2 is highly expressed in hepatocytes, we investigated if this protein affects Ca(2+) dynamics in this cell type. We found that in hepatocytes isolated from Hint2(-/-) mice, the frequency of Ca(2+) oscillations induced by 1 μM noradrenaline was 150% higher than in the wild-type. Using spectrophotometry, we analyzed the rates of Ca(2+) pumping in suspensions of mitochondria prepared from hepatocytes of either wild-type or Hint2(-/-) mice; we found that Hint2 accelerates Ca(2+) pumping into mitochondria. We then resorted to computational modeling to elucidate the possible molecular target of Hint2 that could explain both observations. On the basis of a detailed model for mitochondrial metabolism proposed in another study, we identified the respiratory chain as the most probable target of Hint2. We then used the model to predict that the absence of Hint2 leads to a premature opening of the mitochondrial permeability transition pore in response to repetitive additions of Ca(2+) in suspensions of mitochondria. This prediction was then confirmed experimentally.
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http://dx.doi.org/10.1016/j.bpj.2013.06.048DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3762358PMC
September 2013

Disruption of the histidine triad nucleotide-binding hint2 gene in mice affects glycemic control and mitochondrial function.

Hepatology 2013 May;57(5):2037-48

Division of Hepatology, Department of Clinical Research, University of Berne, Berne, Switzerland.

Unlabelled: The histidine triad nucleotide-binding (HINT2) protein is a mitochondrial adenosine phosphoramidase expressed in the liver and pancreas. Its physiological function is unknown. To elucidate the role of HINT2 in liver physiology, the mouse Hint2 gene was deleted. Hint2(-/-) and Hint2(+/+) mice were generated in a mixed C57Bl6/J × 129Sv background. At 20 weeks, the phenotypic changes in Hint2(-/-) relative to Hint2(+/+) mice were an accumulation of hepatic triglycerides, decreased tolerance to glucose, a defective counter-regulatory response to insulin-provoked hypoglycemia, and an increase in plasma interprandial insulin but a decrease in glucose-stimulated insulin secretion and defective thermoregulation upon fasting. Leptin messenger RNA (mRNA) in adipose tissue and plasma leptin were elevated. In mitochondria from Hint2(-/-) hepatocytes, state 3 respiration was decreased, a finding confirmed in HepG2 cells where HINT2 mRNA was silenced. The linked complex II-III electron transfer was decreased in Hint2(-/-) mitochondria, which was accompanied by a lower content of coenzyme Q. Hypoxia-inducible factor-2α expression and the generation of reactive oxygen species were increased. Electron microscopy of mitochondria in Hint2(-/-) mice aged 12 months revealed clustered, fused organelles. The hepatic activities of 3-hydroxyacyl-coenzyme A dehydrogenase short chain and glutamate dehydrogenase (GDH) were decreased by 68% and 60%, respectively, without a change in protein expression. GDH activity was similarly decreased in HINT2-silenced HepG2 cells. When measured in the presence of purified sirtuin 3, latent GDH activity was recovered (126% in Hint2(-/-) versus 83% in Hint2(+/+) ). This suggests a greater extent of acetylation in Hint2(-/-) than in Hint2(+/+) .

Conclusion: Hint2/HINT2 positively regulates mitochondrial lipid metabolism and respiration and glucose homeostasis. The absence of Hint2 provokes mitochondrial deformities and a change in the pattern of acetylation of selected proteins.
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http://dx.doi.org/10.1002/hep.26060DOI Listing
May 2013

Arbitrary protein-protein docking targets biologically relevant interfaces.

BMC Biophys 2012 May 6;5. Epub 2012 May 6.

Université Lyon 1; CNRS, UMR 5086; Bases Moléculaires et Structurales des Systèmes Infectieux, IBCP, 7 passage du, Vercors, F-69367, France.

Background: Protein-protein recognition is of fundamental importance in the vast majority of biological processes. However, it has already been demonstrated that it is very hard to distinguish true complexes from false complexes in so-called cross-docking experiments, where binary protein complexes are separated and the isolated proteins are all docked against each other and scored. Does this result, at least in part, reflect a physical reality? False complexes could reflect possible nonspecific or weak associations.

Results: In this paper, we investigate the twilight zone of protein-protein interactions, building on an interesting outcome of cross-docking experiments: false complexes seem to favor residues from the true interaction site, suggesting that randomly chosen partners dock in a non-random fashion on protein surfaces. Here, we carry out arbitrary docking of a non-redundant data set of 198 proteins, with more than 300 randomly chosen "probe" proteins. We investigate the tendency of arbitrary partners to aggregate at localized regions of the protein surfaces, the shape and compositional bias of the generated interfaces, and the potential of this property to predict biologically relevant binding sites. We show that the non-random localization of arbitrary partners after protein-protein docking is a generic feature of protein structures. The interfaces generated in this way are not systematically planar or curved, but tend to be closer than average to the center of the proteins. These results can be used to predict biological interfaces with an AUC value up to 0.69 alone, and 0.72 when used in combination with evolutionary information. An appropriate choice of random partners and number of docking models make this method computationally practical. It is also noted that nonspecific interfaces can point to alternate interaction sites in the case of proteins with multiple interfaces. We illustrate the usefulness of arbitrary docking using PEBP (Phosphatidylethanolamine binding protein), a kinase inhibitor with multiple partners.

Conclusions: An approach using arbitrary docking, and based solely on physical properties, can successfully identify biologically pertinent protein interfaces.
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http://dx.doi.org/10.1186/2046-1682-5-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3441232PMC
May 2012

Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs.

BMC Bioinformatics 2011 Jun 20;12:247. Epub 2011 Jun 20.

INSERM, U973, Paris F-75013, France.

Background: One of the strategies for protein function annotation is to search particular structural motifs that are known to be shared by proteins with a given function.

Results: Here, we present a systematic extraction of structural motifs of seven residues from protein loops and we explore their correspondence with functional sites. Our approach is based on the structural alphabet HMM-SA (Hidden Markov Model - Structural Alphabet), which allows simplification of protein structures into uni-dimensional sequences, and advanced pattern statistics adapted to short sequences. Structural motifs of interest are selected by looking for structural motifs significantly over-represented in SCOP superfamilies in protein loops. We discovered two types of structural motifs significantly over-represented in SCOP superfamilies: (i) ubiquitous motifs, shared by several superfamilies and (ii) superfamily-specific motifs, over-represented in few superfamilies. A comparison of ubiquitous words with known small structural motifs shows that they contain well-described motifs as turn, niche or nest motifs. A comparison between superfamily-specific motifs and biological annotations of Swiss-Prot reveals that some of them actually correspond to functional sites involved in the binding sites of small ligands, such as ATP/GTP, NAD(P) and SAH/SAM.

Conclusions: Our findings show that statistical over-representation in SCOP superfamilies is linked to functional features. The detection of over-represented motifs within structures simplified by HMM-SA is therefore a promising approach for prediction of functional sites and annotation of uncharacterized proteins.
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http://dx.doi.org/10.1186/1471-2105-12-247DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158783PMC
June 2011

Hit proteins, mitochondria and cancer.

Biochim Biophys Acta 2011 Jun 1;1807(6):626-32. Epub 2011 Mar 1.

Institute of Clinical Pharmacology and Visceral Research, University of Bern, Switzerland.

The histidine triad (HIT) superfamily comprises proteins that share the histidine triad motif, His-ϕ-His-ϕ-His-ϕ-ϕ, where ϕ is a hydrophobic amino acid. HIT proteins are ubiquitous in prokaryotes and eukaryotes. HIT proteins bind nucleotides and exert dinucleotidyl hydrolase, nucleotidylyl transferase or phosphoramidate hydrolase enzymatic activity. In humans, 5 families of HIT proteins are recognized. The accumulated epidemiological and experimental evidence indicates that two branches of the superfamily, the HINT (Histidine Triad Nucleotide Binding) members and FHIT (Fragile Histidine Triad), have tumor suppressor properties but a conclusive physiological role can still not be assigned to these proteins. Aprataxin forms another discrete branch of the HIT superfamily, is implicated in DNA repair mechanisms and unlike the HINT and FHIT members, a defective protein can be conclusively linked to a disease, ataxia with oculomotor apraxia type 1. The scavenger mRNA decapping enzyme, DcpS, forms a fourth branch of the HIT superfamily. Finally, the GalT enzymes, which exert specific nucleoside monophosphate transferase activity, form a fifth branch that is not implicated in tumorigenesis. The molecular mechanisms by which the HINT and FHIT proteins participate in bioenergetics of cancer are just beginning to be unraveled. Their purported actions as tumor suppressors are highlighted in this review.
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http://dx.doi.org/10.1016/j.bbabio.2011.02.001DOI Listing
June 2011

Ablation of the tumor suppressor histidine triad nucleotide binding protein 1 is protective against hepatic ischemia/reperfusion injury.

Hepatology 2011 Jan 7;53(1):243-52. Epub 2010 Dec 7.

Institute of Clinical Pharmacology and Visceral Research, University of Bern, Bern, Switzerland.

Unlabelled: The identification of cellular pathways capable of limiting ischemia/reperfusion (I/R) injury remains a frontier in medicine, and its clinical relevance is urgent. Histidine triad nucleotide binding protein 1 (HINT1) is a tumor suppressor that influences apoptosis. Because apoptotic pathways are a feature of I/R injury, we asked whether Hint1 influences hepatic I/R injury. Hint1(-/-) and C57BL/6 mice were subjected to 70% liver ischemia followed by reperfusion for 3 or 24 hours or to a sham operation. The serum aminotransferase levels, histological lesions, apoptosis, reactive oxygen species, and expression of B cell lymphoma 2-associated X protein (Bax), heme oxygenase 1 (HO-1), interleukin-6 (IL-6), IL-10, tumor necrosis factor-a, Src, nuclear factor kappa B (p65/RelA), and c-Jun were quantified. The responses to toll-like receptor ligands and nicotinamide adenine dinucleotide phosphate oxidase activity in Kupffer cells were compared in Hint1(-/-) mice and C57BL/6 mice. After I/R, the levels of serum aminotransferases, parenchymal necrosis, and hepatocellular apoptosis were significantly lower in Hint1(-/-) mice versus control mice. Furthermore, Bax expression decreased more than 2-fold in Hint1(-/-) mice, and the increases in reactive oxygen species and HO-1 expression that were evident in wild-type mice after I/R were absent in Hint1(-/-) mice. The phosphorylation of Src and the nuclear translocation of p65 were increased in Hint1(-/-) mice, whereas the nuclear expression of phosphorylated c-Jun was decreased. The levels of the protective cytokines IL-6 and IL-10 were increased in Hint1(-/-) mice. These effects increased survival after I/R in mice lacking Hint1. Hint1(-/-) Kupffer cells were less activated than control cells after stimulation with lipopolysaccharides.

Conclusion: The Hint1 protein influences the course of I/R injury, and its ablation in Kupffer cells may limit the extent of the injury.
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http://dx.doi.org/10.1002/hep.23978DOI Listing
January 2011