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Abstract: Molecular dynamics simulation method is used to assess the contribution of a disease-associated salt bridge in the early stages of the conformational rearrangement of human prion protein upon Arg208→His mutation, which causes Creutzfeldt–Jakob disease. Previous investigations have suggested that the breakage of this putative salt bridge (D144/E146 ↔Arg208) between helix 1 and helix 3 is responsible for such a mutation-driven process. So far, no experimental data has been reported in order to distinguish the contribution of this single salt bridge in the initial steps of amyloid formation. Consequently, we decided to investigate the role of this salt bridge in early conformational rearrangements. To remove the salt bridge without perturbations in the backbone structure, the neutralized states of the involved residues were used. Three 10-ns molecular dynamics simulations on three initial structures have been performed. The results revealed that the early stages of the conformational rearrangements, against common belief, are mainly associated with the mutation-induced global changes in the backbone dynamics but not with the breaking of the salt bridge. [Copyright &y& Elsevier]

Abstract: We decided to investigate the influence of the presence of disulfide bonds on the pattern of force distribution in the functional site of scorpion toxin BMK M1 in its functional state. Therefore, a series of short time molecular dynamics (MD) simulations were performed on this toxin in the native state and disulfide bond broken states. The comparison of disulfide bond broken states with the native state showed that the electrostatic potential energy of important functional residues in the reverse turn and C-terminal regions were modulated by the cooperative effect of all disulfide bonds in the molecule. Furthermore, our results revealed that disulfide bonds also play a cooperative role in modulating (1) the amplitude of the fluctuations of the functional segments and (2) the correlation of motions between important functional residue pairs in this toxin. Therefore, we can conclude that the disulfide bonds have cooperation to adjust the pattern of force distribution in the functional site of this toxin in its functional state. [Copyright &y& Elsevier]

Photoinactivation is a common phenomenon in bioluminescence ctenophore photoproteins ( e.g mnemiopsin, berovin and BfosPP) with still unknown mechanism. The activity of coelenterate photoproteins ( e.g aequorin), which has high structural similarity with ctenophore photoproteins, is not affected by light. Recently, we have characterized the effects of light on ctenophore photoprotein mnemiopsin, in different conformations, which has demonstrated light induced structural changes, uniquely secondary structures, of both apo and holo mnemiopsin. This paper is further expansion of our previous work, by applying molecular dynamics simulations to investigate photoinactivation related dynamics of berovin at atomistic level, in comparison with aequorin, under the influence of electric component of electromagnetic field. The results have indicated that the intense electric filed could influence structure of both berovin and aequorin but in different manner, whereas moderate electric field only effects on berovin's structure remarkably. In this case, increased helicity of residues E180-M193 and decreased helical contents of L38-D46 and L125-D138 segments are considerable in berovin as well as flexibility elevation of calcium binding loops. These changes cause structural expansion of berovin, especially at N-terminal domain, in direction of electric field. In conclusion, the induced structural changes of mentioned helical parts together with elevated fluctuation of their adjacent segments, N26-D46 and M193-Y206, indicate the influence of light on substrate stabilizing residues, Arg41 and Y204. This condition could presumably leads to inactivation of bioluminescence reaction due to separation of substrate from the cavity of the protein. [ABSTRACT FROM AUTHOR]

Surface modification of the substrate as a component of in vitro cell culture and tissue engineering, using bio-active molecules including extracellular matrix (ECM) proteins or peptides derived ECM proteins can modulate the surface properties and thereby induce the desired signaling pathways in cells. The aim of this study was to evaluate the behavior of human bone marrow mesenchymal stem cells (hBM-MSCs) on glass substrates modified with fibronectin (Fn), collagen (Coll), RGD peptides (RGD) and designed peptide (R-pept) as bio-active molecules. The glass coverslips were coated with fibronectin, collagen, RGD peptide and R-peptide. Bone marrow mesenchymal stem cells were cultured on different substrates and the adhesion behavior in early incubation times was investigated using scanning electron microscopy (SEM) and confocal microscopy. The MTT assay was performed to evaluate the effect of different bio-active molecules on MSCs proliferation rate during 24 and 72 h. Formation of filopodia and focal adhesion (FA) complexes, two steps of cell adhesion process, were observed in MSCs cultured on bio-active molecules modified coverslips, specifically in Fn coated and R-pept coated groups. SEM image showed well adhesion pattern for MSCs cultured on Fn and R-pept after 2 h incubation, while the shape of cells cultured on Coll and RGD substrates indicated that they might experience stress condition in early hours of culture. Investigation of adhesion behavior, as well as proliferation pattern, suggests R-peptide as a promising bio-active molecule to be used for surface modification of substrate in supporting and inducing cell adhesion and proliferation. [ABSTRACT FROM AUTHOR]

The first cDNA from lampyridae encoding a glow-worm luciferase from lantern mRNA of Lampyris turkestanicus has been cloned, sequenced, the amino acid sequence predicted, and the sequence reported to GenBank. The cDNA was 1644 base pairs in length and coding a 547-residue protein. The deduced amino acid sequence of the luciferase gene of L. turkestanicus showed 98.7% and 95.8% identity to Lampyris noctiluca and Pyrocoelia rufa, respectively. Phylogenetic analysis further confirmed that the deduced amino acid sequences of L. turkestanicus luciferase gene belong to the same subfamily, Lampyrinae. The cDNA encoding the luciferase of L. turkestanicus was expressed as a 62kDa band in recombinant Escherichia coli and showed green luminescence in the presence of luciferin. Amongst amino acid differences of L. turkestanicus and L. noctiluca (its clade) there are two important substitutions. Signature amino-acid sequences and motifs found in the deduced sequence are CK2-phospho site, ASN-glycosylation, myristoylation site, PKC-phospho site, microbodies C-terminal targeting signal, and AMP-binding domain. [Copyright &y& Elsevier]