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The Ramachandran plots of glycine and pre-proline
Bosco K Ho, Robert Brasseur
BMC Structural Biology , 2005, DOI: 10.1186/1472-6807-5-14
Abstract: In glycine, the ψ angle is typically clustered at ψ = 180° and ψ = 0°. We show that these clusters correspond to conformations where either the Ni+1 or O atom is sandwiched between the two Hα atoms of glycine. We show that the shape of the 5 distinct regions of density (the α, αL, βS, βP and βPR regions) can be reproduced with electrostatic dipole-dipole interactions. In pre-proline, we analyse the origin of the ζ region of the Ramachandran plot, a region unique to pre-proline. We show that it is stabilized by a COi-1···CδHδi+1 weak hydrogen bond. This is analogous to the COi-1···NHi+1 hydrogen bond that stabilizes the γ region in the generic Ramachandran plot.We have identified the specific interactions that affect the backbone of glycine and pre-proline. Knowledge of these interactions will improve current force-fields, and help understand structural motifs containing these residues.The Ramachandran plot [1] is the 2d plot of the φ-ψ torsion angles of the protein backbone. It provides a simple view of the conformation of a protein. The φ-ψ angles cluster into distinct regions in the Ramachandran plot where each region corresponds to a particular secondary structure. There are four basic types of Ramachandran plots, depending on the stereo-chemistry of the amino acid: generic (which refers to the 18 non-glycine non-proline amino acids), glycine, proline, and pre-proline (which refers to residues preceding a proline [2]). The generic and proline Ramachandran plots are now well understood [3] but the glycine and pre-proline Ramachandran plots are not.The generic Ramachandran plot was first explained by Ramachandran and co-workers in terms of steric clashes [1]. This has become the standard explanation for the observed regions in the Ramachandran plot [4,5]. However, recent studies found significant discrepancies between the classic steric map and the Ramachandran plot of high-resolution protein structures [6-9]. These discrepancies have now been resolved. The first d
A new in-silico method for determination of helical transmembrane domains based on the PepLook scan: application to IL-2Rβ and IL-2Rγc receptor chains
Yan Charlois, Laurence Lins, Robert Brasseur
BMC Structural Biology , 2011, DOI: 10.1186/1472-6807-11-26
Abstract: Using sequences whose NMR-structures are already known (GpA, EphA1 and Erb2-HER2), we first determined that the hydrophobic to hydrophilic accessible surface area ratio (ASAr) was the best criterion for delimiting the TMD sequence. The length of the helical structure and the Impala method further supported the determination of the TMD limits. This method was applied to the IL-2Rβ and IL-2Rγ TMD sequences of Homo sapiens, Rattus norvegicus, Mus musculus and Bos taurus.We succeeded in reducing the variation in the TMD limits to only 2 residues and in gaining structural information.IL-2 and IL-15 are two structurally close hematopoietic cytokines, both presenting a functional redundancy and both involved in immunology and inflammatory diseases. IL-2 was implicated in the first metastatic melanoma immunotherapy [1] and is used in adoptive immunotherapy with tumor infiltrating lymphocytes (TILs). Most treatments require high doses of IL-2 [2,3] and induce a systemic toxicity similar to GM-CSF (Granulocyte Macrophage-Colony Stimulating Factor) treatments [4]. These secondary effects restrict the therapy and have led to investigations into other forms of treatment, such as the promising IL-15 therapy.Transduction receptor chains IL-2Rβ and IL-2Rγc (class I hematopoietic receptors) form an intermediate-affinity complex capable of binding IL-2 and IL-15. Whereas the IL-2Rβ chain is restricted to dimeric receptor for IL-15 and IL-2 [5] or to specific trimeric receptors (IL-2Rβ/IL-2Rγ/IL-2Rα and IL-2Rβ/IL-2Rγ/IL-15Rα), the IL-2Rγc chain is involved in γc-family receptors, that is to say the IL-2, IL-4, IL-7, IL-9, IL-15, IL-21 and GM-CSF receptors[6]. γc-deficit is implicated in immunodeficiency, such as X-linked Severe Combined ImmunoDeficiency (X-SCID)[7].Fluorescence resonance energy transfer (FRET) studies suggest that IL-2Rα, IL-7Rα and IL-15Rα chains are co-localized[8] with IL-2Rβ and γc chains within lipid rafts[9]. IL-2Rα and IL-15Rα chains also appear to co-localize
Distantly related lipocalins share two conserved clusters of hydrophobic residues: use in homology modeling
Benoit Adam, Benoit Charloteaux, Jerome Beaufays, Luc Vanhamme, Edmond Godfroid, Robert Brasseur, Laurence Lins
BMC Structural Biology , 2008, DOI: 10.1186/1472-6807-8-1
Abstract: The pairwise sequence identity is low among this family, often below 30%, despite a well conserved tertiary structure. Under the 30% identity threshold, alignment methods do not correctly assign and align proteins. The only safe way to assign a sequence to that family is by experimental determination. However, these procedures are long and costly and cannot always be applied. A way to circumvent the experimental approach is sequence and structure analyze. To further help in that task, the residues implicated in the stabilisation of the lipocalin fold were determined. This was done by analyzing the conserved interactions for ten lipocalins having a maximum pairwise identity of 28% and various functions.It was determined that two hydrophobic clusters of residues are conserved by analysing the ten lipocalin structures and sequences. One cluster is internal to the barrel, involving all strands and the 310 helix. The other is external, involving four strands and the helix lying parallel to the barrel surface. These clusters are also present in RaHBP2, a unusual "outlier" lipocalin from tick Rhipicephalus appendiculatus. This information was used to assess assignment of LIR2 a protein from Ixodes ricinus and to build a 3D model that helps to predict function. FTIR data support the lipocalin fold for this protein.By sequence and structural analyzes, two conserved clusters of hydrophobic residues in interactions have been identified in lipocalins. Since the residues implicated are not conserved for function, they should provide the minimal subset necessary to confer the lipocalin fold. This information has been used to assign LIR2 to lipocalins and to investigate its structure/function relationship. This study could be applied to other protein families with low pairwise similarity, such as the structurally related fatty acid binding proteins or avidins.Lipocalins are small secreted proteins (160–200 residues), typically structured in a 8 strands up and down β-barrel. A 310
SAHBNET, an Accessible Surface-Based Elastic Network: An Application to Membrane Protein
Nicolas Dony,Jean Marc Crowet,Bernard Joris,Robert Brasseur,Laurence Lins
International Journal of Molecular Sciences , 2013, DOI: 10.3390/ijms140611510
Abstract: Molecular Dynamics is a method of choice for membrane simulations and the rising of coarse-grained forcefields has opened the way to longer simulations with reduced calculations times. Here, we present an elastic network, SAHBNET (Surface Accessibility Hydrogen-Bonds elastic NETwork), that will maintain the structure of soluble or membrane proteins based on the hydrogen bonds present in the atomistic structure and the proximity between buried residues. This network is applied on the coarse-grained beads defined by the MARTINI model, and was designed to be more physics-based than a simple elastic network. The SAHBNET model is evaluated against atomistic simulations, and compared with ELNEDYN models. The SAHBNET is then used to simulate two membrane proteins inserted in complex lipid bilayers. These bilayers are formed by self-assembly and the use of a modified version of the GROMACS tool genbox (which is accessible through the gcgs.gembloux.ulg.ac.be website). The results show that SAHBNET keeps the structure close to the atomistic one and is successfully used for the simulation of membrane proteins.
Editorial. La bio-informatique restera-t-elle une exception ou deviendra-t-elle la normalité dans la communauté scientifique ?
Brasseur, R.
Biotechnologie, Agronomie, Société et Environnement , 2000,
Abstract:
Human babesiosis in Europe
Brasseur, P.;Gorenflot, A.;
Memórias do Instituto Oswaldo Cruz , 1992, DOI: 10.1590/S0074-02761992000700019
Abstract: human babesiosis in europe came to medical attention in 1957 and until now 19 cases have been reported, most of them due to babesia divergens. the onset of the disease is characterized by hemoglobinuria, high fever and renal failure ensue rapidly. the patients were generally asplenic and resident in a rural area. intraerythrocytic pleomorphic parasites (1-3 μm) observed in stained thin blood smears are essential for genus diagnosis. parasitemia varyed from 5 to 80% of red blood cells. massive blood exchange transfusion (2-3 blood volumes) followed by intravenous clindamycine (3-4 times daily) and oral quinine (600 mg base, 3 times daily) were successfully used in the treatment of three recent cases. splenectomised individuals should be aware for prevention.
Some monotonicity results for general systems of nonlinear elliptic PDEs
Julien Brasseur,Serena Dipierro
Mathematics , 2015,
Abstract: In this paper we show that minima and stable solutions of a general energy functional of the form $$ \int_{\Omega} F(\nabla u,\nabla v,u,v,x)dx $$ enjoy some monotonicity properties, under an assumption on the growth at infinity of the energy. Our results are quite general, and comprise some rigidity results which are known in the literature.
Ixodes ricinus Tick Lipocalins: Identification, Cloning, Phylogenetic Analysis and Biochemical Characterization
Jér?me Beaufays, Beno?t Adam, Yves Decrem, Pierre-Paul Prév?t, Sébastien Santini, Robert Brasseur, Michel Brossard, Laurence Lins, Luc Vanhamme, Edmond Godfroid
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0003941
Abstract: Background During their blood meal, ticks secrete a wide variety of proteins that interfere with their host's defense mechanisms. Among these proteins, lipocalins play a major role in the modulation of the inflammatory response. Methodology/Principal Findings Screening a cDNA library in association with RT-PCR and RACE methodologies allowed us to identify 14 new lipocalin genes in the salivary glands of the Ixodes ricinus hard tick. A computational in-depth structural analysis confirmed that LIRs belong to the lipocalin family. These proteins were called LIR for “Lipocalin from I. ricinus” and numbered from 1 to 14 (LIR1 to LIR14). According to their percentage identity/similarity, LIR proteins may be assigned to 6 distinct phylogenetic groups. The mature proteins have calculated pM and pI varying from 21.8 kDa to 37.2 kDa and from 4.45 to 9.57 respectively. In a western blot analysis, all recombinant LIRs appeared as a series of thin bands at 50–70 kDa, suggesting extensive glycosylation, which was experimentally confirmed by treatment with N-glycosidase F. In addition, the in vivo expression analysis of LIRs in I. ricinus, examined by RT-PCR, showed homogeneous expression profiles for certain phylogenetic groups and relatively heterogeneous profiles for other groups. Finally, we demonstrated that LIR6 codes for a protein that specifically binds leukotriene B4. Conclusions/Significance This work confirms that, regarding their biochemical properties, expression profile, and sequence signature, lipocalins in Ixodes hard tick genus, and more specifically in the Ixodes ricinus species, are segregated into distinct phylogenetic groups suggesting potential distinct function. This was particularly demonstrated by the ability of LIR6 to scavenge leukotriene B4. The other LIRs did not bind any of the ligands tested, such as 5-hydroxytryptamine, ADP, norepinephrine, platelet activating factor, prostaglandins D2 and E2, and finally leukotrienes B4 and C4.
Black Carbon Instead of Particle Mass Concentration as an Indicator for the Traffic Related Particles in the Brussels Capital Region  [PDF]
Peter Vanderstraeten, Michael Forton, Olivier Brasseur, Zvi Y. Offer
Journal of Environmental Protection (JEP) , 2011, DOI: 10.4236/jep.2011.25060
Abstract: The Brussels Capital Region has difficulties in meeting the stringent EU daily limit value for PM10 in all its measuring sites. Postponing the attainment of the deadline was not granted by the EU Commission, mainly due to insufficient judged measures to reduce road traffic emissions. However, a thorough analysis of the data makes clear that neither the particle mass concentration (PM10 and PM2.5) nor the particle number concentration are specific metrics for evaluating the particle pollution originated by traffic. In fact, increased formation of secondary aerosol, together with adverse meteorological conditions and the (re) suspension of the coarser fraction are by far the three main explanations for the numerous PM10 exceeding values. From our experience, amongst the particles measured, only the results for Black Carbon (BC), mainly present in the lower submicron range, are reflective of the direct influence of local traffic. Measured at two traffic sites along with PM mass and number concentrations, the data for Black Carbon show a striking correlation with nitrogen monoxide, a parameter strongly related with the proximity of the local traffic. The correlation factor between Black Carbon data and NO or NOX is much higher than between Black Carbon and the PM mass or number concentration. Therefore the assessment of traffic related particles should consider Black Carbon rather than PM10 or PM2.5.
The Invalidity of the Laplace Law for Biological Vessels and of Estimating Elastic Modulus from Total Stress vs. Strain: a New Practical Method
Francesco Costanzo,James G. Brasseur
Physics , 2013,
Abstract: The quantification of the stiffness of tubular biological structures is often obtained, both in vivo and in vitro, as the slope of total transmural hoop stress plotted against hoop strain. Total hoop stress is typically estimated using the "Laplace law." We show that this procedure is fundamentally flawed for two reasons: Firstly, the Laplace law predicts total stress incorrectly for biological vessels. Furthermore, because muscle and other biological tissue are closely volume-preserving, quantifications of elastic modulus require the removal of the contribution to total stress from incompressibility. We show that this hydrostatic contribution to total stress has a strong material-dependent nonlinear response to deformation that is difficult to predict or measure. To address this difficulty, we propose a new practical method to estimate a mechanically viable modulus of elasticity that can be applied both in vivo and in vitro using the same measurements as current methods, with care taken to record the reference state. To be insensitive to incompressibility, our method is based on shear stress rather than hoop stress, and provides a true measure of the elastic response without application of the Laplace law. We demonstrate the accuracy of our method using a mathematical model of tube inflation with multiple constitutive models. We also re-analyze an in vivo study from the gastro-intestinal literature that applied the standard approach and concluded that a drug-induced change in elastic modulus depended on the protocol used to distend the esophageal lumen. Our new method removes this protocol-dependent inconsistency in the previous result.
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