Top PDF The isoelectric region of proteins: a systematic analysis.

The isoelectric region of proteins: a systematic analysis.

The isoelectric region of proteins: a systematic analysis.

Ion exchange chromatography (IEC) is a widely applied method in protein purification. It is well established, efficient, and applicable to large scale purification [1,2]. Protein binding in IEC is primarily determined by electrostatic interactions between the charge of the protein and the charged stationary phase [3,4,5]. As a consequence, optimal pH values for binding to or elution from an ion exchange column can be predicted by the isoelectric point (pI) for many proteins [6] with loading pHs about 0.5–1 pH units above or below the pI of the respective protein [7,8]. However, it has been shown that for some proteins the pI is not predictive, but binding to or elution from the column only occurs for pH values far from the pI of the protein [6,9]. A detailed investigation of pH values at which bound proteins eluted from an anion exchange chromatography column were performed using a pH gradient as the method of elution. It demonstrated that for proteins with pI values between 6 and 8, the elution occurred at pH values considerably higher than their pI. Proteins with a pI lower than 6 or higher than 8 however eluted at pH values close to their pI [6]. The unique behaviour of proteins with a pI between 6 and 8 was explained by the observation that their titration curves had a broad region of almost zero charge near their pI which extended over several pH units [6]. In this work, we term this region the isoelectric region (IER). A large IER has also been shown to influence the binding of proteins to ion exchange columns which has been demonstrated for the lipase B from Candida antarctica [9]. The purification of this protein by ion exchange chromatography had not been achieved before. Only by
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Systematic analysis and prediction of pupylation sites in prokaryotic proteins.

Systematic analysis and prediction of pupylation sites in prokaryotic proteins.

This investigation focuses on the analysis of ubiquitin-like protein conjugated lysine in prokaryotes. In ubiquitin-like protein conjugation, the region of the ubiquitin-like protein conjugated lysine residues is in directly contact with the proteasome accessory factor A (PafA) catalytic center [18,19]. Since PafA has a substrate binding specificity, whether the region of ubiquitin-like protein conjugated lysine conservative amino acid motifs for PafA recognition must be explored. After the duplicated sequences of experimental pupylation sites were removed, as shown in Figure S1, a web-based tool TwoSampleLogo [20] was adapted to generate the graphical sequence logo (P,0.01; t-test) that detects and displays statistically significant differences in position-specific symbol compositions between two sets of multiple sequence alignments. One interesting feature is the absence of additional lysines at positions that are immediately adjacent to the pupylation site. For example, lysines are depleted at positions 22 and 2 (see Figure S1). This suggests that pupylation sites do not have a tendency to cluster, perhaps due to the structural constrains that would prevent simultaneous attachment of two or more bulky ubiquitin-like protein molecules in close proximity to each other on the same substrate. Another interesting feature is the upstream and adjacent amino acid residues in pupylated sites, which may be close to pupylated lysine residues in three-dimensional structure, have notable difference between pupylation sites and non- pupylation sites.
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A DIseAse MOdule Detection (DIAMOnD) algorithm derived from a systematic analysis of connectivity patterns of disease proteins in the human interactome.

A DIseAse MOdule Detection (DIAMOnD) algorithm derived from a systematic analysis of connectivity patterns of disease proteins in the human interactome.

Taken together, these results show that disease proteins exhibit distinct interaction patterns among each other that suggest the existence of specific disease modules within the Interactome. Yet, these modules apparently do not coincide with topological communities of densely inter- connected proteins. In principle, this discrepancy could be either a mere consequence of in- complete Interactome and gene-disease association data [5,10,26], or reflect an inherent fundamental difference between disease and topological modules. To investigate this question, we compared the behavior of the two relevant measures, local modularity and connectivity sig- nificance, for different levels of completeness of the underlying network. Fig. 1I shows that the connectivity significance of disease genes slowly drops as more and more links are removed. Conversely, this trend indicates that the predictive power of the connectivity significance should continuously increase as the Interactome becomes more and more complete. For the local modularity measure, however, we see a very different behavior. Fig. 1J shows that the modularity remains roughly constant as the network completeness decreases or even slightly increases, similar to the behavior observed for random expectation. The reason for this some- what unintuitive behavior is that random removal affects links between disease proteins to the same extent as links to other proteins, thereby leaving their relative relationship, on average, unchanged (Fig. 1K). We therefore expect that with increasing network completeness, the local modularity among disease proteins will not significantly increase. These results suggest that to- pological communities are not able to significantly capture disease proteins, regardless of the level of network completeness. Connectivity significance, on the other hand, captures the inter- action patterns between disease proteins more and more distinctively as the network ap- proaches the complete network.
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Chitinases as Antibacterial Proteins: A Systematic Review

Chitinases as Antibacterial Proteins: A Systematic Review

the purification of Hypotin, a protein from peanut (Arachis hypogaea) seeds which showed antifungal activity towards a variety of fungi species as well as antibacterial activity towards Staphylococcus aureus. The clas- sification of Hypotin as a chitinase was based on the similarity of its N-terminal amino acid sequence with already known plant chitinases. However, those authors did not show any experimental evidence on the ability of Hypotin to degrade chitin or chitin derivatives, and their work was not included in our analysis.
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Accessible surfaces of beta proteins increase with increasing protein molecular mass more rapidly than those of other proteins.

Accessible surfaces of beta proteins increase with increasing protein molecular mass more rapidly than those of other proteins.

Here we present a systematic analysis of accessible surface areas and hydrogen bonds of 2554 globular proteins from four structural classes (all-a, all-b, a/b and a+b proteins) that is aimed to learn in which structural class the accessible surface area increases with increasing protein molecular mass more rapidly than in other classes, and what structural peculiarities are responsible for this effect. The beta structural class of proteins was found to be the leader, with the following possible explanations of this fact. First, in beta structural proteins, the fraction of residues not included in the regular secondary structure is the largest, and second, the accessible surface area of packaged elements of the beta-structure increases more rapidly with increasing molecular mass in comparison with the alpha-structure. Moreover, in the beta structure, the probability of formation of backbone hydrogen bonds is higher than that in the alpha helix for all residues of a+b proteins (the average probability is 0.7360.01 for the beta-structure and 0.6060.01 for the alpha-structure without proline) and a/b proteins, except for asparagine, aspartic acid, glycine, threonine, and serine (0.7060.01 for the beta-structure and 0.6060.01 for the alpha-structure without the proline residue). There is a linear relationship between the number of hydrogen bonds and the number of amino acid residues in the protein (Number of hydrogen bonds~0:678:number of residues{3:350).
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Genome analysis and phylogenetic relatedness of Gallibacterium anatis strains from poultry.

Genome analysis and phylogenetic relatedness of Gallibacterium anatis strains from poultry.

Clustered regularly interspaced short palindromic repeats (CRISPRs) are arrays or repeats common among bacteria and archaeae that provide protection against foreign DNA [34]. These loci are identified by their possession of cas gene clusters, and the presence of non-contiguous direct repeats separated by variable spacer regions. Several CRISPR loci were identified within the three G. anatis genomes sequenced [35]. The first CRISPR locus was found between UMN179_2281 and UMN179_2300 and was present in UMN179 and 12656-12 on GI44 (Table 3). This region contained the genes csm1-csm2-csm3-csm4-csm5-cas6-csx16-csm6- csx1-cas2-cas1-cas2, with 31 direct repeats in UMN179 and 15 direct repeats in 12656-12. A second CRISPR locus was identified between UMN179_2337 and UMN179_2343 and was present in all three genomes. This locus contained cas3-cys4-cys3-cys2-cys1 and had 8 direct repeats in UMN179, and 7 direct repeats each in F149 T and 12656-12. A third locus was present in strains F149 T and 12656-12, but absent in UMN179, situated between UMN179_173 and UMN179_174. This region contained cas3- cas5-csd1-csd2-cas4-cas1-cas2 and had 6 direct repeats in 12656-12 and 48 direct repeats in F149 T . None of the spacers within any of the three strains shared significant nucleotide similarity with spacers of other strains. Similarly, none of the three CRISPR loci Figure 5. Inferred phylogeny of the TopB proteins of integrative conjugative elements (ICEs) of UMN179, F149, and 12656-12 and similar ICEs in the NCBI database. Data was analyzed using the Maximum Likelihood method based on the JTT matrix-based model conducted in MEGA5. There were a total of 596 positions in the final dataset and 500 bootstrap replicates were included.
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Synthesis Of Arts In Architecture Of Uzbekistan Of The Ancient Period

Synthesis Of Arts In Architecture Of Uzbekistan Of The Ancient Period

the walls of buildings. It could be decorative niches (of spiral form in the Hall of Warriors), small rectangular "shelves" (in the Hall of Victories), rectangular niches with arched ends (Surkh-Kotal), arches of different contour (semicircular ones or pointed upwards). "An arch as a compositional basis for the image of Buddha was known in stone sculpture of Buddhist monuments in Northern Bactria [31, 597p]. For example, in Square Hall at Old Nisa (III-II centuries BC) the statues were placed on the top tier in intercolumniation Corinthian order, in special niches in one interval. In Buddhist sanctuary DT-1the wall sculpture in the "Hall of Kings" and joss-houses were placed over the socle of the stupa, in the temple of Ai-Khanum - on sufa, bending round the cella, in Ayrtam - on capital-like block, in the sanctuary of Dt-9 - on a low sufa "at the level of viewing by those who comes to worship [14, 214p]. In the monastery complex in Karatepa an arrangement of niche, which was previously the location of a statue of seated Buddha, was not accidental: "It seemed to be directing the attention of those who enter the monastery to the face of "Great teacher."Stone sculpture in ground monastery of Fayaztepa was a high relief with the image of Buddha surrounded by 2 monks arranged into keeled arch [32]. In Khoresm, in the Hall of Kings, a special boxes were designed for the sculptures (23-24) at a height of 1.1 meters, separated by partitions, "the very architecture of the Hall of the Kings was largely subordinated to the necessity to position the sacred statue" [33, 120p]. In Toprak-Kala, in the "Hall of Dancing Masks", in addition to the three major niches in the walls of the room there were found smaller niches
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Investigating The Use Of Mobile Computing In Zimbabwe Polytechnics Case Of A Polytechnic In Zimbabwe

Investigating The Use Of Mobile Computing In Zimbabwe Polytechnics Case Of A Polytechnic In Zimbabwe

outside staff and lecture rooms, send and receive emails and communicate on social networks. This Polytechnic in particular, was one of the first institutions to install the wireless access points that accessed internet through the main fibre backbone. In 2009 it went on to procure laptops for staff members, starting with senior management, the Heads of departments and finally lectures. Students were then allowed to bring their own devices which could be configured to be able to access institutional WIFI (The Polytechnic ICT policy document, 2010). This was the beginning of mobile computing at the Polytechnic. Since then further strides were made in such areas as installation of applications that run on mobile devices through wireless connections, increasing internet bandwidth to improve speed as demand for internet went up, upgrading wireless access points to improve strength of connectivity, upgrading of servers to handle the demand and volumes and expansion of campus area network to cover the whole Polytechnic, procurement of more mobile devices. And the institution now boasts of such things as e-learning, m- learning, m-education, among other technologies that are giving it a competitive advantage over sister Polytechnics.
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Model of knowledge representation about materials in the form of a relational database for CAPCAST system

Model of knowledge representation about materials in the form of a relational database for CAPCAST system

Checking the dependency of attributes is done to omit the un- necessary attributes, the step which can be of crucial importance in optimising the decision-making process. A smaller number of attributes means less of a dialogue with the user and quicker search of the rule base looking for adequate procedure of reason- ing. In the case of decision tables that contain very large sets of redundant attributes (created during the operations associated with data mining), the possibilities of reduction can become critical elements in building of a knowledge base. A totally different situation occurs when the decision table is created by knowledge engineers in a controlled manner, based on e.g. literature, expert knowledge, and/or standards, when the set of attributes is authori- tatively created basing on the available knowledge about the phenomena. In this case, the reduction of attributes is not neces- sary, as it can be assumed that the number of unnecessary attributes (if any) shall not deteriorate the model classificability.
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Unique proteomic signatures distinguish macrophages and dendritic cells.

Unique proteomic signatures distinguish macrophages and dendritic cells.

Figure 1. The plasma membrane proteome of macrophages. Panel A: Bone marrow-derived macrophages (BmM) were derived from bone marrow precursor cells of C57BL/6 mice cultured with M-CSF. Classically activated macrophages (M1) and alternatively activated macrophages (M2) were derived from BmMs by treatment with IFN-c and LPS or with IL-4. Panel B: qRT-PCR of markers used to detect M1 and M2 macrophages. Results (means and SEMs, N = 6) were standardized to 18S, expressed relative to the cell type with the highest expression of each gene, and are representative of 3 independent analyses. Panel C: LC-ESI-MS/MS analysis of plasma membrane proteins isolated from differentially activated macrophages. Proteins were quantified by spectral counting (total number of peptides identified for a given protein) and subjected to sequential criteria to identify 192 plasma membrane proteins that were reproducibly detected with high confidence. Panel D: Quantification of the membrane proteomes of M1 and M2 macrophages. Differentially expressed proteins (red, upregulated; green, downregulated; gray, not significantly different) were identified based on t-test and G-test statistics. Significance cutoffs (dashed lines; p,0.05 and G-statistic .1.5 or ,21.5) were determined based on permutation analysis (estimated FDR,5%). Panel E: Quantification of the membrane proteomes of M1 macrophages and BmMs. Proteins differentially expressed by M1 cells relative to both BmMs and M2 cells are indicated with colored dots (red, upregulated; green, downregulated). Proteins differentially expressed by M1 and M2 cells (Panel D) but not differentially expressed by M1 and BmMs are indicated by gray dots. Panel F: Examples of proteins that distinguish M1 cells from both BmM and M2 cells (CSF1R, ITGAL). Results (N = 6 per group) are means and SDs. Panel G: Examples of proteins that fail to distinguish M1 cells from both BmM and M2 cells (CD14, ITGAV). Panel H: Plasma membrane proteins differentially expressed by M1 cells (36 proteins), M2 cells (35 proteins), and BmMs (17 proteins).
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Joint Analysis of the Discount Factor and Payoff Parameters in Dynamic Discrete Choice Games

Joint Analysis of the Discount Factor and Payoff Parameters in Dynamic Discrete Choice Games

criterion makes full information on the underlying parameter on the empirical model and has impli- cations for all two-step estimation methods that wish to estimate the discount factor. One can of course argue that analogous analysis can be performed with other loss functions. However, without pro…ling, an exhaustive search with other loss functions, e.g. those based on the choice probabilities (e.g. maximum likelihood, moments or asymptotic least squares) may not be feasible. Especially when there are many payo¤ parameters, it may not be trivial to locate the global minimizer even for a single candidate value of the discount factor. We also provide conditions when switching costs can be identi…ed in closed-form under independently of the discount factor and speci…cation of other payo¤ components (linear or otherwise). The latter gives a closed-form estimator for the switching costs that can be used for speci…cation testing, which for example can use to test for the mode of competition between …rms. We illustrate the scope of its applications in a Monte Carlo study and an empirical game using real data.
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The modification process of AlSi21CuNi silumin and its effect on change of mechanical properties of the alloy

The modification process of AlSi21CuNi silumin and its effect on change of mechanical properties of the alloy

Pouring temperature belongs to very important factors in obtainment of correct results of the modification. Hypereutectoid silumins are characteristic of good castability even in temperatures close to liquidus curve, what suggests implementation of low temperature of casting. However, such method of casting creates conditions to easy coarsening of primary crystals of silicon and their non-uniform distribution on microstructure of the casting. Rate of cooling of the alloy poured into mould has also an effect on results of the modification.
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The comparison of the structure and microhardness of the tool steel C90 and HS 6-5-2 remelted with the electric arc

The comparison of the structure and microhardness of the tool steel C90 and HS 6-5-2 remelted with the electric arc

The samples were remelted on the surface with the electric arc with the use of the FALTIG 315AC/DC apparatus. The single remelting was applied. The treatment parameters were used: amperage of the electric arc I = 100 A, speed of the electrode movement v=200 mm/min. As the plasma formative gas, the argon was used. The treatment has been conducted at the depart- ment of Foundry and Welding of Rzeszow University of Tech- nology. After the remelting, there has been the conventional tempering done 1x1 hour in a temperature of 200°C for the steel C90 and 2x2 hours in the temperature of 560 °C for the steel HS 6- 5-2. Parameters of tempering (temperature, time and multiplicity) of the tested steels were selected according to the standard PN-EN ISO 4957:2002U. The microhardeness measurements were made with the Hanemanna objective mph 100. The load used was 0,064 N, the operating time of the load was 10 s. Metallographic tests were conducted on the optical microscope - Neophot 2 and Tesla BS-340 electronic scanning microscope.
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Analysis of Structure and Abrasion Resistance of the Metal Composite Based on an Intermetallic FeAl Phase with VC and TiC Precipitates

Analysis of Structure and Abrasion Resistance of the Metal Composite Based on an Intermetallic FeAl Phase with VC and TiC Precipitates

Intermetals are creep-resistant materials with unique properties intermediate between the properties of metals and ceramics. Their low density, high strength and resistance to oxidation, combined with sufficient ductility and fracture toughness, make them an attractive material for machine elements operating at elevated temperatures and in corrosive environments. Intermetallic phases based on Fe and Al (called intermetallics) are intermetallic compounds very interesting in terms of the technological properties, which combine the properties of metals and ceramics. From the Fe-Al phase equilibrium diagram it follows that the widest use could have two phases: FeAl and Fe 3 Al. Of these two phases, more useful seems be the FeAl
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An analysis of the region of the Phocaea dynamical family

An analysis of the region of the Phocaea dynamical family

At the end of this preliminary analysis of the Phocaea family region there is a general vision of the origin and evolution of aster- oids in the region that is starting taking shape. While it is certain that the Phocaea group is indeed in a stable island surrounded by very unstable dynamical regions (Kneˇzevi´c & Milani 2003), the fact that most of the S-type objects are associated with the dynamical Phocaea families seems to suggest that the Phocaea cluster should indeed be a real collisional family. No local background was iden- tified in the cumulative H distribution, and it seems that the region, apart from a few large C-type objects, is dominated by the Phocaea family. This may suggest that very few bodies reached the highly inclined region studied here and, of those, one, the parent body of the Phocaea family, was targeted in the collision that created the family possibly up to 2.2 Byr ago. Values of collision probabilities suggest that the impactor may have come from the low i inner main
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Assessment Of Some Acceleration Schemes In The Solution Of Systems Of Linear Equations.

Assessment Of Some Acceleration Schemes In The Solution Of Systems Of Linear Equations.

The results of the numerical experiments are presented in Tables 1 to 12. From Table 1 all the methods (the stationary methods, the accelerated schemes and the Krylov subspace acceleration methods) converged for the system considered. The Accelerated gradient scheme (AGS) converged faster than all the other methods (after just one or two iterations). The minimum and maximum optimal relaxation parameters for the stationary and acceleration schemes were 1.01 and 1.25 respectively. The number of iterations for both the acceleration schemes and Krylov subspace acceleration methods reduced drastically with the exception of that of Richardson with the stationary iterative methods. The speed indicates fast converges of the method even though it is relative, depending on the type of computer used. Each method has small relative residual which show that the approximation to the solution is stable and accurate.
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Nanoscale roughness and morphology affect the IsoElectric Point of titania surfaces.

Nanoscale roughness and morphology affect the IsoElectric Point of titania surfaces.

length, surface roughness, asperity separation…) influences the relative strength of different contributions to the interaction energy (van der Waals, electrostatic, Lewis acid-base acidity…). Duval et al. have explicitly included in their calculation of interfacial electrostatic interactions the charging mechanisms of the surfaces, developing a theoretical/numerical framework to account for local morpholog- ical (though calculations are implemented only for LEGO-like corrugated interfaces) as well as chemical heterogeneities of the surfaces. Their model takes into account the fine structure of the electrostatic double layer and boundary conditions beyond the limits of the linearized PB equations, allowing therefore to account for spatially-resolved charge regulation mechanisms and surface roughness effects [40]. Daikhin et al. have considered a statistical representation of surface morphology (in terms of height distributions) rather than on simplified geometrical constructions [41,42,43]; yet, their focus is limited to the calculation of some measurable electrochemical observables, typically the double layer capacitance. None of the works discussed so far present explicit calculations of the interaction force between rough surfaces in electrolyte solutions, and for this reason a direct application of theories for the analysis of experimental data acquired at complex rough interfaces is not straightforward.
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Modeling and Analysis of Queuing Systems in Banks A case study of Ghana Commercial Bank Ltd. Kumasi Main Branch

Modeling and Analysis of Queuing Systems in Banks A case study of Ghana Commercial Bank Ltd. Kumasi Main Branch

Data for this study was collected from the banking hall of Ghana Commercial Bank (GCB) Ltd. Kumasi Main Branch. The methods used during the data collection were direct observation and personal interview and questionnaire administering. The data gathered were the daily record of queuing system over a month. The variables measured included arrival and service rate per hour. They were analyzed for simultaneous efficiency in customer satisfaction and economic cost minimization through the use of a multi-channel single-line queuing model, which were compared for a number of queue performances such as; the average number of customers in the queue and in the system, average time each customer spends in the queue and in the system and the probability of the system being idle. The following assumptions were made for modeling the queuing system at Ghana Commercial Bank (GCB) Ltd. Kumasi Main Branch.
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Analysis of proteins from marine molluscs

Analysis of proteins from marine molluscs

Marine molluscs, particularly mussels, oysters, and clams, have been used worldwide as bioindicators to assess the impact of pol- lutants in coastal marine ecosystems and their health status. More recently, the discovery in 1997 of large mussel beds in deep sea hydrothermal vents (1) , particularly in the Mid-Atlantic Ridge, has attracted much scientific attention due to their capacity to live in one of the most extreme environments on earth characterized by high temperature and pressure, low pH, enriched in toxic sul- phide species (2) , radionuclides, and naturally high bioavailable metal concentrations that would be toxic or even lethal to coastal marine species (3, 4) . Therefore these species have been consid- ered as models to assess pollution effects in natural contaminated environments (5) .
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Rev. Bras. Anestesiol.  vol.64 número5

Rev. Bras. Anestesiol. vol.64 número5

The article entitled ‘‘Comparison between continuous tho- racic epidural and paravertebral blocks for postoperative analgesia in patients undergoing thoracotomy: systematic review’’, recently published in the Journal Revista Brasileira de Anestesiologia, brings out the authors’ concern to show the anesthetic therapy effectiveness for treating postopera- tive pain in chest surgery. 1

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