On the early events of the calcium-induced activation of coagulation factor XIII-A2 and tissue transglutaminase: an in silico study.

Both coagulation factor XIII-A2 (FXIII-A2) and tissue transglutaminase (TG2) play distinctive and important roles in homeostasis by crosslinking proteins or peptides via isopeptide bonds. In this present study, a series of microsecond-long all-atom molecular dynamics (MD) simulations were carried out in order to reveal the dynamic, atomic-level events which may contribute to the activation of these proteins via the binding of calcium ions. In addition to previously conducted in vitro and crystallographic studies, further suggestions have been made concerning the calcium binding features of these enzymes. The different systems used for running the simulations were based on the zymogen, computationally cleaved and even the activation peptide (AP-FXIII) free FXIII-A2' homodimer form. The effects of various ionic environments have also been explored in the simulations of FXIII-A2. Our results suggest that the presence of calcium ions can cause increased AP fluctuations, which ultimately could lead to their relocation on the homodimer surface. The release of these APs seems to be crucial for rotation of the A subunits based on equilibrium MD simulations. The primary evidence for this assumption comes from the predicted principal component eigenvector which is considered as the first, large-scale event of the overall activation process. To get a more accurate atomic-level description, the calcium binding sites of TG2 have also been investigated in our extensive in silico experiments, which suggests the presence of previously unidentified binding sites as well.Communicated by Ramaswamy H. Sarma.

Calcium binding of the antifungal protein PAF: Structure, dynamics and function aspects by NMR and MD simulations.

Calcium ions (Ca2+) play an important role in the toxicity of the cysteine-rich and cationic antifungal protein PAF from Penicillium chrysogenum: high extracellular Ca2+ levels reduce the toxicity of PAF in the sensitive model fungus Neurospora crassa in a concentration dependent way. However, little is known about the mechanistic details of the Ca2+ ion impact and the Ca2+ binding capabilities of PAF outside the fungal cell, which might be the reason for the activity loss. Using nuclear magnetic resonance (NMR), isothermal titration calorimetry and molecular dynamics (MD) simulations we demonstrated that PAF weakly, but specifically binds Ca2+ ions. MD simulations of PAF predicted one major Ca2+ binding site at the C-terminus involving Asp53 and Asp55, while Asp19 was considered as putative Ca2+ binding site. The exchange of Asp19 to serine had little impact on the Ca2+ binding, however caused the loss of antifungal activity, as was shown in our recent study. Now we replaced the C-terminal aspartates and expressed the serine variant PAFD53S/D55S. The specific Ca2+ binding affinity of PAFD53S/D55S decreased significantly if compared to PAF, whereas the antifungal activity was retained. To understand more details of Ca2+ interactions, we investigated the NMR and MD structure/dynamics of the free and Ca2+-bound PAF and PAFD53S/D55S. Though we found some differences between these protein variants and the Ca2+ complexes, these effects cannot explain the observed Ca2+ influence. In conclusion, PAF binds Ca2+ ions selectively at the C-terminus; however, this Ca2+ binding does not seem to play a direct role in the previously documented modulation of the antifungal activity of PAF.

Antithrombin Debrecen (p.Leu205Pro) - Clinical and molecular characterization of a novel mutation associated with severe thrombotic tendency.

INTRODUCTION: Hereditary antithrombin (AT) deficiency is a rare thrombophilic disorder with heterogeneous genetic background and various clinical presentations. In this study we identified a novel AT mutation. Genotype-phenotype correlations, molecular characteristics and thrombotic manifestations of the mutation were investigated. MATERIALS AND METHODS: Thirty-one members of a single family were included. Clinical data was collected regarding thrombotic history. The mutation was identified by direct sequencing of the SERPINC1 gene. HEK293 cells were transfected with wild type and mutant SERPINC1 plasmids. Western blotting, ELISA and functional amidolytic assay were used to detect wild type and mutant AT. After double immunostaining, confocal laser scanning microscopy was used to localize mutant AT in the cells. Molecular modeling was carried out to study the structural-functional consequences of the mutation. RESULTS: Unprovoked venous thrombotic events at early age, fatal first episodes and recurrences were observed in the affected individuals. The median AT activity was 59%. Genetic analysis revealed heterozygous form of the novel mutation p.Leu205Pro (AT Debrecen). The mutant AT was expressed and synthesized in HEK293 cells but only a small amount was secreted. The majority was trapped intracellularly in the trans­Golgi and 26S proteasome. The mutation is suspected to cause considerable structural distortion of the protein. The low specific activity of the mutant AT suggested functional abnormality. CONCLUSIONS: AT Debrecen was associated with very severe thrombotic tendency. The mutation led to misfolded AT, impaired secretion and altered function. Detailed clinical and molecular characterization of a pathogenic mutation might provide valuable information for individualized management.

Modeling the archetype cysteine protease reaction using dispersion corrected density functional methods in ONIOM-type hybrid QM/MM calculations; the proteolytic reaction of papain.

A proteolytic reaction of papain with a simple peptide model substrate N-methylacetamide has been studied. Our aim was twofold: (i) we proposed a plausible reaction mechanism with the aid of potential energy surface scans and second geometrical derivatives calculated at the stationary points, and (ii) we investigated the applicability of the dispersion corrected density functional methods in comparison with the popular hybrid generalized gradient approximations (GGA) method (B3LYP) without such a correction in the QM/MM calculations for this particular problem. In the resting state of papain the ion pair and neutral forms of the Cys-His catalytic dyad have approximately the same energy and they are separated by only a small barrier. Zero point vibrational energy correction shifted this equilibrium slightly to the neutral form. On the other hand, the electrostatic solvation free energy corrections, calculated using the Poisson-Boltzmann method for the structures sampled from molecular dynamics simulation trajectories, resulted in a more stable ion-pair form. All methods we applied predicted at least a two elementary step acylation process via a zwitterionic tetrahedral intermediate. Using dispersion corrected DFT methods the thioester S-C bond formation and the proton transfer from histidine occur in the same elementary step, although not synchronously. The proton transfer lags behind (or at least does not precede) the S-C bond formation. The predicted transition state corresponds mainly to the S-C bond formation while the proton is still on the histidine Nδ atom. In contrast, the B3LYP method using larger basis sets predicts a transition state in which the S-C bond is almost fully formed and the transition state can be mainly featured by the Nδ(histidine) to N(amid) proton transfer. Considerably lower activation energy was predicted (especially by the B3LYP method) for the next amide bond breaking elementary step of acyl-enzyme formation. Deacylation appeared to be a single elementary step process in all the methods we applied.

Molecular characterization of p.Asp77Gly and the novel p.Ala163Val and p.Ala163Glu mutations causing protein C deficiency.

INTRODUCTION: Protein C (PC) is a major anticoagulant and numerous distinct mutations in its coding gene result in quantitative or qualitative PC deficiency with high thrombosis risk. Homozygous or compound heterozygous PC deficiency usually leads to life-threatening thrombosis in neonates. PATIENTS AND METHODS: The molecular consequences of 3 different missense mutations of two patients have been investigated. The first patient suffered from neonatal purpura fulminans and was a compound heterozygote for p.Asp77Gly and p.Ala163Glu mutations. The second patient had severe deep venous thrombosis in young adulthood and carried the p.Ala163Val mutation. The fate of mutant proteins expressed in HEK cells was monitored by ELISA, by Western blotting, by investigation of polyubiquitination and by functional assays. Their intracellular localization was examined by immunostaining and confocal laser scanning microscopy. Molecular modeling and dynamics simulations were also carried out. RESULTS AND CONCLUSIONS: The 163Val and 163Glu mutants had undetectable levels in the culture media, showed intracellular co-localization with the 26S proteasome and were polyubiquitinated. The 77Gly mutant was secreted to the media showing similar activity as the wild type. There was no difference among intracellular PC levels of wild type and mutant proteins. The 163Val and 163Glu mutations caused significant changes in the relative positions of the EGF2 domains suggesting misfolding with the consequence of secretion defect. No major structural alteration was observed in case of 77Gly mutant; it might influence the stability of protein complexes in which PC participates and may have an impact on the clearance of PC requiring further research.

Dynamic properties of the native free antithrombin from molecular dynamics simulations: computational evidence for solvent- exposed Arg393 side chain.

While antithrombin (AT) has small basal inhibitory activity, it reaches its full inhibitory potential against activated blood coagulation factors, FXa, FIXa, and FIIa (thrombin), via an allosteric and/or template (bridging) mechanism by the action of heparin, heparan sulfate, or heparin-mimetic pentasaccharides (PS). From the numerous X-ray structures available for different conformational states of AT, only indirect and incomplete conclusions can be drawn on the inherently dynamic properties of AT. As a typical example, the basal inhibitory activity of AT cannot be interpreted on the basis of "non-activated" free antithrombin X-ray structures since the Arg393 side chain, playing crucial role in antithrombin-proteinase interaction, is not exposed. In order to reveal the intrinsic dynamic properties and the reason of basal inhibitory activity of antithrombin, 2 µs molecular dynamics simulations were carried out on its native free-forms. It was shown from the simulation trajectories that the reactive center loop which is functioning as "bait" for proteases, even without any biasing potential can populate conformational state in which the Arg393 side chain is solvent exposed. It is revealed from the trajectory analysis that the peptide sequences correspond to the helix D extension, and new helix P formation can be featured with especially large root-mean-square fluctuations. Mutual information analyses of the trajectory showed remarkable (generalized) correlation between those regions of antithrombin which changed their conformations as the consequence of AT-PS complex formation. This suggests that allosteric information propagation pathways are present even in the non-activated native form of AT.

New way to reconstruct severe injuries to the lower extremity.

The combined use of an avascular cadaver bone graft, and a reverse flow fibular osteoperiosteal and soleus muscle flap is a reliable option for the reconstruction of severe injury to the lower extremity because of the segmental blood supply from the fibular artery.

Effect of network structure on phase transitions in queuing networks.

Recently, De Martino et al. [J. Stat. Mech. (2009) P08023; Phys. Rev. E 79, 015101 (2009)] have presented a general framework for the study of transportation phenomena on random networks with annealed disorder. One of their most significant achievements was a deeper understanding of the phase transition from the uncongested to the congested phase at a critical traffic load on uncorrelated networks. In this paper, we also study phase transition in transportation networks using a discrete time random walk model. Our aim is to establish a direct connection between the structure of an uncorrelated random graph with quenched disorder and the value of the critical traffic load. We show that if the network is dense, the quenched and annealed formulas for the critical loading probability coincide. For sparse graphs, higher-order corrections, related to the local structure of the network, appear.

Shortest path discovery of complex networks.

In this Rapid Communication we present an analytic study of sampled networks in the case of some important shortest-path sampling models. We present analytic formulas for the probability of edge discovery in the case of an evolving and a static network model. We also show that the number of discovered edges in a finite network scales much more slowly than predicted by earlier mean-field models. Finally, we calculate the degree distribution of sampled networks and we demonstrate that they are analogous to a destroyed network obtained by randomly removing edges from the original network.

Distribution of edge load in scale-free trees.

Node betweenness has been studied recently by a number of authors, but until now less attention has been paid to edge betweenness. In this paper, we present an exact analytic study of edge betweenness in evolving scale-free and non-scale-free trees. We aim at the probability distribution of edge betweenness under the condition that a local property, the in-degree of the "younger" node of a randomly selected edge, is known. En route to the conditional distribution of edge betweenness the exact joint distribution of cluster size and in-degree, and its one-dimensional marginal distributions have been presented in the paper as well. From the derived probability distributions the expectation values of different quantities have been calculated. Our results provide an exact solution not only for infinite, but for finite networks as well.

Public-key encryption with chaos.

We propose public-key encryption algorithms based on chaotic maps, which are generalization of well-known and commercially used algorithms: Rivest-Shamir-Adleman (RSA), ElGamal, and Rabin. For the case of generalized RSA algorithm we discuss in detail its software implementation and properties. We show that our algorithm is as secure as RSA algorithm.