Tr-Noe and MD studies of Leishmania gp63 SRYD-containing sequences bound to anti-SRYD monoclonal antibody

The I²⁵⁰ASRYDQL²⁵⁷ synthetic octapeptideof the Leishmania major surface glycoproteingp63, which efficiently inhibits parasite attachmentto the macrophage receptors and mimics antigenicallyand functionally the RGDS sequence of fibronectin, wasstudied by 2D TR-NOESY in the presence of an anti-SRYDmonoclonal antibody (mAbSRYD) that recognizes bothSRYD-containing peptides and the cognate protein onintact parasites. Molecular modeling was performedusing distance constraints obtained from TR-NOEs. Thebound structure was compared with that of the freepeptide in DMSO solution and with the crystalstructure of the RYD fragment of the OPG2 Fab, anantireceptor antibody that mimics an RGD cell adhesion site.     

PhyloMeasures: a package for computing phylogenetic biodiversity measures and their statistical moments

We present PhyloMeasures, a new software package including both a C++ and R version, that provides very fast computation of popular phylogenetic diversity measures. PhyloMeasures introduces two major advances over existing methods. First, it uses efficient algorithms for calculating basic phylogenetic metrics (such as Faith's PD and the mean pairwise distance, MPD) and two‐sample measures (such as common branch length, CBL, and the unique fraction) that are designed to perform well even on very large trees. Second, it computes exact richness‐standardised versions of these measures (such as the widely used net relatedness index, NRI) by efficiently evaluating analytical expressions for the mean and variance of the basic measures, rather than by the slow and inexact randomization techniques that are the current standard. Together, these lead to massive improvements in performance compared to the current state of the art. For example, running on a standard laptop, PhyloMeasures functions can provide the NRI for 20 samples from a tree of 100 000 tips in about 1.5 s, compared to an estimated 37 d using standard resampling approaches. This will allow analyses on larger data sets than were previously possible.     

Simple chalcones and bis-chalcones ethers as possible pleiotropic agents

The synthesis, the antioxidative properties and the lipoxygenase (LOX) and acetylcholinesterase (AChE) inhibition of a number of 4-hydroxy-chalcones diversely substituted as well as of a series of bis-chalcones ether derivatives are reported. The chalcones derivatives were readily produced using a Claisen–Schmidt condensation in a ultra sound bath in good yields. The structures of the synthesized compounds were confirmed by spectral and elemental analysis. Their lipophilicity is experimentally determined by reversed-phase thin-layer chromatography method. Most of them are potent in vitro inhibitors of lipid peroxidation and of LOX. Compounds b2 and b3 were found to be the most potent LOX and AChE inhibitors among the tested derivatives with a significant anti-lipid peroxidation profile. The results led us to propose these enone derivatives as new multifunctional compounds against Alzheimer's disease. The results are discussed in terms of structural and physicochemical characteristics of the compounds. Moreover, the pharmacokinetic profile of these compounds was investigated using computational methods.     

Thermal denaturation of the BRCT tandem repeat region of human tumour suppressor gene product BRCA1

Reduced stability of the tandem BRCT domains of human BReast CAncer 1 (BRCA1) due to missense mutations may be critical for loss of function in DNA repair and damage-induced checkpoint control. In the present thermal denaturation study of the BRCA1 BRCT region, high-precision differential scanning calorimetry (DSC) and circular dichroism (CD) spectroscopy provide evidence for the existence of a denatured state that is structurally very similar to the native. Consistency between theoretical structure-based estimates of the enthalpy (DeltaH) and heat capacity change (DeltaCp) and the calorimetric results is obtained when considering partial thermal unfolding contained in the region of the conserved hydrophobic pocket formed at the interface of the two BRCT repeats. The structural integrity of this region has been shown to be crucial for the interaction of BRCA1 with phosphorylated peptides. In addition, cancer-causing missense mutations located at the inter-BRCT-repeat interface have been linked to the destabilization of the tandem BRCT structure.     

Skeletal muscle reperfusion injury is mediated by neutrophils and the complement membrane attack complex

The relative inflammatory roles ofneutrophils, selectins, and terminal complement components areinvestigated in this study of skeletal muscle reperfusion injury. Miceunderwent 2 h of hindlimb ischemia followed by 3 h ofreperfusion. The role of neutrophils was defined by immunodepletion,which reduced injury by 38%, as did anti-selectin therapy withrecombinant soluble P-selectin glycoprotein ligand-immunoglobulin (Ig)fusion protein. Injury in C5-deficient and soluble complement receptortype 1-treated wild-type mice was 48% less than that of untreatedwild-type animals. Injury was restored in C5-deficient micereconstituted with wild-type serum, indicating the effector role ofC5-9. Neutropenic C5-deficient animals showed additive reductionin injuries (71%), which was lower than C5-deficientneutrophil-replete mice, indicating neutrophil activity withoutC5a. Hindlimb histological injury was worse in ischemicwild-type and C5-deficient animals reconstituted with wild-type serum.In conclusion, the membrane attack complex and neutrophils actadditively to mediate skeletal muscle reperfusion injury. Neutrophilactivity is independent of C5a but is dependent on selectin-mediated adhesion.

     

Phosphorylated and nonphosphorylated epitopes of the La/SSB autoantigen: comparison of their antigenic and conformational characteristics

La/SSB phosphoprotein is the target antigen of autoantibodies in sera of patients with Sj?gren's syndrome (SS) and systemic lupus erythematosus (SLE). Among other structural and function motifs, four phosphorylation sites are encompassed in the primary sequence of La/SSB. Two of them (Thr-362 and Ser-366) are located within GSGKGKVQFQGKKTKFASDD (346-368) and one (Thr-302) within VTWEVLEGEVEKEALKKI (301-318), which are main B-cell epitopes of La/SSB. With the aim to investigate how phosphorylation, one of the most common posttranslational protein modifications, affects the antigenic and conformational characteristics of the La/SSB epitopes, we synthesized and studied the phosphorylated epitopes La/SSB(346-368)-P, La/SSB(359-368)-P, and La/SSB(301-318)-P with respect to their nonphosphorylated counterparts. Anti-La/SSB positive sera from SS and SLE patients are better recognized by the phosphorylated epitopes compared to their nonphosphorylated counterparts. Conformational analysis by (1)H nuclear magnetic resonance spectroscopy and molecular dynamics showed that the phosphorylated epitopes adopt different structural characteristics from those of the corresponding nonphosphorylated epitopes. It is concluded that phosphorylation can create neoepitopes with altered functions, compared to the nonphosphorylated epitopes, which might be seen from the immune system as "foreign."     

HLA‐DQ7 β1 and β2 derived peptides as immunomodulators

Modulation of protein–protein interactions involved in the immune system by using small molecular mimics of the contact interfaces may lead to the blockage of the autoimmune response and the development of drugs for immunotherapy. The nonpolymorphic β‐regions, exposed to the microenvironment, of the modeled HLA‐DQ7, which is genetically linked to autoimmune diseases, were determined. Peptides 132–141 and 58–67, located at the β₁ and β₂ domains of HLA‐DQ7, respectively, were tested for their involvement in the interactions with CD4⁺ T lymphocytes. Linear, cyclic, and dimeric analogs that mimic the exposed surfaces of HLA‐DQ7 were designed and synthesized. Their immunosuppressory activities, found in the secondary, humoral immune response to sheep erythrocytes (SRBC) in mice in vitro, ranged from 11% to 53%. The significance of the total charge of the peptides, the pattern of the hydrogen bonding, and the presence of secondary structure were investigated in relation to the immunomodulatory effect of the peptides. Two dimeric analogs of the HLA‐DQ7 58–67 fragment, consisting of the two monomers covalently linked by a polyethylene glycol (PEG) spacer, able to mimic the superdimers, were also synthesized and studied. As the 58–67 segment is located at the β₁ region of HLA‐DQ7, close to the major histocompatibility complex (MHC) groove, one may assume that the 58–67 peptide could accommodate the association between T‐cell receptor (TCR) and human leukocyte antigen (HLA) by activating a co‐stimulatory molecule of the TCR/HLA interaction. This hypothesis is supported by the confocal laser image of the fluorescein‐labeled 58–67 peptide and by the fact that it is an immunostimulator at low concentration. Copyright © 2009 European Peptide Society and John Wiley & Sons, Ltd.