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Of Proteins (of + protein)
Kinds of Of Proteins Selected AbstractsNew angle-dependent potential energy function for backbone,backbone hydrogen bond in protein,protein interactionsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 5 2010Hwanho Choi Abstract Backbone,backbone hydrogen bonds (BBHBs) are one of the most abundant interactions at the interface of protein,protein complex. Here, we propose an angle-dependent potential energy function for BBHB based on density functional theory (DFT) calculations and the operation of a genetic algorithm to find the optimal parameters in the potential energy function. The angular part of the energy funtion is assumed to be the product of the power series of sine and cosine functions with respect to the two angles associated with BBHB. Two radial functions are taken into account in this study: Morse and Leonard-Jones 12-10 potential functions. Of these two functions under consideration, the former is found to be more accurate than the latter in terms of predicting the binding energies obtained from DFT calculations. The new HB potential function also compares well with the knowledge-based potential derived by applying Boltzmann statistics for a variety of protein,protein complexes in protein data bank. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Bovine Serum Albumin and Lysozyme Adsorption on Calcium Phosphate ParticlesADVANCED ENGINEERING MATERIALS, Issue 1-2 2010Berit Mueller Two model proteins that are oppositely charged at neutral pH , bovine serum albumin (BSA) and lysozyme, with acidic and alkaline isoelectric points, respectively , are used to investigate the protein adsorption behaviour of hydroxyapatite and beta-tricalcium phosphate (, -TCP) particles. Both calcium phosphate based particles are highly relevant for the fabrication of bioactive and resorbable bone implants. The investigations are carried out by combining zeta potential and Vis spectroscopy measurements. The changes of zeta potential and isoelectric point are determined as a function of added protein. Both proteins form a monolayer on , -TCP, while on hydroxyapatite only semi-monolayers were measured. For BSA, a side-on adsorption mode is suggested, whereas end-on adsorption appears to be most likely for lysozyme. The zeta potential curves as a function of adsorbed protein show that plateaus of the protein amounts adsorbed increase with charge saturation. In addition, the spatial charge distribution of both proteins is modelled to get a further understanding of the initial adsorption orientation of the biomolecules, supporting the findings from the experimental data. The reported findings can be transferred to the adsorption behaviour of a variety of proteins on calcium phosphate surfaces and are helpful for the fabrication of bone-analogous calcium phosphate/protein nanocomposites. [source] Changes in chromatin structure and methylation of the human interleukin-1, gene during monopoiesisIMMUNOLOGY, Issue 3 2010Inga Wessels Summary Interleukin-1, (IL-1,) induces the expression of a variety of proteins responsible for acute inflammation and chronic inflammatory diseases. However, the molecular regulation of IL-1, expression in myeloid differentiation has not been elucidated. In this study the chromatin structure of the IL-1, promoter and the impact of methylation on IL-1, expression in monocytic development were examined. The results revealed that the IL-1, promoter was inaccessible in undifferentiated promyeloid HL-60 cells but highly accessible in differentiated monocytic cells which additionally acquired the ability to produce IL-1,. Accessibilities of differentiated cells were comparable to those of primary monocytes. Lipopolysaccharide (LPS) stimulation did not affect promoter accessibility in promyeloid and monocytic HL-60 cells, demonstrating that the chromatin remodelling of the IL-1, promoter depends on differentiation and not on the transcriptional status of the cell. Demethylation via 5-aza-2,-deoxycytodine led to the induction of IL-1, expression in undifferentiated and differentiated cells, which could be increased after LPS stimulation. Our data indicate that the IL-1, promoter is reorganized into an open poised conformation during monopoiesis being a privilege of mature monocytes but not of the entire myeloid lineage. As a second mechanism, IL-1, expression is regulated by methylation acting independently of the developmental stage of myeloid cells. [source] Signaling mechanisms that regulate actin-based motility processes in the nervous systemJOURNAL OF NEUROCHEMISTRY, Issue 3 2002Gary Meyer Abstract Actin-based motility is critical for nervous system development. Both the migration of neurons and the extension of neurites require organized actin polymerization to push the cell membrane forward. Numerous extracellular stimulants of motility and axon guidance cues regulate actin-based motility through the rho GTPases (rho, rac, and cdc42). The rho GTPases reorganize the actin cytoskeleton, leading to stress fiber, filopodium, or lamellipodium formation. The activity of the rho GTPases is regulated by a variety of proteins that either stimulate GTP uptake (activation) or hydrolysis (inactivation). These proteins potentially link extracellular signals to the activation state of rho GTPases. Effectors downstream of the rho GTPases that directly influence actin polymerization have been identified and are involved in neurite development. The Arp2/3 complex nucleates the formation of new actin branches that extend the membrane forward. Ena/VASP proteins can cause the formation of longer actin filaments, characteristic of growth cone actin morphology, by preventing the capping of barbed ends. Actin-depolymerizing factor (ADF)/cofilin depolymerizes and severs actin branches in older parts of the actin meshwork, freeing monomers to be re-incorporated into actively growing filaments. The signaling mechanisms by which extracellular cues that guide axons to their targets lead to direct effects on actin filament dynamics are becoming better understood. [source] The red-ox status of a penicillin-binding protein is an on/off switch for spore peptidoglycan synthesis in Bacillus subtilisMOLECULAR MICROBIOLOGY, Issue 1 2010Patrick Eichenberger Summary Thiol-disulphide oxidoreductases catalyse the formation or breakage of disulphide bonds to control the red-ox status of a variety of proteins. Their activity is compartmentalized, as exemplified by the distinct roles these enzymes play in the cytoplasm and periplasm of Gram-negative bacteria. In this issue of Molecular Microbiology, an article from Lars Hederstedt and collaborators at Lund University sheds light on another member of this superfamily of proteins, the thioredoxin-like protein StoA from Bacillus subtilis. Interestingly, StoA function is required in yet another subcellular compartment: the intermembrane space that separates forespores from mother cells in endospore-forming bacteria. Specifically, this study demonstrates that the high-molecular-weight penicillin-binding protein SpoVD, which contains two exposed cysteine residues and whose extracellular domain is located in the intermembrane space, is a substrate of StoA. As formation of a disulphide bond most likely inactivates SpoVD activity, the converse breakage of that bond in a process catalysed by StoA appears to be the trigger that initiates peptidoglycan synthesis in sporulating cells. [source] Identification of protein differences between two clinical isolates of Streptococcus mutans by proteomic analysisMOLECULAR ORAL MICROBIOLOGY, Issue 2 2008L. H. Guo Introduction:,Streptococcus mutans is generally considered to be the principal etiological agent for dental caries. Different strains of S. mutans may display different virulence mechanisms, so the isolation of the differential proteins is illuminating. Methods:,S. mutans strains 9-1 and 9-2, which both colonized the same oral cavity, were selected after screening for the possession of suspected virulence traits. The soluble cellular proteins were extracted from steady-state planktonic cells of strains 9-1 and 9-2 and were analyzed using high-resolution two-dimensional gel electrophoresis. Then, replicate maps of proteins from the two strains were generated. Proteins expressed only in strain 9-1 or 9-2 were excised and digested with trypsin by using an in-gel protocol. Tryptic digests were analyzed using matrix-assisted laser desorption/ionization time of flight mass spectrometry, by which peptide mass fingerprints were generated, and these were used to assign putative functions according to their homology with the translated sequences in the S. mutans genomic database. Results:, There were 12 proteins only expressed in strain 9-1 and three proteins only expressed in strain 9-2. They were involved in protein biosynthesis, protein folding, cell wall biosynthesis, fatty acid biosynthesis, nucleotide biosynthesis, repair of DNA damage, carbohydrate metabolism, signal transduction, and translation. Conclusion:, The identification of proteins differentially expressed between strains 9-1 and 9-2 provides new information concerning the mechanisms of cariogenesis. [source] A charged residue at the subunit interface of PCNA promotes trimer formation by destabilizing alternate subunit interactionsACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2009Bret D. Freudenthal Eukaryotic proliferating cell nuclear antigen (PCNA) is an essential replication accessory factor that interacts with a variety of proteins involved in DNA replication and repair. Each monomer of PCNA has an N-terminal domain A and a C-terminal domain B. In the structure of the wild-type PCNA protein, domain A of one monomer interacts with domain B of a neighboring monomer to form a ring-shaped trimer. Glu113 is a conserved residue at the subunit interface in domain A. Two distinct X-ray crystal structures have been determined of a mutant form of PCNA with a substitution at this position (E113G) that has previously been studied because of its effect on translesion synthesis. The first structure was the expected ring-shaped trimer. The second structure was an unanticipated nontrimeric form of the protein. In this nontrimeric form, domain A of one PCNA monomer interacts with domain A of a neighboring monomer, while domain B of this monomer interacts with domain B of a different neighboring monomer. The B,B interface is stabilized by an antiparallel ,-sheet and appears to be structurally similar to the A,B interface observed in the trimeric form of PCNA. The A,A interface, in contrast, is primarily stabilized by hydrophobic interactions. Because the E113G substitution is located on this hydrophobic surface, the A,A interface should be less favorable in the case of the wild-type protein. This suggests that the side chain of Glu113 promotes trimer formation by destabilizing these possible alternate subunit interactions. [source] Probing protein colloidal behavior in membrane-based separation processes using spectrofluorometric Rayleigh scattering dataBIOTECHNOLOGY PROGRESS, Issue 3 2010Rand Elshereef Abstract One of the primary problems in membrane-based protein separation is membrane fouling. In this study we explored the feasibility of employing Rayleigh light scattering data from fluorescence studies combined with chemometric techniques to determine whether a correlation could be established with membrane fouling phenomena. Membrane flux was measured in a dead-end UF filtration system and the effect of protein solution properties on the flux decline was systematically investigated. A variety of proteins were used as a test case in this study. In parallel, the colloidal behavior of the protein solutions was assessed by employing multiwavelength Rayleigh scattering measurements. To assess the usefulness of Rayleigh scattering measurements for probing the colloidal behavior of proteins, a protein solution of ,-lactoglobulin was used as a base-case scenario. The colloidal behavior of different ,-lactoglobulin solutions was inferred based on published data for this protein, under identical solution conditions, where techniques other than Rayleigh scattering had been used. Using this approach, good agreement was observed between scattering data and the colloidal behavior of this protein. To test the hypothesis that a high degree of aggregation will lead to increased membrane fouling, filtration data was used to find whether the Rayleigh scattering intensity correlated with permeate flux changes. It was found that for protein solutions which were stable and did not aggregate, fouling was reduced and these solutions exhibited reduced Rayleigh scattering. When the aggregation behavior of the solution was favored, significant flux declines occurred and were highly correlated with increased Rayleigh scattering. © 2010 American Institute of Chemical Engineers Biotechnol. Prog., 2010 [source] | ||||||||||||||||