188 research outputs found
Universal geometrical factor of protein conformations as a consequence of energy minimization
The biological activity and functional specificity of proteins depend on
their native three-dimensional structures determined by inter- and
intra-molecular interactions. In this paper, we investigate the geometrical
factor of protein conformation as a consequence of energy minimization in
protein folding. Folding simulations of 10 polypeptides with chain length
ranging from 183 to 548 residues manifest that the dimensionless ratio
(V/(A)) of the van der Waals volume V to the surface area A and average
atomic radius of the folded structures, calculated with atomic radii
setting used in SMMP [Eisenmenger F., et. al., Comput. Phys. Commun., 138
(2001) 192], approach 0.49 quickly during the course of energy minimization. A
large scale analysis of protein structures show that the ratio for real and
well-designed proteins is universal and equal to 0.491\pm0.005. The fractional
composition of hydrophobic and hydrophilic residues does not affect the ratio
substantially. The ratio also holds for intrinsically disordered proteins,
while it ceases to be universal for polypeptides with bad folding properties.Comment: 6 pages, 1 table, 4 figure
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A novel transport mechanism for MOMP in Chlamydophila pneumoniae and its putative role in immune-therapy
Major outer membrane proteins (MOMPs) of Gram negative bacteria are one of the most intensively studied membrane proteins. MOMPs are essential for maintaining the structural integrity of bacterial outer membranes and in adaptation of parasites to their hosts. There is evidence to suggest a role for purified MOMP from Chlamydophila pneumoniae and corresponding MOMP-derived peptides in immune-modulation, leading to a reduced atherosclerotic phenotype in apoEâ/â mice via a characteristic dampening of MHC class II activity. The work reported herein tests this hypothesis by employing a combination of homology modelling and docking to examine the detailed molecular interactions that may be responsible. A three-dimensional homology model of the C. pneumoniae MOMP was constructed based on the 14 transmembrane ÎČ-barrel crystal structure of the fatty acid transporter from Escherichia coli, which provides a plausible transport mechanism for MOMP. Ligand docking experiments were used to provide details of the possible molecular interactions driving the binding of MOMP-derived peptides to MHC class II alleles known to be strongly associated with inflammation. The docking experiments were corroborated by predictions from conventional immuno-informatic algorithms. This work supports further the use of MOMP in C. pneumoniae as a possible vaccine target and the role of MOMP-derived peptides as vaccine candidates for immune-therapy in chronic inflammation that can result in cardiovascular events
Etude de la matiÚre organique réfractaire à la coagulation-floculation et à son procédé alternatif, l'électrocoagulation, lors du traitement d'un lixiviat stabilisé
International audienceThe organic matter (OM) and more specially humic substances (HS) represents the major organic constituent of a landfill leachate. It plays a dual but a very important role in both biogeochemistry of medium and pollutant chemistry. The removal of this organic matter can be realised by the use of the classical coagulation-flocculation process or by the electrocoagulation process. The organic matter fractionation of a stabilised landfill leachate has been realised by the Malcolm & Mac Carty (1992) fractionation protocol which combines the use of non-ionic XAD resins assembled in series (DAX-8 & XAD-4) in order to divide up the organic matter in more numerous fractions. The analysis of the size of the OM has been realised by ultrafiltration (30KDa, 3KDa and 0,5KDa).The quantity of the residual organic matter is the same for the two processes but the composition of this residual matter appears different: electrocoagulation show a more important pourcent of small organic molecules.LâĂ©limination de la matiĂšre organique (MO) contenue dans un lixiviat de dĂ©charge dâordures mĂ©nagĂšres peut ĂȘtre rĂ©alisĂ©e Ă lâaide du procĂ©dĂ© de coagulation-floculation classique ou dâĂ©lectrocoagulation. La caractĂ©risation de la fraction rĂ©siduelle aprĂšs traitement peut se faire par analyse de la taille des composĂ©s et par fractionnement sur rĂ©sine en fonction de lâhydrophobicitĂ© des composĂ©s. LâĂ©tude menĂ©e sur un lixiviat dit « stabilisĂ© », donc composĂ© majoritairement de macromolĂ©cules organiques, met en Ă©vidence un abattement quantitativement identique de la charge organique pour les deux procĂ©dĂ©s de traitement. La MO rĂ©fractaire est cependant qualitativement diffĂ©rente puisque lâĂ©lectrocoagulation conduit Ă la formation de composĂ©s de plus petite taille
Ăvaluation de la fixation sur quelques sols des dĂ©rivĂ©s du diuron, de l'atrazine et de la simazine seuls ou en mĂ©lange
La contamination des sols et des eaux par les herbicides et leurs dĂ©rivĂ©s est devenue une situation prĂ©occupante qui nĂ©cessite plus que jamais la plus grande attention. Dans l'environnement, le devenir de ces produits est gouvernĂ© par de nombreux processus dont les phĂ©nomĂšnes de rĂ©tention. Le travail entrepris a pour objectif d'Ă©tudier la rĂ©tention du diuron, de l'atrazine, de la simazine et de leurs dĂ©rivĂ©s dans les sols Ă l'aide d'essais cinĂ©tiques et d'isothermes de fixation. Les rĂ©sultats rapportent des observations similaires entre les cinĂ©tiques et les isothermes de fixation. Les coefficients d'adsorption obtenus Ă partir des reprĂ©sentations directes (KD) et suivant le modĂšle de Freundlich des isothermes rĂ©vĂšlent que tous les composĂ©s sont mieux retenus sur les sols et les horizons les plus riches en matiĂšre organique. L'utilisation du coefficient KCO, permettant de considĂ©rer la rĂ©tention et intrinsĂšquement la mobilitĂ© comme facteur uniquement du carbone organique du sol, permet de proposer un comportement gĂ©nĂ©ral des composĂ©s sur les sols. DĂ©fait, il apparaĂźt que les s-triazines (KCOatrazine = 155L.kg-1 et KCOsimazine = 120 L.kg-l) et surtout leurs dĂ©rivĂ©s dĂ©alkylĂ©s (dĂ©Ă©thylatrazine, dĂ©isopropylatrazine et dĂ©dialkylatrazine) sont trĂšs peu retenus par les sols, au contraire des dĂ©rivĂ©s hydroxylĂ©s (hydroxyatrazine et ammeline). La fixation d'un mĂ©lange laisse entrevoir des compĂ©titions entre l'atrazine - la dĂ©Ă©thylatrazine qui favoriseraient une augmentation de leurs mobilitĂ©s. Le diuron (KCOdiuron = 520 L.kg-1), est moins retenu que ses dĂ©rivĂ©s (dichlorophĂ©nylmĂ©thyl-urĂ©e, dichlorophĂ©nyl-urĂ©e et 3-4 dichloroaniline), mais ces derniers s'avĂšrent tout de mĂȘme mobiles, surtout s'ils se retrouvent dans un mĂ©lange. En effet, le diuron et ses dĂ©rivĂ©s dĂ©mĂ©thylĂ©s apparaissent compĂ©titeurs pour l'adsorption dans les sols alors que la 3-4 dichloroaniline ne souffre d'aucune compĂ©tition et verrait mĂȘme sa rĂ©tention facilitĂ©e dans des mĂ©langes peu concentrĂ©s
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