P1 Site Research Articles

A new Kunitz-type plasmin inhibitor from scorpion venom

Kunitz-type peptides from venomous animals are an important source of lead drug candidates towards human plasmin, a target of protease-associated diseases. However, no Kunitz-type plasmin inhibitor from venomous scorpion has been characterized. Here, we first investigated plasmin inhibiting activities of eight known Kunitz-type scorpion toxins Hg1, BmKTT-1, BmKTT-2, BmKTT-3, LmKTT-1a, LmKTT-1b, LmKTT-1c and BmKPI, and found a new plasmin inhibitor BmKTT-2, a Kunitz-type toxin peptide from the scorpion Buthus martensi karch. Protease inhibitory activity assay showed that BmKTT-2 potently inhibited plasmin with a Ki value of 8.75 ± 2.05 nM. Structure–function relationship studies between BmKTT-2 and plasmin showed that BmKTT-2 is a classical Kunitz-type plasmin inhibitor: Lys13 in BmKTT-2 is the P1 site, and Ala14 in BmKTT-2 is the P1′ site. Interestingly, BmKTT-2 has potent inhibiting activities towards three important digestive serine proteases trypsin, chymotrypsin and elastase, suggesting a good stability for administering oral medications. To the best of our knowledge, BmKTT-2 is the first Kunitz-type human plasmin inhibitor from scorpion venom, providing novel insights into drug developments targeting human plasmin protease.

Pyrite as a proxy for the identification of former coastal lagoons in semiarid NE Brazil

This work aimed to test the suitability of pyrite (FeS2) as a proxy for reconstructing past marine environmental conditions along the semiarid coast of Brazil. Morphological description combined with physicochemical analyses including Fe partitioning were conducted for soil depth profiles (30 and 60 cm depths) at three sites in two contrasting lagoons of the state of Ceara: a suspected former lagoon that would have been transformed into a freshwater “lake” at a site vegetated by Juncus effusus (site P1), and another lagoon with connection to the sea at sites vegetated by J. effusus (site P2) or Portulaca oleracea (site P3). Soil samples were collected in September 2010. Site P3 had more reducing conditions, reaching Eh values of –132 mV in the surface layer (0–10 cm), whereas minimum values for the P1 and P2 sites were +219 and +85 mV, respectively. Lower pyritic Fe values were found at site P1, with a degree of pyritization (DOP) ranging from 10 to 13%. At sites P2 and P3, DOP ranged from 9 to 67% and from 55 to 72%, respectively. These results are consistent with an interruption of tidal channels by eolian dune migration inducing strong changes in the hydrodynamics and physicochemical characteristics (lower salinity, oxidizing conditions) of these sites, causing the dieback of suspected former mangroves and a succession to freshwater marshes with an intermediate salt marsh stage. Together with other physicochemical signatures, pyrite can evidently serve as a useful proxy in tracking environmental changes in such ecotones, with implications for coastal management.

Hippocampal involvement in glucose facilitation of recognition memory: Event-related potential components in a dual-task paradigm

BACKGROUND: Glucose administration may facilitate hippocampus-mediated recognition memory (‘remember’ rather than familiarity ‘know’ responses). OBJECTIVE: This study aimed to investigate the electrophysiological correlates of this phenomenon in a cohort of older individuals. METHODS: In this double-blind placebo-controlled cross-over study, 12 older participants (mean age = 69.33 ± 1.69 years) completed the remember-know paradigm both with and without a concurrent tracking task while recording event-related potentials (ERPs). RESULTS: Counter to predictions, glucose reduced overall accuracy. No treatment effects were found for proportion of Remember, Know and Guess responses, although there was a trend towards greater accuracy for ‘Remember’ responses following glucose. There was weak evidence for dissociation of drink effects on tracking with glucose being associated with preferential allocation of resources to ‘Remember’ over ‘Know’ responses. At P3 and F3 electrode sites, a significantly greater left parietal (LP) recollection effect and greater FN400 effect respectively were found for glucose. CONCLUSIONS: These findings do not support task effort modulation of the memory-enhancing effects of glucose. There was evidence of a greater glucose facilitatory effect for hippocampus-mediated LP recollection.

Tu1454 Inter-Rater Agreement for Analysis of Pharyngeal High Resolution Manometry Parameters

Introduction: Pharyngeal manometry using high resolution technology is a developing field that is being advocated for evaluation of dysphagic symptoms that are not explained by a conclusive or objective finding on routine evaluation such as radiography. Fundamental to the success of this approach, automated analysis techniques not withstanding, is the reliability and reproducibility of the measurements performed by the clinicians. Our aim was to determine the inter-rater reliability for measurements of deglutitive pharyngeal peristaltic pressure wave characteristics such as peak peristaltic amplitude, pharyngeal contractile integral (PCI), nadir upper esophageal sphincter (UES) deglutitive pressure and intrabolus pressure (IBP). Methods: We studied 11 healthy individuals (age 56±25 years, 6F) by high resolution manometry using a catheter with 36 recording sites spaced at 1 cm intervals that recorded from the entire pharyngeal contractile zone, UES and proximal esophagus. Each volunteer swallowed 0.5 ml of room temperature water 40 times with 20 seconds intervals between swallows. Three raters (one seasoned, two with recent training) each independently analyzed a total of 3080 pressure signatures, 440 pharyngeal contractile integrals and 440 intra-bolus pressures. Measured parameters included peak peristaltic wave pressures at specific manometric locations 2, 3, 4, 5, 6, 7, and 8 cm above the upper margin of the UES high pressure zone, as well as PCI, nadir UES deglutitive pressure and IBP. Inter-rater agreement was evaluated using Bland-Altman intra-class correlation coefficient (ICC) analysis. Results: As seen in the table, agreement among the three raters all for all manometric locations was highly significant (p<0.001) with sites p2 and p3 (2 and 3cm above the upper margin of the UES) having the lowest levels of agreement. Furthermore, metrics with a single value for each swallow like PCI and UES nadir pressure also showed highly significant agreement whereas IBP measurements did not. A graphical depiction of intra-rater agreement is shown in the figure for PCI as a representative parameter. Conclusion: Analysis of pharyngeal pressure parameters by individuals with proper training is reproducible as evidenced by high level of agreement between the results obtained independently by three different raters. Supported in part by EOPH grant and PPG. Supported in part by R01DK025731 and P01DK068051

Mapping of reciprocal space of La0.30CoO2 in 3D: Analysis of superstructure diffractions and intergrowths with Co3O4

We have used electron diffraction tomography and powder X-ray diffraction to elucidate the structural properties of layered cobaltate γ-La0.30CoO2. The structure consists of hexagonal sheets of edge-sharing CoO6 octahedra interleaved by lanthanum monolayers. The La3+ cations occupy only one third of available P2 sites, forming a 2-dimensional a√3×a√3 superstructure in a–b plane. The results show that there exists no order in the mutual relative shift between the neighbouring La interlayers within the a–b plane. This is manifested in the observed monotonous decrease of the diffracted intensity of the superstructure diffractions along c⁎ in both X-ray and electron diffraction data. The observed lack of stacking order differentiates the LaxCoO2 from its Ca and Sr analogues where at least a partial stacking order of the cationic interlayers is manifested in experimental data published in literature.

Phospholipid-binding Sites of Phosphatase and Tensin Homolog (PTEN): EXPLORING THE MECHANISM OF PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE ACTIVATION

The lipid phosphatase activity of the tumor suppressor phosphatase and tensin homolog (PTEN) is enhanced by the presence of its biological product, phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2). This enhancement is suggested to occur via the product binding to the N-terminal region of the protein. PTEN effects on short-chain phosphoinositide (31)P linewidths and on the full field dependence of the spin-lattice relaxation rate (measured by high resolution field cycling (31)P NMR using spin-labeled protein) are combined with enzyme kinetics with the same short-chain phospholipids to characterize where PI(4,5)P2 binds on the protein. The results are used to model a discrete site for a PI(4,5)P2 molecule close to, but distinct from, the active site of PTEN. This PI(4,5)P2 site uses Arg-47 and Lys-13 as phosphate ligands, explaining why PTEN R47G and K13E can no longer be activated by that phosphoinositide. Placing a PI(4,5)P2 near the substrate site allows for proper orientation of the enzyme on interfaces and should facilitate processive catalysis.

Potential Assessment of Tidal Stream Energy Around Hulu Island, China

Tidal stream energy is one of most promising resources of marine renewable energy, and it has attracted more and more attention in the recent years. Hulu Island which is located at Zhoushan, China is with a maximal current velocity more than 2.0 m/s, showing a great potential in utilization of tidal stream energy. Meanwhile, a demonstration project for exploiting tidal stream energy, supported by the State Oceanic Administration, People's Republic of China, is planned in this coastal area. This study develops a two-dimensional mathematical model for the simulation of tidal hydrodynamics and potential assessment of tidal stream energy around Hulu Island. The numerical results of tidal elevation and current velocity are compared with those data from field observations (one for water level and two for tidal current), and the good agreement between simulation and measurement indicates a great ability of the model. Distributions of mean and maximal energy densities of tidal stream in the vicinity of Hulu Island are provided, and two possible sites for deploying tidal stream turbines are recommended. At each possible site, velocity profile and power density curve are numerically investigated for a 15-day period for covering the spring-neap tide cycle. The results show the candidate site P1 and P2 hold the mean power density as 0.62kW/m2 and 1.81kW/m2, respectively.

MOLECULAR MODEL OF CYTOTOXIN-1 FROM NAJA MOSSAMBICA MOSSAMBICA VENOM IN COMPLEX WITH CHYMOTRYPSIN.

Snake venom is a myriad of biologically active proteins and peptides. Three finger toxins are highly conserved in their molecular structure, but interestingly possess diverse biological functions. During the course of evolution the introduction of subtle mutations in loop regions and slight variations in the three dimensional structure, has resulted in their functional versatility. Cytotoxin-1 (UniProt ID: P01467), isolated from Naja mossambica mossambica, showed the potential to inhibit chymotrypsin and the chymotryptic activity of the 20S proteasome. In the present work we describe a molecular model of cytotoxin-1 in complex with chymotrypsin, prepared by the online server ClusPro. Analysis of the molecular model shows that Cytotoxin-1 (P01467) binds to chymotrypsin through its loop I located near the N-terminus. The concave side of loop I of the toxin fits well in the substrate binding pocket of the protease. We propose Phe10 as the dedicated P1 site of the ligand. Being a potent inhibitor of the 20S proteasome, cytotoxin-1 (P01467) can serve as a potential antitumor agent. Already snake venom cytotoxins have been investigated for their ability as an anticancer agent. The molecular model of cytotoxin-1 in complex with chymotrypsin provides important information towards understanding the complex formation.

Impact of viral activators and epigenetic regulators on HIV-1 LTRs containing naturally occurring single nucleotide polymorphisms.

Following human immunodeficiency virus type 1 (HIV-1) integration into host cell DNA, the viral promoter can become transcriptionally silent in the absence of appropriate signals and factors. HIV-1 gene expression is dependent on regulatory elements contained within the long terminal repeat (LTR) that drive the synthesis of viral RNAs and proteins through interaction with multiple host and viral factors. Previous studies identified single nucleotide polymorphisms (SNPs) within CCAAT/enhancer binding protein (C/EBP) site I and Sp site III (3T, C-to-T change at position 3, and 5T, C-to-T change at position 5 of the binding site, respectively, when compared to the consensus B sequence) that are low affinity binding sites and correlate with more advanced stages of HIV-1 disease. Stably transfected cell lines containing the wild type, 3T, 5T, and 3T5T LTRs were developed utilizing bone marrow progenitor, T, and monocytic cell lines to explore the LTR phenotypes associated with these genotypic changes from an integrated chromatin-based microenvironment. Results suggest that in nonexpressing cell clones LTR-driven gene expression occurs in a SNP-specific manner in response to LTR activation or treatment with trichostatin A treatment, indicating a possible cell type and SNP-specific mechanism behind the epigenetic control of LTR activation.

Fused-ring structure of decahydroisoquinolin as a novel scaffold for SARS 3CL protease inhibitors

The design and evaluation of a novel decahydroisoquinolin scaffold as an inhibitor for severe acute respiratory syndrome (SARS) chymotrypsin-like protease (3CLpro) are described. Focusing on hydrophobic interactions at the S2 site, the decahydroisoquinolin scaffold was designed by connecting the P2 site cyclohexyl group of the substrate-based inhibitor to the main-chain at the α-nitrogen atom of the P2 position via a methylene linker. Starting from a cyclohexene enantiomer obtained by salt resolution, trans-decahydroisoquinolin derivatives were synthesized. All decahydroisoquinolin inhibitors synthesized showed moderate but clear inhibitory activities for SARS 3CLpro, which confirmed the fused ring structure of the decahydroisoquinolin functions as a novel scaffold for SARS 3CLpro inhibitor. X-ray crystallographic analyses of the SARS 3CLpro in a complex with the decahydroisoquinolin inhibitor revealed the expected interactions at the S1 and S2 sites, as well as additional interactions at the N-substituent of the inhibitor.

Economic weights for performance and survival traits of growing pigs.

The objective of this paper was to derive economic weights for performance and survival traits of growing pigs including feed conversion ratio (FCR), daily feed intake (DFI), ADG, postweaning survival of the growing pig (SG), and carcass fat depth at the P2 site (CFD). An independent model was developed for each trait to derive economic values directly based on a typical Australian production system. This flexible approach may be used to customize economic values for different production systems and alternative trait combinations in breeding objectives. Discounted genetic expressions were used as a means of taking into account differences in frequency and timing of expression of traits to obtain economic weights. Economic values for SG were derived based on a cost-saving and a lost-revenue approach. The correct formulation of the economic value of ADG depends on how feed cost is included in the breeding objective. If FCR is defined as a breeding objective trait, then savings in feed costs through earlier slaughter should not be counted in the economic value of ADG. In contrast, if DFI is included in the breeding objective instead of FCR, then feed-cost savings through earlier slaughter need to be attributed to the economic value for ADG, as a benefit from faster ADG. The paper also demonstrates that economic weightings in indexes for FCR can potentially be overestimated by 70% when it is assumed that DFI or FCR records taken from a limited duration test period reflect the corresponding trait over the full lifetime of the growing pig destined for slaughter. Postweaning survival of the growing pig was the most important breeding objective trait of growing pigs. The relative importance of each breeding objective trait in a sire-line index based on the genetic SD of each trait was 44.5, 27.0, 17.4, and 11.1% for SG, FCR, ADG, and CFD, respectively. Further studies to better clarify the extent of genetic variation that exists in SG under nucleus-farm and commercial-farm conditions are warranted, given the high economic importance of this survival trait of growing pigs.

Anisotropic covalency contributions to superexchange pathways in type one copper active sites.

Type one (T1) Cu sites deliver electrons to catalytic Cu active sites: the mononuclear type two (T2) Cu site in nitrite reductases (NiRs) and the trinuclear Cu cluster in the multicopper oxidases (MCOs). The T1 Cu and the remote catalytic sites are connected via a Cys-His intramolecular electron-transfer (ET) bridge, which contains two potential ET pathways: P1 through the protein backbone and P2 through the H-bond between the Cys and the His. The high covalency of the T1 Cu–S(Cys) bond is shown here to activate the T1 Cu site for hole superexchange via occupied valence orbitals of the bridge. This covalency-activated electronic coupling (HDA) facilitates long-range ET through both pathways. These pathways can be selectively activated depending on the geometric and electronic structure of the T1 Cu site and thus the anisotropic covalency of the T1 Cu–S(Cys) bond. In NiRs, blue (π-type) T1 sites utilize P1 and green (σ-type) T1 sites utilize P2, with P2 being more efficient. Comparing the MCOs to NiRs, the second-sphere environment changes the conformation of the Cys-His pathway, which selectively activates HDA for superexchange by blue π sites for efficient turnover in catalysis. These studies show that a given protein bridge, here Cys-His, provides different superexchange pathways and electronic couplings depending on the anisotropic covalencies of the donor and acceptor metal sites.

Bioinformatic analyses of male and female Amblyomma americanum tick expressed serine protease inhibitors (serpins)

Serine protease inhibitors (serpins) are a diverse family of proteins that is conserved across taxa. The diversity of Amblyomma americanum serpins (AAS) is far more complex than previously thought as revealed by discovery of 57 and 33 AAS transcripts that are respectively expressed in male and female A. americanum ticks, with 30 found in both. While distinct reproductively, both male and female metastriate ticks, such as A. americanum, require a blood meal. Thus, 30 AAS sequences found in both male and female ticks could play important role(s) in regulating tick feeding and thus represent attractive candidates for anti-tick vaccine development. Of significant interest, 19 AAS sequences expressed in male and female ticks are also part of the 48 AAS sequences expressed in fed female tick salivary glands or midguts; two organs through which the tick interacts with host blood and immune response factors. Considered the most important domain for serpin function, the reactive center loop (RCL) is further characterized by a single ‘P1’ site amino acid residue, which is central to determining the protease regulated by the serpin. In this study, a diversity of 17 different P1 site amino acid residues were predicted, suggesting that A. americanum serpins potentially regulate a large number of proteolytic pathways. Our data also indicate that some serpins in this study could regulate target protease common to all tick species, in that more than 40% of AAS show 58–97% inter-species amino acid conservation. Of significance, 24% of AAS showed 62–100% inter-species conservation within the functional RCL domain, with 10 RCLs showing ≥90–100% conservation. In vertebrates, serpins with basic residues at the P1 site regulate key host defense pathways, which the tick must evade to feed successfully. Interestingly, we found that AAS sequences with basic or polar uncharged residues at the putative P1 site are more likely to be conserved across tick species. Another notable observation from our data is that AAS sequences found only in female ticks and those found in both males and females, but not those found only in male ticks, were highly conserved in other tick species. While descriptive, this study provides the basis for more in-depth studies exploring the roles of serpins in tick feeding physiology.

Using S-transform in EEG analysis for measuring an alert versus mental fatigue state.

This paper presents research that investigated the effects of mental fatigue on brain activity using electroencephalogram (EEG) signals. Since EEG signals are considered to be non-stationary, time-frequency analysis has frequently been used for analysis. The S-transform is a time-frequency analysis method and is used in this paper to analyze EEG signals during alert and fatigue states during a driving simulator task. Repeated-measure MANOVA results show significant differences between alert and fatigue states within the alpha (8-13Hz) frequency band. The two sites demonstrating the greatest increases in alpha activity during fatigue were the Cz and P4 sites. The results show that S-transform analysis can be used to distinguish between alert and fatigue states in the EEG and also supports the use of the S-transform for EEG analysis.

The P2/P2′ sites affect the substrate cleavage of TNF-α converting enzyme (TACE)

Tumor necrosis factor-alpha converting enzyme (TACE) is a proteinase that releases over eighty soluble proteins from their membrane-bound forms, and it has long been an intriguing therapeutic target in auto-immune diseases, and recently, in cancers. However, a haunting question is how TACE recognizes its substrates. In this work, we applied computational and experimental methods to study the role of the P2 site and the P2′ site of the substrate peptide in the substrate cleavage of TACE. In the computational complex model, the sidechains of these residues do not form key interactions with TACE, but experimentally, the mutations at these two positions largely affect the peptide cleavage efficiency in the enzymatic assay. We then showed that the P2/P2′ sites could affect the efficiency of the conformation search for the correct peptide orientation, which in turn affects the substrate cleavage efficiency. Our result provides new information to the better understanding of the enzymatic mechanism of TACE, and could be useful in the design of novel TACE inhibitors.

Dissolved copper speciation in the Tasman Sea, SW Pacific Ocean

The speciation of copper (Cu) in seawater is dominated by organic complexation but the sources, distribution and nature of these natural organic ligands remain unclear. The spatial distribution and character of organic copper binding ligands at two sites in the Tasman Sea were investigated using competitive ligand exchange adsorptive cathodic stripping voltammetry, utilising salicylaldoxime as the competing ligand. The first station was located in the oligotrophic north Tasman Sea and was contrasted with a second, mesotrophic, station in the south of the region where sampling coincided with a coccolithophore bloom. The northern P1 site (0–3000m) was characterised by detection of a single, strong, class of ligand with a uniformly distributed conditional stability constant (log K′CuL=12.97±0.26). At the two shallowest depths of the southern P3 site (13 and 28m), two ligands were detected. A single, stronger, ligand was detected at all other depths for this site. Below 120m, conditional stability constants at the southern P3 site (0–3500m) were uniformly distributed (log K′CuL=13.32±0.21). At both stations, ligand concentrations usually exceeded the total dissolved Cu concentration and mirrored the bio-intermediate Cu profile at depth. Dissolved Cu was more than 99% complexed by organic ligands at all depths except one, when dissolved Cu concentration exceeds the dissolve ligand concentration. The variability in ligand concentrations was greatest in the top 0–50m at the northern P1 site and 0–80m at the southern site. Based on a combination of phototrophic cell counts and biomarker pigment concentrations, the source of organic Cu-binding ligands in the north Tasman Sea is thought to be from cyanobacterial production, namely Synechococcus spp which dominates in the region. The detection of two organic Cu binding ligand classes at the southern P3 station indicates a more complex Cu-binding ligand pool in the surface waters. At this site, the ligands are likely sourced from cyanobacteria and eukaryotes, namely coccolithophores. At the northern P1 station only, a relationship between the proportion of unbound ligand available and the dissolved oxygen concentration was obtained. Given the simpler ligand pool dynamics of the northern station relative to the south, this relationship may reveal that complexation of organic Cu-binding ligands is important to prevent or slow ligand degradation in the deep sea.

Functional properties of the HIV-1 long terminal repeat containing single-nucleotide polymorphisms in Sp site III and CCAAT/enhancer binding protein site I.

BackgroundHIV-1 gene expression is driven by the long terminal repeat (LTR), which contains many binding sites shown to interact with an array of host and viral factors. Selective pressures within the host as well as the low fidelity of reverse transcriptase lead to changes in the relative prevalence of genetic variants within the HIV-1 genome, including the LTR, resulting in viral quasispecies that can be differentially regulated and can potentially establish niches within specific cell types and tissues.MethodsUtilizing flow cytometry and electromobility shift assays, specific single-nucleotide sequence polymorphisms (SNPs) were shown to alter both the phenotype of LTR-driven transcription and reactivation. Additional studies also demonstrated differential loading of transcription factors to probes derived from the double-variant LTR as compared to probes from the wild type.ResultsThis study has identified specific SNPs within CCAAT/enhancer binding protein (C/EBP) site I and Sp site III (3 T, C-to-T change at position 3, and 5 T, C-to-T change at position 5 of the binding site, respectively) that alter LTR-driven gene transcription and may alter the course of viral latency and reactivation. The HIV-1 LAI LTRs containing the SNPs of interest were coupled to a plasmid encoding green fluorescent protein (GFP), and polyclonal HIV-1 LTR-GFP stable cell lines utilizing bone marrow progenitor, T, and monocytic cell lines were constructed and utilized to explore the LTR phenotype associated with these genotypic changes.ConclusionsAlthough the 3 T and 5 T SNPs have been shown to be low-affinity binding sites, the fact that they can still result in effective HIV-1 LTR-driven gene expression, particularly within the TF-1 cell line, has suggested that the low binding site affinities associated with the 3 T C/EBP site I and 5 T Sp site III are potentially compensated for by the interaction of nuclear factor-κB with its corresponding binding sites under selected physiological and cellular conditions. Additionally, tumor necrosis factor-α and Tat can enhance basal transcription of each SNP-specific HIV-1 LTR; however, differential regulation of the LTR is both SNP- and cell type-specific.

Gamma Power and Cognition in Patients with Schizophrenia and Their First-Degree Relatives

Background: Gamma oscillations are essential for functional neural assembly formation underlying higher cerebral functions. Previous studies concerning gamma band power in schizophrenia have yielded diverse results. Methods: In this study, we assessed gamma band power in minimally treated patients with schizophrenia, their first-degree relatives and healthy controls during an oddball paradigm performance, as well as the relation between gamma power and cognitive performance. Results: We found a higher gamma power in the patient group than in the healthy controls at the P3, P4, Fz, Pz and T5 sites. Compared with their relatives, gamma power in the patients was only marginally higher over P3 and P4. We found a nearly significant inverse association between gamma power at F4 and Tower of London performance in the patients, as well as a significant inverse association between gamma power at T5 and verbal memory and working memory scores in the relatives. Conclusion: These results support higher total gamma power in association with schizophrenia and its inverse association with cognitive performance in patients and their first-degree relatives.

Key Binding and Susceptibility of NS3/4A Serine Protease Inhibitors against Hepatitis C Virus

Hepatitis C virus (HCV) causes an infectious disease that manifests itself as liver inflammation, cirrhosis, and can lead to the development of liver cancer. Its NS3/4A serine protease is a potent target for drug design and development since it is responsible for cleavage of the scissile peptide bonds in the polyprotein important for the HCV life cycle. Herein, the ligand-target interactions and the binding free energy of the four current NS3/4A inhibitors (boceprevir, telaprevir, danoprevir, and BI201335) were investigated by all-atom molecular dynamics simulations with three different initial atomic velocities. The per-residue free energy decomposition suggests that the key residues involved in inhibitor binding were residues 41-43, 57, 81, 136-139, 155-159, and 168 in the NS3 domain. The van der Waals interactions yielded the main driving force for inhibitor binding at the protease active site for the cleavage reaction. In addition, the highest number of hydrogen bonds was formed at the reactive P1 site of the four studied inhibitors. Although the hydrogen bond patterns of these inhibitors were different, their P3 site was most likely to be recognized by the A157 backbone. Both molecular mechanic (MM)/Poisson-Boltzmann surface area and MM/generalized Born surface area approaches predicted the relative binding affinities of the four inhibitors in a somewhat similar trend to their experimentally derived biological activities.

Seasonal variability of basic pollution parameters in atmospheric precipitation in Strzelin

Abstract Electrical conductivity and pH are the basic indices of rainfall pollution, constituting the basis for evaluation of the general nature of rainwater. This article presents an analysis of these two parameters in samples of rainfall collected in the years 2008-2010 (in the heating season and outside it) in three measurement sites P1, P2 and P3, located in the city and commune Strzelin (Lower Silesian Voivodeship). Preliminary results show a high variation of pH and electrical conductivity of rainfall occurring in the analysed area. Approximately 30% of the samples were characterised by a pH that allowed to qualify them, according to JANSEN et al. [1988], as normal rainfall. A similar share in all the collected samples represented rainfall of pH &lt; 5.1 that was classified as slightly, considerably and highly acidic. The problem of acid rain occurred in the analysed area mainly during the heating season, when rainfall of pH &lt; 5.1 accounted for a considerable share in all rainfall samples collected in the said period. The electrical conductivity of most samples fell below 60 μS·cm-1, which allowed us to classify them as slightly polluted rainfall (site P2), considerably polluted (site P3) and highly polluted (site P1).