Science.gov

Sample records for seo proteins results

  1. Calcium powered phloem protein of SEO gene family “Forisome” functions in wound sealing and act as biomimetic smart materials

    PubMed Central

    Srivastava, Vineet Kumar; Tuteja, Narendra

    2014-01-01

    Forisomes protein belongs to SEO gene family and is unique to Fabaceae family. These proteins are located in sieve tubes of phloem and function to prevent loss of nutrient-rich photoassimilates, upon mechanical injury/wounding. Forisome protein is also known as ATP independent, mechanically active proteins. Despite the wealth of information role of forisome in plants are not yet fully understood. Recent reports suggest that forisomes protein can act as ideal model to study self assembly mechanism for development of nanotechnological devices like microfluidic system application in space exploration mission. Improvement in micro instrument is highly demanding and has been a key technology by NASA in future space exploration missions. Based on its physical parameters, forisome are found to be ideal biomimetic materials for micro fluidic system because the conformational shifts can be replicated in vitro and are fully reversible over large number of cycles. By the use of protein engineering forisome recombinant protein can be tailored. Due to its unique ability to convert chemical energy into mechanical energy forisome has received much attention. For nanotechnological application and handling biomolecules such as DNA, RNA, protein and cell as a whole microfluidic system will be the most powerful technology. The discovery of new biomimetic smart materials has been a key factor in development of space science and its requirements in such a challenging environment. The field of microfludic, particularly in terms of development of its components along with identification of new biomimetic smart materials, deserves more attention. More biophysical investigation is required to characterize it to make it more suitable under parameters of performance. PMID:25763691

  2. CEOS SEO and GISS Meeting

    NASA Technical Reports Server (NTRS)

    Killough, Brian; Stover, Shelley

    2008-01-01

    The Committee on Earth Observation Satellites (CEOS) provides a brief to the Goddard Institute for Space Studies (GISS) regarding the CEOS Systems Engineering Office (SEO) and current work on climate requirements and analysis. A "system framework" is provided for the Global Earth Observation System of Systems (GEOSS). SEO climate-related tasks are outlined including the assessment of essential climate variable (ECV) parameters, use of the "systems framework" to determine relevant informational products and science models and the performance of assessments and gap analyses of measurements and missions for each ECV. Climate requirements, including instruments and missions, measurements, knowledge and models, and decision makers, are also outlined. These requirements would establish traceability from instruments to products and services allowing for benefit evaluation of instruments and measurements. Additionally, traceable climate requirements would provide a better understanding of global climate models.

  3. Pb4V6O16(SeO3)3(H2O), Pb2VO2(SeO3)2Cl, and PbVO2(SeO3)F: new lead(II)-vanadium(V) mixed-metal selenites featuring novel anionic skeletons.

    PubMed

    Cao, Xue-Li; Kong, Fang; Hu, Chun-Li; Xu, Xiang; Mao, Jiang-Gao

    2014-08-18

    Hydrothermal reactions of PbCO3 (or PbCl2), V2O5, and SeO2 in KOH solution or HF solution resulted in three new lead(II)-vanadium(V) mixed-metal selenites, namely, Pb4V6O16(SeO3)3(H2O) (1), Pb2VO2(SeO3)2Cl (2), and PbVO2(SeO3)F (3). Compounds 1 and 2 are polar (space group P21), whereas compound 3 is centrosymmetric (space group Pbca). Compound 1 displays an unusual [V6O16(SeO3)3](8-) anionic chain, which is composed by a 1D [V4O12](2-) anionic chain that is further decorated by dimeric [V2O6(SeO3)3](8-) units via corner-sharing. Compound 2 features two types of 1D chains, a cationic [Pb2Cl](3+) chain and a [VO2(SeO3)2](3-) anionic chain, whereas compound 3 contains dimeric [V2O4(SeO3)2F2](2-) units. The powder second-harmonic-generating (SHG) measurements indicate that compound 1 shows a weak SHG response of about 0.2 × KDP (KH2PO4) under 1400 nm laser radiation. Thermal stability and optical properties as well as theoretical calculations based on density functional theory methods were also performed. PMID:25102013

  4. Earth resources applications of the Synchronous Earth Observatory Satellite (SEOS)

    NASA Technical Reports Server (NTRS)

    Lowe, D. S.; Cook, J. J.

    1973-01-01

    The results are presented of a four month study to define earth resource applications which are uniquely suited to data collection by a geosynchronous satellite. While such a satellite could also perform many of the functions of ERTS, or its low orbiting successors, those applications were considered in those situations where requirements for timely observation limit the capability of ERTS or EOS. Thus, the application presented could be used to justify a SEOS.

  5. RNA adducts with Na 2SeO 4 and Na 2SeO 3 - Stability and structural features

    NASA Astrophysics Data System (ADS)

    Nafisi, Shohreh; Manouchehri, Firouzeh; Montazeri, Maryam

    2011-12-01

    Selenium compounds are widely available in dietary supplements and have been extensively studied for their antioxidant and anticancer properties. Low blood Se levels were found to be associated with an increased incidence and mortality from various types of cancers. Although many in vivo and clinical trials have been conducted using these compounds, their biochemical and chemical mechanisms of efficacy are the focus of much current research. This study was designed to examine the interaction of Na 2SeO 4 and Na 2SeO 3 with RNA in aqueous solution at physiological conditions, using a constant RNA concentration (6.25 mM) and various sodium selenate and sodium selenite/polynucleotide (phosphate) ratios of 1/80, 1/40, 1/20, 1/10, 1/5, 1/2 and 1/1. Fourier transform infrared, UV-Visible spectroscopic methods were used to determine the drug binding modes, the binding constants, and the stability of Na 2SeO 4 and Na 2SeO 3-RNA complexes in aqueous solution. Spectroscopic evidence showed that Na 2SeO 4 and Na 2SeO 3 bind to the major and minor grooves of RNA ( via G, A and U bases) with some degree of the Se-phosphate (PO 2) interaction for both compounds with overall binding constants of K(Na 2SeO 4-RNA) = 8.34 × 10 3 and K(Na 2SeO 3-RNA) = 4.57 × 10 3 M -1. The order of selenium salts-biopolymer stability was Na 2SeO 4-RNA > Na 2SeO 3-RNA. RNA aggregations occurred at higher selenium concentrations. No biopolymer conformational changes were observed upon Na 2SeO 4 and Na 2SeO 3 interactions, while RNA remains in the A-family structure.

  6. Resource Seminar 2007: Introduction to Linux Eun-seo Choi

    E-print Network

    Choi, Eunseo

    Resource Seminar 2007: Introduction to Linux Eun-seo Choi Oct 11, 2007 1 Resources · Senior grads and magazines ­ Google, Wikipedia, etc. ­ Linux Journal (http://www.linuxjournal.com/), Linux Magazine (http://www. linux-mag.com/), Linux Format (http://www.linuxformat.co.uk/), and many others (http://en.wikipedia.org/wiki/List_of_Linux

  7. Investigation of local symmetry in LiH3(SeO3)2 single crystals by 1H and 7Li nuclear magnetic resonance

    NASA Astrophysics Data System (ADS)

    Lim, Ae Ran

    2013-10-01

    The local environments of 1H and 7Li nuclei in LiH3(SeO3)2 crystals were investigated using FT NMR. The 7Li spectrum does changes from three resonance lines to one resonance line near Tm (=383 K). The variation in the splitting of the 7Li resonance lines with temperature indicates that the EFG at the Li sites produced by the (SeO3)2- groups varies with temperature. The changes in the temperature dependence of the intensity, line width, and spin-lattice relaxation time T1 near Tm for the 1H and 7Li nuclei coincide with the distortion of the structural framework surrounding each 1H and 7Li ion. Finally, the NMR results obtained here are compared to MH3(SeO3)2 (M = Na, K, and Cs) crystals previously reported.

  8. Proteins in electric fields and pressure fields: experimental results.

    PubMed

    Fidy, J; Balog, E; Köhler, M

    1998-08-18

    Experimental results obtained by Stark effect and pressure tuning optical spectroscopy are discussed with the emphasis on studies aimed at unraveling the coupling of prosthetic groups to proteins. A comparative, detailed analysis is given concerning the coupling of the heme group to the apoprotein in various heme proteins based on spectral hole burning data. Electrochromism and electric dichroism experiments related to the coupling problem are also discussed in the context of other protein systems. PMID:9733987

  9. Detection of calcium by a confocal laser scanning microscope in Na2SeO3-treated SW480 human colonic carcinoma cells

    NASA Astrophysics Data System (ADS)

    Wang, Haitao; Liu, Yafeng; Zhang, Zhihong; Yang, Xiangliang; Xu, Hui-Bie F.

    2002-04-01

    A number of studies have demonstrated that perturbed cellular calcium homeostasis has been implicated in apoptosis. Some studies showed that selenium compounds were able to induce cell apoptosis. The main objective of this study is to evaluate effect of Na2SeO3 on intracellular Ca2+ levels in SW480 human colonic carcinoma cells. When SW480 cells were exposed to 25 to 100 micrometers ol/L Na2SeO3, we also found that Na2SeO3 was able to induce [Ca2+]i, disruption of mitochondrial membrane potential ((Delta) (psi) m) in SW480 cells by using a confocal laser scanning microscope. Ca2+ channel inhibitor CoCl2 and an intracellular Ca2+ chelator BAPTA completely inhibited [Ca2+]i increase. CoCl2, BAPTA and ruthenium red also inhibited disruption of (Delta) (psi) m. The results suggest that Na2SeO3 is able to increase [Ca2+]i mitochondria permeability transition and Ca2+ is from extracellular Ca2+.

  10. Structure and properties of a non-traditional glass containing TeO2, SeO2 and MoO3

    NASA Astrophysics Data System (ADS)

    Bachvarova-Nedelcheva, A.; Iordanova, R.; Kostov, K. L.; Yordanov, St.; Ganev, V.

    2012-09-01

    A glass containing SeO2, TeO2, MoO3 and La2O3 was obtained at high oxygen pressure (P = 36 MPa) using pure oxides as precursors. The real bulk chemical composition of the glass according to LA-ICP-MS analysis is 17SeO2·50TeO2·32MoO3·1La2O3 (wt.%). The glass was characterized by X-ray diffraction, scanning electron microscopy (SEM), differential thermal analysis (DTA), UV-Vis, XPS, IR and EPR spectroscopy. According to DTA the glass transition temperature (Tg) is below 300 °C. By IR and X-ray photoelectron spectroscopy was determined the main building units (TeO3, TeO4, SeO3, Mo2O8) and the existing of mixed bridging bonds only, which build up the amorphous network. It was established by UV-Vis that the glass is transparent above 490 nm. As a result of a lengthy heat treatment, crystallization took place and crystals rich in SeO2 and TeO2 were found incorporated into the amorphous part containing all components.

  11. Syntheses, structures, and properties of Ag 4(Mo 2O 5)(SeO 4) 2(SeO 3) and Ag 2(MoO 3) 3SeO 3

    NASA Astrophysics Data System (ADS)

    Ling, Jie; Albrecht-Schmitt, Thomas E.

    2007-05-01

    Ag 4(Mo 2O 5)(SeO 4) 2(SeO 3) has been synthesized by reacting AgNO 3, MoO 3, and selenic acid under mild hydrothermal conditions. The structure of this compound consists of cis-MoO 22+ molybdenyl units that are bridged to neighboring molybdenyl moieties by selenate anions and by a bridging oxo anion. These dimeric units are joined by selenite anions to yield zigzag one-dimensional chains that extended down the c-axis. Individual chains are polar with the C2 distortion of the Mo(VI) octahedra aligning on one side of each chain. However, the overall structure is centrosymmetric because neighboring chains have opposite alignment of the C2 distortion. Upon heating Ag 4(Mo 2O 5)(SeO 4) 2(SeO 3) looses SeO 2 in two distinct steps to yield Ag 2MoO 4. Crystallographic data: (193 K; Mo K?, ?=0.71073 Ĺ): orthorhombic, space group Pbcm, a=5.6557(3), b=15.8904(7), c=15.7938(7) Ĺ, V=1419.41(12), Z=4, R( F)=2.72% for 121 parameters with 1829 reflections with I>2 ?( I). Ag 2(MoO 3) 3SeO 3 was synthesized by reacting AgNO 3 with MoO 3, SeO 2, and HF under hydrothermal conditions. The structure of Ag 2(MoO 3) 3SeO 3 consists of three crystallographically unique Mo(VI) centers that are in 2+2+2 coordination environments with two long, two intermediate, and two short bonds. These MoO 6 units are connected to form a molybdenyl ribbon that extends along the c-axis. These ribbons are further connected together through tridentate selenite anions to form two-dimensional layers in the [ bc] plane. Crystallographic data: (193 K; Mo K?, ?=0.71073 Ĺ): monoclinic, space group P2 1/n, a=7.7034(5), b=11.1485(8), c=12.7500(9) Ĺ, ?=105.018(1) V=1002.7(2), Z=4, R( F)=3.45% for 164 parameters with 2454 reflections with I>2 ?( I). Ag 2(MoO 3) 3SeO 3 decomposes to Ag 2Mo 3O 10 on heating above 550 °C.

  12. A physical approach to protein structure prediction: CASP4 results

    SciTech Connect

    Crivelli, Silvia; Eskow, Elizabeth; Bader, Brett; Lamberti, Vincent; Byrd, Richard; Schnabel, Robert; Head-Gordon, Teresa

    2001-02-27

    We describe our global optimization method called Stochastic Perturbation with Soft Constraints (SPSC), which uses information from known proteins to predict secondary structure, but not in the tertiary structure predictions or in generating the terms of the physics-based energy function. Our approach is also characterized by the use of an all atom energy function that includes a novel hydrophobic solvation function derived from experiments that shows promising ability for energy discrimination against misfolded structures. We present the results obtained using our SPSC method and energy function for blind prediction in the 4th Critical Assessment of Techniques for Protein Structure Prediction (CASP4) competition, and show that our approach is more effective on targets for which less information from known proteins is available. In fact our SPSC method produced the best prediction for one of the most difficult targets of the competition, a new fold protein of 240 amino acids.

  13. An empirical analysis of health care IPOs and SEOs.

    PubMed

    Brau, James C; Holloway, Jonathan M

    2009-01-01

    This article reviews the extant literature regarding the three new issues phenomena: hot issue markets, first-day underpricing, and poor long-run performance as they apply to the heath care industry. Given the "creeping corporatization" of the heath care industry and the unique influence of nonmarket forces on it, we examine whether the three IPO phenomena exist within the industry. We find that hot issue markets, initial underpricing, and negative long-run abnormal returns and sales growth occur among both heath care IPOs and SEOs. Of particular interest, we find that firms are able to issue during times of excess heath care spending and subsequently underperform the market, apparently exploiting windows of opportunity. PMID:20515009

  14. Effects of sodium and potassium ions on a novel SeO2-B2O3-SiO2-P2O5-CaO bioactive system

    NASA Astrophysics Data System (ADS)

    Trandafir, D. L.; Ponta, O.; Ciceo-Lucacel, R.; Simon, V.

    2015-01-01

    The study is focused on Na2O and/or K2O influence on a new sol-gel derived SeO2-B2O3-SiO2-P2O5-CaO bioactive system. The structural changes induced by Na2O and/or K2O addition were correlated with the samples behavior in simulated biological media. X-ray diffraction (XRD) and Fourier transform infrared (FTIR) spectroscopy were used to characterize the structure and the type of the chemical bonds. The morphology of the samples was characterized through scanning electron microscopy (SEM). XRD results pointed out a prevalent vitreous structure with an incipient hydroxyapatite (HA) crystalline phase. FTIR results revealed a complex network consisting of silicate, phosphate and borate units, as well as the development of both A- and B-type of carbonate-substituted HA. The bioactivity of the samples was tested in vitro following the evolution of the apatite layers self-assembled on the samples surface in simulated body fluid. Their biocompatibility was investigated after samples surface functionalization with protein. The results indicate that sodium and potassium addition improves the biocompatibility by enhancement of protein adherence on samples surface and without to prevent the samples bioactivity.

  15. DMBC: SEO (Search Engine Optimization) Search Engine Optimization is the practice of increasing the visibility of a website within

    E-print Network

    Stowell, Michael

    & Keywords Site Popularity · How many people have previously searched for (and clicked on) your site vsDMBC: SEO (Search Engine Optimization) SEO · Search Engine Optimization is the practice of increasing the visibility of a website within search engines in a natural, non-promoted or advertised way

  16. Crystal chemistry of selenates with mineral-like structures: VII. The structure of (H3O)[(UO2)(SeO4)(SeO2OH)] and some structural features of selenite-selenates

    NASA Astrophysics Data System (ADS)

    Krivovichev, S. V.

    2009-12-01

    The crystal structure of a new compound, (H3O)[(UO2)(SeO4)(SeO2OH)] (monoclinic, P21/ n, a = 8.6682(19), b = 10.6545(16), c = 9.846(2) Ĺ, ? = 97.881(17)°, V = 900.7(3) Ĺ3), was solved by direct methods and refined to R 1 = 0.050. The structure contains two symmetrically different Se atoms. The Se1 site is coordinated by three O atoms as is characteristic of Se4+ cations. The Se2 site is coordinated by four O atoms and forms selenate anion SeO{4/2-}. The structure is based on selenite-selenate sheets [(UO2)(SeO4)(SeO2OH)]- linked by the interlayer H3O- ions. The sheets are parallel to (101). The structure is compared to that of schmiederite, Pb2Cu2(SeO3)(SeO4)(OH)4.

  17. Short Signatures From Diffie-Hellman: Realizing Short Public Key Jae Hong Seo

    E-print Network

    International Association for Cryptologic Research (IACR)

    between the public key and random tags, which are part of signatures. Roughly speaking, we canShort Signatures From Diffie-Hellman: Realizing Short Public Key Jae Hong Seo Department short public key of ( log ) group elements. Then, we developed a new technique for asymmetric trade

  18. Automatic Modeling of Virtual Humans and Body Clothing Nadia Magnenat-Thalmann, Hyewon Seo, Frederic Cordier

    E-print Network

    Cordier, Frederic

    of the human body. In the market, there are now available several systems that are optimized eitherAutomatic Modeling of Virtual Humans and Body Clothing Nadia Magnenat-Thalmann, Hyewon Seo, parameterization techniques for modeling static shape (the variety of human body shapes) and dynamic shape (how

  19. Diet SODA: A Power-Efficient Processor for Digital Cameras Sangwon Seo1

    E-print Network

    Kambhampati, Subbarao

    Diet SODA: A Power-Efficient Processor for Digital Cameras Sangwon Seo1 , Ronald G. Dreslinski1 devices. This paper proposes a power-efficient SIMD ar- chitecture, referred to as Diet SODA, for DSP data (SIMD) architecture to significantly lower the power consumption. The major features of Diet SODA

  20. Factors controlling the variations in the mid-ocean ridge segmentation Eun-seo Choi1

    E-print Network

    Choi, Eunseo

    T31B-0449 Factors controlling the variations in the mid-ocean ridge segmentation Eun-seo Choi1 of the orthogonal pattern characterizing mid-ocean ridges and transform faults are studied using numerical models. Thermal stresses are isotropic, but mid-ocean ridges themselves and numerous ridge parallel faults can

  1. Automating the DEVS Modeling and Simulation Interface to Web Services Chungman Seo

    E-print Network

    Automating the DEVS Modeling and Simulation Interface to Web Services Chungman Seo Bernard P, zeigler@ece.arizona.edu Keywords: DEVS, Web Services, WSDL, Dynamic Web Service Invocation, Web Service Execution Language Abstract Web service technology is used to augment software reusability and composability

  2. Ribosomal Protein Mutations Result in Constitutive p53 Protein Degradation through Impairment of the AKT Pathway.

    PubMed

    Antunes, Ana T; Goos, Yvonne J; Pereboom, Tamara C; Hermkens, Dorien; Wlodarski, Marcin W; Da Costa, Lydie; MacInnes, Alyson W

    2015-07-01

    Mutations in ribosomal protein (RP) genes can result in the loss of erythrocyte progenitor cells and cause severe anemia. This is seen in patients with Diamond-Blackfan anemia (DBA), a pure red cell aplasia and bone marrow failure syndrome that is almost exclusively linked to RP gene haploinsufficiency. While the mechanisms underlying the cytopenia phenotype of patients with these mutations are not completely understood, it is believed that stabilization of the p53 tumor suppressor protein may induce apoptosis in the progenitor cells. In stark contrast, tumor cells from zebrafish with RP gene haploinsufficiency are unable to stabilize p53 even when exposed to acute DNA damage despite transcribing wild type p53 normally. In this work we demonstrate that p53 has a limited role in eliciting the anemia phenotype of zebrafish models of DBA. In fact, we find that RP-deficient embryos exhibit the same normal p53 transcription, absence of p53 protein, and impaired p53 response to DNA damage as RP haploinsufficient tumor cells. Recently we reported that RP mutations suppress activity of the AKT pathway, and we show here that this suppression results in proteasomal degradation of p53. By re-activating the AKT pathway or by inhibiting GSK-3, a downstream modifier that normally represses AKT signaling, we are able to restore the stabilization of p53. Our work indicates that the anemia phenotype of zebrafish models of DBA is dependent on factors other than p53, and may hold clinical significance for both DBA and the increasing number of cancers revealing spontaneous mutations in RP genes. PMID:26132763

  3. Emulating exhalative chemistry: synthesis and structural characterization of ilinskite, Na[Cu5O2](SeO3)2Cl3, and its K-analogue

    NASA Astrophysics Data System (ADS)

    Kovrugin, Vadim M.; Siidra, Oleg I.; Colmont, Marie; Mentré, Olivier; Krivovichev, Sergey V.

    2015-08-01

    The K- and Na-synthetic analogues of the fumarolic mineral ilinskite have been synthesized by the chemical vapor transport (CVT) reactions method. The A[Cu5O2](SeO3)2Cl3 ( A + = K+, Na+) compounds crystallize in the orthorhombic space group Pnma: a = 18.1691(6) Ĺ, b = 6.4483(2) Ĺ, c = 10.5684(4) Ĺ, V = 1238.19(7) Ĺ3, R 1 = 0.018 for 1957 unique reflections with F > 4? F for K[Cu5O2](SeO3)2Cl3 ( KI), and a = 17.7489(18) Ĺ, b = 6.4412(6) Ĺ, c = 10.4880(12) Ĺ, V = 1199.0(2) Ĺ3, R 1 = 0.049 for 1300 unique reflections with F > 4? F for Na[Cu5O2](SeO3)2Cl3 ( NaI). The crystal structures of KI and NaI are based upon the [O2Cu5]6+ sheets consisting of corner-sharing (OCu4)6+ tetrahedra. The Na-for-K substitution results in the significant expansion of the interlayer space and changes in local coordination of some of the Cu2+ cations. The A + cation coordination changes from fivefold (for Na+) to ninefold (for K+). The CVT reactions method provides a unique opportunity to model physicochemical conditions existing in fumarolic environments and may be used not only to model exhalative processes, but also to predict possible mineral phases that may form in fumaroles. In particular, the K analogue of ilinskite is not known in nature, whereas it may well form from volcanic gases in a K-rich local geochemical environment.

  4. Consumption of Milk Protein or Whey Protein Results in a Similar Increase in Muscle Protein Synthesis in Middle Aged Men

    PubMed Central

    Mitchell, Cameron J.; McGregor, Robin A.; D’Souza, Randall F.; Thorstensen, Eric B.; Markworth, James F.; Fanning, Aaron C.; Poppitt, Sally D.; Cameron-Smith, David

    2015-01-01

    The differential ability of various milk protein fractions to stimulate muscle protein synthesis (MPS) has been previously described, with whey protein generally considered to be superior to other fractions. However, the relative ability of a whole milk protein to stimulate MPS has not been compared to whey. Sixteen healthy middle-aged males ingested either 20 g of milk protein (n = 8) or whey protein (n = 8) while undergoing a primed constant infusion of ring 13C6 phenylalanine. Muscle biopsies were obtained 120 min prior to consumption of the protein and 90 and 210 min afterwards. Resting myofibrillar fractional synthetic rates (FSR) were 0.019% ± 0.009% and 0.021% ± 0.018% h?1 in the milk and whey groups respectively. For the first 90 min after protein ingestion the FSR increased (p < 0.001) to 0.057% ± 0.018% and 0.052% ± 0.024% h?1 in the milk and whey groups respectively with no difference between groups (p = 0.810). FSR returned to baseline in both groups between 90 and 210 min after protein ingestion. Despite evidence of increased rate of digestion and leucine availability following the ingestion of whey protein, there was similar activation of MPS in middle-aged men with either 20 g of milk protein or whey protein. PMID:26506377

  5. A new phase in the MnII-SeIV-MoVI-O system, Mn(MoO3)(SeO3)(H2O): Hydrothermal synthesis, crystal structure and properties

    NASA Astrophysics Data System (ADS)

    Zhen, Yanzhong; Wang, Danjun; Liu, Bin; Fu, Feng; Xue, Ganglin

    2013-11-01

    A new phase in the MnII-SeIV-MoVI-O system, Mn(MoO3)(SeO3)(H2O) (1), has been hydrothermally synthesized with a high yield (82%), and characterized by IR, TG-DSC, magnetism measurement and single crystal X-ray diffraction. The structure of Mn(MoO3)(SeO3)(H2O) features a complicated 3D network composed of the 1D molybdenum(VI) oxide chains and the 1D manganese(II) selenite chains interconnected via Se-O-Mo and Mn-O-Mo bridges. It is stable up to approximately 340 °C, and losses water molecule at 340 °C, then release SeO2 at about 420 °C. The result of magnetic property measurements has indicated that there exist antiferromagnetic interactions between Mn(II) centers. Photocatalysis experimental result illustrates that the compound exhibits good photocatalytic performance for degradation of RhB under visible light irradiation.

  6. Protein crystal growth results from shuttle flight 51-F

    NASA Technical Reports Server (NTRS)

    Bugg, C. E.

    1985-01-01

    The protein crystal growth (PCG) experiments run on 51-F were analyzed. It was found that: (1) sample stability is increased over that observed during the experiments on flight 51-D; (2) the dialysis experiments produced lysozyme crystals that were significantly larger than those obtained in our identical ground-based studies; (3) temperature fluctuations apparently caused problems during the crystallization experiments on 51-F; (4) it is indicated that teflon tape stabilizes droplets on the syringe tips; (5) samples survived during the reentry and landing in glass tips that were not stoppered with plungers; (6) from the ground-based studies, it was expected that equilibration should be complete within 2 to 4 days for all of these vapor-diffusion experiments, thus it appears that the vapor diffusion rates are somewhat slower under microgravity conditions; (7) drop tethering was highly successful, all four of the tethered drops were stable, even though they contained MPD solutions; (8) the PCG experiments on 51-F were done to assess the hardware and experimental procedures that are developed for future flights, when temperature control will be available. Lysozyme crystals obtained by microdialysis are considerably larger than those obtained on the ground, using the identical apparatus and procedures.

  7. Evolutionary Rate Covariation in Meiotic Proteins Results from Fluctuating Evolutionary Pressure in Yeasts and Mammals

    PubMed Central

    Clark, Nathan L.; Alani, Eric; Aquadro, Charles F.

    2013-01-01

    Evolutionary rates of functionally related proteins tend to change in parallel over evolutionary time. Such evolutionary rate covariation (ERC) is a sequence-based signature of coevolution and a potentially useful signature to infer functional relationships between proteins. One major hypothesis to explain ERC is that fluctuations in evolutionary pressure acting on entire pathways cause parallel rate changes for functionally related proteins. To explore this hypothesis we analyzed ERC within DNA mismatch repair (MMR) and meiosis proteins over phylogenies of 18 yeast species and 22 mammalian species. We identified a strong signature of ERC between eight yeast proteins involved in meiotic crossing over, which seems to have resulted from relaxation of constraint specifically in Candida glabrata. These and other meiotic proteins in C. glabrata showed marked rate acceleration, likely due to its apparently clonal reproductive strategy and the resulting infrequent use of meiotic proteins. This correlation between change of reproductive mode and change in constraint supports an evolutionary pressure origin for ERC. Moreover, we present evidence for similar relaxations of constraint in additional pathogenic yeast species. Mammalian MMR and meiosis proteins also showed statistically significant ERC; however, there was not strong ERC between crossover proteins, as observed in yeasts. Rather, mammals exhibited ERC in different pathways, such as piRNA-mediated defense against transposable elements. Overall, if fluctuation in evolutionary pressure is responsible for ERC, it could reveal functional relationships within entire protein pathways, regardless of whether they physically interact or not, so long as there was variation in constraint on that pathway. PMID:23183665

  8. Tuning of protein-surfactant interaction to modify the resultant structure

    NASA Astrophysics Data System (ADS)

    Mehan, Sumit; Aswal, Vinod K.; Kohlbrecher, Joachim

    2015-09-01

    Small-angle neutron scattering and dynamic light scattering studies have been carried out to examine the interaction of bovine serum albumin (BSA) protein with different surfactants under varying solution conditions. We show that the interaction of anionic BSA protein (p H 7 ) with surfactant and the resultant structure are strongly modified by the charge head group of the surfactant, ionic strength of the solution, and mixed surfactants. The protein-surfactant interaction is maximum when two components are oppositely charged, followed by components being similarly charged through the site-specific binding, and no interaction in the case of a nonionic surfactant. This interaction of protein with ionic surfactants is characterized by the fractal structure representing a bead-necklace structure of micellelike clusters adsorbed along the unfolded protein chain. The interaction is enhanced with ionic strength only in the case of site-specific binding of an anionic surfactant with an anionic protein, whereas it is almost unchanged for other complexes of cationic and nonionic surfactants with anionic proteins. Interestingly, the interaction of BSA protein with ionic surfactants is significantly suppressed in the presence of nonionic surfactant. These results with mixed surfactants thus can be used to fold back the unfolded protein as well as to prevent surfactant-induced protein unfolding. For different solution conditions, the results are interpreted in terms of a change in fractal dimension, the overall size of the protein-surfactant complex, and the number of micelles attached to the protein. The interplay of electrostatic and hydrophobic interactions is found to govern the resultant structure of complexes.

  9. Cs(TaO2)3(SeO3)2 and Cs(TiOF)3(SeO3)2: structural and second harmonic generation changes induced by the different d(0)-TM coordination octahedra.

    PubMed

    Cao, Xue-Li; Hu, Chun-Li; Kong, Fang; Mao, Jiang-Gao

    2015-04-20

    Two new cesium selenites containing TaO6 or TiO4F2 octahedra, namely, Cs(TaO2)3(SeO3)2 (1) and Cs(TiOF)3(SeO3)2 (2), have been prepared using standard high temperature solid-state method and hydrothermal reaction, respectively. Compound 1 crystallizes in P3?m1 and features an unusual [(TaO2)3(SeO3)2](-) sandwich-like double layer in which two [Ta(1)O3(SeO3)](3-) layers are bridged by central Ta(2)O6 octahedra via corner-sharing, whereas Cs(TiOF)3(SeO3)2 with a polar space group P63mc features an interesting hexagonal tungsten oxide (HTO) layered topology and presents a strong second harmonic generation (SHG) of about 5 × KDP (KH2PO4), which is much larger than those of A(VO2)3(QO3)2 (A = K, Tl, Rb, Cs, or NH4; Q = Se, Te) with a similar HTO layered structure. Cs(TiOF)3(SeO3)2 is also type-I phase matching. The SHG of above-mentioned HTO materials can be enhanced greatly with the replacement of VO6 octahedra by TiO4F2 octahedra. Furthermore, thermal stabilities, UV-vis diffuse reflectance spectra, infrared spectra, relationship between crystal structure and SHG, and theoretical calculations were also reported. PMID:25835387

  10. 31 CFR 30.3 - Q-3: How are the SEOs and most highly compensated employees identified for purposes of compliance...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 31 Money and Finance: Treasury 1 2010-07-01 2010-07-01 false Q-3: How are the SEOs and most highly compensated employees identified for purposes of compliance with this part? 30.3 Section 30.3 Money and... GOVERNANCE § 30.3 Q-3: How are the SEOs and most highly compensated employees identified for purposes...

  11. TiO2-SEO Block Copolymer Nanocomposites as Solid-State Electrolytes for Lithium Metal Batteries

    NASA Astrophysics Data System (ADS)

    Gurevitch, Inna; Buonsanti, Raffaella; Teran, Alexander; Cabana, Jordi; Balsara, Nitash

    2013-03-01

    Replacing the liquid electrolyte in lithium batteries by a solid has been a long-standing goal of the battery industry due to the promise of better safety and the potential to produce batteries with higher energy densities. Recently, symmetric polystyrene-block-poly(ethylene oxide) (SEO) copolymers/LiX salt mixtures with high ionic conductivity and high shear modulus were developed as solid electrolytes. For an enhancement in mechanical properties and its effect on the dendrite growth from lithium metal electrodes, we study the effect of adding TiO2 nanoparticles to the SEO/LiX mixtures. We find that TiO2/SEO/LiX nanocomposite electrolytes have stable performance against the lithium metal electrodes. There appears to be a correlation between the stability of the electrolytes, morphology, and mechanical properties.

  12. Recent results and new hardware developments for protein crystal growth in microactivity

    NASA Technical Reports Server (NTRS)

    Delucas, L. J.; Long, M. M.; Moore, K. M.; Smith, C.; Carson, M.; Narayana, S. V. L.; Carter, D.; Clark, A. D., Jr.; Nanni, R. G.; Ding, J.

    1993-01-01

    Protein crystal growth experiments have been performed on 16 space shuttle missions since April, 1985. The initial experiments utilized vapor diffusion crystallization techniques similar to those used in laboratories for earth-based experiments. More recent experiments have utilized temperature induced crystallization as an alternative method for growing high quality protein crystals in microgravity. Results from both vapor diffusion and temperature induced crystallization experiments indicate that proteins grown in microgravity may be larger, display more uniform morphologies, and yield diffraction data to significantly higher resolutions than the best crystals of these proteins grown on earth.

  13. Programmers' Build Errors: A Case Study (at Google) Hyunmin Seo

    E-print Network

    Cortes, Corinna

    - tivity. Programming is often described as an "edit-compile- debug" cycle in which a programmer makes a change, com- piles, and tests the resulting binary, then repeats the cycle until the program behaves@google.com ABSTRACT Building is an integral part of the software development pro- cess. However, little is known about

  14. Theoretical study of potential energy curves, spectroscopic constants, and radiative lifetimes of low-lying states in an SeO molecule

    NASA Astrophysics Data System (ADS)

    Li, Rui; Lian, Ke-Yan; Li, Qi-Nan; Miao, Feng-Juan; Yan, Bing; Jin, Ming-Xing

    2012-12-01

    The low-lying potential energy curves of the SeO molecule are computed by means of an ab initio multireference configuration interaction technique, taking into account relativistic (scalar plus spin—orbit coupling) effects. The spectroscopic constants of ? states for X3?-, a1?, b1?+, A3?, A'3?, and A? 3?+ states are obtained, and they are in good accordance with available experimental values. The Franck—Condon factors and transition dipole moments to the ground state are computed, and the natural radiative lifetimes of low-lying ? states are theoretically obtained. Comparisons of the natural lifetimes of ? states with previous experimental results and those of isovalent TeO molecule are made.

  15. Hoyoung Seo (C.V.) Page 1 of 3 Hoyoung Seo, Ph.D., P.E.

    E-print Network

    Chen, Xinzhong

    Murray, Canada: Interpretation of results from 1) Static compressive, tensile, and lateral load tests on 406 analysis of piles for machine foundation · Vopak Terminal Expansion, Vopak, The Bahamas: Analysis

  16. Direct Synthesis of Gallium Nitride Nanowires Coated with Boron Carbonitride Layers Hee Won Seo, Seung Yong Bae, and Jeunghee Park*

    E-print Network

    Kim, Bongsoo

    Direct Synthesis of Gallium Nitride Nanowires Coated with Boron Carbonitride Layers Hee Won Seo-701, South Korea ReceiVed: January 1, 2003; In Final Form: April 30, 2003 Gallium nitride nanowires coated of gallium, gallium oxide, boron oxide, and carbon nanotubes under an ammonia atmosphere. The average

  17. High-pressure single-crystal X-ray diffraction of Tl 2SeO 4

    NASA Astrophysics Data System (ADS)

    Grzechnik, Andrzej; Breczewski, Tomasz; Friese, Karen

    2008-11-01

    The effect of pressure on the crystal structure of thallium selenate (Tl 2SeO 4) ( Pmcn, Z=4), containing the Tl + cations with electron lone pairs, has been studied with single-crystal X-ray diffraction in a diamond anvil cell up to 3.64 GPa at room temperature. No phase transition has been observed. The compressibility data are fitted by a Murnaghan equation of state with the zero-pressure bulk modulus B0=29(1) GPa and the unit-cell volume at ambient pressure V0=529.6(8) Ĺ 3 ( B'=4.00). Tl 2SeO 4 is the least compressible in the c direction, while the pressure-induced changes of the a and b lattice parameters are quite similar. These observations can be explained by different pressure effects on the nine- and 11-fold coordination polyhedra around the two non-equivalent Tl atoms. The SeO 42- tetrahedra are not rigid units and become more distorted. Their contribution to the compressibility is small. The effect of pressure on the isotypical oxide materials A 2TO 4 with the ?-K 2SO 4 structure is discussed. It appears that the presence of electron lone pairs on the Tl + cation does not seem to influence the compressibility of Tl 2SeO 4.

  18. Success in Mathematics within a Challenged Minority: The Case of Students of Ethiopian Origin in Israel (SEO)

    ERIC Educational Resources Information Center

    Mulat, Tiruwork; Arcavi, Abraham

    2009-01-01

    Many studies have reported on the economical, social, and educational difficulties encountered by Ethiopian Jews since their immigration to Israel. Furthermore, the overall academic underachievement and poor representation of students of Ethiopian origin (SEO) in the advanced mathematics and science classes were highlighted and described. Yet,…

  19. Spectral line-by-line pulse shaping Z. Jiang, D. S. Seo,* D. E. Leaird, and A. M. Weiner

    E-print Network

    Purdue University

    Spectral line-by-line pulse shaping Z. Jiang, D. S. Seo,* D. E. Leaird, and A. M. Weiner School 47907-2035 Received January 3, 2005 We experimentally demonstrate pulse-shaping experiments in which, centered at 1542 nm) are resolved. The shaped pulses overlap in time, and this leads to a new way

  20. Bioactive protein-based nanofibers interact with intestinal biological components resulting in transepithelial permeation of a therapeutic protein.

    PubMed

    Stephansen, Karen; García-Díaz, María; Jessen, Flemming; Chronakis, Ioannis S; Nielsen, Hanne Mřrck

    2015-11-10

    Proteins originating from natural sources may constitute a novel type of material for use in drug delivery. However, thorough understanding of the behavior and effects of such a material when processed into a matrix together with a drug is crucial prior to further development into a drug product. In the present study the potential of using bioactive electrospun fish sarcoplasmic proteins (FSP) as a carrier matrix for small therapeutic proteins was demonstrated in relation to the interactions with biological components of the intestinal tract. The inherent structural and chemical properties of FSP as a biomaterial facilitated interactions with cells and enzymes found in the gastrointestinal tract and displayed excellent biocompatibility. More specifically, insulin was efficiently encapsulated into FSP fibers maintaining its conformation, and subsequent controlled release was obtained in simulated intestinal fluid. The encapsulation of insulin into FSP fibers provided protection against chymotrypsin degradation, and resulted in an increase in insulin transport to around 12% without compromising the cellular viability. This increased transport was driven by interactions upon contact between the nanofibers and the Caco-2 cell monolayer leading to the opening of the tight junction proteins. Overall, electrospun FSP may constitute a novel material for oral delivery of biopharmaceuticals. PMID:26320547

  1. Protein Radical Formation Resulting from Eosinophil Peroxidase-catalyzed Oxidation of Sulfite.

    PubMed

    Ranguelova, Kalina; Chatterjee, Saurabh; Ehrenshaft, Marilyn; Ramirez, Dario C; Summers, Fiona A; Kadiiska, Maria B; Mason, Ronald P

    2010-07-30

    Eosinophil peroxidase (EPO) is an abundant heme protein in eosinophils that catalyzes the formation of cytotoxic oxidants implicated in asthma, allergic inflammatory disorders, and cancer. It is known that some proteins with peroxidase activity (horseradish peroxidase and prostaglandin hydroperoxidase) can catalyze oxidation of bisulfite (hydrated sulfur dioxide), leading to the formation of sulfur trioxide anion radical ((.)SO(3)(-)). This free radical further reacts with oxygen to form peroxymonosulfate anion radical ((-)O(3)SOO(.)) and the very reactive sulfate anion radical (SO(4)()), which is nearly as strong an oxidant as the hydroxyl radical. However, the ability of EPO to generate reactive sulfur radicals has not yet been reported. Here we demonstrate that eosinophil peroxidase/H(2)O(2) is able to oxidize bisulfite, ultimately forming the sulfate anion radical (SO(4)()), and that these reactive intermediates can oxidize target proteins to protein radicals, thereby initiating protein oxidation. We used immuno-spin trapping and confocal microscopy to study protein oxidation by EPO/H(2)O(2) in the presence of bisulfite in a pure enzymatic system and in human promyelocytic leukemia HL-60 clone 15 cells, maturated to eosinophils. Polyclonal antiserum raised against the spin trap 5,5-dimethyl-1-pyrroline N-oxide (DMPO) detected the presence of DMPO covalently attached to the proteins resulting from the DMPO trapping of protein free radicals. We found that sulfite oxidation mediated by EPO/H(2)O(2) induced the formation of radical-derived DMPO spin-trapped human serum albumin and, to a lesser extent, of DMPO-EPO. These studies suggest that EPO-dependent oxidative damage may play a role in tissue injury in bisulfite-exacerbated eosinophilic inflammatory disorders. PMID:20501663

  2. Ablation of retinal ciliopathy protein RPGR results in altered photoreceptor ciliary composition

    PubMed Central

    Rao, Kollu N.; Li, Linjing; Anand, Manisha; Khanna, Hemant

    2015-01-01

    Cilia regulate several developmental and homeostatic pathways that are critical to survival. Sensory cilia of photoreceptors regulate phototransduction cascade for visual processing. Mutations in the ciliary protein RPGR (retinitis pigmentosa GTPase regulator) are a prominent cause of severe blindness disorders due to degeneration of mature photoreceptors. However, precise function of RPGR is still unclear. Here we studied the involvement of RPGR in ciliary trafficking by analyzing the composition of photoreceptor sensory cilia (PSC) in Rpgrko retina. Using tandem mass spectrometry analysis followed by immunoblotting, we detected few alterations in levels of proteins involved in proteasomal function and vesicular trafficking in Rpgrko PSC, prior to onset of degeneration. We also found alterations in the levels of high molecular weight soluble proteins in Rpgrko PSC. Our data indicate RPGR regulates entry or retention of soluble proteins in photoreceptor cilia but spares the trafficking of key structural and phototransduction-associated proteins. Given a frequent occurrence of RPGR mutations in severe photoreceptor degeneration due to ciliary disorders, our results provide insights into pathways resulting in altered mature cilia function in ciliopathies. PMID:26068394

  3. Small structural differences of targeted anti-tumor toxins result in strong variation of protein expression.

    PubMed

    Gilabert-Oriol, Roger; Thakur, Mayank; Weise, Christoph; Dernedde, Jens; von Mallinckrodt, Benedicta; Fuchs, Hendrik; Weng, Alexander

    2013-09-01

    Targeted anti-tumor toxins consist of a toxic functional moiety that is chemically linked or recombinantly fused to a cell-directing ligand. Ribosome-inactivating proteins (RIPs), especially type I RIPs such as saporin or dianthin, are commonly used as toxin components. Although expression of type I RIP-based fusion proteins is well reported, the achievement of higher protein yields in heterologous expression systems through innovative strategies is of major interest. In the present study, the targeted toxins (his)saporin-EGF (SE) and (his)dianthin-EGF (DE) were expressed as fusion proteins under identical expression conditions. However, the total amount of DE was nearly two-times higher than SE. The identity of the heterologously expressed targeted toxins was confirmed by mass spectrometric studies. Their biological specific activity, monitored in real time, was almost equal. Sequence alignment shows 84% identity and a structural comparison revealed five major differences, two of which affect the secondary structure resulting in a loop (SE) to ?-strand (DE) conversion and one introduces a gap in SE (after position 57). In conclusion, these structural variations resulted in different protein expression levels while codon usage and toxicity to bacteria were excluded as a cause. Minor structural differences identified in this study may be considered responsible for the protection of DE from bacterial proteases and therefore may serve as a lead to modify certain domains in type I RIP-based targeted toxins. PMID:23867360

  4. Arenavirus budding resulting from viral-protein-associated cell membrane curvature

    PubMed Central

    Schley, David; Whittaker, Robert J.; Neuman, Benjamin W.

    2013-01-01

    Viral replication occurs within cells, with release (and onward infection) primarily achieved through two alternative mechanisms: lysis, in which virions emerge as the infected cell dies and bursts open; or budding, in which virions emerge gradually from a still living cell by appropriating a small part of the cell membrane. Virus budding is a poorly understood process that challenges current models of vesicle formation. Here, a plausible mechanism for arenavirus budding is presented, building on recent evidence that viral proteins embed in the inner lipid layer of the cell membrane. Experimental results confirm that viral protein is associated with increased membrane curvature, whereas a mathematical model is used to show that localized increases in curvature alone are sufficient to generate viral buds. The magnitude of the protein-induced curvature is calculated from the size of the amphipathic region hypothetically removed from the inner membrane as a result of translation, with a change in membrane stiffness estimated from observed differences in virion deformation as a result of protein depletion. Numerical results are based on experimental data and estimates for three arenaviruses, but the mechanisms described are more broadly applicable. The hypothesized mechanism is shown to be sufficient to generate spontaneous budding that matches well both qualitatively and quantitatively with experimental observations. PMID:23864502

  5. Loss of Photoreceptors Results in Upregulation of Synaptic Proteins in Bipolar Cells and Amacrine Cells

    PubMed Central

    Dagar, Sushma; Nagar, Saumya; Goel, Manvi; Cherukuri, Pitchaiah; Dhingra, Narender K.

    2014-01-01

    Deafferentation is known to cause significant changes in the postsynaptic neurons in the central nervous system. Loss of photoreceptors, for instance, results in remarkable morphological and physiological changes in bipolar cells and horizontal cells. Retinal ganglion cells (RGCs), which send visual information to the brain, are relatively preserved, but show aberrant firing patterns, including spontaneous bursts of spikes in the absence of photoreceptors. To understand how loss of photoreceptors affects the circuitry presynaptic to the ganglion cells, we measured specific synaptic proteins in two mouse models of retinal degeneration. We found that despite the nearly total loss of photoreceptors, the synaptophysin protein and mRNA levels in retina were largely unaltered. Interestingly, the levels of synaptophysin in the inner plexiform layer (IPL) were higher, implying that photoreceptor loss results in increased synaptophysin in bipolar and/or amacrine cells. The levels of SV2B, a synaptic protein expressed by photoreceptors and bipolar cells, were reduced in whole retina, but increased in the IPL of rd1 mouse. Similarly, the levels of syntaxin-I and synapsin-I, synaptic proteins expressed selectively by amacrine cells, were higher after loss of photoreceptors. The upregulation of syntaxin-I was evident as early as one day after the onset of photoreceptor loss, suggesting that it did not require any massive or structural remodeling, and therefore is possibly reversible. Together, these data show that loss of photoreceptors results in increased synaptic protein levels in bipolar and amacrine cells. Combined with previous reports of increased excitatory and inhibitory synaptic currents in RGCs, these results provide clues to understand the mechanism underlying the aberrant spiking in RGCs. PMID:24595229

  6. Photocrosslinking and Photodamage in Protein-Nucleic Acid Systems Resulting from UV and IR Radiation.

    NASA Astrophysics Data System (ADS)

    Kozub, John Andrew

    1995-01-01

    Photocrosslinking of protein-nucleic acid complexes with low intensity UV has frequently been used to study biological systems. We have investigated the photochemistry of protein-nucleic acid systems using nanosecond UV pulses from a Nd:YAG-pumped dye laser system, low-intensity continuous UV from a typical germicidal lamp, and high-intensity mid -IR pulses from the Vanderbilt Free Electron Laser. Quantum yields for UV-induced nucleic acid damage from laser pulses and the germicidal lamp were found to be nearly equivalent. We have demonstrated the general applicability of the laser to this technique by successfully crosslinking hnRNP protein to RNA, yeast TATA-binding protein to dsDNA, and gene 32 protein to ssDNA with UV laser pulses. Our results indicate that UV-crosslinking has an intrinsic specificity for nucleic acid sites containing thymidine (or uridine), forcing a distinction between preferred binding sites and favorable crosslinking sites. We have found in each system that protein and nucleic acid photodamage competes with crosslinking, limits the yield, and may interfere with subsequent analysis. The distribution of photoproducts in the gene 32 protein-ssDNA system was investigated as a function of the total dose of UV radiation and the intensity of UV laser pulses. It was found that laser pulses providing up to 50 photons per nucleic acid base induce a linear response from the system; the absolute and relative yields of photoproducts depend only on the total dose of UV and not on the rate of delivery. At higher intensities, the yield of crosslinks per incident photon was reduced. A single pulse at the optimum intensity (about 100-200 photons per nucleic acid base) induced roughly 80% of the maximum attainable yield of crosslinks in this system. The early results of our search for photochemistry induced by Free Electron Laser pulses indicate the potential to induce a unique photoreaction in the gene 32 protein -ssDNA system. The yield is apparently enhanced by simultaneous exposure to UV pulses. Future experiments will test the potential of IR and UV irradiations to increase the specificity for photocrosslinks.

  7. Bi6(SeO3)3O5Br2: A new bismuth oxo-selenite bromide

    NASA Astrophysics Data System (ADS)

    Berdonosov, Peter S.; Olenev, Andrei V.; Kirsanova, Maria A.; Lebed, Julia B.; Dolgikh, Valery A.

    2012-12-01

    A new bismuth oxo-selenite bromide Bi6(SeO3)3O5Br2 was synthesized and structurally characterized. The crystal structure belongs to the triclinic system (space group P1Ż, Z=2, a=7.1253(7) Ĺ, b=10.972(1) Ĺ, c=12.117(1) Ĺ, ?=67.765(7)°, ?=82.188(8)°, ?=78.445(7)°) and is unrelated to those of other known oxo-selenite halides. It can be considered as an open framework composed of BiOx or BiOyBrz polyhedrons forming channels running along [1 0 0] direction which contain the selenium atoms in pyramidal shape oxygen coordination (SeO3E). The spectroscopic properties and thermal stability were studied. The new compound is stable up to 400 °C.

  8. Caspase-independent Mitochondrial Cell Death Results from Loss of Respiration, Not Cytotoxic Protein Release

    PubMed Central

    Lartigue, Lydia; Kushnareva, Yulia; Seong, Youngmo; Lin, Helen; Faustin, Benjamin

    2009-01-01

    In apoptosis, mitochondrial outer membrane permeabilization (MOMP) triggers caspase-dependent death. However, cells undergo clonogenic death even if caspases are blocked. One proposed mechanism involved the release of cytotoxic proteins (e.g., AIF and endoG) from mitochondria. To initiate MOMP directly without side effects, we created a tamoxifen-switchable BimS fusion protein. Surprisingly, even after MOMP, caspase-inhibited cells replicated DNA and divided for ?48 h before undergoing proliferation arrest. AIF and endoG remained in mitochondria. However, cells gradually lost mitochondrial membrane potential and ATP content, and DNA synthesis slowed to a halt by 72 h. These defects resulted from a partial loss of respiratory function, occurring 4–8 h after MOMP, that was not merely due to dispersion of cytochrome c. In particular, Complex I activity was completely lost, and Complex IV activity was reduced by ?70%, whereas Complex II was unaffected. Later, cells exhibited a more profound loss of mitochondrial protein constituents. Thus, under caspase inhibition, MOMP-induced clonogenic death results from a progressive loss of mitochondrial function, rather than the release of cytotoxic proteins from mitochondria. PMID:19793916

  9. Infrared evidence for multiple structural transitions in single crystal Cu3(SeO3)2 Cl

    NASA Astrophysics Data System (ADS)

    Miller, Kevin H.; Berger, Helmuth; Tanner, David B.

    2013-03-01

    Infrared reflection and transmission over a broad temperature range (10-300 K) have been measured on the anisotropic single-crystal Cu3(SeO3)2 Cl. Two distinct space groups have previously been reported for Cu3(SeO3)2 Cl at 300 K (monoclinic C2/m and triclinic P1bar). Comparing the number of observed infrared active phonons with group theoretical predictions points towards the existence of the triclinic structure at 300 K; however, an impurity-rich monoclinic structure cannot be ruled out. New phonon modes are observed upon cooling below 90 K, and again upon cooling below 40 K. The latter temperature range corresponds to the onset of long range magnetic order in the material. The structural and magnetic properties of Cu3(SeO3)2 Cl will be discussed in terms of our infrared spectra, group theoretical predictions, and comparisons to related compounds. Supported by the US DOE through contract DE-FG02-02ER45984 at UF.

  10. Enzymatic hydrolysis of brewers' spent grain proteins and technofunctional properties of the resulting hydrolysates.

    PubMed

    Celus, Inge; Brijs, Kristof; Delcour, Jan A

    2007-10-17

    Brewers' spent grain (BSG) is the insoluble residue of barley malt resulting from the manufacture of wort. Although it is the main byproduct of the brewing industry, it has received little attention as a marketable commodity and is mainly used as animal feed. Our work focuses on one of the main constituents of BSG, i.e., the proteins. The lack of solubility of BSG proteins is one of the limitations for their more extensive use in food processing. We therefore aimed to generate BSG protein hydrolysates with improved technofunctional properties. BSG protein concentrate (BPC) was prepared by alkaline extraction of BSG and subsequent acid precipitation. BPC was enzymatically hydrolyzed in a pH-stat setup by several commercially available proteases (Alcalase, Flavourzyme, and Pepsin) for different times and/or with different enzyme concentrations in order to obtain hydrolysates with different degrees of hydrolysis (DH). Physicochemical properties, such as molecular weight (MW) distribution and hydrophobicity, as well as technofunctional properties, such as solubility, color, and emulsifying and foaming properties, were determined. Enzymatic hydrolysis of BPC improved emulsion and/or foam-forming properties. However, for the hydrolysates prepared with Alcalase and Pepsin, an increasing DH generally decreased emulsifying and foam-forming capacities. Moreover, the type of enzyme impacted the resulting technofunctional properties. Hydrolysates prepared with Flavourzyme showed good technofunctional properties, independent of the DH. Physicochemical characterization of the hydrolysates indicated the importance of protein fragments with relatively high MW (exceeding 14.5 k) and high surface hydrophobicity for favorable technofunctional properties. PMID:17896813

  11. Aging results in an unusual expression of Drosophila heat shock proteins

    SciTech Connect

    Fleming, J.E.; Walton, J.K.; Dubitsky, R.; Bensch, K.G. )

    1988-06-01

    The authors used high-resolution two-dimensional polyacrylamide gel electrophoresis to evaluate the effect of aging on the heat shock response in Drosophila melanogaster. Although the aging process is not well understood at the molecular level, recent observations suggest that quantitative changes in gene expression occur as these fruit flies approach senescence. Such genetic alterations are in accord with our present data, which clearly show marked differences in the synthesis of heat shock proteins between young and old fruit flies. In 10-day-old flies, a heat shock of 20 min results in the expression of 14 new proteins as detectable by two-dimensional electrophoresis of ({sup 35}S)methionine-labeled polypeptides, whereas identical treatment of 45-day-old flies leads to the expression of at least 50 new or highly up-regulated proteins. In addition, there is also a concomitant increase in the rate of synthesis of a number of the normal proteins in the older animals. Microdensitometric determinations of the low molecular weight heat shock polypeptides on autoradiographs of five age groups revealed that their maximum expression occurs at 47 days for a population of flies with a mean life span of 33.7 days. Moreover, a heat shock effect similar to that observed in senescent flies occurs in young flies fed canavanine, an arginine analogue, before heat shock.

  12. Protein crystal growth results from the United States Microgravity Laboratory-1 mission

    NASA Technical Reports Server (NTRS)

    Delucas, Lawrence J.; Moore, K. M.; Vanderwoerd, M.; Bray, T. L.; Smith, C.; Carson, M.; Narayana, S. V. L.; Rosenblum, W. M.; Carter, D.; Clark, A. D, Jr.

    1994-01-01

    Protein crystal growth experiments have been performed by this laboratory on 18 Space Shuttle missions since April, 1985. In addition, a number of microgravity experiments also have been performed and reported by other investigators. These Space Shuttle missions have been used to grow crystals of a variety of proteins using vapor diffusion, liquid diffusion, and temperature-induced crystallization techniques. The United States Microgravity Laboratory - 1 mission (USML-1, June 25 - July 9, 1992) was a Spacelab mission dedicated to experiments involved in materials processing. New protein crystal growth hardware was developed to allow in orbit examination of initial crystal growth results, the knowledge from which was used on subsequent days to prepare new crystal growth experiments. In addition, new seeding hardware and techniques were tested as well as techniques that would prepare crystals for analysis by x-ray diffraction, a capability projected for the planned Space Station. Hardware that was specifically developed for the USML-1 mission will be discussed along with the experimental results from this mission.

  13. Divergent Evolution of CHD3 Proteins Resulted in MOM1 Refining Epigenetic Control in Vascular Plants

    PubMed Central

    ?aikovski, Marian; Yokthongwattana, Chotika; Habu, Yoshiki; Nishimura, Taisuke; Mathieu, Olivier; Paszkowski, Jerzy

    2008-01-01

    Arabidopsis MOM1 is required for the heritable maintenance of transcriptional gene silencing (TGS). Unlike many other silencing factors, depletion of MOM1 evokes transcription at selected loci without major changes in DNA methylation or histone modification. These loci retain unusual, bivalent chromatin properties, intermediate to both euchromatin and heterochromatin. The structure of MOM1 previously suggested an integral nuclear membrane protein with chromatin-remodeling and actin-binding activities. Unexpected results presented here challenge these presumed MOM1 activities and demonstrate that less than 13% of MOM1 sequence is necessary and sufficient for TGS maintenance. This active sequence encompasses a novel Conserved MOM1 Motif 2 (CMM2). The high conservation suggests that CMM2 has been the subject of strong evolutionary pressure. The replacement of Arabidopsis CMM2 by a poplar motif reveals its functional conservation. Interspecies comparison suggests that MOM1 proteins emerged at the origin of vascular plants through neo-functionalization of the ubiquitous eukaryotic CHD3 chromatin remodeling factors. Interestingly, despite the divergent evolution of CHD3 and MOM1, we observed functional cooperation in epigenetic control involving unrelated protein motifs and thus probably diverse mechanisms. PMID:18725928

  14. Correlating labeling chemistry and in-vitro test results with the biological behavior of radiolabeled proteins

    SciTech Connect

    Srivastava, S.C.; Meinken, G.E.

    1985-01-01

    Monoclonal antibodies possess enormous potential for delivery of therapeutic amounts of radionuclides to target antigens in vivo, in particular for tumor imaging and therapy. Translation of this concept into practice has encountered numerous problems. Specifically whereas general protein radiolabeling methods are applicable to antibodies, immunological properties of the antibodies are often compromised resulting in reduced in-vivo specificity for the target antigens. The bifunctional chelating agent approach shows the most promise, however, development of other agents will be necessary for widespread usefulness of this technique. The effects of labeling chemistry on the in-vivo behavior of several monoclonal antibodies are described. 30 refs., 4 figs., 10 tabs.

  15. Deficiency of a protein-repair enzyme results in the accumulation of altered proteins, retardation of growth, and fatal seizures in?mice

    PubMed Central

    Kim, Edward; Lowenson, Jonathan D.; MacLaren, Duncan C.; Clarke, Steven; Young, Stephen G.

    1997-01-01

    l-Asparaginyl and l-aspartyl residues in proteins are subject to spontaneous degradation reactions that generate isomerized and racemized aspartyl derivatives. Proteins containing l-isoaspartyl and d-aspartyl residues can have altered structures and diminished biological activity. These residues are recognized by a highly conserved cytosolic enzyme, the protein l-isoaspartate(d-aspartate) O-methyltransferase (EC 2.1.1.77). The enzymatic methyl esterification of these abnormal residues in vitro can lead to their conversion (i.e., repair) to normal l-aspartyl residues and should therefore prevent the accumulation of potentially dysfunctional proteins in vivo as cells and tissues age. Particularly high levels of the repair methyltransferase are present in the brain, although enyzme activity is present in all vertebrate tissues. To define the physiological relevance of this protein-repair pathway and to determine whether deficient protein repair would cause central nervous system dysfunction, we used gene targeting in mouse embryonic stem cells to generate protein l-isoaspartate(d-aspartate) O-methyltransferase-deficient mice. Analyses of tissues from methyltransferase knockout mice revealed a striking accumulation of protein substrates for this enzyme in the cytosolic fraction of brain, heart, liver, and erythrocytes. The knockout mice showed significant growth retardation and succumbed to fatal seizures at an average of 42 days after birth. These results suggest that the ability of mice to repair l-isoaspartyl- and d-aspartyl-containing proteins is essential for normal growth and for normal central nervous system function. PMID:9177182

  16. HIV-1 Tat Protein Increases Microglial Outward K+ Current and Resultant Neurotoxic Activity

    PubMed Central

    Liu, Jianuo; Xu, Peng; Collins, Cory; Liu, Han; Zhang, Jingdong; Keblesh, James P.; Xiong, Huangui

    2013-01-01

    Microglia plays a crucial role in the pathogenesis of HIV-1-associated neurocognitive disorders. Increasing evidence indicates the voltage-gated potassium (Kv) channels are involved in the regulation of microglia function, prompting us to hypothesize Kv channels may also be involved in microglia-mediated neurotoxic activity in HIV-1-infected brain. To test this hypothesis, we investigated the involvement of Kv channels in the response of microglia to HIV-1 Tat protein. Treatment of rat microglia with HIV-1 Tat protein (200 ng/ml) resulted in pro-inflammatory microglial activation, as indicated by increases in TNF-?, IL-1?, reactive oxygen species, and nitric oxide, which were accompanied by enhanced outward K+ current and Kv1.3 channel expression. Suppression of microglial Kv1.3 channel activity, either with Kv1.3 channel blockers Margatoxin, 5-(4-Phenoxybutoxy)psoralen, or broad-spectrum K+ channel blocker 4-Aminopyridine, or by knockdown of Kv1.3 expression via transfection of microglia with Kv1.3 siRNA, was found to abrogate the neurotoxic activity of microglia resulting from HIV-1 Tat exposure. Furthermore, HIV-1 Tat-induced neuronal apoptosis was attenuated with the application of supernatant collected from K+ channel blocker-treated microglia. Lastly, the intracellular signaling pathways associated with Kv1.3 were investigated and enhancement of microglial Kv1.3 was found to correspond with an increase in Erk1/2 mitogen-activated protein kinase activation. These data suggest targeting microglial Kv1.3 channels may be a potential new avenue of therapy for inflammation-mediated neurological disorders. PMID:23738010

  17. Inhibition of protein kinase C results in decreased expression of bovine leukemia virus.

    PubMed Central

    Jensen, W A; Wicks-Beard, B J; Cockerell, G L

    1992-01-01

    The in vitro expression of bovine leukemia virus (BLV) in short-term cultured bovine peripheral blood mononuclear cells (PBMC) is associated with increased spontaneous lymphocyte blastogenesis. The purpose of this study was to determine whether intracellular pathways responsible for antigen- or mitogen-induced lymphocyte blastogenesis were also responsible for induction of BLV expression. The protein kinase C (PKC) inhibitor 1-(5-isoquinolinylsulfonyl)-3-methylpiperazine dihydrochloride (3-methyl H7) decreased blastogenesis in a dose-dependent manner, as measured by [3H]thymidine incorporation, in unstimulated, lipopolysaccharide-stimulated and phorbol ester (PMA)-stimulated BLV-infected PBMC. Similarly, 3-methyl H7 decreased BLV expression, as measured by production of gp51 envelope antigen or p24gag antigen, in BLV-infected PBMC under the same conditions. Using an RNase protection assay, the inhibition of BLV expression by 3-methyl H7 was shown to be due to decreased transcriptional activity. The cyclic GMP-dependent protein kinase and cyclic AMP-dependent protein kinase inhibitor N-(2-guanidinoethyl)-5-isoquinolinesulfonamide (HA1004) did not inhibit either BLV expression or blastogenesis of BLV-infected bovine PBMC. Additional evidence for the PKC-dependent expression of BLV was obtained by using a persistently BLV-infected B-lymphocyte cell line, NBC-13. Activation of PKC by PMA in NBC-13 cells increased BLV expression. 3-methyl H7 decreased the PMA-induced expression of BLV in NBC-13 cells in a dose-dependent manner, whereas HA1004 did not inhibit this expression. These results identify a mechanism for the induction of BLV expression through PKC activation and therefore indicate that latency and replication of BLV is controlled by normal B-lymphocyte intracellular signaling pathways. Images PMID:1318412

  18. Switching kinetics of the ferroelectric transition in K2SeO4 studied by stroboscopic ?-ray diffraction

    NASA Astrophysics Data System (ADS)

    Leist, J.; Gibhardt, H.; Eckold, G.

    2013-11-01

    The kinetics of the ferroelectric lock-in transition in potassium selenate (K2SeO4) was studied on a millisecond timescale using high-resolution ?-ray diffraction. A large change of the line width and wavevector of the first order satellite is observed during the switching process. This is attributed to a loss of long-range order under the influence of the electric field. In addition, the incommensurate phase is stabilized by the pulsed field and the transition to the pure commensurate phase is shifted to lower temperatures. Strains that may build up during the rapid switching process are supposed to be the reason for this behaviour.

  19. Lead (II) selenite halides Pb3(SeO3)2 X 2 ( X = Br, I): Synthesis and crystal structure

    NASA Astrophysics Data System (ADS)

    Berdonosov, P. S.; Olenev, A. V.; Dolgikh, V. A.

    2012-03-01

    Two lead selenite halides, Pb3(SeO3)2Br2 and Pb3(SeO3)2I2, have been prepared by solid-phase synthesis and structurally characterized. These compounds are isotypic and can be considered 3D with a microporous framework composed of lead polyhedra (distorted Archimedean antiprisms formed by oxygen and halogen atoms). The framework contains channels oriented in the [010] direction. These channels contain selenium atoms, which are bound with framework oxygen atoms belonging to different lead polyhedra.

  20. Abstract--Most high-throughput experimental results of protein-protein interactions (PPIs) are seemingly inconsistent

    E-print Network

    of individual proteins to interact and, therefore, create apparent differences among PPIs, the physical nature determine the activity of a functional cell. A comprehensive and accurate definition of various interactomes, in part, by the U.S. Army's Network Science Initiative through the Military Operational Medicine Research

  1. SANS study of interaction of silica nanoparticles with BSA protein and their resultant structure

    SciTech Connect

    Yadav, Indresh Aswal, V. K.; Kohlbrecher, J.

    2014-04-24

    Small angle neutron scattering (SANS) has been carried out to study the interaction of anionic silica nanoparticles (88 Ĺ) with globular protein Bovine Serum Albumin (BSA) (M.W. 66.4 kD) in aqueous solution. The measurements have been carried out on fixed concentration (1 wt %) of Ludox silica nanoparticles with varying concentration of BSA (0–5 wt %) at pH7. Results show that silica nanoparticles and BSA coexist as individual entities at low concentration of BSA where electrostatic repulsive interactions between them prevent their aggregation. However, as the concentration of BSA increases (? 0.5 wt %), it induces the attractive depletion interaction among nanoparticles leading to finally their aggregation at higher BSA concentration (2 wt %). The aggregates are found to be governed by the diffusion limited aggregation (DLA) morphology of fractal nature having fractal dimension about 2.4.

  2. Immunohistochemistry staining for mismatch repair proteins: the endoscopic biopsy material provides useful and coherent results.

    PubMed

    Vilkin, Alex; Leibovici-Weissman, Ya'ara; Halpern, Marisa; Morgenstern, Sara; Brazovski, Eli; Gingold-Belfer, Rachel; Wasserberg, Nir; Brenner, Baruch; Niv, Yaron; Sneh-Arbib, Orly; Levi, Zohar

    2015-11-01

    Immunohistochemistry (IHC) testing for mismatch repair proteins (MMRP) in patients with colorectal cancer can be performed on endoscopic biopsy material or the surgical resection material. Data are continuing to accumulate regarding the deleterious effect of neoadjuvant chemoradiation on MMRP expression. However, despite continuing rise in the use of endoscopic biopsies for IHC, most pathology departments still use mainly the surgical materials for IHC testing. In this study we compared the quality of stains among 96 colon cancer subjects with paired endoscopic and surgical material available for MLH1, MSH2, MSH6, and PMS2 stains (96 × 4, yielding 384 paired stains). Each slide received both a quantitative score (immunoreactivity [0-3] × percent positivity [0-4]) and a qualitative score (absent; weak and focal; strong). The quantitative scores of all MMRP were significantly higher among the endoscopic material (P<.001 for all). In 358 pairs (93.2%), both the endoscopic and operative material stained either strong (322, 83.9%) or absent (36, 9.4%). In 26 pairs (6.8%), the endoscopic material stained strong, whereas the operative material stained focal and weak. No endoscopic biopsy materials stained focal and weak. Our findings indicate that the biopsy material may provide more coherent results. Although these results may indicate that biopsy material provides coherent and useful results, it is yet to be determined if the demonstrated differences pose a real clinical problem in interpreting final results of IHC staining of such kind. Hence, we suggest that when available, the endoscopic material rather than the operative one should serve as the primary substrate for IHC staining. PMID:26359539

  3. Ordering of the O(2)…D… O(2) bonds near the phase transition in KD3(SeO3)2 single crystals by D nuclear magnetic resonance

    NASA Astrophysics Data System (ADS)

    Lim, Ae Ran; Jeong, Se-Young

    2013-01-01

    Deuterium resonance investigations of KD3(SeO3)2 single crystals have been performed near the phase transition temperature T C . There are two types of deuterium bonds in these crystals with different behaviors at this phase transition. Our experimental results show that there are significant changes in the D spinlattice relaxation time T 1 at T C ; the abrupt decrease in T 1 near T C can be explained by the critical slowing down of an overdamped soft pseudospin-type deuteron mode. Further, the ordering of the O(2)…D… O(2) bonds is affected by the phase transition, whereas the ordering of the O(1)-D… O(3) bonds is unaffected. The D NMR measurements also show that the D(2) deuteron disordering above T C is dynamic and not static.

  4. Pooled Results From 5 Validation Studies of Dietary Self-Report Instruments Using Recovery Biomarkers for Energy and Protein Intake

    PubMed Central

    Freedman, Laurence S.; Commins, John M.; Moler, James E.; Arab, Lenore; Baer, David J.; Kipnis, Victor; Midthune, Douglas; Moshfegh, Alanna J.; Neuhouser, Marian L.; Prentice, Ross L.; Schatzkin, Arthur; Spiegelman, Donna; Subar, Amy F.; Tinker, Lesley F.; Willett, Walter

    2014-01-01

    We pooled data from 5 large validation studies of dietary self-report instruments that used recovery biomarkers as references to clarify the measurement properties of food frequency questionnaires (FFQs) and 24-hour recalls. The studies were conducted in widely differing US adult populations from 1999 to 2009. We report on total energy, protein, and protein density intakes. Results were similar across sexes, but there was heterogeneity across studies. Using a FFQ, the average correlation coefficients for reported versus true intakes for energy, protein, and protein density were 0.21, 0.29, and 0.41, respectively. Using a single 24-hour recall, the coefficients were 0.26, 0.40, and 0.36, respectively, for the same nutrients and rose to 0.31, 0.49, and 0.46 when three 24-hour recalls were averaged. The average rate of under-reporting of energy intake was 28% with a FFQ and 15% with a single 24-hour recall, but the percentages were lower for protein. Personal characteristics related to under-reporting were body mass index, educational level, and age. Calibration equations for true intake that included personal characteristics provided improved prediction. This project establishes that FFQs have stronger correlations with truth for protein density than for absolute protein intake, that the use of multiple 24-hour recalls substantially increases the correlations when compared with a single 24-hour recall, and that body mass index strongly predicts under-reporting of energy and protein intakes. PMID:24918187

  5. Heterologous Activation of Protein Kinase C Stimulates Phosphorylation of -Opioid Receptor at Serine 344, Resulting

    E-print Network

    Tian, Weidong

    Heterologous Activation of Protein Kinase C Stimulates Phosphorylation of -Opioid Receptor of the current study is to investigate the effect of opioid-independent, heterologous activation of protein kinase C (PKC) on the responsiveness of opioid receptor and the underlying molecular mechanisms. Our

  6. Preparation and characterization of SeO2/TiO2 composite photocatalyst with excellent performance for sunset yellow azo dye degradation under natural sunlight illumination

    NASA Astrophysics Data System (ADS)

    Rajamanickam, D.; Dhatshanamurthi, P.; Shanthi, M.

    2015-03-01

    To improve the solar light induced photocatalytic application performances of TiO2, in this study, the SeO2 modified TiO2 composite photocatalysts with various ratios of SeO2 to TiO2 were prepared by sol-gel method. The catalyst was characterized by X-ray diffraction (XRD), high resolution scanning electron microscope (HR-SEM), energy dispersive spectra (EDS), diffuse reflectance spectra (DRS), photoluminescence spectra (PL), X-ray photoelectron spectroscopy (XPS) and Brunauer-Emmett-Teller (BET) surface area measurement methods. The photocatalytic activity of SeO2/TiO2 was investigated for the degradation of sunset yellow (SY) in aqueous solution using solar light. The SeO2/TiO2 is found to be more efficient than prepared TiO2 and TiO2-P25 at pH 7 for the mineralization of SY. The effects of operational parameters such as the amount of photocatalyst, dye concentration and initial pH on photo mineralization of SY have been analyzed. The degradation was strongly enhanced in the presence of electron acceptors such as oxone, KIO4 and KBrO3. The kinetics of SY photodegradation was found to follow the pseudo-first order rate law and could be described in terms of Langmuir-Hinshelwood model. The mineralization of SY has been confirmed by COD measurements. The catalyst is found to be reusable.

  7. Bio-LDH nanohybrid for gene therapy Seo-Young Kwak, Yong-Joo Jeong, Jong-Sang Park, Jin-Ho Choy*

    E-print Network

    Park, Jong-Sang

    Bio-LDH nanohybrid for gene therapy Seo-Young Kwak, Yong-Joo Jeong, Jong-Sang Park, Jin-Ho Choy. Introduction Gene therapy is gaining growing attention for the treatment of genetic deficiencies and life of a targeting ligand and a DNA-binding moiety, have great potential for gene therapy due to their safety

  8. Formation energy of -carbide using ab initio calculations Seung-Woo Seo, You Young Song, In Gee Kim, H. K. D. H. Bhadeshia

    E-print Network

    Cambridge, University of

    Formation energy of -carbide using ab initio calculations Seung-Woo Seo, You Young Song, In Gee Kim(Fe,Mn)3C with an anti-perovskite structure, known as -carbide, is easily found in strong, low is enhanced by the precipitation of -carbide, which is coherent with austenite, causes a shear band induced

  9. Sr3Bi2(SeO3)6·H2O: A novel anionic layer consisting of second-order Jahn-Teller (SOJT) distortive cations

    NASA Astrophysics Data System (ADS)

    Ahn, Hyun Sun; Lee, Eun Pyo; Chang, Hong-Young; Lee, Dong Woo; Ok, Kang Min

    2015-01-01

    A new layered bismuth selenite hydrate material, Sr3Bi2(SeO3)6·H2O has been synthesized through a hydrothermal reaction using SrCO3, Bi2O3, SeO2, and water as reagents. The crystal structure of the reported material has been determined by single crystal X-ray diffraction analysis. The anionic layered framework of Sr3Bi2(SeO3)6·H2O consists of polyhedra of second-order Jahn-Teller (SOJT) distortive cations, Bi3+ and Se4+. Attributable to the variable and asymmetric coordination geometry of the constituent cations, a rich structural chemistry including uni-dimensional bands and linkers is observed in the layer. The material is thermally stable up to about 390 °C and starts decomposing due to the sublimation of SeO2 above the temperature. The UV-vis diffuse reflectance spectrum suggests a band gap of 3.3 eV. Elemental analysis, infrared spectrum, local dipole moment calculations, and electronic structure calculations are also reported.

  10. Halophilic Protein Adaptation Results from Synergistic Residue-Ion Interactions in the Folded and Unfolded States.

    PubMed

    Ortega, Gabriel; Diercks, Tammo; Millet, Oscar

    2015-12-17

    Halophilic organisms thrive in environments with extreme salt concentrations and have adapted by allowing molar quantities of cosolutes, mainly KCl, to accumulate in their cytoplasm. To cope with this high intracellular salinity, halophilic organisms modified the chemical composition of their proteins to enrich their surface with acidic and short polar side chains, while lysines and bulky hydrophobic residues got depleted. We have emulated the evolutionary process of haloadaptation with natural and designed halophilic polypeptides and applied novel nuclear magnetic resonance (NMR) methodology to study the different mechanisms contributing to protein haloadaptation at a per residue level. Our analysis of an extensive set of NMR observables, determined over several proteins, allowed us to disentangle the synergistic contributions of protein haloadaptation: cation exclusion and electrostatic repulsion between negatively charged residues destabilize the denatured state ensemble while cumulative weak cation-protein interactions stabilize the folded conformations. PMID:26628359

  11. The Structural Biology Center 19ID undulator beamline: facility specifications and protein crystallographic results

    PubMed Central

    Rosenbaum, Gerd; Alkire, Randy W.; Evans, Gwyndaf; Rotella, Frank J.; Lazarski, Krzystof; Zhang, Rong-Guang; Ginell, Stephan L.; Duke, Norma; Naday, Istvan; Lazarz, Jack; Molitsky, Michael J.; Keefe, Lisa; Gonczy, John; Rock, Larry; Sanishvili, Ruslan; Walsh, Martin A.; Westbrook, Edwin; Joachimiak, Andrzej

    2008-01-01

    The 19ID undulator beamline of the Structure Biology Center has been designed and built to take full advantage of the high flux, brilliance and quality of X-ray beams delivered by the Advanced Photon Source. The beamline optics are capable of delivering monochromatic X-rays with photon energies from 3.5 to 20 keV (3.5–0.6 Ĺ wavelength) with fluxes up to 8–18 × 1012 photons s?1 (depending on photon energy) onto cryogenically cooled crystal samples. The size of the beam (full width at half-maximum) at the sample position can be varied from 2.2 mm × 1.0 mm (horizontal × vertical, unfocused) to 0.083 mm × 0.020 mm in its fully focused configuration. Specimen-to-detector distances of between 100 mm and 1500 mm can be used. The high flexibility, inherent in the design of the optics, coupled with a ?-geometry goniometer and beamline control software allows optimal strategies to be adopted in protein crystallographic experiments, thus maximizing the chances of their success. A large-area mosaic 3 × 3 CCD detector allows high-quality diffraction data to be measured rapidly to the crystal diffraction limits. The beamline layout and the X-ray optical and endstation components are described in detail, and the results of representative crystallographic experiments are presented. PMID:16371706

  12. Vascular endothelial dysfunction resulting from l-arginine deficiency in a patient with lysinuric protein intolerance

    PubMed Central

    Kamada, Yoshihiro; Nagaretani, Hiroyuki; Tamura, Shinji; Ohama, Tohru; Maruyama, Takao; Hiraoka, Hisatoyo; Yamashita, Shizuya; Yamada, Akira; Kiso, Shinichi; Inui, Yoshiaki; Ito, Nobuyuki; Kayanoki, Yoshiro; Kawata, Sumio; Matsuzawa, Yuji

    2001-01-01

    Although L-arginine is the only substrate for nitric oxide (NO) production, no studies have yet been reported on the effect of an L-arginine deficiency on vascular function in humans. Lysinuric protein intolerance (LPI) is a rare autosomal recessive defect of dibasic amino acid transport caused by mutations in the SLC7A7 gene, resulting in an L-arginine deficiency. Vascular endothelial function was examined in an LPI patient who was shown to be a compound heterozygote for two mutations in the gene (5.3-kbp Alu-mediated deletion, IVS3+1G??). The lumen diameter of the brachial artery was measured in this patient and in healthy controls at rest, during reactive hyperemia (endothelium-dependent vasodilation [EDV]), and after sublingual nitroglycerin administration (endothelium-independent vasodilation [EIV]) using ultrasonography. Both EDV and NOx concentrations were markedly reduced in the patient compared with those for the controls. They became normal after an L-arginine infusion. EIV was not significantly different between the patient and controls. Positron emission tomography of the heart and a treadmill test revealed ischemic changes in the patient, which were improved by the L-arginine infusion. Thus, in the LPI patient, L-arginine deficiency caused vascular endothelial dysfunction via a decrease in NO production. PMID:11544277

  13. Loss of Clcc1 Results in ER Stress, Misfolded Protein Accumulation, and Neurodegeneration

    PubMed Central

    Jia, Yichang; Jucius, Thomas J.; Cook, Susan A.

    2015-01-01

    Folding of transmembrane and secretory proteins occurs in the lumen of the endoplasmic reticulum (ER) before transportation to the cell surface and is monitored by the unfolded protein response (UPR) signaling pathway. The accumulation of unfolded proteins in the ER activates the UPR that restores ER homeostasis by regulating gene expression that leads to an increase in the protein-folding capacity of the ER and a decrease in the ER protein-folding load. However, prolonged UPR activity has been associated with cell death in multiple pathological conditions, including neurodegeneration. Here, we report a spontaneous recessive mouse mutation that causes progressive cerebellar granule cell death and peripheral motor axon degeneration. By positional cloning, we identify the mutation in this strain as a retrotransposon insertion in the Clcc1 gene, which encodes a putative chloride channel localized to the ER. Furthermore, we demonstrate that the C3H/HeSnJ inbred strain has late onset cerebellar degeneration due to this mutation. Interestingly, acute knockdown of Clcc1 expression in cultured cells increases sensitivity to ER stress. In agreement, GRP78, the major HSP70 family chaperone in the ER, is upregulated in Clcc1-deficient granule cells in vivo, and ubiquitinated proteins accumulate in these neurons before their degeneration. These data suggest that disruption of chloride homeostasis in the ER disrupts the protein-folding capacity of the ER, leading to eventual neuron death. PMID:25698737

  14. Moderate energy restriction with high protein diet results in healthier outcome in women

    PubMed Central

    2010-01-01

    Background The present study compares two different weight reduction regimens both with a moderately high protein intake on body composition, serum hormone concentration and strength performance in non-competitive female athletes. Methods Fifteen normal weighted women involved in recreational resistance training and aerobic training were recruited for the study (age 28.5 ± 6.3 yr, height 167.0 ± 7.0 cm, body mass 66.3 ± 4.2 kg, body mass index 23.8 ± 1.8, mean ± SD). They were randomized into two groups. The 1 KG group (n = 8; energy deficit 1100 kcal/day) was supervised to reduce body weight by 1 kg per week and the 0.5 KG group (n = 7; energy deficit 550 kcal/day) by 0.5 kg per week, respectively. In both groups protein intake was kept at least 1.4 g/kg body weight/day and the weight reduction lasted four weeks. At the beginning of the study the energy need was calculated using food and training diaries. The same measurements were done before and after the 4-week weight reduction period including total body composition (DXA), serum hormone concentrations, jumping ability and strength measurements Results During the 4-week weight reduction period there were no changes in lean body mass and bone mass, but total body mass, fat mass and fat percentage decreased significantly in both groups. The changes were greater in the 1 KG group than in the 0.5 KG group in total body mass (p < 0.001), fat mass (p < 0.001) and fat percentage (p < 0.01). Serum testosterone concentration decreased significantly from 1.8 ± 1.0 to 1.4 ± 0.9 nmol/l (p < 0.01) in 1 KG and the change was greater in 1 KG (30%, p < 0.001) than in 0.5 KG (3%). On the other hand, SHBG increased significantly in 1 KG from 63.4 ± 17.7 to 82.4 ± 33.0 nmol/l (p < 0.05) during the weight reducing regimen. After the 4-week period there were no changes in strength performance in 0.5 KG group, however in 1 KG maximal strength in bench press decreased (p < 0.05) while endurance strength in squat and counter movement jump improved (p < 0.05) Conclusion It is concluded that a weight reduction by 0.5 kg per week with ~1.4 g protein/kg body weight/day can be recommended to normal weighted, physically active women instead of a larger (e.g. 1 kg per week) weight reduction because the latter may lead to a catabolic state. Vertical jumping performance is improved when fat mass and body weight decrease. Thus a moderate weight reduction prior to a major event could be considered beneficial for normal built athletes in jumping events. PMID:20205751

  15. Reduced functionality of PSE-like chicken breast meat batter resulting from alterations in protein conformation.

    PubMed

    Li, K; Zhao, Y Y; Kang, Z L; Wang, P; Han, M Y; Xu, X L; Zhou, G H

    2015-01-01

    The objectives of this study were to evaluate protein thermal stability, water-protein interaction, microstructure, and protein conformation between PSE-like and normal chicken breast meat batters. Sixty pale, soft, and exudative (PSE)-like (L*>53, pH24 h<5.7) and 60 normal (46protein and 2% salt, and they were analyzed for the protein changes and the microstructure using differential scanning calorimetry, low-field (LF)-NMR, SEM, and Raman spectroscopy. PSE-like meat batter had lower gel strength, water-holding capacity, and salt-soluble protein extraction (P<0.05). Heated PSE-like meat batter formed an aggregated gel matrix, while normal meat batter produced a compact gel network with fine, cross-linked strands by many protein filaments. LF-NMR revealed an increase in the water mobility in heated PSE-like meat batter with an increasing amount of loosely bound water (P<0.05). No significant changes were observed in the electrophoretic patterns of salt-soluble protein extracts by SDS-PAGE. However, differential scanning calorimetry showed that PSE-like meat had greater myosin and sarcoplasmic proteins/collagen denaturation (P<0.05). In PSE-like meat, actin denaturation was particular evident after salt addition (P<0.05) using differential scanning calorimetry. Moreover, Raman spectroscopy indicated that PSE-like meat batter had less unfolded ?-helix and ?-sheet structure formation, reduced exposure of hydrophobic and tyrosine residues (P<0.05), and changes in the microenvironment of aliphatic residues and tryptophan, which affected salt-soluble protein extraction, gel properties, and water-holding capacity. In conclusion, the inferior functional properties of PSE-like meat were attributed to not only myosin denaturation, but also actin denaturation after salt addition and different protein structural states. PMID:25577798

  16. Total protein concentration and diagnostic test results for gray wolf (Canis lupus) serum using Nobuto filter paper strips.

    PubMed

    Jara, Rocío F; Sepúlveda, Carolina; Ip, Hon S; Samuel, Michael D

    2015-04-01

    Nobuto filter paper strips are widely used for storing blood-serum samples, but the recovery of proteins from these strips following rehydration is unknown. Poor recovery of proteins could reduce the concentration of antibodies and antigens and reduce the sensitivity of diagnostic assays. We compared the protein concentration, and its association with test sensitivity, of eluted Nobuto strip samples with paired sera. We collected and froze serum from five gray wolves (Canis lupus) for 8 mo. When thawed, we used a spectrophotometer (absorbance 280 nm) to determine the serum protein concentration for paired sera and Nobuto eluates for each animal in 2-fold serial dilutions. Total protein concentration was similar for both sample storage methods (Nobuto eluates and control sera), except for the undiluted samples in which Nobuto eluates had higher total protein concentrations. Both sample storage methods appear to produce similar results using the SNAP® 4Dx® Test to detect antibodies against pathogens causing Lyme disease, anaplasmosis, and ehrlichiosis as well as antigen for canine heartworm disease. PMID:25574804

  17. Presynaptic Deletion of GIT Proteins Results in Increased Synaptic Strength at a Mammalian Central Synapse.

    PubMed

    Montesinos, Mónica S; Dong, Wei; Goff, Kevin; Das, Brati; Guerrero-Given, Debbie; Schmalzigaug, Robert; Premont, Richard T; Satterfield, Rachel; Kamasawa, Naomi; Young, Samuel M

    2015-12-01

    A cytomatrix of proteins at the presynaptic active zone (CAZ) controls the strength and speed of neurotransmitter release at synapses in response to action potentials. However, the functional role of many CAZ proteins and their respective isoforms remains unresolved. Here, we demonstrate that presynaptic deletion of the two G protein-coupled receptor kinase-interacting proteins (GITs), GIT1 and GIT2, at the mouse calyx of Held leads to a large increase in AP-evoked release with no change in the readily releasable pool size. Selective presynaptic GIT1 ablation identified a GIT1-specific role in regulating release probability that was largely responsible for increased synaptic strength. Increased synaptic strength was not due to changes in voltage-gated calcium channel currents or activation kinetics. Quantitative electron microscopy revealed unaltered ultrastructural parameters. Thus, our data uncover distinct roles for GIT1 and GIT2 in regulating neurotransmitter release strength, with GIT1 as a specific regulator of presynaptic release probability. PMID:26637799

  18. Proteins.

    ERIC Educational Resources Information Center

    Doolittle, Russell F.

    1985-01-01

    Examines proteins which give rise to structure and, by virtue of selective binding to other molecules, make genes. Binding sites, amino acids, protein evolution, and molecular paleontology are discussed. Work with encoding segments of deoxyribonucleic acid (exons) and noncoding stretches (introns) provides new information for hypotheses. (DH)

  19. Mutations in the DI-DII Linker of Human Parainfluenza Virus Type 3 Fusion Protein Result in Diminished Fusion Activity

    PubMed Central

    Xie, Wenyan; Wen, Hongling; Chu, Fulu; Yan, Shaofeng; Lin, Bin; Xie, Wenli; Liu, Ying; Ren, Guijie; Zhao, Li; Song, Yanyan; Sun, Chengxi; Wang, Zhiyu

    2015-01-01

    Human parainfluenza virus type 3 (HPIV3) can cause severe respiratory tract diseases in infants and young children, but no licensed vaccines or antiviral agents are currently available for treatment. Fusing the viral and target cell membranes is a prerequisite for its entry into host cells and is directly mediated by the fusion (F) protein. Although several domains of F are known to have important effects on regulating the membrane fusion activity, the roles of the DI-DII linker (residues 369–374) of the HPIV3 F protein in the fusogenicity still remains ill-defined. To facilitate our understanding of the role of this domain might play in F-induced cell-cell fusion, nine single mutations were engineered into this domain by site-directed mutagenesis. A vaccinia virus-T7 RNA polymerase transient expression system was employed to express the wild-type or mutated F proteins. These mutants were analyzed for membrane fusion activity, cell surface expression, and interaction between F and HN protein. Each of the mutated F proteins in this domain has a cell surface expression level similar to that of wild-type F. All of them resulted in a significant reduction in fusogenic activity in all steps of membrane fusion. Furthermore, all these fusion-deficient mutants reduced the amount of the HN-F complexes at the cell surface. Together, the results of our work suggest that this region has an important effect on the fusogenic activity of F. PMID:26305905

  20. Overexpression of Drosophila juvenile hormone esterase binding protein results in anti-JH effects and reduced pheromone abundance

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The titer of juvenile hormone (JH), which has wide ranging physiological effects in insects, is regulated in part by JH esterase (JHE). We show that overexpression in Drosophila melanogaster of the JHE binding protein, DmP29 results in a series of apparent anti-JH effects. We hypothesize that DmP29 ...

  1. Local structure of Rb2Li4(SeO4)3·2H2O by the modeling of X-ray diffuse scattering — from average-structure to microdomain model

    NASA Astrophysics Data System (ADS)

    Komornicka, Dorota; Wo?cyrz, Marek; Pietraszko, Adam

    2012-08-01

    Local structure of dirubidium tetralithium tris(selenate(VI)) dihydrate — Rb2Li4(SeO4)3· 2H2O has been determined basing on the modeling of X-ray diffuse scattering. The origin of observed structured diffuse streaks is SeO4 tetrahedra switching between two alternative positions in two quasi-planar layers existing in each unit cell and formation of domains with specific SeO4 tetrahedra configuration locally fulfilling condition for C-centering in the 2a×2b×c superstructure cell. The local structure solution is characterized by a uniform distribution of rather large domains (ca. thousand of unit cells) in two layers, but also monodomains can be taken into account. Inside a single domain SeO4 tetrahedra are ordered along ab-diagonal forming two-string ribbons. Inside the ribbons SeO4 and LiO4 tetrahedra share the oxygen corners, whereas ribbons are bound to each other by a net of hydrogen bonds and fastened by corner sharing SeO4 tetrahedra of the neighboring layers.

  2. H295R expression of melanocortin 2 receptor accessory protein results in ACTH responsiveness.

    PubMed

    Nanba, Kazutaka; Chen, Andrew X; Turcu, Adina F; Rainey, William E

    2016-02-01

    The H295R adrenocortical cell line is widely used for molecular analysis of adrenal functions but is known to have only modest ACTH responsiveness. The lack of ACTH response was linked to a low expression of its receptor, melanocortin 2 receptor (MC2R). We hypothesized that increasing the MC2R accessory protein (MRAP), which is required to traffic MC2R from the endoplasmic reticulum to the cell surface, would increase ACTH responsiveness. Lentiviral particles containing human MRAP-open reading frame were generated and transduced in H295R cells. Using antibiotic resistance, 18 clones were isolated for characterization. The most ACTH-responsive steroidogenic clone, H295RA, was used for further experiments. Successful induction of MRAP and increased expression of MC2R in H295RA cells was confirmed by quantitative real-time RT-PCR and protein analysis. Treatment with ACTH significantly increased aldosterone, cortisol, and dehydroepiandrosterone production in H295RA cells. ACTH also significantly increased transcript levels for all of the steroidogenic enzymes required to produce aldosterone, cortisol, and dehydroepiandrosterone, as well as MC2R mRNA. Using liquid chromatography/tandem mass spectrometry, we further revealed that the main unconjugated steroids produced in H295RA cells were 11-deoxycortisol, cortisol, and androstenedione. Treatment of H295RA cells with ACTH also acutely increased cAMP production and cellular protein levels for total and phosphorylated steroidogenic acute regulatory protein. In summary, through genetic manipulation, we have developed an ACTH-responsive human adrenocortical cell line. The cell line will provide a powerful in vitro tool for molecular analysis of physiologic and pathologic conditions involving the hypothalamic-pituitary-adrenal axis. PMID:26576642

  3. Analysis of proteins in bronchoalveolar lavage fluids during pulmonary edema resulting from nitrogen dioxide and cadmium exposure

    SciTech Connect

    Gurley, L.R.; London, J.E.; Dethloff, L.A.; Lehnert, B.E.

    1988-01-01

    We have developed a new HPLC method by which quantitative measurements can be made on the biochemical constituents of the extracellular fluid lining of the lung as sampled by bronchoalveolar lavage. Nine of the fractions are proteins, two are phospholipids, and two fractions remained unidentified. Rats were subjected to the intrapulmonary deposition of cadmium, a treatment model known to induce pulmonary edema and cause a translocation of blood compartment proteins into the lung's alveolar space compartment. Resulting pulmonary edema was hallmarked by /approximately/25-fold increases in three major blood compartment-derived HPLC protein fractions, two of which have been identified as albumin and immunoglobulin(s). Analysis of lavage fluid from rats exposed to 100 ppM NO/sub 2/ for 15 min, an exposure regimen which also produces pulmonary edema, indicated that the three blood compartment proteins in the lavage fluids were elevated 35- to 72-fold over controls 24 h after exposure. These results demonstrate that HPLC can be used to provide a highly sensitive method for detection and quantitation of pulmonary edema that can occur in acute lung injuries resulting from environmental insults.

  4. Protein

    MedlinePLUS

    ... Go lean with protein. • Choose lean meats and poultry. Lean beef cuts include round steaks (top loin, ... main dishes. • Use nuts to replace meat or poultry, not in addition to meat or poultry (i. ...

  5. Protein

    MedlinePLUS

    ... Fruits Fats and Cholesterol Types of Fat Cholesterol Dietary fat and disease Calcium and Milk Vitamins Healthy Drinks ... the high protein diet saw improvements in blood lipids and blood pressure. ( 11 ) A more recent study ...

  6. Natriuretic Peptide Receptor-3 Gene (NPR3) Nonsynonymous Polymorphism Results in Significant Reduction in Protein Expression Because of Accelerated Degradation

    PubMed Central

    Pereira, Naveen L.; Lin, Dong; Pelleymounter, Linda; Moon, Irene; Stilling, Gail; Eckloff, Bruce W.; Wieben, Eric D.; Redfield, Margaret M.; Burnett, John C.; Yee, Vivien C.; Weinshilboum, Richard M.

    2013-01-01

    Background The primary role of natriuretic peptide receptor-3 (NPR3) or NPR-C is in the clearance of natriuretic peptides that play an important role in modulating intravascular volume and vascular tone. Genetic variation in NPR3 has been associated with variation in blood pressure and obesity. Despite the importance of NPR3, sequence variation in the gene has not been addressed using DNA from different ethnic populations. We set out to identify and functionally characterize genetic variation in NPR3 in 3 ethnic groups. Methods and Results DNA samples from 96 European American, 96 African American, and 96 Han Chinese American healthy subjects were used to resequence NPR3 exons, splice junctions, and flanking regions. We identified 105 polymorphisms, 50 of which were novel, including 8 nonsynonymous single-nucleotide polymorphisms, 7 were novel. Expression constructs were created for the nonsynonymous single-nucleotide polymorphisms. HEK293 cells were transfected with constructs for wild type and variant allozymes; and recombinant proteins were measured by quantitative Western blot analysis. The most significant change in NPR3 protein was observed for the Arg146 variant allozyme, with 20% of wild-type protein, primarily because of autophagy-dependent degradation. NPR3 structural modeling confirmed that the Arg146 variant protein was not compatible with wild-type conformation and could result in protein misfolding or instability. Conclusions Multiple novel NPR3 genetic polymorphisms were identified in 3 ethnic groups. The Arg146 allozyme displayed a significant decrease in protein quantity because of degradation mediated predominantly by autophagy. This genetic variation could have a significant effect on the metabolism of natriuretic peptides with potential clinical implications. PMID:23493048

  7. Vibrational spectroscopic study of the uranyl selenite mineral derriksite Cu4UO2(SeO3)2(OH)6?H2O

    NASA Astrophysics Data System (ADS)

    Frost, Ray L.; ?ejka, Ji?í; Scholz, Ricardo; López, Andrés; Theiss, Frederick L.; Xi, Yunfei

    2014-01-01

    Raman spectrum of the mineral derriksite Cu4UO2(SeO3)2(OH)6?H2O was studied and complemented by the infrared spectrum of this mineral. Both spectra were interpreted and partly compared with the spectra of demesmaekerite, marthozite, larisaite, haynesite and piretite. Observed Raman and infrared bands were attributed to the (UO2)2+, (SeO3)2-, (OH)- and H2O vibrations. The presence of symmetrically distinct hydrogen bonded molecule of water of crystallization and hydrogen bonded symmetrically distinct hydroxyl ions was inferred from the spectra in the derriksite unit cell. Approximate U-O bond lengths in uranyl and O-H⋯O hydrogen bond lengths were calculated from the Raman and infrared spectra of derriksite.

  8. Structural and conductivity studies of CsK(SO4)0.32(SeO4)0.68Te(OH)6

    NASA Astrophysics Data System (ADS)

    Djemel, M.; Abdelhedi, M.; Zouari, N.; Dammak, M.; Kolsi, A. W.

    2012-12-01

    The compound CsK(SO4)0.32(SeO4)0.68Te(OH)6 crystallizes in the monoclinic P21/n space group. It was analyzed, at room temperature, using X-ray diffractometer data. The main feature of these atomic arrangements is the coexistence of three and different anions (SO42-, SeO42- and TeO66-groups) in the unit cell, connected by hydrogen bonds which make the building of the crystal. The thermal analysis of the title compound shows three distinct endothermal peaks at 435, 460 and 475 K. Complex impedance measurements are performed on this material as a function of both temperature and frequency. The electric conduction has been studied. The temperature dependence on the conductivity indicates that the sample became an ionic conductor at high temperature.

  9. Electrophoretic analysis of sheep plasma protein labeled with Na2 75SeO3 in vivo

    SciTech Connect

    Davidson, W.B.; McMurray, C.H.

    1987-05-01

    Following an intravenous injection of /sup 75/Se, sodium selenite plasma samples were analyzed by two-dimensional electrophoresis. /sup 75/Se was detected by indirect autoradiography. From 0.5 to 53 hr postinjection of /sup 75/Se, 21 /sup 75/Se peptides were detected. Both the isoelectric points and molecular weights of these peptides are reported. The molecular weights of the peptides ranged from 20,000 to 70,000 daltons.

  10. Results.

    ERIC Educational Resources Information Center

    Zemsky, Robert; Shaman, Susan; Shapiro, Daniel B.

    2001-01-01

    Describes the Collegiate Results Instrument (CRI), which measures a range of collegiate outcomes for alumni 6 years after graduation. The CRI was designed to target alumni from institutions across market segments and assess their values, abilities, work skills, occupations, and pursuit of lifelong learning. (EV)

  11. Transiting Exoplanet Survey Satellite (TESS) Community Observer Program including the Science Enhancement Option Box (SEO Box) - 12 TB On-board Flash Memory for Serendipitous Science

    NASA Astrophysics Data System (ADS)

    Schingler, Robert; Villasenor, J. N.; Ricker, G. R.; Latham, D. W.; Vanderspek, R. K.; Ennico, K. A.; Lewis, B. S.; Bakos, G.; Brown, T. M.; Burgasser, A. J.; Charbonneau, D.; Clampin, M.; Deming, L. D.; Doty, J. P.; Dunham, E. W.; Elliot, J. L.; Holman, M. J.; Ida, S.; Jenkins, J. M.; Jernigan, J. G.; Kawai, N.; Laughlin, G. P.; Lissauer, J. J.; Martel, F.; Sasselov, D. D.; Seager, S.; Torres, G.; Udry, S.; Winn, J. N.; Worden, S. P.

    2010-01-01

    The Transiting Exoplanet Survey Satellite (TESS) will perform an all-sky survey in a low-inclination, low-Earth orbit. TESS's 144 GB of raw data collected each orbit will be stacked, cleaned, cut, compressed and downloaded. The Community Observer Program is a Science Enhancement Option (SEO) that takes advantage of the low-radiation environment, technology advances in flash memory, and the vast amount of astronomical data collected by TESS. The Community Observer Program requires the addition of a 12 TB "SEO Box” inside the TESS Bus. The hardware can be built using low-cost Commercial Off-The-Shelf (COTS) components and fits within TESS's margins while accommodating GSFC gold rules. The SEO Box collects and stores a duplicate of the TESS camera data at a "raw” stage ( 4.3 GB/orbit, after stacking and cleaning) and makes them available for on-board processing. The sheer amount of onboard storage provided by the SEO Box allows the stacking and storing of several months of data, allowing the investigator to probe deeper in time prior to a given event. Additionally, with computation power and data in standard formats, investigators can utilize data-mining techniques to investigate serendipitous phenomenon, including pulsating stars, eclipsing binaries, supernovae or other transient phenomena. The Community Observer Program enables ad-hoc teams of citizen scientists to propose, test, refine and rank algorithms for on-board analysis to support serendipitous science. Combining "best practices” of online collaboration, with careful moderation and community management, enables this `crowd sourced’ participatory exploration with a minimal risk and impact on the core TESS Team. This system provides a powerful and independent tool opening a wide range of opportunity for science enhancement and secondary science. Support for this work has been provided by NASA, the Kavli Foundation, Google, and the Smithsonian Institution.

  12. Committee on Earth Observation Satellites (CEOS) Systems Engineering Office (SEO). Ocean Surface Topography (OST) Workshop, Ruedesheim an Rhein, Germany. [CEOS SEO Status Report

    NASA Technical Reports Server (NTRS)

    Killough, Brian D., Jr.

    2008-01-01

    The CEOS Systems Engineering Office will present a 2007 status report of the CEOS constellation process, present a new systems engineering framework, and analysis results from the GEO Societal Benefit Area (SBA) assessment and the OST constellation requirements assessment.

  13. Lack of the Lysosomal Membrane Protein, GLMP, in Mice Results in Metabolic Dysregulation in Liver

    PubMed Central

    Kong, Xiang Yi; Kase, Eili Tranheim; Herskedal, Anette; Schjalm, Camilla; Damme, Markus; Nesset, Cecilie Kasi; Thoresen, G. Hege; Rustan, Arild C.; Eskild, Winnie

    2015-01-01

    Ablation of glycosylated lysosomal membrane protein (GLMP, formerly known as NCU-G1) has been shown to cause chronic liver injury which progresses into liver fibrosis in mice. Both lysosomal dysfunction and chronic liver injury can cause metabolic dysregulation. Glmpgt/gt mice (formerly known as Ncu-g1gt/gtmice) were studied between 3 weeks and 9 months of age. Body weight gain and feed efficiency of Glmpgt/gt mice were comparable to wild type siblings, only at the age of 9 months the Glmpgt/gt siblings had significantly reduced body weight. Reduced size of epididymal fat pads was accompanied by hepatosplenomegaly in Glmpgt/gt mice. Blood analysis revealed reduced levels of blood glucose, circulating triacylglycerol and non-esterified fatty acids in Glmpgt/gt mice. Increased flux of glucose, increased de novo lipogenesis and lipid accumulation were detected in Glmpgt/gt primary hepatocytes, as well as elevated triacylglycerol levels in Glmpgt/gt liver homogenates, compared to hepatocytes and liver from wild type mice. Gene expression analysis showed an increased expression of genes involved in fatty acid uptake and lipogenesis in Glmpgt/gt liver compared to wild type. Our findings are in agreement with the metabolic alterations observed in other mouse models lacking lysosomal proteins, and with alterations characteristic for advanced chronic liver injury. PMID:26047317

  14. Synonymous modification results in high-fidelity gene expression of repetitive protein and nucleotide sequences

    PubMed Central

    Wu, Bin; Miskolci, Veronika; Sato, Hanae; Tutucci, Evelina; Kenworthy, Charles A.; Donnelly, Sara K.; Yoon, Young J.; Cox, Dianne

    2015-01-01

    Repetitive nucleotide or amino acid sequences are often engineered into probes and biosensors to achieve functional readouts and robust signal amplification. However, these repeated sequences are notoriously prone to aberrant deletion and degradation, impacting the ability to correctly detect and interpret biological functions. Here, we introduce a facile and generalizable approach to solve this often unappreciated problem by modifying the nucleotide sequences of the target mRNA to make them nonrepetitive but still functional (“synonymous”). We first demonstrated the procedure by designing a cassette of synonymous MS2 RNA motifs and tandem coat proteins for RNA imaging and showed a dramatic improvement in signal and reproducibility in single-RNA detection in live cells. The same approach was extended to enhancing the stability of engineered fluorescent biosensors containing a fluorescent resonance energy transfer (FRET) pair of fluorescent proteins on which a great majority of systems thus far in the field are based. Using the synonymous modification to FRET biosensors, we achieved correct expression of full-length sensors, eliminating the aberrant truncation products that often were assumed to be due to nonspecific proteolytic cleavages. Importantly, the biological interpretations of the sensor are significantly different when a correct, full-length biosensor is expressed. Thus, we show here a useful and generally applicable method to maintain the integrity of expressed genes, critical for the correct interpretation of probe readouts. PMID:25877922

  15. Tethering of SUUR and HP1 proteins results in delayed replication of euchromatic regions in Drosophila melanogaster polytene chromosomes.

    PubMed

    Pokholkova, Galina V; Koryakov, Dmitry E; Pindyurin, Alexey V; Kozhevnikova, Elena N; Belyakin, Stepan N; Andreyenkov, Oleg V; Belyaeva, Elena S; Zhimulev, Igor F

    2015-06-01

    We analyze how artificial targeting of Suppressor of Under-Replication (SUUR) and HP1 proteins affects DNA replication in the "open," euchromatic regions. Normally these regions replicate early in the S phase and display no binding of either SUUR or HP1. These proteins were expressed as fusions with DNA-binding domain of GAL4 and recruited to multimerized UAS integrated in three euchromatic sites of the polytene X chromosome: 3B, 8D, and 18B. Using PCNA staining as a marker of ongoing replication, we showed that targeting of SUUR(GAL4DBD) and HP1(GAL4DBD) results in delayed replication of appropriate euchromatic regions. Specifically, replication at these regions starts early, much like in the absence of the fusion proteins; however, replication completion is significantly delayed. Notably, delayed replication was insufficient to induce underreplication. Recruitment of SUUR(GAL4DBD) and HP1(GAL4DBD) had distinct effects on expression of a mini-white reporter, found near UAS. Whereas SUUR(GAL4DBD) had no measurable influence on mini-white expression, HP1(GAL4DBD) targeting silenced mini-white, even in the absence of functional SU(VAR)3-9. Furthermore, recruitment of SUUR(GAL4DBD) and HP1(GAL4DBD) had distinct effects on the protein composition of target regions. HP1(GAL4DBD) but not SUUR(GAL4DBD) could displace an open chromatin marker, CHRIZ, from the tethering sites. PMID:25398563

  16. Transduction of the TAT-FLIP fusion protein results in transient resistance to Fas-induced apoptosis in vivo.

    PubMed

    Krautwald, Stefan; Ziegler, Ekkehard; Tiede, Karen; Pust, Rainer; Kunzendorf, Ulrich

    2004-10-15

    Although tightly regulated programmed cell death (apoptosis) possesses great importance for tissue homeostasis, several pathologic processes are associated with organ failure due to adversely activated cell apoptosis. Transient increase in apoptosis has been shown to cause organ damage during fulminant hepatitis B, autoimmune diseases, ischemia-reperfusion injury, sepsis, or allograft rejection. A defined and temporary inhibition of cell apoptosis may therefore be of high clinical relevance. Activation of death receptors results in caspase-8 recruitment to the death-inducing signaling complex, which initiates the apoptotic process through cleavage of caspase-8 and downstream substrates. This initial step may be inhibited by the caspase-8 inhibitor FLIP (FLICE inhibitory protein). To specifically inhibit the initiation of death receptor-mediated apoptosis we constructed a fusion protein containing FLIP fused N-terminally to the human immunodeficiency virus TAT domain. This TAT domain allows the fusion protein to cross the cell membrane and thus makes the FLIP domain able to interfere with the death-inducing signaling complex inside of the cell. We observed that incubation of lymphocytic Jurkat or BJAB cells with TAT-FLIPS proteins significantly inhibits Fas-induced activation of procaspase-8 and downstream caspases, preventing cells from undergoing apoptosis. Systemic application of TAT-FLIPS prolongs survival and reduces multi-organ failure due to Fas-receptor-mediated lethal apoptosis in mice. Therefore, application of cellular FLIPS in the form of a TAT fusion protein may open a promising, easily applicable new tool for providing protection against transient, pathologically increased apoptosis in various diseases. PMID:15304499

  17. Size- and shape-controlled synthesis of ZnSe nanocrystals using SeO2 as selenium precursor.

    PubMed

    Shen, Huaibin; Niu, Jin Zhong; Wang, Hongzhe; Li, Xiaomin; Li, Lin Song; Chen, Xia

    2010-12-21

    Here we report a low-cost and "green" phosphine-free route for the size- and shape-controlled synthesis of high-quality zinc blende (cubic) ZnSe nanocrystals. To avoid the use of expensive and toxic solvents such as trioctylphosphine (TOP) or tributylphosphine (TBP), SeO(2) was dispersed in 1-octadecene (ODE) as a chalcogen precursor. It has been found that the temperature and the surface ligand influenced the nucleation, the reaction speed and the formation of different shapes. Absorption spectroscopy, fluorescence spectroscopy, powder X-ray diffraction (XRD) and transmission electron microscopy (TEM) were used for the characterization of the as-synthesized ZnSe nanocrystals. The size-dependent photoluminescence (PL) range of the as-prepared ZnSe nanocrystals was between 390 and 450 nm, with the PL full width at half-maximum (FWHM) well controlled between 14 and 18 nm and PL quantum yields reached up to 40% at room temperature. Moreover, this new selenium precursor can be used to form tetrapod-shaped ZnSe nanocrystals when zinc acetylacetonate was introduced as the zinc precursor with a one-pot method. PMID:20976341

  18. EXPRESSION OF AN INSECT (DENDROIDES CANADENSIS) ANTIFREEZE PROTEIN IN ARABIDOPSIS THALIANA RESULTS IN A DECREASE IN PLANT FREEZING TEMPERATURE

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Transgenic Arabidopsis thaliana plants which express genes encoding insect, Dendroides canadensis, antifreeze proteins (AFP) were produced by Agrobacterium-mediated transformation. The antifreeze protein genes, both with and without the signal peptide sequence (for protein secretion), were expresse...

  19. Hydrothermal synthesis, structures and optical properties of A2Zn3(SeO3)4·XH2O (A=Li, Na, K; X=2 or 0)

    NASA Astrophysics Data System (ADS)

    Liu, Yunsheng; Mei, Dajiang; Xu, Jingli; Wu, Yuandong

    2015-12-01

    New alkali metal zinc selenites, A2Zn3(SeO3)4·XH2O (A=Li, Na, K; X=2 or 0) were prepared through hydrothermal reactions. Li2Zn3(SeO3)4·2H2O (1) crystallizes in the monoclinic space group P21/c with lattice parameters a=8.123(4), b=9.139(4), c=7.938(3) Ĺ, ?=112.838(9)°. Na2Zn3(SeO3)4·2H2O (2) crystallizes in the monoclinic space group C2/c with lattice parameters a=15.7940(18), b=6.5744(8), c=14.6787(17) Ĺ, ?=107.396(3)°. K2Zn3(SeO3)4 (3) crystallizes in the monoclinic space group C2/c with lattice parameters a=11.3584(12), b=8.6091(9), c=13.6816(14) Ĺ, ?=93.456(2)°. The anionic structures are composed of [Zn3O12]18- sheets, chains, and "isolated" units in compound 1, 2, 3, respectively, and trigonal pyramids SeO32-. The compounds were characterized by the solid state UV-vis-NIR diffuse reflectance spectroscopy, infrared spectra and thermogravimetric analysis.

  20. Resistance of Dynamin-related Protein 1 Oligomers to Disassembly Impairs Mitophagy, Resulting in Myocardial Inflammation and Heart Failure.

    PubMed

    Cahill, Thomas J; Leo, Vincenzo; Kelly, Matthew; Stockenhuber, Alexander; Kennedy, Nolan W; Bao, Leyuan; Cereghetti, Grazia; Harper, Andrew R; Czibik, Gabor; Lao, Chunyan; Bellahcene, Mohamed; Steeples, Violetta; Ghaffari, Safar; Yavari, Arash; Mayer, Alice; Poulton, Joanna; Ferguson, David J P; Scorrano, Luca; Hettiarachchi, Nishani T; Peers, Chris; Boyle, John; Hill, R Blake; Simmons, Alison; Watkins, Hugh; Dear, T Neil; Ashrafian, Houman

    2015-10-23

    We have reported previously that a missense mutation in the mitochondrial fission gene Dynamin-related protein 1 (Drp1) underlies the Python mouse model of monogenic dilated cardiomyopathy. The aim of this study was to investigate the consequences of the C452F mutation on Drp1 protein function and to define the cellular sequelae leading to heart failure in the Python monogenic dilated cardiomyopathy model. We found that the C452F mutation increased Drp1 GTPase activity. The mutation also conferred resistance to oligomer disassembly by guanine nucleotides and high ionic strength solutions. In a mouse embryonic fibroblast model, Drp1 C452F cells exhibited abnormal mitochondrial morphology and defective mitophagy. Mitochondria in C452F mouse embryonic fibroblasts were depolarized and had reduced calcium uptake with impaired ATP production by oxidative phosphorylation. In the Python heart, we found a corresponding progressive decline in oxidative phosphorylation with age and activation of sterile inflammation. As a corollary, enhancing autophagy by exposure to a prolonged low-protein diet improved cardiac function in Python mice. In conclusion, failure of Drp1 disassembly impairs mitophagy, leading to a downstream cascade of mitochondrial depolarization, aberrant calcium handling, impaired ATP synthesis, and activation of sterile myocardial inflammation, resulting in heart failure. PMID:26370078

  1. Nonsense Mutations in SMPX, Encoding a Protein Responsive to Physical Force, Result in X-Chromosomal Hearing Loss

    PubMed Central

    Huebner, Antje K.; Gandia, Marta; Frommolt, Peter; Maak, Anika; Wicklein, Eva M.; Thiele, Holger; Altmüller, Janine; Wagner, Florian; Vińuela, Antonio; Aguirre, Luis A.; Moreno, Felipe; Maier, Hannes; Rau, Isabella; Gießelmann, Sebastian; Nürnberg, Gudrun; Gal, Andreas; Nürnberg, Peter; Hübner, Christian A.; del Castillo, Ignacio; Kurth, Ingo

    2011-01-01

    The fact that hereditary hearing loss is the most common sensory disorder in humans is reflected by, among other things, an extraordinary allelic and nonallelic genetic heterogeneity. X-chromosomal hearing impairment represents only a minor fraction of all cases. In a study of a Spanish family the locus for one of the X-chromosomal forms was assigned to Xp22 (DFNX4). We mapped the disease locus in the same chromosomal region in a large German pedigree with X-chromosomal nonsyndromic hearing impairment by using genome-wide linkage analysis. Males presented with postlingual hearing loss and onset at ages 3–7, whereas onset in female carriers was in the second to third decades. Targeted DNA capture with high-throughput sequencing detected a nonsense mutation in the small muscle protein, X-linked (SMPX) of affected individuals. We identified another nonsense mutation in SMPX in patients from the Spanish family who were previously analyzed to map DFNX4. SMPX encodes an 88 amino acid, cytoskeleton-associated protein that is responsive to mechanical stress. The presence of Smpx in hair cells and supporting cells of the murine cochlea indicates its role in the inner ear. The nonsense mutations detected in the two families suggest a loss-of-function mechanism underlying this form of hearing impairment. Results obtained after heterologous overexpression of SMPX proteins were compatible with this assumption. Because responsivity to physical force is a characteristic feature of the protein, we propose that long-term maintenance of mechanically stressed inner-ear cells critically depends on SMPX function. PMID:21549336

  2. Neonatal presentation of familial glucocorticoid deficiency resulting from a novel splice mutation in the melanocortin 2 receptor accessory protein

    PubMed Central

    Jain, V; Metherell, L A; David, A; Sharma, R; Sharma, P K; Clark, A J L; Chan, L F

    2011-01-01

    Background Familial glucocorticoid deficiency (FGD) is a rare autosomal recessive disorder characterised by isolated glucocorticoid deficiency. Mutations in the ACTH receptor/melanocortin 2 receptor (MC2R), the MC2R accessory protein (MRAP) or the STAR protein (STAR) cause FGD types 1, 2 and 3, respectively, accounting for ?50% of all cases. Patient and methods We report a neonate of Indian origin, who was diagnosed with FGD in the first few days of life. He presented with hypoglycaemic seizures and was noted to have generalised intense hyperpigmentation and normal male genitalia. Biochemical investigations revealed hypocortisolaemia (cortisol 0.223??g/dl; NR 1–23??g/dl) and elevated plasma ACTH (170?pg/ml). Serum electrolytes, aldosterone and plasma renin activity were normal. Peak cortisol following a standard synacthen test was 0.018??g/dl. He responded to hydrocortisone treatment and continues on replacement. Patient DNA was analysed by direct sequencing. The effect of the novel mutation was assessed by an in vitro splicing assay using wild type and mutant heterologous minigenes. Results A novel homozygous mutation c.106+2_3dupTA was found in the MRAP gene. Both parents were heterozygous for the mutation. In an in vitro splicing assay, the mutation resulted in the skipping of exon 3. Conclusion We have identified a novel MRAP mutation where disruption of the intron 3 splice-site results in a prematurely terminated translation product. This protein (if produced) would lack the transmembrane domain that is essential for MC2R interaction. We predict that this would cause complete lack of ACTH response thus explaining the early presentation in this case. PMID:21951701

  3. Disruption of the basal body protein POC1B results in autosomal-recessive cone-rod dystrophy.

    PubMed

    Roosing, Susanne; Lamers, Ideke J C; de Vrieze, Erik; van den Born, L Ingeborgh; Lambertus, Stanley; Arts, Heleen H; Peters, Theo A; Hoyng, Carel B; Kremer, Hannie; Hetterschijt, Lisette; Letteboer, Stef J F; van Wijk, Erwin; Roepman, Ronald; den Hollander, Anneke I; Cremers, Frans P M

    2014-08-01

    Exome sequencing revealed a homozygous missense mutation (c.317C>G [p.Arg106Pro]) in POC1B, encoding POC1 centriolar protein B, in three siblings with autosomal-recessive cone dystrophy or cone-rod dystrophy and compound-heterozygous POC1B mutations (c.199_201del [p.Gln67del] and c.810+1G>T) in an unrelated person with cone-rod dystrophy. Upon overexpression of POC1B in human TERT-immortalized retinal pigment epithelium 1 cells, the encoded wild-type protein localized to the basal body of the primary cilium, whereas this localization was lost for p.Arg106Pro and p.Gln67del variant forms of POC1B. Morpholino-oligonucleotide-induced knockdown of poc1b translation in zebrafish resulted in a dose-dependent small-eye phenotype, impaired optokinetic responses, and decreased length of photoreceptor outer segments. These ocular phenotypes could partially be rescued by wild-type human POC1B mRNA, but not by c.199_201del and c.317C>G mutant human POC1B mRNAs. Yeast two-hybrid screening of a human retinal cDNA library revealed FAM161A as a binary interaction partner of POC1B. This was confirmed in coimmunoprecipitation and colocalization assays, which both showed loss of FAM161A interaction with p.Arg106Pro and p.Gln67del variant forms of POC1B. FAM161A was previously implicated in autosomal-recessive retinitis pigmentosa and shown to be located at the base of the photoreceptor connecting cilium, where it interacts with several other ciliopathy-associated proteins. Altogether, this study demonstrates that POC1B mutations result in a defect of the photoreceptor sensory cilium and thus affect cone and rod photoreceptors. PMID:25018096

  4. Vitiligo-inducing phenols activate the unfolded protein response in melanocytes resulting in upregulation of IL6 and IL8.

    PubMed

    Toosi, Siavash; Orlow, Seth J; Manga, Prashiela

    2012-11-01

    Vitiligo is characterized by depigmented skin patches caused by loss of epidermal melanocytes. Oxidative stress may have a role in vitiligo onset, while autoimmunity contributes to disease progression. In this study, we sought to identify mechanisms that link disease triggers and spreading of lesions. A hallmark of melanocytes at the periphery of vitiligo lesions is dilation of the endoplasmic reticulum (ER). We hypothesized that oxidative stress results in redox disruptions that extend to the ER, causing accumulation of misfolded peptides, which activates the unfolded protein response (UPR). We used 4-tertiary butyl phenol and monobenzyl ether of hydroquinone, known triggers of vitiligo. We show that expression of key UPR components, including the transcription factor X-box-binding protein 1 (XBP1), is increased following exposure of melanocytes to phenols. XBP1 activation increases production of immune mediators IL6 and IL8. Co-treatment with XBP1 inhibitors reduced IL6 and IL8 production induced by phenols, while overexpression of XBP1 alone increased their expression. Thus, melanocytes themselves produce cytokines associated with activation of an immune response following exposure to chemical triggers of vitiligo. These results expand our understanding of the mechanisms underlying melanocyte loss in vitiligo and pathways linking environmental stressors and autoimmunity. PMID:22696056

  5. Synthesis, crystal structure and characterization of Na3H(SO4)1.78(SeO4)0.22

    NASA Astrophysics Data System (ADS)

    Ben Hassen, C.; Boujelbene, M.; Mhiri, T.

    2013-05-01

    Synthesis, crystal structure, Raman, IR and TG/DTA characterization are given for Trisodium hydrogen bisulfate selenite Na3H(SO4)1.78(SeO4)0.22. This compound crystallizes in the monoclinic system with space group P21/c and cell parameters: a = 8.6787 (4) Ĺ, b = 9.6631 (6) Ĺ, c = 9.2070 (5) Ĺ, ß = 108.825 (4)°, Z = 4 and V = 730.83 (7) Ĺ3. The refinement of 2492 observed reflections (I > 2?(I)) leads to R1 = 0.045 and wR2 = 0.125. The structure is characterized by S/SeO4 tetrahedra which are linked into isolated pairs by hydrogen bonds which form dimers of composition [H(SO)2]. The existence of O-H and (S/Se)-O bonds in the structure at room temperature has been confirmed by IR and Raman spectroscopy in the frequency ranges 50-1300 and 500-4000 cm-1, respectively. Thermogravimetric analysis (TGA) and differential thermal analysis (DTA) measurements have been carried out on Na3H(SO4)1.78(SeO4)0.22 crystal in the temperature range between 50 and 600 °C. Water evolution and major thermal decomposition take place with onset temperatures of approximately 282 °C and 395 °C, respectively. A Raman study of the decomposition of Na3H(SO4)1.78(SeO4)0.22 as a function of temperature supports a reaction sequence and possible intermediates during the process.

  6. Persistence of glucose residues on core oligosaccharides prevents association of TCR alpha and TCR beta proteins with calnexin and results specifically in accelerated degradation of nascent TCR alpha proteins within the endoplasmic reticulum.

    PubMed

    Kearse, K P; Williams, D B; Singer, A

    1994-08-15

    The alpha beta T-cell antigen receptor (TCR) is a multisubunit transmembrane complex composed of at least six different proteins (alpha, beta, gamma, delta, epsilon and zeta) that are assembled in the endoplasmic reticulum (ER). In this report we have examined the role of oligosaccharide processing on survival and assembly of nascent TCR proteins within the ER and their associations with molecular chaperone proteins important in TCR assembly. We found that treatment of BW5147 T cells with the glucosidase inhibitor castanospermine resulted in markedly accelerated degradation of nascent TCR alpha proteins with a half-life of approximately 20 min. Accelerated degradation was unique to TCR alpha proteins, as the stability of nascent TCR beta and CD3 gamma,epsilon chains was unaltered. Consistent with a requirement for glucose (Glc) trimming for survival of nascent TCR alpha proteins within the ER, we found that newly synthesized TCR alpha chains were innately unstable in the glucosidase II-deficient BW5147 mutant cell line PHAR2.7. In addition to destabilizing nascent TCR alpha proteins we found that persistence of Glc residues on core oligosaccharides markedly interfered with association of both TCR alpha and TCR beta glycoproteins with the molecular chaperone calnexin. Finally, using 2B4 T hybridoma cells in which TCR complexes are efficiently assembled, we found that rapid degradation of nascent TCR alpha proteins induced by impaired Glc trimming severely limits assembly of TCR alpha proteins with TCR beta proteins.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:7915231

  7. Tamm-Horsfall protein in patients with kidney dama...[Urol Res. 2004] -PubMed Result Urol Res. 2004 May;32(2):79-83. Links

    E-print Network

    Abraham, Nader G.

    Tamm-Horsfall protein in patients with kidney dama...[Urol Res. 2004] - PubMed Result Urol Res. 2004 May;32(2):79-83. Links Tamm-Horsfall protein in patients with kidney damage and diabetes in diabetic and control kidney tissue specimens with or without kidney damage. Immunogold labeling

  8. Dynamic Hyperparameter Scaling Method for LVQ Algorithms Sambu Seo and Klaus Obermayer

    E-print Network

    Wichmann, Felix

    ], the analysis of gene expression profiles of primary breast tumor cells [6] and cancer class prediction from, the on-line learning process, and the structure of the resulting classifier. Motivated by the results we. More importantly, however, the number of learning trials for different values of the hyperparameters

  9. Mutual Fund Trading Pressure: Firm-Level Stock Price Impact and Timing of SEOs

    E-print Network

    Khan, Mozaffar Nayim

    We use price pressure resulting from purchases by mutual funds with large capital inflows to identify overvalued equity. This is a relatively exogenous overvaluation indicator as it is associated with who is buying—buyers ...

  10. Complex Expression of the UL136 Gene of Human Cytomegalovirus Results in Multiple Protein Isoforms with Unique Roles in Replication

    PubMed Central

    Caviness, Katie; Cicchini, Louis; Rak, Michael; Umashankar, Mahadevaiah

    2014-01-01

    ABSTRACT Human cytomegalovirus (HCMV) is a complex DNA virus with a 230-kb genome encoding 170 and up to 750 proteins. The upper limit of this coding capacity suggests the evolution of complex mechanisms to substantially increase the coding potential from the 230-kb genome. Our work examines the complexity of one gene, UL136, encoded within the ULb? region of the genome that is lost during serial passage of HCMV in cultured fibroblasts. UL136 is expressed as five protein isoforms. We mapped these isoforms and demonstrate that they originate from both a complex transcriptional profile and, possibly, the usage of multiple translation initiation sites. Intriguingly, the pUL136 isoforms exhibited distinct subcellular distributions with varying association with the Golgi apparatus. The subcellular localization of membrane-bound isoforms of UL136 differed between when they were expressed exogenously and when they were expressed in the context of viral infection, suggesting that the trafficking of these isoforms is mediated by infection-specific factors. While UL136, like most ULb? genes, was dispensable for replication in fibroblasts, the soluble 23- and 19-kDa isoforms suppressed virus replication. In CD34+ hematopoietic progenitor cells (HPCs) infected in vitro, disruption of the 23- and 19-kDa isoforms resulted in increased replication and a loss of the latency phenotype, similar to the effects of the UL138 latency determinant encoded within the same genetic locus. Our work suggests a complex interplay between the UL136 isoforms which balances viral replication in multiple cell types and likely contributes to the cell type-dependent phenotypes of the UL133/8 locus and the outcome of HCMV infection. IMPORTANCE HCMV is a significant cause of morbidity in immunocompromised individuals, including transplant patients. The lifelong persistence of the virus results in a high seroprevalence worldwide and may contribute to age-related pathologies, such as atherosclerosis. The mechanisms of viral persistence are poorly understood; however, understanding the molecular basis of persistence is imperative for the development of new treatments. In this work, we characterize a complex HCMV gene, UL136, which is expressed as five protein isoforms. These isoforms arise predominantly from complex transcriptional mechanisms, which contribute to an increased coding capacity of the virus. Further, the UL136 isoforms oppose the activity of one another to balance HCMV replication in multiple cell types. We identify soluble isoforms of UL136 that function to suppress virus replication in fibroblasts and in CD34+ HPCs for latency. PMID:25297993

  11. Synthesis, magnetic structure, and properties of a layered cobalt-hydroxide ferromagnet, Co5(OH)6(SeO4)2(H2O)4.

    PubMed

    Maalej, Wassim; Vilminot, Serge; André, Gilles; Kurmoo, Mohamedally

    2010-03-15

    The synthesis and nuclear and magnetic structures from the powder diffraction of Co(II)(5)(OH)(6)(SeO(4))(2)(H(2)O)(4) and its deuterated analogues as well as their infrared spectral, thermal, and magnetic properties are reported. The nuclear structure consists of brucite-like cobalt hydroxide layers connected by ...OSeO(3)-Co(H(2)O)(4)-O(3)SeO... bridges. The two independent cobalt atoms within the layer are arranged in chains along the b axis creating an anisotropy within each layer. The interlayer distance (10.718 A) is the only parameter to increase compared to the sulfate analogue (10.273 A). The infrared spectra and thermal properties are similar to those reported for the sulfate analogue. Due to the ferromagnetic exchange between the nearest-neighbor cobalt atoms within the layer, satisfying the Goodenough-Kanamori rule, and the weak interlayer exchange, an overall ferromagnet is obtained. The ferromagnetic order at 9 K was confirmed by the ac susceptibilities, the saturation magnetization, and most importantly the enhancement of some Bragg diffraction peaks below the Curie temperature. The moments of all the cobalt atoms were found to be aligned along the b axis with a moment of 3.25(8) mu(B) each giving the best fit. The increase in layer distance and the electron density by replacing sulfur by selenium lowers the Curie temperature. PMID:20151687

  12. X-ray diffraction, Raman study and electrical properties of the new mixed compound Rb1.7K0.3(SO4)0.88(SeO4)0.12Te(OH)6

    NASA Astrophysics Data System (ADS)

    Djemel, M.; Abdelhedi, M.; Ktari, L.; Dammak, M.

    2013-09-01

    At room temperature, the new compound Rb1.7K0.3(SO4)0.88(SeO4)0.12Te(OH)6 crystallizes in the monoclinic system with space group C2. The unit cell parameters are: a = 11.4168 (4), b = 6.6321 (4), c = 13.6078 (6), ? = 106.975 (3), V = 985.46 (8), Z = 4 and ?cal = 3.25 g cm-1. The title compound undergoes a superionic phase transition at T = 479 K. This transition was confirmed by an abrupt increase of conductivity. Differential scanning calorimetry of Rb1.7K0.3(SO4)0.88(SeO4)0.12Te(OH)6 material showed three anomalies at 411, 461, and 479 K, respectively. Raman and IR spectra of Rb1.7K0.3(SO4)0.88(SeO4)0.12Te(OH)6, recorded at room temperature in the frequency 50-4000 cm-1 show that the SO42-, SeO42- and TeO66- groups coexist in the crystal independently.

  13. Supplemental Figure 1. Root lengths of S. pinnata and S. albescens grown on vertically placed agar plates after 30 days of growth from germination. Plants treated without () Se (open bars) and with (+) 20 M SeO4

    E-print Network

    plates after 30 days of growth from germination. Plants treated without (­) Se (open bars) and with (+) 20 M SeO4 2- (gray bars). Data represent the average of 4-5 different plants ± SE. P-values using of four authentic seleno-amino acid standards. Mixture of selenomethionine, selenocystine

  14. ACUTE EXPOSURE OF THE NEONATAL RAT TO TRIETHYLTIN RESULTS IN PERSISTENT CHANGES IN NEUROTYPIC AND GLIOTYPIC PROTEINS (JOURNAL VERSION)

    EPA Science Inventory

    Measurements of neuron-specific (neurotypic) and glia-specific (fliotypic) proteins were used to characterize the toxic effects of TET on the developing CNS. Six proteins, each of which is associated with specific aspects of neuronal and glial development, were evaluated as follo...

  15. Loss of the Synaptic Vesicle Protein SV2B Results in Reduced Neurotransmission and Altered Synaptic Vesicle Protein Expression in the Retina

    PubMed Central

    Burton, Kimberly; Idzerda, Rejean; McKnight, G. Stanley; Bajjalieh, Sandra M.

    2009-01-01

    The Synaptic Vesicle Protein 2 (SV2) family of transporter-like proteins is expressed exclusively in vesicles that undergo calcium-regulated exocytosis. Of the three isoforms expressed in mammals, SV2B is the most divergent. Here we report studies of SV2B location and function in the retina. Immunolabeling studies revealed that SV2B is detected in rod photoreceptor synaptic terminals where it is the primary isoform. In mice lacking SV2B, synaptic transmission at the synapse between photoreceptors and bipolar neurons was decreased, as evidenced by a significant reduction in the amplitude of the b-wave in electroretinogram recordings. Quantitative immunoblot analyses of whole eyes revealed that loss of SV2B was associated with reduced levels of synaptic vesicle proteins including synaptotagmin, VAMP, synaptophysin and the vesicular glutamate transporter V-GLUT1. Immunolabeling studies revealed that SV2B is detected in rod photoreceptor synaptic terminals where it is the primary isoform. Thus, SV2B contributes to the modulation of synaptic vesicle exocytosis and plays a significant role in regulating synaptic protein content. PMID:19381277

  16. Surfactant Protein D Binds to Coxiella burnetii and Results in a Decrease in Interactions with Murine Alveolar Macrophages

    PubMed Central

    Soltysiak, Kelly A.; van Schaik, Erin J.; Samuel, James E.

    2015-01-01

    Coxiella burnetii is a Gram-negative, obligate intracellular bacterium and the causative agent of Q fever. Infections are usually acquired after inhalation of contaminated particles, where C. burnetii infects its cellular target cells, alveolar macrophages. Respiratory pathogens encounter the C-type lectin surfactant protein D (SP-D) during the course of natural infection. SP-D is a component of the innate immune response in the lungs and other mucosal surfaces. Many Gram-negative pulmonary pathogens interact with SP-D, which can cause aggregation, bactericidal effects and aid in bacterial clearance. Here we show that SP-D binds to C. burnetii in a calcium-dependent manner with no detectable bacterial aggregation or bactericidal effects. Since SP-D interactions with bacteria often alter macrophage interactions, it was determined that SP-D treatment resulted in a significant decrease in C. burnetii interactions to a mouse alveolar macrophage model cell line MH-S indicating SP-D causes a significant decrease in phagocytosis. The ability of SP-D to modulate macrophage activation by C. burnetii was tested and it was determined that SP-D does not alter the correlates measured for macrophage activation. Taken together these studies support those demonstrating limited activation of alveolar macrophages with C. burnetii and demonstrate interactions with SP-D participate in reduction of phagocyte attachment and phagocytosis. PMID:26366725

  17. Surfactant Protein D Binds to Coxiella burnetii and Results in a Decrease in Interactions with Murine Alveolar Macrophages.

    PubMed

    Soltysiak, Kelly A; van Schaik, Erin J; Samuel, James E

    2015-01-01

    Coxiella burnetii is a Gram-negative, obligate intracellular bacterium and the causative agent of Q fever. Infections are usually acquired after inhalation of contaminated particles, where C. burnetii infects its cellular target cells, alveolar macrophages. Respiratory pathogens encounter the C-type lectin surfactant protein D (SP-D) during the course of natural infection. SP-D is a component of the innate immune response in the lungs and other mucosal surfaces. Many Gram-negative pulmonary pathogens interact with SP-D, which can cause aggregation, bactericidal effects and aid in bacterial clearance. Here we show that SP-D binds to C. burnetii in a calcium-dependent manner with no detectable bacterial aggregation or bactericidal effects. Since SP-D interactions with bacteria often alter macrophage interactions, it was determined that SP-D treatment resulted in a significant decrease in C. burnetii interactions to a mouse alveolar macrophage model cell line MH-S indicating SP-D causes a significant decrease in phagocytosis. The ability of SP-D to modulate macrophage activation by C. burnetii was tested and it was determined that SP-D does not alter the correlates measured for macrophage activation. Taken together these studies support those demonstrating limited activation of alveolar macrophages with C. burnetii and demonstrate interactions with SP-D participate in reduction of phagocyte attachment and phagocytosis. PMID:26366725

  18. Extended networks, porous sheets, and chiral frameworks. Thorium materials containing mixed geometry anions: Structures and properties of Th(SeO 3)(SeO 4), Th(IO 3) 2(SeO 4)(H 2O) 3·H 2O, and Th(CrO 4)(IO 3) 2

    NASA Astrophysics Data System (ADS)

    Sullens, Tyler A.; Almond, Philip M.; Byrd, Jessica A.; Beitz, James V.; Bray, Travis H.; Albrecht-Schmitt, Thomas E.

    2006-04-01

    Three novel Th(IV) compounds containing heavy oxoanions, Th(SeO 3)(SeO 4) ( 1), Th(IO 3) 2(SeO 4)(H 2O) 3·H 2O ( 2), and Th(CrO 4)(IO 3) 2 ( 3), have been synthesized under mild hydrothermal conditions. Each of these three distinct structures contain trigonal pyramidal and tetrahedral oxoanions. Compound 1 adopts a three-dimensional structure formed from ThO 9 tricapped trigonal prisms, trigonal pyramidal selenite, SeO 32-, anions containing Se(IV), and tetrahedral selenate, SeO 42-, anions containing Se(VI). The structure of 2 contains two-dimensional porous sheets and occluded water molecules. The Th centers are found as isolated ThO 9 tricapped trigonal prisms and are bound by four trigonal pyramidal iodate anions, two tetrahedral selenate anions, and three coordinating water molecules. In the structure of 3, the Th(IV) cations are found as ThO 9 tricapped trigonal prisms. Each Th center is bound by six IO 31- anions and three CrO 42- anions forming a chiral three-dimensional structure. Second-harmonic generation of 532 nm light from 1064 nm radiation by a polycrystalline sample of 3 was observed. Crystallographic data (193 K, Mo K?, ?=0.71073): 1; monoclinic, P2 1/ c; a=7.0351(5) Ĺ, b=9.5259(7) Ĺ, c=9.0266(7) Ĺ, ?=103.128(1), Z=4, R(F)=2.47% for 91 parameters with 1462 reflections with I>2?(I); 2, monoclinic, P2 1/ n, a=7.4889(9) Ĺ, b=8.002(1) Ĺ, c=20.165(3) Ĺ, ?=100.142(2), Z=4, R(F)=4.71% for 158 parameters with 2934 reflections with I>2?(I); 3, orthorhombic, P2 12 12 1, a=7.3672(5) Ĺ, b=9.3617(6) Ĺ, c=11.9201(7) Ĺ, Z=4, R(F)=2.04% for 129 parameters with 2035 reflections with I>2?(I).

  19. Life-cycle and genetic characterization of Astiotrema odhneri Bhalerao, 1936 sensu Cho & Seo 1977 from the Primorsky Region (Russian Far East).

    PubMed

    Besprozvannykh, V V; Atopkin, D M; Ermolenko, A V; Kharitonova, A V; Khamatova, A Yu

    2015-12-01

    Adult Astiotrema odhneri Bhalerao, 1936 sensu Cho & Seo 1977 were found in the intestine of a freshwater turtle, Pelodiscus sinensis (Wiegmann), from the Komissarovka River Basin, Primorsky Region, Russia. It was established that the first intermediate host of this parasite is a snail, Anisus centrifugops, and that the second intermediate hosts include the snails, Helicorbis sujfunensis and A. centrifugops, tadpoles of the frog Rana dybowskii, and the fish Perccottus glenii. The development of A. odhneri includes the formation of sporocyst and xiphidiocercariae, which is typical for species belonging to Plagiorchioidea. Phylogenetic analysis based on 28S rRNA gene sequences showed that A. odhneri, together with Astiotrema monticellii, form a monophyletic clade that was closer to Opisthorchioidea than to any other taxon represented in the tree. However, phylogenetic analysis without outgroup taxon indicated a high degree of differentiation of Astiotrema from both Plagiorchioidea and Opisthorchioidea. PMID:26232633

  20. Mechanisms of cross-talk between G-protein-coupled receptors resulting in enhanced release of intracellular Ca2+.

    PubMed Central

    Werry, Tim D; Wilkinson, Graeme F; Willars, Gary B

    2003-01-01

    Alteration in [Ca(2+)](i) (the intracellular concentration of Ca(2+)) is a key regulator of many cellular processes. To allow precise regulation of [Ca(2+)](i) and a diversity of signalling by this ion, cells possess many mechanisms by which they are able to control [Ca(2+)](i) both globally and at the subcellular level. Among these are many members of the superfamily of GPCRs (G-protein-coupled receptors), which are characterized by the presence of seven transmembrane domains. Typically, those receptors able to activate PLC (phospholipase C) enzymes cause release of Ca(2+) from intracellular stores and influence Ca(2+) entry across the plasma membrane. It has been well documented that Ca(2+) signalling by one type of GPCR can be influenced by stimulation of a different type of GPCR. Indeed, many studies have demonstrated heterologous desensitization between two different PLC-coupled GPCRs. This is not surprising, given our current understanding of negative-feedback regulation and the likely shared components of the signalling pathway. However, there are also many documented examples of interactions between GPCRs, often coupling preferentially to different signalling pathways, which result in a potentiation of Ca(2+) signalling. Such interactions have important implications for both the control of cell function and the interpretation of in vitro cell-based assays. However, there is currently no single mechanism that adequately accounts for all examples of this type of cross-talk. Indeed, many studies either have not addressed this issue or have been unable to determine the mechanism(s) involved. This review seeks to explore a range of possible mechanisms to convey their potential diversity and to provide a basis for further experimental investigation. PMID:12790797

  1. NCYM, a Cis-Antisense Gene of MYCN, Encodes a De Novo Evolved Protein That Inhibits GSK3? Resulting in the Stabilization of MYCN in Human Neuroblastomas

    PubMed Central

    Suenaga, Yusuke; Islam, S. M. Rafiqul; Alagu, Jennifer; Kaneko, Yoshiki; Kato, Mamoru; Tanaka, Yukichi; Kawana, Hidetada; Hossain, Shamim; Matsumoto, Daisuke; Yamamoto, Mami; Shoji, Wataru; Itami, Makiko; Shibata, Tatsuhiro; Nakamura, Yohko; Ohira, Miki; Haraguchi, Seiki; Takatori, Atsushi; Nakagawara, Akira

    2014-01-01

    The rearrangement of pre-existing genes has long been thought of as the major mode of new gene generation. Recently, de novo gene birth from non-genic DNA was found to be an alternative mechanism to generate novel protein-coding genes. However, its functional role in human disease remains largely unknown. Here we show that NCYM, a cis-antisense gene of the MYCN oncogene, initially thought to be a large non-coding RNA, encodes a de novo evolved protein regulating the pathogenesis of human cancers, particularly neuroblastoma. The NCYM gene is evolutionally conserved only in the taxonomic group containing humans and chimpanzees. In primary human neuroblastomas, NCYM is 100% co-amplified and co-expressed with MYCN, and NCYM mRNA expression is associated with poor clinical outcome. MYCN directly transactivates both NCYM and MYCN mRNA, whereas NCYM stabilizes MYCN protein by inhibiting the activity of GSK3?, a kinase that promotes MYCN degradation. In contrast to MYCN transgenic mice, neuroblastomas in MYCN/NCYM double transgenic mice were frequently accompanied by distant metastases, behavior reminiscent of human neuroblastomas with MYCN amplification. The NCYM protein also interacts with GSK3?, thereby stabilizing the MYCN protein in the tumors of the MYCN/NCYM double transgenic mice. Thus, these results suggest that GSK3? inhibition by NCYM stabilizes the MYCN protein both in vitro and in vivo. Furthermore, the survival of MYCN transgenic mice bearing neuroblastoma was improved by treatment with NVP-BEZ235, a dual PI3K/mTOR inhibitor shown to destabilize MYCN via GSK3? activation. In contrast, tumors caused in MYCN/NCYM double transgenic mice showed chemo-resistance to the drug. Collectively, our results show that NCYM is the first de novo evolved protein known to act as an oncopromoting factor in human cancer, and suggest that de novo evolved proteins may functionally characterize human disease. PMID:24391509

  2. Experimental study on protein transmission through the human muscle fascia: preliminary results and application theory in lymphedema.

    PubMed

    Vettorello, G F; Rubbini, M; Nastruzzi, C; Menegatti, E; Esposito, E; Mascoli, F; Pozza, E; Cataldi, A; Donini, I G

    1996-08-01

    The presence of proteins (albumin and globulins) in lymphedematous tissue not only gives rise to colloidosmotic pressure but also produces an electrostatic charge endowing the proteins with individual features and different migration rates. The working hypothesis of the experimental study is to transfer lymph proteins from the upper fascia accumulation area to a subfascial drainage area by subjecting them to an adequate difference in potential. A double chamber, variable volume system with separation wall able to contain a 1 cm square of muscle fascia, was designed and built; the aim of the apparatus was to reproduce the subcutaneus zone separated by the fascia interposition, from the muscle-vascular zone. At the system was applied a variable electric field in six different experiments: 4 using porous synthetic membranes and 2 using human muscle fascia. PMID:8698777

  3. Bovine papillomavirus type 1 E1 ATPase activity does not depend on binding to DNA nor to viral E2 protein.

    PubMed

    Santucci, S; Bonne-Andréa, C; Clertant, P

    1995-05-01

    Replication of bovine papillomavirus type 1 (BPV-1) DNA has been shown to require two viral proteins known to interact in a molecular complex: E2, a transcription activator, and E1, another nuclear phosphoprotein, which binds to the replication origin and for which helicase/ATPase activities have previously been reported. Here we characterize the BPV-1 E1 ATPase activity. In contrast to Seo et al. (Proceedings of the National Academy of Sciences, USA, 90, 702-706, 1993), we were able to detect this activity in the absence of nucleic acid in partially purified preparations of either E1 protein or of E1-E2 protein complex. Measurements of specific activity and kinetic parameters gave similar values for preparations of various kinds. ATPase activity was quantitatively retained by immunoprecipitates obtained by using anti-E1 or, in the case of E1-E2 complex, anti-E2 antibodies. Significantly, preparations of bacterially expressed glutathione S-transferase-E1 fusion protein exhibited levels of DNA-independent ATPase activity comparable to those of baculovirus-expressed E1. The presence of nucleic acids of various types, including stoichiometric amounts of a BPV-1 ori DNA fragment containing E1 and E2 binding sites, did not grossly affect E1 ATPase activity, the most notable effect being a 2-fold stimulation by unspecific ssDNA. Altogether, our results indicate that BPV-1 E1 possesses an intrinsic ATPase activity which does not depend on the presence of nucleic acid; moreover, they render unlikely any modulation of E1 ATPase activity due to binding either E2 protein or target DNA sequences, or as a result of protein phosphorylation. PMID:7730798

  4. Insertional Inactivation of Genes Encoding the Crystalline Inclusion Proteins of Photorhabdus luminescens Results in Mutants with Pleiotropic Phenotypes

    PubMed Central

    Bintrim, Scott B.; Ensign, Jerald C.

    1998-01-01

    The entomopathogenic bacterium Photorhabdus luminescens exhibits phase variation when cultured in vitro. The variant forms of P. luminescens are pleiotropic and are designated phase I and phase II variants. One of the characteristic phenotypes of phase I cells is the production of two types of intracellular protein inclusions. The genes encoding the protein monomers that form these inclusions, designated cipA and cipB, were cloned and characterized. cipA and cipB encode hydrophobic proteins of 11,648 and 11,308 Da, respectively. The deduced amino acid sequences of CipA and CipB have no significant amino acid sequence similarity to any other known protein but have 25% identity and 49% similarity to each other. Insertional inactivation of cipA or cipB in phase I cells of P. luminescens produced mutants that differ from phase I cells in bioluminescence, the pattern and activities of extracellular products, biochemical traits, adsorption of dyes, and ability to support nematode growth and reproduction. In general, the cip mutants were phenotypically more similar to each other than to either phase I or phase II variants. PMID:9495767

  5. Conformational changes of hapten-protein conjugates resulting in improved broad-specificity and sensitivity of an ELISA for organophosphorus pesticides

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The type of hapten linkage to the carrier protein can play an important role in determining the nature of the resulting antibody response. Generic haptens using three types of linkers were synthesized (a monocarboxylic acid, an unsaturated hydrocarbon, and a carboxamido spacer). These haptens were...

  6. Combined growth hormone/insulin-like growth factor I in addition to glutamine-supplemented TPN results in net protein anabolism in critical illness.

    PubMed

    Carroll, Paul V; Jackson, Nicola C; Russell-Jones, David L; Treacher, David F; Sönksen, Peter H; Umpleby, A Margot

    2004-01-01

    Protein loss leading to reduced lean body mass is recognized to contribute to the high levels of morbidity and mortality seen in critical illness. This prospective, randomized, controlled study compared the effects of conventional parenteral nutrition (TPN), glutamine-supplemented (0.4 g.kg-1.day-1) TPN (TPNGLN), and TPNGLN with combined growth hormone (GH, 0.2 IU.kg-1.day-1) and IGF-I (160 microg.kg-1.day-1) on protein metabolism in critical illness. Nineteen mechanically ventilated subjects [64 +/- 3 yr, body mass index (BMI) 23.8 +/- 1.3, kg/m2] were initially studied in the fasting state (study 1) and subsequently after 3 days of nutritional with/without hormonal support (study 2). All had recently been admitted to the ICU and the majority were postemergency abdominal surgery (APACHE II 17.5 +/- 1.0). Protein metabolism was assessed using a primed constant infusion of [1-13C]leucine. Conventional TPN contained mixed amino acids, Intralipid, and 50% dextrose. TPNGLN, unlike TPN alone, resulted in an increase in plasma glutamine concentration ( approximately 50%, P < 0.05). Both TPN and TPNGLN decreased the rate of protein breakdown (TPN 15%, P < 0.002; TPNGLN 16%, P < 0.05), but during these treatments the patients remained in a net negative protein balance. Combined treatment with TPNGLN + GH/IGF-I increased plasma IGF-I levels (10.3 +/- 0.8 vs. 48.1 +/- 9.1 nmol/l, study 1 vs. study 2, P < 0.05), and in contrast to therapy with nutrition alone, resulted in net protein gain (-0.75 +/- 0.14 vs. 0.33 +/- 0.12 g protein.kg-1.day-1, study 1 vs. study 2, P < 0.05). Therapy with GH/IGF-I + TPNGLN, unlike nutrition alone, resulted in net positive protein balance in a group of critically ill patients. PMID:12759221

  7. Chemical and structural evolution in the Th-SeO3(2-)/SeO4(2-) system: from simple selenites to cluster-based selenate compounds.

    PubMed

    Xiao, Bin; Langer, Eike; Dellen, Jakob; Schlenz, Hartmut; Bosbach, Dirk; Suleimanov, Evgeny V; Alekseev, Evgeny V

    2015-03-16

    While extensive success has been gained in the structural chemistry of the U-Se system, the synthesis and characterization of Th-based Se structures are widely unexplored. Here, four new Th-Se compounds, ?-Th(SeO3)2, ?-Th(SeO3)2, Th(Se2O5)2, and Th3O2(OH)2(SeO4)3, have been obtained from mild hydrothermal or low-temperature (180-220 °C) flux conditions and were subsequently structurally and spectroscopically characterized. The crystal structures of ?-Th(SeO3)2 and ?-Th(SeO3)2 are based on ThO8 and SeO3 polyhedra, respectively, featuring a three-dimensional (3D) network with selenite anions filling in the Th channels along the a axis. Th(Se2O5)2 is a 3D framework composed of isolated ThO8 polyhedra interconnected by [Se2O5](2-) dimers. Th3O2(OH)2(SeO4)3 is also a 3D framework constructed by octahedral hexathorium clusters [Th6(?3-O)4(?3-OH)4](12+), which are interlinked by selenate groups SeO4(2-). The positions of the vibrational modes associated with both Se(IV)O3(2-) and Se(VI)O4(2-) units, respectively, were determined for four compounds, and the Raman spectra of ?- and ?-Th(SeO3)2 are compared and discussed in detail. PMID:25719971

  8. Crystal chemistry of selenates with mineral-like structures: VIII. Butlerite chains in the structure of K(UO2)(SeO4)(OH)(H2O)

    NASA Astrophysics Data System (ADS)

    Gurzhii, V. V.; Bessonov, A. A.; Krivovichev, S. V.; Tananaev, I. G.; Armbruster, T.; Myasoedov, B. F.

    2009-12-01

    A new potassium uranyl selenate compound K(UO2)(SeO4)(OH)(H2O) has been synthesized for the first time using the technique of evaporation from water solution. Its crystal structure has been solved by direct methods (monoclinic, P21/ c, a = 8.0413(9) Ĺ, b = 8.0362(9) Ĺ, c = 11.6032(14) Ĺ, ? = 106.925(2)°, V = 717.34(14) Ĺ3) and refined to R 1 = 0.0319 ( wR 2 = 0.0824) for 1285 reflections with | F 0| > 4? F . The structure consists of [(UO2(SeO4)(OH)(H2O)]- chains extending along axis b. In the chains, the uranyl pentagonal bipyramids are linked via bridged hydroxyl anions and tetrahedral oxoanions [SeO4]2-. Potassium ions are situated between these chains. No chains of that type have been observed in uranyl compounds earlier, but they had been detected in the structures of butlerite, parabutlerite, uklonskovite, fibroferrite, and a number of synthetic compounds.

  9. Crystal chemistry of selenates with mineral-like structures. III. Heteropolyhedral chains in the crystal structure of [Mg(H2O)4(SeO4)]2(H2O)

    NASA Astrophysics Data System (ADS)

    Krivovichev, S. V.

    2007-12-01

    The crystal structure of a new compound [Mg(H2O)4(SeO4)]2(H2O) (monoclinic, P2 1/ a, a = 7.2549(12), b = 20.059(5), c = 10.3934(17) Ĺ, ? = 101.989(13), V = 1479.5(5) Ĺ3) has been solved by direct methods and refined to R 1 = 0.059 for 2577 observed reflections with | F hkl | ? 4?| F hkl |. The structure consists of [Mg(H2O)4(SeO4)]0 chains formed by alternating corner-sharing Mg octahedrons and (SeO4)2- tetrahedrons. O atoms of Mg octahedrons that are shared with selenate tetrahedrons are in a trans orientation. The heteropoly-hedral octahedral-tetrahedral chains are parallel to the c axis and undulate within the (010) plane. The adjacent chains are linked by hydrogen bonds involving H2O molecules not bound with M2+ cations.

  10. The human cytomegalovirus UL11 protein interacts with the receptor tyrosine phosphatase CD45, resulting in functional paralysis of T cells.

    PubMed

    Gabaev, Ildar; Steinbrück, Lars; Pokoyski, Claudia; Pich, Andreas; Stanton, Richard J; Schwinzer, Reinhard; Schulz, Thomas F; Jacobs, Roland; Messerle, Martin; Kay-Fedorov, Penelope C

    2011-12-01

    Human cytomegalovirus (CMV) exerts diverse and complex effects on the immune system, not all of which have been attributed to viral genes. Acute CMV infection results in transient restrictions in T cell proliferative ability, which can impair the control of the virus and increase the risk of secondary infections in patients with weakened or immature immune systems. In a search for new immunomodulatory proteins, we investigated the UL11 protein, a member of the CMV RL11 family. This protein family is defined by the RL11 domain, which has homology to immunoglobulin domains and adenoviral immunomodulatory proteins. We show that pUL11 is expressed on the cell surface and induces intercellular interactions with leukocytes. This was demonstrated to be due to the interaction of pUL11 with the receptor tyrosine phosphatase CD45, identified by mass spectrometry analysis of pUL11-associated proteins. CD45 expression is sufficient to mediate the interaction with pUL11 and is required for pUL11 binding to T cells, indicating that pUL11 is a specific CD45 ligand. CD45 has a pivotal function regulating T cell signaling thresholds; in its absence, the Src family kinase Lck is inactive and signaling through the T cell receptor (TCR) is therefore shut off. In the presence of pUL11, several CD45-mediated functions were inhibited. The induction of tyrosine phosphorylation of multiple signaling proteins upon TCR stimulation was reduced and T cell proliferation was impaired. We therefore conclude that pUL11 has immunosuppressive properties, and that disruption of T cell function via inhibition of CD45 is a previously unknown immunomodulatory strategy of CMV. PMID:22174689

  11. Acquired ability of Staphylococcus aureus to produce toxic shock-associated protein and resulting illness in a rabbit model.

    PubMed Central

    Rasheed, J K; Arko, R J; Feeley, J C; Chandler, F W; Thornsberry, C; Gibson, R J; Cohen, M L; Jeffries, C D; Broome, C V

    1985-01-01

    Staphylococcus aureus from patients with toxic shock syndrome (TSS) produce TSS toxin 1. We transferred, by a bacteriophage, the ability to produce TSS toxin 1 from a TSS toxin 1-positive to a TSS toxin 1-negative strain of S. aureus. This recombinant strain produced TSS toxin 1 as confirmed by isoelectric focusing, immunodiffusion, radioimmunoassay, and autoradiography. The recombinant produced TSS-like illness in rabbits, and was significantly (P less than 0.001) more lethal than the recipient strain. Both strains produced fever and diarrhea, but, in addition, rabbits challenged with the recombinant also developed lowered blood pressure (P = 0.002), conjunctival hyperemia, erythroderma, and respiratory distress. Histopathological findings in rabbits challenged with the recombinant strain were remarkably similar to those described for humans with TSS, e.g., erythrophagocytosis, liver "triaditis," and vasodilatation. This study demonstrates that this protein may contribute to the pathogenesis of the TSS. Images PMID:3156093

  12. Accumulation of radium in ferruginous protein bodies formed in lung tissue: association of resulting radiation hotspots with malignant mesothelioma and other malignancies.

    PubMed

    Nakamura, Eizo; Makishima, Akio; Hagino, Kyoko; Okabe, Kazunori

    2009-01-01

    While exposure to fibers and particles has been proposed to be associated with several different lung malignancies including mesothelioma, the mechanism for the carcinogenesis is not fully understood. Along with mineralogical observation, we have analyzed forty-four major and trace elements in extracted asbestos bodies (fibers and proteins attached to them) with coexisting fiber-free ferruginous protein bodies from extirpative lungs of individuals with malignant mesothelioma. These observations together with patients' characteristics suggest that inhaled iron-rich asbestos fibers and dust particles, and excess iron deposited by continuous cigarette smoking would induce ferruginous protein body formation resulting in ferritin aggregates in lung tissue. Chemical analysis of ferruginous protein bodies extracted from lung tissues reveals anomalously high concentrations of radioactive radium, reaching millions of times higher concentration than that of seawater. Continuous and prolonged internal exposure to hotspot ionizing radiation from radium and its daughter nuclides could cause strong and frequent DNA damage in lung tissue, initiate different types of tumour cells, including malignant mesothelioma cells, and may cause cancers. PMID:19644223

  13. Accumulation of radium in ferruginous protein bodies formed in lung tissue: association of resulting radiation hotspots with malignant mesothelioma and other malignancies

    PubMed Central

    Nakamura, Eizo; Makishima, Akio; Hagino, Kyoko; Okabe, Kazunori

    2009-01-01

    While exposure to fibers and particles has been proposed to be associated with several different lung malignancies including mesothelioma, the mechanism for the carcinogenesis is not fully understood. Along with mineralogical observation, we have analyzed forty-four major and trace elements in extracted asbestos bodies (fibers and proteins attached to them) with coexisting fiber-free ferruginous protein bodies from extirpative lungs of individuals with malignant mesothelioma. These observations together with patients’ characteristics suggest that inhaled iron-rich asbestos fibers and dust particles, and excess iron deposited by continuous cigarette smoking would induce ferruginous protein body formation resulting in ferritin aggregates in lung tissue. Chemical analysis of ferruginous protein bodies extracted from lung tissues reveals anomalously high concentrations of radioactive radium, reaching millions of times higher concentration than that of seawater. Continuous and prolonged internal exposure to hotspot ionizing radiation from radium and its daughter nuclides could cause strong and frequent DNA damage in lung tissue, initiate different types of tumour cells, including malignant mesothelioma cells, and may cause cancers. PMID:19644223

  14. Altered levels of the Taraxacum kok-saghyz (Russian dandelion) small rubber particle protein, TkSRPP3, result in qualitative and quantitative changes in rubber metabolism.

    PubMed

    Collins-Silva, Jillian; Nural, Aise Taban; Skaggs, Amanda; Scott, Deborah; Hathwaik, Upul; Woolsey, Rebekah; Schegg, Kathleen; McMahan, Colleen; Whalen, Maureen; Cornish, Katrina; Shintani, David

    2012-07-01

    Several proteins have been identified and implicated in natural rubber biosynthesis, one of which, the small rubber particle protein (SRPP), was originally identified in Hevea brasiliensis as an abundant protein associated with cytosolic vesicles known as rubber particles. While previous in vitro studies suggest that SRPP plays a role in rubber biosynthesis, in vivo evidence is lacking to support this hypothesis. To address this issue, a transgene approach was taken in Taraxacum kok-saghyz (Russian dandelion or Tk) to determine if altered SRPP levels would influence rubber biosynthesis. Three dandelion SRPPs were found to be highly abundant on dandelion rubber particles. The most abundant particle associated SRPP, TkSRPP3, showed temporal and spatial patterns of expression consistent with patterns of natural rubber accumulation in dandelion. To confirm its role in rubber biosynthesis, TkSRPP3 expression was altered in Russian dandelion using over-expression and RNAi methods. While TkSRPP3 over-expressing lines had slightly higher levels of rubber in their roots, relative to the control, TkSRPP3 RNAi lines showed significant decreases in root rubber content and produced dramatically lower molecular weight rubber than the control line. Not only do results here provide in vivo evidence of TkSRPP proteins affecting the amount of rubber in dandelion root, but they also suggest a function in regulating the molecular weight of the cis-1, 4-polyisoprene polymer. PMID:22609069

  15. Proton Dynamics in the Anti-ferroelectric CsH3(SeO3)2 by using 1H NMR Measurements

    NASA Astrophysics Data System (ADS)

    Lee, Moohee; Ndiaye, B.; Kang, K.; Kim, H.; Sim, J.; Lim, Ae Ran

    2014-03-01

    1H NMR techniques have been employed on the anti-ferroelectric CsH3(SeO3)2 to measure spectrum, shift, T1 and T2 from 300 K down to 80 K at 4.85 T. The 1H NMR spectrum at 300 K shows a composite structure; one dominant broad peak and two small narrow peaks. From the temperature dependences of both intensity and T1 for each peak, we identify that the narrow peaks come from rapidly moving protons whereas the broad peaks originate from rigid protons. The spectra below 200 K show several peaks associated with six nonequivalent proton sites and also the T1 decays show a non-exponential curve coming from many proton sites. T1 is very long even at 300 K and becomes even longer at low temperature. By analyzing T1 decays with T1S and T1L, we confirm that 1/T1(T) show an activated behavior; the short component originates from proton dynamics with activation energy of ~ 140 K and the long component is associated with that of ~ 100 K. Further analysis suggests that some protons show an abrupt change in both shift and T1L across Tc and may be responsible for the phase transition.

  16. Influence of buffer composition on the distribution of inkjet printed protein molecules and the resulting spot morphology.

    PubMed

    Mujawar, Liyakat Hamid; van Amerongen, Aart; Norde, Willem

    2012-08-30

    Producing high quality protein microarrays on inexpensive substrates like polystyrene is a big challenge in the field of diagnostics. Using a non-contact inkjet printer we have produced microarrays on polystyrene slides for two different biotinylated biomolecules, bovine serum albumin (BSA-biotin) and immunoglobulin-G (IgG-biotin), and studied the influence of buffer (composition and pH) on the spot morphology and signal intensity. Atomic force microscopy revealed the morphological pattern of the (biomolecule) spots printed from phosphate buffer (pH 7.4), phosphate buffered saline (pH 7.4) and carbonate buffer (pH 9.6). The spots showed an irregular crust-like appearance when printed in phosphate buffered saline (pH 7.4), mainly due to the high NaCl content, whereas spots of biomolecules printed in carbonate buffer (pH 9.6) showed a smooth morphology. In addition, the rinsing of these dried spots led to the loss of a considerable fraction of the biomolecules, leaving behind a small fraction that is compatible with the (mono)layer. It was confirmed by confocal laser microscopy that the quality of the spots with respect to the uniformity and distribution of the biomolecules therein was superior when printed in carbonate buffer (pH 9.6) as compared to other buffer systems. Particularly, spotting in PBS yielded spots having a very irregular distribution and morphology. PMID:22939120

  17. Partial loss of the DNA repair scaffolding protein, Xrcc1, results in increased brain damage and reduced recovery from ischemic stroke in mice.

    PubMed

    Ghosh, Somnath; Canugovi, Chandrika; Yoon, Jeong Seon; Wilson, David M; Croteau, Deborah L; Mattson, Mark P; Bohr, Vilhelm A

    2015-07-01

    Oxidative DNA damage is mainly repaired by base excision repair (BER). Previously, our laboratory showed that mice lacking the BER glycosylases 8-oxoguanine glycosylase 1 (Ogg1) or nei endonuclease VIII-like 1 (Neil1) recover more poorly from focal ischemic stroke than wild-type mice. Here, a mouse model was used to investigate whether loss of 1 of the 2 alleles of X-ray repair cross-complementing protein 1 (Xrcc1), which encodes a nonenzymatic scaffold protein required for BER, alters recovery from stroke. Ischemia and reperfusion caused higher brain damage and lower functional recovery in Xrcc1(+/-) mice than in wild-type mice. Additionally, a greater percentage of Xrcc1(+/-) mice died as a result of the stroke. Brain samples from human individuals who died of stroke and individuals who died of non-neurological causes were assayed for various steps of BER. Significant losses of thymine glycol incision, abasic endonuclease incision, and single nucleotide incorporation activities were identified, as well as lower expression of XRCC1 and NEIL1 proteins in stroke brains compared with controls. Together, these results suggest that impaired BER is a risk factor in ischemic brain injury and contributes to its recovery. PMID:25971543

  18. Depletion of the RNA-Binding Protein RBP33 Results in Increased Expression of Silenced RNA Polymerase II Transcripts in Trypanosoma brucei

    PubMed Central

    Fernández-Moya, Sandra M.; Carrington, Mark; Estévez, Antonio M.

    2014-01-01

    We have characterized the RNA-binding protein RBP33 in Trypanosoma brucei, and found that it localizes to the nucleus and is essential for viability. The subset of RNAs bound to RBP33 was determined by immunoprecipitation of ribonucleoprotein complexes followed by deep sequencing. Most RBP33-bound transcripts are predicted to be non-coding. Among these, over one-third are located close to the end of transcriptional units (TUs) or have an antisense orientation within a TU. Depletion of RBP33 resulted in an increase in the level of RNAs derived from regions that are normally silenced, such as strand-switch regions, retroposon and repeat sequences. Our work provides the first example of an RNA-binding protein involved in the regulation of gene silencing in trypanosomes. PMID:25215501

  19. Nonablative skin rejuvenation devices and the role of heat shock protein 70: results of a human skin explant model

    NASA Astrophysics Data System (ADS)

    Helbig, Doris; Moebius, Anne; Simon, Jan C.; Paasch, Uwe

    2010-05-01

    Nonablative thermal laser therapy with a 1540-nm laser induces controlled, spatially determined thermal damage, allowing subsequent collagen remodeling while preserving the epidermis. A photorejuvenation effect using nonthermal nonablative stimulation of cells with low energy and narrow band light has been termed photomodulation. Light emitting diodes (LEDs) are narrow band emitters that lead to photomodulation via stimulation of mitochondrial cell organelles. In a previous study, we demonstrated in a human skin explant model that heat shock protein 70 (HSP70) plays a pivotal role in the initiation of skin remodeling after ablative fractional photothermolysis. To test its importance in nonablative laser therapy and photomodulation, the spatio-temporal expression of HSP70 is investigated in response to a 1540-nm laser treatment and six different LED therapies. An Er:glass laser is used with a 1-Hz repetition rate, 30-J/cm2 fluence, and a hand piece with a 2-mm spot size. Nonthermal nonablative treatment is performed using two LED (LEDA SCR red light: 635 nm, 40 to 120 W/cm2, 40 to 120 J/cm2 LEDA SCR yellow light: 585 nm, 16 to 35 W/cm2, 20 to 100 J/cm2 spot size 16×10 cm). Immediate responses as well as responses 1, 3, or 7 days postprocedure are studied; untreated skin explants serve as control. Immunohistochemical investigation (HSP70) is performed in all native, nontreated, and Er:glass laser- or LED-treated samples (n=175). Nonablative laser therapy leads to a clear time-dependent induction of epidermally expressed HSP70, peaking between one to three days post-treatment. In contrast, none of the various LED treatments up-regulated the HSP70 expression in our skin explant model. HSP70 is up-regulated by nonablative but thermal laser devices, but does not seem to play a significant role in the induction of skin remodeling induced by photomodulation. The maximum of HSP70 expression is reached later after Er:glass laser intervention compared to ablative fractional (AFP) treatment.

  20. Feeding soy protein isolate prevents impairment of bone acquisition by western diets as a result of insulin signaling in bone

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Excessive consumption of high fat/high cholesterol “Western” diets during postnatal life results in increased energy intake, development of obesity and systemic insulin resistance. However, how this diet impairs bone development and remodeling is not well understood, and no effective dietary interve...

  1. Differences in folate?protein interactions result in differing inhibition of native rat liver and recombinant glycine N-methyltransferase by 5-methyltetrahydrofolate

    SciTech Connect

    Luka, Zigmund; Pakhomova, Svetlana; Loukachevitch, Lioudmila V.; Newcomer, Marcia E.; Wagner, Conrad

    2012-06-27

    Glycine N-methyltransferase (GNMT) is a key regulatory enzyme in methyl group metabolism. In mammalian liver it reduces S-adenosylmethionine levels by using it to methylate glycine, producing N-methylglycine (sarcosine) and S-adenosylhomocysteine. GNMT is inhibited by binding two molecules of 5-methyltetrahydrofolate (mono- or polyglutamate forms) per tetramer of the active enzyme. Inhibition is sensitive to the status of the N-terminal valine of GNMT and to polyglutamation of the folate inhibitor. It is inhibited by pentaglutamate form more efficiently compared to monoglutamate form. The native rat liver GNMT contains an acetylated N-terminal valine and is inhibited much more efficiently compared to the recombinant protein expressed in E. coli where the N-terminus is not acetylated. In this work we used a protein crystallography approach to evaluate the structural basis for these differences. We show that in the folate-GNMT complexes with the native enzyme, two folate molecules establish three and four hydrogen bonds with the protein. In the folate-recombinant GNMT complex only one hydrogen bond is established. This difference results in more effective inhibition by folate of the native liver GNMT activity compared to the recombinant enzyme.

  2. Epigenetic and oncogenic regulation of SLC16A7 (MCT2) results in protein over-expression, impacting on signalling and cellular phenotypes in prostate cancer

    PubMed Central

    Pertega-Gomes, Nelma; Vizcaino, Jose R.; Felisbino, Sergio; Warren, Anne Y.; Shaw, Greg; Kay, Jonathan; Whitaker, Hayley; Lynch, Andy G.

    2015-01-01

    Monocarboxylate Transporter 2 (MCT2) is a major pyruvate transporter encoded by the SLC16A7 gene. Recent studies pointed to a consistent overexpression of MCT2 in prostate cancer (PCa) suggesting MCT2 as a putative biomarker and molecular target. Despite the importance of this observation the mechanisms involved in MCT2 regulation are unknown. Through an integrative analysis we have discovered that selective demethylation of an internal SLC16A7/MCT2 promoter is a recurrent event in independent PCa cohorts. This demethylation is associated with expression of isoforms differing only in 5?-UTR translational control motifs, providing one contributing mechanism for MCT2 protein overexpression in PCa. Genes co-expressed with SLC16A7/MCT2 also clustered in oncogenic-related pathways and effectors of these signalling pathways were found to bind at the SLC16A7/MCT2 gene locus. Finally, MCT2 knock-down attenuated the growth of PCa cells. The present study unveils an unexpected epigenetic regulation of SLC16A7/MCT2 isoforms and identifies a link between SLC16A7/MCT2, Androgen Receptor (AR), ETS-related gene (ERG) and other oncogenic pathways in PCa. These results underscore the importance of combining data from epigenetic, transcriptomic and protein level changes to allow more comprehensive insights into the mechanisms underlying protein expression, that in our case provide additional weight to MCT2 as a candidate biomarker and molecular target in PCa. PMID:26035357

  3. Genetic Deletion of Rnd3/RhoE Results in Mouse Heart Calcium Leakage Through Upregulation of Protein Kinase A Signaling

    PubMed Central

    Lin, Xi; Yue, Xiaojing; Wang, Qiongling; Wang, Guoliang; Fu, Qin; Ai, Xun; Chiang, David Y.; Miyake, Christina Y.; Wehrens, Xander H.T.; Chang, Jiang

    2014-01-01

    Rationale Rnd3, a small Rho GTPase, is involved in the regulation of cell actin cytoskeleton dynamics, cell migration, and proliferation. The biological function of Rnd3 in the heart remains unexplored. Objective To define the functional role of the Rnd3 gene in the animal heart and investigate the associated molecular mechanism. Methods and Results By loss-of-function approaches, we discovered that Rnd3 is involved in calcium regulation in cardiomyocytes. Rnd3-null mice died at the embryonic stage with fetal arrhythmias. The deletion of Rnd3 resulted in severe Ca2+ leakage through destabilized ryanodine receptor type 2 (RyR2) Ca2+ release channels. We further found that downregulation of Rnd3 attenuated ?2-adrenergic receptor (?2AR) lysosomal targeting and ubiquitination, which in turn resulted in the elevation of ?2AR protein levels leading to the hyperactivation of protein kinase A (PKA) signaling. The PKA activation destabilized RyR2 channels. This irregular spontaneous Ca2+ release can be curtailed by PKA inhibitor treatment. Increases in the PKA activity along with elevated cyclic adenosine monophosphate (cAMP) levels were detected in Rnd3-null embryos, in neonatal rat cardiomyocytes, and non-cardiac cell lines with Rnd3 knockdown, suggesting a general mechanism for Rnd3-mediated PKA signaling activation. ?2AR blocker treatment reduced arrhythmia and improved cardiac function. Conclusion Rnd3 is a novel factor involved in intracellular Ca2+ homeostasis regulation in the heart. Deficiency of the protein induces RyR2 dysfunction by a mechanism that attenuates Rnd3-mediated ?2AR ubiquitination, which leads to the activation of PKA signaling. Increased PKA signaling in turn promotes RyR2 hyperphosphorylation, which contributes to arrhythmogenesis and heart failure. PMID:25348166

  4. soaPDB: a web application for searching the Protein Data Bank, organizing results, and receiving automatic email alerts

    PubMed Central

    Lesburg, Charles A.; Duca, José S.

    2008-01-01

    soaPDB is a web application that allows generation and organization of saved PDB searches, and offers automatic email alerts. This tool is used from a web interface to store PDB searches and results in a backend relational database. Written using the Ruby on Rails open-source web framework, soaPDB is easy to deploy, maintain and customize. soaPDB is freely available upon request for local installation and is also available at http://soapdb.dyndns.org:3000. PMID:18487276

  5. Acute leukemias of different lineages have similar MLL gene fusions encoding related chimeric proteins resulting from chromosomal translocation

    SciTech Connect

    Corral, J.; Forster, A.; Thompson, S.; Rabbitts, T.H. ); Lampert, F. ); Kaneko, Y. ); Slater, R.; Kroes, W.G. ); Van Der Schoot, C.E. ); Ludwig, W.D. ); Karpas, A. ); Pocock, C.; Cotter, F. )

    1993-09-15

    The MLL gene, on human chromosome 11q23, undergoes chromosomal translocation in acute leukemias, resulting in gene fusion with AF4 (chromosome 4) and ENL (chromosome 19). The authors report here translocation of MLL with nine different chromosomes and two paracentric chromosome 11 deletions in early B cell, B- or T-cell lineage, or nonlymphocytic acute leukemias. The mRNA translocation junction from 22t(4;11) patients, including six adult leukemias, and nine t(11;19) tumors reveals a remarkable conservation of breakpoints within MLL, AF4, or ENL genes, irrespective of tumor phenotype. Typically, the breakpoints are upstream of the zinc-finger region of MLL, and deletion of this region can accompany translocation, supporting the der(11) chromosome as the important component in leukemogenesis. Partial sequence of a fusion between MLL and the AFX1 gene from chromosome X shows the latter to be rich in Ser/Pro codons, like the ENL mRNA. These data suggest that the heterogeneous 11q23 abnormalities might cause attachment of Ser/Pro-rich segments to the NH[sub 2] terminus of MLL, lacking the zinc-finger region, and that translocation occurs in early hematopoietic cells, before commitment to distinct lineages. 36 refs., 2 figs.

  6. Association between Sleep Quality and C-Reactive Protein: Results from National Health and Nutrition Examination Survey, 2005-2008

    PubMed Central

    Liu, Rong; Liu, Xin; Zee, Phyllis C.; Hou, Lifang; Zheng, Zheng; Wei, Yongxiang; Du, Jie

    2014-01-01

    Objective Our objective was to explore the association between poor sleep quality and hs_CRP in an adult U.S. population. Methods This study focused on 9,317 participants in the National Health and Nutrition Examination Survey (NHANES) from 2005–2008 who were aged 20–85 years, completed a sleep disorder questionnaire, and had available information on serum hs_CRP. Sleep quality was classified into three categories (good, moderate, poor) based on the responses of participants to the NHANES sleep disorder questionnaire. High CRP was defined as hs-CRP >1 md/dL. Linear regression model was applied to investigate the association between poor sleep quality and log-transformed hs_CRP. And logistic regression model was fitted to evaluate the association between sleep quality and the risk of high CRP. Results Females were more likely to report poor sleep quality than males (26% vs. 19%, p<0.0001). Each sleep disorder was significantly associated with increased hs_CRP and correlative to other sleep disorders. In fully-adjusted linear regression model, poor sleep quality was significantly associated with elevated hs_CRP (log transformed) among the overall sample and in females only (??=?0.10, se?=?0.03, p<0.01 and ??=?0.13, se?=?0.04, p<0.01, respectively). In fully-adjusted logistics regression model, poor sleep quality was linked with risk of high CRP(OR: 1.42, 95%CI: 1.15–1.76 in overall sample and OR: 1.59, 95%CI: 1.18–2.14 in females, respectively). Conclusion We found that poor sleep quality was independently associated with elevated hs_CRP in females but not in males in a U.S. adult population. PMID:24663098

  7. Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database

    SciTech Connect

    Omenn, Gilbert; States, David J.; Adamski, Marcin; Blackwell, Thomas W.; Menon, Rajasree; Hermjakob, Henning; Apweiler, Rolf; Haab, Brian B.; Simpson, Richard; Eddes, James; Kapp, Eugene; Moritz, Rod; Chan, Daniel W.; Rai, Alex J.; Admon, Arie; Aebersold, Ruedi; Eng, Jimmy K.; Hancock, William S.; Hefta, Stanley A.; Meyer, Helmut; Paik, Young-Ki; Yoo, Jong-Shin; Ping, Peipei; Pounds, Joel G.; Adkins, Joshua N.; Qian, Xiaohong; Wang, Rong; Wasinger, Valerie; Wu, Chi Yue; Zhao, Xiaohang; Zeng, Rong; Archakov, Alexander; Tsugita, Akira; Beer, Ilan; Pandey, Akhilesh; Pisano, Michael; Andrews, Philip; Tammen, Harald; Speicher, David W.; Hanash, Samir M.

    2005-08-13

    HUPO initiated the Plasma Proteome Project (PPP) in 2002. Its pilot phase has (1) evaluated advantages and limitations of many depletion, fractionation, and MS technology platforms; (2) compared PPP reference specimens of human serum and EDTA, heparin, and citrate-anticoagulated plasma; and (3) created a publicly-available knowledge base (www.bioinformatics. med.umich.edu/hupo/ppp; www.ebi.ac.uk/pride). Thirty-five participating laboratories in 13 countries submitted datasets. Working groups addressed (a) specimen stability and protein concentrations; (b) protein identifications from 18 MS/MS datasets; (c) independent analyses from raw MS-MS spectra; (d) search engine performance, subproteome analyses, and biological insights; (e) antibody arrays; and (f) direct MS/SELDI analyses. MS-MS datasets had 15 710 different International Protein Index (IPI) protein IDs; our integration algorithm applied to multiple matches of peptide sequences yielded 9504 IPI proteins identified with one or more peptides and 3020 proteins identified with two or more peptides (the Core Dataset). These proteins have been characterized with Gene Ontology, InterPro, Novartis Atlas, OMIM, and immunoassay based concentration determinations. The database permits examination of many other subsets, such as 1274 proteins identified with three or more peptides. Reverse protein to DNA matching identified proteins for 118 previously unidentified ORFs. We recommend use of plasma instead of serum, with EDTA (or citrate) for anticoagulation. To improve resolution, sensitivity and reproducibility of peptide identifications and protein matches, we recommend combinations of depletion, fractionation, and MS/MS technologies, with explicit criteria for evaluation of spectra, use of search algorithms, and integration of homologous protein matches. This Special Issue of PROTEOMICS presents papers integral to the collaborative analysis plus many reports of supplementary work on various aspects of the PPP workplan. These PPP results on complexity, dynamic range, incomplete sampling, false-positive matches, and integration of diverse datasets for plasma and serum proteins lay a foundation for development and validation of circulating protein biomarkers in health and disease.

  8. Rapamycin and chloroquine: the in vitro and in vivo effects of autophagy-modifying drugs show promising results in valosin containing protein multisystem proteinopathy.

    PubMed

    Nalbandian, Angčle; Llewellyn, Katrina J; Nguyen, Christopher; Yazdi, Puya G; Kimonis, Virginia E

    2015-01-01

    Mutations in the valosin containing protein (VCP) gene cause hereditary Inclusion body myopathy (hIBM) associated with Paget disease of bone (PDB), frontotemporal dementia (FTD), more recently termed multisystem proteinopathy (MSP). Affected individuals exhibit scapular winging and die from progressive muscle weakness, and cardiac and respiratory failure, typically in their 40s to 50s. Histologically, patients show the presence of rimmed vacuoles and TAR DNA-binding protein 43 (TDP-43)-positive large ubiquitinated inclusion bodies in the muscles. We have generated a VCPR155H/+ mouse model which recapitulates the disease phenotype and impaired autophagy typically observed in patients with VCP disease. Autophagy-modifying agents, such as rapamycin and chloroquine, at pharmacological doses have previously shown to alter the autophagic flux. Herein, we report results of administration of rapamycin, a specific inhibitor of the mechanistic target of rapamycin (mTOR) signaling pathway, and chloroquine, a lysosomal inhibitor which reverses autophagy by accumulating in lysosomes, responsible for blocking autophagy in 20-month old VCPR155H/+ mice. Rapamycin-treated mice demonstrated significant improvement in muscle performance, quadriceps histological analysis, and rescue of ubiquitin, and TDP-43 pathology and defective autophagy as indicated by decreased protein expression levels of LC3-I/II, p62/SQSTM1, optineurin and inhibiting the mTORC1 substrates. Conversely, chloroquine-treated VCPR155H/+ mice revealed progressive muscle weakness, cytoplasmic accumulation of TDP-43, ubiquitin-positive inclusion bodies and increased LC3-I/II, p62/SQSTM1, and optineurin expression levels. Our in vitro patient myoblasts studies treated with rapamycin demonstrated an overall improvement in the autophagy markers. Targeting the mTOR pathway ameliorates an increasing list of disorders, and these findings suggest that VCP disease and related neurodegenerative multisystem proteinopathies can now be included as disorders that can potentially be ameliorated by rapalogs. PMID:25884947

  9. Rapamycin and Chloroquine: The In Vitro and In Vivo Effects of Autophagy-Modifying Drugs Show Promising Results in Valosin Containing Protein Multisystem Proteinopathy

    PubMed Central

    Nalbandian, Angčle; Llewellyn, Katrina J.; Nguyen, Christopher; Yazdi, Puya G.; Kimonis, Virginia E.

    2015-01-01

    Mutations in the valosin containing protein (VCP) gene cause hereditary Inclusion body myopathy (hIBM) associated with Paget disease of bone (PDB), frontotemporal dementia (FTD), more recently termed multisystem proteinopathy (MSP). Affected individuals exhibit scapular winging and die from progressive muscle weakness, and cardiac and respiratory failure, typically in their 40s to 50s. Histologically, patients show the presence of rimmed vacuoles and TAR DNA-binding protein 43 (TDP-43)-positive large ubiquitinated inclusion bodies in the muscles. We have generated a VCPR155H/+ mouse model which recapitulates the disease phenotype and impaired autophagy typically observed in patients with VCP disease. Autophagy-modifying agents, such as rapamycin and chloroquine, at pharmacological doses have previously shown to alter the autophagic flux. Herein, we report results of administration of rapamycin, a specific inhibitor of the mechanistic target of rapamycin (mTOR) signaling pathway, and chloroquine, a lysosomal inhibitor which reverses autophagy by accumulating in lysosomes, responsible for blocking autophagy in 20-month old VCPR155H/+ mice. Rapamycin-treated mice demonstrated significant improvement in muscle performance, quadriceps histological analysis, and rescue of ubiquitin, and TDP-43 pathology and defective autophagy as indicated by decreased protein expression levels of LC3-I/II, p62/SQSTM1, optineurin and inhibiting the mTORC1 substrates. Conversely, chloroquine-treated VCPR155H/+ mice revealed progressive muscle weakness, cytoplasmic accumulation of TDP-43, ubiquitin-positive inclusion bodies and increased LC3-I/II, p62/SQSTM1, and optineurin expression levels. Our in vitro patient myoblasts studies treated with rapamycin demonstrated an overall improvement in the autophagy markers. Targeting the mTOR pathway ameliorates an increasing list of disorders, and these findings suggest that VCP disease and related neurodegenerative multisystem proteinopathies can now be included as disorders that can potentially be ameliorated by rapalogs. PMID:25884947

  10. The crystal structure of ilinskite, NaCu5O2(SeO3)2Cl3, and review of mixed-ligand CuOmCln coordination geometries in minerals and inorganic compounds

    NASA Astrophysics Data System (ADS)

    Krivovichev, Sergey V.; Filatov, Stanislav K.; Vergasova, Lidiya P.

    2013-04-01

    The crystal structure of ilinskite, NaCu5O2(SeO3)2Cl3, a rare copper selenite chloride from volcanic fumaroles of the Great fissure Tolbachik eruption (Kamchatka peninsula, Russia), has been solved by direct methods and refined to R 1 = 0.044 on the basis of 2720 unique observed reflections. The mineral is orthorhombic, Pnma, a = 17.769(7), b = 6.448(3), c = 10.522(4) Ĺ, V = 1205.6(8) Ĺ3, Z = 4. The The CuOmCln coordination polyhedra share edges to form tetramers that have 'additional' O1 and O2 atoms as centers. The O1Cu4 and O2Cu4 tetrahedra share common Cu atoms to form [O2Cu5]6+ sheets. The SeO3 groups and Cl atoms are adjacent to the [O2Cu5]6+ sheets to form complex layers parallel to (100). The Na+ cations are located in between the layers. A review of mixed-ligand CuOmCln coordination polyhedra in minerals and inorganic compounds is given. There are in total 26 stereochemically different mixed-ligand Cu-O-Cl coordinations.

  11. Dityrosine, 3,4-dihydroxyphenylalanine (DOPA), and radical formation from tyrosine residues on milk proteins with globular and flexible structures as a result of riboflavin-mediated photo-oxidation.

    PubMed

    Dalsgaard, Trine K; Nielsen, Jacob H; Brown, Bronwyn E; Stadler, Nadina; Davies, Michael J

    2011-07-27

    Riboflavin-mediated photo-oxidative damage to protein Tyr residues has been examined to determine whether protein structure influences competing protein oxidation pathways in single proteins and protein mixtures. EPR studies resulted in the detection of Tyr-derived o-semiquione radicals, with this species suggested to arise from oxidation of 3,4-dihydroxyphenylalanine (DOPA). The yield of this radical was lower in samples containing ?-casein than in samples containing only globular proteins. Consistent with this observation, the yield of DOPA detected on ?-casein was lower than that on two globular proteins, BSA and ?-lactoglobulin. In contrast, samples with ?-casein gave higher yields of dityrosine than samples containing BSA and ?-lactoglobulin. These results indicate that the flexible structure of ?-casein favors radical-radical termination of tyrosyl radicals to give dityrosine, whereas the less flexible structure of globular proteins decreases the propensity for tyrosyl radicals to dimerize, with this resulting in higher yields of DOPA and its secondary radical. PMID:21696221

  12. Lipid Raft- and Protein Kinase C-mediated Synergism between Glucocorticoid- and Gonadotropin-releasing Hormone Signaling Results in Decreased Cell Proliferation*

    PubMed Central

    Wehmeyer, Lancelot; Du Toit, Andrea; Lang, Dirk M.; Hapgood, Janet P.

    2014-01-01

    Cross-talk between the glucocorticoid receptor (GR) and other receptors is emerging as a mechanism for fine-tuning cellular responses. We have previously shown that gonadotropin-releasing hormone (GnRH) ligand-independently activates the GR and synergistically modulates glucocorticoid-induced transcription of an endogenous gene in L?T2 pituitary gonadotrope precursor cells. Here, we investigated GR and GnRH receptor (GnRHR) cross-talk that involves co-localization with lipid rafts in L?T2 cells. We report that the GnRHR and a small population of the GR co-localize with the lipid raft protein flotillin-1 (Flot-1) at the plasma membrane and that the GR is present in a complex with Flot-1, independent of the presence of ligands. We found that the SGK-1 gene is up-regulated by Dex and GnRH alone, whereas a combination of both ligands resulted in a synergistic increase in SGK-1 mRNA levels. Using siRNA-mediated knockdown and antagonist strategies, we show that the gene-specific synergistic transcriptional response requires the GR, GnRHR, and Flot-1 as well as the protein kinase C pathway. Interestingly, although several GR cofactors are differentially recruited to the SGK-1 promoter in the presence of Dex and GnRH, GR levels remain unchanged compared with Dex treatment alone, suggesting that lipid raft association of the GR has a role in enhancing its transcriptional output in the nucleus. Finally, we show that Dex plus GnRH synergistically inhibit cell proliferation in a manner dependent on SGK-1 and Flot-1. Collectively the results support a mechanism whereby GR and GnRHR cross-talk within Flot-1-containing lipid rafts modulates cell proliferation via PKC activation and SGK-1 up-regulation. PMID:24558046

  13. 31 CFR 30.4 - Q-4: What actions are necessary for a TARP recipient to comply with the standards established...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... risk officers the SEO compensation plans to ensure that the SEO compensation plans do not encourage... fiscal year, provide a narrative description of how the SEO compensation plans do not encourage the SEOs... these SEO compensation plans do not encourage behavior focused on short-term results rather than...

  14. 31 CFR 30.4 - Q-4: What actions are necessary for a TARP recipient to comply with the standards established...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... risk officers the SEO compensation plans to ensure that the SEO compensation plans do not encourage... fiscal year, provide a narrative description of how the SEO compensation plans do not encourage the SEOs... these SEO compensation plans do not encourage behavior focused on short-term results rather than...

  15. 31 CFR 30.4 - Q-4: What actions are necessary for a TARP recipient to comply with the standards established...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... risk officers the SEO compensation plans to ensure that the SEO compensation plans do not encourage... fiscal year, provide a narrative description of how the SEO compensation plans do not encourage the SEOs... these SEO compensation plans do not encourage behavior focused on short-term results rather than...

  16. 31 CFR 30.4 - Q-4: What actions are necessary for a TARP recipient to comply with the standards established...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... risk officers the SEO compensation plans to ensure that the SEO compensation plans do not encourage... fiscal year, provide a narrative description of how the SEO compensation plans do not encourage the SEOs... these SEO compensation plans do not encourage behavior focused on short-term results rather than...

  17. Immunization with a Lymphocytic Choriomeningitis Virus Peptide Mixed with Heat Shock Protein 70 Results in Protective Antiviral Immunity and Specific Cytotoxic T Lymphocytes

    PubMed Central

    Ciupitu, Anne-Marie T.; Petersson, Max; O'Donnell, Carey L.; Williams, Kevin; Jindal, Satish; Kiessling, Rolf; Welsh, Raymond M.

    1998-01-01

    Heat shock proteins (hsp's) isolated from murine cancer cells can elicit protective immunity and specific cytotoxic T lymphocytes (CTLs) by channeling tumor-derived peptides bound to hsp's to the major histocompatibility class I antigen presentation pathway. Here we have investigated if hsp70 can be used in a novel peptide vaccine for the induction of protective antiviral immunity and memory CTLs. A CTL epitope from the well-defined lymphocytic choriomeningitis virus (LCMV) system was mixed with recombinant hsp70 in vitro under conditions that optimize peptide binding to hsp70. Mice were immunized with the hsp70–peptide mixture and challenged with LCMV. Virus titers were reduced 10–100-fold in these mice compared to control mice. Immunization with the hsp70–peptide mixture resulted in the development of CTL memory cells that could be reactivated during LCMV infection, and that in a 51Cr-release assay could lyse cells pulsed with the same peptide, but not cells pulsed with another LCMV peptide. These results show that hsp70 can be used with CTL epitopes to induce efficient protective antiviral immunity and the generation of peptide-specific CTLs. The results also demonstrate the usefulness of hsp70 as an alternative to adjuvants and DNA vectors for the delivery of CTL epitopes to antigen-presenting cells. PMID:9480978

  18. Reactive oxygen species derived from xanthine oxidase interrupt dimerization of breast cancer resistance protein, resulting in suppression of uric acid excretion to the intestinal lumen.

    PubMed

    Ogura, Jiro; Kuwayama, Kaori; Sasaki, Shunichi; Kaneko, Chihiro; Koizumi, Takahiro; Yabe, Keisuke; Tsujimoto, Takashi; Takeno, Reiko; Takaya, Atsushi; Kobayashi, Masaki; Yamaguchi, Hiroaki; Iseki, Ken

    2015-09-01

    The prevalence of hyperuricemia/gout increases with aging. However, the effect of aging on function for excretion of uric acid to out of the body has not been clarified. We found that ileal uric acid clearance in middle-aged rats (11-12 months) was decreased compared with that in young rats (2 months). In middle-aged rats, xanthine oxidase (XO) activity in the ileum was significantly higher than that in young rats. Inosine-induced reactive oxygen species (ROS), which are derived from XO, also decreased ileal uric acid clearance. ROS derived from XO decreased the active homodimer level of breast cancer resistance protein (BCRP), which is a uric acid efflux transporter, in the ileum. Pre-administration of allopurinol recovered the BCRP homodimer level, resulting in the recovering ileal uric acid clearance. Moreover, we investigated the effects of ROS derived from XO on BCRP homodimer level directly in Caco-2 cells using hypoxanthine. Treatment with hypoxanthine decreased BCRP homodimer level. Treatment with hypoxanthine induced mitochondrial dysfunction, suggesting that the decreasing BCRP homodimer level might be caused by mitochondrial dysfunction. In conclusion, ROS derived from XO decrease BCRP homodimer level, resulting in suppression of function for uric acid excretion to the ileal lumen. ROS derived from XO may cause the suppression of function of the ileum for the excretion of uric acid with aging. The results of our study provide a new insight into the causes of increasing hyperuricemia/gout prevalence with aging. PMID:26119820

  19. ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank.

    PubMed

    Sehnal, David; Svobodová Va?eková, Radka; Pravda, Lukáš; Ionescu, Crina-Maria; Geidl, Stanislav; Horský, Vladimír; Jaiswal, Deepti; Wimmerová, Michaela; Ko?a, Jaroslav

    2015-01-01

    Following the discovery of serious errors in the structure of biomacromolecules, structure validation has become a key topic of research, especially for ligands and non-standard residues. ValidatorDB (freely available at http://ncbr.muni.cz/ValidatorDB) offers a new step in this direction, in the form of a database of validation results for all ligands and non-standard residues from the Protein Data Bank (all molecules with seven or more heavy atoms). Model molecules from the wwPDB Chemical Component Dictionary are used as reference during validation. ValidatorDB covers the main aspects of validation of annotation, and additionally introduces several useful validation analyses. The most significant is the classification of chirality errors, allowing the user to distinguish between serious issues and minor inconsistencies. Other such analyses are able to report, for example, completely erroneous ligands, alternate conformations or complete identity with the model molecules. All results are systematically classified into categories, and statistical evaluations are performed. In addition to detailed validation reports for each molecule, ValidatorDB provides summaries of the validation results for the entire PDB, for sets of molecules sharing the same annotation (three-letter code) or the same PDB entry, and for user-defined selections of annotations or PDB entries. PMID:25392418

  20. Downregulation of Cellular c-Jun N-Terminal Protein Kinase and NF-?B Activation by Berberine May Result in Inhibition of Herpes Simplex Virus Replication

    PubMed Central

    Song, Siwei; Qiu, Min; Chu, Ying; Chen, Deyan; Wang, Xiaohui; Su, Airong

    2014-01-01

    Berberine is a quaternary ammonium salt from the protoberberine group of isoquinoline alkaloids. Some reports show that berberine exhibits anti-inflammatory, antitumor, and antiviral properties by modulating multiple cellular signaling pathways, including p53, nuclear factor ?B (NF-?B), and mitogen-activated protein kinase. In the present study, we investigated the antiviral effect of berberine against herpes simplex virus (HSV) infection. Current antiherpes medicines such as acyclovir can lessen the recurring activation when used early at infection but are unable to prevent or cure infections where treatment has selected for resistant mutants. In searching for new antiviral agents against herpesvirus infection, we found that berberine reduced viral RNA transcription, protein synthesis, and virus titers in a dose-dependent manner. To elucidate the mechanism of its antiviral activity, the effect of berberine on the individual steps of viral replication cycle of HSV was investigated via time-of-drug addition assay. We found that berberine acted at the early stage of HSV replication cycle, between viral attachment/entry and genomic DNA replication, probably at the immediate-early gene expression stage. We further demonstrated that berberine significantly reduced HSV-induced NF-?B activation, as well as I?B-? degradation and p65 nuclear translocation. Moreover, we found that berberine also depressed HSV-induced c-Jun N-terminal kinase (JNK) phosphorylation but had little effect on p38 phosphorylation. Our results suggest that the berberine inhibition of HSV infection may be mediated through modulating cellular JNK and NF-?B pathways. PMID:24913175

  1. Rats fed soy protein isolate (SPI) have impaired hepatic CYP1A1 induction by polycyclic aromatic hydrocarbons as a result of interference with aryl hydrocarbon receptor signaling

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Consumption of soy diet has been found to reduce cancer incidence in animals and is associated with reduced cancer risk in humans. Previously, we have demonstrated that female Sprague-Dawley rats fed purified AIN-93G diets with soy protein isolate (SPI) as the sole protein source had reduced CYP1A1 ...

  2. Absence of myotonic dystrophy protein kinase (DMPK) mRNA as a result of a triplet repeat expansion in myotonic dystrophy

    SciTech Connect

    Carango, P.; Noble, J.E.; Funanage, V.L.; Marks, H.G. )

    1993-11-01

    Myotonic dystrophy is an autosomally dominant inherited disease in which system-wide abnormalities are caused by a triplet repeat expansion within the 3[prime] untranslated region of the myotonic dystrophy protein kinase (DMPK) gene. To determine the effect an expanded repeat region has on DMPK expression, the authors have separated the chromosome 19 homologues from a 36-year-old woman with myotonic dystrophy into different cell lines by way of somatic cell hybridization. Hybrid DM9101 contains the normal DMPK allele (13 repeats), whereas hybrid DM1115 harbors the mutant allele ([approximately]133 repeats). Reverse transcription/polymerase chain reaction (RT/PCR) amplification of coding sequences from the DMPK gene has shown both reduced levels of primary DMPK transcripts and impaired processing of these transcripts in hybrid cell line DM1115. These findings suggest that the presence of a large number of repeats in the 3[prime] untranslated region of the DMPK gene reduces both the synthesis and the processing of DMPK mRNA, resulting in undetectable levels of processed DMPK mRNA from the mutant allele. 41 refs., 6 figs., 1 tab.

  3. Transfer of 15-lipoxygenase gene into rabbit iliac arteries results in the appearance of oxidation-specific lipid-protein adducts characteristic of oxidized low density lipoprotein.

    PubMed Central

    Ylä-Herttuala, S; Luoma, J; Viita, H; Hiltunen, T; Sisto, T; Nikkari, T

    1995-01-01

    Oxidized low density lipoprotein (LDL) possesses several atherogenic properties. The mechanisms by which LDL becomes oxidized in vivo remain unknown, but previous studies have suggested that 15-lipoxygenase may be one of the factors involved in the initiation of LDL oxidation in the arterial wall. 3 wk after a retrovirus-mediated 15-lipoxygenase gene transfer into iliac arteries of normocholesterolemic rabbits there was a threefold increase in 15-lipoxygenase activity but no signs of LDL oxidation. However, when animals were made moderately hypercholesterolemic by feeding a 0.13% cholesterol diet for 2-3 wk starting from day 4 after the gene transfer, oxidation-specific lipid-protein adducts characteristic of oxidized LDL were detected in 15-lipoxygenase-transduced arteries. Control experiments in which contralateral iliac arteries were transduced with beta-galactosidase-containing retroviruses showed only occasional signs of the presence of oxidation-specific adducts. The results support the hypothesis that products derived from the 15-lipoxygenase activity are involved in the induction of LDL oxidation within the arterial wall, provided that sufficient concentrations of lipoproteins are present in the artery. Images PMID:7769108

  4. A missense mutation in the transmembrane domain of CESA4 affects protein abundance in the plasma membrane and results in abnormal cell wall biosynthesis in rice.

    PubMed

    Zhang, Baocai; Deng, Lingwei; Qian, Qian; Xiong, Guangyan; Zeng, Dali; Li, Rui; Guo, Longbiao; Li, Jiayang; Zhou, Yihua

    2009-11-01

    Cellulose synthase (CESA) is a critical catalytic subunit of the cellulose synthase complex responsible for glucan chain elongation. Our knowledge about how CESA functions is still very limited. Here, we report the functional characterization of a rice mutant, brittle culm11, that shows growth retardation and dramatically reduced plant strength. Map-based cloning revealed that all the mutant phenotypes result from a missense mutation in OsCESA4 (G858R), a highly conserved residue at the end of the fifth transmembrane domain. The aberrant secondary cell wall of the mutant plants is attributed to significantly reduced cellulose content, abnormal secondary wall structure of sclerenchyma cells, and overall altered wall composition, as detected by chemical analyses and immunochemical staining. Importantly, we have found that this point mutation decreases the abundance of OsCESA4 in the plasma membrane, probably due to a defect in the process of CESA complex secretion. The data from our biochemical, genetic, and pharmacological analyses indicate that this residue is critical for maintaining the normal level of CESA proteins in the plasma membrane. PMID:19697141

  5. Proteins wriggle.

    PubMed Central

    Cahill, Michael; Cahill, Sean; Cahill, Kevin

    2002-01-01

    We propose an algorithmic strategy for improving the efficiency of Monte Carlo searches for the low-energy states of proteins. Our strategy is motivated by a model of how proteins alter their shapes. In our model, when proteins fold under physiological conditions, their backbone dihedral angles change synchronously in groups of four or more to avoid steric clashes and respect the kinematic conservation laws. They wriggle; they do not thrash. We describe a simple algorithm that can be used to incorporate wriggling in Monte Carlo simulations of protein folding. We have tested this wriggling algorithm against a code in which the dihedral angles are varied independently (thrashing). Our standard of success is the average root-mean-square distance (rmsd) between the alpha-carbons of the folding protein and those of its native structure. After 100,000 Monte Carlo sweeps, the relative decrease in the mean rmsd, as one switches from thrashing to wriggling, rises from 11% for the protein 3LZM with 164 amino acids (aa) to 40% for the protein 1A1S with 313 aa and 47% for the protein 16PK with 415 aa. These results suggest that wriggling is useful and that its utility increases with the size of the protein. One may implement wriggling on a parallel computer or a computer farm. PMID:11964253

  6. N-Octanoyl Dopamine Treatment of Endothelial Cells Induces the Unfolded Protein Response and Results in Hypometabolism and Tolerance to Hypothermia

    PubMed Central

    Stamellou, Eleni; Fontana, Johann; Wedel, Johannes; Ntasis, Emmanouil; Sticht, Carsten; Becker, Anja; Pallavi, Prama; Wolf, Kerstin; Krämer, Bernhard K.; Hafner, Mathias; van Son, Willem J.; Yard, Benito A.

    2014-01-01

    Aim N-acyl dopamines (NADD) are gaining attention in the field of inflammatory and neurological disorders. Due to their hydrophobicity, NADD may have access to the endoplasmic reticulum (ER). We therefore investigated if NADD induce the unfolded protein response (UPR) and if this in turn influences cell behaviour. Methods Genome wide gene expression profiling, confirmatory qPCR and reporter assays were employed on human umbilical vein endothelial cells (HUVEC) to validate induction of UPR target genes and UPR sensor activation by N-octanoyl dopamine (NOD). Intracellular ATP, apoptosis and induction of thermotolerance were used as functional parameters to assess adaptation of HUVEC. Results NOD, but not dopamine dose dependently induces the UPR. This was also found for other synthetic NADD. Induction of the UPR was dependent on the redox activity of NADD and was not caused by selective activation of a particular UPR sensor. UPR induction did not result in cell apoptosis, yet NOD strongly impaired cell proliferation by attenuation of cells in the S-G2/M phase. Long-term treatment of HUVEC with low NOD concentration showed decreased intracellular ATP concentration paralleled with activation of AMPK. These cells were significantly more resistant to cold inflicted injury. Conclusions We provide for the first time evidence that NADD induce the UPR in vitro. It remains to be assessed if UPR induction is causally associated with hypometabolism and thermotolerance. Further pharmacokinetic studies are warranted to address if the NADD concentrations used in vitro can be obtained in vivo and if this in turn shows therapeutic efficacy. PMID:24926788

  7. Effect of increased leptin and C-reactive protein levels on mortality: Results from the National Health and Nutrition Examination Survey

    PubMed Central

    Amrock, Stephen M.; Weitzman, Michael

    2014-01-01

    Objective Leptin and C-reactive protein (CRP) have each been linked to adverse cardiovascular events, and prior cross-sectional research suggests that increased levels of both biomarkers pose an even greater risk. The effect of increased levels of both leptin and CRP on mortality has not, however, been previously assessed. Methods We used data from the third National Health and Nutrition Examination Survey (NHANES III) to estimate the mortality effect of high leptin and high CRP levels. Outcomes were compared with the use of inverse-probability-weighting adjustment. Among 6,259 participants included in the analysis, 766 were in their sex-specific, population-weighted highest quartiles of both leptin and CRP. Median follow-up time was 14.3 years. Results There was no significant difference in adjusted all-cause mortality between the groups (risk ratio 1.22, 95% confidence interval [CI], 0.97 to 1.54). Similar results were noted with the use of several different analytic methods and in many subgroups, though high leptin and CRP levels may increase all-cause mortality in males (hazard ratio, 1.80, 95% CI, 1.32 to 2.46; P for interaction, 0.011). A significant difference in cardiovascular mortality was also noted (risk ratio, 1.54, 95% CI, 1.08 to 2.18), though that finding was not confirmed in all sensitivity analyses. Conclusions In this observational study, no significant difference in overall all-cause mortality rates in those with high leptin and high CRP levels was found, though high leptin and CRP levels appear associated with increased mortality in males. High leptin and CRP levels also likely increase risk for cardiovascular death. PMID:24998933

  8. Elevated Levels of Synthesis of over 20 Proteins Results after Mutation of the Rhizobium leguminosarum Exopolysaccharide Synthesis Gene pssA

    PubMed Central

    Guerreiro, Nelson; Ksenzenko, Vladimir N.; Djordjevic, Michael A.; Ivashina, Tanya V.; Rolfe, Barry G.

    2000-01-01

    The protein expression profiles of Rhizobium leguminosarum strains in response to specific genetic perturbations in exopolysaccharide (EPS) biosynthesis genes were examined using two-dimensional gel electrophoresis. Lesions in either pssA, pssD, or pssE of R. leguminosarum bv. viciae VF39 or in pssA of R. leguminosarum bv. trifolii ANU794 not only abolished the capacity of these strains to synthesize EPS but also had a pleiotropic effect on protein synthesis levels. A minimum of 22 protein differences were observed for the two pssA mutant strains. The differences identified in the pssD and pssE mutants of strain VF39 were a distinct subset of the same protein synthesis changes that occurred in the pssA mutant. The pssD and pssE mutant strains shared identical alterations in the proteins synthesized, suggesting that they share a common function in the biosynthesis of EPS. In contrast, a pssC mutant that produces 38% of the EPS level of the parental strain showed no differences in its protein synthesis patterns, suggesting that the absence of EPS itself was contributing to the changes in protein synthesis and that there may be a complex interconnection of the EPS biosynthetic pathway with other metabolic pathways. Genetic complementation of pssA can restore wild-type protein synthesis levels, indicating that many of the observed differences in protein synthesis are also a specific response to a dysfunctional PssA. The relevance of these proteins, which are grouped as members of the pssA mutant stimulon, remains unclear, as the majority lacked a homologue in the current sequence databases and therefore possibly represent a novel functional network(s). These findings have illustrated the potential of proteomics to reveal unexpected higher-order processes of protein function and regulation that arise from mutation. In addition, it is evident that enzymatic pathways and regulatory networks are more interconnected and more sensitive to structural changes in the cell than is often appreciated. In these cases, linking the observed phenotype directly to the mutated gene can be misleading, as the phenotype could be attributable to downstream effects of the mutation. PMID:10913086

  9. Elevated levels of synthesis of over 20 proteins results after mutation of the Rhizobium leguminosarum exopolysaccharide synthesis gene pssA.

    PubMed

    Guerreiro, N; Ksenzenko, V N; Djordjevic, M A; Ivashina, T V; Rolfe, B G

    2000-08-01

    The protein expression profiles of Rhizobium leguminosarum strains in response to specific genetic perturbations in exopolysaccharide (EPS) biosynthesis genes were examined using two-dimensional gel electrophoresis. Lesions in either pssA, pssD, or pssE of R. leguminosarum bv. viciae VF39 or in pssA of R. leguminosarum bv. trifolii ANU794 not only abolished the capacity of these strains to synthesize EPS but also had a pleiotropic effect on protein synthesis levels. A minimum of 22 protein differences were observed for the two pssA mutant strains. The differences identified in the pssD and pssE mutants of strain VF39 were a distinct subset of the same protein synthesis changes that occurred in the pssA mutant. The pssD and pssE mutant strains shared identical alterations in the proteins synthesized, suggesting that they share a common function in the biosynthesis of EPS. In contrast, a pssC mutant that produces 38% of the EPS level of the parental strain showed no differences in its protein synthesis patterns, suggesting that the absence of EPS itself was contributing to the changes in protein synthesis and that there may be a complex interconnection of the EPS biosynthetic pathway with other metabolic pathways. Genetic complementation of pssA can restore wild-type protein synthesis levels, indicating that many of the observed differences in protein synthesis are also a specific response to a dysfunctional PssA. The relevance of these proteins, which are grouped as members of the pssA mutant stimulon, remains unclear, as the majority lacked a homologue in the current sequence databases and therefore possibly represent a novel functional network(s). These findings have illustrated the potential of proteomics to reveal unexpected higher-order processes of protein function and regulation that arise from mutation. In addition, it is evident that enzymatic pathways and regulatory networks are more interconnected and more sensitive to structural changes in the cell than is often appreciated. In these cases, linking the observed phenotype directly to the mutated gene can be misleading, as the phenotype could be attributable to downstream effects of the mutation. PMID:10913086

  10. Technical decision making with higher order structure data: utilization of differential scanning calorimetry to elucidate critical protein structural changes resulting from oxidation.

    PubMed

    Arthur, Kelly K; Dinh, Nikita; Gabrielson, John P

    2015-04-01

    Differential scanning calorimetry (DSC) is a useful tool for monitoring thermal stability of the molecular conformation of proteins. Here, we present an example of the sensitivity of DSC to changes in stability arising from a common chemical degradation pathway, oxidation. This Note is part of a series of industry case studies demonstrating the application of higher order structure data for technical decision making. For this study, six protein products from three structural classes were evaluated at multiple levels of oxidation. For each protein, the melting temperature (Tm ) decreased linearly as a function of oxidation; however, differences in the rate of change in Tm , as well as differences in domain Tm stability were observed across and within structural classes. For one protein, analysis of the impact of oxidation on protein function was also performed. For this protein, DSC was shown to be a leading indicator of decreased antigen binding suggesting a subtle conformation change may be underway that can be detected using DSC prior to any observable impact on product potency. Detectable changes in oxidized methionine by mass spectrometry (MS) occurred at oxidation levels below those with a detectable conformational or functional impact. Therefore, by using MS, DSC, and relative potency methods in concert, the intricate relationship between a primary structural modification, changes in conformational stability, and functional impact can be elucidated. PMID:25561411

  11. Identification of precursor to cytomegalovirus capsid assembly protein and evidence that processing results in loss of its carboxy-terminal end.

    PubMed Central

    Gibson, W; Marcy, A I; Comolli, J C; Lee, J

    1990-01-01

    The 37-kilodalton (kDa) assembly protein of cytomegalovirus (strain Colburn) B capsids is shown to have a 40-kDa precursor. Pulse-chase radiolabeling experiments revealed that conversion of the precursor to the product was slow, requiring over 6 h for completion, and correlated with movement from the cytoplasmic to the nuclear fraction of Nonidet P-40-disrupted cells. Of these two proteins, only the 40-kDa precursor was synthesized in vitro from infected-cell RNA, consistent with its being the primary translation product. Amino acid sequence data obtained from CNBr-treated, high-performance liquid chromatography-purified assembly protein indicated that precursor translation begins at the first of two closely spaced potential initiation sites and that precursor maturation involves the loss of at least 32 amino acids from its carboxy-terminal end. It is also shown by immunological cross-reactivity and peptide similarity that three low-abundance B-capsid proteins (i.e., the 45-kilodalton [45K], 39K, and 38K proteins) are closely related to the assembly protein; the nature of this relatedness is discussed. Images PMID:2154607

  12. A rhizobium selenitireducens protein showing selenite reductase activity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Biobarriers remove, via precipitation, the metalloid selenite (SeO3–2) from groundwater; a process that involves the biological reduction of soluble SeO3–2 to insoluble elemental red selenium (Se0). The enzymes associated with this reduction process are poorly understood. In Rhizobium selenitiredu...

  13. Results of a phase I/II open-label, safety and efficacy trial of coagulation factor IX (recombinant), albumin fusion protein in haemophilia B patients

    PubMed Central

    Martinowitz, U; Lissitchkov, T; Lubetsky, A; Jotov, G; Barazani-Brutman, T; Voigt, C; Jacobs, I; Wuerfel, T; Santagostino, E

    2015-01-01

    Introduction rIX-FP is a coagulation factor IX (recombinant), albumin fusion protein with more than fivefold half-life prolongation over other standard factor IX (FIX) products available on the market. Aim This prospective phase II, open-label study evaluated the safety and efficacy of rIX-FP for the prevention of bleeding episodes during weekly prophylaxis and assessed the haemostatic efficacy for on-demand treatment of bleeding episodes in previously treated patients with haemophilia B. Methods The study consisted of a 10–14 day evaluation of rIX-FP pharmacokinetics (PK), and an 11 month safety and efficacy evaluation period with subjects receiving weekly prophylaxis treatment. Safety was evaluated by the occurrence of related adverse events, and immunogenic events, including development of inhibitors. Efficacy was evaluated by annualized spontaneous bleeding rate (AsBR), and the number of injections to achieve haemostasis. Results Seventeen subjects participated in the study, 13 received weekly prophylaxis and 4 received episodic treatment only. No inhibitors were detected in any subject. The mean and median AsBR were 1.25, and 1.13 respectively in the weekly prophylaxis arm. All bleeding episodes were treated with 1 or 2 injections of rIX-FP. Three prophylaxis subjects who were treated on demand prior to study entry had >85% reduction in AsBR compared to the bleeding rate prior to study entry. Conclusion This study demonstrated the efficacy for weekly routine prophylaxis of rIX-FP to prevent spontaneous bleeding episodes and for the treatment of bleeding episodes. In addition no safety issues were detected during the study and an improved PK profile was demonstrated. PMID:25990590

  14. BBS7 is required for BBSome formation and its absence in mice results in Bardet-Biedl syndrome phenotypes and selective abnormalities in membrane protein trafficking

    PubMed Central

    Zhang, Qihong; Nishimura, Darryl; Vogel, Tim; Shao, Jianqiang; Swiderski, Ruth; Yin, Terry; Searby, Charles; Carter, Calvin S.; Kim, GunHee; Bugge, Kevin; Stone, Edwin M.; Sheffield, Val C.

    2013-01-01

    Summary Bardet-Biedl Syndrome (BBS) is a pleiotropic and genetically heterozygous disorder caused independently by numerous genes (BBS1–BBS17). Seven highly conserved BBS proteins (BBS1, 2, 4, 5, 7, 8 and 9) form a complex known as the BBSome, which functions in ciliary membrane biogenesis. BBS7 is both a unique subunit of the BBSome and displays direct physical interaction with a second BBS complex, the BBS chaperonin complex. To examine the in vivo function of BBS7, we generated Bbs7 knockout mice. Bbs7?/? mice show similar phenotypes to other BBS gene mutant mice including retinal degeneration, obesity, ventriculomegaly and male infertility characterized by abnormal spermatozoa flagellar axonemes. Using tissues from Bbs7?/? mice, we show that BBS7 is required for BBSome formation, and that BBS7 and BBS2 depend on each other for protein stability. Although the BBSome serves as a coat complex for ciliary membrane proteins, BBS7 is not required for the localization of ciliary membrane proteins polycystin-1, polycystin-2, or bitter taste receptors, but absence of BBS7 leads to abnormal accumulation of the dopamine D1 receptor to the ciliary membrane, indicating that BBS7 is involved in specific membrane protein localization to cilia. PMID:23572516

  15. S1. Sample applications of the PRS method In this section we provide results from the PRS method on different protein systems. Each

    E-print Network

    Yanikoglu, Berrin

    lobes moving relative to each other upon binding the substrate. Its apo- and holo (lysine bound induced by the ligand. We have applied the PRS method to both the apo and the holo forms of this protein (102 residues have Ci 0.8). The holo form, on the other hand, is stabilized by the ligand

  16. Feeding soy protein isolate (SPI) does not result in an estrogenic gene expression profile in the mammary of ovariectomized (OVX) female rats

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Concerns of increased breast cancer risk in women consuming soy exist because of the perceived estrogenicity of soy isoflavones. Female Sprague-Dawley rats (N equals 20/group) were fed AIN-93G diets with casein or SPI as the protein from PND30. On PND50 rats were OVX and 10/group infused s.c. with 5...

  17. TAT-Mediated Transduction of MafA Protein In Utero Results in Enhanced Pancreatic Insulin Expression and Changes in Islet Morphology

    PubMed Central

    Vargas, Nancy; Fort, Nicholas M.; Cechin, Sirlene; García, Enrique; Espino-Grosso, Pedro; Fraker, Christopher A.; Ricordi, Camillo; Inverardi, Luca; Pastori, Ricardo L.; Domínguez-Bendala, Juan

    2011-01-01

    Alongside Pdx1 and Beta2/NeuroD, the transcription factor MafA has been shown to be instrumental in the maintenance of the beta cell phenotype. Indeed, a combination of MafA, Pdx1 and Ngn3 (an upstream regulator of Beta2/NeuroD) was recently reported to lead to the effective reprogramming of acinar cells into insulin-producing beta cells. These experiments set the stage for the development of new strategies to address the impairment of glycemic control in diabetic patients. However, the clinical applicability of reprogramming in this context is deemed to be poor due to the need to use viral vehicles for the delivery of the above factors. Here we describe a recombinant transducible version of the MafA protein (TAT-MafA) that penetrates across cell membranes with an efficiency of 100% and binds to the insulin promoter in vitro. When injected in utero into living mouse embryos, TAT-MafA significantly up-regulates target genes and induces enhanced insulin production as well as cytoarchitectural changes consistent with faster islet maturation. As the latest addition to our armamentarium of transducible proteins (which already includes Pdx1 and Ngn3), the purification and characterization of a functional TAT-MafA protein opens the door to prospective therapeutic uses that circumvent the use of viral delivery. To our knowledge, this is also the first report on the use of protein transduction in utero. PMID:21857924

  18. [Taxonomic classification of the Oil Destructing Bacterium Using Mass Spectrometry Methods by the Results of Analysis of Cellular Proteins and Study of Cellular Fatty Acids].

    PubMed

    Korshunova, T Y; Mukhamatdyarova, S R; Loginov, O N

    2015-01-01

    Species classification of a strain of the bacterium oil-destructor Acinetobacter sp. I B DT-5.1/l is established by means of gas chromatography-mass spectrometry fatty acid methyl esters in the cell wall and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry of proteins of a cell. PMID:26349232

  19. Preliminary results on the effects of grape (Vitis vinifera) seed condensed tannins on in vitro intestinal digestibility of the lupin (Lupinus angustifolius) seed protein fraction in small ruminants.

    PubMed

    Bruno-Soares, A M; Soares-Pereira, A L; Matos, T J S; Ricardo-da-Silva, J M

    2011-08-01

    Condensed tannins (CT) from grape seeds (Vitis vinifera L.) were added to complex the protein fraction of Lupinus angustifolius seeds. Three CT/protein ratios were used: 96 mg/g (T(1)), 180 mg/g (T(2)) and 0 mg/g (T(0)). The CP losses in the rumen were assessed by the nylon-bag technique and CP intestinal digestibility (CPID) was estimated using an in vitro assay applying a three-step procedure: samples were subject to rumen degradation (in situ, 16 h) and the remaining residues were subject to the digestive enzymes of the abomasum and pancreas in vitro. A positive effect (p < 0.05) of the level of CT on the immediately soluble faction a and the insoluble degradable fraction b was observed between T(0) and T(2) . In the presence of CT the rumen degradation rate was reduced (p < 0.05) from 0.0763/h (T(0)) to 0.0443/h (T(2)). The application of CT showed a reduction (around 10% for T(1)) of effective rumen CP degradability. The CPID did not seem to be affected (p > 0.05) by the presence of CT. These findings suggest that the use of grape seed CT might have the potential to improve the efficiency of utilisation of the protein fraction from lupin seeds. PMID:21039934

  20. Genotypic Variation under Fe Deficiency Results in Rapid Changes in Protein Expressions and Genes Involved in Fe Metabolism and Antioxidant Mechanisms in Tomato Seedlings (Solanum lycopersicum L.)

    PubMed Central

    Muneer, Sowbiya; Jeong, Byoung Ryong

    2015-01-01

    To investigate Fe deficiency tolerance in tomato cultivars, quantification of proteins and genes involved in Fe metabolism and antioxidant mechanisms were performed in “Roggusanmaru” and “Super Doterang”. Fe deficiency (Moderate, low and –Fe) significantly decreased the biomass, total, and apoplastic Fe concentration of “Roggusanmaru”, while a slight variation was observed in “Super Doterang” cultivar. The quantity of important photosynthetic pigments such as total chlorophyll and carotenoid contents significantly decreased in “Roggusanmaru” than “Super Doterang” cultivar. The total protein profile in leaves and roots determines that “Super Doterang” exhibited an optimal tolerance to Fe deficiency compared to “Roggusanmaru” cultivar. A reduction in expression of PSI (photosystem I), PSII (photosystem II) super-complexes and related thylakoid protein contents were detected in “Roggusanmaru” than “Super Doterang” cultivar. Moreover, the relative gene expression of SlPSI and SlPSII were well maintained in “Super Doterang” than “Roggusanmaru” cultivar. The relative expression of genes involved in Fe-transport (SlIRT1 and SlIRT2) and Fe(III) chelates reductase oxidase (SlFRO1) were relatively reduced in “Roggusanmaru”, while increased in “Super Doterang” cultivar under Fe deficient conditions. The H+-ATPase relative gene expression (SlAHA1) in roots were maintained in “Super Doterang” compared to “Roggusanmaru”. Furthermore, the gene expressions involved in antioxidant defense mechanisms (SlSOD, SlAPX and SlCAT) in leaves and roots showed that these genes were highly increased in “Super Doterang”, whereas decreased in “Roggusanmaru” cultivar under Fe deficiency. The present study suggested that “Super Doterang” is better tomato cultivar than “Roggusanmaru” for calcareous soils. PMID:26602920

  1. Rats fed soy protein isolate (SPI) have impaired hepatic CYP1A1 induction by polycyclic aromatic hydrocarbons as a result of interference with aryl hydrocarbon receptor signaling

    SciTech Connect

    Singhal, Rohit; Badger, Thomas M.; Ronis, Martin J.

    2008-03-01

    Consumption of soy diets has been found to reduce cancer incidence in animals and is associated with reduced cancer risk in humans. Previously, we have demonstrated that female Sprague-Dawley rats fed purified AIN-93G diets with soy protein isolate (SPI) as the sole protein source had reduced CYP1A1 induction and basal aryl hydrocarbon receptor (AhR) levels relative to those fed the same diet containing casein (CAS). In the present study, the molecular mechanisms underlying reduced AhR expression have been studied. The SPI-effect on AhR was not observed after feeding diets containing the purified soy isoflavones genistein or daidzein. Rat hepatoma FGC-4 cells were treated with the serum obtained from rats fed CAS- or SPI-containing diets. Reduced AhR levels (P < 0.05) were observed after 24 h exposure to SPI-serum without any changes in the overall expression of chaperone proteins-HSP90 and XAP2. SPI-serum-stimulated AhR degradation was inhibited by treating the cells with the proteasome inhibitor, MG132, and was observed to be preceded by ubiquitination of the receptor. A reduced association of XAP2 with the immunoprecipitated AhR complex was observed. SPI-serum-mediated AhR degradation was preceded by nuclear translocation of the receptor. However, the translocated receptor was found to be unable to heterodimerize with ARNT or to bind to XRE elements on the CYP1A1 enhancer. These data suggest that feeding SPI-containing diets antagonizes AhR signaling by a novel mechanism which differs from those established for known AhR antagonists.

  2. Genotypic Variation under Fe Deficiency Results in Rapid Changes in Protein Expressions and Genes Involved in Fe Metabolism and Antioxidant Mechanisms in Tomato Seedlings (Solanum lycopersicum L.).

    PubMed

    Muneer, Sowbiya; Jeong, Byoung Ryong

    2015-01-01

    To investigate Fe deficiency tolerance in tomato cultivars, quantification of proteins and genes involved in Fe metabolism and antioxidant mechanisms were performed in "Roggusanmaru" and "Super Doterang". Fe deficiency (Moderate, low and -Fe) significantly decreased the biomass, total, and apoplastic Fe concentration of "Roggusanmaru", while a slight variation was observed in "Super Doterang" cultivar. The quantity of important photosynthetic pigments such as total chlorophyll and carotenoid contents significantly decreased in "Roggusanmaru" than "Super Doterang" cultivar. The total protein profile in leaves and roots determines that "Super Doterang" exhibited an optimal tolerance to Fe deficiency compared to "Roggusanmaru" cultivar. A reduction in expression of PSI (photosystem I), PSII (photosystem II) super-complexes and related thylakoid protein contents were detected in "Roggusanmaru" than "Super Doterang" cultivar. Moreover, the relative gene expression of SlPSI and SlPSII were well maintained in "Super Doterang" than "Roggusanmaru" cultivar. The relative expression of genes involved in Fe-transport (SlIRT1 and SlIRT2) and Fe(III) chelates reductase oxidase (SlFRO1) were relatively reduced in "Roggusanmaru", while increased in "Super Doterang" cultivar under Fe deficient conditions. The H?-ATPase relative gene expression (SlAHA1) in roots were maintained in "Super Doterang" compared to "Roggusanmaru". Furthermore, the gene expressions involved in antioxidant defense mechanisms (SlSOD, SlAPX and SlCAT) in leaves and roots showed that these genes were highly increased in "Super Doterang", whereas decreased in "Roggusanmaru" cultivar under Fe deficiency. The present study suggested that "Super Doterang" is better tomato cultivar than "Roggusanmaru" for calcareous soils. PMID:26602920

  3. Unique thermodynamic relationships for ?fHo and ?fGo for crystalline inorganic salts. I. Predicting the possible existence and synthesis of Na2SO2 and Na2SeO2.

    PubMed

    Vegas, Angel; Liebman, Joel F; Jenkins, H Donald Brooke

    2012-10-01

    The concept that equates oxidation and pressure has been successfully utilized in explaining the structural changes observed in the M(2)S subnets of M(2)SO(x) (x = 3, 4) compounds (M = Na, K) when compared with the structures (room- and high-pressure phases) of their parent M(2)S `alloy' [Martínez-Cruz et al. (1994), J. Solid State Chem. 110, 397-398; Vegas (2000), Crystallogr. Rev. 7, 189-286; Vegas et al. (2002), Solid State Sci. 4, 1077-1081]. These structural changes suggest that if M(2)SO(2) would exist, its cation array might well have an anti-CaF(2) structure. On the other hand, in an analysis of the existing thermodynamic data for M(2)S, M(2)SO(3) and M(2)SO(4) we have identified, and report, a series of unique linear relationships between the known ?(f)H(o) and ?(f)G(o) values of the alkali metal (M) sulfide (x = 0) and their oxyanion salts M(2)SO(x) (x = 3 and 4), and the similarly between M(2)S(2) disulfide (x = 0) and disulfur oxyanion salts M(2)S(2)O(x) (x = 3, 4, 5, 6 and 7) and the number of O atoms in their anions x. These linear relationships appear to be unique to sulfur compounds and their inherent simplicity permits us to interpolate thermochemical data (?(f)H(o)) for as yet unprepared compounds, M(2)SO (x = 1) and M(2)SO(2) (x = 2). The excellent linearity indicates the reliability of the interpolated data. Making use of the volume-based thermodynamics, VBT [Jenkins et al. (1999), Inorg. Chem. 38, 3609-3620], the values of the absolute entropies were estimated and from them, the standard ?(f)S(o) values, and then the ?(f)G(o) values of the salts. A tentative proposal is made for the synthesis of Na(2)SO(2) which involves bubbling SO(2) through a solution of sodium in liquid ammonia. For this attractive thermodynamic route, we estimate ?G(o) to be approximately -500 kJ mol(-1). However, examination of the stability of Na(2)SO(2) raises doubts and Na(2)SeO(2) emerges as a more attractive target material. Its synthesis is likely to be easier and it is stable to disproportionation into Na(2)S and Na(2)SeO(4). Like Na(2)SO(2), this compound is predicted to have an anti-CaF(2) Na(2)Se subnet. PMID:22992796

  4. A single amino acid change resulting in loss of fluorescence of eGFP in a viral fusion protein confers fitness and growth advantage to the recombinant vesicular stomatitis virus

    SciTech Connect

    Dinh, Phat X.; Panda, Debasis; Das, Phani B.; Das, Subash C.; Das, Anshuman; The Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, Nebraska 68583-0900 ; Pattnaik, Asit K.

    2012-10-25

    Using a recombinant vesicular stomatitis virus encoding eGFP fused in-frame with an essential viral replication protein, the phosphoprotein P, we show that during passage in culture, the virus mutates the nucleotide C289 within eGFP of the fusion protein PeGFP to A or T, resulting in R97S/C amino acid substitution and loss of fluorescence. The resultant non-fluorescent virus exhibits increased fitness and growth advantage over its fluorescent counterpart. The growth advantage of the non-fluorescent virus appears to be due to increased transcription and replication activities of the PeGFP protein carrying the R97S/C substitution. Further, our results show that the R97S/C mutation occurs prior to accumulation of mutations that can result in loss of expression of the gene inserted at the G-L gene junction. These results suggest that fitness gain is more important for the recombinant virus than elimination of expression of the heterologous gene.

  5. Research Results

    NASA Astrophysics Data System (ADS)

    2011-12-01

    Research on Global Carbon Emission and Sequestration NSFC Funded Project Made Significant Progress in Quantum Dynamics Functional Human Blood Protein Obtained from Rice How Giant Pandas Thrive on a Bamboo Diet New Evidence of Interpersonal Violence from 129,000 Years Ago Found in China Aptamer-Mediated Efficient Capture and Release of T Lymphocytes on Nanostructured Surfaces BGI Study Results on Resequencing 50 Accessions of Rice Cast New Light on Molecular Breeding BGI Reports Study Results on Frequent Mutation of Genes Encoding UMPP Components in Kidney Cancer Research on Habitat Shift Promoting Species Diversification

  6. Selection for low or high primary dormancy in Lolium rigidum Gaud seeds results in constitutive differences in stress protein expression and peroxidase activity

    PubMed Central

    Goggin, Danica E.; Powles, Stephen B.; Steadman, Kathryn J.

    2011-01-01

    Seed dormancy in wild Lolium rigidum Gaud (annual ryegrass) populations is highly variable and not well characterized at the biochemical level. To identify some of the determinants of dormancy level in these seeds, the proteomes of subpopulations selected for low and high levels of primary dormancy were compared by two-dimensional polyacrylamide gel electrophoresis of extracts from mature, dry seeds. High-dormancy seeds showed higher expression of small heat shock proteins, enolase, and glyoxalase I than the low-dormancy seeds. The functional relevance of these differences in protein expression was confirmed by the fact that high-dormancy seeds were more tolerant to high temperatures imposed at imbibition and had consistently higher glyoxalase I activity over 0–42?d dark stratification. Higher expression of a putative glutathione peroxidase in low-dormancy seeds was not accompanied by higher activity, but these seeds had a slightly more oxidized glutathione pool and higher total peroxidase activity. Overall, these biochemical and physiological differences suggest that L. rigidum seeds selected for low dormancy are more prepared for rapid germination via peroxidase-mediated cell wall weakening, whilst seeds selected for high dormancy are constitutively prepared to survive environmental stresses, even in the absence of stress during seed development. PMID:20974739

  7. Bacteriophage protein-protein interactions.

    PubMed

    Häuser, Roman; Blasche, Sonja; Dokland, Terje; Haggĺrd-Ljungquist, Elisabeth; von Brunn, Albrecht; Salas, Margarita; Casjens, Sherwood; Molineux, Ian; Uetz, Peter

    2012-01-01

    Bacteriophages T7, ?, P22, and P2/P4 (from Escherichia coli), as well as ?29 (from Bacillus subtilis), are among the best-studied bacterial viruses. This chapter summarizes published protein interaction data of intraviral protein interactions, as well as known phage-host protein interactions of these phages retrieved from the literature. We also review the published results of comprehensive protein interaction analyses of Pneumococcus phages Dp-1 and Cp-1, as well as coliphages ? and T7. For example, the ?55 proteins encoded by the T7 genome are connected by ?43 interactions with another ?15 between the phage and its host. The chapter compiles published interactions for the well-studied phages ? (33 intra-phage/22 phage-host), P22 (38/9), P2/P4 (14/3), and ?29 (20/2). We discuss whether different interaction patterns reflect different phage lifestyles or whether they may be artifacts of sampling. Phages that infect the same host can interact with different host target proteins, as exemplified by E. coli phage ? and T7. Despite decades of intensive investigation, only a fraction of these phage interactomes are known. Technical limitations and a lack of depth in many studies explain the gaps in our knowledge. Strategies to complete current interactome maps are described. Although limited space precludes detailed overviews of phage molecular biology, this compilation will allow future studies to put interaction data into the context of phage biology. PMID:22748812

  8. Vaccination with a Fusion Protein That Introduces HIV-1 Gag Antigen into a Multitrimer CD40L Construct Results in Enhanced CD8+ T Cell Responses and Protection from Viral Challenge by Vaccinia-Gag

    PubMed Central

    Gupta, Sachin; Termini, James M.; Raffa, Francesca N.; Williams, Cindi-Ann; Kornbluth, Richard S.

    2014-01-01

    CD40 ligand (CD40L, CD154) is a membrane protein that is important for the activation of dendritic cells (DCs) and DC-induced CD8+ T cell responses. To be active, CD40L must cluster CD40 receptors on responding cells. To produce a soluble form of CD40L that clusters CD40 receptors necessitates the use of a multitrimer construct. With this in mind, a tripartite fusion protein was made from surfactant protein D (SPD), HIV-1 Gag as a test antigen, and CD40L, where SPD serves as a scaffold for the multitrimer protein complex. This SPD-Gag-CD40L protein activated CD40-bearing cells and bone marrow-derived DCs in vitro. Compared to a plasmid for Gag antigen alone (pGag), DNA vaccination of mice with pSPD-Gag-CD40L induced an increased number of Gag-specific CD8+ T cells with increased avidity for major histocompatibility complex class I-restricted Gag peptide and improved vaccine-induced protection from challenge by vaccinia-Gag virus. The importance of the multitrimeric nature of the complex was shown using a plasmid lacking the N terminus of SPD that produced a single trimer fusion protein. This plasmid, pTrimer-Gag-CD40L, was only weakly active on CD40-bearing cells and did not elicit strong CD8+ T cell responses or improve protection from vaccinia-Gag challenge. An adenovirus 5 (Ad5) vaccine incorporating SPD-Gag-CD40L was much stronger than Ad5 expressing Gag alone (Ad5-Gag) and induced complete protection (i.e., sterilizing immunity) from vaccinia-Gag challenge. Overall, these results show the potential of a new vaccine design in which antigen is introduced into a construct that expresses a multitrimer soluble form of CD40L, leading to strongly protective CD8+ T cell responses. PMID:24227853

  9. Interactive intoxicating and ameliorating effects of tannic acid, aluminum (Al3+), copper (Cu2+), and selenate (SeO42-) in wheat roots. A descriptive and mathematical assessment

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tannic acids and tannins are polyphenolic compounds produced by plants and are important components of soil and water organic matter. Tannic acids and tannins form complexes with proteins, metals, and soil particulate matter and perform several physiological and ecological functions. The tannic ac...

  10. Knock-out of SO1377 gene, which encodes the member of a conserved hypothetical bacterial protein family COG2268, results in alteration of iron metabolism, increased spontaneous mutation and hydrogen peroxide sensitivity in Shewanella oneidensis MR-1

    PubMed Central

    Gao, Weimin; Liu, Yongqing; Giometti, Carol S; Tollaksen, Sandra L; Khare, Tripti; Wu, Liyou; Klingeman, Dawn M; Fields, Matthew W; Zhou, Jizhong

    2006-01-01

    Background Shewanella oneidensis MR-1 is a facultative, gram-negative bacterium capable of coupling the oxidation of organic carbon to a wide range of electron acceptors such as oxygen, nitrate and metals, and has potential for bioremediation of heavy metal contaminated sites. The complete 5-Mb genome of S. oneidensis MR-1 was sequenced and standard sequence-comparison methods revealed approximately 42% of the MR-1 genome encodes proteins of unknown function. Defining the functions of hypothetical proteins is a great challenge and may need a systems approach. In this study, by using integrated approaches including whole genomic microarray and proteomics, we examined knockout effects of the gene encoding SO1377 (gi24372955), a member of the conserved, hypothetical, bacterial protein family COG2268 (Clusters of Orthologous Group) in bacterium Shewanella oneidensis MR-1, under various physiological conditions. Results Compared with the wild-type strain, growth assays showed that the deletion mutant had a decreased growth rate when cultured aerobically, but not affected under anaerobic conditions. Whole-genome expression (RNA and protein) profiles revealed numerous gene and protein expression changes relative to the wild-type control, including some involved in iron metabolism, oxidative damage protection and respiratory electron transfer, e. g. complex IV of the respiration chain. Although total intracellular iron levels remained unchanged, whole-cell electron paramagnetic resonance (EPR) demonstrated that the level of free iron in mutant cells was 3 times less than that of the wild-type strain. Siderophore excretion in the mutant also decreased in iron-depleted medium. The mutant was more sensitive to hydrogen peroxide and gave rise to 100 times more colonies resistant to gentamicin or kanamycin. Conclusion Our results showed that the knock-out of SO1377 gene had pleiotropic effects and suggested that SO1377 may play a role in iron homeostasis and oxidative damage protection in S. oneidensis MR-1. PMID:16600046

  11. Hepatitis B virus surface protein mutations clustered mainly in CTL immune epitopes in chronic carriers: results of an Iranian nationwide study.

    PubMed

    Khedive, A; Norouzi, M; Ramezani, F; Karimzadeh, H; Alavian, S M; Malekzadeh, R; Montazeri, G; Nejatizadeh, A; Ziaee, M; Abedi, F; Ataei, B; Yaran, M; Sayad, B; Somi, M H; Sarizadeh, G; Sanei-Moghaddam, I; Mansour-Ghanaei, F; Rafatpanah, H; Pourhosseingholi, M A; Keyvani, H; Kalantari, E; Saberifiroozi, M; Judaki, M A; Ghamari, S; Daram, M; Mahabadi, M; Fazeli, Z; Goodarzi, Z; Poortahmasebi, V; Jazayeri, S M

    2013-07-01

    Mutations within the coding region of hepatitis B surface antigen (HBsAg) have been found naturally in chronic carriers. To characterize the mutations of HBsAg from Iranian chronic carriers who were vaccine and/or medication naive. The surface genes from 360 patients were amplified and directly sequenced. The distribution of amino acid substitutions was classified according to different immune epitopes of the surface protein. All isolates belonged to genotype D. 222 (61.6%) of 360 patients contained at least one amino acid substitution. 404 (74.5%) of 542 amino acid changes occurred in different immune epitopes of HBsAg, of which 112 (27.7%) in 32 residues of B-cell epitopes (62 in the 'a' determinant); 111 (27.4%) in 32 residues of T helper; and 197 (48.7%) in 32 residues inside cytotoxic T lymphocyte (CTL) epitopes. One Th (186-197) and two CTL (28-51 and 206-215) epitopes were found to be hotspot motifs for the occurrence of 213 (52.7%) substitutions. 20 stop codons were identified in different epitopes. There was a significant association between amino acid substitutions and anti-HBe seropositivity; however, the correlation between such changes with viral load and ALT levels was not significant. In chronic hepatitis B virus(HBV) carriers, positive selection in particular outside the 'a' determinant appeared to exert influence on the surface proteins. These changes could be immune escape mutations naturally occurring due to the host immune surveillance especially at the T-cell level. PMID:23730843

  12. Solid-state synthesis, structure and properties of a novel open-framework cadmium selenite bromide: [Cd10(SeO3)8Br4]·HBr·H2O

    NASA Astrophysics Data System (ADS)

    Chen, Wen-Tong; Wang, Ming-Sheng; Wang, Guan-E.; Chen, Hui-Fen; Guo, Guo-Cong

    2013-08-01

    A novel open-framework cadmium selenite bromide, [Cd10(SeO3)8Br4]·HBr·H2O (1), has been obtained by a solid-state reaction at 450 °C, and the structure has been determined by single-crystal X-ray diffraction analysis. Compound 1 crystallizes in Pbcm of the orthorhombic system: a=10.882(3), b=16.275(5), c=18.728(6) Ĺ, V=3317(2) Ĺ3, R1/wR2=0.0411/0.0659. Compound 1 is characteristic of a novel 3-D open-framework structure, composing ?2[CdSeO3] layers and the pillars of edge-shared CdO3Br2 square pyramids. The lattice water molecules and the HBr molecules locate in the voids of the framework. Optical absorption spectrum of 1 reveals the presence of an optical gap of 1.65 eV. Solid-state photoluminescent study indicates that compound 1 exhibits strong violet emission. TG-DSC measurement shows that compound 1 is thermally stable up to 200 °C.

  13. Placental amino acid transport may be regulated by maternal vitamin D and vitamin D-binding protein: results from the Southampton Women's Survey.

    PubMed

    Cleal, J K; Day, P E; Simner, C L; Barton, S J; Mahon, P A; Inskip, H M; Godfrey, K M; Hanson, M A; Cooper, C; Lewis, R M; Harvey, N C

    2015-06-28

    Both maternal 25-hydroxyvitamin D (25(OH)D) concentrations during pregnancy and placental amino acid transporter gene expression have been associated with development of the offspring in terms of body composition and bone structure. Several amino acid transporter genes have vitamin D response elements in their promoters suggesting the possible linkage of these two mechanisms. We aimed to establish whether maternal 25(OH)D and vitamin D-binding protein (VDBP) levels relate to expression of placental amino acid transporters. RNA was extracted from 102 placental samples collected in the Southampton Women's Survey, and gene expression was analysed using quantitative real-time PCR. Gene expression data were normalised to the geometric mean of three housekeeping genes, and related to maternal factors and childhood body composition. Maternal serum 25(OH)D and VDBP levels were measured by radioimmunoassay. Maternal 25(OH)D and VDBP levels were positively associated with placental expression of specific genes involved in amino acid transport. Maternal 25(OH)D and VDBP concentrations were correlated with the expression of specific placental amino acid transporters, and thus may be involved in the regulation of amino acid transfer to the fetus. The positive correlation of VDBP levels and placental transporter expression suggests that delivery of vitamin D to the placenta may be important. This exploratory study identifies placental amino acid transporters which may be altered in response to modifiable maternal factors and provides a basis for further studies. PMID:25940599

  14. Protein Crystallization

    NASA Technical Reports Server (NTRS)

    Chernov, Alexander A.

    2005-01-01

    Nucleation, growth and perfection of protein crystals will be overviewed along with crystal mechanical properties. The knowledge is based on experiments using optical and force crystals behave similar to inorganic crystals, though with a difference in orders of magnitude in growing parameters. For example, the low incorporation rate of large biomolecules requires up to 100 times larger supersaturation to grow protein, rather than inorganic crystals. Nucleation is often poorly reproducible, partly because of turbulence accompanying the mixing of precipitant with protein solution. Light scattering reveals fluctuations of molecular cluster size, its growth, surface energies and increased clustering as protein ages. Growth most often occurs layer-by-layer resulting in faceted crystals. New molecular layer on crystal face is terminated by a step where molecular incorporation occurs. Quantitative data on the incorporation rate will be discussed. Rounded crystals with molecularly disordered interfaces will be explained. Defects in crystals compromise the x-ray diffraction resolution crucially needed to find the 3D atomic structure of biomolecules. The defects are immobile so that birth defects stay forever. All lattice defects known for inorganics are revealed in protein crystals. Contribution of molecular conformations to lattice disorder is important, but not studied. This contribution may be enhanced by stress field from other defects. Homologous impurities (e.g., dimers, acetylated molecules) are trapped more willingly by a growing crystal than foreign protein impurities. The trapped impurities induce internal stress eliminated in crystals exceeding a critical size (part of mni for ferritin, lysozyme). Lesser impurities are trapped from stagnant, as compared to the flowing, solution. Freezing may induce much more defects unless quickly amorphysizing intracrystalline water.

  15. Surface Mediated Protein Disaggregation

    NASA Astrophysics Data System (ADS)

    Radhakrishna, Mithun; Kumar, Sanat K.

    2014-03-01

    Preventing protein aggregation is of both biological and industrial importance. Biologically these aggregates are known to cause amyloid type diseases like Alzheimer's and Parkinson's disease. Protein aggregation leads to reduced activity of the enzymes in industrial applications. Inter-protein interactions between the hydrophobic residues of the protein are known to be the major driving force for protein aggregation. In the current paper we show how surface chemistry and curvature can be tuned to mitigate these inter-protein interactions. Our results calculated in the framework of the Hydrophobic-Polar (HP) lattice model show that, inter-protein interactions can be drastically reduced by increasing the surface hydrophobicity to a critical value corresponding to the adsorption transition of the protein. At this value of surface hydrophobicity, proteins lose inter-protein contacts to gain surface contacts and thus the surface helps in reducing the inter-protein interactions. Further, we show that the adsorption of the proteins inside hydrophobic pores of optimal sizes are most efficient both in reducing inter-protein contacts and simultaneously retaining most of the native-contacts due to strong protein-surface interactions coupled with stabilization due to the confinement. Department of Energy (Grant No DE-FG02-11ER46811).

  16. Rhizobium selenitireducens proteins involved in the reduction of selenite to elemental selenium

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microbial based bioremediation barriers can remove the metalloid selenite (SeO3–2) from flowing groundwater. The organisms associated with the process include microorganisms from within the bacterial and archaeal domains that can reduce soluble SeO3–2 to the insoluble and reddish-colored elemental ...

  17. Protein folding.

    PubMed

    Rossmann, M G; Argos, P

    1981-01-01

    After some general remarks on protein structure, there follows a discussion on primary, secondary, and tertiary organization. The account of primary structure includes a discussion of the conformation of disulfide bonds. Types of helices, sheets, and turns are described in the section on secondary structure, followed by a discussion of super-secondary structure and the effects of metals and prosthetic groups of protein fold. The crux of the review lies in an examination of tertiary structure, or specifically of domains that are defined, in part, as functional units within a polypeptide chain. An assembly of domains can in turn result in a protein whose function is quite sophisticated. Some consideration of domain recognition is given in the section on taxonomy and in the appendix. The key part of the tertiary structure section concentrates on a taxonomic protein classification dependent not only on structure but also on function. A discussion of the requirements by quaternary structure on a fold are omitted in this review. Finally, no review of this kind can escape a discussion of evolutionary convergence and divergence. PMID:7023364

  18. High temperature redox reactions with uranium: Synthesis and characterization of Cs(UO2)Cl(SeO3), Rb2(UO2)3O2(SeO3)2, and RbNa5U2(SO4)7

    NASA Astrophysics Data System (ADS)

    Babo, Jean-Marie; Albrecht-Schmitt, Thomas E.

    2013-10-01

    Cs(UO2)Cl(SeO3) (1), Rb2(UO2)3O2(SeO3)3 (2), and RbNa5U2(SO4)7 (3) single crystals were synthesized using CsCl, RbCl, and a CuCl/NaCl eutectic mixture as fluxes, respectively. Their lattice parameters and space groups are as follows: P21/n (a=6.548(1) Ĺ, b=11.052(2) Ĺ, c=10.666(2) Ĺ and ?=93.897(3)°), P1bar (a=7.051(2) Ĺ, b=7.198(2) Ĺ, c=8.314(2) Ĺ, ?=107.897(3)°, ?=102.687(3)° and ?=100.564(3)°) and C2/c (a=17.862(4) Ĺ, b=6.931(1) Ĺ, c=20.133(4) Ĺ and ?=109.737(6)°. The small anionic building units found in these compounds are SeO32- and SO42- tetrahedra, oxide, and chloride. The crystal structure of the first compound is composed of [(UO2)2Cl2(SeO3)2]2- chains separated by Cs+ cations. The structure of (2) is constructed from [(UO2)3O11]16- chains further connected through selenite units into layers stacked perpendicularly to the [0 1 0] direction, with Rb+ cations intercalating between them. The structure of compound (3) is made of uranyl sulfate layers formed by edge and vertex connections between dimeric [U2O16] and [SO4] polyhedra. These layers contain unusual sulfate-metal connectivity as well as large voids.

  19. Thermodynamic model for the solubility of BaSeO4(cr) in the aqueous Ba2+-SeO42--Na+-H+-OH--H2O system: Extending to high selenate concentrations

    SciTech Connect

    Rai, Dhanpat; Felmy, Andrew R.; Moore, Dean A.; Kitamura, Akira; Yoshikawa, Hideki; Doi, Reisuke; Yoshida, Yasushi

    2014-09-15

    The solubility of Ba(SeO4, SO4) precipitates was determined as a function of the BaSeO4 mole fractions, ranging from 0.0015 to 0.3830, and time with an equilibration period extending to as long as 302 days. Equilibrium/steady state conditions in this system are reached in ? 65 days. Pitzer’s ion interaction model was used to calculate solid and aqueous phase activity coefficients. Thermodynamic analyses showed that the data do not satisfy Gibbs-Duhem equation, thereby demonstrating that a single-solid solution phase does not control both the selenate and sulfate concentrations. Our extensive data with log10 [Ba]) ranging from -3.6 to -5.9 mol.kg-1, log10 [SeO4]) ranging from -3.6 to -5.2 mol.kg-1, and log10 [SO4] ranging from -4.0 to -5.3 mol.kg-1 can be explained with the formation of an ideal BaSeO4 solid solution phase that controls the selenium concentrations and a slightly disordered/less-crystalline BaSO4(s) (log10 K0sp = -9.5 instead of -10.05 for barite) that controls the sulfate concentrations. In these experiments the BaSO4 component of the solid solution phase never reaches thermodynamic equilibrium with the aqueous phase. Thermodynamic interpretations of the data show that both the ideal BaSeO4 solid solution phase and less-crystalline BaSO4(s) phase are in equilibrium with each other in the entire range of BaSeO4 mole fractions investigated in this study.

  20. Protein Condensation

    NASA Astrophysics Data System (ADS)

    Gunton, James D.; Shiryayev, Andrey; Pagan, Daniel L.

    2007-09-01

    Preface; 1. Introduction; 2. Globular protein structure; 3. Experimental methods; 4. Thermodynamics and statistical mechanics; 5. Protein-protein interactions; 6. Theoretical studies of equilibrium; 7. Nucleation theory; 8. Experimental studies of nucleation; 9. Lysozyme; 10. Some other globular proteins; 11. Membrane proteins; 12. Crystallins and cataracts; 13. Sickle hemoglobin and sickle cell anemia; 14, Alzheimer's disease; Index.

  1. Protein Condensation

    NASA Astrophysics Data System (ADS)

    Gunton, James D.; Shiryayev, Andrey; Pagan, Daniel L.

    2014-07-01

    Preface; 1. Introduction; 2. Globular protein structure; 3. Experimental methods; 4. Thermodynamics and statistical mechanics; 5. Protein-protein interactions; 6. Theoretical studies of equilibrium; 7. Nucleation theory; 8. Experimental studies of nucleation; 9. Lysozyme; 10. Some other globular proteins; 11. Membrane proteins; 12. Crystallins and cataracts; 13. Sickle hemoglobin and sickle cell anemia; 14, Alzheimer's disease; Index.

  2. Calcium-energized motor protein forisome controls damage in phloem: potential applications as biomimetic "smart" material.

    PubMed

    Srivastava, Vineet Kumar; Tuteja, Renu; Tuteja, Narendra

    2015-06-01

    Forisomes are ATP independent, mechanically active proteins from the Fabaceae family (also called Leguminosae). These proteins are located in sieve tubes of phloem and function to prevent loss of nutrient-rich photoassimilates, upon mechanical injury/wounding. Forisomes are SEO (sieve element occlusion) gene family proteins that have recently been shown to be involved in wound sealing mechanism. Recent findings suggest that forisomes could act as an ideal model to study self assembly mechanism for the development of nanotechnological devices like microinstruments, the microfluidic system frequently used in space exploration missions. Technology enabling improvement in micro instruments has been identified as a key technology by NASA in future space exploration missions. Forisomes are designated as biomimetic smart materials which are calcium-energized motor proteins. Since forisomes are biomolecules from plant systems it can be doctored through genetic engineering. In contrast, "smart" materials which are not derived from plants are difficult to modify in their properties. Current levels of understanding about forisomes conformational shifts with respect to calcium ions and pH changes requires supplement of future advances with relation to its 3D structure to understand self assembly processes. In plant systems it forms blood clots in the form of occlusions to prevent nutrient fluid leakage and thus proves to be a unique damage control system of phloem tissue. PMID:24020505

  3. Reduced ?-lactoglobulin IgE binding upon in vitro digestion as a result of the interaction of the protein with casein glycomacropeptide.

    PubMed

    Martinez, María J; Martos, Gustavo; Molina, Elena; Pilosof, Ana M R

    2016-02-01

    The aim of this work was to evaluate the effect of the presence of casein glycomacropeptide (CMP) on the in vitro digestibility and potential allergenicity of ?-lactoglobulin (?-lg)-CMP mixtures. The digestion products were analyzed by RP-HPLC and RP-HPLC-ESI-MS/MS. The potential allergenicity of the digestion products was studied by human IgE binding by inhibition ELISA with serum samples from children with clinical allergic symptoms to ?-lg. No differences were observed by HPLC in the mixtures hydrolysates due to CMP-?-lg interactions. RP-HPLC-ESI-MS/MS results showed different peptides occurring in the mixtures hydrolysates. Additionally, it was observed a significant reduction of ?-lg IgE binding in the presence of CMP. The disappearance of epitopes in the digested mixtures could explain the lower IgE binding observed in these systems compared to ?-lg. It can be concluded that the presence of CMP in products containing ?-lg may modify the digestion products that may reduce the potential allergenicity of ?-lg. PMID:26304433

  4. Structure?Activity Relationships in Peptide Modulators of ?-Amyloid Protein Aggregation: Variation in ?,?-Disubstitution Results in Altered Aggregate Size and Morphology

    PubMed Central

    2010-01-01

    Neuronal cytotoxicity observed in Alzheimer’s disease (AD) is linked to the aggregation of ?-amyloid peptide (A?) into toxic forms. Increasing evidence points to oligomeric materials as the neurotoxic species, not A? fibrils; disruption or inhibition of A? self-assembly into oligomeric or fibrillar forms remains a viable therapeutic strategy to reduce A? neurotoxicity. We describe the synthesis and characterization of amyloid aggregation mitigating peptides (AAMPs) whose structure is based on the A? “hydrophobic core” A?17?20, with ?,?-disubstituted amino acids (??AAs) added into this core as potential disrupting agents of fibril self-assembly. The number, positional distribution, and side-chain functionality of ??AAs incorporated into the AAMP sequence were found to influence the resultant aggregate morphology as indicated by ex situ experiments using atomic force microscopy (AFM) and transmission electron microscopy (TEM). For instance, AAMP-5, incorporating a sterically hindered ??AA with a diisobutyl side chain in the core sequence, disrupted A?1?40 fibril formation. However, AAMP-6, with a less sterically hindered ??AA with a dipropyl side chain, altered fibril morphology, producing shorter and larger sized fibrils (compared with those of A?1?40). Remarkably, ??AA-AAMPs caused disassembly of existing A? fibrils to produce either spherical aggregates or protofibrillar structures, suggesting the existence of equilibrium between fibrils and prefibrillar structures. PMID:22778850

  5. Total protein

    MedlinePLUS

    The total protein test measures the total amount of two classes of proteins found in the fluid portion of your blood. These are albumin and globulin. Proteins are important parts of all cells and tissues. ...

  6. Protein C

    MedlinePLUS

    Protein C is a normal substance in the body that prevents blood clotting. A blood test can be done ... forming (anticoagulants), such as warfarin (Coumadin), decrease protein C and protein S levels. Your doctor may ask you ...

  7. Increasing the metabolizable protein supply enhanced growth performance and led to variable results on innate and humoral immune response of preconditioning beef steers.

    PubMed

    Moriel, P; Artioli, L F A; Poore, M H; Confer, A W; Marques, R S; Cooke, R F

    2015-09-01

    We evaluated the effects of MP supply on growth performance before and after preconditioning and measurements of innate and humoral immune response of beef steers following vaccination. Angus steers ( = 36; BW = 231 ± 21 kg; age = 184 ± 18 d) were weaned on d -6, stratified by BW and age on d 0, and randomly assigned to 1 of 18 drylot pens (2 steers/pen). Treatments were assigned to pens (6 pens/treatment) and consisted of corn silage-based diets formulated to provide 85%, 100%, or 115% of the daily MP requirements of a beef steer gaining 1.1 kg/d from d 0 to 42. Steers were vaccinated against infectious bovine rhinotracheitis virus, bovine viral diarrhea (BVDV) types 1 and 2 viruses, and clostridium on d 14 and 28. Blood samples were collected on d 0, 14, 15, 17, 21, 28, 29, 30, 35, and 42. Body weight did not differ ( ? 0.17) among treatments from d 0 to 28. On d 42, 115% MP steers were heaviest, 100% MP steers were intermediate, and 85% MP steers were lightest ( = 0.05; 297, 290, and 278 ± 7 kg, respectively). Overall, ADG and G:F did not differ ( ? 0.13) between 100% and 115% MP steers and were least ( < 0.01) for 85% MP steers (1.2, 1.4, and 0.8 ± 0.07 kg/d and 0.23, 0.24, and 0.19 ± 0.008, respectively). Plasma haptoglobin (Hp) concentrations did not differ among treatments ( ? 0.46), whereas plasma ceruloplasmin (Cp) concentrations were greatest ( ? 0.04) for 85% MP steers, intermediate for 100% MP steers, and least for 115% MP steers on d 30, 35, and 42. Plasma cortisol concentrations were greater ( ? 0.03) for 85% vs. 100% and 115% MP steers on d 14 and 28. Liver mRNA expression of Cp and Hp and muscle mRNA expression of m-calpain, mammalian target of rapamycin, and ubiquitin did not differ among treatments ( ? 0.17). Serum neutralization titers to BVDV-1b titers were greater ( ? 0.02) for 115% vs. 85% and 100% MP steers on d 42 (5.8, 3.0, and 3.7 ± 0.60 log, respectively), whereas mean serum leukotoxin titers were greater for 85% vs. 100% and 115% MP steers (3.1, 2.4, and 2.5 ± 0.21 log, respectively). Preconditioning MP supply did not affect ( ? 0.26) ubsequent finishing growth performance and carcass characteristics. Thus, increasing MP supply from 85% to 115% of daily requirement of preconditioning beef steers had variable results on innate and humoral immune response and enhanced growth performance during a 42-d preconditioning period without affecting carcass characteristics at slaughter. PMID:26440347

  8. Computational Prediction of Protein–Protein Interaction Networks: Algo-rithms and Resources

    PubMed Central

    Zahiri, Javad; Bozorgmehr, Joseph Hannon; Masoudi-Nejad, Ali

    2013-01-01

    Protein interactions play an important role in the discovery of protein functions and pathways in biological processes. This is especially true in case of the diseases caused by the loss of specific protein-protein interactions in the organism. The accuracy of experimental results in finding protein-protein interactions, however, is rather dubious and high throughput experimental results have shown both high false positive beside false negative information for protein interaction. Computational methods have attracted tremendous attention among biologists because of the ability to predict protein-protein interactions and validate the obtained experimental results. In this study, we have reviewed several computational methods for protein-protein interaction prediction as well as describing major databases, which store both predicted and detected protein-protein interactions, and the tools used for analyzing protein interaction networks and improving protein-protein interaction reliability. PMID:24396273

  9. Computational Prediction of Protein-Protein Interaction Networks: Algo-rithms and Resources.

    PubMed

    Zahiri, Javad; Bozorgmehr, Joseph Hannon; Masoudi-Nejad, Ali

    2013-09-01

    Protein interactions play an important role in the discovery of protein functions and pathways in biological processes. This is especially true in case of the diseases caused by the loss of specific protein-protein interactions in the organism. The accuracy of experimental results in finding protein-protein interactions, however, is rather dubious and high throughput experimental results have shown both high false positive beside false negative information for protein interaction. Computational methods have attracted tremendous attention among biologists because of the ability to predict protein-protein interactions and validate the obtained experimental results. In this study, we have reviewed several computational methods for protein-protein interaction prediction as well as describing major databases, which store both predicted and detected protein-protein interactions, and the tools used for analyzing protein interaction networks and improving protein-protein interaction reliability. PMID:24396273

  10. Protein solubility modeling.

    PubMed

    Agena, S M; Pusey, M L; Bogle, I D

    1999-07-20

    A thermodynamic framework (UNIQUAC model with temperature dependent parameters) is applied to model the salt-induced protein crystallization equilibrium, i.e., protein solubility. The framework introduces a term for the solubility product describing protein transfer between the liquid and solid phase and a term for the solution behavior describing deviation from ideal solution. Protein solubility is modeled as a function of salt concentration and temperature for a four-component system consisting of a protein, pseudo solvent (water and buffer), cation, and anion (salt). Two different systems, lysozyme with sodium chloride and concanavalin A with ammonium sulfate, are investigated. Comparison of the modeled and experimental protein solubility data results in an average root mean square deviation of 5.8%, demonstrating that the model closely follows the experimental behavior. Model calculations and model parameters are reviewed to examine the model and protein crystallization process. PMID:10397850

  11. Protein solubility modeling

    NASA Technical Reports Server (NTRS)

    Agena, S. M.; Pusey, M. L.; Bogle, I. D.

    1999-01-01

    A thermodynamic framework (UNIQUAC model with temperature dependent parameters) is applied to model the salt-induced protein crystallization equilibrium, i.e., protein solubility. The framework introduces a term for the solubility product describing protein transfer between the liquid and solid phase and a term for the solution behavior describing deviation from ideal solution. Protein solubility is modeled as a function of salt concentration and temperature for a four-component system consisting of a protein, pseudo solvent (water and buffer), cation, and anion (salt). Two different systems, lysozyme with sodium chloride and concanavalin A with ammonium sulfate, are investigated. Comparison of the modeled and experimental protein solubility data results in an average root mean square deviation of 5.8%, demonstrating that the model closely follows the experimental behavior. Model calculations and model parameters are reviewed to examine the model and protein crystallization process. Copyright 1999 John Wiley & Sons, Inc.

  12. Protein-Protein Interfaces in Viral Capsids Are Structurally Unique.

    PubMed

    Cheng, Shanshan; Brooks, Charles L

    2015-11-01

    Viral capsids exhibit elaborate and symmetrical architectures of defined sizes and remarkable mechanical properties not seen with cellular macromolecular complexes. Given the uniqueness of the higher-order organization of viral capsid proteins in the virosphere, we explored the question of whether the patterns of protein-protein interactions within viral capsids are distinct from those in generic protein complexes. Our comparative analysis involving a non-redundant set of 551 inter-subunit interfaces in viral capsids from VIPERdb and 20,014 protein-protein interfaces in non-capsid protein complexes from the Protein Data Bank found 418 generic protein-protein interfaces that share similar physicochemical patterns with some protein-protein interfaces in the capsid set, using the program PCalign we developed for comparing protein-protein interfaces. This overlap in the structural space of protein-protein interfaces is significantly small, with a p-value <0.0001, based on a permutation test on the total set of protein-protein interfaces. Furthermore, the generic protein-protein interfaces that bear similarity in their spatial and chemical arrangement with capsid ones are mostly small in size with fewer than 20 interfacial residues, which results from the relatively limited choices of natural design for small interfaces rather than having significant biological implications in terms of functional relationships. We conclude based on this study that protein-protein interfaces in viral capsids are non-representative of patterns in the smaller, more compact cellular protein complexes. Our finding highlights the design principle of building large biological containers from repeated, self-assembling units and provides insights into specific targets for antiviral drug design for improved efficacy. PMID:26375252

  13. Diets containing soy or rice protein isolate increase insulin sensitivity and improve lipid homeostasis in weanling rats fed high fat, high cholesterol Western diets as a result of activation of PPAR and LXR-mediated pathways

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The current study examined the effects of feeding soy protein isolate (SPI) and rice protein isolate (RPI) on insulin sensitivity and fat breakdown in weanling rats consuming high fat/high cholesterol diets. Male Sprague-Dawley rats were placed on semi-purified diets containing the milk protein case...

  14. Protein Complexes in Bacteria

    PubMed Central

    Caufield, J. Harry; Abreu, Marco; Wimble, Christopher; Uetz, Peter

    2015-01-01

    Large-scale analyses of protein complexes have recently become available for Escherichia coli and Mycoplasma pneumoniae, yielding 443 and 116 heteromultimeric soluble protein complexes, respectively. We have coupled the results of these mass spectrometry-characterized protein complexes with the 285 “gold standard” protein complexes identified by EcoCyc. A comparison with databases of gene orthology, conservation, and essentiality identified proteins conserved or lost in complexes of other species. For instance, of 285 “gold standard” protein complexes in E. coli, less than 10% are fully conserved among a set of 7 distantly-related bacterial “model” species. Complex conservation follows one of three models: well-conserved complexes, complexes with a conserved core, and complexes with partial conservation but no conserved core. Expanding the comparison to 894 distinct bacterial genomes illustrates fractional conservation and the limits of co-conservation among components of protein complexes: just 14 out of 285 model protein complexes are perfectly conserved across 95% of the genomes used, yet we predict more than 180 may be partially conserved across at least half of the genomes. No clear relationship between gene essentiality and protein complex conservation is observed, as even poorly conserved complexes contain a significant number of essential proteins. Finally, we identify 183 complexes containing well-conserved components and uncharacterized proteins which will be interesting targets for future experimental studies. PMID:25723151

  15. Forces Stabilizing Proteins

    PubMed Central

    Pace, C. Nick; Scholtz, J. Martin; Grimsley, Gerald R.

    2014-01-01

    The goal of this article is to summarize what has been learned about the major forces stabilizing proteins since the late 1980s when site-directed mutagenesis became possible. The following conclusions are derived from experimental studies of hydrophobic and hydrogen bonding variants. 1. Based on studies of 138 hydrophobic interaction variants in 11 proteins, burying a –CH2– group on folding contributes 1.1 ± 0.5 kcal/mol to protein stability. 2. The burial of nonpolar side chains contributes to protein stability in two ways: first, a term that depends on the removal of the side chains from water and, more importantly, the enhanced London dispersion forces that result from the tight packing in the protein interior. 3. Based on studies of 151 hydrogen bonding variants in 15 proteins, forming a hydrogen bond on folding contributes 1.1 ± 0.8 kcal/mol to protein stability. 4. The contribution of hydrogen bonds to protein stability is strongly context dependent. 5. Hydrogen bonds by side chains and peptide groups make similar contributions to protein stability. 6. Polar group burial can make a favorable contribution to protein stability even if the polar group is not hydrogen bonded. 7. Hydrophobic interactions and hydrogen bonds both make large contributions to protein stability. PMID:24846139

  16. Exploring NMR ensembles of calcium binding proteins: Perspectives to design inhibitors of protein-protein interactions

    PubMed Central

    2011-01-01

    Background Disrupting protein-protein interactions by small organic molecules is nowadays a promising strategy employed to block protein targets involved in different pathologies. However, structural changes occurring at the binding interfaces make difficult drug discovery processes using structure-based drug design/virtual screening approaches. Here we focused on two homologous calcium binding proteins, calmodulin and human centrin 2, involved in different cellular functions via protein-protein interactions, and known to undergo important conformational changes upon ligand binding. Results In order to find suitable protein conformations of calmodulin and centrin for further structure-based drug design/virtual screening, we performed in silico structural/energetic analysis and molecular docking of terphenyl (a mimicking alpha-helical molecule known to inhibit protein-protein interactions of calmodulin) into X-ray and NMR ensembles of calmodulin and centrin. We employed several scoring methods in order to find the best protein conformations. Our results show that docking on NMR structures of calmodulin and centrin can be very helpful to take into account conformational changes occurring at protein-protein interfaces. Conclusions NMR structures of protein-protein complexes nowadays available could efficiently be exploited for further structure-based drug design/virtual screening processes employed to design small molecule inhibitors of protein-protein interactions. PMID:21569443

  17. Myeloma Patient's Guide to Understanding Your Test Results

    MedlinePLUS

    ... and liver function test results. n S erum Protein Electrophoresis (SPEP) Assesses the amount of abnormal (monoclonal) protein. n U rine Protein Electrophoresis (UPEP) Shows the amount of monoclonal protein in ...

  18. Protein- protein interaction detection system using fluorescent protein microdomains

    DOEpatents

    Waldo, Geoffrey S. (Santa Fe, NM); Cabantous, Stephanie (Los Alamos, NM)

    2010-02-23

    The invention provides a protein labeling and interaction detection system based on engineered fragments of fluorescent and chromophoric proteins that require fused interacting polypeptides to drive the association of the fragments, and further are soluble and stable, and do not change the solubility of polypeptides to which they are fused. In one embodiment, a test protein X is fused to a sixteen amino acid fragment of GFP (.beta.-strand 10, amino acids 198-214), engineered to not perturb fusion protein solubility. A second test protein Y is fused to a sixteen amino acid fragment of GFP (.beta.-strand 11, amino acids 215-230), engineered to not perturb fusion protein solubility. When X and Y interact, they bring the GFP strands into proximity, and are detected by complementation with a third GFP fragment consisting of GFP amino acids 1-198 (strands 1-9). When GFP strands 10 and 11 are held together by interaction of protein X and Y, they spontaneous association with GFP strands 1-9, resulting in structural complementation, folding, and concomitant GFP fluorescence.

  19. Beyond proteins.

    PubMed

    Robson, B

    1999-08-01

    Increased understanding of the biological principles of protein structure and folding, combined with advances in protein-synthetic chemistry, should not only allow us to borrow from biology but also to depart from it and so produce protein-like, but non-protein, molecules and molecular devices. However, radical departures from protein-like forms into more-robust and truly novel 'smart' polymers and materials first require a solution to the protein-folding problem using only fundamental physicochemical principles. Any such practical solution may not come from raw computing power alone but rather from a deeper understanding of topological principles. PMID:10407402

  20. Toxicity of selenium (Na sub 2 SeO sub 3 ) and mercury (HgCl sub 2 ) on the planarian Dugesia gonocephala

    SciTech Connect

    Congiu, A.M.; Casu, S.; Ugazio, G. )

    1989-10-01

    The toxicity of selenium (Na{sub 2}SeO{sub 3}) and mercury (HgCl{sub 2}) was determined by using a freshwater planarian which is particularly sensitive to pollution, and belongs to a fissiparous breed of Dugesia gonocephala. The mortality and fissiparity frequency of the subjects were studied. They were exposed to intense treatments (48 hours) or for medium to long periods of time (21 days) to either the single compounds or a combination of both, and were fed or fasting. The lethal effect of sodium selenite is correlated to the food intake, whereas the toxicity of mercurous chloride is probably the result of a fixative effect which does not depend on feeding. The 21-day treatment with the first compound has a non-negligible lethal effect which is probably due to an accumulation phenomenon. At doses where an antioxidant effect prevails, fissiparity is stimulated. On the other hand, the second compound reduces reproduction frequency to half the base values. Compared to the Paracentrotus lividus, the Dugesia gonocephala offers various advantages concerning toxicological experiments; besides being easier to handle in the laboratory, it is available all year round and is not subject to seasonal cycles. It is also more susceptible to the toxic effect of mercury, which is a common and highly toxic pollutant, than the sea urchin.

  1. The temperature-sensitive (ts) phenotype of a cold-passaged (cp) live attenuated respiratory syncytial virus vaccine candidate, designated cpts530, results from a single amino acid substitution in the L protein.

    PubMed Central

    Juhasz, K; Whitehead, S S; Bui, P T; Biggs, J M; Crowe, J E; Boulanger, C A; Collins, P L; Murphy, B R

    1997-01-01

    cpts530, a candidate live-virus vaccine, is an attenuated strain of human respiratory syncytial virus (RSV). It was derived by subjecting a cold-passaged (cp) strain of RSV to a single round of chemical mutagenesis. cpts530 is a temperature-sensitive (ts) mutant that is attenuated in mice and chimpanzees, and its ts phenotype exhibits a high level of stability during replication in both species. In the present study, the complete nucleotide sequence of cpts530 RSV was determined. The five mutations known to be present in the parent cpRSV were retained in its cpts530 derivative, and one additional nucleotide change was identified at nucleotide (nt) 10060, which resulted in a phenylalanine-to-leucine change at amino acid 521 in the large polymerase (L) protein. To determine if this single amino acid substitution was indeed responsible for the ts phenotype of cpts530, it was introduced alone or in combination with the cp mutations into the full-length cDNA clone of the wild-type A2 RSV. Analysis of infectious viruses recovered from mutant cDNAs indicated that this single mutation specified complete restriction of plaque formation of recombinant cp530 in HEp-2 cell monolayer cultures at 40 degrees C, and the level of temperature sensitivity was not influenced by the presence of the five cpRSV mutations. These findings identify the phenylalanine-to-leucine change at amino acid 521 in the L protein as the mutation that specifies the ts phenotype of cpts530. Furthermore, these findings illustrate the feasibility of using the cDNA-based recovery system to analyze and construct defined attenuated vaccine viruses. PMID:9223470

  2. Physics of protein motility and motor proteins

    NASA Astrophysics Data System (ADS)

    Kolomeisky, Anatoly B.

    2013-09-01

    Motor proteins are enzymatic molecules that transform chemical energy into mechanical motion and work. They are critically important for supporting various cellular activities and functions. In the last 15 years significant progress in understanding the functioning of motor proteins has been achieved due to revolutionary breakthroughs in single-molecule experimental techniques and strong advances in theoretical modelling. However, microscopic mechanisms of protein motility are still not well explained, and the collective efforts of many scientists are needed in order to solve these complex problems. In this special section the reader will find the latest advances on the difficult road to mapping motor proteins dynamics in various systems. Recent experimental developments have allowed researchers to monitor and to influence the activity of single motor proteins with a high spatial and temporal resolution. It has stimulated significant theoretical efforts to understand the non-equilibrium nature of protein motility phenomena. The latest results from all these advances are presented and discussed in this special section. We would like to thank the scientists from all over the world who have reported their latest research results for this special section. We are also grateful to the staff and editors of Journal of Physics: Condensed Matter for their invaluable help in handling all the administrative and refereeing activities. The field of motor proteins and protein motility is fast moving, and we hope that this collection of articles will be a useful source of information in this highly interdisciplinary area. Physics of protein motility and motor proteins contents Physics of protein motility and motor proteinsAnatoly B Kolomeisky Identification of unique interactions between the flexible linker and the RecA-like domains of DEAD-box helicase Mss116 Yuan Zhang, Mirkó Palla, Andrew Sun and Jung-Chi Liao The load dependence of the physical properties of a molecular motor Xianchao Meng, Min Yu and Yunxin Zhang Microtubule organization by kinesin motors and microtubule crosslinking protein MAP65 Joshua Pringle, Amutha Muthukumar, Amanda Tan, Laura Crankshaw, Leslie Conway and Jennifer L Ross Backtracking dynamics of RNA polymerase: pausing and error correction Mamata Sahoo and Stefan Klumpp First-passage problems in DNA replication: effects of template tension on stepping and exonuclease activities of a DNA polymerase motor Ajeet K Sharma and Debashish Chowdhury

  3. Protein Microarrays

    NASA Astrophysics Data System (ADS)

    Ricard-Blum, S.

    Proteins are key actors in the life of the cell, involved in many physiological and pathological processes. Since variations in the expression of messenger RNA are not systematically correlated with variations in the protein levels, the latter better reflect the way a cell functions. Protein microarrays thus supply complementary information to DNA chips. They are used in particular to analyse protein expression profiles, to detect proteins within complex biological media, and to study protein-protein interactions, which give information about the functions of those proteins [3-9]. They have the same advantages as DNA microarrays for high-throughput analysis, miniaturisation, and the possibility of automation. Section 18.1 gives a brief overview of proteins. Following this, Sect. 18.2 describes how protein microarrays can be made on flat supports, explaining how proteins can be produced and immobilised on a solid support, and discussing the different kinds of substrate and detection method. Section 18.3 discusses the particular format of protein microarrays in suspension. The diversity of protein microarrays and their applications are then reported in Sect. 18.4, with applications to therapeutics (protein-drug interactions) and diagnostics. The prospects for future developments of protein microarrays are then outlined in the conclusion. The bibliography provides an extensive list of reviews and detailed references for those readers who wish to go further in this area. Indeed, the aim of the present chapter is not to give an exhaustive or detailed analysis of the state of the art, but rather to provide the reader with the basic elements needed to understand how proteins are designed and used.

  4. Protein Structure

    ERIC Educational Resources Information Center

    Asmus, Elaine Garbarino

    2007-01-01

    Individual students model specific amino acids and then, through dehydration synthesis, a class of students models a protein. The students clearly learn amino acid structure, primary, secondary, tertiary, and quaternary structure in proteins and the nature of the bonds maintaining a protein's shape. This activity is fun, concrete, inexpensive and…

  5. How Many Protein-Protein Interactions Types Exist in Nature?

    PubMed Central

    Mitra, Pralay; Zhang, Yang

    2012-01-01

    Protein quaternary structure universe” refers to the ensemble of all protein-protein complexes across all organisms in nature. The number of quaternary folds thus corresponds to the number of ways proteins physically interact with other proteins. This study focuses on answering two basic questions: Whether the number of protein-protein interactions is limited and, if yes, how many different quaternary folds exist in nature. By all-to-all sequence and structure comparisons, we grouped the protein complexes in the protein data bank (PDB) into 3,629 families and 1,761 folds. A statistical model was introduced to obtain the quantitative relation between the numbers of quaternary families and quaternary folds in nature. The total number of possible protein-protein interactions was estimated around 4,000, which indicates that the current protein repository contains only 42% of quaternary folds in nature and a full coverage needs approximately a quarter century of experimental effort. The results have important implications to the protein complex structural modeling and the structure genomics of protein-protein interactions. PMID:22719985

  6. Protein-protein interactions: methods for detection and analysis.

    PubMed Central

    Phizicky, E M; Fields, S

    1995-01-01

    The function and activity of a protein are often modulated by other proteins with which it interacts. This review is intended as a practical guide to the analysis of such protein-protein interactions. We discuss biochemical methods such as protein affinity chromatography, affinity blotting, coimmunoprecipitation, and cross-linking; molecular biological methods such as protein probing, the two-hybrid system, and phage display: and genetic methods such as the isolation of extragenic suppressors, synthetic mutants, and unlinked noncomplementing mutants. We next describe how binding affinities can be evaluated by techniques including protein affinity chromatography, sedimentation, gel filtration, fluorescence methods, solid-phase sampling of equilibrium solutions, and surface plasmon resonance. Finally, three examples of well-characterized domains involved in multiple protein-protein interactions are examined. The emphasis of the discussion is on variations in the approaches, concerns in evaluating the results, and advantages and disadvantages of the techniques. PMID:7708014

  7. Prediction protein--protein interaction sites heterocomplexes with neural networks

    E-print Network

    Pazos, Florencio

    % residues involved protein interactions in a selected database comprising 226 heterodimers. analysis. propose the predictor significantly complement results structural and func­ tional proteomics. Keywords--protein interaction through isolation protein complexes under way, and map proteomics adds a to efficiently study

  8. Secure Binary Field Multiplication Hwajeong Seo1

    E-print Network

    International Association for Cryptologic Research (IACR)

    is regarded as a relatively secure approach because LUT access can be conducted in a regular and atomic form multi- plication. The attack exploits the horizontal Correlation Power Analysis (CPA) on weights of LUT

  9. Replication Proteins and Human Disease

    PubMed Central

    Jackson, Andrew P.; Laskey, Ronald A.; Coleman, Nicholas

    2014-01-01

    In this article, we discuss the significance of DNA replication proteins in human disease. There is a broad range of mutations in genes encoding replication proteins, which result in several distinct clinical disorders that share common themes. One group of replication proteins, the MCMs, has emerged as effective biomarkers for early detection of a range of common cancers. They offer practical and theoretical advantages over other replication proteins and have been developed for widespread clinical use. PMID:23881941

  10. Protein crystallization in microgravity.

    PubMed

    Aibara, S; Shibata, K; Morita, Y

    1997-12-01

    A space experiment involving protein crystallization was conducted in a microgravity environment using the space shuttle "Endeavour" of STS-47, on a 9-day mission from September 12th to 20th in 1992. The crystallization was carried out according to a batch method, and 5 proteins were selected as flight samples for crystallization. Two of these proteins: hen egg-white lysozyme and co-amino acid: pyruvate aminotransferase from Pseudomonas sp. F-126, were obtained as single crystals of good diffraction quality. Since 1992 we have carried out several space experiments for protein crystallization aboard space shuttles and the space station MIR. Our experimental results obtained mainly from hen egg-white lysozyme are described below, focusing on the effects of microgravity on protein crystal growth. PMID:11541767

  11. Protein aggregation and prionopathies.

    PubMed

    Renner, M; Melki, R

    2014-06-01

    Prion protein and prion-like proteins share a number of characteristics. From the molecular point of view, they are constitutive proteins that aggregate following conformational changes into insoluble particles. These particles escape the cellular clearance machinery and amplify by recruiting the soluble for of their constituting proteins. The resulting protein aggregates are responsible for a number of neurodegenerative diseases such as Creutzfeldt-Jacob, Alzheimer, Parkinson and Huntington diseases. In addition, there are increasing evidences supporting the inter-cellular trafficking of these aggregates, meaning that they are "transmissible" between cells. There are also evidences that brain homogenates from individuals developing Alzheimer and Parkinson diseases propagate the disease in recipient model animals in a manner similar to brain extracts of patients developing Creutzfeldt-Jacob's disease. Thus, the propagation of protein aggregates from cell to cell may be a generic phenomenon that contributes to the evolution of neurodegenerative diseases, which has important consequences on human health issues. Moreover, although the distribution of protein aggregates is characteristic for each disease, new evidences indicate the possibility of overlaps and crosstalk between the different disorders. Despite the increasing evidences that support prion or prion-like propagation of protein aggregates, there are many unanswered questions regarding the mechanisms of toxicity and this is a field of intensive research nowadays. PMID:24698014

  12. Protein Attachment on Nanodiamonds.

    PubMed

    Lin, Chung-Lun; Lin, Cheng-Huang; Chang, Huan-Cheng; Su, Meng-Chih

    2015-07-16

    A recent advance in nanotechnology is the scale-up production of small and nonaggregated diamond nanoparticles suitable for biological applications. Using detonation nanodiamonds (NDs) with an average diameter of ?4 nm as the adsorbents, we have studied the static attachment of three proteins (myoglobin, bovine serum albumin, and insulin) onto the nanoparticles by optical spectroscopy, mass spectrometry, and dynamic light scattering, and electrophoretic zeta potential measurements. Results show that the protein surface coverage is predominantly determined by the competition between protein-protein and protein-ND interactions, giving each protein a unique and characteristic structural configuration in its own complex. Specifically, both myoglobin and bovine serum albumin show a Langmuir-type adsorption behavior, forming 1:1 complexes at saturation, whereas insulin folds into a tightly bound multimer before adsorption. The markedly different adsorption patterns appear to be independent of the protein concentration and are closely related to the affinity of the individual proteins for the NDs. The present study provides a fundamental understanding for the use of NDs as a platform for nanomedical drug delivery. PMID:25815400

  13. Interfacial Protein-Protein Associations

    PubMed Central

    Langdon, Blake B.; Kastantin, Mark; Walder, Robert; Schwartz, Daniel K.

    2014-01-01

    While traditional models of protein adsorption focus primarily on direct protein-surface interactions, recent findings suggest that protein-protein interactions may play a central role. Using high-throughput intermolecular resonance energy transfer (RET) tracking, we directly observed dynamic, protein-protein associations of bovine serum albumin on poly(ethylene glycol) modified surfaces. The associations were heterogeneous and reversible, and associating molecules resided on the surface for longer times. The appearance of three distinct RET states suggested a spatially heterogeneous surface – with areas of high protein density (i.e. strongly-interacting clusters) coexisting with mobile monomers. Distinct association states exhibited characteristic behavior, i.e. partial-RET (monomer-monomer) associations were shorter-lived than complete-RET (protein-cluster) associations. While the fractional surface area covered by regions with high protein density (i.e. clusters) increased with increasing concentration, the distribution of contact times between monomers and clusters was independent of solution concentration, suggesting that associations were a local phenomenon, and independent of the global surface coverage. PMID:24274729

  14. Dietary Proteins

    MedlinePLUS

    ... This means they supply all of the amino acids the body can't make on its own. Plant proteins are incomplete. You must combine different types of plant proteins to get all of the amino acids your body needs. It is important to get ...

  15. Proteins : paradigms of complexity /

    SciTech Connect

    Frauenfelder, Hans,

    2001-01-01

    Proteins are the working machines of living systems. Directed by the DNA, of the order of a few hundred building blocks, selected from twenty different amino acids, are covalently linked into a linear polypeptide chain. In the proper environment, the chain folds into the working protein, often a globule of linear dimensions of a few nanometers. The biologist considers proteins units from which living systems are built. Many physical scientists look at them as systems in which the laws of complexity can be studied better than anywhere else. Some of the results of such studies will be sketched.

  16. Protein based Block Copolymers

    PubMed Central

    Rabotyagova, Olena S.; Cebe, Peggy; Kaplan, David L.

    2011-01-01

    Advances in genetic engineering have led to the synthesis of protein-based block copolymers with control of chemistry and molecular weight, resulting in unique physical and biological properties. The benefits from incorporating peptide blocks into copolymer designs arise from the fundamental properties of proteins to adopt ordered conformations and to undergo self-assembly, providing control over structure formation at various length scales when compared to conventional block copolymers. This review covers the synthesis, structure, assembly, properties, and applications of protein-based block copolymers. PMID:21235251

  17. Ranking Docked Models of Protein-Protein Complexes Using Predicted Partner-Specific Protein-Protein Interfaces: A Preliminary Study

    PubMed Central

    Xue, Li C.; Jordan, Rafael A.; EL-Manzalawy, Yasser; Dobbs, Drena; Honavar, Vasant

    2015-01-01

    Computational protein-protein docking is a valuable tool for determining the conformation of complexes formed by interacting proteins. Selecting near-native conformations from the large number of possible models generated by docking software presents a significant challenge in practice. We introduce a novel method for ranking docked conformations based on the degree of overlap between the interface residues of a docked conformation formed by a pair of proteins with the set of predicted interface residues between them. Our approach relies on a method, called PS-HomPPI, for reliably predicting protein-protein interface residues by taking into account information derived from both interacting proteins. PS-HomPPI infers the residues of a query protein that are likely to interact with a partner protein based on known interface residues of the homo-interologs of the query-partner protein pair, i.e., pairs of interacting proteins that are homologous to the query protein and partner protein. Our results on Docking Benchmark 3.0 show that the quality of the ranking of docked conformations using our method is consistently superior to that produced using ClusPro cluster-size-based and energy-based criteria for 61 out of the 64 docking complexes for which PS-HomPPI produces interface predictions. An implementation of our method for ranking docked models is freely available at: http://einstein.cs.iastate.edu/DockRank/. PMID:25905110

  18. Inactivation of Two Dictyostelium discoideum Genes, DdPIK1 and DdPIK2, Encoding Proteins Related to Mammalian Phosphatidylinositide 3-kinases, Results in Defects in Endocytosis, Lysosome to Postlysosome Transport, and Actin Cytoskeleton Organization

    PubMed Central

    Buczynski, Greg; Grove, Bryon; Nomura, Anson; Kleve, Maurice; Bush, John; Firtel, Richard A.; Cardelli, James

    1997-01-01

    Phosphatidylinositide 3-kinases (PI 3-kinases) have been implicated in controlling cell proliferation, actin cytoskeleton organization, and the regulation of vesicle trafficking between intracellular organelles. There are at least three genes in Dictyostelium discoideum, DdPIK1, DdPIK2, and DdPIK3, encoding proteins most closely related to the mammalian 110-kD PI-3 kinase in amino acid sequence within the kinase domain. A mutant disrupted in DdPIK1 and DdPIK2 (?ddpik1/ddpik2) grows slowly in liquid medium. Using FITC-dextran (FD) as a fluid phase marker, we determined that the mutant strain was impaired in pinocytosis but normal in phagocytosis of beads or bacteria. Microscopic and biochemical approaches indicated that the transport rate of fluid-phase from acidic lysosomes to non-acidic postlysosomal vacuoles was reduced in mutant cells resulting in a reduction in efflux of fluid phase. Mutant cells were also almost completely devoid of large postlysosomal vacuoles as determined by transmission EM. However, ?ddpik1/ddpik2 cells functioned normally in the regulation of other membrane traffic. For instance, radiolabel pulse-chase experiments indicated that the transport rates along the secretory pathway and the sorting efficiency of the lysosomal enzyme ?-mannosidase were normal in the mutant strain. Furthermore, the contractile vacuole network of membranes (probably connected to the endosomal pathway by membrane traffic) was functionally and morphologically normal in mutant cells. Light microscopy revealed that ?ddpik1/ddpik2 cells appeared smaller and more irregularly shaped than wild-type cells; 1–3% of the mutant cells were also connected by a thin cytoplasmic bridge. Scanning EM indicated that the mutant cells contained numerous filopodia projecting laterally and vertically from the cell surface, and fluorescent microscopy indicated that these filopodia were enriched in F-actin which accumulated in a cortical pattern in control cells. Finally, ?ddpik1/ddpik2 cells responded and moved more rapidly towards cAMP. Together, these results suggest that Dictyostelium DdPIK1 and DdPIK2 gene products regulate multiple steps in the endosomal pathway, and function in the regulation of cell shape and movement perhaps through changes in actin organization. PMID:9087443

  19. Polymorphisms in the Low-Density Lipoprotein Receptor-Related Protein 5 (LRP5) Gene Are Associated with Peak Bone Mass in Non-sedentary Men: Results from the Odense Androgen Study

    PubMed Central

    Beckers, S.; Peeters, A.; Piters, E.; Balemans, W.; Nielsen, T. L.; Wraae, K.; Bathum, L.; Brasen, C.; Hagen, C.; Andersen, M.; Van Hul, W.; Abrahamsen, B.

    2007-01-01

    Purpose To investigate the impact of the Ala1330Val (rs3736228, exon 18) and Val667Met (rs4988321, exon 9) polymorphisms of the low-density lipoprotein receptor-related protein 5 (LRP5) gene on peak bone mass in young men. Methods The Odense Androgen Study (OAS) is a population-based study comprising 783 Caucasian men aged 20-30 years. Genotyping was performed using real-time polymerase chain reaction (PCR) or fluorescence polarization. Bone mineral density (BMD) measurements were performed using dual-energy X-ray absorptiometry. Results The CC, CT, and TT genotypes in Ala1330Val were found in 75.6%, 21.8%, and 2.6% of the participants, respectively. Similarly, the GG, GA, and AA genotypes of Val667Met were found in 89.7%, 9.8%, and 0.5%, respectively. For the Ala1330Val polymorphism, no significant differences between the genotypes were found regarding BMD in the overall study population. However, when analysis was restricted to non-sedentary men (n = 589), a significant association between the number of T-alleles and BMD in the spine and whole body were found. Each copy of the T-allele changed the Z-score of the spine by (median and 95% confidence interval) ?0.21 [95% CI: ?0.40; ?0.03] (p < 0.02). Analysis suggested an association between the AA genotype in the Val667Met polymorphism and increased body height and decreased BMD of the femoral neck; however, no significant gene-dose effect of the A-allele could be demonstrated in the whole population. When the analysis was restricted to non-sedentary subjects, however, each number of A-alleles was associated with a change in Z-score of ?0.26 [95% CI: ?0.51; ?0.01] (p = 0.04). No further significant results emerged with haplotype analysis. Conclusion The Ala1330Val and Val667Met polymorphisms in the LRP5 gene are significantly associated with peak bone mass in physically active men. PMID:18058054

  20. Impact of Protein Supplementation and Care and Support on Body Composition and CD4 Count among HIV-Infected Women Living in Rural India: Results from a Randomized Pilot Clinical Trial

    PubMed Central

    Nyamathi, Adeline; Sinha, Sanjeev; Ganguly, Kalyan K; Ramakrishna, Padma; Suresh, P.; Carpenter, Catherine L

    2013-01-01

    Body composition in HIV-infected individuals is subject to many influences. We conducted a pilot six-month randomized trial of 68 WLA (women living with AIDS) from rural India. High protein intervention combined with education and supportive care delivered by HIV-trained village women (Asha [Activated Social Health Activist] Life [AL]) was compared to standard protein with usual care delivered by village community assistants (Usual Care [UC]). Measurements included CD4 counts, ART adherence, socio-demographics, disease characteristics (questionnaires); and anthropometry (bioimpedance analyzer). Repeated measures analysis of variance modeled associations. AL significantly gained in BMI, muscle mass, fat mass, ART adherence, and CD4 counts compared to UC, with higher weight and muscle mass gains among ART adherent (? 66%) participants who had healthier immunity (CD4 ? 450). BMI of WLA improved through high protein supplementation combined with education and supportive care. Future research is needed to determine which intervention aspect was most responsible. PMID:23370835

  1. Isolation of protein subpopulations undergoing protein-protein interactions.

    PubMed

    Nelson, Thomas J; Backlund, Peter S; Yergey, Alfred L; Alkon, Daniel L

    2002-03-01

    A new method is described for isolating and identifying proteins participating in protein-protein interactions in a complex mixture. The method uses a cyanogen bromide-activated Sepharose matrix to isolate proteins that are non-covalently bound to other proteins. Because the proteins are accessible to chemical manipulation, mass spectrometric identification of the proteins can yield information on specific classes of interacting proteins, such as calcium-dependent or substrate-dependent protein interactions. This permits selection of a subpopulation of proteins from a complex mixture on the basis of specified interaction criteria. The new method has the advantage of screening the entire proteome simultaneously, unlike the two-hybrid system or phage display, which can only detect proteins binding to a single bait protein at a time. The method was tested by selecting rat brain extract for proteins exhibiting calcium-dependent protein interactions. Of 12 proteins identified by mass spectrometry, eight were either known calcium-binding proteins or proteins with known calcium-dependent protein interactions, indicating that the method is capable of enriching a subpopulation of proteins from a complex mixture on the basis of a specific class of protein interactions. Because only naturally occurring interactions of proteins in their native state are observed, this method will have wide applicability to studies of protein interactions in tissue samples and autopsy specimens, for screening for perturbations of protein-protein interactions by signaling molecules, pharmacological agents or toxins, and screening for differences between cancerous and untransformed cells. PMID:12096125

  2. Proteins interacting with cloning scars: a source of false positive protein-protein interactions

    PubMed Central

    Banks, Charles A. S.; Boanca, Gina; Lee, Zachary T.; Florens, Laurence; Washburn, Michael P.

    2015-01-01

    A common approach for exploring the interactome, the network of protein-protein interactions in cells, uses a commercially available ORF library to express affinity tagged bait proteins; these can be expressed in cells and endogenous cellular proteins that copurify with the bait can be identified as putative interacting proteins using mass spectrometry. Control experiments can be used to limit false-positive results, but in many cases, there are still a surprising number of prey proteins that appear to copurify specifically with the bait. Here, we have identified one source of false-positive interactions in such studies. We have found that a combination of: 1) the variable sequence of the C-terminus of the bait with 2) a C-terminal valine “cloning scar” present in a commercially available ORF library, can in some cases create a peptide motif that results in the aberrant co-purification of endogenous cellular proteins. Control experiments may not identify false positives resulting from such artificial motifs, as aberrant binding depends on sequences that vary from one bait to another. It is possible that such cryptic protein binding might occur in other systems using affinity tagged proteins; this study highlights the importance of conducting careful follow-up studies where novel protein-protein interactions are suspected. PMID:25704442

  3. EDITORIAL: Precision proteins Precision proteins

    NASA Astrophysics Data System (ADS)

    Demming, Anna

    2010-06-01

    Since the birth of modern day medicine, during the times of Hippocrates in ancient Greece, the profession has developed from the rudimentary classification of disease into a rigorous science with an inspiring capability to treat and cure. Scientific methodology has distilled clinical diagnostic tools from the early arts of prognosis, which used to rely as much on revelation and prophecy, as intuition and judgement [1]. Over the past decade, research into the interactions between proteins and nanosystems has provided some ingenious and apt techniques for delving into the intricacies of anatomical systems. In vivo biosensing has emerged as a vibrant field of research, as much of medical diagnosis relies on the detection of substances or an imbalance in the chemicals in the body. The inherent properties of nanoscale structures, such as cantilevers, make them well suited to biosensing applications that demand the detection of molecules at very low concentrations. Measurable deflections in cantilevers functionalised with antibodies provide quantitative indicators of the presence of specific antigens when the two react. Such developments have roused mounting interest in the interactions of proteins with nanostructures, such as carbon nanotubes [3], which have demonstrated great potential as generic biomarkers. Plasmonic properties are also being exploited in sensing applications, such as the molecular sentinel recently devised by researchers in the US. The device uses the plasmonic properties of a silver nanoparticle linked to a Raman labelled hairpin DNA probe to signal changes in the probe geometry resulting from interactions with substances in the environment. Success stories so far include the detection of two specific genes associated with breast cancer [4]. A greater understanding of how RNA interference regulates gene expression has highlighted the potential of using this natural process as another agent for combating disease in personalized medicine. However, the large molecular weight, net negative charge and hydrophilicity of synthetic small interfering RNAs makes it hard for the molecules to cross the plasma membrane and enter the cell cytoplasm. Immune responses can also diminish the effectiveness of this approach. In this issue, Shiri Weinstein and Dan Peer from Tel Aviv University provide an overview of the challenges and recent progress in the use of nanocarriers for delivering RNAi effector molecules into target tissues and cells more effectively [5]. Also in this issue, researchers in Korea report new results that demonstrate the potential of nanostructures in neural network engineering [6]. Min Jee Jang et al report directional growth of neurites along linear carbon nanotube patterns, demonstrating great progress in neural engineering and the scope for using nanotechnology to treat neural diseases. Modern medicine cannot claim to have abolished the pain and suffering that accompany disease. But a comparison between the ghastly and often ineffective iron implements of early medicine and the smart gadgets and treatments used in hospitals today speaks volumes for the extraordinary progress that has been made, and the motivation behind this research. References [1] Wallis F 2000 Signs and senses: diagnosis and prognosis in early medieval pulse and urine texts Soc. Hist. Med. 13 265-78 [2] Arntz Y, Seelig J D, Lang H P, Zhang J, Hunziker P, Ramseyer J P, Meyer E, Hegner M and Gerber Ch 2003 Label-free protein assay based on a nanomechanical cantiliever array Nanotechnology 14 86-90 [3] Gowtham S, Scheicher R H, Pandey R, Karna S P and Ahuja R 2008 First-principles study of physisorption of nucleic acid bases on small-diameter carbon nanotubes Nanotechnology 19 125701 [4] Wang H-N and Vo-Dinh T 2009 Multiplex detection of breast cancer biomarkers using plasmonic molecular sentinel nanoprobes Nanotechnology 20 065101 [5] Weinstein S and Peer D 2010 RNAi nanomedicines: challenges and opportunities within the immune system Nanotechnology 21 232001 [6] Jang M J, Namgung S, Hong S, and Nam Y 2010 Directional neurite gro

  4. The FOLDX results suggest that CSL motifs with C at position 1 will have higher binding energies, in contrast to the canonical PWM and to the logo derived from the protein binding microarrays (PBMs). To investigate CSL

    E-print Network

    Jackson, Sophie

    , in contrast to the canonical PWM and to the logo derived from the protein binding microarrays (PBMs to generate a binding logo and this was compared with the previously used TRANSFAC logo [3]. UNDERSTANDING-domain communication are indicated by orange spheres. C: Comparison of energy logos obtained from FOLDX predictions

  5. Whey protein supplementation does not alter plasma branched-chained amino acid profiles but results in unique metabolomics patterns in obese women enrolled in an 8-week weight loss trial

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: It has been suggested that perturbations in branched-chain amino acid (BCAA) catabolism are associated with insulin resistance and contribute to elevated systemic BCAAs. Evidence in rodents suggests dietary protein rich in BCAAs can increase BCAA catabolism, but there is limited evidence...

  6. Protein dynamics. Direct observation of hierarchical protein dynamics.

    PubMed

    Lewandowski, Józef R; Halse, Meghan E; Blackledge, Martin; Emsley, Lyndon

    2015-05-01

    One of the fundamental challenges of physical biology is to understand the relationship between protein dynamics and function. At physiological temperatures, functional motions arise from the complex interplay of thermal motions of proteins and their environments. Here, we determine the hierarchy in the protein conformational energy landscape that underlies these motions, based on a series of temperature-dependent magic-angle spinning multinuclear nuclear-magnetic-resonance relaxation measurements in a hydrated nanocrystalline protein. The results support strong coupling between protein and solvent dynamics above 160 kelvin, with fast solvent motions, slow protein side-chain motions, and fast protein backbone motions being activated consecutively. Low activation energy, small-amplitude local motions dominate at low temperatures, with larger-amplitude, anisotropic, and functionally relevant motions involving entire peptide units becoming dominant at temperatures above 220 kelvin. PMID:25931561

  7. Measurements of Protein-Protein Interactions in Solutions by Chromatography

    NASA Astrophysics Data System (ADS)

    Berejnov, V.; Bloustine, J.; Fraden, S.

    2003-03-01

    The protein-protein interaction in solutions have generated a great deal of interest among structural biologists since [1] showed a correlation between protein crystallisability and a virial coefficient B2 describing such interaction. The work [1] demonstrated that many proteins crystallize in conditions where the B2 becomes slightly negative, indicating net attractive interactions between protein molecules. We present a new efficient method for extracting second virial coefficients B2 of protein solutions from retention time measurements in size exclusion chromatography (SEC). We measure B2 by analyzing the concentration dependance of the chromatographic partition coefficient. We show the ability of this method to track the evolution of B2 from positive to negative values in lysozyme and bovine serum albumin solutions. Our SEC results agree quantitatively with data obtained by light scattering. 1. A.George and W.W.Wilson, Predicting protein crystallization from a dilute solution property. Acta. Cryst., D50:361--365, 1994.

  8. Discover Protein Complexes in Protein-Protein Interaction Networks Using Parametric Local Modularity

    PubMed Central

    2010-01-01

    Background Recent advances in proteomic technologies have enabled us to create detailed protein-protein interaction maps in multiple species and in both normal and diseased cells. As the size of the interaction dataset increases, powerful computational methods are required in order to effectively distil network models from large-scale interactome data. Results We present an algorithm, miPALM (Module Inference by Parametric Local Modularity), to infer protein complexes in a protein-protein interaction network. The algorithm uses a novel graph theoretic measure, parametric local modularity, to identify highly connected sub-networks as candidate protein complexes. Using gold standard sets of protein complexes and protein function and localization annotations, we show our algorithm achieved an overall improvement over previous algorithms in terms of precision, recall, and biological relevance of the predicted complexes. We applied our algorithm to predict and characterize a set of 138 novel protein complexes in S. cerevisiae. Conclusions miPALM is a novel algorithm for detecting protein complexes from large protein-protein interaction networks with improved accuracy than previous methods. The software is implemented in Matlab and is freely available at http://www.medicine.uiowa.edu/Labs/tan/software.html. PMID:20958996

  9. Protein crystal growth in microgravity

    NASA Technical Reports Server (NTRS)

    Rosenblum, William M.; Delucas, Lawrence J.; Wilson, William W.

    1989-01-01

    Major advances have been made in several of the experimental aspects of protein crystallography, leaving protein crystallization as one of the few remaining bottlenecks. As a result, it has become important that the science of protein crystal growth is better understood and that improved methods for protein crystallization are developed. Preliminary experiments with both small molecules and proteins indicate that microgravity may beneficially affect crystal growth. For this reason, a series of protein crystal growth experiments using the Space Shuttle was initiated. The preliminary space experiments were used to evolve prototype hardware that will form the basis for a more advanced system that can be used to evaluate effects of gravity on protein crystal growth. Various optical techniques are being utilized to monitor the crystal growth process from the incipient or nucleation stage and throughout the growth phase. The eventual goal of these studies is to develop a system which utilizes optical monitoring for dynamic control of the crystallization process.

  10. Protein-protein interactions and cancer: targeting the central dogma.

    PubMed

    Garner, Amanda L; Janda, Kim D

    2011-01-01

    Between 40,000 and 200,000 protein-protein interactions have been predicted to exist within the human interactome. As these interactions are of a critical nature in many important cellular functions and their dysregulation is causal of disease, the modulation of these binding events has emerged as a leading, yet difficult therapeutic arena. In particular, the targeting of protein-protein interactions relevant to cancer is of fundamental importance as the tumor-promoting function of several aberrantly expressed proteins in the cancerous state is directly resultant of its ability to interact with a protein-binding partner. Of significance, these protein complexes play a crucial role in each of the steps of the central dogma of molecular biology, the fundamental processes of genetic transmission. With the many important discoveries being made regarding the mechanisms of these genetic process, the identification of new chemical probes are needed to better understand and validate the druggability of protein-protein interactions related to the central dogma. In this review, we provide an overview of current small molecule-based protein-protein interaction inhibitors for each stage of the central dogma: transcription, mRNA splicing and translation. Importantly, through our analysis we have uncovered a lack of necessary probes targeting mRNA splicing and translation, thus, opening up the possibility for expansion of these fields. PMID:21320057

  11. Cutting Edge: Codeletion of the Ras GTPase-Activating Proteins (RasGAPs) Neurofibromin 1 and p120 RasGAP in T Cells Results in the Development of T Cell Acute Lymphoblastic Leukemia.

    PubMed

    Lubeck, Beth A; Lapinski, Philip E; Oliver, Jennifer A; Ksionda, Olga; Parada, Luis F; Zhu, Yuan; Maillard, Ivan; Chiang, Mark; Roose, Jeroen; King, Philip D

    2015-07-01

    Ras GTPase-activating proteins (RasGAPs) inhibit signal transduction initiated through the Ras small GTP-binding protein. However, which members of the RasGAP family act as negative regulators of T cell responses is not completely understood. In this study, we investigated potential roles for the RasGAPs RASA1 and neurofibromin 1 (NF1) in T cells through the generation and analysis of T cell-specific RASA1 and NF1 double-deficient mice. In contrast to mice lacking either RasGAP alone in T cells, double-deficient mice developed T cell acute lymphoblastic leukemia/lymphoma, which originated at an early point in T cell development and was dependent on activating mutations in the Notch1 gene. These findings highlight RASA1 and NF1 as cotumor suppressors in the T cell lineage. PMID:26002977

  12. Protein Solubilization: A Novel Approach

    PubMed Central

    Johnson, David H.; Wilson, W. William; DeLucas, Lawrence J.

    2014-01-01

    Formulation development presents significant challenges with respect to protein therapeutics. One component of these challenges is to attain high protein solubility (> 50 mg/ml for immunoglobulins) with minimal aggregation. Protein-protein interactions contribute to aggregation and the integral sum of these interactions can be quantified by a thermodynamic parameter known as the osmotic second virial coefficient (B-value). The method presented here utilizes high-throughput measurement of B-values to identify the influence of additives on protein-protein interactions. The experiment design uses three tiers of screens to arrive at final solution conditions that improve protein solubility. The first screen identifies individual additives that reduce protein interactions. A second set of B-values are then measured for different combinations of these additives via an incomplete factorial screen. Results from the incomplete factorial screen are used to train an artificial neural network (ANN). The “trained” ANN enables predictions of B-values for more than 4,000 formulations that include additive combinations not previously experimentally measured. Validation steps are incorporated throughout the screening process to ensure that 1) the protein’s thermal and aggregation stability characteristics are not reduced and 2) the artificial neural network predictive model is accurate. The ability of this approach to reduce aggregation and increase solubility is demonstrated using an IgG protein supplied by Minerva Biotechnologies, Inc. PMID:25270058

  13. Cotton and Protein Interactions

    SciTech Connect

    Goheen, Steven C.; Edwards, J. V.; Rayburn, Alfred R.; Gaither, Kari A.; Castro, Nathan J.

    2006-06-30

    The adsorbent properties of important wound fluid proteins and cotton cellulose are reviewed. This review focuses on the adsorption of albumin to cotton-based wound dressings and some chemically modified derivatives targeted for chronic wounds. Adsorption of elastase in the presence of albumin was examined as a model to understand the interactive properties of these wound fluid components with cotton fibers. In the chronic non-healing wound, elastase appears to be over-expressed, and it digests tissue and growth factors, interfering with the normal healing process. Albumin is the most prevalent protein in wound fluid, and in highly to moderately exudative wounds, it may bind significantly to the fibers of wound dressings. Thus, the relative binding properties of both elastase and albumin to wound dressing fibers are of interest in the design of more effective wound dressings. The present work examines the binding of albumin to two different derivatives of cotton, and quantifies the elastase binding to the same derivatives following exposure of albumin to the fiber surface. An HPLC adsorption technique was employed coupled with a colorimetric enzyme assay to quantify the relative binding properties of albumin and elastase to cotton. The results of wound protein binding are discussed in relation to the porosity and surface chemistry interactions of cotton and wound proteins. Studies are directed to understanding the implications of protein adsorption phenomena in terms of fiber-protein models that have implications for rationally designing dressings for chronic wounds.

  14. Protein-protein interaction as a predictor of subcellular location

    PubMed Central

    Shin, Chang Jin; Wong, Simon; Davis, Melissa J; Ragan, Mark A

    2009-01-01

    Background Many biological processes are mediated by dynamic interactions between and among proteins. In order to interact, two proteins must co-occur spatially and temporally. As protein-protein interactions (PPIs) and subcellular location (SCL) are discovered via separate empirical approaches, PPI and SCL annotations are independent and might complement each other in helping us to understand the role of individual proteins in cellular networks. We expect reliable PPI annotations to show that proteins interacting in vivo are co-located in the same cellular compartment. Our goal here is to evaluate the potential of using PPI annotation in determining SCL of proteins in human, mouse, fly and yeast, and to identify and quantify the factors that contribute to this complementarity. Results Using publicly available data, we evaluate the hypothesis that interacting proteins must be co-located within the same subcellular compartment. Based on a large, manually curated PPI dataset, we demonstrate that a substantial proportion of interacting proteins are in fact co-located. We develop an approach to predict the SCL of a protein based on the SCL of its interaction partners, given sufficient confidence in the interaction itself. The frequency of false positive PPIs can be reduced by use of six lines of supporting evidence, three based on type of recorded evidence (empirical approach, multiplicity of databases, and multiplicity of literature citations) and three based on type of biological evidence (inferred biological process, domain-domain interactions, and orthology relationships), with biological evidence more-effective than recorded evidence. Our approach performs better than four existing prediction methods in identifying the SCL of membrane proteins, and as well as or better for soluble proteins. Conclusion Understanding cellular systems requires knowledge of the SCL of interacting proteins. We show how PPI data can be used more effectively to yield reliable SCL predictions for both soluble and membrane proteins. Scope exists for further improvement in our understanding of cellular function through consideration of the biological context of molecular interactions. PMID:19243629

  15. Protein damage, repair and proteolysis.

    PubMed

    Chondrogianni, Niki; Petropoulos, Isabelle; Grimm, Stefanie; Georgila, Konstantina; Catalgol, Betul; Friguet, Bertrand; Grune, Tilman; Gonos, Efstathios S

    2014-02-01

    Proteins are continuously affected by various intrinsic and extrinsic factors. Damaged proteins influence several intracellular pathways and result in different disorders and diseases. Aggregation of damaged proteins depends on the balance between their generation and their reversal or elimination by protein repair systems and degradation, respectively. With regard to protein repair, only few repair mechanisms have been evidenced including the reduction of methionine sulfoxide residues by the methionine sulfoxide reductases, the conversion of isoaspartyl residues to L-aspartate by L-isoaspartate methyl transferase and deglycation by phosphorylation of protein-bound fructosamine by fructosamine-3-kinase. Protein degradation is orchestrated by two major proteolytic systems, namely the lysosome and the proteasome. Alteration of the function for both systems has been involved in all aspects of cellular metabolic networks linked to either normal or pathological processes. Given the importance of protein repair and degradation, great effort has recently been made regarding the modulation of these systems in various physiological conditions such as aging, as well as in diseases. Genetic modulation has produced promising results in the area of protein repair enzymes but there are not yet any identified potent inhibitors, and, to our knowledge, only one activating compound has been reported so far. In contrast, different drugs as well as natural compounds that interfere with proteolysis have been identified and/or developed resulting in homeostatic maintenance and/or the delay of disease progression. PMID:23107776

  16. On the role of electrostatics on protein-protein interactions

    PubMed Central

    Zhang, Zhe; Witham, Shawn; Alexov, Emil

    2011-01-01

    The role of electrostatics on protein-protein interactions and binding is reviewed in this article. A brief outline of the computational modeling, in the framework of continuum electrostatics, is presented and basic electrostatic effects occurring upon the formation of the complex are discussed. The role of the salt concentration and pH of the water phase on protein-protein binding free energy is demonstrated and indicates that the increase of the salt concentration tends to weaken the binding, an observation that is attributed to the optimization of the charge-charge interactions across the interface. It is pointed out that the pH-optimum (pH of optimal binding affinity) varies among the protein-protein complexes, and perhaps is a result of their adaptation to particular subcellular compartment. At the end, the similarities and differences between hetero- and homo-complexes are outlined and discussed with respect to the binding mode and charge complementarity. PMID:21572182

  17. Protein Adsorption in Three Dimensions

    PubMed Central

    Vogler, Erwin A.

    2011-01-01

    Recent experimental and theoretical work clarifying the physical chemistry of blood-protein adsorption from aqueous-buffer solution to various kinds of surfaces is reviewed and interpreted within the context of biomaterial applications, especially toward development of cardiovascular biomaterials. The importance of this subject in biomaterials surface science is emphasized by reducing the “protein-adsorption problem” to three core questions that require quantitative answer. An overview of the protein-adsorption literature identifies some of the sources of inconsistency among many investigators participating in more than five decades of focused research. A tutorial on the fundamental biophysical chemistry of protein adsorption sets the stage for a detailed discussion of the kinetics and thermodynamics of protein adsorption, including adsorption competition between two proteins for the same adsorbent immersed in a binary-protein mixture. Both kinetics and steady-state adsorption can be rationalized using a single interpretive paradigm asserting that protein molecules partition from solution into a three-dimensional (3D) interphase separating bulk solution from the physical-adsorbent surface. Adsorbed protein collects in one-or-more adsorbed layers, depending on protein size, solution concentration, and adsorbent surface energy (water wettability). The adsorption process begins with the hydration of an adsorbent surface brought into contact with an aqueous-protein solution. Surface hydration reactions instantaneously form a thin, pseudo-2D interface between the adsorbent and protein solution. Protein molecules rapidly diffuse into this newly-formed interface, creating a truly 3D interphase that inflates with arriving proteins and fills to capacity within milliseconds at mg/mL bulk-solution concentrations CB. This inflated interphase subsequently undergoes time-dependent (minutes-to-hours) decrease in volume VI by expulsion of either-or-both interphase water and initially-adsorbed protein. Interphase protein concentration CI increases as VI decreases, resulting in slow reduction in interfacial energetics. Steady-state is governed by a net partition coefficient P=(/CBCI). In the process of occupying space within the interphase, adsorbing protein molecules must displace an equivalent volume of interphase water. Interphase water is itself associated with surface-bound water through a network of transient hydrogen bonds. Displacement of interphase water thus requires an amount of energy that depends on the adsorbent surface chemistry/energy. This “adsorption-dehydration” step is the significant free-energy cost of adsorption that controls the maximum amount of protein that can be adsorbed at steady state to a unit adsorbent-surface area (the adsorbent capacity). As adsorbent hydrophilicity increases, protein adsorption monotonically decreases because the energetic cost of surface dehydration increases, ultimately leading to no protein adsorption near an adsorbent water wettability (surface energy) characterized by a water contact angle ? ? 65°. Consequently, protein does not adsorb (accumulate at interphase concentrations greater than bulk solution) to more hydrophilic adsorbents exhibiting ? < 65° . For adsorbents bearing strong Lewis acid/base chemistry such as ion-exchange resins, protein/surface interactions can be highly favorable, causing protein to adsorb in multilayers in a relatively thick interphase. A straightforward, three-component free energy relationship captures salient features of protein adsorption to all surfaces predicting that the overall free energy of protein adsorption ?Gadso is a relatively small multiple of thermal energy for any surface chemistry (except perhaps for bioengineered surfaces bearing specific ligands for adsorbing protein) because a surface chemistry that interacts chemically with proteins must also interact with water through hydrogen bonding. In this way, water moderates protein adsorption to any surface by competing with

  18. Essential protein identification based on essential protein-protein interaction prediction by Integrated Edge Weights.

    PubMed

    Jiang, Yuexu; Wang, Yan; Pang, Wei; Chen, Liang; Sun, Huiyan; Liang, Yanchun; Blanzieri, Enrico

    2015-07-15

    Essential proteins play a crucial role in cellular survival and development process. Experimentally, essential proteins are identified by gene knockouts or RNA interference, which are expensive and often fatal to the target organisms. Regarding this, an alternative yet important approach to essential protein identification is through computational prediction. Existing computational methods predict essential proteins based on their relative densities in a protein-protein interaction (PPI) network. Degree, betweenness, and other appropriate criteria are often used to measure the relative density. However, no matter what criterion is used, a protein is actually ordered by the attributes of this protein per se. In this research, we presented a novel computational method, Integrated Edge Weights (IEW), to first rank protein-protein interactions by integrating their edge weights, and then identified sub PPI networks consisting of those highly-ranked edges, and finally regarded the nodes in these sub networks as essential proteins. We evaluated IEW on three model organisms: Saccharomyces cerevisiae (S. cerevisiae), Escherichia coli (E. coli), and Caenorhabditis elegans (C. elegans). The experimental results showed that IEW achieved better performance than the state-of-the-art methods in terms of precision-recall and Jackknife measures. We had also demonstrated that IEW is a robust and effective method, which can retrieve biologically significant modules by its highly-ranked protein-protein interactions for S. cerevisiae, E. coli, and C. elegans. We believe that, with sufficient data provided, IEW can be used to any other organisms' essential protein identification. A website about IEW can be accessed from http://digbio.missouri.edu/IEW/index.html. PMID:25892709

  19. Proteins aggregation and human diseases

    NASA Astrophysics Data System (ADS)

    Hu, Chin-Kun

    2015-04-01

    Many human diseases and the death of most supercentenarians are related to protein aggregation. Neurodegenerative diseases include Alzheimer's disease (AD), Huntington's disease (HD), Parkinson's disease (PD), frontotemporallobar degeneration, etc. Such diseases are due to progressive loss of structure or function of neurons caused by protein aggregation. For example, AD is considered to be related to aggregation of A?40 (peptide with 40 amino acids) and A?42 (peptide with 42 amino acids) and HD is considered to be related to aggregation of polyQ (polyglutamine) peptides. In this paper, we briefly review our recent discovery of key factors for protein aggregation. We used a lattice model to study the aggregation rates of proteins and found that the probability for a protein sequence to appear in the conformation of the aggregated state can be used to determine the temperature at which proteins can aggregate most quickly. We used molecular dynamics and simple models of polymer chains to study relaxation and aggregation of proteins under various conditions and found that when the bending-angle dependent and torsion-angle dependent interactions are zero or very small, then protein chains tend to aggregate at lower temperatures. All atom models were used to identify a key peptide chain for the aggregation of insulin chains and to find that two polyQ chains prefer anti-parallel conformation. It is pointed out that in many cases, protein aggregation does not result from protein mis-folding. A potential drug from Chinese medicine was found for Alzheimer's disease.

  20. Protein-protein complexation in bioluminescence

    E-print Network

    Zhijie, Liu

    REVIEW Protein-protein complexation in bioluminescence Maxim S. Titushin1 , Yingang Feng2 , John towards understanding the role of protein-protein interactions in the function of various bioluminescence on methodology used to detect and characterize these interactions. In some bioluminescence systems, protein

  1. Correlation of C-reactive protein haplotypes with serum C-reactive protein level and response to anti-tumor necrosis factor therapy in UK rheumatoid arthritis patients: results from the Biologics in Rheumatoid Arthritis Genetics and Genomics Study Syndicate cohort

    PubMed Central

    2012-01-01

    Introduction In many European countries, restrictions exist around the prescription of anti-tumor necrosis factor (anti-TNF) treatments for rheumatoid arthritis (RA). Eligibility and response to treatment is assessed by using the disease activity score 28 (DAS28) algorithm, which incorporates one of two inflammatory markers, erythrocyte sedimentation rate (ESR) or C-reactive protein (CRP). Although DAS28-CRP provides a more reliable measure of disease activity, functional variants exist within the CRP gene that affect basal CRP production. Therefore, we aimed to determine the relation between functional genetic variants at the CRP gene locus and levels of serum CRP in RA patients, and whether these variants, alone or in combination, are correlated with DAS28-CRP and change in DAS28-CRP after anti-TNF treatment. Methods DNA samples from the Biologics in Rheumatoid Arthritis Genetics and Genomics Study Syndicate (BRAGGSS) were genotyped for rs1205, rs1800947, and rs3091244 by using either TaqMan or the Sequenom MassARRAY iPLEX system. Estimated haplotypes were constructed for each sample by using the expectation maximization algorithm implemented in the haplo.stats package within the R statistical program. CRP values were log transformed, and the association between single nucleotide polymorphisms (SNPs), haplotypes of SNPs and baseline CRP, baseline DAS28-CRP, and change in DAS28-CRP were evaluated by using linear regression in STATA v.10. Results Baseline CRP measurements were available for 599 samples with 442 also having data 6 months after treatment with an anti-TNF. For these 442 samples, the study had > 80% power to detect a clinically meaningful difference of 0.6 DAS28 Units for an allele frequency of 5%. Estimated haplotype frequencies corresponded with previous frequencies reported in the literature. Overall, no significant association was observed between any of the markers investigated and baseline CRP levels. Further, CRP haplotypes did not correlate with baseline CRP (P = 0.593), baseline DAS28-CRP (P = 0.540), or change in DAS28-CRP after treatment with an anti-TNF over a 6-month period (P = 0.302). Conclusions Although CRP genotype may influence baseline CRP levels, in patients with very active disease, no such association was found. This suggests that genetic variation at the CRP locus does not influence DAS28-CRP, which may continue to be used in determining eligibility for and response to anti-TNF treatment, without adjusting for CRP genotype. PMID:23039402

  2. The Biological Value of Protein.

    PubMed

    Moore, Daniel R; Soeters, Peter B

    2015-11-01

    The biological value of a protein extends beyond its amino-acid composition and digestibility, and can be influenced by additional factors in a tissue-specific manner. In healthy individuals, the slow appearance of dietary amino acids in the portal vein and subsequently in the systemic circulation in response to bolus protein ingestion improves nitrogen retention and decreases urea production. This is promoted by slow absorption when only protein is ingested (e.g. casein). When a full meal is ingested, whey achieves slightly better nitrogen retention than soy or casein, which is very likely achieved by its high content of essential amino acids (especially leucine). Elderly people exhibit 'anabolic resistance' implying that more protein is required to reach maximal rates of muscle protein synthesis compared to young individuals. Protein utilization in inflammatory or traumatic conditions increases substantially in the splanchnic tissues containing most of the immune system, and in wounds and growing tissues. This happens especially in the elderly, which often suffer from chronic inflammatory activity due to disease, physical inactivity and/or the aging process itself. Consequently, the proportion of protein absorbed in the gut and utilized for muscle protein synthesis decreases in these situations. This compromises dietary-protein-induced stimulation of muscle protein synthesis and ultimately results in increased requirements of protein (?1.2 g/kg body weight/day) to limit gradual muscle loss with age. To optimally preserve muscle mass, physical exercise is required. Exercise has both direct effects on muscle mass and health, and indirect effects by increasing the utilization of dietary protein (especially whey) to enhance rates of muscle protein synthesis. PMID:26545252

  3. Protein function prediction using neighbor relativity in protein-protein interaction network.

    PubMed

    Moosavi, Sobhan; Rahgozar, Masoud; Rahimi, Amir

    2013-04-01

    There is a large gap between the number of discovered proteins and the number of functionally annotated ones. Due to the high cost of determining protein function by wet-lab research, function prediction has become a major task for computational biology and bioinformatics. Some researches utilize the proteins interaction information to predict function for un-annotated proteins. In this paper, we propose a novel approach called "Neighbor Relativity Coefficient" (NRC) based on interaction network topology which estimates the functional similarity between two proteins. NRC is calculated for each pair of proteins based on their graph-based features including distance, common neighbors and the number of paths between them. In order to ascribe function to an un-annotated protein, NRC estimates a weight for each neighbor to transfer its annotation to the unknown protein. Finally, the unknown protein will be annotated by the top score transferred functions. We also investigate the effect of using different coefficients for various types of functions. The proposed method has been evaluated on Saccharomyces cerevisiae and Homo sapiens interaction networks. The performance analysis demonstrates that NRC yields better results in comparison with previous protein function prediction approaches that utilize interaction network. PMID:23314240

  4. Structural basis for protein–protein interactions in the 14-3-3 protein family

    PubMed Central

    Yang, Xiaowen; Lee, Wen Hwa; Sobott, Frank; Papagrigoriou, Evangelos; Robinson, Carol V.; Grossmann, J. Günter; Sundström, Michael; Doyle, Declan A.; Elkins, Jonathan M.

    2006-01-01

    The seven members of the human 14-3-3 protein family regulate a diverse range of cell signaling pathways by formation of protein–protein complexes with signaling proteins that contain phosphorylated Ser/Thr residues within specific sequence motifs. Previously, crystal structures of three 14-3-3 isoforms (zeta, sigma, and tau) have been reported, with structural data for two isoforms deposited in the Protein Data Bank (zeta and sigma). In this study, we provide structural detail for five 14-3-3 isoforms bound to ligands, providing structural coverage for all isoforms of a human protein family. A comparative structural analysis of the seven 14-3-3 proteins revealed specificity determinants for binding of phosphopeptides in a specific orientation, target domain interaction surfaces and flexible adaptation of 14-3-3 proteins through domain movements. Specifically, the structures of the beta isoform in its apo and peptide bound forms showed that its binding site can exhibit structural flexibility to facilitate binding of its protein and peptide partners. In addition, the complex of 14-3-3 beta with the exoenzyme S peptide displayed a secondary structural element in the 14-3-3 peptide binding groove. These results show that the 14-3-3 proteins are adaptable structures in which internal flexibility is likely to facilitate recognition and binding of their interaction partners. PMID:17085597

  5. PocketQuery: protein-protein interaction inhibitor starting points from protein-protein interaction structure.

    PubMed

    Koes, David Ryan; Camacho, Carlos J

    2012-07-01

    PocketQuery (http://pocketquery.csb.pitt.edu) is a web interface for exploring the properties of protein-protein interaction (PPI) interfaces with a focus on the discovery of promising starting points for small-molecule design. PocketQuery rapidly focuses attention on the key interacting residues of an interaction using a 'druggability' score that provides an estimate of how likely the chemical mimicry of a cluster of interface residues would result in a small-molecule inhibitor of an interaction. These residue clusters are chemical starting points that can be seamlessly exported to a pharmacophore-based drug discovery workflow. PocketQuery is updated on a weekly basis to contain all applicable PPI structures deposited in the Protein Data Bank and allows users to upload their own custom structures for analysis. PMID:22523085

  6. Prediction of Protein-Protein Interaction Sites Based on Naive Bayes Classifier

    PubMed Central

    Geng, Haijiang; Lu, Tao; Lin, Xiao; Liu, Yu; Yan, Fangrong

    2015-01-01

    Protein functions through interactions with other proteins and biomolecules and these interactions occur on the so-called interface residues of the protein sequences. Identifying interface residues makes us better understand the biological mechanism of protein interaction. Meanwhile, information about the interface residues contributes to the understanding of metabolic, signal transduction networks and indicates directions in drug designing. In recent years, researchers have focused on developing new computational methods for predicting protein interface residues. Here we creatively used a 181-dimension protein sequence feature vector as input to the Naive Bayes Classifier- (NBC-) based method to predict interaction sites in protein-protein complexes interaction. The prediction of interaction sites in protein interactions is regarded as an amino acid residue binary classification problem by applying NBC with protein sequence features. Independent test results suggested that Naive Bayes Classifier-based method with the protein sequence features as input vectors performed well. PMID:26697220

  7. A Proteomic Approach to Characterize Protein Shedding

    SciTech Connect

    Ahram, Mamoun; Adkins, Joshua N.; Auberry, Deanna L.; Wunschel, David S.; Springer, David L.

    2005-01-01

    Shedding (i.e., proteolysis of ectodomains of membrane proteins) plays an important pathophysiological role. In order to study the feasibility of identifying shed proteins, we analyzed serum-free media of human mammary epithelial cells by mass spectrometry following induction of shedding by the phorbol ester, 4?-phorbol 12-myristate 13-acetate (PMA). Different means of sample preparation, including biotinylation of cell surface proteins, isolation of glycosylated proteins, and preparation of crude protein fraction, were carried out to develop the optimal method of sample processing. The collected proteins were digested with trypsin and analyzed by reversed-phase capillary liquid chromatography interfaced to an ion-trap mass spectrometer. The resulting peptide spectra were interpreted using the program SEQUEST. Analyzing the sample containing the crude protein mixture without chemical modification or separation resulted in the greatest number of identifications, including putatively shed proteins. Overall, 93 membrane-associated proteins were identified including 57 that contain at least one transmembrane domain and 36 that indirectly associate with the extracellular surface of the plasma membrane. Of the 57 transmembrane proteins, 43 were identified by extracellular peptides providing strong evidence for them originating from regulated proteolysis or shedding processes. We combined results from the different experiments and used a peptide count method to estimate changes in protein abundance. Using this approach, we identified 2 proteins, syndecan-4 and hepatoma-derived growth factor, whose abundances increased in media of cells treated with PMA. We also detected proteins whose abundances decreased after PMA treatment such as 78-kDa glucose-regulated protein and calreticulin. Further analysis using immunoblotting validated the abundance changes for syndecan-4 and 78-kDa glucose-regulated protein as a result of PMA treatment. These results demonstrate that mass spectrometry can be used to identify low-abundance shed proteins and to estimate changes in protein abundances.

  8. Benchtop Detection of Proteins

    NASA Technical Reports Server (NTRS)

    Scardelletti, Maximilian C.; Varaljay, Vanessa

    2007-01-01

    A process, and a benchtop-scale apparatus for implementing the process, have been developed to detect proteins associated with specific microbes in water. The process and apparatus may also be useful for detection of proteins in other, more complex liquids. There may be numerous potential applications, including monitoring lakes and streams for contamination, testing of blood and other bodily fluids in medical laboratories, and testing for microbial contamination of liquids in restaurants and industrial food-processing facilities. A sample can be prepared and analyzed by use of this process and apparatus within minutes, whereas an equivalent analysis performed by use of other processes and equipment can often take hours to days. The process begins with the conjugation of near-infrared-fluorescent dyes to antibodies that are specific to a particular protein. Initially, the research has focused on using near-infrared dyes to detect antigens or associated proteins in solution, which has proven successful vs. microbial cells, and streamlining the technique in use for surface protein detection on microbes would theoretically render similar results. However, it is noted that additional work is needed to transition protein-based techniques to microbial cell detection. Consequently, multiple such dye/antibody pairs could be prepared to enable detection of multiple selected microbial species, using a different dye for each species. When excited by near-infrared light of a suitable wavelength, each dye fluoresces at a unique longer wavelength that differs from those of the other dyes, enabling discrimination among the various species. In initial tests, the dye/antibody pairs are mixed into a solution suspected of containing the selected proteins, causing the binding of the dye/antibody pairs to such suspect proteins that may be present. The solution is then run through a microcentrifuge that includes a membrane that acts as a filter in that it retains the dye/antibody/protein complexes while allowing any remaining unbound dye/antibody pairs to flow away. The retained dye/antibody/protein complexes are transferred to a cuvette, wherein they are irradiated with light from a miniature near-infrared laser delivered via a fiber-optic cable. The resulting fluorescence from the dye(s) is measured by use of a miniature spectrometer, the output of which is digitized, then analyzed by laptop computer. The software running in the computer identifies the protein species by the wavelengths of their spectral peaks and determines the amounts of the proteins, and thus, one day, microbes of the various species from the intensities of the peaks. The abovementioned removal of the unbound dye/antibody pairs during centrifugation prevents false positive readings. The process proves successful in detecting proteins in solution and thus can now be employed for use in microbe detection.

  9. Exploring the repeat protein universe through computational protein design.

    PubMed

    Brunette, T J; Parmeggiani, Fabio; Huang, Po-Ssu; Bhabha, Gira; Ekiert, Damian C; Tsutakawa, Susan E; Hura, Greg L; Tainer, John A; Baker, David

    2015-12-24

    A central question in protein evolution is the extent to which naturally occurring proteins sample the space of folded structures accessible to the polypeptide chain. Repeat proteins composed of multiple tandem copies of a modular structure unit are widespread in nature and have critical roles in molecular recognition, signalling, and other essential biological processes. Naturally occurring repeat proteins have been re-engineered for molecular recognition and modular scaffolding applications. Here we use computational protein design to investigate the space of folded structures that can be generated by tandem repeating a simple helix-loop-helix-loop structural motif. Eighty-three designs with sequences unrelated to known repeat proteins were experimentally characterized. Of these, 53 are monomeric and stable at 95?°C, and 43 have solution X-ray scattering spectra consistent with the design models. Crystal structures of 15 designs spanning a broad range of curvatures are in close agreement with the design models with root mean square deviations ranging from 0.7 to 2.5?Ĺ. Our results show that existing repeat proteins occupy only a small fraction of the possible repeat protein sequence and structure space and that it is possible to design novel repeat proteins with precisely specified geometries, opening up a wide array of new possibilities for biomolecular engineering. PMID:26675729

  10. Novel computational methods to design protein-protein interactions

    NASA Astrophysics Data System (ADS)

    Zhou, Alice Qinhua; O'Hern, Corey; Regan, Lynne

    2014-03-01

    Despite the abundance of structural data, we still cannot accurately predict the structural and energetic changes resulting from mutations at protein interfaces. The inadequacy of current computational approaches to the analysis and design of protein-protein interactions has hampered the development of novel therapeutic and diagnostic agents. In this work, we apply a simple physical model that includes only a minimal set of geometrical constraints, excluded volume, and attractive van der Waals interactions to 1) rank the binding affinity of mutants of tetratricopeptide repeat proteins with their cognate peptides, 2) rank the energetics of binding of small designed proteins to the hydrophobic stem region of the influenza hemagglutinin protein, and 3) predict the stability of T4 lysozyme and staphylococcal nuclease mutants. This work will not only lead to a fundamental understanding of protein-protein interactions, but also to the development of efficient computational methods to rationally design protein interfaces with tunable specificity and affinity, and numerous applications in biomedicine. NSF DMR-1006537, PHY-1019147, Raymond and Beverly Sackler Institute for Biological, Physical and Engineering Sciences, and Howard Hughes Medical Institute.

  11. DONUT results

    SciTech Connect

    Furukawa, Tomoko

    2008-02-21

    The DONUT experiment succeeded in observing tau-neutrino CC interactions for the first time in 2000. The analysis using total sample is presented in this paper, based on 3.5x10{sup 17} protons on target. The number of identified {nu}{sub {tau}} CC interactions is 9 from 581 neutrino interactions located in the emulsion. The result of the first measurement of {nu}{sub {tau}} CC cross section is consistent with the expectation from the Standard Model.

  12. Protein Chemistry Core

    Cancer.gov

    The Protein Chemistry Core has expertise in the analysis of protein modifications via radioactive and non-radioactive methods.  The core provides the following services to the NCI community:  Protein and peptide sequencing Protein phosphorylation site map

  13. TGF-beta signaling proteins and the Protein Ontology

    PubMed Central

    Arighi, Cecilia N; Liu, Hongfang; Natale, Darren A; Barker, Winona C; Drabkin, Harold; Blake, Judith A; Smith, Barry; Wu, Cathy H

    2009-01-01

    Background The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or post-translational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. Results PRO is manually curated on the basis of PrePRO, an automatically generated file with content derived from standard protein data sources. Manual curation ensures that the treatment of the protein classes and the internal and external relationships conform to the PRO framework. The current release of PRO is based upon experimental data from mouse and human proteins wherein equivalent protein forms are represented by single terms. In addition to the PRO ontology, the annotation of PRO terms is released as a separate PRO association file, which contains, for each given PRO term, an annotation from the experimentally characterized sub-types as well as the corresponding database identifiers and sequence coordinates. The annotations are added in the form of relationship to other ontologies. Whenever possible, equivalent forms in other species are listed to facilitate cross-species comparison. Splice and allelic variants, gene fusion products and modified protein forms are all represented as entities in the ontology. Therefore, PRO provides for the representation of protein entities and a resource for describing the associated data. This makes PRO useful both for proteomics studies where isoforms and modified forms must be differentiated, and for studies of biological pathways, where representations need to take account of the different ways in which the cascade of events may depend on specific protein modifications. Conclusion PRO provides a framework for the formal representation of protein classes and protein forms in the OBO Foundry. It is designed to enable data retrieval and integration and machine reasoning at the molecular level of proteins, thereby facilitating cross-species comparisons, pathway analysis, disease modeling and the generation of new hypotheses. PMID:19426460

  14. Protein-protein and protein-salt interactions in aqueous protein solutions containing concentrated electrolytes

    SciTech Connect

    Curtis, R.A.; Blanch, H.W.; Prausnitz, J.M.

    1998-01-05

    Protein-protein and protein-salt interactions have been obtained for ovalbumin in solutions of ammonium sulfate and for lysozyme in solutions of ammonium sulfate, sodium chloride, potassium isothiocyanate, and potassium chloride. The two-body interactions between ovalbumin molecules in concentrated ammonium-sulfate solutions can be described by the DLVO potentials plus a potential that accounts for the decrease in free volume available to the protein due to the presence of the salt ions. The interaction between ovalbumin and ammonium sulfate is unfavorable, reflecting the kosmotropic nature of sulfate anions. Lysozyme-lysozyme interactions cannot be described by the above potentials because anion binding to lysozyme alters these interactions. Lysozyme-isothiocyanate complexes are strongly attractive due to electrostatic interactions resulting from bridging by the isothiocyanate ion. Lysozyme-lysozyme interactions in sulfate solutions are more repulsive than expected, possibly resulting from a larger excluded volume of a lysozyme-sulfate bound complex or perhaps, hydration forces between the lysozyme-sulfate complexes.

  15. Protein Design Zhilei Chen

    E-print Network

    Zhao, Huimin

    Protein Design Zhilei Chen Center for Biophysics and Computational Biology, University of Illinois of Illinois, Urbana, Illinois, U.S.A. INTRODUCTION Protein design refers to the ability to alter protein structure to achieve the desired protein function. Of the two classes of proteins (binding proteins

  16. Health Benefits of Texturized Whey Proteins

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Whey proteins are an important class of food ingredients used in many functional foods to boost protein content. Using the extrusion texturization process to partially open the native globular structures of whey proteins changed their conformation to the molten globular state, resulting in a new cla...

  17. Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells

    PubMed Central

    Filteau, Marie; Leducq, Jean-Baptiste; Dubé, Alexandre K.; Landry, Christian R.

    2015-01-01

    Proteins are the building blocks, effectors and signal mediators of cellular processes. A protein’s function, regulation and localization often depend on its interactions with other proteins. Here, we describe a protocol for the yeast protein-fragment complementation assay (PCA), a powerful method to detect direct and proximal associations between proteins in living cells. The interaction between two proteins, each fused to a dihydrofolate reductase (DHFR) protein fragment, translates into growth of yeast strains in presence of the drug methotrexate (MTX). Differential fitness, resulting from different amounts of reconstituted DHFR enzyme, can be quantified on high-density colony arrays, allowing to differentiate interacting from non-interacting bait-prey pairs. The high-throughput protocol presented here is performed using a robotic platform that parallelizes mating of bait and prey strains carrying complementary DHFR-fragment fusion proteins and the survival assay on MTX. This protocol allows to systematically test for thousands of protein-protein interactions (PPIs) involving bait proteins of interest and offers several advantages over other PPI detection assays, including the study of proteins expressed from their endogenous promoters without the need for modifying protein localization and for the assembly of complex reporter constructs. PMID:25867901

  18. Mercury-binding proteins of Mytilus edulis

    SciTech Connect

    Roesijadi, G.; Morris, J.E.; Calabrese, A.

    1981-11-01

    Mytilus edulis possesses low molecular weight, mercury-binding proteins. The predominant protein isolated from gill tissue is enriched in cysteinyl residues (8%) and possesses an amino acid composition similar to cadmium-binding proteins of mussels and oysters. Continuous exposure of mussels to 5 ..mu..g/l mercury results in spillover of mercury from these proteins to high molecular weight proteins. Antibodies to these proteins have been isolated, and development of immunoassays is presently underway. Preliminary studies to determine whether exposure of adult mussels to mercury will result in induction of mercury-binding proteins in offspring suggest that such proteins occur in larvae although additional studies are indicated for a conclusive demonstration.

  19. Photolytic Crosslinking to Probe Protein-Protein and Protein-Matrix Interactions In Lyophilized Powders

    PubMed Central

    Iyer, Lavanya K.; Moorthy, Balakrishnan S.; Topp, Elizabeth M.

    2015-01-01

    Protein structure and local environment in lyophilized formulations were probed using high-resolution solid-state photolytic crosslinking with mass spectrometric analysis (ssPC-MS). In order to characterize structure and microenvironment, protein-protein, protein-excipient and protein-water interactions in lyophilized powders were identified. Myoglobin (Mb) was derivatized in solution with the heterobifunctional probe succinimidyl 4,4’-azipentanoate (SDA) and the structural integrity of the labeled protein (Mb-SDA) confirmed using CD spectroscopy and liquid chromatography / mass spectrometry (LC-MS). Mb-SDA was then formulated with and without excipients (raffinose, guanidine hydrochloride (Gdn HCl)) and lyophilized. The freeze-dried powder was irradiated with ultraviolet light at 365 nm for 30 min to produce crosslinked adducts that were analyzed at the intact protein level and after trypsin digestion. SDA-labeling produced Mb carrying up to 5 labels, as detected by LC-MS. Following lyophilization and irradiation, crosslinked peptide-peptide, peptide-water and peptide-raffinose adducts were detected. The exposure of Mb side chains to the matrix was quantified based on the number of different peptide-peptide, peptide-water and peptide-excipient adducts detected. In the absence of excipients, peptide-peptide adducts involving the CD, DE and EF loops and helix H were common. In the raffinose formulation, peptide-peptide adducts were more distributed throughout the molecule. The Gdn HCl formulation showed more protein-protein and protein-water adducts than the other formulations, consistent with protein unfolding and increased matrix interactions. The results demonstrate that ssPC-MS can be used to distinguish excipient effects and characterize the local protein environment in lyophilized formulations with high resolution. PMID:26204425

  20. Jesse Rinehart, PhD Proteins: Proteomics & Protein-Protein Interactions

    E-print Network

    Gerstein, Mark

    Jesse Rinehart, PhD Proteins: Proteomics & Protein-Protein Interactions Part I #12;DNA RNA PROTEIN Purification - Quantitative Proteomics · Applications - Representative Studies · Putting it all together.... - Databases & Pathways Proteins: Proteomics & Protein-Protein Interactions #12;Overview · Techniques

  1. Measurements of Protein Crystal Face Growth Rates

    NASA Technical Reports Server (NTRS)

    Gorti, S.

    2014-01-01

    Protein crystal growth rates will be determined for several hyperthermophile proteins.; The growth rates will be assessed using available theoretical models, including kinetic roughening.; If/when kinetic roughening supersaturations are established, determinations of protein crystal quality over a range of supersaturations will also be assessed.; The results of our ground based effort may well address the existence of a correlation between fundamental growth mechanisms and protein crystal quality.

  2. Conformational dynamics data bank: a database for conformational proteins and supramolecular protein assemblies

    E-print Network

    Kim, Do-Nyun

    The conformational dynamics data bank (CDDB, http://www.cdyn.org) is a database that aims to provide comprehensive results on the conformational dynamics of high molecular weight proteins and protein assemblies. Analysis ...

  3. Synthesis of milligram quantities of proteins using a reconstituted in vitro protein synthesis system.

    PubMed

    Kazuta, Yasuaki; Matsuura, Tomoaki; Ichihashi, Norikazu; Yomo, Tetsuya

    2014-11-01

    In this study, the amount of protein synthesized using an in vitro protein synthesis system composed of only highly purified components (the PURE system) was optimized. By varying the concentrations of each system component, we determined the component concentrations that result in the synthesis of 0.38 mg/mL green fluorescent protein (GFP) in batch mode and 3.8 mg/mL GFP in dialysis mode. In dialysis mode, protein concentrations of 4.3 and 4.4 mg/mL were synthesized for dihydrofolate reductase and ?-galactosidase, respectively. Using the optimized system, the synthesized protein represented 30% (w/w) of the total protein, which is comparable to the level of overexpressed protein in Escherichia coli cells. This optimized reconstituted in vitro protein synthesis system may potentially be useful for various applications, including in vitro directed evolution of proteins, artificial cell assembly, and protein structural studies. PMID:24880499

  4. Dietary protein to support muscle hypertrophy.

    PubMed

    van Loon, Luc J C; Gibala, Martin J

    2011-01-01

    Intact protein, protein hydrolysates, and free amino acids are popular ingredients in contemporary sports nutrition, and have been suggested to augment post-exercise recovery. Protein and/or amino acid ingestion stimulates skeletal muscle protein synthesis, inhibits protein breakdown and, as such, stimulates muscle protein accretion following resistance and endurance type exercise. This has been suggested to lead to a greater adaptive response to each successive exercise bout, resulting in more effective muscle reconditioning. Despite limited evidence, some basic guidelines can be defined regarding the preferred type, amount, and timing of dietary protein that should be ingested to maximize post-exercise muscle protein accretion. Whey protein seems most effective in stimulating muscle protein synthesis during acute post-exercise recovery. This is likely attributable to its rapid digestion and absorption kinetics and specific amino acid composition. Ingestion of approximately 20 g protein during and/or immediately after exercise is sufficient to maximize post-exercise muscle protein synthesis rates. Coingestion of a large amount of carbohydrate or free leucine is not warranted to further augment post- exercise muscle protein synthesis when ample protein is already ingested. Future research should focus on the relevance of the acute anabolic response following exercise to optimize the skeletal muscle adaptive response to exercise training. PMID:22301837

  5. Protein patterns and proteins that identify subtypes of glioblastoma multiforme.

    PubMed

    Furuta, Makoto; Weil, Robert J; Vortmeyer, Alexander O; Huang, Steve; Lei, Jingqi; Huang, Tai-Nan; Lee, Youn-Soo; Bhowmick, Deb A; Lubensky, Irina A; Oldfield, Edward H; Zhuang, Zhengping

    2004-09-01

    Glioblastoma multiforme (GBM) has been subdivided into two types based on clinical and genetic findings: primary tumors, which arise de novo, and secondary tumors, which progress from lower grade gliomas to GBMs. To analyse this dichotomy at the protein level, we employed selective tissue microdissection to obtain pure populations of tumor cells, which we studied using two-dimensional protein gel electrophoresis (2-DGE) and protein sequencing of select target proteins. Protein patterns were analysed in a blinded manner from the clinical and genetic data. 2-DGE clearly identified two distinct populations of tumors. 2-DGE was reproducible and reliable, as multiple samples analysed from the same patient gave identical results. In addition, we isolated and sequenced 11 proteins that were uniquely expressed in either the primary or the secondary GBMs, but not both. We demonstrate that specific proteomic patterns can be reproducibly identified by two-dimensional gel electrophoresis from limited numbers of selectively procured, microdissected tumor cells and that two patterns of GBMs, primary versus secondary, previously distinguished by clinical and genetic differences, can be recognized at the protein level. Proteins that are expressed distinctively may have important implications for the diagnosis, prognosis, and treatment of patients with GBM. PMID:15286718

  6. Length, protein protein interactions, and complexity

    NASA Astrophysics Data System (ADS)

    Tan, Taison; Frenkel, Daan; Gupta, Vishal; Deem, Michael W.

    2005-05-01

    The evolutionary reason for the increase in gene length from archaea to prokaryotes to eukaryotes observed in large-scale genome sequencing efforts has been unclear. We propose here that the increasing complexity of protein-protein interactions has driven the selection of longer proteins, as they are more able to distinguish among a larger number of distinct interactions due to their greater average surface area. Annotated protein sequences available from the SWISS-PROT database were analyzed for 13 eukaryotes, eight bacteria, and two archaea species. The number of subcellular locations to which each protein is associated is used as a measure of the number of interactions to which a protein participates. Two databases of yeast protein-protein interactions were used as another measure of the number of interactions to which each S. cerevisiae protein participates. Protein length is shown to correlate with both number of subcellular locations to which a protein is associated and number of interactions as measured by yeast two-hybrid experiments. Protein length is also shown to correlate with the probability that the protein is encoded by an essential gene. Interestingly, average protein length and number of subcellular locations are not significantly different between all human proteins and protein targets of known, marketed drugs. Increased protein length appears to be a significant mechanism by which the increasing complexity of protein-protein interaction networks is accommodated within the natural evolution of species. Consideration of protein length may be a valuable tool in drug design, one that predicts different strategies for inhibiting interactions in aberrant and normal pathways.

  7. The N and C Termini of ZO-1 Are Surrounded by Distinct Proteins and Functional Protein Networks*

    PubMed Central

    Van Itallie, Christina M.; Aponte, Angel; Tietgens, Amber Jean; Gucek, Marjan; Fredriksson, Karin; Anderson, James Melvin

    2013-01-01

    The proteins and functional protein networks of the tight junction remain incompletely defined. Among the currently known proteins are barrier-forming proteins like occludin and the claudin family; scaffolding proteins like ZO-1; and some cytoskeletal, signaling, and cell polarity proteins. To define a more complete list of proteins and infer their functional implications, we identified the proteins that are within molecular dimensions of ZO-1 by fusing biotin ligase to either its N or C terminus, expressing these fusion proteins in Madin-Darby canine kidney epithelial cells, and purifying and identifying the resulting biotinylated proteins by mass spectrometry. Of a predicted proteome of ?9000, we identified more than 400 proteins tagged by biotin ligase fused to ZO-1, with both identical and distinct proteins near the N- and C-terminal ends. Those proximal to the N terminus were enriched in transmembrane tight junction proteins, and those proximal to the C terminus were enriched in cytoskeletal proteins. We also identified many unexpected but easily rationalized proteins and verified partial colocalization of three of these proteins with ZO-1 as examples. In addition, functional networks of interacting proteins were tagged, such as the basolateral but not apical polarity network. These results provide a rich inventory of proteins and potential novel insights into functions and protein networks that should catalyze further understanding of tight junction biology. Unexpectedly, the technique demonstrates high spatial resolution, which could be generally applied to defining other subcellular protein compartmentalization. PMID:23553632

  8. Protein mediated membrane adhesion

    NASA Astrophysics Data System (ADS)

    Carlson, Andreas; Mahadevan, L.

    2015-05-01

    Adhesion in the context of mechanical attachment, signaling, and movement in cellular dynamics is mediated by the kinetic interactions between membrane-embedded proteins in an aqueous environment. Here, we present a minimal theoretical framework for the dynamics of membrane adhesion that accounts for the kinetics of protein binding, the elastic deformation of the membrane, and the hydrodynamics of squeeze flow in the membrane gap. We analyze the resulting equations using scaling estimates to characterize the spatiotemporal features of the adhesive patterning and corroborate them using numerical simulations. In addition to characterizing aspects of cellular dynamics, our results might also be applicable to a range of phenomena in physical chemistry and materials science where flow, deformation, and kinetics are coupled to each other in slender geometries.

  9. Protein accumulation and rumen stability of wheat ?-gliadin fusion proteins in tobacco and alfalfa.

    PubMed

    Sun, Xiaodong; Chi-Ham, Cecilia L; Cohen-Davidyan, Tamar; DeBen, Christopher; Getachow, Girma; DePeters, Edward; Putnam, Daniel; Bennett, Alan

    2015-09-01

    The nutritional value of various crops can be improved by engineering plants to produce high levels of proteins. For example, because methionine deficiency limits the protein quality of Medicago Sativa (alfalfa) forage, producing alfalfa plants that accumulate high levels of a methionine-rich protein could increase the nutritional value of that crop. We used three strategies in designing methionine-rich recombinant proteins that could accumulate to high levels in plants and thereby serve as candidates for improving the protein quality of alfalfa forage. In tobacco, two fusion proteins, ?-gliadin-?-zein and ?-?-zein, as well as ?-zein co-expressed with ?-zein, all formed protein bodies. However, the ?-gliadin-?-zein fusion protein accumulated to the highest level, representing up to 1.5% of total soluble protein (TSP) in one transformant. In alfalfa, ?-gliadin-?-zein accumulated to 0.2% of TSP, and in an in vitro rumen digestion assay, ?-gliadin-?-zein was more resistant to microbial degradation than Rubisco. Additionally, although it did not form protein bodies, a ?-gliadin-GFP fusion protein accumulated to much higher levels, 7% of TSP, than a recombinant protein comprised of an ER localization signal fused to GFP in tobacco. Based on our results, we conclude that ?-gliadin-?-zein is a potential candidate protein to use for enhancing methionine levels in plants and for improving rumen stability of forage protein. ?-gliadin fusion proteins may provide a general platform for increasing the accumulation of recombinant proteins in transgenic plants. PMID:25659597

  10. Text Mining for Protein Docking

    PubMed Central

    Badal, Varsha D.; Kundrotas, Petras J.; Vakser, Ilya A.

    2015-01-01

    The rapidly growing amount of publicly available information from biomedical research is readily accessible on the Internet, providing a powerful resource for predictive biomolecular modeling. The accumulated data on experimentally determined structures transformed structure prediction of proteins and protein complexes. Instead of exploring the enormous search space, predictive tools can simply proceed to the solution based on similarity to the existing, previously determined structures. A similar major paradigm shift is emerging due to the rapidly expanding amount of information, other than experimentally determined structures, which still can be used as constraints in biomolecular structure prediction. Automated text mining has been widely used in recreating protein interaction networks, as well as in detecting small ligand binding sites on protein structures. Combining and expanding these two well-developed areas of research, we applied the text mining to structural modeling of protein-protein complexes (protein docking). Protein docking can be significantly improved when constraints on the docking mode are available. We developed a procedure that retrieves published abstracts on a specific protein-protein interaction and extracts information relevant to docking. The procedure was assessed on protein complexes from Dockground (http://dockground.compbio.ku.edu). The results show that correct information on binding residues can be extracted for about half of the complexes. The amount of irrelevant information was reduced by conceptual analysis of a subset of the retrieved abstracts, based on the bag-of-words (features) approach. Support Vector Machine models were trained and validated on the subset. The remaining abstracts were filtered by the best-performing models, which decreased the irrelevant information for ~ 25% complexes in the dataset. The extracted constraints were incorporated in the docking protocol and tested on the Dockground unbound benchmark set, significantly increasing the docking success rate. PMID:26650466

  11. Computational approaches for detecting protein complexes from protein interaction networks: a survey

    PubMed Central

    2010-01-01

    Background Most proteins form macromolecular complexes to perform their biological functions. However, experimentally determined protein complex data, especially of those involving more than two protein partners, are relatively limited in the current state-of-the-art high-throughput experimental techniques. Nevertheless, many techniques (such as yeast-two-hybrid) have enabled systematic screening of pairwise protein-protein interactions en masse. Thus computational approaches for detecting protein complexes from protein interaction data are useful complements to the limited experimental methods. They can be used together with the experimental methods for mapping the interactions of proteins to understand how different proteins are organized into higher-level substructures to perform various cellular functions. Results Given the abundance of pairwise protein interaction data from high-throughput genome-wide experimental screenings, a protein interaction network can be constructed from protein interaction data by considering individual proteins as the nodes, and the existence of a physical interaction between a pair of proteins as a link. This binary protein interaction graph can then be used for detecting protein complexes using graph clustering techniques. In this paper, we review and evaluate the state-of-the-art techniques for computational detection of protein complexes, and discuss some promising research directions in this field. Conclusions Experimental results with yeast protein interaction data show that the interaction subgraphs discovered by various computational methods matched well with actual protein complexes. In addition, the computational approaches have also improved in performance over the years. Further improvements could be achieved if the quality of the underlying protein interaction data can be considered adequately to minimize the undesirable effects from the irrelevant and noisy sources, and the various biological evidences can be better incorporated into the detection process to maximize the exploitation of the increasing wealth of biological knowledge available. PMID:20158874

  12. [ALR, the multifunctional protein].

    PubMed

    Balogh, Tibor; Szarka, András

    2015-03-29

    ALR is a mystic protein. It has a so called "long" 22 kDa and a "short" 15 kDa forms. It has been described after partial hepatectomy and it has just been considered as a key protein of liver regeneration. At the beginning of the 21st century it has been revealed that the "long" form is localized in the mitochondrial intermembrane space and it is an element of the mitochondrial protein import and disulphide relay system. Several proteins of the substrates of the mitochondrial disulphide relay system are necessary for the proper function of the mitochondria, thus any mutation of the ALR gene leads to mitochondrial diseases. The "short" form of ALR functions as a secreted extracellular growth factor and it promotes the protection, regeneration and proliferation of hepatocytes. The results gained on the recently generated conditional ALR mutant mice suggest that ALR can play an important role in the pathogenesis of alcoholic and non-alcoholic steatosis. Since the serum level of ALR is modified in several liver diseases it can be a promising marker molecule in laboratory diagnostics. PMID:25796277

  13. Dynamics of protein conformations

    NASA Astrophysics Data System (ADS)

    Stepanova, Maria

    2010-10-01

    A novel theoretical methodology is introduced to identify dynamic structural domains and analyze local flexibility in proteins. The methodology employs a multiscale approach combining identification of essential collective coordinates based on the covariance analysis of molecular dynamics trajectories, construction of the Mori projection operator with these essential coordinates, and analysis of the corresponding generalized Langevin equations [M.Stepanova, Phys.Rev.E 76(2007)051918]. Because the approach employs a rigorous theory, the outcomes are physically transparent: the dynamic domains are associated with regions of relative rigidity in the protein, whereas off-domain regions are relatively soft. This also allows scoring the flexibility in the macromolecule with atomic-level resolution [N.Blinov, M.Berjanskii, D.S.Wishart, and M.Stepanova, Biochemistry, 48(2009)1488]. The applications include the domain coarse-graining and characterization of conformational stability in protein G and prion proteins. The results are compared with published NMR experiments. Potential applications for structural biology, bioinformatics, and drug design are discussed.

  14. The late addition of core lipids to nascent apolipoprotein B100, resulting in the assembly and secretion of triglyceride-rich lipoproteins, is independent of both microsomal triglyceride transfer protein activity and new triglyceride synthesis.

    PubMed

    Pan, Meihui; Liang Js, Jun-shan; Fisher, Edward A; Ginsberg, Henry N

    2002-02-01

    Although microsomal triglyceride transfer protein (MTP) and newly synthesized triglyceride (TG) are critical for co-translational targeting of apolipoprotein B (apoB100) to lipoprotein assembly in hepatoma cell lines, their roles in the later stages of lipoprotein assembly remain unclear. Using N-acetyl-Leu-Leu-norleucinal to prevent proteasomal degradation, HepG2 cells were radiolabeled and chased for 0-90 min (chase I). The medium was changed and cells chased for another 150 min (chase II) in the absence (control) or presence of Pfizer MTP inhibitor CP-10447 (CP). As chase I was extended, inhibition of apoB100 secretion by CP during chase II decreased from 75.9% to only 15% of control (no CP during chase II). Additional studies were conducted in which chase I was either 0 or 90 min, and chase II was in the presence of [(3)H]glycerol and either BSA (control), CP (inhibits both MTP activity and TG synthesis),BMS-1976360-1) (BMS) (inhibits only MTP activity), or triacsin C (TC) (inhibits only TG synthesis). When chase I was 0 min, CP, BMS, and TC reduced apoB100 secretion during chase II by 75.3, 73.9, and 53.9%. However, when chase I was 90 min, those agents reduced apoB100 secretion during chase II by only 16.0, 19.2, and 13.9%. Of note, all three inhibited secretion of newly synthesized TG during chase II by 80, 80, and 40%, whether chase I was 0 or 90 min. In both HepG2 cells and McA-RH7777 cells, if chase I was at least 60 min, inhibition of TG synthesis and/or MTP activity did not affect the density of secreted apoB100-lipoproteins under basal conditions. Oleic acid increased secretion of TG-enriched apoB100-lipoproteins similarly in the absence or presence of either of CP, BMS, or TC. We conclude that neither MTP nor newly synthesized TG is necessary for the later stages of apoB100-lipoprotein assembly and secretion in either HepG2 or McA-RH7777 cells. PMID:11704664

  15. Protein compressibility, dynamics, and pressure.

    PubMed Central

    Kharakoz, D P

    2000-01-01

    The relationship between the elastic and dynamic properties of native globular proteins is considered on the basis of a wide set of reported experimental data. The formation of a small cavity, capable of accommodating water, in the protein interior is associated with the elastic deformation, whose contribution to the free energy considerably exceeds the heat motion energy. Mechanically, the protein molecule is a highly nonlinear system. This means that its compressibility sharply decreases upon compression. The mechanical nonlinearity results in the following consequences related to the intramolecular dynamics of proteins: 1) The sign of the electrostriction effect in the protein matrix is opposite that observed in liquids-this is an additional indication that protein behaves like a solid particle. 2) The diffusion of an ion from the solvent to the interior of a protein should depend on pressure nonmonotonically: at low pressure diffusion is suppressed, while at high pressure it is enhanced. Such behavior is expected to display itself in any dynamic process depending on ion diffusion. Qualitative and quantitative expectations ensuing from the mechanical properties are concordant with the available experimental data on hydrogen exchange in native proteins at ambient and high pressure. PMID:10866977

  16. Water at interface with proteins

    E-print Network

    Giancarlo Franzese; Valentino Bianco; Svilen Iskrov

    2010-12-07

    Water is essential for the activity of proteins. However, the effect of the properties of water on the behavior of proteins is only partially understood. Recently, several experiments have investigated the relation between the dynamics of the hydration water and the dynamics of protein. These works have generated a large amount of data whose interpretation is debated. New experiments measure the dynamics of water at low temperature on the surface of proteins, finding a qualitative change (crossover) that might be related to the slowing down and stop of the protein's activity (protein glass transition), possibly relevant for the safe preservation of organic material at low temperature. To better understand the experimental data several scenarios have been discussed. Here, we review these experiments and discuss their interpretations in relation with the anomalous properties of water. We summarize the results for the thermodynamics and dynamics of supercooled water at an interface. We consider also the effect of water on protein stability, making a step in the direction of understanding, by means of Monte Carlo simulations and theoretical calculations, how the interplay of water cooperativity and hydrogen bonds interfacial strengthening affects the protein cold denaturation.

  17. HMPAS: Human Membrane Protein Analysis System

    PubMed Central

    2013-01-01

    Background Membrane proteins perform essential roles in diverse cellular functions and are regarded as major pharmaceutical targets. The significance of membrane proteins has led to the developing dozens of resources related with membrane proteins. However, most of these resources are built for specific well-known membrane protein groups, making it difficult to find common and specific features of various membrane protein groups. Methods We collected human membrane proteins from the dispersed resources and predicted novel membrane protein candidates by using ortholog information and our membrane protein classifiers. The membrane proteins were classified according to the type of interaction with the membrane, subcellular localization, and molecular function. We also made new feature dataset to characterize the membrane proteins in various aspects including membrane protein topology, domain, biological process, disease, and drug. Moreover, protein structure and ICD-10-CM based integrated disease and drug information was newly included. To analyze the comprehensive information of membrane proteins, we implemented analysis tools to identify novel sequence and functional features of the classified membrane protein groups and to extract features from protein sequences. Results We constructed HMPAS with 28,509 collected known membrane proteins and 8,076 newly predicted candidates. This system provides integrated information of human membrane proteins individually and in groups organized by 45 subcellular locations and 1,401 molecular functions. As a case study, we identified associations between the membrane proteins and diseases and present that membrane proteins are promising targets for diseases related with nervous system and circulatory system. A web-based interface of this system was constructed to facilitate researchers not only to retrieve organized information of individual proteins but also to use the tools to analyze the membrane proteins. Conclusions HMPAS provides comprehensive information about human membrane proteins including specific features of certain membrane protein groups. In this system, user can acquire the information of individual proteins and specified groups focused on their conserved sequence features, involved cellular processes, and diseases. HMPAS may contribute as a valuable resource for the inference of novel cellular mechanisms and pharmaceutical targets associated with the human membrane proteins. HMPAS is freely available at http://fcode.kaist.ac.kr/hmpas. PMID:24564858

  18. Solubility of commercial milk protein concentrates and milk protein isolates.

    PubMed

    Sikand, V; Tong, P S; Roy, S; Rodriguez-Saona, L E; Murray, B A

    2011-12-01

    High-protein milk protein concentrate (MPC) and milk protein isolate (MPI) powders may have lower solubility than low-protein MPC powders, but information is limited on MPC solubility. Our objectives in this study were to (1) characterize the solubility of commercially available powder types with differing protein contents such as MPC40, MPC80, and MPI obtained from various manufacturers (sources), and (2) determine if such differences could be associated with differences in mineral, protein composition, and conformational changes of the powders. To examine possible predictors of solubility as measured by percent suspension stability (%SS), mineral analysis, Fourier transform infrared (FTIR) spectroscopy, and quantitative protein analysis by HPLC was performed. After accounting for overall differences between powder types, %SS was found to be strongly associated with the calcium, magnesium, phosphorus, and sodium content of the powders. The FTIR score plots were in agreement with %SS results. A principal component analysis of FTIR spectra clustered the highly soluble MPC40 separately from the rest of samples. Furthermore, 2 highly soluble MPI samples were clustered separately from the rest of the MPC80 and MPI samples. We found that the 900 to 1,200 cm?ą region exhibited the highest discriminating power, with dominant bands at 1,173 and 968 cm?ą, associated with phosphate vibrations. The 2 highly soluble MPI powders were observed to have lower ?-casein and ?-(S1)-casein contents and slightly higher whey protein contents than the other powders. The differences in the solubility of MPC and MPI were associated with a difference in mineral composition, which may be attributed to differences in processing conditions. Additional studies on the role of minerals composition on MPC80 solubility are warranted. Such a study would provide a greater understanding of factors associated with differences in solubility and can provide insight on methods to improve solubility of high-protein milk protein concentrates. PMID:22118108

  19. Electrostatic design of protein-protein association rates.

    PubMed

    Schreiber, Gideon; Shaul, Yossi; Gottschalk, Kay E

    2006-01-01

    De novo design and redesign of proteins and protein complexes have made promising progress in recent years. Here, we give an overview of how to use available computer-based tools to design proteins to bind faster and tighter to their protein-complex partner by electrostatic optimization between the two proteins. Electrostatic optimization is possible because of the simple relation between the Debye-Huckel energy of interaction between a pair of proteins and their rate of association. This can be used for rapid, structure-based calculations of the electrostatic attraction between the two proteins in the complex. Using these principles, we developed two computer programs that predict the change in k(on), and as such the affinity, on introducing charged mutations. The two programs have a web interface that is available at www.weizmann.ac.il/home/bcges/PARE.html and http://bip.weizmann.ac.il/hypare. When mutations leading to charge optimization are introduced outside the physical binding site, the rate of dissociation is unchanged and therefore the change in k(on) parallels that of the affinity. This design method was evaluated on a number of different protein complexes resulting in binding rates and affinities of hundreds of fold faster and tighter compared to wild type. In this chapter, we demonstrate the procedure and go step by step over the methodology of using these programs for protein-association design. Finally, the way to easily implement the principle of electrostatic design for any protein complex of choice is shown. PMID:16957340

  20. Evolutionary optimization of protein folding.

    PubMed

    Debčs, Cédric; Wang, Minglei; Caetano-Anollés, Gustavo; Gräter, Frauke

    2013-01-01

    Nature has shaped the make up of proteins since their appearance, [Formula: see text]3.8 billion years ago. However, the fundamental drivers of structural change responsible for the extraordinary diversity of proteins have yet to be elucidated. Here we explore if protein evolution affects folding speed. We estimated folding times for the present-day catalog of protein domains directly from their size-modified contact order. These values were mapped onto an evolutionary timeline of domain appearance derived from a phylogenomic analysis of protein domains in 989 fully-sequenced genomes. Our results show a clear overall increase of folding speed during evolution, with known ultra-fast downhill folders appearing rather late in the timeline. Remarkably, folding optimization depends on secondary structure. While alpha-folds showed a tendency to fold faster throughout evolution, beta-folds exhibited a trend of folding time increase during the last [Formula: see text]1.5 billion years that began during the "big bang" of domain combinations. As a consequence, these domain structures are on average slow folders today. Our results suggest that fast and efficient folding of domains shaped the universe of protein structure. This finding supports the hypothesis that optimization of the kinetic and thermodynamic accessibility of the native fold reduces protein aggregation propensities that hamper cellular functions. PMID:23341762

  1. Protein imprinting in polyacrylamide-based gels.

    PubMed

    Zayats, Maya; Brenner, Andrew J; Searson, Peter C

    2014-10-01

    Protein imprinting in hydrogels is a method to produce materials capable of selective recognition and capture of a target protein. Here we report on the imprinting of fluorescently-labeled maltose binding protein (MBP) in acrylamide (AAm)/N-isopropylacrylamide (NIPAm) hydrogels. The targeting efficiency and selectivity of protein recognition is usually characterized by the imprinting factor, which in the simplest case is the ratio of protein uptake in an imprinted film divided by the uptake by the corresponding non-imprinted film. Our objective in this work is to study the dynamics of protein binding and elution in imprinted and non-imprinted films to elucidate the processes that control protein recognition. Protein elution from imprinted and non-imprinted films suggests that imprinting results in sites with a distribution of binding energies, and that only a relatively small fraction of these sites exhibit strong binding. PMID:25034963

  2. Protein imprinting in polyacrylamide-based gels

    PubMed Central

    Zayats, Maya; Brenner, Andrew J.; Searson, Peter C.

    2015-01-01

    Protein imprinting in hydrogels is a method to produce materials capable of selective recognition and capture of a target protein. Here we report on the imprinting of fluorescently-labeled maltose binding protein (MBP) in acrylamide (AAm)/N-isopropylacrylamide (NIPAm) hydrogels. The targeting efficiency and selectivity of protein recognition is usually characterized by the imprinting factor, which in the simplest case is the ratio of protein uptake in an imprinted film divided by the uptake by the corresponding non-imprinted film. Our objective in this work is to study the dynamics of protein binding and elution in imprinted and non-imprinted films to elucidate the processes that control protein recognition. Protein elution from imprinted and non-imprinted films suggests that imprinting results in sites with a distribution of binding energies, and that only a relatively small fraction of these sites exhibit strong binding. PMID:25034963

  3. Distinguishing Proteins From Arbitrary Amino Acid Sequences

    PubMed Central

    Yau, Stephen S.-T.; Mao, Wei-Guang; Benson, Max; He, Rong Lucy

    2015-01-01

    What kinds of amino acid sequences could possibly be protein sequences? From all existing databases that we can find, known proteins are only a small fraction of all possible combinations of amino acids. Beginning with Sanger's first detailed determination of a protein sequence in 1952, previous studies have focused on describing the structure of existing protein sequences in order to construct the protein universe. No one, however, has developed a criteria for determining whether an arbitrary amino acid sequence can be a protein. Here we show that when the collection of arbitrary amino acid sequences is viewed in an appropriate geometric context, the protein sequences cluster together. This leads to a new computational test, described here, that has proved to be remarkably accurate at determining whether an arbitrary amino acid sequence can be a protein. Even more, if the results of this test indicate that the sequence can be a protein, and it is indeed a protein sequence, then its identity as a protein sequence is uniquely defined. We anticipate our computational test will be useful for those who are attempting to complete the job of discovering all proteins, or constructing the protein universe. PMID:25609314

  4. Graph pyramids for protein function prediction

    PubMed Central

    2015-01-01

    Background Uncovering the hidden organizational characteristics and regularities among biological sequences is the key issue for detailed understanding of an underlying biological phenomenon. Thus pattern recognition from nucleic acid sequences is an important affair for protein function prediction. As proteins from the same family exhibit similar characteristics, homology based approaches predict protein functions via protein classification. But conventional classification approaches mostly rely on the global features by considering only strong protein similarity matches. This leads to significant loss of prediction accuracy. Methods Here we construct the Protein-Protein Similarity (PPS) network, which captures the subtle properties of protein families. The proposed method considers the local as well as the global features, by examining the interactions among 'weakly interacting proteins' in the PPS network and by using hierarchical graph analysis via the graph pyramid. Different underlying properties of the protein families are uncovered by operating the proposed graph based features at various pyramid levels. Results Experimental results on benchmark data sets show that the proposed hierarchical voting algorithm using graph pyramid helps to improve computational efficiency as well the protein classification accuracy. Quantitatively, among 14,086 test sequences, on an average the proposed method misclassified only 21.1 sequences whereas baseline BLAST score based global feature matching method misclassified 362.9 sequences. With each correctly classified test sequence, the fast incremental learning ability of the proposed method further enhances the training model. Thus it has achieved more than 96% protein classification accuracy using only 20% per class training data. PMID:26044522

  5. Shotgun protein sequencing.

    SciTech Connect

    Faulon, Jean-Loup Michel; Heffelfinger, Grant S.

    2009-06-01

    A novel experimental and computational technique based on multiple enzymatic digestion of a protein or protein mixture that reconstructs protein sequences from sequences of overlapping peptides is described in this SAND report. This approach, analogous to shotgun sequencing of DNA, is to be used to sequence alternative spliced proteins, to identify post-translational modifications, and to sequence genetically engineered proteins.

  6. Protein Crystal Based Nanomaterials

    NASA Technical Reports Server (NTRS)

    Bell, Jeffrey A.; VanRoey, Patrick

    2001-01-01

    This is the final report on a NASA Grant. It concerns a description of work done, which includes: (1) Protein crystals cross-linked to form fibers; (2) Engineering of protein to favor crystallization; (3) Better knowledge-based potentials for protein-protein contacts; (4) Simulation of protein crystallization.

  7. Association of bovine ?-casein protein variant I with milk production and milk protein composition.

    PubMed

    Visker, M H P W; Dibbits, B W; Kinders, S M; van Valenberg, H J F; van Arendonk, J A M; Bovenhuis, H

    2011-04-01

    The aim of this study was to detect new polymorphisms in the bovine ?-casein (?-CN) gene and to evaluate association of (new) ?-CN protein variants with milk production traits and milk protein composition. Screening of the ?-CN gene in genomic DNA from 72 Holstein Friesian (HF) bulls resulted in detection of 19 polymorphisms and revealed the presence of ?-CN protein variant I in the Dutch HF population. Studies of association of ?-CN protein variants with milk composition usually do not discriminate protein variant I from variant A2. Association of ?-CN protein variants with milk composition was studied in 1857 first-lactation HF cows and showed that associations of protein variants A2 and I were quite different for several traits. ?-CN protein variant I was significantly associated with protein percentage and protein yield, and with ?s1 -casein (?s1 -CN), ?s2 -casein (?s2 -CN), ?-casein (?-CN), ?-lactalbumin (?-LA), ?-lactoglobulin (?-LG), casein index and casein yield. Inferring ?-?-CN haplotypes showed that ?-CN protein variant I occurred only with ?-CN variant B. Consequently, associations of ?-?-CN haplotype IB with protein percentage, ?-CN, ?-LA, ?-LG and casein index are likely resulting from associations of ?-CN protein variant B, while associations of ?-?-CN haplotype IB with ?s1 -CN and ?s2 -CN seem to be resulting from associations of ?-CN variant I. PMID:24725229

  8. An ontology-based search engine for protein-protein interactions

    PubMed Central

    2010-01-01

    Background Keyword matching or ID matching is the most common searching method in a large database of protein-protein interactions. They are purely syntactic methods, and retrieve the records in the database that contain a keyword or ID specified in a query. Such syntactic search methods often retrieve too few search results or no results despite many potential matches present in the database. Results We have developed a new method for representing protein-protein interactions and the Gene Ontology (GO) using modified Gödel numbers. This representation is hidden from users but enables a search engine using the representation to efficiently search protein-protein interactions in a biologically meaningful way. Given a query protein with optional search conditions expressed in one or more GO terms, the search engine finds all the interaction partners of the query protein by unique prime factorization of the modified Gödel numbers representing the query protein and the search conditions. Conclusion Representing the biological relations of proteins and their GO annotations by modified Gödel numbers makes a search engine efficiently find all protein-protein interactions by prime factorization of the numbers. Keyword matching or ID matching search methods often miss the interactions involving a protein that has no explicit annotations matching the search condition, but our search engine retrieves such interactions as well if they satisfy the search condition with a more specific term in the ontology. PMID:20122195

  9. De novo protein design: how do we expand into the universe of possible protein structures?

    PubMed

    Woolfson, Derek N; Bartlett, Gail J; Burton, Antony J; Heal, Jack W; Niitsu, Ai; Thomson, Andrew R; Wood, Christopher W

    2015-08-01

    Protein scientists are paving the way to a new phase in protein design and engineering. Approaches and methods are being developed that could allow the design of proteins beyond the confines of natural protein structures. This possibility of designing entirely new proteins opens new questions: What do we build? How do we build into protein-structure space where there are few, if any, natural structures to guide us? To what uses can the resulting proteins be put? And, what, if anything, does this pursuit tell us about how natural proteins fold, function and evolve? We describe the origins of this emerging area of fully de novo protein design, how it could be developed, where it might lead, and what challenges lie ahead. PMID:26093060

  10. Small Water Islands in Proteins

    NASA Astrophysics Data System (ADS)

    Helms, V.; Wade, R. C.; McCammon, J. A.

    1998-03-01

    Proteins often contain water-filled cavities. Their presence may have functional reasons or may be related to protein folding. In any case, they are integral parts of the protein. Here, results from molecular dynamics simulations for two systems are presented. First, we analyzed the hydration of an empty buried enzyme active site, cytochrome P450cam. A hydration free energy landscape was obtained by calculating free energy differences for hydrating the active site with 5 to 8 water molecules. In agreement with the crystal structure and with experiments performed under high hydrostatic pressure, 6 water molecules were found to be most favourable thermodynamically [Helms & Wade, Proteins, submited]. Long-lived hydrogen bond networks exist between the water molecules in the active site and result in a significant ordering. Secondly, results are presented from 5 simulations of green fluorescent protein (GFP) of 1 ns length each. The crystal structures of different forms of GFP contain a cluster of five water molecules next to the chromophore. The water cluster seems to play a crucial part in allowing the protein to switch between a fluorescent and a dark state [Dickson et al., Nature, 388, 385-8]. In the simulations, the water molecules are again strongly ordered by a long-lived hydrogen bond network. Both scenarios are discussed in the context of bulk liquid water.

  11. Geometrical aspects of protein folding

    E-print Network

    Jay Banavar; Amos Maritan; Cristian Micheletti; Flavio Seno

    2001-05-10

    These lectures will address two questions. Is there a simple variational principle underlying the existence of secondary motifs in the native state of proteins? Is there a general approach which can qualitatively capture the salient features of the folding process and which may be useful for interpreting and guiding experiments? Here, we present three different approaches to the first question, which demonstrate the key role played by the topology of the native state of proteins. The second question pertaining to the folding dynamics of proteins remains a challenging problem -- a detailed description capturing the interactions between amino acids among each other and with the solvent is a daunting task. We address this issue building on the lessons learned in tackling the first question and apply the resulting method to the folding of various proteins including HIV protease and membrane proteins. The results that will be presented open a fascinating perspective: the two questions appear to be intimately related. The variety of results reported here all provide evidence in favour of the special criteria adopted by nature in the selection of viable protein folds, ranging from optimal compactness to maximum dynamical and geometrical accessibility of the native states.

  12. Conformational search of Proteins and Protein Loops

    E-print Network

    Venkataramani, Ranjitha

    2008-02-26

    This thesis focuses on understanding the structure and dynamics of proteins using simulations. The main system of interest in our case was cytochrome b5, an electron transport protein, which exists in both Microsomal and Outer Mitochondrial isoforms...

  13. Comparative effects of selenite and selenate on nitrate assimilation in barley seedlings

    NASA Technical Reports Server (NTRS)

    Aslam, M.; Harbit, K. B.; Huffaker, R. C.

    1990-01-01

    The effect of SeO3= and SeO4= on NO3- assimilation in 8-d-old barley (Hordeum vulgare L.) seedlings was studied over a 24-h period. Selenite at 0.1 mol m-3 in the uptake solutions severely inhibited the induction of NO3- uptake and active nitrate reductases. Selenate, at 1.0 mol m-3 in the nutrient solution, had little effect on induction of activities of these systems until after 12 h; however, when the seedlings were pretreated with 1.0 mol m-3 SeO4= for 24 h, subsequent NO3- uptake from SeO4(=) -free solutions was inhibited about 60%. Sulphate partially alleviated the inhibitory effect of SeO3= when supplied together in the ambient solutions, but had no effect in seedlings pretreated with SeO3=. By contrast, SO4= partially alleviated the inhibitory effect of SeO4= even in seedlings pretreated with SeO4=. Since uptake of NO3- by intact seedlings was also inhibited by SO3=, the percentage of the absorbed NO3- that was reduced was not affected. By contrast, SeO4=, which affected NO3- uptake much less, inhibited the percentage reduced of that absorbed. However, when supplied to detached leaves, both SeO3= and SeO4= inhibited the in vivo reduction of NO3- as well as induction of nitrate reductase and nitrite reductase activities. Selenite was more inhibitory than SeO4= ; approximately a five to 10 times higher concentration of SeO4= than SeO3= was required to achieve similar inhibition. In detached leaves, the inhibitory effect of both SeO3= and SeO4= on in vivo NO3- reduction as well as on the induction of nitrate reductase activity was partially alleviated by SO4=. The inhibitory effects of Se salts on the induction of the nitrite reductase were, however, completely alleviated by SO4=. The results show that in barley seedlings SeO3= is more toxic than SeO4=. The reduction of SeO4= to SeO3= may be a rate limiting step in causing Se toxicity.

  14. Electric field induced changes in protein conformation.

    PubMed

    Bekard, Innocent; Dunstan, Dave E

    2014-01-21

    The effect of a low strength oscillating electric field on the conformation of Bovine Serum Albumin (BSA) and Lysozyme in solution has been measured. A purpose built cell has been used to measure the real time autofluorescence and Circular Dichroism of the protein solutions exposed to electric fields of differing strength and frequency. Exposure to the electric fields results in protein unfolding for both Lysozyme and BSA. The applied field strengths are extremely small compared to the protein inter-chain intra-molecular forces. We propose a model whereby the electrophoretic motion of the proteins leads to a frictional force that results in protein unfolding. For BSA and Lysozyme in the electric fields used in this study, the shear rates at the protein surface under electrophoretic motion are of order 10(3) and 10(4) s(-1) respectively. Prolonged electric field exposure results in significant frictional energy dissipation in the proteins. The energy dissipated in the proteins results in protein unfolding, which is a critical initial step for protein aggregation and potentially amyloid fibril formation. PMID:24652412

  15. Protein designs in HP models

    NASA Astrophysics Data System (ADS)

    Gupta, Arvind; Khodabakhshi, Alireza Hadj; Ma?uch, Ján; Rafiey, Arash; Stacho, Ladislav

    2009-07-01

    The inverse protein folding problem is that of designing an amino acid sequence which folds into a prescribed shape. This problem arises in drug design where a particular structure is necessary to ensure proper protein-protein interactions and could have applications in nanotechnology. A major challenge in designing proteins with native folds that attain a specific shape is to avoid proteins that have multiple native folds (unstable proteins). In this technical note we present our results on protein designs in the variant of Hydrophobic-Polar (HP) model introduced by Dill [6] on 2D square lattice. The HP model distinguishes only polar and hydrophobic monomers and only counts the number of hydrophobic contacts in the energy function. To achieve better stability of our designs we use the Hydrophobic-Polar-Cysteine (HPC) model which distinguishes the third type of monomers called "cysteines" and incorporates also the disulfid bridges (SS-bridges) into the energy function. We present stable designs in 2D square lattice and 3D hexagonal prism lattice in the HPC model.

  16. Systematic Characterization of Human Protein Complexes Identifies Chromosome Segregation Proteins

    PubMed Central

    Hutchins, James R.A.; Toyoda, Yusuke; Hegemann, Björn; Poser, Ina; Hériché, Jean-Karim; Sykora, Martina M.; Augsburg, Martina; Hudecz, Otto; Buschhorn, Bettina A.; Bulkescher, Jutta; Conrad, Christian; Comartin, David; Schleiffer, Alexander; Sarov, Mihail; Pozniakovsky, Andrei; Slabicki, Mikolaj Michal; Schloissnig, Siegfried; Steinmacher, Ines; Leuschner, Marit; Ssykor, Andrea; Lawo, Steffen; Pelletier, Laurence; Stark, Holger; Nasmyth, Kim; Ellenberg, Jan; Durbin, Richard; Buchholz, Frank; Mechtler, Karl; Hyman, Anthony A.; Peters, Jan-Michael

    2010-01-01

    Chromosome segregation and cell division are essential, highly ordered processes that depend on numerous protein complexes. Results from recent RNA interference (RNAi) screens indicate that the identity and composition of these protein complexes is incompletely understood. Using gene tagging on bacterial artificial chromosomes, protein localization and tandem affinity purification-mass spectrometry, the MitoCheck consortium has analyzed about 100 human protein complexes, many of which had not or only incompletely been characterized. This work has led to the discovery of previously unknown, evolutionarily conserved subunits of the anaphase-promoting complex (APC/C) and the ?-tubulin ring complex (?-TuRC), large complexes which are essential for spindle assembly and chromosome segregation. The approaches we describe here are generally applicable to high throughput follow-up analyses of phenotypic screens in mammalian cells. PMID:20360068

  17. Rescuing Recombinant Proteins by Sequestration Into the P22 VLP

    PubMed Central

    Patterson, Dustin P.; LaFrance, Benjamin; Douglas, Trevor

    2013-01-01

    Here we report the use of a self-assembling protein cage to sequester and solubilize recombinant proteins which are usually trafficked to insoluble inclusion bodies. Our results suggest that protein cages can be used as novel vehicles to rescue and produce soluble proteins that are otherwise difficult to obtain using conventional methods. PMID:24079011

  18. The Evolution of Multimeric Protein Assemblages Michael Lynch*,1

    E-print Network

    Lynch, Michael

    . The resultant theory demonstrates that the likelihoods of alternative pathways for the emergence of proteinThe Evolution of Multimeric Protein Assemblages Michael Lynch*,1 1 Department of Biology, Indiana problems of evolu- tionary biology, it is clear that the emergence of new protein­protein interactions

  19. Origins of Myc Proteins – Using Intrinsic Protein Disorder to Trace Distant Relatives

    PubMed Central

    Mahani, Amir; Henriksson, Johan; Wright, Anthony P. H.

    2013-01-01

    Mammalian Myc proteins are important determinants of cell proliferation as well as the undifferentiated state of stem cells and their activity is frequently deregulated in cancer. Based mainly on conservation in the C-terminal DNA-binding and dimerization domain, Myc-like proteins have been reported in many simpler organisms within and outside the Metazoa but they have not been found in fungi or plants. Several important signature motifs defining mammalian Myc proteins are found in the N-terminal domain but the extent to which these are found in the Myc-like proteins from simpler organisms is not well established. The extent of N-terminal signature sequence conservation would give important insights about the evolution of Myc proteins and their current function in mammalian physiology and disease. In a systematic study of Myc-like proteins we show that N-terminal signature motifs are not readily detectable in individual Myc-like proteins from invertebrates but that weak similarities to Myc boxes 1 and 2 can be found in the N-termini of the simplest Metazoa as well as the unicellular choanoflagellate, Monosiga brevicollis, using multiple protein alignments. Phylogenetic support for the connections of these proteins to established Myc proteins is however poor. We show that the pattern of predicted protein disorder along the length of Myc proteins can be used as a complementary approach to making dendrograms of Myc proteins that aids the classification of Myc proteins. This suggests that the pattern of disorder within Myc proteins is more conserved through evolution than their amino acid sequence. In the disorder-based dendrograms the Myc-like proteins from simpler organisms, including M. brevicollis, are connected to established Myc proteins with a higher degree of certainty. Our results suggest that protein disorder based dendrograms may be of general significance for studying distant relationships between proteins, such as transcription factors, that have high levels of intrinsic disorder. PMID:24086436

  20. Oxidative stress causes plasma protein modification.

    PubMed

    Tetik, Sermin; Kiliç, Arzu; Aksoy, Halil; Rizaner, Nahit; Ahmad, Sarfraz; Yardimci, Turay

    2015-01-01

    We investigated the effect of oxidative systems on plasma proteins using Chloramine-T, a source of free radicals. Plasma specimens from 10 healthy volunteers were treated with 40 mmol/L Chloramine-T (1:1 v/v). Total protein and plasma carbonyl levels were evaluated spectrophotometrically. Identification of plasma proteins modifications was performed by SDS-PAGE, protein and lipid electrophoresis. Protein fragmentation was evaluated by HPLC. Total protein levels of oxidised plasmas were significantly lower (4.08 ± 0.12 g/dL) than control (7.86 ± 0.03 g/dL) (P < 0.01). Plasma carbonyl levels were higher (1.94 ± 0.38 nmol/mg protein) in oxidised plasma than that of control (0.03 ± 0.01 nmol/mg protein) (P < 0.01). Plasma oxidation had no significant effect on the levels of proteins and lipids. Protein fragmentations were detected in oxidised groups compared to those of the control. We conclude that protein modifications have direct effect on the protein functions, which are related to stress agent, its treatment period(s), and the methodology used for evaluating such experimental results. PMID:25675708

  1. PPLook: an automated data mining tool for protein-protein interaction

    PubMed Central

    2010-01-01

    Background Extracting and visualizing of protein-protein interaction (PPI) from text literatures are a meaningful topic in protein science. It assists the identification of interactions among proteins. There is a lack of tools to extract PPI, visualize and classify the results. Results We developed a PPI search system, termed PPLook, which automatically extracts and visualizes protein-protein interaction (PPI) from text. Given a query protein name, PPLook can search a dataset for other proteins interacting with it by using a keywords dictionary pattern-matching algorithm, and display the topological parameters, such as the number of nodes, edges, and connected components. The visualization component of PPLook enables us to view the interaction relationship among the proteins in a three-dimensional space based on the OpenGL graphics interface technology. PPLook can also provide the functions of selecting protein semantic class, counting the number of semantic class proteins which interact with query protein, counting the literature number of articles appearing the interaction relationship about the query protein. Moreover, PPLook provides heterogeneous search and a user-friendly graphical interface. Conclusions PPLook is an effective tool for biologists and biosystem developers who need to access PPI information from the literature. PPLook is freely available for non-commercial users at http://meta.usc.edu/softs/PPLook. PMID:20550717

  2. A method for investigating protein-protein interactions related to Salmonella typhimurium pathogenesis

    SciTech Connect

    Chowdhury, Saiful M.; Shi, Liang; Yoon, Hyunjin; Ansong, Charles; Rommereim, Leah M.; Norbeck, Angela D.; Auberry, Kenneth J.; Moore, R. J.; Adkins, Joshua N.; Heffron, Fred; Smith, Richard D.

    2009-03-01

    We successfully modified an existing method to investigate protein-protein interactions in the pathogenic bacterium Salmonella typhimurium (STM). This method includes i) addition of a histidine-biotin-histidine tag to the bait proteins via recombinant DNA techniques; ii) in vivo cross-linking with formaldehyde; iii) tandem affinity purification of bait proteins under fully denaturing conditions; and iv) identification of the proteins cross-linked to the bait proteins by liquid-chromatography in conjunction with tandem mass-spectrometry. In vivo cross-linking stabilized protein interactions permitted the subsequent two-step purification step conducted under denaturing conditions. The two-step purification greatly reduced nonspecific binding of non-cross-linked proteins to bait proteins. Two different negative controls were employed to reduce false-positive identification. In an initial demonstration of this approach, we tagged three selected STM proteins? HimD, PduB and PhoP? with known binding partners that ranged from stable (e.g., HimD) to transient (i.e., PhoP). Distinct sets of interacting proteins were identified with each bait protein, including the known binding partners such as HimA for HimD, as well as anticipated and unexpected binding partners. Our results suggest that novel protein-protein interactions may be critical to pathogenesis by Salmonella typhimurium. .

  3. Peptidomimetics to mimic protein-protein interactions 

    E-print Network

    Xia, Zebin

    2005-08-29

    Butler-Purry (Member) (Head of Department) May 2004 Major Subject: Interdisciplinary Engineering iii ABSTRACT Peptidomimetics to Mimic Protein-Protein Interactions. (May 2004) Zebin Xia, B.S., Hunan Normal University, P.R.China; M.S.... They are important in the normal function of signal transduction,1-3 immune response,4,5 protein enzyme inhibitors6,7 etc. The abnormal protein-protein interactions are key factors in the development of some pathological processes, for example, Alzheimer?s disease,8...

  4. Prophylaxis vs. on-demand treatment with BAY 81-8973, a full-length plasma protein-free recombinant factor VIII product: results from a randomized trial (LEOPOLD II)

    PubMed Central

    Kavakli, K; Yang, R; Rusen, L; Beckmann, H; Tseneklidou-Stoeter, D; Maas Enriquez, M

    2015-01-01

    Background BAY 81-8973 is a new full-length human recombinant factor VIII product manufactured with technologies to improve consistency in glycosylation and expression to optimize clinical performance. Objectives To demonstrate superiority of prophylaxis vs. on-demand therapy with BAY 81-8973 in patients with severe hemophilia A. Patients/Methods In this multinational, randomized, open-label crossover study (LEOPOLD II; ClinicalTrials.gov identifier: NCT01233258), males aged 12–65 years with severe hemophilia A were randomized to twice-weekly prophylaxis (20–30 IU kg?1), 3-times-weekly prophylaxis (30–40 IU kg?1), or on-demand treatment with BAY 81-8973. Potency labeling for BAY 81-8973 was based on the chromogenic substrate assay or adjusted to the one-stage assay. Primary efficacy endpoint was annualized number of all bleeds (ABR). Adverse events (AEs) and immunogenicity were also assessed. Results Eighty patients (on demand, n = 21; twice-weekly prophylaxis, n = 28; 3-times-weekly prophylaxis, n = 31) were treated and analyzed. Mean ± SD ABR was significantly lower with prophylaxis (twice-weekly, 5.7 ± 7.2; 3-times-weekly, 4.3 ± 6.5; combined, 4.9 ± 6.8) vs. on-demand treatment (57.7 ± 24.6; P < 0.0001, anova). Median ABR was reduced by 97% with prophylaxis (twice-weekly, 4.0; 3-times-weekly, 2.0; combined, 2.0) vs. on-demand treatment (60.0). Median ABR was higher with twice-weekly vs. 3-times-weekly prophylaxis during the first 6-month treatment period (4.1 vs. 2.0) but was comparable in the second 6-month period (1.1 vs. 2.0). Few patients reported treatment-related AEs (4%); no treatment-related serious AEs or inhibitors were reported. Conclusions Twice-weekly or 3-times-weekly prophylaxis with BAY 81-8973 reduced median ABR by 97% compared with on-demand therapy, confirming the superiority of prophylaxis. Treatment with BAY 81-8973 was well tolerated. PMID:25546368

  5. Origins of Protein Functions in Cells

    NASA Technical Reports Server (NTRS)

    Seelig, Burchard; Pohorille, Andrzej

    2011-01-01

    In modern organisms proteins perform a majority of cellular functions, such as chemical catalysis, energy transduction and transport of material across cell walls. Although great strides have been made towards understanding protein evolution, a meaningful extrapolation from contemporary proteins to their earliest ancestors is virtually impossible. In an alternative approach, the origin of water-soluble proteins was probed through the synthesis and in vitro evolution of very large libraries of random amino acid sequences. In combination with computer modeling and simulations, these experiments allow us to address a number of fundamental questions about the origins of proteins. Can functionality emerge from random sequences of proteins? How did the initial repertoire of functional proteins diversify to facilitate new functions? Did this diversification proceed primarily through drawing novel functionalities from random sequences or through evolution of already existing proto-enzymes? Did protein evolution start from a pool of proteins defined by a frozen accident and other collections of proteins could start a different evolutionary pathway? Although we do not have definitive answers to these questions yet, important clues have been uncovered. In one example (Keefe and Szostak, 2001), novel ATP binding proteins were identified that appear to be unrelated in both sequence and structure to any known ATP binding proteins. One of these proteins was subsequently redesigned computationally to bind GTP through introducing several mutations that introduce targeted structural changes to the protein, improve its binding to guanine and prevent water from accessing the active center. This study facilitates further investigations of individual evolutionary steps that lead to a change of function in primordial proteins. In a second study (Seelig and Szostak, 2007), novel enzymes were generated that can join two pieces of RNA in a reaction for which no natural enzymes are known. Recently it was found that, as in the previous case, the proteins have a structure unknown among modern enzymes. In this case, in vitro evolution started from a small, non-enzymatic protein. A similar selection process initiated from a library of random polypeptides is in progress. These results not only allow for estimating the occurrence of function in random protein assemblies but also provide evidence for the possibility of alternative protein worlds. Extant proteins might simply represent a frozen accident in the world of possible proteins. Alternative collections of proteins, even with similar functions, could originate alternative evolutionary paths.

  6. Heat Shock Protein 70 Enhances Vascular Bone Morphogenetic Protein-4 Signaling by Binding Matrix Gla Protein

    PubMed Central

    Yao, Yucheng; Watson, Andrew D.; Ji, Sheng; Boström, Kristina I.

    2009-01-01

    Rationale Matrix Gla protein (MGP) is a calcification inhibitor, which binds and inhibits bone morphogenetic protein (BMP)-2 and -4. Objective The objective was to determine if MGP also binds other proteins, which could interfere with its function. Methods and Results We transfected bovine aortic endothelial cells with N-terminally FLAG-tagged MGP, and used immunoprecipitation and LC-MS/MS-analysis to identify MGP-binding proteins. Heat shock protein 70 (HSP70), a stress-induced protein expressed in atherosclerotic lesions and soluble in serum, was identified as a novel MGP-binding protein. The interaction between MGP and HSP70 was confirmed by co-immunoprecipitation and chemical crosslinking, and blocked the interaction between MGP and BMP-4. In endothelial cells, HSP70 enhanced BMP-4-induced proliferation and tube formation, and in calcifying vascular cells (CVC), HSP70 enhanced BMP-induced calcium deposition. In addition, HSP70 mediated the procalcific effect of interleukin (IL)-6 on CVC. In apolipoprotein E null mice, a model for atherosclerosis, levels of BMP-4, HSP70, MGP and IL-6 were elevated in the aortic wall. Levels of BMP-4, HSP70 and IL-6 were also elevated in serum, and anti-HSP70 antibodies diminished its procalcific effect on CVC. Conclusion HSP70 binds MGP and enhances BMP activity, thereby functioning as a potential link between cellular stress, inflammation and BMP-signaling. PMID:19661459

  7. Macromolecular crowding and protein stability.

    PubMed

    Wang, Yaqiang; Sarkar, Mohona; Smith, Austin E; Krois, Alexander S; Pielak, Gary J

    2012-10-10

    An understanding of cellular chemistry requires knowledge of how crowded environments affect proteins. The influence of crowding on protein stability arises from two phenomena, hard-core repulsions and soft (i.e., chemical) interactions. Most efforts to understand crowding effects on protein stability, however, focus on hard-core repulsions, which are inherently entropic and stabilizing. We assessed these phenomena by measuring the temperature dependence of NMR-detected amide proton exchange and used these data to extract the entropic and enthalpic contributions of crowding to the stability of ubiquitin. Contrary to expectations, the contribution of chemical interactions is large and in many cases dominates the contribution from hardcore repulsions. Our results show that both chemical interactions and hard-core repulsions must be considered when assessing the effects of crowding and help explain previous observations about protein stability and dynamics in cells. PMID:22954326

  8. Infrared Protein Crystallography

    SciTech Connect

    J Sage; Y Zhang; J McGeehan; R Ravelli; M Weik; J van Thor

    2011-12-31

    We consider the application of infrared spectroscopy to protein crystals, with particular emphasis on exploiting molecular orientation through polarization measurements on oriented single crystals. Infrared microscopes enable transmission measurements on individual crystals using either thermal or nonthermal sources, and can accommodate flow cells, used to measure spectral changes induced by exposure to soluble ligands, and cryostreams, used for measurements of flash-cooled crystals. Comparison of unpolarized infrared measurements on crystals and solutions probes the effects of crystallization and can enhance the value of the structural models refined from X-ray diffraction data by establishing solution conditions under which they are most relevant. Results on several proteins are consistent with similar equilibrium conformational distributions in crystal and solutions. However, the rates of conformational change are often perturbed. Infrared measurements also detect products generated by X-ray exposure, including CO{sub 2}. Crystals with favorable symmetry exhibit infrared dichroism that enhances the synergy with X-ray crystallography. Polarized infrared measurements on crystals can distinguish spectral contributions from chemically similar sites, identify hydrogen bonding partners, and, in opportune situations, determine three-dimensional orientations of molecular groups. This article is part of a Special Issue entitled: Protein Structure and Function in the Crystalline State.

  9. Nonlinear features in protein circuitry

    NASA Astrophysics Data System (ADS)

    Liu, Bo; Yan, Shiwei

    2011-07-01

    The noise involved in protein circuit can result in fluctuations in protein concentrations. Then we have explored the effect of such noise on the feedback loop between p53 and its repressor Mdm2, the negative feedback dynamics and oscillatory activities are presented. Recent experimental results show that under certain conditions, the activity of the average protein level of p53 behaves with dampened oscillation in response to DNA damage, and it has non-decaying oscillatory behavior in individual cells, and we show that the dampening is induced by intrinsic noise, namely the uncertainty associated with chemical kinetics in dealing with when and in what order reactions take place in the p53 system. Furthermore, the experimental results are reproduced in this paper.

  10. A combinatorial perspective of the protein inference problem.

    PubMed

    Yang, Chao; He, Zengyou; Yu, Weichuan

    2013-01-01

    In a shotgun proteomics experiment, proteins are the most biologically meaningful output. The success of proteomics studies depends on the ability to accurately and efficiently identify proteins. Many methods have been proposed to facilitate the identification of proteins from peptide identification results. However, the relationship between protein identification and peptide identification has not been thoroughly explained before. In this paper, we devote ourselves to a combinatorial perspective of the protein inference problem. We employ combinatorial mathematics to calculate the conditional protein probabilities (protein probability means the probability that a protein is correctly identified) under three assumptions, which lead to a lower bound, an upper bound, and an empirical estimation of protein probabilities, respectively. The combinatorial perspective enables us to obtain an analytical expression for protein inference. Our method achieves comparable results with ProteinProphet in a more efficient manner in experiments on two data sets of standard protein mixtures and two data sets of real samples. Based on our model, we study the impact of unique peptides and degenerate peptides (degenerate peptides are peptides shared by at least two proteins) on protein probabilities. Meanwhile, we also study the relationship between our model and ProteinProphet. We name our program ProteinInfer. Its Java source code, our supplementary document and experimental results are available at: >http://bioinformatics.ust.hk/proteininfer. PMID:24407311

  11. Biochemical Approaches for Discovering Protein-Protein Interactions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Protein-protein interactions or protein complexes are indigenous to nearly all cellular processes, ranging from metabolism to structure. Elucidating both individual protein associations and complex protein interaction networks, while challenging, is an essential goal of functional genomics. For ex...

  12. PREFACE: Protein protein interactions: principles and predictions

    NASA Astrophysics Data System (ADS)

    Nussinov, Ruth; Tsai, Chung-Jung

    2005-06-01

    Proteins are the `workhorses' of the cell. Their roles span functions as diverse as being molecular machines and signalling. They carry out catalytic reactions, transport, form viral capsids, traverse membranes and form regulated channels, transmit information from DNA to RNA, making possible the synthesis of new proteins, and they are responsible for the degradation of unnecessary proteins and nucleic acids. They are the vehicles of the immune response and are responsible for viral entry into the cell. Given their importance, considerable effort has been centered on the prediction of protein function. A prime way to do this is through identification of binding partners. If the function of at least one of the components with which the protein interacts is known, that should let us assign its function(s) and the pathway(s) in which it plays a role. This holds since the vast majority of their chores in the living cell involve protein-protein interactions. Hence, through the intricate network of these interactions we can map cellular pathways, their interconnectivities and their dynamic regulation. Their identification is at the heart of functional genomics; their prediction is crucial for drug discovery. Knowledge of the pathway, its topology, length, and dynamics may provide useful information for forecasting side effects. The goal of predicting protein-protein interactions is daunting. Some associations are obligatory, others are continuously forming and dissociating. In principle, from the physical standpoint, any two proteins can interact, but under what conditions and at which strength? The principles of protein-protein interactions are general: the non-covalent interactions of two proteins are largely the outcome of the hydrophobic effect, which drives the interactions. In addition, hydrogen bonds and electrostatic interactions play important roles. Thus, many of the interactions observed in vitro are the outcome of experimental overexpression. Protein disorder is important in protein-protein association. It has been estimated that a large fraction of cellular proteins are `natively disordered', i.e., unstable in solution. The disordered state has a significant residual structure. In this state, a protein exists in an ensemble of rapidly interconverting conformers. They play roles in cell-cycle control, signal transduction, transcriptional and translational regulation, and in large macromolecular complexes. It has been suggested that natively disordered proteins are more `adaptive', and thus advantageous in regulation and in binding diverse ligands. Alternatively, since the native conformation is still likely to be the most abundant within the ensemble, disordered proteins, which typically have larger interface to size ratios, lead to smaller protein, genome and cell sizes, and thus are functionally advantageous. To be able to predict protein-protein interactions, we need to discern various aspects of their associations: from their shape complementarity to the organization and relative contributions of the different physical components to their stability. They involve the static and the dynamic. Proteins interact through their surfaces. Thus, to analyze their interactions, we typically study residues (or atoms) which are in contact across the two-chain interface. In addition, we often inspect the residues in their vicinity, exploring their supporting matrix. The hope is that through the understanding of the principles and mechanisms of the interactions, we shall eventually be able to solve the protein-protein interaction puzzle.

  13. UMBCUMBCUMBC Protein Image Alignment

    E-print Network

    Potra, Florian

    UMBCUMBCUMBC Protein Image Alignment via Quadratic Programming Florian A. Potra potra Research supported by NIH, Grant No. R01GM075298-01 Protein Image Alignment via Quadratic Programming ­ p.1-scale analysis of complex protein mixtures focusing on the qualitative and quantitative variations of protein

  14. Whey protein fractionation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Concentrated whey protein products from cheese whey, such as whey protein concentrate (WPC) and whey protein isolate (WPI), contain more than seven different types of proteins: alpha-lactalbumin (alpha-LA), beta-lactoglobulin (beta-LG), bovine serum albumin (BSA), immunoglobulins (Igs), lactoferrin ...

  15. Sorghum and millet proteins

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sorghum and millet proteins are an important source of dietary protein for significant numbers of people living throughout Africa and parts of Asia. Compared to other food proteins, such as those found in milk, eggs and wheat, little is known about the functionality of sorghum and millet proteins. ...

  16. Apoptosis related protein 3 is a lysosomal membrane protein.

    PubMed

    Ding, XiaoDong; Chen, YuanWen; Han, LianShu; Qiu, WenJuan; Gu, XueFan; Zhang, HuiWen

    2015-05-15

    Apoptosis Related Protein 3 (APR3) is an important protein which is involved in retinoic acid-induced apoptosis, osteoblast differentiation and cervical squamous cell carcinoma progression. Although it was predicted to be a trans-membrane protein, its cellular localization is not clear. In this study, we analyzed APR3 with bioinformatic tools and found that APR3 contains a potential signal peptide, a transmembrane region and 3 N-glycosylation sites, all of which are characteristics of lysosomal proteins. Western blot with isolated lysosomes demonstrated that APR3 was mainly present in lysosomes, specially in the lysosomal membrane fraction, but not in endoplasmic reticulum. Concomitantly, double immunofluorescence confirmed that APR3 co-localized with lysosomal membrane protein, LAMP1, as well as lysosomal specific marker, Lyso-Tracker Red. Moreover, we showed that APR3 was highly expressed in the lung, liver, spleen, kidney and adipose tissue, but expressed at the low level in the heart, pancreas, stomach and intestine. Interestingly, APR3 expression was elevated in multiple hepatocellular carcinoma cell lines comparing to normal liver cells. Collectively, our results proved that APR3 is a novel lysosomal membrane protein and shed light on its possible functions. PMID:25839652

  17. Protein sequence comparison and protein evolution

    SciTech Connect

    Pearson, W.R.

    1995-12-31

    This tutorial was one of eight tutorials selected to be presented at the Third International Conference on Intelligent Systems for Molecular Biology which was held in the United Kingdom from July 16 to 19, 1995. This tutorial examines how the information conserved during the evolution of a protein molecule can be used to infer reliably homology, and thus a shared proteinfold and possibly a shared active site or function. The authors start by reviewing a geological/evolutionary time scale. Next they look at the evolution of several protein families. During the tutorial, these families will be used to demonstrate that homologous protein ancestry can be inferred with confidence. They also examine different modes of protein evolution and consider some hypotheses that have been presented to explain the very earliest events in protein evolution. The next part of the tutorial will examine the technical aspects of protein sequence comparison. Both optimal and heuristic algorithms and their associated parameters that are used to characterize protein sequence similarities are discussed. Perhaps more importantly, they survey the statistics of local similarity scores, and how these statistics can both be used to improve the selectivity of a search and to evaluate the significance of a match. They them examine distantly related members of three protein families, the serine proteases, the glutathione transferases, and the G-protein-coupled receptors (GCRs). Finally, the discuss how sequence similarity can be used to examine internal repeated or mosaic structures in proteins.

  18. My 65 years in protein chemistry.

    PubMed

    Scheraga, Harold A

    2015-05-01

    This is a tour of a physical chemist through 65 years of protein chemistry from the time when emphasis was placed on the determination of the size and shape of the protein molecule as a colloidal particle, with an early breakthrough by James Sumner, followed by Linus Pauling and Fred Sanger, that a protein was a real molecule, albeit a macromolecule. It deals with the recognition of the nature and importance of hydrogen bonds and hydrophobic interactions in determining the structure, properties, and biological function of proteins until the present acquisition of an understanding of the structure, thermodynamics, and folding pathways from a linear array of amino acids to a biological entity. Along the way, with a combination of experiment and theoretical interpretation, a mechanism was elucidated for the thrombin-induced conversion of fibrinogen to a fibrin blood clot and for the oxidative-folding pathways of ribonuclease A. Before the atomic structure of a protein molecule was determined by x-ray diffraction or nuclear magnetic resonance spectroscopy, experimental studies of the fundamental interactions underlying protein structure led to several distance constraints which motivated the theoretical approach to determine protein structure, and culminated in the Empirical Conformational Energy Program for Peptides (ECEPP), an all-atom force field, with which the structures of fibrous collagen-like proteins and the 46-residue globular staphylococcal protein A were determined. To undertake the study of larger globular proteins, a physics-based coarse-grained UNited-RESidue (UNRES) force field was developed, and applied to the protein-folding problem in terms of structure, thermodynamics, dynamics, and folding pathways. Initially, single-chain and, ultimately, multiple-chain proteins were examined, and the methodology was extended to protein-protein interactions and to nucleic acids and to protein-nucleic acid interactions. The ultimate results led to an understanding of a variety of biological processes underlying natural and disease phenomena. PMID:25850343

  19. Comparison of tertiary structures of proteins in protein-protein complexes with unbound forms suggests prevalence of allostery in signalling proteins

    PubMed Central

    2012-01-01

    Background Most signalling and regulatory proteins participate in transient protein-protein interactions during biological processes. They usually serve as key regulators of various cellular processes and are often stable in both protein-bound and unbound forms. Availability of high-resolution structures of their unbound and bound forms provides an opportunity to understand the molecular mechanisms involved. In this work, we have addressed the question “What is the nature, extent, location and functional significance of structural changes which are associated with formation of protein-protein complexes?” Results A database of 76 non-redundant sets of high resolution 3-D structures of protein-protein complexes, representing diverse functions, and corresponding unbound forms, has been used in this analysis. Structural changes associated with protein-protein complexation have been investigated using structural measures and Protein Blocks description. Our study highlights that significant structural rearrangement occurs on binding at the interface as well as at regions away from the interface to form a highly specific, stable and functional complex. Notably, predominantly unaltered interfaces interact mainly with interfaces undergoing substantial structural alterations, revealing the presence of at least one structural regulatory component in every complex. Interestingly, about one-half of the number of complexes, comprising largely of signalling proteins, show substantial localized structural change at surfaces away from the interface. Normal mode analysis and available information on functions on some of these complexes suggests that many of these changes are allosteric. This change is largely manifest in the proteins whose interfaces are altered upon binding, implicating structural change as the possible trigger of allosteric effect. Although large-scale studies of allostery induced by small-molecule effectors are available in literature, this is, to our knowledge, the first study indicating the prevalence of allostery induced by protein effectors. Conclusions The enrichment of allosteric sites in signalling proteins, whose mutations commonly lead to diseases such as cancer, provides support for the usage of allosteric modulators in combating these diseases. PMID:22554255

  20. Quantitative study of protein-protein interactions by quartz nanopipettes

    NASA Astrophysics Data System (ADS)

    Tiwari, Purushottam Babu; Astudillo, Luisana; Miksovska, Jaroslava; Wang, Xuewen; Li, Wenzhi; Darici, Yesim; He, Jin

    2014-08-01

    In this report, protein-modified quartz nanopipettes were used to quantitatively study protein-protein interactions in attoliter sensing volumes. As shown by numerical simulations, the ionic current through the conical-shaped nanopipette is very sensitive to the surface charge variation near the pore mouth. With the appropriate modification of negatively charged human neuroglobin (hNgb) onto the inner surface of a nanopipette, we were able to detect concentration-dependent current change when the hNgb-modified nanopipette tip was exposed to positively charged cytochrome c (Cyt c) with a series of concentrations in the bath solution. Such current change is due to the adsorption of Cyt c to the inner surface of the nanopipette through specific interactions with hNgb. In contrast, a smaller current change with weak concentration dependence was observed when Cyt c was replaced with lysozyme, which does not specifically bind to hNgb. The equilibrium dissociation constant (KD) for the Cyt c-hNgb complex formation was derived and the value matched very well with the result from surface plasmon resonance measurement. This is the first quantitative study of protein-protein interactions by a conical-shaped nanopore based on charge sensing. Our results demonstrate that nanopipettes can potentially be used as a label-free analytical tool to quantitatively characterize protein-protein interactions.In this report, protein-modified quartz nanopipettes were used to quantitatively study protein-protein interactions in attoliter sensing volumes. As shown by numerical simulations, the ionic current through the conical-shaped nanopipette is very sensitive to the surface charge variation near the pore mouth. With the appropriate modification of negatively charged human neuroglobin (hNgb) onto the inner surface of a nanopipette, we were able to detect concentration-dependent current change when the hNgb-modified nanopipette tip was exposed to positively charged cytochrome c (Cyt c) with a series of concentrations in the bath solution. Such current change is due to the adsorption of Cyt c to the inner surface of the nanopipette through specific interactions with hNgb. In contrast, a smaller current change with weak concentration dependence was observed when Cyt c was replaced with lysozyme, which does not specifically bind to hNgb. The equilibrium dissociation constant (KD) for the Cyt c-hNgb complex formation was derived and the value matched very well with the result from surface plasmon resonance measurement. This is the first quantitative study of protein-protein interactions by a conical-shaped nanopore based on charge sensing. Our results demonstrate that nanopipettes can potentially be used as a label-free analytical tool to quantitatively characterize protein-protein interactions. Electronic supplementary information (ESI) available: Determination of nanopipette diameter; surface modification scheme; numerical simulation; noise analysis; SPR experiments. See DOI: 10.1039/c4nr02964j

  1. Antioxidant activities of buttermilk proteins, whey proteins, and their enzymatic hydrolysates.

    PubMed

    Conway, Valérie; Gauthier, Sylvie F; Pouliot, Yves

    2013-01-16

    The oxygen radical absorbance capacities (ORAC) and metal chelating capacities (MCC) of protein concentrates prepared from buttermilk and cheese whey by ultrafiltration were compared with those of skim milk protein. Samples were also heat-denatured and hydrolyzed by pepsin for 2 h followed by trypsin for 3 h. The highest MCC was obtained for hydrolyzed skim milk protein. ORAC values ranged from 554.4 to 1319.6 ?mol Trolox equivalents/g protein, with the highest value obtained for hydrolyzed buttermilk protein. Liquid-phase isoelectric focusing (IEF) of this hydrolysate yielded peptide fractions with lower ORAC values. LC-MS analysis of the hydrolyzed skim milk and buttermilk proteins and IEF fractions of the latter showed that peptides derived from milk fat globule membrane proteins, primarily butyrophilin, could be responsible for the superior antioxidant activity of buttermilk. These results suggest overall that hydrolyzed buttermilk protein could be used as a source of natural antioxidants. PMID:23244578

  2. Therapeutic Protein Aggregation: Mechanisms, Design, and Control

    PubMed Central

    Roberts, Christopher J.

    2014-01-01

    While it is well known that proteins are only marginally stable in their folded states, it is often less well appreciated that most proteins are inherently aggregation-prone in their unfolded or partially unfolded states, and the resulting aggregates can be extremely stable and long-lived. For therapeutic proteins, aggregates are a significant risk factor for deleterious immune responses in patients, and can form via a variety of mechanisms. Controlling aggregation using a mechanistic approach may allow improved design of therapeutic protein stability, as a complement to existing design strategies that target desired protein structures and function. Recent results highlight the importance of balancing protein environment with the inherent aggregation propensities of polypeptide chains. PMID:24908382

  3. Protein Sequence, Structure, Stability and Functionality

    E-print Network

    J. C. Phillips

    2008-02-25

    Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. Proteins are peptide chains decorated by amino acids, and protein scientists have long described protein-water interactions in terms of qualitative amino acid hydrophobicity scales. Here we examine several recent scales and argue plausibly (in terms of self-organized criticality) that one of them should be regarded as an absolute scale (within the protein universe), analogous to the dielectric scale of bond ionicity in inorganic octet compounds. Applications to repeat proteins (containing upwards of 900 amino acids) are successful, far beyond reasonable expectations, in all cases studied so far. While some of the results are obvious and can be obtained from the ex vitro spatial structures alone, many are hidden from plain view, and can be called phantom relations. As a byproduct, the network theory explains the exceptional functionality of leucine in zippers, heptads, and repeat consensus sites.

  4. Infrared techniques for quantifying protein structural stability.

    PubMed

    Vrettos, John S; Meuse, Curtis W

    2009-07-01

    Biopharmaceutical and biotechnology companies and regulatory agencies require novel methods to determine the structural stabilities of proteins and the integrity of protein-protein, protein-ligand, and protein-membrane interactions that can be applied to a variety of sample states and environments. Infrared spectroscopy is a favorable method for a number of reasons: it is adequately sensitive to minimal sample amounts and is not limited by the molecular weight of the sample; yields spectra that are simple to evaluate; does not require protein modifications, a special supporting matrix, or internal standard; and is applicable to soluble and membrane proteins. In this paper, we investigate the application of infrared spectroscopy to the quantification of protein structural stability by measuring the extent of amide hydrogen/deuterium exchange in buffers containing D(2)O for proteins in solution and interacting with ligands and lipid membranes. We report the thermodynamic stability of several protein preparations, including chick egg-white lysozyme, trypsin bound by benzamidine inhibitors, and cytochrome c interacting with lipid membranes of varying net-negative surface charge density. The results demonstrate that infrared spectroscopy can be used to compare protein stability as determined by amide hydrogen/deuterium exchange for a variety of cases. PMID:19327337

  5. Evolutionary aspect of protein self-organization

    NASA Astrophysics Data System (ADS)

    Rapis, E.

    2008-06-01

    Numerous experimental data (published in 1988 2006) show that, when an open protein-water system far from thermodynamic equilibrium is dehydrated (dried), abiogenic self-organization of the protein invariably takes place, which complicates the structure and also results in the formation of a 3D supramolecular architecture with synchronous replication of spiral vortices and domains (cells) with nuclei having spiral clockwise and counterclockwise symmetry typical of protein in the living organism. When a solvent evaporates, say, from a multicomponent solution, such as blood serum, a protein structure arises the morphology of which copies the morphology of the protein one-component system. Thus, the competing activity of protein is observed when it experiences phase transition in the course of self-organization. In light of a new evolutionary chemical theory based on the Rudenko concept, these data allow one to put forward a hypothesis that protein exhibits evolutionary properties under conditions far from thermodynamic equilibrium. This hypothesis relies on the assumption that the energetically active structure of protein self-organizing in the course of its phase transition may generate energy necessary for catalysis and autocatalysis when a one-component protein-water system dries out. An important piece of evidence in favor of this hypothesis is the presence of the basic type of symmetry (spiral mirror clockwise or counterclockwise symmetry) under the given nonequilibrium conditions in vitro, which is characteristic of animate nature, protein in the living organism in vivo, and abiogenic self-organization of protein in vitro.

  6. The continuity of protein structure space is an intrinsic property of proteins

    PubMed Central

    Skolnick, Jeffrey; Arakaki, Adrian K.; Lee, Seung Yup; Brylinski, Michal

    2009-01-01

    The classical view of the space of protein structures is that it is populated by a discrete set of protein folds. For proteins up to 200 residues long, by using structural alignments and building upon ideas of the completeness and continuity of structure space, we show that nearly any structure is significantly related to any other using a transitive set of no more than 7 intermediate structurally related proteins. This result holds for all structures in the Protein Data Bank, even when structural relationships between evolutionary related proteins (as detected by threading or functional analyses) are excluded. A similar picture holds for an artificial library of compact, hydrogen-bonded, homopolypeptide structures. The 3 sets share the global connectivity features of random graphs, in which the local connectivity of each node (i.e., the number of neighboring structures per protein) is preserved. This high connectivity supports the continuous view of single-domain protein structure space. More importantly, these results do not depend on evolution, rather just on the physics of protein structures. The fact that evolutionary divergence need not be invoked to explain the continuous nature of protein structure space has implications for how the universe of protein structures might have originated, and how function should be transferred between proteins of similar structure. PMID:19805219

  7. Coevolution of gene expression among interacting proteins

    SciTech Connect

    Fraser, Hunter B.; Hirsh, Aaron E.; Wall, Dennis P.; Eisen,Michael B.

    2004-03-01

    Physically interacting proteins or parts of proteins are expected to evolve in a coordinated manner that preserves proper interactions. Such coevolution at the amino acid-sequence level is well documented and has been used to predict interacting proteins, domains, and amino acids. Interacting proteins are also often precisely coexpressed with one another, presumably to maintain proper stoichiometry among interacting components. Here, we show that the expression levels of physically interacting proteins coevolve. We estimate average expression levels of genes from four closely related fungi of the genus Saccharomyces using the codon adaptation index and show that expression levels of interacting proteins exhibit coordinated changes in these different species. We find that this coevolution of expression is a more powerful predictor of physical interaction than is coevolution of amino acid sequence. These results demonstrate previously uncharacterized coevolution of gene expression, adding a different dimension to the study of the coevolution of interacting proteins and underscoring the importance of maintaining coexpression of interacting proteins over evolutionary time. Our results also suggest that expression coevolution can be used for computational prediction of protein protein interactions.

  8. Dietary Protein Intake in Dutch Elderly People: A Focus on Protein Sources

    PubMed Central

    Tieland, Michael; Borgonjen-Van den Berg, Karin J.; Van Loon, Luc J. C.; de Groot, Lisette C. P. G. M.

    2015-01-01

    Introduction: Sufficient high quality dietary protein intake is required to prevent or treat sarcopenia in elderly people. Therefore, the intake of specific protein sources as well as their timing of intake are important to improve dietary protein intake in elderly people. Objectives: to assess the consumption of protein sources as well as the distribution of protein sources over the day in community-dwelling, frail and institutionalized elderly people. Methods: Habitual dietary intake was evaluated using 2- and 3-day food records collected from various studies involving 739 community-dwelling, 321 frail and 219 institutionalized elderly people. Results: Daily protein intake averaged 71 ± 18 g/day in community-dwelling, 71 ± 20 g/day in frail and 58 ± 16 g/day in institutionalized elderly people and accounted for 16% ± 3%, 16% ± 3% and 17% ± 3% of their energy intake, respectively. Dietary protein intake ranged from 10 to 12 g at breakfast, 15 to 23 g at lunch and 24 to 31 g at dinner contributing together over 80% of daily protein intake. The majority of dietary protein consumed originated from animal sources (?60%) with meat and dairy as dominant sources. Thus, 40% of the protein intake in community-dwelling, 37% in frail and 29% in institutionalized elderly originated from plant based protein sources with bread as the principle source. Plant based proteins contributed for >50% of protein intake at breakfast and between 34% and 37% at lunch, with bread as the main source. During dinner, >70% of the protein intake originated from animal protein, with meat as the dominant source. Conclusion: Daily protein intake in these older populations is mainly (>80%) provided by the three main meals, with most protein consumed during dinner. More than 60% of daily protein intake consumed is of animal origin, with plant based protein sources representing nearly 40% of total protein consumed. During dinner, >70% of the protein intake originated from animal protein, while during breakfast and lunch a large proportion of protein is derived from plant based protein sources. PMID:26610565

  9. Protein Adsorption in Microengraving Immunoassays

    PubMed Central

    Song, Qing

    2015-01-01

    Microengraving is a novel immunoassay forcharacterizing multiple protein secretions from single cells. During the immunoassay, characteristic diffusion and kinetic time scales ?D and ?K determine the time for molecular diffusion of proteins secreted from the activated single lymphocytes and subsequent binding onto the glass slide surface respectively. Our results demonstrate that molecular diffusion plays important roles in the early stage of protein adsorption dynamics which shifts to a kinetic controlled mechanism in the later stage. Similar dynamic pathways are observed for protein adsorption with significantly fast rates and rapid shifts in transport mechanisms when C0* is increased a hundred times from 0.313 to 31.3. Theoretical adsorption isotherms follow the trend of experimentally obtained data. Adsorption isotherms indicate that amount of proteins secreted from individual cells and subsequently captured on a clean glass slide surface increases monotonically with time. Our study directly validates that protein secretion rates can be quantified by the microengraving immunoassay. This will enable us to apply microengraving immunoassays to quantify secretion rates from 104–105 single cells in parallel, screen antigen-specific cells with the highest secretion rate for clonal expansion and quantitatively reveal cellular heterogeneity within a small cell sample. PMID:26501282

  10. Protein complex detection with semi-supervised learning in protein interaction networks

    PubMed Central

    2011-01-01

    Background Protein-protein interactions (PPIs) play fundamental roles in nearly all biological processes. The systematic analysis of PPI networks can enable a great understanding of cellular organization, processes and function. In this paper, we investigate the problem of protein complex detection from noisy protein interaction data, i.e., finding the subsets of proteins that are closely coupled via protein interactions. However, protein complexes are likely to overlap and the interaction data are very noisy. It is a great challenge to effectively analyze the massive data for biologically meaningful protein complex detection. Results Many people try to solve the problem by using the traditional unsupervised graph clustering methods. Here, we stand from a different point of view, redefining the properties and features for protein complexes and designing a “semi-supervised” method to analyze the problem. In this paper, we utilize the neural network with the “semi-supervised” mechanism to detect the protein complexes. By retraining the neural network model recursively, we could find the optimized parameters for the model, in such a way we can successfully detect the protein complexes. The comparison results show that our algorithm could identify protein complexes that are missed by other methods. We also have shown that our method achieve better precision and recall rates for the identified protein complexes than other existing methods. In addition, the framework we proposed is easy to be extended in the future. Conclusions Using a weighted network to represent the protein interaction network is more appropriate than using a traditional unweighted network. In addition, integrating biological features and topological features to represent protein complexes is more meaningful than using dense subgraphs. Last, the “semi-supervised” learning model is a promising model to detect protein complexes with more biological and topological features available. PMID:22165896

  11. Protein structure prediction using hybrid AI methods

    SciTech Connect

    Guan, X.; Mural, R.J.; Uberbacher, E.C.

    1993-11-01

    This paper describes a new approach for predicting protein structures based on Artificial Intelligence methods and genetic algorithms. We combine nearest neighbor searching algorithms, neural networks, heuristic rules and genetic algorithms to form an integrated system to predict protein structures from their primary amino acid sequences. First we describe our methods and how they are integrated, and then apply our methods to several protein sequences. The results are very close to the real structures obtained by crystallography. Parallel genetic algorithms are also implemented.

  12. Finding Occurrences of Protein Complexes in Protein-Protein Interaction Graphs ,

    E-print Network

    Fertin, Guillaume

    Finding Occurrences of Protein Complexes in Protein-Protein Interaction Graphs , Guillaume Fertin analysis of protein-protein interaction graphs, we use a graph-based formalism to detect the preservation of a given protein complex G in the protein-protein interaction graph H of another species with respect to (w

  13. Protein Models Docking Benchmark 2

    PubMed Central

    Anishchenko, Ivan; Kundrotas, Petras J.; Tuzikov, Alexander V.; Vakser, Ilya A.

    2015-01-01

    Structural characterization of protein-protein interactions is essential for our ability to understand life processes. However, only a fraction of known proteins have experimentally determined structures. Such structures provide templates for modeling of a large part of the proteome, where individual proteins can be docked by template-free or template-based techniques. Still, the sensitivity of the docking methods to the inherent inaccuracies of protein models, as opposed to the experimentally determined high-resolution structures, remains largely untested, primarily due to the absence of appropriate benchmark set(s). Structures in such a set should have pre-defined inaccuracy levels and, at the same time, resemble actual protein models in terms of structural motifs/packing. The set should also be large enough to ensure statistical reliability of the benchmarking results. We present a major update of the previously developed benchmark set of protein models. For each interactor, six models were generated with the model-to-native C? RMSD in the 1 to 6 Ĺ range. The models in the set were generated by a new approach, which corresponds to the actual modeling of new protein structures in the “real case scenario,” as opposed to the previous set, where a significant number of structures were model-like only. In addition, the larger number of complexes (165 vs. 63 in the previous set) increases the statistical reliability of the benchmarking. We estimated the highest accuracy of the predicted complexes (according to CAPRI criteria), which can be attained using the benchmark structures. The set is available at http://dockground.bioinformatics.ku.edu. PMID:25712716

  14. Protein models docking benchmark 2.

    PubMed

    Anishchenko, Ivan; Kundrotas, Petras J; Tuzikov, Alexander V; Vakser, Ilya A

    2015-05-01

    Structural characterization of protein-protein interactions is essential for our ability to understand life processes. However, only a fraction of known proteins have experimentally determined structures. Such structures provide templates for modeling of a large part of the proteome, where individual proteins can be docked by template-free or template-based techniques. Still, the sensitivity of the docking methods to the inherent inaccuracies of protein models, as opposed to the experimentally determined high-resolution structures, remains largely untested, primarily due to the absence of appropriate benchmark set(s). Structures in such a set should have predefined inaccuracy levels and, at the same time, resemble actual protein models in terms of structural motifs/packing. The set should also be large enough to ensure statistical reliability of the benchmarking results. We present a major update of the previously developed benchmark set of protein models. For each interactor, six models were generated with the model-to-native C(?) RMSD in the 1 to 6 Ĺ range. The models in the set were generated by a new approach, which corresponds to the actual modeling of new protein structures in the "real case scenario," as opposed to the previous set, where a significant number of structures were model-like only. In addition, the larger number of complexes (165 vs. 63 in the previous set) increases the statistical reliability of the benchmarking. We estimated the highest accuracy of the predicted complexes (according to CAPRI criteria), which can be attained using the benchmark structures. The set is available at http://dockground.bioinformatics.ku.edu. PMID:25712716

  15. Characterization of wheat puroindoline proteins.

    PubMed

    Day, Li; Bhandari, Dhan G; Greenwell, Philip; Leonard, Steven A; Schofield, J David

    2006-12-01

    Puroindoline proteins were purified from selected UK-grown hexaploid wheats. Their identities were confirmed on the basis of capillary electrophoresis mobilities, relative molecular mass and N-terminal amino acid sequencing. Only one form of puroindoline-a protein was found in those varieties, regardless of endosperm texture. Three allelic forms of puroindoline-b protein were identified. Nucleotide sequencing of cDNA produced by RT-PCR of isolated mRNA indicated that these were the 'wild-type', found in soft wheats, puroindoline-b containing a Gly-->Ser amino acid substitution (position 46) and puroindoline-b containing a Trp-->Arg substitution (position 44). The latter two were found in hard wheats. Microheterogeneity, due to short extensions and/or truncations at the N-terminus and C-terminus, was detected for both puroindoline-a and puroindoline-b. The type of microheterogeneity observed was more consistent for puroindoline-a than for puroindoline-b, and may arise through slightly different post-translational processing pathways. A puroindoline-b allele corresponding to a Leu-->Pro substitution (position 60) was identified from the cDNA sequence of the hard variety Chablis, but no mature puroindoline-b protein was found in this or two other European varieties known to possess this puroindoline-b allele. Wheats possessing the puroindoline-b proteins with point mutations appeared to contain lower amounts of puroindoline protein. Such wheats have a hard endosperm texture, as do wheats from which puroindoline-a or puroindoline-b are absent. Our results suggest that point mutations in puroindoline-b genes may confer hard endosperm texture through accumulation of allelic forms of puroindoline-b proteins with altered functional properties and/or through lower amounts of puroindoline proteins. PMID:17076702

  16. Computational prediction of protein-protein interactions.

    PubMed

    Ehrenberger, Tobias; Cantley, Lewis C; Yaffe, Michael B

    2015-01-01

    The prediction of protein-protein interactions and kinase-specific phosphorylation sites on individual proteins is critical for correctly placing proteins within signaling pathways and networks. The importance of this type of annotation continues to increase with the continued explosion of genomic and proteomic data, particularly with emerging data categorizing posttranslational modifications on a large scale. A variety of computational tools are available for this purpose. In this chapter, we review the general methodologies for these types of computational predictions and present a detailed user-focused tutorial of one such method and computational tool, Scansite, which is freely available to the entire scientific community over the Internet. PMID:25859943

  17. Hyperquenching for protein cryocrystallography

    PubMed Central

    Warkentin, Matthew; Berejnov, Viatcheslav; Husseini, Naji S.; Thorne, Robert E.

    2010-01-01

    When samples having volumes characteristic of protein crystals are plunge cooled in liquid nitrogen or propane, most cooling occurs in the cold gas layer above the liquid. By removing this cold gas layer, cooling rates for small samples and modest plunge velocities are increased to 1.5 × 104 K s?1, with increases of a factor of 100 over current best practice possible with 10 ?m samples. Glycerol concentrations required to eliminate water crystallization in protein-free aqueous mixtures drop from ?28% w/v to as low as 6% w/v. These results will allow many crystals to go from crystallization tray to liquid cryogen to X-ray beam without cryoprotectants. By reducing or eliminating the need for cryoprotectants in growth solutions, they may also simplify the search for crystallization conditions and for optimal screens. The results presented here resolve many puzzles, such as why plunge cooling in liquid nitrogen or propane has, until now, not yielded significantly better diffraction quality than gas-stream cooling. PMID:20461232

  18. Proteins as "dopable" bio-electronic materials

    NASA Astrophysics Data System (ADS)

    Cahen, David

    2013-02-01

    Proteins are surprisingly good solid-state electronic conductors. This holds also for proteins without any known biological electron transfer function. How do they do it? To answer this question we measure solid-state electron transport (ETp) across proteins that are "dry" (only tightly bound water, to retain the conformation, still present). We compare results for the electron transfer (ET) protein, Azurin (Az), the proton-pumping membrane protein Bacteriorhodopsin (bR), and for Human and Bovine Serum Albumin (HSA and BSA). Clear differences between these proteins are seen, which preserve their structure in the solid state measurement configuration. Importantly for future bioelectronics, the results are sensitive to protein modification, e.g., removing or disconnecting the retinal in bR and removing or replacing the Cu redox centre in Az. These cofactors can thus be viewed as natural dopants for proteins. Insight in the ETp mechanism comes from temperature-dependent studies. Az shows 40-360K temperature-independent ETp across its 3.5 nm long axis, until its denaturation temperature, indicative of tunneling. Cu removal, replacement (by Zn) or deuteration changes this to thermally activated ETp. This suggests hopping and involvement of the amide backbone in the ETp. The latter, which rhymes with indications from ETp experiments on oligopeptide and simulations of ET in proteins, opens the way for modeling what otherwise is an awfully complex system. Below 200K all proteins and their variants show temperature-independent ETp. We can furthermore make a totally electrically inactive protein, HSA, into an efficient ETp medium by doping it with natural poly-ene. Putting our data in perspective by comparing them to all known protein ETp data in the literature, we conclude that, in general, proteins are well described as dopable molecular wires.

  19. Urine Protein and Urine Protein to Creatinine Ratio

    MedlinePLUS

    ... Visit Global Sites Search Help? Urine Protein and Urine Protein to Creatinine Ratio Share this page: Was this page helpful? ... Urine Protein; Urine Total Protein; Urine Protein to Creatinine Ratio; UPCR Formal name: Urine Protein Related tests: Urinalysis ; Albumin ; Microalbumin ; Protein Electrophoresis ; ...

  20. Discover protein sequence signatures from protein-protein interaction data

    E-print Network

    Fang, Jianwen; Haasl, R. J.; Dong, Yinghua; Lushington, Gerald H.

    2005-11-23

    Bioinformatics Open Access Research article Discover protein sequence signatures from protein-protein interaction data Jianwen Fang* 1,2 , Ryan J Haasl 1 , Yinghua Dong 1 and Gerald H Lushington 1,3 Address: 1 Bioinformatics Core Facility, University of Kansas...@ku.edu; Ryan J Haasl - rh2@medicine.wisc.edu; Yinghua Dong - yinghua@ku.edu; Gerald H Lushington - glushington@ku.edu * Corresponding author Abstract Background: The development of high-throughput technologies such as yeast two-hybrid systems and mass...

  1. ProtPhylo: identification of protein-phenotype and protein-protein functional associations via phylogenetic profiling.

    PubMed

    Cheng, Yiming; Perocchi, Fabiana

    2015-07-01

    ProtPhylo is a web-based tool to identify proteins that are functionally linked to either a phenotype or a protein of interest based on co-evolution. ProtPhylo infers functional associations by comparing protein phylogenetic profiles (co-occurrence patterns of orthology relationships) for more than 9.7 million non-redundant protein sequences from all three domains of life. Users can query any of 2048 fully sequenced organisms, including 1678 bacteria, 255 eukaryotes and 115 archaea. In addition, they can tailor ProtPhylo to a particular kind of biological question by choosing among four main orthology inference methods based either on pair-wise sequence comparisons (One-way Best Hits and Best Reciprocal Hits) or clustering of orthologous proteins across multiple species (OrthoMCL and eggNOG). Next, ProtPhylo ranks phylogenetic neighbors of query proteins or phenotypic properties using the Hamming distance as a measure of similarity between pairs of phylogenetic profiles. Candidate hits can be easily and flexibly prioritized by complementary clues on subcellular localization, known protein-protein interactions, membrane spanning regions and protein domains. The resulting protein list can be quickly exported into a csv text file for further analyses. ProtPhylo is freely available at http://www.protphylo.org. PMID:25956654

  2. Protein structure networks.

    PubMed

    Greene, Lesley H

    2012-11-01

    The application of the field of network science to the scientific disciplines of structural biology and biochemistry, have yielded important new insights into the nature and determinants of protein structures, function, dynamics and the folding process. Advancements in further understanding protein relationships through network science have also reshaped the way we view the connectivity of proteins in the protein universe. The canonical hierarchical classification can now be visualized for example, as a protein fold continuum. This review will survey several key advances in the expanding area of research being conducted to study protein structures and folding using network approaches. PMID:23042823

  3. Protein and Older Persons.

    PubMed

    Bauer, Juergen M; Diekmann, Rebecca

    2015-08-01

    An optimal protein intake is important for the preservation of muscle mass, functionality, and quality of life in older persons. In recent years, new recommendations regarding the optimal intake of protein in this population have been published. Based on the available scientific literature, 1.0 to 1.2 g protein/kg body weight (BW)/d are recommended in healthy older adults. In certain disease states, a daily protein intake of more than 1.2 g/kg BW may be required. The distribution of protein intake over the day, the amount per meal, and the amino acid profile of proteins are also discussed. PMID:26195093

  4. Protein quality control in the mammalian endoplasmic reticulum

    E-print Network

    Klemm, Elizabeth J. (Elizabeth Joanna)

    2011-01-01

    Quality control is an important part of protein biogenesis. Aberrant proteins must be destroyed before they aggregate and cause deleterious effects. Failure to do so can result in cell death or malfunction and, ultimately, ...

  5. Predicting protein functions from PPI networks using functional aggregation.

    PubMed

    Hou, Jingyu; Chi, Xiaoxiao

    2012-11-01

    Predicting protein functions computationally from massive protein-protein interaction (PPI) data generated by high-throughput technology is one of the challenges and fundamental problems in the post-genomic era. Although there have been many approaches developed for computationally predicting protein functions, the mutual correlations among proteins in terms of protein functions have not been thoroughly investigated and incorporated into existing prediction methods, especially in voting based prediction methods. In this paper, we propose an innovative method to predict protein functions from PPI data by aggregating the functional correlations among relevant proteins using the Choquet-Integral in fuzzy theory. This functional aggregation measures the real impact of each relevant protein function on the final prediction results, and reduces the impact of repeated functional information on the prediction. Accordingly, a new protein similarity and a new iterative prediction algorithm are proposed in this paper. The experimental evaluations on real PPI datasets demonstrate the effectiveness of our method. PMID:22732317

  6. New Uses for Rendered Protein

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The history of rendering shows that current uses for rendered protein are a result of value-adding research. Feed nutritionists discovered how to use this formerly very low value by-product as an important component of formulated livestock feed. Today the feed market is mature and has been severel...

  7. Robust co-regulation of tyrosine phosphorylation sites on proteins reveals novel protein interactions†

    PubMed Central

    Naegle, Kristen M.; White, Forest M.; Lauffenburger, Douglas A.; Yaffe, Michael B.

    2012-01-01

    Cell signaling networks propagate information from extracellular cues via dynamic modulation of protein–protein interactions in a context-dependent manner. Networks based on receptor tyrosine kinases (RTKs), for example, phosphorylate intracellular proteins in response to extracellular ligands, resulting in dynamic protein–protein interactions that drive phenotypic changes. Most commonly used methods for discovering these protein–protein interactions, however, are optimized for detecting stable, longer-lived complexes, rather than the type of transient interactions that are essential components of dynamic signaling networks such as those mediated by RTKs. Substrate phosphorylation downstream of RTK activation modifies substrate activity and induces phospho-specific binding interactions, resulting in the formation of large transient macromolecular signaling complexes. Since protein complex formation should follow the trajectory of events that drive it, we reasoned that mining phosphoproteomic datasets for highly similar dynamic behavior of measured phosphorylation sites on different proteins could be used to predict novel, transient protein–protein interactions that had not been previously identified. We applied this method to explore signaling events downstream of EGFR stimulation. Our computational analysis of robustly co-regulated phosphorylation sites, based on multiple clustering analysis of quantitative time-resolved mass-spectrometry phosphoproteomic data, not only identified known sitewise-specific recruitment of proteins to EGFR, but also predicted novel, a priori interactions. A particularly intriguing prediction of EGFR interaction with the cytoskeleton-associated protein PDLIM1 was verified within cells using co-immunoprecipitation and in situ proximity ligation assays. Our approach thus offers a new way to discover protein–protein interactions in a dynamic context- and phosphorylation site-specific manner. PMID:22851037

  8. Assessing Energetic Contributions to Binding from a Disordered Region in a Protein-Protein Interaction

    SciTech Connect

    S Cho; C Swaminathan; D Bonsor; M Kerzic; R Guan; J Yang; C Kieke; P Anderson; D Kranz; et al.

    2011-12-31

    Many functional proteins are at least partially disordered prior to binding. Although the structural transitions upon binding of disordered protein regions can influence the affinity and specificity of protein complexes, their precise energetic contributions to binding are unknown. Here, we use a model protein-protein interaction system in which a locally disordered region has been modified by directed evolution to quantitatively assess the thermodynamic and structural contributions to binding of disorder-to-order transitions. Through X-ray structure determination of the protein binding partners before and after complex formation and isothermal titration calorimetry of the interactions, we observe a correlation between protein ordering and binding affinity for complexes along this affinity maturation pathway. Additionally, we show that discrepancies between observed and calculated heat capacities based on buried surface area changes in the protein complexes can be explained largely by heat capacity changes that would result solely from folding the locally disordered region. Previously developed algorithms for predicting binding energies of protein-protein interactions, however, are unable to correctly model the energetic contributions of the structural transitions in our model system. While this highlights the shortcomings of current computational methods in modeling conformational flexibility, it suggests that the experimental methods used here could provide training sets of molecular interactions for improving these algorithms and further rationalizing molecular recognition in protein-protein interactions.

  9. Stabilizing membrane proteins through protein engineering.

    PubMed

    Scott, Daniel J; Kummer, Lutz; Tremmel, Dirk; Plückthun, Andreas

    2013-06-01

    Integral membrane proteins (IMPs) are crucial components of all cells but are difficult to study in vitro because they are generally unstable when removed from their native membranes using detergents. Despite the major biomedical relevance of IMPs, less than 1% of Protein Data Bank (PDB) entries are IMP structures, reflecting the technical gap between studies of soluble proteins compared to IMPs. Stability can be engineered into IMPs by inserting stabilizing mutations, thereby generating proteins that can be successfully applied to biochemical and structural studies when solubilized in detergent micelles. The identification of stabilizing mutations is not trivial, and this review will focus on the methods that have been used to identify stabilized membrane proteins, including alanine scanning and screening, directed evolution and computational design. PMID:23639904

  10. Origins of the protein synthesis cycle

    NASA Technical Reports Server (NTRS)

    Fox, S. W.

    1981-01-01

    Largely derived from experiments in molecular evolution, a theory of protein synthesis cycles has been constructed. The sequence begins with ordered thermal proteins resulting from the self-sequencing of mixed amino acids. Ordered thermal proteins then aggregate to cell-like structures. When they contained proteinoids sufficiently rich in lysine, the structures were able to synthesize offspring peptides. Since lysine-rich proteinoid (LRP) also catalyzes the polymerization of nucleoside triphosphate to polynucleotides, the same microspheres containing LRP could have synthesized both original cellular proteins and cellular nucleic acids. The LRP within protocells would have provided proximity advantageous for the origin and evolution of the genetic code.

  11. Can protein levels be economically increased?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    One result from the 2010 hard red winter wheat harvest was an increase of discussions on protein values across the southern great plains. The crop garnered relatively low protein values for several reasons, many of which were directly related to the weather patterns and environmental conditions. T...

  12. Increased Adipose Protein Carbonylation in Human Obesity

    PubMed Central

    Frohnert, Brigitte I.; Sinaiko, Alan R.; Serrot, Federico J.; Foncea, Rocio E.; Moran, Antoinette; Ikramuddin, Sayeed; Choudry, Umar; Bernlohr, David A.

    2015-01-01

    Insulin resistance is associated with obesity but mechanisms controlling this relationship in humans are not fully understood. Studies in animal models suggest a linkage between adipose reactive oxygen species (ROS) and insulin resistance. ROS oxidize cellular lipids to produce a variety of lipid hydroperoxides that in turn generate reactive lipid aldehydes that covalently modify cellular proteins in a process termed carbonylation. Mammalian cells defend against reactive lipid aldehydes and protein carbonylation by glutathionylation using glutathione-S-transferase A4 (GSTA4) or carbonyl reduction/oxidation via reductases and/or dehydrogenases. Insulin resistance in mice is linked to ROS production and increased level of protein carbonylation, mitochondrial dysfunction, decreased insulin-stimulated glucose transport, and altered adipokine secretion. To assess protein carbonylation and insulin resistance in humans, eight healthy participants underwent subcutaneous fat biopsy from the periumbilical region for protein analysis and frequently sampled intravenous glucose tolerance testing to measure insulin sensitivity. Soluble proteins from adipose tissue were analyzed using two-dimensional gel electrophoresis and the major carbonylated proteins identified as the adipocyte and epithelial fatty acid–binding proteins. The level of protein carbonylation was directly correlated with adiposity and serum free fatty acids (FFAs). These results suggest that in human obesity oxidative stress is linked to protein carbonylation and such events may contribute to the development of insulin resistance. PMID:21593812

  13. An activity coefficient model for proteins.

    PubMed

    Agena, S M; Bogle, I D; Pessoa, F L

    1997-07-01

    Modeling of the properties of biochemical components is gaining increasing interest due to its potential for further application within the area of biochemical process development. Generally protein solution properties such as protein solubility are expressed through component activity coefficients which are studied here. The original UNIQUAC model is chosen for the representation of protein activity coefficients and, to the best of our knowledge, this is the first time it has been directly applied to protein solutions. Ten different protein-salt-water systems with four different proteins, serum albumin, alphacymotrypsin, beta-lactoglobulin and ovalbumin, are investigated. A root-mean-squared deviation of 0.54% is obtained for the model by comparing calculated protein activity coefficients and protein activity coefficients deduced from osmotic measurements through virial expansion. Model predictions are used to analyze the effect of salt concentrations, pH, salt types, and temperature on protein activity coefficients and also on protein solubility and demonstrate consistency with results from other references. PMID:18636445

  14. Predicting protein dynamics from structural ensembles

    NASA Astrophysics Data System (ADS)

    Copperman, J.; Guenza, M. G.

    2015-12-01

    The biological properties of proteins are uniquely determined by their structure and dynamics. A protein in solution populates a structural ensemble of metastable configurations around the global fold. From overall rotation to local fluctuations, the dynamics of proteins can cover several orders of magnitude in time scales. We propose a simulation-free coarse-grained approach which utilizes knowledge of the important metastable folded states of the protein to predict the protein dynamics. This approach is based upon the Langevin Equation for Protein Dynamics (LE4PD), a Langevin formalism in the coordinates of the protein backbone. The linear modes of this Langevin formalism organize the fluctuations of the protein, so that more extended dynamical cooperativity relates to increasing energy barriers to mode diffusion. The accuracy of the LE4PD is verified by analyzing the predicted dynamics across a set of seven different proteins for which both relaxation data and NMR solution structures are available. Using experimental NMR conformers as the input structural ensembles, LE4PD predicts quantitatively accurate results, with correlation coefficient ? = 0.93 to NMR backbone relaxation measurements for the seven proteins. The NMR solution structure derived ensemble and predicted dynamical relaxation is compared with molecular dynamics simulation-derived structural ensembles and LE4PD predictions and is consistent in the time scale of the simulations. The use of the experimental NMR conformers frees the approach from computationally demanding simulations.

  15. Predicting protein dynamics from structural ensembles.

    PubMed

    Copperman, J; Guenza, M G

    2015-12-28

    The biological properties of proteins are uniquely determined by their structure and dynamics. A protein in solution populates a structural ensemble of metastable configurations around the global fold. From overall rotation to local fluctuations, the dynamics of proteins can cover several orders of magnitude in time scales. We propose a simulation-free coarse-grained approach which utilizes knowledge of the important metastable folded states of the protein to predict the protein dynamics. This approach is based upon the Langevin Equation for Protein Dynamics (LE4PD), a Langevin formalism in the coordinates of the protein backbone. The linear modes of this Langevin formalism organize the fluctuations of the protein, so that more extended dynamical cooperativity relates to increasing energy barriers to mode diffusion. The accuracy of the LE4PD is verified by analyzing the predicted dynamics across a set of seven different proteins for which both relaxation data and NMR solution structures are available. Using experimental NMR conformers as the input structural ensembles, LE4PD predicts quantitatively accurate results, with correlation coefficient ? = 0.93 to NMR backbone relaxation measurements for the seven proteins. The NMR solution structure derived ensemble and predicted dynamical relaxation is compared with molecular dynamics simulation-derived structural ensembles and LE4PD predictions and is consistent in the time scale of the simulations. The use of the experimental NMR conformers frees the approach from computationally demanding simulations. PMID:26723616

  16. Macromolecular recognition in the Protein Data Bank

    SciTech Connect

    Janin, Joël; Rodier, Francis; Chakrabarti, Pinak

    2007-01-01

    X-ray structures in the PDB illustrate both the specific recognition of two polypeptide chains in protein–protein complexes and dimeric proteins and their nonspecific interaction at crystal contacts. Crystal structures deposited in the Protein Data Bank illustrate the diversity of biological macromolecular recognition: transient interactions in protein–protein and protein–DNA complexes and permanent assemblies in homodimeric proteins. The geometric and physical chemical properties of the macromolecular interfaces that may govern the stability and specificity of recognition are explored in complexes and homodimers compared with crystal-packing interactions. It is found that crystal-packing interfaces are usually much smaller; they bury fewer atoms and are less tightly packed than in specific assemblies. Standard-size interfaces burying 1200–2000 Ĺ{sup 2} of protein surface occur in protease–inhibitor and antigen–antibody complexes that assemble with little or no conformation changes. Short-lived electron-transfer complexes have small interfaces; the larger size of the interfaces observed in complexes involved in signal transduction and homodimers correlates with the presence of conformation changes, often implicated in biological function. Results of the CAPRI (critical assessment of predicted interactions) blind prediction experiment show that docking algorithms efficiently and accurately predict the mode of assembly of proteins that do not change conformation when they associate. They perform less well in the presence of large conformation changes and the experiment stimulates the development of novel procedures that can handle such changes.

  17. Structural anatomy of telomere OB proteins

    PubMed Central

    Horvath, Martin P.

    2015-01-01

    Telomere DNA-binding proteins protect the ends of chromosomes in eukaryotes. A subset of these proteins are constructed with one or more OB folds and bind with G+T-rich single-stranded DNA found at the extreme termini. The resulting DNA-OB protein complex interacts with other telomere components to coordinate critical telomere functions of DNA protection and DNA synthesis. While the first crystal and NMR structures readily explained protection of telomere ends, the picture of how single-stranded DNA becomes available to serve as primer and template for synthesis of new telomere DNA is only recently coming into focus. New structures of telomere OB fold proteins alongside insights from genetic and biochemical experiments have made significant contributions towards understanding how protein-binding OB proteins collaborate with DNA-binding OB proteins to recruit telomerase and DNA polymerase for telomere homeostasis. This review surveys telomere OB protein structures alongside highly comparable structures derived from replication protein A (RPA) components, with the goal of providing a molecular context for understanding telomere OB protein evolution and mechanism of action in protection and synthesis of telomere DNA. PMID:21950380

  18. A simple method for finding a protein’s ligand-binding pockets

    PubMed Central

    2014-01-01

    Background This paper provides a simple and rapid method for a protein-clustering strategy. The basic idea implemented here is to use computational geometry methods to predict and characterize ligand-binding pockets of a given protein structure. In addition to geometrical characteristics of the protein structure, we consider some simple biochemical properties that help recognize the best candidates for pockets in a protein’s active site. Results Our results are shown to produce good agreement with known empirical results. Conclusions The method presented in this paper is a low-cost rapid computational method that could be used to classify proteins and other biomolecules, and furthermore could be useful in reducing the cost and time of drug discovery. PMID:25038637

  19. Protein Structure Analysis Iosif Vaisman

    E-print Network

    Vaisman, Iosif

    Protein Structure Analysis Iosif Vaisman 2010 BINF 731 http://binf.gmu.edu/vaisman/binf731/ Protein sequence (helices, beta-sheets, turns) ·Tertiary - the three-dimensional fold of a protein subunit prediction Protein structure classification Protein representations Protein representations Protein

  20. Towards a detailed atlas of protein-protein interactions.

    PubMed

    Mosca, Roberto; Pons, Tirso; Céol, Arnaud; Valencia, Alfonso; Aloy, Patrick

    2013-12-01

    Protein interaction maps are the key to understand the complex world of biological processes inside the cell. Public protein databases have already catalogued hundreds of thousands of experimentally discovered interactions, and struggle to curate all the existing information dispersed through the literature. However, to be most efficient, standard protocols need to be implemented for direct submission of new interaction sets directly into databases. At the same time, great efforts are invested to expand the coverage of the interaction space and unveil the molecular details of such interactions up to the atomistic level. The net result will be the definition of a detailed atlas spanning the universe of protein interactions to guide the everyday work of the biologist. PMID:23896349

  1. Human T-lymphotropic Virus Type 1-infected Cells Secrete Exosomes That Contain Tax Protein*S

    E-print Network

    Vertes, Akos

    Human T-lymphotropic Virus Type 1-infected Cells Secrete Exosomes That Contain Tax Protein College of Medicine, Doylestown, Pennsylvania 18902 Background: Extracellular exosomes contain various functional elements. Results: Exosomal Tax protein causes phenotypic changes in uninfected cells. Conclusion

  2. Co-translational assembly of protein complexes.

    PubMed

    Wells, Jonathan N; Bergendahl, L Therese; Marsh, Joseph A

    2015-12-01

    The interaction of biological macromolecules is a fundamental attribute of cellular life. Proteins, in particular, often form stable complexes with one another. Although the importance of protein complexes is widely recognized, we still have only a very limited understanding of the mechanisms underlying their assembly within cells. In this article, we review the available evidence for one such mechanism, namely the coupling of protein complex assembly to translation at the polysome. We discuss research showing that co-translational assembly can occur in both prokaryotic and eukaryotic organisms and can have important implications for the correct functioning of the complexes that result. Co-translational assembly can occur for both homomeric and heteromeric protein complexes and for both proteins that are translated directly into the cytoplasm and those that are translated into or across membranes. Finally, we discuss the properties of proteins that are most likely to be associated with co-translational assembly. PMID:26614664

  3. Localization of peroxisomal matrix proteins by photobleaching

    SciTech Connect

    Buch, Charlotta; Soedertoerns University, Life Sciences, SE-141 89 Huddinge ; Hunt, Mary C.; Alexson, Stefan E.H.; Hallberg, Einar

    2009-10-16

    The distribution of some enzymes between peroxisomes and cytosol, or a dual localization in both these compartments, can be difficult to reconcile. We have used photobleaching in live cells expressing green fluorescent protein (GFP)-fusion proteins to show that imported bona fide peroxisomal matrix proteins are retained in the peroxisome. The high mobility of the GFP-fusion proteins in the cytosol and absence of peroxisomal escape makes it possible to eliminate the cytosolic fluorescence by photobleaching, to distinguish between exclusively cytosolic proteins and proteins that are also present at low levels in peroxisomes. Using this technique we found that GFP tagged bile acid-CoA:amino acid N-acyltransferase (BAAT) was exclusively localized in the cytosol in HeLa cells. We conclude that the cytosolic localization was due to its carboxyterminal non-consensus peroxisomal targeting signal (-SQL) since mutation of the -SQL to -SKL resulted in BAAT being efficiently imported into peroxisomes.

  4. Preparation of Soluble Proteins from Escherichia coli

    PubMed Central

    Wingfield, Paul T.

    2014-01-01

    Purification of human IL-1? is used in this unit as an example of the preparation of soluble proteins from E. coli. Bacteria containing IL-1? are lysed, and IL-1 ? in the resulting supernatant is purified by anion-exchange chromatography, salt precipitation and cation-exchange chromatography, and then concentrated. Finally, the IL-1 ? protein is applied to a gel-filtration column to separate it from remaining higher- and lower-molecular-weight contaminants, the purified protein is stored frozen or is lyophilized. The purification protocol described is typical for a protein that is expressed in fairly high abundance (i.e., >5% total protein) and accumulates in a soluble state. Also, the purification procedure serves as an example of how use classical protein purifications methods which may also be used in conjunction with the affinity-based methods now more commonly used. PMID:25367009

  5. Membrane protein expression: no cells required.

    PubMed

    Katzen, Federico; Peterson, Todd C; Kudlicki, Wieslaw

    2009-08-01

    Structural and functional studies of membrane proteins have been severely hampered by difficulties in producing sufficient quantities of properly folded protein products. It is well established that cell-based expression of membrane proteins is generally problematic and frequently results in low yield, cell toxicity, protein aggregation and misfolding. Owing to its inherent open nature, cell-free protein expression has become a highly promising tool for the fast and efficient production of these difficult-to-express proteins. Here we review the most recent advances in this field, underscoring the potentials and weaknesses of the newly developed approaches and place specific emphasis on the use of nanolipoprotein particles (NLPs or nanodiscs). PMID:19616329

  6. Microbial production of spider silk proteins.

    PubMed

    Fahnestock, S R; Yao, Z; Bedzyk, L A

    2000-08-01

    The remarkable properties of spider dragline silk and related protein polymers will find many applications if the materials can be produced economically. We have demonstrated the production of high molecular weight spider dragline silk analog proteins encoded by synthetic genes in several microbial systems, including Escherichia coli and Pichia pastoris. In E. coli, proteins of up to 1000 amino acids in length could be produced efficiently, but the yield and homogeneity of higher molecular weight silk proteins were found to be limited by truncated synthesis, probably as a result of ribosome termination errors. No such phenomenon was observed in the yeast P. pastoris, where higher molecular weight silk proteins could be produced without heterogeneity due to truncated synthesis. Spider dragline silk analog proteins could be secreted by P. pastoris when fused to both the signal sequence and N-terminal pro-sequence of the Saccharomyces cerevisiae alpha-mating factor gene. PMID:11763501

  7. Protein Arginine Methyltransferase 8: Tetrameric Structure and Protein Substrate Specificity.

    PubMed

    Lee, Wei-Chao; Lin, Wen-Ling; Matsui, Tsutomu; Chen, Eric S-W; Wei, Tong-You Wade; Lin, Wen-Hsuan; Hu, Hao; Zheng, Yujun George; Tsai, Ming-Daw; Ho, Meng-Chiao

    2015-12-29

    Type I protein arginine methyltransferases (PRMTs) catalyze asymmetric dimethylation of various proteins, and their dysregulations often correlate with tumorigenesis or developmental deficiency. Recent studies have focused on the in vivo substrate identification and the enzyme mechanism with peptide substrates. However, how PRMTs recognize substrates at the protein level remains unknown. PRMT8 is one of the least characterized type I PRMTs, and its crystal structure has not been reported. Here, we report the crystal structure of the PRMT8:SAH complex, identify a new non-histone protein substrate NIFK, and uncover a previously unknown regulatory region specifically required for recognizing NIFK. Instead of the canonical dimeric structure for other type I PRMTs, PRMT8 exists as a tetramer in solution. Using X-ray crystallography in combination with small-angle X-ray scattering experiments, the dimer of dimers architecture in which two PRMT8 dimers are held together mainly by ? strand interactions was proposed. Mutation of PRMT8-?15 impedes the methylation of NIFK but still allows methylation of the histone H2A/H2B dimer or a peptide substrate, suggesting a possible structural basis for recognition of protein substrates. Lastly, we observed two PRMT8 dimer orientations resulting in open (without SAH) and closed (with SAH bound) conformations. The comparison between open and closed conformations may provide useful information for PRMT1/8 inhibitor design. PMID:26529540

  8. Exploring strategies for protein trapping in Drosophila

    SciTech Connect

    Quinones-Coello, Ana T.; Petrella, Lisa N.; Ayers, Kathleen; Melillo, Anthony; Mazzalupo, Stacy; Hudson, Andrew M.; Wang, Shu; Castiblanco, Claudia; Buszczak, Michael; Hoskins, Roger A.; Cooley, Lynn

    2006-12-18

    The use of fluorescent protein tags has had a huge impact oncell biological studies in virtually every experimental system.Incorporation of coding sequence for fluorescent proteins such as greenfluorescent protein (GFP) into genes at their endogenous chromosomalposition is especially useful for generating GFP-fusion proteins thatprovide accurate cellular and subcellular expression data. We testedmodifications of a transposon-based protein trap screening procedure inDrosophila to optimize the rate of recovering useful protein traps andtheir analysis. Transposons carrying the GFP-coding sequence flanked bysplice acceptor and donor sequences were mobilized, and new insertionsthat resulted in production of GFP were captured using an automatedembryo sorter. Individual stocks were established, GFP expression wasanalyzed during oogenesis, and insertion sites were determined bysequencing genomic DNA flanking the insertions. The resulting collectionincludes lines with protein traps in which GFP was spliced into mRNAs andembedded within endogenous proteins or enhancer traps in which GFPexpression depended on splicing into transposon-derived RNA. We report atotal of 335 genes associated with protein or enhancer traps and aweb-accessible database for viewing molecular information and expressiondata for these genes.

  9. The Physics of Protein Crystallization

    NASA Technical Reports Server (NTRS)

    Vekilov, P. G.; Chernov, A. A.

    2002-01-01

    This paper covers review of recent research on protein crystal properties, nucleation, growth and perfection. Mechanical properties of crystals built of molecules strongly exceeding the range of molecular forces are very different from conventional ones. Similar scaling is responsible for specificity of phase equilibrium for macromolecular systems of which thermodynamics is discussed. Nucleation and growth peculiarity and similarity in protein solutions as compared to inorganic solutions is addressed. Hypotheses on why and when microgravity (lack of convection) conditions may result in more perfect crystals are discussed.

  10. Characterizing Protein Conformation Space

    E-print Network

    Nigham, Anshul

    In this work, we propose a radical approach for exploring the space of all possible protein structures. We present techniques to explore the clash-free conformation space, which comprises all protein structures whose atoms ...

  11. Protein electrophoresis - serum

    MedlinePLUS

    This lab test measures the types of protein in the fluid (serum) part of a blood sample. Other electrophoresis tests that measure proteins in the serum include: Immunoelectrophoresis Immunofixation Globulin electrophoresis

  12. Learning about Proteins

    MedlinePLUS

    ... body, and protecting you from disease. All About Amino Acids When you eat foods that contain protein, the ... called amino (say: uh-MEE-no) acids. The amino acids then can be reused to make the proteins ...

  13. Protein carbamylation and cardiovascular disease.

    PubMed

    Verbrugge, Frederik H; Tang, W H Wilson; Hazen, Stanley L

    2015-09-01

    Carbamylation constitutes a posttranslational modification of proteins or amino acids and results from different pathways in vivo. First is the non-enzymatic reaction between isocyanic acid, a decomposition product of urea, and either the N-terminus or the ?-amino group of lysine residues. Isocyanic acid levels, while low in vivo, are in equilibrium with urea and are thus increased in chronic and end-stage renal diseases. An alternative pathway involves the leukocyte heme protein myeloperoxidase, which catalyzes the oxidation of thiocyanate in the presence of hydrogen peroxide, producing isocyanate at inflammation sites. Notably, plasma thiocyanate levels are increased in smokers, and leukocyte-driven protein carbamylation occurs both within human and animal atherosclerotic plaques, as well as on plasma proteins. Protein carbamylation is considered a hallmark of molecular aging and is implicated in many pathological conditions. Recently, it has been shown that carbamylated low-density lipoprotein (LDL) induces endothelial dysfunction via lectin-like-oxidized LDL receptor-1 activation and increased reactive oxygen species production, leading to endothelial nitric oxide synthase uncoupling. Moreover, carbamylated LDL harbors atherogenic activities, including both binding to macrophage scavenger receptors inducing cholesterol accumulation and foam-cell formation, as well as promoting vascular smooth muscle proliferation. In contrast, high-density lipoprotein loses its anti-apoptotic activity after carbamylation, contributing to endothelial cell death. In addition to involvement in atherogenesis, protein carbamylation levels have emerged as a particularly strong predictor of both prevalent and incident cardiovascular disease risk. Recent studies also suggest that protein carbamylation may serve as a potential therapeutic target for the prevention of atherosclerotic heart disease. PMID:26061545

  14. Screening of the Binding of Small Molecules to Proteins by Desorption Electrospray Ionization Mass Spectrometry Combined with Protein Microarray

    NASA Astrophysics Data System (ADS)

    Yao, Chenxi; Wang, Tao; Zhang, Buqing; He, Dacheng; Na, Na; Ouyang, Jin

    2015-11-01

    The interaction between bioactive small molecule ligands and proteins is one of the important research areas in proteomics. Herein, a simple and rapid method is established to screen small ligands that bind to proteins. We designed an agarose slide to immobilize different proteins. The protein microarrays were allowed to interact with different small ligands, and after washing, the microarrays were screened by desorption electrospray ionization mass spectrometry (DESI MS). This method can be applied to screen specific protein binding ligands and was shown for seven proteins and 34 known ligands for these proteins. In addition, a high-throughput screening was achieved, with the analysis requiring approximately 4 s for one sample spot. We then applied this method to determine the binding between the important protein matrix metalloproteinase-9 (MMP-9) and 88 small compounds. The molecular docking results confirmed the MS results, demonstrating that this method is suitable for the rapid and accurate screening of ligands binding to proteins.

  15. How to image a single protein

    E-print Network

    Jean-Nicolas Longchamp; Stephan Rauschenbach; Sabine Abb; Conrad Escher; Tatiana Latychevskaia; Klaus Kern; Hans-Werner Fink

    2015-12-30

    Imaging a single protein has been a long-standing dream for advancing structural biology and with this various fields in natural science. In particular, revealing the distinct conformations of an individual protein is of outermost importance. To do so, one needs to master and combine three requirements. At first, a method for isolating individual proteins for further inspection has to be at hand; quite the opposite to the current challenge of assembling proteins into a crystal for X-ray analysis. Furthermore, technologies are required for keeping a single protein fixed in space long enough to accumulate sufficient structural information from a scattering experiment. Last but not least, gentle radiation with a wavelength small enough to uncover structural details while ensuring that radiation damage does not decompose the protein during observation as it is available by low-energy electron holography is vital for imaging. Here we show that soft-landing electrospray beam deposition allows for specific selection and sound deposition of individual proteins and protein complexes onto ultraclean freestanding graphene in an ultra-high vacuum environment. Due to the fact that graphene is transparent for low-energy electrons and since the latter do not damage biological molecules, we were able to acquire high signal-to-noise ratio electron holograms of individual proteins (Cytochrome C and BSA) as well as of protein complexes (haemoglobin). The numerical hologram reconstructions reveal the overall shape of single proteins. With this, images of individual folded proteins and protein complexes, not being the result of an averaging process, have been obtained for the first time.

  16. Moonlighting proteins in sperm-egg interactions.

    PubMed

    Petit, François M; Serres, Catherine; Auer, Jana

    2014-12-01

    Sperm-egg interaction is a highly species-specific step during the fertilization process. The first steps consist of recognition between proteins on the sperm head and zona pellucida (ZP) glycoproteins, the acellular coat that protects the oocyte. We aimed to determine which sperm head proteins interact with ZP2, ZP3 and ZP4 in humans. Two approaches were combined to identify these proteins: immunoblotting human spermatozoa targeted by antisperm antibodies (ASAs) from infertile men and far-Western blotting of human sperm proteins overlaid by each of the human recombinant ZP (hrZP) proteins. We used a proteomic approach with 2D electrophoretic separation of sperm protein revealed using either ASAs eluted from infertile patients or recombinant human ZP glycoproteins expressed in Chinese-hamster ovary (CHO) cells. Only spots highlighted by both methods were analysed by MALDI-MS/MS for identification. We identified proteins already described in human spermatozoa, but implicated in different metabolic pathways such as glycolytic enzymes [phosphokinase type 3 (PK3), enolase 1 (ENO1), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), aldolase A (ALDOA) and triose phosphate isomerase (TPI)], detoxification enzymes [GST Mu (GSTM) and phospholipid hydroperoxide glutathione peroxidase (PHGPx) 4], ion channels [voltage-dependent anion channel 2 (VDAC2)] or structural proteins (outer dense fibre 2). Several proteins were localized on the sperm head by indirect immunofluorescence, and their interaction with ZP proteins was confirmed by co-precipitation experiments. These results confirm the complexity of the sperm-ZP recognition process in humans with the implication of different proteins interacting with the main three ZP glycoproteins. The multiple roles of these proteins suggest that they are multifaceted or moonlighting proteins. PMID:25399599

  17. Proteins and Complexity

    NASA Astrophysics Data System (ADS)

    Murray, Joelle; Gibbon, Dana; Runyon, Alissa; Bajracharya, Arun

    2015-03-01

    A protein's tertiary structure determines its function in living organisms. The different functions proteins serve necessitate variety in native structures. How is variation in tertiary structure created from a common set of amino acids and molecular forces? In other words, what generates complexity in structures across all types of native proteins? To explore this question, a simple HP model of protein folding was explored for evidence of self-organized criticality, a potential generator of complexity.

  18. Proteins of Norwalk virus.

    PubMed

    Greenberg, H B; Valdesuso, J R; Kalica, A R; Wyatt, R G; McAuliffe, V J; Kapikian, A Z; Chanock, R M

    1981-03-01

    The proteins of the Norwalk virus were studied by polyacrylamide gel electrophoresis. Highly purified specifically immunoprecipitated virions appeared to contain a single primary structural protein with a molecular weight of 59,000. In addition, a soluble Norwalk viral protein with a molecular weight of 30,000 was identified in fecal specimens containing Norwalk virus. The protein structure of the virion is similar to that of the Calciviridae family. PMID:6785451

  19. Proteins of Norwalk virus.

    PubMed Central

    Greenberg, H B; Valdesuso, J R; Kalica, A R; Wyatt, R G; McAuliffe, V J; Kapikian, A Z; Chanock, R M

    1981-01-01

    The proteins of the Norwalk virus were studied by polyacrylamide gel electrophoresis. Highly purified specifically immunoprecipitated virions appeared to contain a single primary structural protein with a molecular weight of 59,000. In addition, a soluble Norwalk viral protein with a molecular weight of 30,000 was identified in fecal specimens containing Norwalk virus. The protein structure of the virion is similar to that of the Calciviridae family. Images PMID:6785451

  20. Lasing from fluorescent protein crystals.

    PubMed

    Oh, Heon Jeong; Gather, Malte C; Song, Ji-Joon; Yun, Seok Hyun

    2014-12-15

    We investigated fluorescent protein crystals for potential photonic applications, for the first time to our knowledge. Rod-shaped crystals of enhanced green fluorescent protein (EGFP) were synthesized, with diameters of 0.5-2 ?m and lengths of 100-200 ?m. The crystals exhibit minimal light scattering due to their ordered structure and generate substantially higher fluorescence intensity than EGFP or dye molecules in solutions. The magnitude of concentration quenching in EGFP crystals was measured to be about 7-10 dB. Upon optical pumping at 485 nm, individual EGFP crystals located between dichroic mirrors generated laser emission with a single-mode spectral line at 513 nm. Our results demonstrate the potential of protein crystals as novel optical elements for self-assembled, micro- or nano-lasers and amplifiers in aqueous environment. PMID:25607090

  1. Sucralose Destabilization of Protein Structure.

    PubMed

    Chen, Lee; Shukla, Nimesh; Cho, Inha; Cohn, Erin; Taylor, Erika A; Othon, Christina M

    2015-04-16

    Sucralose is a commonly employed artificial sweetener that behaves very differently than its natural disaccharide counterpart, sucrose, in terms of its interaction with biomolecules. The presence of sucralose in solution is found to destabilize the native structure of two model protein systems: the globular protein bovine serum albumin and an enzyme staphylococcal nuclease. The melting temperature of these proteins decreases as a linear function of sucralose concentration. We correlate this destabilization to the increased polarity of the molecule. The strongly polar nature is manifested as a large dielectric friction exerted on the excited-state rotational diffusion of tryptophan using time-resolved fluorescence anisotropy. Tryptophan exhibits rotational diffusion proportional to the measured bulk viscosity for sucrose solutions over a wide range of concentrations, consistent with a Stokes-Einstein model. For sucralose solutions, however, the diffusion is dependent on the concentration, strongly diverging from the viscosity predictions, and results in heterogeneous rotational diffusion. PMID:26263149

  2. Neutron protein crystallography in JAERI

    NASA Astrophysics Data System (ADS)

    Tanaka, I.

    2004-07-01

    Neutron diffraction provides an experimental method of directly locating hy- drogen atoms in proteins. After developing an original neutron detector (neutron imaging plate) and a novel practical neutron monochromator (elastically bent perfect Si monochro- mator), BIX-type diffractometers which were equipped with these tools were e+/-ciently constructed at JRR-3 in Japan Atomic Energy Research Institute (JAERI), Japan and they have finished many protein crystallographic measurements and interesting results have come one after another. At the same time a method of growing large protein single crystals and a database of hydrogen and hydration have also been developed. In the near future, a pulsed neutron diffractometer for biological macromolecules has been proposed at J-PARC in JAERI.

  3. DC Protein Assay Instruction

    E-print Network

    Lebendiker, Mario

    the addition of reagents. The assay is based on the reaction of protein with an alkaline copper tartrate: The reaction between protein and copper in an alkaline medium, and the subsequent reduction of Folin reagentDC Protein Assay Instruction Manual For Technical Service Call Your Local Bio-Rad Office

  4. Modeling Protein Domain Function

    ERIC Educational Resources Information Center

    Baker, William P.; Jones, Carleton "Buck"; Hull, Elizabeth

    2007-01-01

    This simple but effective laboratory exercise helps students understand the concept of protein domain function. They use foam beads, Styrofoam craft balls, and pipe cleaners to explore how domains within protein active sites interact to form a functional protein. The activity allows students to gain content mastery and an understanding of the…

  5. CSF total protein

    MedlinePLUS

    CSF total protein is a test to determine the amount of protein in your spinal fluid, also called cerebrospinal fluid (CSF). ... The normal protein range varies from lab to lab, but is typically about 15 to 60 mg/dL. Note: mg/dL = ...

  6. CSF myelin basic protein

    MedlinePLUS

    CSF myelin basic protein is a test to measure the level of myelin basic protein (MBP) in the cerebrospinal fluid (CSF). The CSF ... less than 4 ng/mL of myelin basic protein in the CSF. Note: ng/mL = nanogram per ...

  7. Texturized dairy proteins

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Dairy proteins are amenable to structural modifications induced by high temperature, shear and moisture; in particular, whey proteins can change conformation to new unfolded states. The change in protein state is a basis for creating new foods. The dairy products, nonfat dried milk (NDM), whey prote...

  8. Protein Identification Database Searching

    E-print Network

    Richardson, David

    ASMS 2005 Protein Identification by Database Searching John Cottrell Matrix Science #12;ASMS 2005 molecular weights from an enzyme digest of a protein #12;ASMS 2005 Henzel, W. J., Billeci, T. M., Stults, J ID: 1. Peptide Mass Fingerprint A set of peptide molecular weights from an enzyme digest of a protein

  9. Destabilized bioluminescent proteins

    DOEpatents

    Allen, Michael S. (Knoxville, TN); Rakesh, Gupta (New Delhi, IN); Gary, Sayler S. (Blaine, TN)

    2007-07-31

    Purified nucleic acids, vectors and cells containing a gene cassette encoding at least one modified bioluminescent protein, wherein the modification includes the addition of a peptide sequence. The duration of bioluminescence emitted by the modified bioluminescent protein is shorter than the duration of bioluminescence emitted by an unmodified form of the bioluminescent protein.

  10. Modeling Protein Self Assembly

    ERIC Educational Resources Information Center

    Baker, William P.; Jones, Carleton Buck; Hull, Elizabeth

    2004-01-01

    Understanding the structure and function of proteins is an important part of the standards-based science curriculum. Proteins serve vital roles within the cell and malfunctions in protein self assembly are implicated in degenerative diseases. Experience indicates that this topic is a difficult one for many students. We have found that the concept…

  11. Overview of Protein Microarrays

    PubMed Central

    Reymond Sutandy, FX; Qian, Jiang; Chen, Chien-Sheng; Zhu, Heng

    2013-01-01

    Protein microarray is an emerging technology that provides a versatile platform for characterization of hundreds of thousands of proteins in a highly parallel and high-throughput way. Two major classes of protein microarrays are defined to describe their applications: analytical and functional protein microarrays. In addition, tissue or cell lysates can also be fractionated and spotted on a slide to form a reverse-phase protein microarray. While the fabrication technology is maturing, applications of protein microarrays, especially functional protein microarrays, have flourished during the past decade. Here, we will first review recent advances in the protein microarray technologies, and then present a series of examples to illustrate the applications of analytical and functional protein microarrays in both basic and clinical research. The research areas will include detection of various binding properties of proteins, study of protein posttranslational modifications, analysis of host-microbe interactions, profiling antibody specificity, and identification of biomarkers in autoimmune diseases. As a powerful technology platform, it would not be surprising if protein microarrays will become one of the leading technologies in proteomic and diagnostic fields in the next decade. PMID:23546620

  12. Protein – Which is Best?

    PubMed Central

    Hoffman, Jay R.; Falvo, Michael J.

    2004-01-01

    Protein intake that exceeds the recommended daily allowance is widely accepted for both endurance and power athletes. However, considering the variety of proteins that are available much less is known concerning the benefits of consuming one protein versus another. The purpose of this paper is to identify and analyze key factors in order to make responsible recommendations to both the general and athletic populations. Evaluation of a protein is fundamental in determining its appropriateness in the human diet. Proteins that are of inferior content and digestibility are important to recognize and restrict or limit in the diet. Similarly, such knowledge will provide an ability to identify proteins that provide the greatest benefit and should be consumed. The various techniques utilized to rate protein will be discussed. Traditionally, sources of dietary protein are seen as either being of animal or vegetable origin. Animal sources provide a complete source of protein (i.e. containing all essential amino acids), whereas vegetable sources generally lack one or more of the essential amino acids. Animal sources of dietary protein, despite providing a complete protein and numerous vitamins and minerals, have some health professionals concerned about the amount of saturated fat common in these foods compared to vegetable sources. The advent of processing techniques has shifted some of this attention and ignited the sports supplement marketplace with derivative products such as whey, casein and soy. Individually, these products vary in quality and applicability to certain populations. The benefits that these particular proteins possess are discussed. In addition, the impact that elevated protein consumption has on health and safety issues (i.e. bone health, renal function) are also reviewed. Key Points Higher protein needs are seen in athletic populations. Animal proteins is an important source of protein, however potential health concerns do exist from a diet of protein consumed from primarily animal sources. With a proper combination of sources, vegetable proteins may provide similar benefits as protein from animal sources. Casein protein supplementation may provide the greatest benefit for increases in protein synthesis for a prolonged duration. PMID:24482589

  13. Nanoelectrochemical Immunosensors for Protein Detection

    NASA Astrophysics Data System (ADS)

    Carpentiero, Alessandro; de Leo, Manuela; Garcia Romero, Ivan; Pozzi Mucelli, Stefano; Reuther, Freimut; Stanta, Giorgio; Tormen, Massimo; Ugo, Paolo; Zamuner, Martina

    Nanoelectrochemical immunosensors fabricated by templated electrodeposition of gold nanoelectrodes inside the pores of polycarbonate (PC) track-etched membranes, followed by the immobilization of the biorecognition elements on the surrounding PC, have proven high sensitivity and specificity for protein detection. The signal transduction scheme involves a suitable redox mediator added to the sample solution to shuttle electrons from the gold nanoelectrodes to the biorecognition layer, both elements being in strict spatial proximity. Highly improved signal-to-background current ratio, which are peculiar of NEEs with respect to other electrochemical transducers, can be exploited in this way. Two detection schemes were tested: one based on the direct immobilization of the target protein on the PC of the NEE (approach A) and the other based on the immobilisation on PC of an antibody to capture the target protein (approach B). The biorecognition process was completed by adding a primary antibody and a secondary antibody with horse radish peroxidase (HRP) as enzyme label; methylene blue was the redox mediator added to the electrolyte solution. Typical target analytes were single chain fragment variable proteins, for approach A, and trastuzumab (also known as Herceptin®), for approach B. NEE-based capture sensors were tested successfully to detect small amounts of the receptor protein HER2 in biological samples. Finally, motivated by the target of a better control of the geometrical characteristics of ensembles of nanoelectrodes (size, density, geometrical arrangement, and degree of recession), and by the positive results obtained with track-etch membranes of PC from the standpoint of protein immobilization, we demonstrated the fabrication of nanobiosensors by patterning ordered arrays of nanoelectrodes (NEAs) by electron beam lithography (EBL) on polycarbonate. EBL results perfectly suitable for the top-down fabrication of arrays of nanobiosensors on thin PC films deposited on gold coated silicon.

  14. Combining Random Gene Fission and Rational Gene Fusion To Discover Near-Infrared Fluorescent Protein Fragments That Report on Protein–Protein Interactions

    PubMed Central

    2015-01-01

    Gene fission can convert monomeric proteins into two-piece catalysts, reporters, and transcription factors for systems and synthetic biology. However, some proteins can be challenging to fragment without disrupting function, such as near-infrared fluorescent protein (IFP). We describe a directed evolution strategy that can overcome this challenge by randomly fragmenting proteins and concomitantly fusing the protein fragments to pairs of proteins or peptides that associate. We used this method to create libraries that express fragmented IFP as fusions to a pair of associating peptides (IAAL-E3 and IAAL-K3) and proteins (CheA and CheY) and screened for fragmented IFP with detectable near-infrared fluorescence. Thirteen novel fragmented IFPs were identified, all of which arose from backbone fission proximal to the interdomain linker. Either the IAAL-E3 and IAAL-K3 peptides or CheA and CheY proteins could assist with IFP fragment complementation, although the IAAL-E3 and IAAL-K3 peptides consistently yielded higher fluorescence. These results demonstrate how random gene fission can be coupled to rational gene fusion to create libraries enriched in fragmented proteins with AND gate logic that is dependent upon a protein–protein interaction, and they suggest that these near-infrared fluorescent protein fragments will be suitable as reporters for pairs of promoters and protein–protein interactions within whole animals. PMID:25265085

  15. The major proteins of bovine seminal plasma interact with caseins and whey proteins of milk extender.

    PubMed

    Lusignan, Marie-France; Bergeron, Annick; Lafleur, Michel; Manjunath, Puttaswamy

    2011-09-01

    Milk has been used routinely as an extender for sperm preservation. Caseins, the major proteins in milk, are proposed to be the protective constituents of milk during sperm preservation. It is unclear whether the whey proteins in milk are also implicated in the protection of sperm. Our previous studies have shown that the major proteins of bovine seminal plasma (recently named as binder of sperm or BSP, which comprises BSP1, BSP3, and BSP5 proteins) mediate a continuous phospholipid and cholesterol efflux from the sperm plasma membrane that is detrimental for sperm preservation. In this study, we investigated whether the protective effect of milk could be due to an interaction between BSP proteins and milk proteins. The binding of BSP proteins to milk proteins was demonstrated by gel filtration chromatography. Milk was fractionated into three fractions: the first containing whey protein aggregates and kappa-casein, the second containing all milk proteins, and the third containing small peptides, salts, and sugars. BSP1 has a higher affinity for the milk proteins in the milk fractions as compared to BSP3 and BSP5. The binding of BSP proteins to milk proteins was further characterized by isothermal titration calorimetry. We demonstrated that BSP1 binds to caseins and the titration could be simulated with a Scatchard approach, leading to an affinity constant (K(a)) of 350 mM(-1) and a stoichiometric parameter for the association (n) of 4.5 BSP1 per casein. The association between BSP1 and alpha-lactalbumin was characterized by a K(a) of 240 mM(-1) and an n value of 0.8. These results indicate the existence of an interaction between BSP proteins and milk proteins that could be the origin of the protection of sperm during preservation in milk. PMID:21593483

  16. Dihydrolipoic acid reduces cytochrome b561 proteins.

    PubMed

    Bérczi, Alajos; Zimányi, László; Asard, Han

    2013-03-01

    Cytochrome b561 (Cyt-b561) proteins constitute a family of trans-membrane proteins that are present in a wide variety of organisms. Two of their characteristic properties are the reducibility by ascorbate (ASC) and the presence of two distinct b-type hemes localized on two opposite sides of the membrane. Here we show that the tonoplast-localized and the putative tumor suppressor Cyt-b561 proteins can be reduced by other reductants than ASC and dithionite. A detailed spectral analysis of the ASC-dependent and dihydrolipoic acid (DHLA)-dependent reduction of these two Cyt-b561 proteins is also presented. Our results are discussed in relation to the known antioxidant capability of DHLA as well as its role in the regeneration of other antioxidant compounds of cells. These results allow us to speculate on new biological functions for the trans-membrane Cyt-b561 proteins. PMID:22526465

  17. Structure and Protein-Protein Interaction Studies on Chlamydia trachomatis Protein CT670 (YscO Homolog)

    SciTech Connect

    Lorenzini, Emily; Singer, Alexander; Singh, Bhag; Lam, Robert; Skarina, Tatiana; Chirgadze, Nickolay Y.; Savchenko, Alexei; Gupta, Radhey S.

    2010-07-28

    Comparative genomic studies have identified many proteins that are found only in various Chlamydiae species and exhibit no significant sequence similarity to any protein in organisms that do not belong to this group. The CT670 protein of Chlamydia trachomatis is one of the proteins whose genes are in one of the type III secretion gene clusters but whose cellular functions are not known. CT670 shares several characteristics with the YscO protein of Yersinia pestis, including the neighboring genes, size, charge, and secondary structure, but the structures and/or functions of these proteins remain to be determined. Although a BLAST search with CT670 did not identify YscO as a related protein, our analysis indicated that these two proteins exhibit significant sequence similarity. In this paper, we report that the CT670 crystal, solved at a resolution of 2 {angstrom}, consists of a single coiled coil containing just two long helices. Gel filtration and analytical ultracentrifugation studies showed that in solution CT670 exists in both monomeric and dimeric forms and that the monomer predominates at lower protein concentrations. We examined the interaction of CT670 with many type III secretion system-related proteins (viz., CT091, CT665, CT666, CT667, CT668, CT669, CT671, CT672, and CT673) by performing bacterial two-hybrid assays. In these experiments, CT670 was found to interact only with the CT671 protein (YscP homolog), whose gene is immediately downstream of ct670. A specific interaction between CT670 and CT671 was also observed when affinity chromatography pull-down experiments were performed. These results suggest that CT670 and CT671 are putative homologs of the YcoO and YscP proteins, respectively, and that they likely form a chaperone-effector pair.

  18. Structure and protein-protein interaction studies on Chlamydia trachomatis protein CT670 (YscO Homolog).

    PubMed

    Lorenzini, Emily; Singer, Alexander; Singh, Bhag; Lam, Robert; Skarina, Tatiana; Chirgadze, Nickolay Y; Savchenko, Alexei; Gupta, Radhey S

    2010-06-01

    Comparative genomic studies have identified many proteins that are found only in various Chlamydiae species and exhibit no significant sequence similarity to any protein in organisms that do not belong to this group. The CT670 protein of Chlamydia trachomatis is one of the proteins whose genes are in one of the type III secretion gene clusters but whose cellular functions are not known. CT670 shares several characteristics with the YscO protein of Yersinia pestis, including the neighboring genes, size, charge, and secondary structure, but the structures and/or functions of these proteins remain to be determined. Although a BLAST search with CT670 did not identify YscO as a related protein, our analysis indicated that these two proteins exhibit significant sequence similarity. In this paper, we report that the CT670 crystal, solved at a resolution of 2 A, consists of a single coiled coil containing just two long helices. Gel filtration and analytical ultracentrifugation studies showed that in solution CT670 exists in both monomeric and dimeric forms and that the monomer predominates at lower protein concentrations. We examined the interaction of CT670 with many type III secretion system-related proteins (viz., CT091, CT665, CT666, CT667, CT668, CT669, CT671, CT672, and CT673) by performing bacterial two-hybrid assays. In these experiments, CT670 was found to interact only with the CT671 protein (YscP homolog), whose gene is immediately downstream of ct670. A specific interaction between CT670 and CT671 was also observed when affinity chromatography pull-down experiments were performed. These results suggest that CT670 and CT671 are putative homologs of the YcoO and YscP proteins, respectively, and that they likely form a chaperone-effector pair. PMID:20348249

  19. The effect of protein depletion and repletion on muscle-protein turnover in the chick.

    PubMed Central

    MacDonald, M L; Swick, R W

    1981-01-01

    Rates of growth and protein turnover in the breast muscle of young chicks were measured in order to assess the roles of protein synthesis and degradation in the regulation of muscle mass. Rates of protein synthesis were measured in vivo by injecting a massive dose of L-[1-14C]valine, and rates of protein degradation were estimated as the difference between the synthesis rate and the growth rate of muscle protein. In chicks fed on a control diet for up to 7 weeks of age, the fractional rate of synthesis decreased from 1 to 2 weeks of age and then changed insignificantly from 2 to 7 weeks of age, whereas DNA activity was constant for 1 to 7 weeks. When 4-week-old chicks were fed on a protein-free diet for 17 days, the total amount of breast-muscle protein synthesized and degraded per day and the amount of protein synthesized per unit of DNA decreased. Protein was lost owing to a greater decrease in the rate of protein synthesis, as a result of the loss of RNA and a lowered RNA activity. When depleted chicks were re-fed the control diet, rapid growth was achieved by a doubling of the fractional synthesis rate by 2 days. Initially, this was a result of increased RNA activity; by 5 days, the RNA/DNA ratio also increased. There was no evidence of a decrease in the fractional degradation rate during re-feeding. These results indicate that dietary-protein depletion and repletion cause changes in breast-muscle protein mass primarily through changes in the rate of protein synthesis. PMID:6171262

  20. The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases

    PubMed Central

    Côté, Richard G; Jones, Philip; Martens, Lennart; Kerrien, Samuel; Reisinger, Florian; Lin, Quan; Leinonen, Rasko; Apweiler, Rolf; Hermjakob, Henning

    2007-01-01

    Background Each major protein database uses its own conventions when assigning protein identifiers. Resolving the various, potentially unstable, identifiers that refer to identical proteins is a major challenge. This is a common problem when attempting to unify datasets that have been annotated with proteins from multiple data sources or querying data providers with one flavour of protein identifiers when the source database uses another. Partial solutions for protein identifier mapping exist but they are limited to specific species or techniques and to a very small number of databases. As a result, we have not found a solution that is generic enough and broad enough in mapping scope to suit our needs. Results We have created the Protein Identifier Cross-Reference (PICR) service, a web application that provides interactive and programmatic (SOAP and REST) access to a mapping algorithm that uses the UniProt Archive (UniParc) as a data warehouse to offer protein cross-references based on 100% sequence identity to proteins from over 70 distinct source databases loaded into UniParc. Mappings can be limited by source database, taxonomic ID and activity status in the source database. Users can copy/paste or upload files containing protein identifiers or sequences in FASTA format to obtain mappings using the interactive interface. Search results can be viewed in simple or detailed HTML tables or downloaded as comma-separated values (CSV) or Microsoft Excel (XLS) files suitable for use in a local database or a spreadsheet. Alternatively, a SOAP interface is available to integrate PICR functionality in other applications, as is a lightweight REST interface. Conclusion We offer a publicly available service that can interactively map protein identifiers and protein sequences to the majority of commonly used protein databases. Programmatic access is available through a standards-compliant SOAP interface or a lightweight REST interface. The PICR interface, documentation and code examples are available at . PMID:17945017

  1. Highly thermostable fluorescent proteins

    SciTech Connect

    Bradbury, Andrew M.; Waldo, Geoffrey S.; Kiss, Csaba

    2011-03-22

    Thermostable fluorescent proteins (TSFPs), methods for generating these and other stability-enhanced proteins, polynucleotides encoding such proteins, and assays and method for using the TSFPs and TSFP-encoding nucleic acid molecules are provided. The TSFPs of the invention show extremely enhanced levels of stability and thermotolerance. In one case, for example, a TSFP of the invention is so stable it can be heated to 99.degree. C. for short periods of time without denaturing, and retains 85% of its fluorescence when heated to 80.degree. C. for several minutes. The invention also provides a method for generating stability-enhanced variants of a protein, including but not limited to fluorescent proteins.

  2. Highly thermostable fluorescent proteins

    DOEpatents

    Bradbury, Andrew M. (Santa Fe, NM); Waldo, Geoffrey S. (Santa Fe, NM); Kiss, Csaba (Los Alamos, NM)

    2011-11-29

    Thermostable fluorescent proteins (TSFPs), methods for generating these and other stability-enhanced proteins, polynucleotides encoding such proteins, and assays and method for using the TSFPs and TSFP-encoding nucleic acid molecules are provided. The TSFPs of the invention show extremely enhanced levels of stability and thermotolerance. In one case, for example, a TSFP of the invention is so stable it can be heated to 99.degree. C. for short periods of time without denaturing, and retains 85% of its fluorescence when heated to 80.degree. C. for several minutes. The invention also provides a method for generating stability-enhanced variants of a protein, including but not limited to fluorescent proteins.

  3. Highly thermostable fluorescent proteins

    DOEpatents

    Bradbury, Andrew M. (Santa Fe, NM); Waldo, Geoffrey S. (Santa Fe, NM); Kiss, Csaba (Los Alamos, NM)

    2012-05-01

    Thermostable fluorescent proteins (TSFPs), methods for generating these and other stability-enhanced proteins, polynucleotides encoding such proteins, and assays and method for using the TSFPs and TSFP-encoding nucleic acid molecules are provided. The TSFPs of the invention show extremely enhanced levels of stability and thermotolerance. In one case, for example, a TSFP of the invention is so stable it can be heated to 99.degree. C. for short periods of time without denaturing, and retains 85% of its fluorescence when heated to 80.degree. C. for several minutes. The invention also provides a method for generating stability-enhanced variants of a protein, including but not limited to fluorescent proteins.

  4. A Second-generation Protein–Protein Interaction Network of Helicobacter pylori*

    PubMed Central

    Häuser, Roman; Ceol, Arnaud; Rajagopala, Seesandra V.; Mosca, Roberto; Siszler, Gabriella; Wermke, Nadja; Sikorski, Patricia; Schwarz, Frank; Schick, Matthias; Wuchty, Stefan; Aloy, Patrick; Uetz, Peter

    2014-01-01

    Helicobacter pylori infections cause gastric ulcers and play a major role in the development of gastric cancer. In 2001, the first protein interactome was published for this species, revealing over 1500 binary protein interactions resulting from 261 yeast two-hybrid screens. Here we roughly double the number of previously published interactions using an ORFeome-based, proteome-wide yeast two-hybrid screening strategy. We identified a total of 1515 protein–protein interactions, of which 1461 are new. The integration of all the interactions reported in H. pylori results in 3004 unique interactions that connect about 70% of its proteome. Excluding interactions of promiscuous proteins we derived from our new data a core network consisting of 908 interactions. We compared our data set to several other bacterial interactomes and experimentally benchmarked the conservation of interactions using 365 protein pairs (interologs) of E. coli of which one third turned out to be conserved in both species. PMID:24627523

  5. Dilution of protein-surfactant complexes: A fluorescence study

    PubMed Central

    Azadi, Glareh; Chauhan, Anuj; Tripathi, Anubhav

    2013-01-01

    Dilution of protein–surfactant complexes is an integrated step in microfluidic protein sizing, where the contribution of free micelles to the overall fluorescence is reduced by dilution. This process can be further improved by establishing an optimum surfactant concentration and quantifying the amount of protein based on the fluorescence intensity. To this end, we study the interaction of proteins with anionic sodium dodecyl sulfate (SDS) and cationic hexadecyl trimethyl ammonium bromide (CTAB) using a hydrophobic fluorescent dye (sypro orange). We analyze these interactions fluourometrically with bovine serum albumin, carbonic anhydrase, and beta-galactosidase as model proteins. The fluorescent signature of protein–surfactant complexes at various dilution points shows three distinct regions, surfactant dominant, breakdown, and protein dominant region. Based on the dilution behavior of protein–surfactant complexes, we propose a fluorescence model to explain the contribution of free and bound micelles to the overall fluorescence. Our results show that protein peak is observed at 3 mM SDS as the optimum dilution concentration. Furthermore, we study the effect of protein concentration on fluorescence intensity. In a single protein model with a constant dye quantum yield, the peak height increases with protein concentration. Finally, addition of CTAB to the protein–SDS complex at mole fractions above 0.1 shifts the protein peak from 3 mM to 4 mM SDS. The knowledge of protein–surfactant interactions obtained from these studies provides significant insights for novel detection and quantification techniques in microfluidics. PMID:23868358

  6. Protein effects on surfactant adsorption suggest the dominant mode of surfactant-mediated stabilization of protein.

    PubMed

    Kim, Hyojin Lee; McAuley, Arnold; McGuire, Joseph

    2014-05-01

    Surfactants stabilize proteins through two major mechanisms: (1) their preferential location at nearby interfaces, in this way precluding protein adsorption; and/or (2) their association with protein into "complexes" that prevent proteins from interacting with surfaces as well as each other. However, selection of surfactants for protein stabilization currently is not typically made with benefit of any quantitative, predictive information to ensure that either mechanism will be enforced. We compared surface tension depression by poloxamer 188, polysorbate (PS) 80, and PS 20 in the presence and absence of lysozyme or a recombinant protein. The kinetic results were interpreted with reference to a mechanism for surfactant adsorption governed by the formation of a rate-limiting structural intermediate (i.e., an "activated complex") composed of surfactant and protein. The presence of protein was seen to increase the rate of surfactant adsorption in relation to surfactant acting alone for the PSs, with very little change in kinetics owing to protein in the case of poloxamer 188. A simple thermodynamic analysis indicated the presence of protein caused a reduction in ?G for the surfactant adsorption process, deriving entirely from a reduction in ?H. Thus, protein likely accelerates the adsorption of these surfactants by disrupting their self-associations, increasing the concentration of surfactant monomers near the interface. PMID:24585710

  7. Sizing Large Proteins and Protein Complexes by Electrospray Ionization Mass Spectrometry and Ion Mobility

    PubMed Central

    Kaddis, Catherine S.; Lomeli, Shirley H.; Yin, Sheng; Berhane, Beniam; Apostol, Marcin I.; Kickhoefer, Valerie A.; Rome, Leonard H.; Loo, Joseph A.

    2009-01-01

    Mass spectrometry (MS) and ion mobility with electrospray ionization (ESI) have the capability to measure and detect large noncovalent protein-ligand and protein-protein complexes. Using an ion mobility method termed GEMMA (Gas-Phase Electrophoretic Mobility Molecular Analysis), protein particles representing a range of sizes can be separated by their electrophoretic mobility in air. Highly charged particles produced from a protein complex solution using electrospray can be manipulated to produce singly charged ions which can be separated and quantified by their electrophoretic mobility. Results from ESI-GEMMA analysis from our laboratory and others were compared to other experimental and theoretically determined parameters, such as molecular mass and cryoelectron microscopy and x-ray crystal structure dimensions. There is a strong correlation between the electrophoretic mobility diameter determined from GEMMA analysis and the molecular mass for protein complexes up to 12 MDa, including the 93 kDa enolase dimer, the 480 kDa ferritin 24-mer complex, the 4.6 MDa cowpea chlorotic mottle virus (CCMV), and the 9 MDa MVP-vault assembly. ESI-GEMMA is used to differentiate a number of similarly sized vault complexes that are composed of different N-terminal protein tags on the MVP subunit. The average effective density of the proteins and protein complexes studied was 0.6 g/cm3. Moreover, there is evidence that proteins and protein complexes collapse or become more compact in the gas phase in the absence of water. PMID:17434746

  8. RNA-Processing Protein TDP-43 Regulates FOXO-Dependent Protein Quality Control in Stress Response

    PubMed Central

    Zhang, Tao; Baldie, Gerard; Periz, Goran; Wang, Jiou

    2014-01-01

    Protein homeostasis is critical for cell survival and functions during stress and is regulated at both RNA and protein levels. However, how the cell integrates RNA-processing programs with post-translational protein quality control systems is unknown. Transactive response DNA-binding protein (TARDBP/TDP-43) is an RNA-processing protein that is involved in the pathogenesis of major neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Here, we report a conserved role for TDP-43, from C. elegans to mammals, in the regulation of protein clearance via activation of FOXO transcription factors. In response to proteotoxic insults, TDP-43 redistributes from the nucleus to the cytoplasm, promoting nuclear translocation of FOXOs and relieving an inhibition of FOXO activity in the nucleus. The interaction between TDP-43 and the FOXO pathway in mammalian cells is mediated by their competitive binding to 14-3-3 proteins. Consistent with FOXO-dependent protein quality control, TDP-43 regulates the levels of misfolded proteins. Therefore, TDP-43 mediates stress responses and couples the regulation of RNA metabolism and protein quality control in a FOXO-dependent manner. The results suggest that compromising the function of TDP-43 in regulating protein homeostasis may contribute to the pathogenesis of related neurodegenerative diseases. PMID:25329970

  9. Monitoring protein-protein interactions in intact eukaryotic cells by beta-galactosidase complementation.

    PubMed

    Rossi, F; Charlton, C A; Blau, H M

    1997-08-01

    We present an approach for monitoring protein-protein interactions within intact eukaryotic cells, which should increase our understanding of the regulatory circuitry that controls the proliferation and differentiation of cells and how these processes go awry in disease states such as cancer. Chimeric proteins composed of proteins of interest fused to complementing beta-galactosidase (beta-gal) deletion mutants permit a novel analysis of protein complexes within cells. In this approach, the beta-gal activity resulting from the forced interaction of nonfunctional weakly complementing beta-gal peptides (Deltaalpha and Deltaomega) serves as a measure of the extent of interaction of the non-beta-gal portions of the chimeras. To test this application of lacZ intracistronic complementation, proteins that form a complex in the presence of rapamycin were used. These proteins, FRAP and FKBP12, were synthesized as fusion proteins with Deltaalpha and Deltaomega, respectively. Enzymatic beta-gal activity served to monitor the formation of the rapamycin-induced chimeric FRAP/FKBP12 protein complex in a time- and dose-dependent manner, as assessed by histochemical, biochemical, and fluorescence-activated cell sorting assays. This approach may prove to be a valuable adjunct to in vitro immunoprecipitation and crosslinking methods and in vivo yeast two-hybrid and fluorescence energy transfer systems. It may also allow a direct assessment of specific protein dimerization interactions in a biologically relevant context, localized in the cell compartments in which they occur, and in the milieu of competing proteins. PMID:9237989

  10. Development of Novel Fluorescence and NMR Reagents for Monitoring Protein-Protein Interactions Between Survivin and Its Protein Binding Partners

    E-print Network

    Bishop, Stephanie Cara

    2015-08-31

    Inhibition of protein-protein interactions is a promising therapeutic strategy for targeting non-enzymatic proteins. One strategy to inhibit protein-protein interactions is to design inhibitors specifically toward the protein-protein interaction...

  11. Protein kinesis: The dynamics of protein trafficking and stability

    SciTech Connect

    1995-12-31

    The purpose of this conference is to provide a multidisciplinary forum for exchange of state-of-the-art information on protein kinesis. This volume contains abstracts of papers in the following areas: protein folding and modification in the endoplasmic reticulum; protein trafficking; protein translocation and folding; protein degradation; polarity; nuclear trafficking; membrane dynamics; and protein import into organelles.

  12. Cryoprotective leaf proteins.

    PubMed

    Volger, H G; Heber, U

    1975-12-15

    Leaves of frost-resistant plants contain a number of soluble proteins which are capable of protecting isolated biomembranes against inactivation during freezing. Such proteins have not been found in non-hardy summer material. The pattern of protective proteins was not uniform in hardy material of different origin and appeared to change with the season. Cryoprotective proteins were isolated by preparative gel electrophoresis. Molecular weights of different proteins as determined by their electrophoretic mobility in sodium dodecyl sulfate gels were between 10000 and 20000. Circular dichroism measurements failed to indicate helical structures. The amino acid composition of 2 active proteins revealed a high content of polar amino acids. The proteins were heat-stable. They were, on a molar basis, more than 1000 times as effective in protecting thylakoid membranes against freezing damage as low-molecular-weight cryoprotectants such as sucrose, glycerol or dimethylsulfoxide. Very low concentrations of the proteins increased cryoprotection provided by sucrose. Of a number of oligopeptides of known composition, only a few were cryoprotective. Their activity was very small as compared with that of the active proteins. The concentration of the cryoprotective proteins in hardy leaves appeared to be high enough for a significant contribution of the proteins to the frost tolerance of resistant plants. PMID:1191683

  13. Protein Structure Analysis Iosif Vaisman

    E-print Network

    Vaisman, Iosif

    Protein Structure Analysis Iosif Vaisman 2013 BINF 731 Secondary Structure: Computational Problems Secondary structure characterization Secondary structure assignment Secondary structure prediction Protein structure classification Structural classes of proteins all all Protein Structure Classification SCOP

  14. Protein Structure Analysis Iosif Vaisman

    E-print Network

    Vaisman, Iosif

    Protein Structure Analysis Iosif Vaisman 2015 BINF 731 Secondary Structure: Computational Problems Secondary structure characterization Secondary structure assignment Secondary structure prediction Protein structure classification Structural classes of proteins all a all b a/b Protein Structure Classification

  15. Characterization of essential proteins based on network topology in proteins interaction networks

    NASA Astrophysics Data System (ADS)

    Bakar, Sakhinah Abu; Taheri, Javid; Zomaya, Albert Y.

    2014-06-01

    The identification of essential proteins is theoretically and practically important as (1) it is essential to understand the minimal surviving requirements for cellular lives, and (2) it provides fundamental for development of drug. As conducting experimental studies to identify essential proteins are both time and resource consuming, here we present a computational approach in predicting them based on network topology properties from protein-protein interaction networks of Saccharomyces cerevisiae. The proposed method, namely EP3NN (Essential Proteins Prediction using Probabilistic Neural Network) employed a machine learning algorithm called Probabilistic Neural Network as a classifier to identify essential proteins of the organism of interest; it uses degree centrality, closeness centrality, local assortativity and local clustering coefficient of each protein in the network for such predictions. Results show that EP3NN managed to successfully predict essential proteins with an accuracy of 95% for our studied organism. Results also show that most of the essential proteins are close to other proteins, have assortativity behavior and form clusters/sub-graph in the network.

  16. ComPPI: a cellular compartment-specific database for protein-protein interaction network analysis.

    PubMed

    Veres, Daniel V; Gyurkó, Dávid M; Thaler, Benedek; Szalay, Kristóf Z; Fazekas, Dávid; Korcsmáros, Tamás; Csermely, Peter

    2015-01-01

    Here we present ComPPI, a cellular compartment-specific database of proteins and their interactions enabling an extensive, compartmentalized protein-protein interaction network analysis (URL: http://ComPPI.LinkGroup.hu). ComPPI enables the user to filter biologically unlikely interactions, where the two interacting proteins have no common subcellular localizations and to predict novel properties, such as compartment-specific biological functions. ComPPI is an integrated database covering four species (S. cerevisiae, C. elegans, D. melanogaster and H. sapiens). The compilation of nine protein-protein interaction and eight subcellular localization data sets had four curation steps including a manually built, comprehensive hierarchical structure of >1600 subcellular localizations. ComPPI provides confidence scores for protein subcellular localizations and protein-protein interactions. ComPPI has user-friendly search options for individual proteins giving their subcellular localization, their interactions and the likelihood of their interactions considering the subcellular localization of their interacting partners. Download options of search results, whole-proteomes, organelle-specific interactomes and subcellular localization data are available on its website. Due to its novel features, ComPPI is useful for the analysis of experimental results in biochemistry and molecular biology, as well as for proteome-wide studies in bioinformatics and network science helping cellular biology, medicine and drug design. PMID:25348397

  17. ComPPI: a cellular compartment-specific database for protein–protein interaction network analysis

    PubMed Central

    Veres, Daniel V.; Gyurkó, Dávid M.; Thaler, Benedek; Szalay, Kristóf Z.; Fazekas, Dávid; Korcsmáros, Tamás; Csermely, Peter

    2015-01-01

    Here we present ComPPI, a cellular compartment-specific database of proteins and their interactions enabling an extensive, compartmentalized protein–protein interaction network analysis (URL: http://ComPPI.LinkGroup.hu). ComPPI enables the user to filter biologically unlikely interactions, where the two interacting proteins have no common subcellular localizations and to predict novel properties, such as compartment-specific biological functions. ComPPI is an integrated database covering four species (S. cerevisiae, C. elegans, D. melanogaster and H. sapiens). The compilation of nine protein–protein interaction and eight subcellular localization data sets had four curation steps including a manually built, comprehensive hierarchical structure of >1600 subcellular localizations. ComPPI provides confidence scores for protein subcellular localizations and protein–protein interactions. ComPPI has user-friendly search options for individual proteins giving their subcellular localization, their interactions and the likelihood of their interactions considering the subcellular localization of their interacting partners. Download options of search results, whole-proteomes, organelle-specific interactomes and subcellular localization data are available on its website. Due to its novel features, ComPPI is useful for the analysis of experimental results in biochemistry and molecular biology, as well as for proteome-wide studies in bioinformatics and network science helping cellular biology, medicine and drug design. PMID:25348397

  18. The Vroman effect: competitive protein exchange with dynamic multilayer protein aggregates.

    PubMed

    Hirsh, Stacey L; McKenzie, David R; Nosworthy, Neil J; Denman, John A; Sezerman, Osman U; Bilek, Marcela M M

    2013-03-01

    The surface immobilization of proteins is an emerging field with applications in a wide range of important areas: biomedical devices, disease diagnosis, biosensing, food processing, biofouling, and bioreactors. Proteins, in Nature, often work synergistically, as in the important enzyme mixture, cellulase. It is necessary to preserve these synergies when utilizing surface immobilized proteins. However, the competitive displacement of earlier adsorbed proteins by other proteins with stronger binding affinities (the "Vroman effect") results in undesired layer instabilities that are difficult to control. Although this nanoscale phenomenon has been extensively studied over the last 40 years, the process through which this competitive exchange occurs is not well understood. This paper uses atomic force microscopy, QCM-D, TOF-SIMS, and in-solution TOF-MS to show that this competitive exchange process can occur through the turning of multilayer protein aggregates. This dynamic process is consistent with earlier postulated "transient complex" models, in which the exchange occurs in three stages: an initial layer adsorbs, another protein layer then embeds itself into the initial layer, forming a "transient complex;" the complex "turns," exposing the first layer to solution; proteins from the first layer desorb resulting in a final adsorbed protein composition that is enriched in proteins from the second layer. PMID:23261559

  19. YouTube SEO Tip Sheet Feinberg Office of Communications

    E-print Network

    Chisholm, Rex L.

    for search engine success. 1. Always upload your video to YouTube. The Northwestern University Feinberg with Google, Communications recommends using YouTube even if you are also uploading your video directly to YouTube on the Office of Communications web page. 2. Do keyword research. Google Keyword Tool

  20. Observing Protein & Energy Nutrition (OPEN) Study

    Cancer.gov

    The Observing Protein and Energy Nutrition (OPEN) Study was designed to assess dietary measurement error by comparing results from self-reported dietary intake data with four dietary biomarkers: doubly labeled water and urinary nitrogen, sodium, and potassium.

  1. Characterization of human N8 protein.

    PubMed

    Chen, S L; Zhang, X K; Halverson, D O; Byeon, M K; Schweinfest, C W; Ferris, D K; Bhat, N K

    1997-11-20

    We have shown before that the N8 mRNA is expressed at higher levels in lung tumor and lung tumor-derived cell lines than normal lung cells. In this paper, we have characterized the N8 protein, and studied its properties. The N8 gene encodes a major 24 kDa protein and its expression correlates well with the N8 mRNA expression pattern observed in different cell lines. N8 protein is capable of forming a homodimer or multimeter in vitro. It is a phosphorylated cytoplasmic protein and phosphorylation occurs mainly at serine residues. N8 protein is expressed at higher levels in epithelial cells than in mesenchymal cells. N8 protein expression is induced in a fibroblast cell line expressing adenoviral Ela protein, which acquired epithelial-like characteristics. Furthermore, ectopic expression of N8 protein in NIH3T3 cells converts them into a spheroid form. These spheroids also have some of the characteristic features of epithelial cells. Taken together, these results suggest that the N8 protein may be associated with the development or maintenance of epithelial cell phenotype. PMID:9399645

  2. Protein phosphorylation: Localization in regenerating optic axons

    SciTech Connect

    Larrivee, D. )

    1990-09-01

    A number of axonal proteins display changes in phosphorylation during goldfish optic nerve regeneration. (1) To determine whether the phosphorylation of these proteins was closely linked to their synthesis in the retinal ganglion cell body, cycloheximide was injected intraocularly into goldfish whose optic nerves had been regenerating for 3 weeks. Cycloheximide reduced the incorporation of (3H)proline and 32P orthophosphate into total nerve protein by 84% and 46%, respectively. Of the 20 individual proteins examined, 17 contained less than 15% of the (3H)proline label measured in corresponding controls, whereas 18 proteins contained 50% or more of the 32P label, suggesting that phosphorylation was largely independent of synthesis. (2) To determine whether the proteins were phosphorylated in the ganglion cell axons, axonal transport of proteins was blocked by intraocular injection of vincristine. Vincristine reduced (3H)proline labeling of total protein by 88% and 32P labeling by 49%. Among the individual proteins (3H)proline labeling was reduced by 90% or more in 18 cases but 32P labeling was reduced only by 50% or less. (3) When 32P was injected into the cranial cavity near the ends of the optic axons, all of the phosphoproteins were labeled more intensely in the optic tract than in the optic nerve. These results suggest that most of the major phosphoproteins that undergo changes in phosphorylation in the course of regeneration are phosphorylated in the optic axons.

  3. Antigenic Properties of N Protein of Hantavirus

    PubMed Central

    Yoshimatsu, Kumiko; Arikawa, Jiro

    2014-01-01

    Hantavirus causes two important rodent-borne viral zoonoses, hemorrhagic fever with renal syndrome (HFRS) in Eurasia and hantavirus pulmonary syndrome (HPS) in North and South America. Twenty-four species that represent sero- and genotypes have been registered within the genus Hantavirus by the International Committee on Taxonomy of Viruses (ICTV). Among the viral proteins, nucleocapsid (N) protein possesses an immunodominant antigen. The antigenicitiy of N protein is conserved compared with that of envelope glycoproteins. Therefore, N protein has been used for serological diagnoses and seroepidemiological studies. An understanding of the antigenic properties of N protein is important for the interpretation of results from serological tests using N antigen. N protein consists of about 430 amino acids and possesses various epitopes. The N-terminal quarter of N protein bears linear and immunodominant epitopes. However, a serotype-specific and multimerization-dependent antigenic site was found in the C-terminal half of N protein. In this paper, the structure, function, and antigenicity of N protein are reviewed. PMID:25123683

  4. Regulation of cardiac C-protein phosphorylation

    SciTech Connect

    Titus, F.L.

    1985-01-01

    Molecular mechanisms of cardiac sympathetic and parasympathetic responses were addressed by studying subcellular changes in protein phosphorylation, cAMP-dependent protein kinase activity and protein phosphatase activity in frog hearts. B-adrenergic agonists increased and muscarinic cholinergic agonists decreased (/sup 32/P)phosphate incorporation into C-protein, a thick filament component. Regulation of protein phosphatase activity by Iso and methacholine (MCh) was assayed using extracts of drug treated frog hearts and (/sup 32/P)phospho-C-protein as substrate. Total phosphatase activity decreased 21% in extracts from hearts perfused with 0.1 ..mu..M Iso and 17% in hearts exposed to Iso plus 1 ..mu..M methacholine. This decrease reflected decreased phosphatase-2A activity. No changes in total phosphatase activity were measurable in broken cells treated with Iso or MCh. The results suggest adrenergic stimulation changes contractile activity in frog hearts by activating cAMP-dependent protein kinase associated with particulate cellular elements and inactivating soluble protein phosphatase-2A. This is the first demonstration of coordinated regulation of these enzymes by B-adrenergic agonists favoring phosphorylation of effector proteins. Coordinated regulation by methacholine in the presence of Iso was not observed.

  5. Multi-level machine learning prediction of protein–protein interactions in Saccharomyces cerevisiae

    PubMed Central

    Zubek, Julian; Tatjewski, Marcin; Boniecki, Adam; Mnich, Maciej; Basu, Subhadip

    2015-01-01

    Accurate identification of protein–protein interactions (PPI) is the key step in understanding proteins’ biological functions, which are typically context-dependent. Many existing PPI predictors rely on aggregated features from protein sequences, however only a few methods exploit local information about specific residue contacts. In this work we present a two-stage machine learning approach for prediction of protein–protein interactions. We start with the carefully filtered data on protein complexes available for Saccharomyces cerevisiae in the Protein Data Bank (PDB) database. First, we build linear descriptions of interacting and non-interacting sequence segment pairs based on their inter-residue distances. Secondly, we train machine learning classifiers to predict binary segment interactions for any two short sequence fragments. The final prediction of the protein–protein interaction is done using the 2D matrix representation of all-against-all possible interacting sequence segments of both analysed proteins. The level-I predictor achieves 0.88 AUC for micro-scale, i.e., residue-level prediction. The level-II predictor improves the results further by a more complex learning paradigm. We perform 30-fold macro-scale, i.e., protein-level cross-validation experiment. The level-II predictor using PSIPRED-predicted secondary structure reaches 0.70 precision, 0.68 recall, and 0.70 AUC, whereas other popular methods provide results below 0.6 threshold (recall, precision, AUC). Our results demonstrate that multi-scale sequence features aggregation procedure is able to improve the machine learning results by more than 10% as compared to other sequence representations. Prepared datasets and source code for our experimental pipeline are freely available for download from: http://zubekj.github.io/mlppi/ (open source Python implementation, OS independent). PMID:26157620

  6. Multi-level machine learning prediction of protein-protein interactions in Saccharomyces cerevisiae.

    PubMed

    Zubek, Julian; Tatjewski, Marcin; Boniecki, Adam; Mnich, Maciej; Basu, Subhadip; Plewczynski, Dariusz

    2015-01-01

    Accurate identification of protein-protein interactions (PPI) is the key step in understanding proteins' biological functions, which are typically context-dependent. Many existing PPI predictors rely on aggregated features from protein sequences, however only a few methods exploit local information about specific residue contacts. In this work we present a two-stage machine learning approach for prediction of protein-protein interactions. We start with the carefully filtered data on protein complexes available for Saccharomyces cerevisiae in the Protein Data Bank (PDB) database. First, we build linear descriptions of interacting and non-interacting sequence segment pairs based on their inter-residue distances. Secondly, we train machine learning classifiers to predict binary segment interactions for any two short sequence fragments. The final prediction of the protein-protein interaction is done using the 2D matrix representation of all-against-all possible interacting sequence segments of both analysed proteins. The level-I predictor achieves 0.88 AUC for micro-scale, i.e., residue-level prediction. The level-II predictor improves the results further by a more complex learning paradigm. We perform 30-fold macro-scale, i.e., protein-level cross-validation experiment. The level-II predictor using PSIPRED-predicted secondary structure reaches 0.70 precision, 0.68 recall, and 0.70 AUC, whereas other popular methods provide results below 0.6 threshold (recall, precision, AUC). Our results demonstrate that multi-scale sequence features aggregation procedure is able to improve the machine learning results by more than 10% as compared to other sequence representations. Prepared datasets and source code for our experimental pipeline are freely available for download from: http://zubekj.github.io/mlppi/ (open source Python implementation, OS independent). PMID:26157620

  7. Identification of Protein-Protein Interactions and Topologies in Living Cells with Chemical Cross-linking and Mass Spectrometry

    SciTech Connect

    Zhang, Haizhen; Tang, Xiaoting; Munske, Gerhard R.; Tolic, Nikola; Anderson, Gordon A.; Bruce, James E.

    2009-03-01

    We present results from a novel strategy that enables concurrent identification of protein-protein interactions and topologies in living cells without specific antibodies or genetic manipulations for immuno/affinity purifications. The strategy consists of: (i) chemical cross-linking reaction: intact cell labeling with a novel class of chemical cross-linkers, protein interaction reporters (PIRs); (ii) two-stage mass spectrometric analysis: stage 1 identification of PIR-labeled proteins and construction of a restricted database by 2D-LC/MS/MS; and stage 2 analysis of PIR-labeled peptides by multiplexed LC/FTICR-MS; (iii) data analysis: identification of cross-linked peptides and proteins of origin using accurate mass and other constraints. The primary advantage of the PIR approach and distinction from current technology is that protein interactions together with topologies are detected in native biological systems by stabilizing protein complexes with new covalent bonds while the proteins are present in the original cellular environment. Thus, weak or transient interactions or interactions that require properly folded, localized, or membrane-bound proteins can be labeled and identified through the PIR approach. This strategy was applied to S. oneidensis bacterial cells and initial studies resulted in identification of a set of protein-protein interactions and their contact/binding regions. Furthermore, most identified interactions involved membrane proteins, suggesting the PIR approach is particularly suited for studies of membrane protein-protein interactions, an area under-represented with current widely-used approaches.

  8. A new view on the role of intrinsic protein disorder

    NASA Astrophysics Data System (ADS)

    Liu, Jintao; Faeder, James; Camacho, Carlos

    2009-03-01

    Recent studies have found that many proteins do not have stable structure by themselves, i.e., are intrinsically disordered, which challenges the conventional view that structure determines protein function and interaction. We have analyzed the Human Protein Reference Database with the VSL2 protein disorder predictor, and find that the amount of disorder in a protein is the result of evolutionary pressure: catalytic proteins interact with substrates rapidly and highly specifically and thus exhibit low levels of disorder; transcription regulators often slide along DNA, which favors flexible or disordered structures; binding proteins have affinities that depend weakly on folding stability, and thus have a broad disorder distribution. Finally, our findings suggest that sequence/structural features such as phosphotyrosine are better indicators of multiple protein-protein interactions than disorder.

  9. Assembly of transmembrane proteins on oil-water interfaces

    NASA Astrophysics Data System (ADS)

    Yunker, Peter; Landry, Corey; Chong, Shaorong; Weitz, David

    2015-03-01

    Transmembrane proteins are difficult to handle by aqueous solution-based biochemical and biophysical approaches, due to the hydrophobicity of transmembrane helices. Detergents can solubilize transmembrane proteins; however, surfactant coated transmembrane proteins are not always functional, and purifying detergent coated proteins in a micellar solution can be difficult. Motivated by this problem, we study the self-assembly of transmembrane proteins on oil-water interfaces. We found that the large water-oil interface of oil drops prevents nascent transmembrane proteins from forming non-functional aggregates. The oil provides a hydrophobic environment for the transmembrane helix, allowing the ectodomain to fold into its natural structure and orientation. Further, modifying the strength or valency of hydrophobic interactions between transmembrane proteins results in the self-assembly of spatially clustered, active proteins on the oil-water interface. Thus, hydrophobic interactions can facilitate, rather than inhibit, the assembly of transmembrane proteins.

  10. Proteomics beyond large-scale protein expression analysis.

    PubMed

    Boersema, Paul J; Kahraman, Abdullah; Picotti, Paola

    2015-08-01

    Proteomics is commonly referred to as the application of high-throughput approaches to protein expression analysis. Typical results of proteomics studies are inventories of the protein content of a sample or lists of differentially expressed proteins across multiple conditions. Recently, however, an explosion of novel proteomics workflows has significantly expanded proteomics beyond the analysis of protein expression. Targeted proteomics methods, for example, enable the analysis of the fine dynamics of protein systems, such as a specific pathway or a network of interacting proteins, and the determination of protein complex stoichiometries. Structural proteomics tools allow extraction of restraints for structural modeling and identification of structurally altered proteins on a proteome-wide scale. Other variations of the proteomic workflow can be applied to the large-scale analysis of protein activity, location, degradation and turnover. These exciting developments provide new tools for multi-level 'omics' analysis and for the modeling of biological networks in the context of systems biology studies. PMID:25636126

  11. Crop rotation impacts on potato protein.

    PubMed

    Honeycutt, C W

    1998-01-01

    The impact of nitrogen (N) fertilization on potato (Solanum tuberosum L.) protein yield and nutritional quality is well documented but of little benefit to growers with limited access to fertilizer or capital (e.g. in lesser developed countries). This study was conducted 1) to evaluate the extent which crude protein yield in potatoes can be influenced by crop rotation with no N fertilizer and 2) to determine if crop rotation and minimal application of N fertilizer can meet the total protein yield of potatoes achieved with recommended quantities of N fertilizer. A field study was conducted in which potatoes followed previous crops of alfalfa (Medicago sativa L. 'Nitro'), hairy vetch (Vicia villosa Roth), white lupin (Lupinus albus L. 'Ultra'), oats (Avena sativa 'Astro'), and potatoes. Tuber protein yield following alfalfa with no N fertilizer was about 50 kg/ha greater than when following potatoes or oats in one study year. In another year, tuber protein yield was greatest following vetch, achieving 149 kg protein/ha with no N fertilizer. These results were directly linked to the N contributions of rotation crop residues and were reflected in the plant-available N levels measured in soil. Applying one-half the recommended rate of N fertilizer resulted in protein yields comparable to a well-fertilized potato-potato rotation in a relatively dry year, but not in a year with more favorable precipitation. Particular crops grown in rotation with potatoes can make significant contributions to the total protein harvested in tubers. PMID:10426115

  12. Protein Structure Analysis Iosif Vaisman

    E-print Network

    Vaisman, Iosif

    Protein Structure Analysis Iosif Vaisman 2012 BINF 731 Protein Function Prediction Enzyme Function for predicting DNA-binding proteins function from protein structure FINDSITE - a threading-based method sites and their properties in evolutionarily related proteins Pandit et al., PSiFR, 2009 Protein

  13. Protein Structure Analysis Iosif Vaisman

    E-print Network

    Vaisman, Iosif

    Protein Structure Analysis Iosif Vaisman 2012 BINF 731 Protein Engineering Protein Engineering stability Increase proteins resistance to proteases Change codon composition Protein Engineering Bornscheueretal.Nature485,185-194(2012) Protein Engineering Bornscheuer et al. Nature 485, 185-194 (2012

  14. Integration of latex protein sequence data provides comprehensive functional overview of latex proteins.

    PubMed

    Cho, Won Kyong; Jo, Yeonhwa; Chu, Hyosub; Park, Sang-Ho; Kim, Kook-Hyung

    2014-03-01

    The laticiferous system is one of the most important conduit systems in higher plants, which produces a milky-like sap known as latex. Latex contains diverse secondary metabolites with various ecological functions. To obtain a comprehensive overview of the latex proteome, we integrated available latex proteins sequences and constructed a comprehensive dataset composed of 1,208 non-redundant latex proteins from 20 various latex-bearing plants. The results of functional analyses revealed that latex proteins are involved in various biological processes, including transcription, translation, protein degradation and the plant response to environmental stimuli. The results of the comparative analysis showed that the functions of the latex proteins are similar to those of phloem, suggesting the functional conservation of plant vascular proteins. The presence of latex proteins in mitochondria and plastids suggests the production of diverse secondary metabolites. Furthermore, using a BLAST search, we identified 854 homologous latex proteins in eight plant species, including three latex-bearing plants, such as papaya, caster bean and cassava, suggesting that latex proteins were newly evolved in vascular plants. Taken together, this study is the largest and most comprehensive in silico analysis of the latex proteome. The results obtained here provide useful resources and information for characterizing the evolution of the latex proteome. PMID:24395295

  15. Heat-induced Protein Structure and Subfractions in Relation to Protein Degradation Kinetics and Intestinal Availability in Dairy Cattle

    SciTech Connect

    Doiron, K.; Yu, P; McKinnon, J; Christensen, D

    2009-01-01

    The objectives of this study were to reveal protein structures of feed tissues affected by heat processing at a cellular level, using the synchrotron-based Fourier transform infrared microspectroscopy as a novel approach, and quantify protein structure in relation to protein digestive kinetics and nutritive value in the rumen and intestine in dairy cattle. The parameters assessed included (1) protein structure a-helix to e-sheet ratio; (2) protein subfractions profiles; (3) protein degradation kinetics and effective degradability; (4) predicted nutrient supply using the intestinally absorbed protein supply (DVE)/degraded protein balance (OEB) system for dairy cattle. In this study, Vimy flaxseed protein was used as a model feed protein and was autoclave-heated at 120C for 20, 40, and 60 min in treatments T1, T2, and T3, respectively. The results showed that using the synchrotron-based Fourier transform infrared microspectroscopy revealed and identified the heat-induced protein structure changes. Heating at 120C for 40 and 60 min increased the protein structure a-helix to e-sheet ratio. There were linear effects of heating time on the ratio. The heating also changed chemical profiles, which showed soluble CP decreased upon heating with concomitant increases in nonprotein nitrogen, neutral, and acid detergent insoluble nitrogen. The protein subfractions with the greatest changes were PB1, which showed a dramatic reduction, and PB2, which showed a dramatic increase, demonstrating a decrease in overall protein degradability. In situ results showed a reduction in rumen-degradable protein and in rumen-degradable dry matter without differences between the treatments. Intestinal digestibility, determined using a 3-step in vitro procedure, showed no changes to rumen undegradable protein. Modeling results showed that heating increased total intestinally absorbable protein (feed DVE value) and decreased degraded protein balance (feed OEB value), but there were no differences between the treatments. There was a linear effect of heating time on the DVE and a cubic effect on the OEB value. Our results showed that heating changed chemical profiles, protein structure a-helix to e-sheet ratio, and protein subfractions; decreased rumen-degradable protein and rumen-degradable dry matter; and increased potential nutrient supply to dairy cattle. The protein structure a-helix to e-sheet ratio had a significant positive correlation with total intestinally absorbed protein supply and negative correlation with degraded protein balance.

  16. New reporters of protein trafficking and protein-protein interactions in live cells

    E-print Network

    Fernández Suárez, Marta

    2008-01-01

    Here, we describe our attempts to harness the exquisite specificity of natural protein and RNA enzymes to develop improved methods to study protein localization and protein-protein interactions in live cells. We first ...

  17. A NEW LOOK AT AN OLD PROTEIN: ALPHA-ZEIN

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Alpha-Zeins are water insoluble storage proteins found in corn protein bodies. Analysis of the protein sequence using probability algorithms, structural studies by circular dichroism, small angle x-ray scattering (SAXS), light scattering, and optical rotatory dispersion results, suggests that the 1...

  18. Protein Design Using Continuous Rotamers

    PubMed Central

    Donald, Bruce R.

    2012-01-01

    Optimizing amino acid conformation and identity is a central problem in computational protein design. Protein design algorithms must allow realistic protein flexibility to occur during this optimization, or they may fail to find the best sequence with the lowest energy. Most design algorithms implement side-chain flexibility by allowing the side chains to move between a small set of discrete, low-energy states, which we call rigid rotamers. In this work we show that allowing continuous side-chain flexibility (which we call continuous rotamers) greatly improves protein flexibility modeling. We present a large-scale study that compares the sequences and best energy conformations in 69 protein-core redesigns using a rigid-rotamer model versus a continuous-rotamer model. We show that in nearly all of our redesigns the sequence found by the continuous-rotamer model is different and has a lower energy than the one found by the rigid-rotamer model. Moreover, the sequences found by the continuous-rotamer model are more similar to the native sequences. We then show that the seemingly easy solution of sampling more rigid rotamers within the continuous region is not a practical alternative to a continuous-rotamer model: at computationally feasible resolutions, using more rigid rotamers was never better than a continuous-rotamer model and almost always resulted in higher energies. Finally, we present a new protein design algorithm based on the dead-end elimination (DEE) algorithm, which we call iMinDEE, that makes the use of continuous rotamers feasible in larger systems. iMinDEE guarantees finding the optimal answer while pruning the search space with close to the same efficiency of DEE. Availability: Software is available under the Lesser GNU Public License v3. Contact the authors for source code. PMID:22279426

  19. Discovering novel protein-protein interactions by measuring the protein semantic similarity from the biomedical literature.

    PubMed

    Chiang, Jung-Hsien; Ju, Jiun-Huang

    2014-12-01

    Protein-protein interactions (PPIs) are involved in the majority of biological processes. Identification of PPIs is therefore one of the key aims of biological research. Although there are many databases of PPIs, many other unidentified PPIs could be buried in the biomedical literature. Therefore, automated identification of PPIs from biomedical literature repositories could be used to discover otherwise hidden interactions. Search engines, such as Google, have been successfully applied to measure the relatedness among words. Inspired by such approaches, we propose a novel method to identify PPIs through semantic similarity measures among protein mentions. We define six semantic similarity measures as features based on the page counts retrieved from the MEDLINE database. A machine learning classifier, Random Forest, is trained using the above features. The proposed approach achieve an averaged micro-F of 71.28% and an averaged macro-F of 64.03% over five PPI corpora, an improvement over the results of using only the conventional co-occurrence feature (averaged micro-F of 68.79% and an averaged macro-F of 60.49%). A relation-word reinforcement further improves the averaged micro-F to 71.3% and averaged macro-F to 65.12%. Comparing the results of the current work with other studies on the AIMed corpus (ranging from 77.58% to 85.1% in micro-F, 62.18% to 76.27% in macro-F), we show that the proposed approach achieves micro-F of 81.88% and macro-F of 64.01% without the use of sophisticated feature extraction. Finally, we manually examine the newly discovered PPI pairs based on a literature review, and the results suggest that our approach could extract novel protein-protein interactions. PMID:25385082

  20. Immuno-spin trapping detection of antioxidant/pro-oxidant properties of zinc or selenium on DNA and protein radical formation via hydrogen peroxide.

    PubMed

    Deletioglu, Vedia; Tuncay, Erkan; Toy, Aysegul; Atalay, Mustafa; Turan, Belma

    2015-11-01

    Trace elements can participate in the catalysis of group-transfer reactions and can serve as their structural components. However, most of them including zinc and selenium have multifunctional roles in biological environments such as antioxidant and/or pro-oxidant effects, as concentration-dependent manner. Although it has been demonstrated the antioxidant actions of either selenium or zinc compounds, there are several documents pointing out their pro-oxidant/oxidant roles in biological systems. Here we have used ELISA-based immuno-spin trapping, a method for detection of free radical formation, to detect whether or not a zinc compound, Zn3(PO4)2, or a selenium compound, Na2SeO3, has antioxidant and/or pro-oxidant effect on 5,5-Dimethyl-1-Pyrroline-N-Oxide (DMPO)-DNA nitrone adducts induced with Cu(II)-H2O2-oxidizing system in in vitro preparations. Second, we examined whether this technique is capable to demonstrate the different DMPO-protein nitrone adduct productions in isolated protein crude of hearts from normal rats (CON) or rats with metabolic syndrome (MetS). Our data demonstrated that either Zn(2+) (100 µM) or [Formula: see text] (50 nM) has very strong antioxidant action against 200 µM H2O2-induced DMPO-DNA nitrone adduct production, whereas their higher concentrations have apparent pro-oxidant actions. We also used verification by Western blotting analysis whether immuno-spin trapping can be used to assess H2O2-induced DMPO-protein nitrone adducts in heart protein crudes. Our Western blot data further confirmed the ELISA-data from proteins and demonstrated how Zn(2+) or [Formula: see text] are dual-functioning ions such as antioxidant at lower concentrations while pro-oxidant at higher concentrations. Particularly, our present data with [Formula: see text] in DMPO-protein nitrone adducts, being in line with our previous observation on its dual-actions in ischemia/reperfusion-induced damaged heart, have shown that this ion has higher pro-oxidant actions over 50 nM in MetS-group compared to that of CON group. PMID:26169985

  1. Measurements of Protein-Protein Interactions by Size Exclusion Chromatography

    E-print Network

    J. Bloustine; V. Berejnov; S. Fraden

    2003-06-12

    A method is presented for determining second virial coefficients B_2 of protein solutions from retention time measurements in size exclusion chromatography (SEC). We determine B_2 by analyzing the concentration dependance of the chromatographic partition coefficient. We show the ability of this method to track the evolution of B_2 from positive to negative values in lysozyme and bovine serum albumin solutions. Our SEC results agree quantitatively with data obtained by light scattering.

  2. F2Dock: Fast Fourier Protein-Protein Docking

    PubMed Central

    Bajaj, Chandrajit; Chowdhury, Rezaul; Siddavanahalli, Vinay

    2009-01-01

    The functions of proteins is often realized through their mutual interactions. Determining a relative transformation for a pair of proteins and their conformations which form a stable complex, reproducible in nature, is known as docking. It is an important step in drug design, structure determination and understanding function and structure relationships. In this paper we extend our non-uniform fast Fourier transform docking algorithm to include an adaptive search phase (both translational and rotational) and thereby speed up its execution. We have also implemented a multithreaded version of the adaptive docking algorithm for even faster execution on multicore machines. We call this protein-protein docking code F2Dock (F2 = Fast Fourier). We have calibrated F2Dock based on an extensive experimental study on a list of benchmark complexes and conclude that F2Dock works very well in practice. Though all docking results reported in this paper use shape complementarity and Coulombic potential based scores only, F2Dock is structured to incorporate Lennard-Jones potential and re-ranking docking solutions based on desolvation energy. PMID:21071796

  3. Comparative Proteomic Analysis of Extracellular Proteins of Edwardsiella tarda

    PubMed Central

    Tan, Y. P.; Lin, Q.; Wang, X. H.; Joshi, S.; Hew, C. L.; Leung, K. Y.

    2002-01-01

    A comparison of extracellular proteins of virulent and avirulent Edwardsiella tarda strains revealed several major, virulent-strain-specific proteins. Proteomic analysis identified two of the proteins in the virulent strain PPD130/91 as flagellin and SseB, which are virulence factors in bacterial pathogens. PCR amplification and DNA sequencing confirmed the presence of the genes that encode these proteins. Our results clearly demonstrated the potency of the proteomic approach in identifying virulence factors. PMID:12379732

  4. Predicting Protein-Protein Interactions from Protein Domains Using a Set Cover Approach

    E-print Network

    Izaguirre, Jesús A.

    Predicting Protein-Protein Interactions from Protein Domains Using a Set Cover Approach Chengbang--One goal of contemporary proteome research is the elucidation of cellular protein interactions. Based on currently available protein-protein interaction and domain data, we introduce a novel method, Maximum

  5. Leveraging Genomics Software to Improve Proteomics Results

    SciTech Connect

    Fodor, I K; Nelson, D O

    2005-09-06

    Rigorous data analysis techniques are essential in quantifying the differential expression of proteins in biological samples of interest. Statistical methods from the microarray literature were applied to the analysis of two-dimensional difference gel electrophoresis (2-D DIGE) proteomics experiments, in the context of technical variability studies involving human plasma. Protein expression measurements were corrected to account for observed intensity-dependent biases within gels, and normalized to mitigate observed gel to gel variations. The methods improved upon the results achieved using the best currently available 2-D DIGE proteomics software. The spot-wise protein variance was reduced by 10% and the number of apparently differentially expressed proteins was reduced by over 50%.

  6. Simultaneous Dual Protein Labeling using a Triorthogonal Reagent

    PubMed Central

    Rashidian, Mohammad; Kumarapperuma, Sidath C.; Gabrielse, Kari; Fegan, Adrian; Wagner, Carston R.; Distefano, Mark D.

    2013-01-01

    Construction of heterofunctional proteins is a rapidly emerging area of biotherapeutics. Combining a protein with other moieties such as a targeting element, a toxic protein or small molecule, a fluorophore or PEG groups, can improve the specificity, functionality, potency, and pharmacokinetic profile of a protein. Protein farnesyltransferase (PFTase) is able to site-specifically and quantitatively prenylate proteins containing a C-terminal CaaX box amino acid sequence with various modified isoprenoids. Here, we describe the design, synthesis and application of a triorthogonal reagent, 1, that can be used to site-specifically incorporate an alkyne and aldehyde group simultaneously into a protein. To illustrate the capabilities of this approach, a protein was enzymatically modified with 1 followed by oxime ligation and click reaction to simultaneously incorporate an azido-TAMRA fluorophore and an aminooxy-PEG moiety. This was done with both a model protein (GFP) as well as a therapeutically useful protein (CNTF). Next, a protein was enzymatically modified with 1 followed by coupling to an azido-bis-methotrexate dimerizer and aminooxy-TAMRA. Incubation of that construct with a DHFR-DHFR-anti-CD3 fusion protein resulted in the self-assembly of nanoring structures that were endocytosed into T-leukemia cells and visualized therein. These results highlight how complex multifunctional protein assemblies can be prepared using this this facile triorthogonal approach. PMID:24134212

  7. Involvement of a cell surface protein and an ecto-protein kinase in myogenesis.

    PubMed Central

    Chen, X Y; Lo, T C

    1991-01-01

    Myogenic differentiation is composed of a sequential cascade of multiple steps leading to the formation of multinucleated myotubes. The interference with any one step would abolish myogenesis. The present investigation examined the cell surface components which might be involved in myogenesis. Studies with subconfluent day 2 cultures of rat L6 myoblasts revealed that a cell surface 112 kDa protein was phosphorylated by a Ca(2+)-, F(-)- and Mg(2+)-dependent ecto-protein kinase [Chen & Lo (1991) Biochem. J. 279, 467-474]. We have shown in the present investigation that adequate ATP was present on the cell surface for efficient functioning of this ecto-protein kinase. The phosphorylation of the 112 kDa protein by this ecto-protein kinase was decrease dramatically in confluent cells and in multinucleated myotubes. The following evidence suggests that both the 112 kDa protein and the ecto-protein kinase may play important roles in myogenesis. (i) The highest phosphorylation activity was observed in subconfluent cultures, i.e. before the onset of morphological differentiation. (ii) Treatment of cells with chemical reagents resulted in a corresponding decrease in the ecto-protein kinase, the 112 kDa protein, the phosphorylated 112 kDa protein (p112) and the ability to form myotubes. (iii) The level of p112 in a conditional myogenesis-defective mutant corresponded with the cells' eventual ability to differentiate. (iv) A mutant defective in the ecto-protein kinase was impaired in the phosphorylation of the 112 kDa protein and in myogenesis. (v) A mutant containing only residual levels of the 112 kDa protein was deficient in both p112 and myogenesis. (vi) Since the level of p112 was normal in another myogenesis-defective mutant, the phosphorylation of this protein was not likely to be a consequence of myogenic differentiation. The above findings suggest that the ecto-protein kinase and the 112 kDa protein may directly or indirectly be associated with the myogenic pathway. Since the levels of the ecto-protein kinase, the 112 kDa protein and p112 decreased dramatically upon the formation of myotubes, these proteins were probably not required once morphological differentiation had been initiated. Images Fig. 3. Fig. 4. Fig. 5. PMID:1953643

  8. Theranostic potential of gold nanoparticle-protein agglomerates.

    PubMed

    Sanpui, Pallab; Paul, Anumita; Chattopadhyay, Arun

    2015-11-28

    Owing to the ever-increasing applications, glittered with astonishing success of gold nanoparticles (Au NPs) in biomedical research as diagnostic and therapeutic agents, the study of Au NP-protein interaction seems critical for maximizing their theranostic efficiency, and thus demands comprehensive understanding. The mutual interaction of Au NPs and proteins at physiological conditions may result in the aggregation of protein, which can ultimately lead to the formation of Au NP-protein agglomerates. In the present article, we try to appreciate the plausible steps involved in the Au NP-induced aggregation of proteins and also the importance of the proteins' three-dimensional structures in the process. The Au NP-protein agglomerates can potentially be exploited for efficient loading and subsequent release of various therapeutically important molecules, including anticancer drugs, with the unique opportunity of incorporating hydrophilic as well as hydrophobic drugs in the same nanocarrier system. Moreover, the Au NP-protein agglomerates can act as 'self-diagnostic' systems, allowing investigation of the conformational state of the associated protein(s) as well as the protein-protein or protein-Au NP interaction within the agglomerates. Furthermore, the potential of these Au NP-protein agglomerates as a novel platform for multifunctional theranostic application along with exciting future-possibilities is highlighted here. PMID:26508277

  9. Theranostic potential of gold nanoparticle-protein agglomerates

    NASA Astrophysics Data System (ADS)

    Sanpui, Pallab; Paul, Anumita; Chattopadhyay, Arun

    2015-11-01

    Owing to the ever-increasing applications, glittered with astonishing success of gold nanoparticles (Au NPs) in biomedical research as diagnostic and therapeutic agents, the study of Au NP-protein interaction seems critical for maximizing their theranostic efficiency, and thus demands comprehensive understanding. The mutual interaction of Au NPs and proteins at physiological conditions may result in the aggregation of protein, which can ultimately lead to the formation of Au NP-protein agglomerates. In the present article, we try to appreciate the plausible steps involved in the Au NP-induced aggregation of proteins and also the importance of the proteins' three-dimensional structures in the process. The Au NP-protein agglomerates can potentially be exploited for efficient loading and subsequent release of various therapeutically important molecules, including anticancer drugs, with the unique opportunity of incorporating hydrophilic as well as hydrophobic drugs in the same nanocarrier system. Moreover, the Au NP-protein agglomerates can act as `self-diagnostic' systems, allowing investigation of the conformational state of the associated protein(s) as well as the protein-protein or protein-Au NP interaction within the agglomerates. Furthermore, the potential of these Au NP-protein agglomerates as a novel platform for multifunctional theranostic application along with exciting future-possibilities is highlighted here.

  10. Toxicological evaluation of proteins introduced into food crops

    PubMed Central

    Kough, John; Herouet-Guicheney, Corinne; Jez, Joseph M.

    2013-01-01

    This manuscript focuses on the toxicological evaluation of proteins introduced into GM crops to impart desired traits. In many cases, introduced proteins can be shown to have a history of safe use. Where modifications have been made to proteins, experience has shown that it is highly unlikely that modification of amino acid sequences can make a non-toxic protein toxic. Moreover, if the modified protein still retains its biological function, and this function is found in related proteins that have a history of safe use (HOSU) in food, and the exposure level is similar to functionally related proteins, then the modified protein could also be considered to be “as-safe-as” those that have a HOSU. Within nature, there can be considerable evolutionary changes in the amino acid sequence of proteins within the same family, yet these proteins share the same biological function. In general, food crops such as maize, soy, rice, canola etc. are subjected to a variety of processing conditions to generate different food products. Processing conditions such as cooking, modification of pH conditions, and mechanical shearing can often denature proteins in these crops resulting in a loss of functional activity. These same processing conditions can also markedly lower human dietary exposure to (functionally active) proteins. Safety testing of an introduced protein could be indicated if its biological function was not adequately characterized and/or it was shown to be structurally/functionally related to proteins that are known to be toxic to mammals. PMID:24164515

  11. Identification of a third protein 4.1 tumor suppressor, protein 4.1R, in meningioma pathogenesis

    SciTech Connect

    Robb, Victoria A.; Li, Wen; Gascard, Philippe; Perry, Arie; Mohandas, Narla; Gutmann, David H.

    2003-06-11

    Meningiomas are common tumors of the central nervous system, however, the mechanisms under lying their pathogenesis are largely undefined. Two members of the Protein 4.1 super family, the neuro fibromatosis 2 (NF2) gene product (merlin/schwannomin) and Protein 4.1B have been implicated as meningioma tumor suppressors. In this report, we demonstrate that another Protein 4.1 family member, Protein 4.1R, also functions as a meningioma tumor suppressor. Based on the assignment of the Protein 4.1R gene to chromosome 1p32-36, a common region of deletion observed in meningiomas, we analyzed Protein 4.1R expression in meningioma cell lines and surgical tumor specimens. We observed loss of Protein 4.1R protein expression in two meningioma cell lines (IOMM-Lee, CH157-MN) by Western blotting as well as in 6 of 15 sporadic meningioma as by immuno histo chemistry (IHC). Analysis of a subset of these sporadic meningiomas by fluorescent in situ hybridization (FISH) with a Protein 4.1R specific probe demonstrated 100 percent concordance with the IHC results. In support of a meningioma tumor suppressor function, over expression of Protein 4.1R resulted in suppression of IOMM-Lee and CH157MN cell proliferation. Similar to the Protein 4.1B and merlin meningioma tumor suppressors, Protein 4.1R localization in the membrane fraction increased significantly under conditions of growth arrest in vitro. Lastly, Protein 4.1R interacted with some known merlin/Protein 4.1B interactors such as CD44 and bII-spectrin, but did not associate with the Protein 4.1B interactors 14-3-3 and PRMT3 or the merlin binding proteins SCHIP-1 and HRS. Collectively, these results suggest that Protein 4.1R functions as an important tumor suppressor important in the molecular pathogenesis of meningioma.

  12. Biofilm Matrix Proteins

    PubMed Central

    Fong, Jiunn N. C.; Yildiz, Fitnat H.

    2015-01-01

    Proteinaceous components of the biofilm matrix include secreted extracellular proteins, cell surface adhesins and protein subunits of cell appendages such as flagella and pili. Biofilm matrix proteins play diverse roles in biofilm formation and dissolution. They are involved in attaching cells to surfaces, stabilizing the biofilm matrix via interactions with exopolysaccharide and nucleic acid components, developing three-dimensional biofilm architectures, and dissolving biofilm matrix via enzymatic degradation of polysaccharides, proteins, and nucleic acids. In this chapter, we will review functions of matrix proteins in a selected set of microorganisms, studies of the matrix proteomes of Vibrio cholerae and Pseudomonas aeruginosa, and roles of outer membrane vesicles and of nucleoid-binding proteins in biofilm formation. PMID:26104709

  13. Functional Protein Microarray Technology

    PubMed Central

    Hu, Shaohui; Xie, Zhi; Qian, Jiang; Blackshaw, Seth; Zhu, Heng

    2010-01-01

    Functional protein microarrays are emerging as a promising new tool for large-scale and high-throughput studies. In this article, we will review their applications in basic proteomics research, where various types of assays have been developed to probe binding activities to other biomolecules, such as proteins, DNA, RNA, small molecules, and glycans. We will also report recent progress of using functional protein microarrays in profiling protein posttranslational modifications, including phosphorylation, ubiquitylation, acetylation, and nitrosylation. Finally, we will discuss potential of functional protein microarrays in biomarker identification and clinical diagnostics. We strongly believe that functional protein microarrays will soon become an indispensible and invaluable tool in proteomics research and systems biology. PMID:20872749

  14. Mayaro virus proteins.

    PubMed

    Mezencio, J M; Rebello, M A

    1993-01-01

    Mayaro virus was grown in BHK-21 cells and purified by centrifugation in a potassium-tartrate gradient (5-50%). The electron microscopy analyses of the purified virus showed an homogeneous population of enveloped particles with 69 +/- 2.3 nm in diameter. Three structural virus proteins were identified and designated p1, p2 and p3. Their average molecular weight were p1, 54 KDa; p2, 50 KDa and p3, 34 KDa. In Mayaro virus infected Aedes albopictus cells and in BHK-21 infected cells we detected six viral proteins, in which three of them are the structural virus proteins and the other three were products from processing of precursors of viral proteins, whose molecular weights are 62 KDa, 64 KDa and 110 KDa. The 34 KDa protein was the first viral protein synthesized at 5 hours post-infection in both cell lines studied. PMID:8107591

  15. Protein crystal growth (5-IML-1)

    NASA Technical Reports Server (NTRS)

    Bugg, Charles E.

    1992-01-01

    Proteins (enzymes, hormones, immunoglobulins) account for 50 pct. or more of the dry weight of most living systems. A detailed understanding of the structural makeup of a protein is essential to any systematic research pertaining to it. Most macromolecules are extremely difficult to crystallize, and many otherwise exciting projects have terminated at the crystal growth stage. In principle, there are several aspects of microgravity that might be exploited to enhance protein crystal growth. The major factor is the elimination of density driven convective flow. Other factors that can be controlled in the absence of gravity is the sedimentation of growing crystals in a gravitational field, and the potential advantage of doing containerless crystal growth. As a result of these theories and facts, one can readily understand why the microgravity environment of an Earth orbiting vehicle seems to offer unique opportunities for the protein crystallographer. This perception has led to the establishment of the Protein Crystal Growth in a Microgravity Environment (PCG/ME) project. The results of experiments already performed during STS missions have in many cases resulted in large protein crystals which are structurally correct. Thus, the near term objective of the PCG/ME project is to continue to improve the techniques, procedures, and hardware systems used to grow protein crystals in Earth orbit.

  16. Immunomodulatory efficiency of Etroplus suratensis muscle protein

    PubMed Central

    Parthasarathy, P.; Jenilarani, D.; Jaiswal, Neelam

    2014-01-01

    The protein extract of Etroplus suratensis (E. suratensis) collected from Bavanisagar dam was found to be effective against all tested organisms with an inhibition zone ranging from 0.2 to 1.9 mm. When the result was compared with standard antibiotic Streptomycin, a moderate efficiency was observed. In vitro, an antibacterial assay was used to assess the efficacy of fish protein in inhibiting the growth of pathogenic microbes. The fish protein of E. suratensis collected from Bavanisagar had a broad spectrum of antibacterial potential. The minimal inhibitory concentrations of E. suratensis against pathogens are the highest in protein collected from Bavanisagar. In the fish protein collected from Bavanisagar, it has been shown that the minimum bactericidal concentration (MBC) value is higher in Bacillus subtilis (0.85/20 µg/ml) and the lowest in Micrococcus (0.1/100 µg/ml). The sub-lethal dose of fish protein was estimated at 1/10 of 96 h LD50 dose (30 µg/ml/Kg), the antibody response was significantly enhanced on day 14 and day 21 (p < 0.01). The highest IgG level was noticed on day 21, which decreased towards day 28. This result showed the antibody production with an increased IgG concentration. The above results demonstrate that fish protein extracts have great potential as immunostimulants against the microorganisms and they can be used in the treatment of infectious diseases caused by the microorganisms. PMID:26155096

  17. Energy design for protein-protein interactions

    PubMed Central

    Ravikant, D. V. S.; Elber, Ron

    2011-01-01

    Proteins bind to other proteins efficiently and specifically to carry on many cell functions such as signaling, activation, transport, enzymatic reactions, and more. To determine the geometry and strength of binding of a protein pair, an energy function is required. An algorithm to design an optimal energy function, based on empirical data of protein complexes, is proposed and applied. Emphasis is made on negative design in which incorrect geometries are presented to the algorithm that learns to avoid them. For the docking problem the search for plausible geometries can be performed exhaustively. The possible geometries of the complex are generated on a grid with the help of a fast Fourier transform algorithm. A novel formulation of negative design makes it possible to investigate iteratively hundreds of millions of negative examples while monotonically improving the quality of the potential. Experimental structures for 640 protein complexes are used to generate positive and negative examples for learning parameters. The algorithm designed in this work finds the correct binding structure as the lowest energy minimum in 318 cases of the 640 examples. Further benchmarks on independent sets confirm the significant capacity of the scoring function to recognize correct modes of interactions. PMID:21842951

  18. C-reactive protein in urologic cancers.

    PubMed

    Huang, Jonathan; Baum, Yoram; Alemozaffar, Mehrdad; Ogan, Kenneth; Harris, Wayne; Kucuk, Omer; Master, Viraj A

    2015-11-01

    C-reactive protein is an acute-phase reactant that is elevated in the setting of systemic infections, trauma, and malignancies. Urologic cancers have been shown to promote changes in c-reactive protein levels. Pre-treatment serum levels can predict disease characteristics, extent of disease, and prognosticate survival after intervention in renal cell carcinoma, prostate cancer, bladder cancer, upper tract urothelial carcinoma, and penile cancer. Changes in post-treatment serum levels have also shown promise in determining survival. As a result, c-reactive protein has been incorporated into various survival nomograms to improve predictive accuracy. While the association between c-reactive protein and survival in testicular cancer has not been studied, elevated serum levels may correlate with treatment side effects, such as cardiovascular disease and chronic cancer-related fatigue. Understanding the relationship between c-reactive protein and urologic cancers can help physicians determine the appropriate course of treatment and improve patient care. PMID:25936279

  19. Stress proteins are induced by space environment

    NASA Astrophysics Data System (ADS)

    Takahashi, Akihisa; Ohnishi, Takeo

    The space environment contains two major biologically significant influences such as space radiations and microgravity. Almost all organisms possess essential recognition and response systems for environmental changes. The famous one of cellular stress responses is the gene induction of heat shock protein (HSP). HSP expression is increased under elevated temperatures, and also increased by other sources of cellular stress, including ionizing radiation, oxidative injury, osmotic stress and the unfolded protein response. HSPs assist in the folding and maintenance of newly translated proteins, the refolding of denatured proteins and the further unfolding of misfolded or destabilized proteins to protect the cell from crisis. Based on our space experiment, we report the results and discussion from the viewpoint of HSP expression after exposure to space environment.

  20. Mapping hydration dynamics around a protein surface

    PubMed Central

    Zhang, Luyuan; Wang, Lijuan; Kao, Ya-Ting; Qiu, Weihong; Yang, Yi; Okobiah, Oghaghare; Zhong, Dongping

    2007-01-01

    Protein surface hydration is fundamental to its structure and activity. We report here the direct mapping of global hydration dynamics around a protein in its native and molten globular states, using a tryptophan scan by site-specific mutations. With 16 tryptophan mutants and in 29 different positions and states, we observed two robust, distinct water dynamics in the hydration layer on a few (?1–8 ps) and tens to hundreds of picoseconds (?20–200 ps), representing the initial local relaxation and subsequent collective network restructuring, respectively. Both time scales are strongly correlated with protein's structural and chemical properties. These results reveal the intimate relationship between hydration dynamics and protein fluctuations and such biologically relevant water–protein interactions fluctuate on picosecond time scales. PMID:18003912

  1. Implications of protein degradation in aging.

    PubMed

    Goto, S; Takahashi, R; Kumiyama, A A; Radák, Z; Hayashi, T; Takenouchi, M; Abe, R

    2001-04-01

    Aging is characterized by accumulation of potentially harmful altered proteins that could lead to gradual deterioration of cellular functions and eventually result in increased probability of death. Metabolic turnover of proteins thus plays an essential role in maintaining the life of an organism. In this article we summarize our current knowledge on age-related changes in protein turnover with special reference to degradation. Increase in half-life of proteins with advancing age is well documented. Qualitative rather than quantitative changes of proteasomes appear to be responsible for this change. Dietary restriction and moderate long-term exercise seem to restore higher proteasome activity and turnover rate of proteins in aged animals. PMID:11795528

  2. A technique to search for functional similarities in protein-protein interaction networks.

    PubMed

    Fionda, Valeria; Palopoli, Luigi; Panni, Simona; Rombo, Simona E

    2009-01-01

    We describe a method to search for similarities across protein-protein interaction networks of different organisms. The technique core consists in computing a maximum weight matching of bipartite graphs resulting from comparing the neighbourhoods of proteins belonging to different networks. Both quantitative and reliability information are exploited. We tested the method on the networks of S. cerevisiae, D. melanogaster and C. elegans. The experiments showed that the technique is able to detect functional orthologs when the sole sequence similarity does not prove itself sufficient. They also demonstrated the capability of our approach in discovering common biological processes involving uncharacterised proteins. PMID:20052906

  3. Protein-detergent interactions in single crystals of membrane proteins studied by neutron crystallography

    SciTech Connect

    Timmins, P.A.; Pebay-Peyroula, E.

    1994-12-31

    The detergent micelles surrounding membrane protein molecules in single crystals can be investigated using neutron crystallography combined with H{sub 2}O/D{sub 2}O contrast variation. If the protein structure is known then the contrast variation method allows phases to be determined at a contrast where the detergent dominates the scattering. The application of various constraints allows the resulting scattering length density map to be realistically modeled. The method has been applied to two different forms of the membrane protein porin. In one case both hydrogenated and partially deuterated protein were used, allowing the head group and tail to be distinguished.

  4. Method for printing functional protein microarrays

    NASA Technical Reports Server (NTRS)

    Delehanty, James B.; Ligler, Frances S.

    2003-01-01

    Piezoelectric dispensing of proteins from borosilicate glass capillaries is a popular method of protein biochip fabrication that offers the advantages of sample recovery and noncontact with the printing substrate. However, little regard has been given to the quantitative aspects of dispensing minute volumes (1 nL or less) at the low protein concentrations (20 micrograms/mL or less) typically used in microprinting. Specifically, loss of protein sample due to nonspecific adsorption to the glass surface of the dispensing capillaries can limit the amount of protein delivered to the substrate. We demonstrate the benefits of a low ionic strength buffer containing the carrier protein BSA that effectively minimizes the ionic strength-dependent phenomenon of nonspecific protein adsorption to borosilicate glass. Over the concentration range of 20-2.5 micrograms/mL, the dispensing of a reference IgG in 10 mM PBS including 0.1% BSA resulted in the deposition of 3.6- to 44-fold more IgG compared to the deposition of IgG in standard 150 mM PBS in the absence of BSA. Furthermore, when the IgG was dispensed with carrier protein, the resulting spots exhibited a more uniform morphology. In a direct immunoassay for cholera toxin, capture antibody spots dispensed in 10 mM PBS containing 0.1% BSA produced fluorescent signals that were 2.8- to 4.3-fold more intense than antibody spots that were dispensed in 150 mM PBS without BSA. Interestingly, no differences were observed in the specific activities of the capture antibodies as a result of printing in the different buffers. The implications of these results on the future development of protein biochips are discussed.

  5. Pressure cryocooling protein crystals

    DOEpatents

    Kim, Chae Un (Ithaca, NY); Gruner, Sol M. (Ithaca, NY)

    2011-10-04

    Preparation of cryocooled protein crystal is provided by use of helium pressurizing and cryocooling to obtain cryocooled protein crystal allowing collection of high resolution data and by heavier noble gas (krypton or xenon) binding followed by helium pressurizing and cryocooling to obtain cryocooled protein crystal for collection of high resolution data and SAD phasing simultaneously. The helium pressurizing is carried out on crystal coated to prevent dehydration or on crystal grown in aqueous solution in a capillary.

  6. Protein-Protein Interaction Site Predictions with Three-Dimensional Probability Distributions of Interacting

    E-print Network

    Hsu, Wen-Lian

    of proteins in packing density and in the physicochemical nature of the amino acid composition. In this work on an independent dataset (consisting of 142 proteins). The residue-based Matthews correlation coefficient.677, and 0.779 respectively. The benchmark results indicate that the optimized machine learning models

  7. Discovering Distinct Functional Modules of Specific Cancer Types Using Protein-Protein Interaction Networks

    PubMed Central

    Shen, Ru; Wang, Xiaosheng; Guda, Chittibabu

    2015-01-01

    Background. The molecular profiles exhibited in different cancer types are very different; hence, discovering distinct functional modules associated with specific cancer types is very important to understand the distinct functions associated with them. Protein-protein interaction networks carry vital information about molecular interactions in cellular systems, and identification of functional modules (subgraphs) in these networks is one of the most important applications of biological network analysis. Results. In this study, we developed a new graph theory based method to identify distinct functional modules from nine different cancer protein-protein interaction networks. The method is composed of three major steps: (i) extracting modules from protein-protein interaction networks using network clustering algorithms; (ii) identifying distinct subgraphs from the derived modules; and (iii) identifying distinct subgraph patterns from distinct subgraphs. The subgraph patterns were evaluated using experimentally determined cancer-specific protein-protein interaction data from the Ingenuity knowledgebase, to identify distinct functional modules that are specific to each cancer type. Conclusion. We identified cancer-type specific subgraph patterns that may represent the functional modules involved in the molecular pathogenesis of different cancer types. Our method can serve as an effective tool to discover cancer-type specific functional modules from large protein-protein interaction networks. PMID:26495282

  8. Prediction of protein functions with gene ontology and interspecies protein homology data.

    PubMed

    Mitrofanova, Antonina; Pavlovic, Vladimir; Mishra, Bud

    2011-01-01

    Accurate computational prediction of protein functions increasingly relies on network-inspired models for the protein function transfer. This task can become challenging for proteins isolated in their own network or those with poor or uncharacterized neighborhoods. Here, we present a novel probabilistic chain-graph-based approach for predicting protein functions that builds on connecting networks of two (or more) different species by links of high interspecies sequence homology. In this way, proteins are able to "exchange" functional information with their neighbors-homologs from a different species. The knowledge of interspecies relationships, such as the sequence homology, can become crucial in cases of limited information from other sources of data, including the protein-protein interactions or cellular locations of proteins. We further enhance our model to account for the Gene Ontology dependencies by linking multiple but related functional ontology categories within and across multiple species. The resulting networks are of significantly higher complexity than most traditional protein network models. We comprehensively benchmark our method by applying it to two largest protein networks, the Yeast and the Fly. The joint Fly-Yeast network provides substantial improvements in precision, accuracy, and false positive rate over networks that consider either of the sources in isolation. At the same time, the new model retains the computational efficiency similar to that of the simpler networks. PMID:21393654

  9. Classifying proteins into functional groups based on all-versus-all BLAST of 10 million proteins.

    PubMed

    Kolker, Natali; Higdon, Roger; Broomall, William; Stanberry, Larissa; Welch, Dean; Lu, Wei; Haynes, Winston; Barga, Roger; Kolker, Eugene

    2011-01-01

    To address the monumental challenge of assigning function to millions of sequenced proteins, we completed the first of a kind all-versus-all sequence alignments using BLAST for 9.9 million proteins in the UniRef100 database. Microsoft Windows Azure produced over 3 billion filtered records in 6 days using 475 eight-core virtual machines. Protein classification into functional groups was then performed using Hive and custom jars implemented on top of Apache Hadoop utilizing the MapReduce paradigm. First, using the Clusters of Orthologous Genes (COG) database, a length normalized bit score (LNBS) was determined to be the best similarity measure for classification of proteins. LNBS achieved sensitivity and specificity of 98% each. Second, out of 5.1 million bacterial proteins, about two-thirds were assigned to significantly extended COG groups, encompassing 30 times more assigned proteins. Third, the remaining proteins were classified into protein functional groups using an innovative implementation of a single-linkage algorithm on an in-house Hadoop compute cluster. This implementation significantly reduces the run time for nonindexed queries and optimizes efficient clustering on a large scale. The performance was also verified on Amazon Elastic MapReduce. This clustering assigned nearly 2 million proteins to approximately half a million different functional groups. A similar approach was applied to classify 2.8 million eukaryotic sequences resulting in over 1 million proteins being assign to existing KOG groups and the remainder clustered into 100,000 functional groups. PMID:21809957

  10. Models of globular proteins in aqueous solutions

    NASA Astrophysics Data System (ADS)

    Wentzel, Nathaniel James

    Protein crystallization is a continuing area of research. Currently, there is no universal theory for the conditions required to crystallize proteins. A better understanding of protein crystallization will be helpful in determining protein structure and preventing and treating certain diseases. In this thesis, we will extend the understanding of globular proteins in aqueous solutions by analyzing various models for protein interactions. Experiments have shown that the liquid-liquid phase separation curves for lysozyme in solution with salt depend on salt type and salt concentration. We analyze a simple square well model for this system whose well depth depends on salt type and salt concentration, to determine the phase coexistence surfaces from experimental data. The surfaces, calculated from a single Monte Carlo simulation and a simple scaling argument, are shown as a function of temperature, salt concentration and protein concentration for two typical salts. Urate Oxidase from Asperigillus flavus is a protein used for studying the effects of polymers on the crystallization of large proteins. Experiments have determined some aspects of the phase diagram. We use Monte Carlo techniques and perturbation theory to predict the phase diagram for a model of urate oxidase in solution with PEG. The model used includes an electrostatic interaction, van der Waals attraction, and a polymerinduced depletion interaction. The results agree quantitatively with experiments. Anisotropy plays a role in globular protein interactions, including the formation of hemoglobin fibers in sickle cell disease. Also, the solvent conditions have been shown to play a strong role in the phase behavior of some aqueous protein solutions. Each has previously been treated separately in theoretical studies. Here we propose and analyze a simple, combined model that treats both anisotropy and solvent effects. We find that this model qualitatively explains some phase behavior, including the existence of a lower critical point under certain conditions.

  11. Engineered Proteins: Redox Properties and Their Applications

    PubMed Central

    Prabhulkar, Shradha; Tian, Hui; Wang, Xiaotang; Zhu, Jun-Jie

    2012-01-01

    Abstract Oxidoreductases and metalloproteins, representing more than one third of all known proteins, serve as significant catalysts for numerous biological processes that involve electron transfers such as photosynthesis, respiration, metabolism, and molecular signaling. The functional properties of the oxidoreductases/metalloproteins are determined by the nature of their redox centers. Protein engineering is a powerful approach that is used to incorporate biological and abiological redox cofactors as well as novel enzymes and redox proteins with predictable structures and desirable functions for important biological and chemical applications. The methods of protein engineering, mainly rational design, directed evolution, protein surface modifications, and domain shuffling, have allowed the creation and study of a number of redox proteins. This review presents a selection of engineered redox proteins achieved through these methods, resulting in a manipulation in redox potentials, an increase in electron-transfer efficiency, and an expansion of native proteins by de novo design. Such engineered/modified redox proteins with desired properties have led to a broad spectrum of practical applications, ranging from biosensors, biofuel cells, to pharmaceuticals and hybrid catalysis. Glucose biosensors are one of the most successful products in enzyme electrochemistry, with reconstituted glucose oxidase achieving effective electrical communication with the sensor electrode; direct electron-transfer-type biofuel cells are developed to avoid thermodynamic loss and mediator leakage; and fusion proteins of P450s and redox partners make the biocatalytic generation of drug metabolites possible. In summary, this review includes the properties and applications of the engineered redox proteins as well as their significance and great potential in the exploration of bioelectrochemical sensing devices. Antioxid. Redox Signal. 17, 1796–1822. PMID:22435347

  12. Moonlighting proteins in cancer.

    PubMed

    Min, Kyung-Won; Lee, Seong-Ho; Baek, Seung Joon

    2016-01-01

    Since the 1980s, growing evidence suggested that the cellular localization of proteins determined their activity and biological functions. In a classical view, a protein is characterized by the single cellular compartment where it primarily resides and functions. It is now believed that when proteins appear in different subcellular locations, the cells surpass the expected activity of proteins given the same genomic information to fulfill complex biological behavior. Many proteins are recognized for having the potential to exist in multiple locations in cells. Dysregulation of translocation may cause cancer or contribute to poorer cancer prognosis. Thus, quantitative and comprehensive assessment of dynamic proteins and associated protein movements could be a promising indicator in determining cancer prognosis and efficiency of cancer treatment and therapy. This review will summarize these so-called moonlighting proteins, in terms of a coupled intracellular cancer signaling pathway. Determination of the detailed biological intracellular and extracellular transit and regulatory activity of moonlighting proteins permits a better understanding of cancer and identification of potential means of molecular intervention. PMID:26499805

  13. PIC: Protein Interactions Calculator.

    PubMed

    Tina, K G; Bhadra, R; Srinivasan, N

    2007-07-01

    Interactions within a protein structure and interactions between proteins in an assembly are essential considerations in understanding molecular basis of stability and functions of proteins and their complexes. There are several weak and strong interactions that render stability to a protein structure or an assembly. Protein Interactions Calculator (PIC) is a server which, given the coordinate set of 3D structure of a protein or an assembly, computes various interactions such as disulphide bonds, interactions between hydrophobic residues, ionic interactions, hydrogen bonds, aromatic-aromatic interactions, aromatic-sulphur interactions and cation-pi interactions within a protein or between proteins in a complex. Interactions are calculated on the basis of standard, published criteria. The identified interactions between residues can be visualized using a RasMol and Jmol interface. The advantage with PIC server is the easy availability of inter-residue interaction calculations in a single site. It also determines the accessible surface area and residue-depth, which is the distance of a residue from the surface of the protein. User can also recognize specific kind of interactions, such as apolar-apolar residue interactions or ionic interactions, that are formed between buried or exposed residues or near the surface or deep inside. PMID:17584791

  14. Human Mitochondrial Protein Database

    National Institute of Standards and Technology Data Gateway

    SRD 131 Human Mitochondrial Protein Database (Web, free access)   The Human Mitochondrial Protein Database (HMPDb) provides comprehensive data on mitochondrial and human nuclear encoded proteins involved in mitochondrial biogenesis and function. This database consolidates information from SwissProt, LocusLink, Protein Data Bank (PDB), GenBank, Genome Database (GDB), Online Mendelian Inheritance in Man (OMIM), Human Mitochondrial Genome Database (mtDB), MITOMAP, Neuromuscular Disease Center and Human 2-D PAGE Databases. This database is intended as a tool not only to aid in studying the mitochondrion but in studying the associated diseases.

  15. Self assembling proteins

    DOEpatents

    Yeates, Todd O.; Padilla, Jennifer; Colovos, Chris

    2004-06-29

    Novel fusion proteins capable of self-assembling into regular structures, as well as nucleic acids encoding the same, are provided. The subject fusion proteins comprise at least two oligomerization domains rigidly linked together, e.g. through an alpha helical linking group. Also provided are regular structures comprising a plurality of self-assembled fusion proteins of the subject invention, and methods for producing the same. The subject fusion proteins find use in the preparation of a variety of nanostructures, where such structures include: cages, shells, double-layer rings, two-dimensional layers, three-dimensional crystals, filaments, and tubes.

  16. Acanthamoeba castellanii STAT protein.

    PubMed

    Kicinska, Anna; Leluk, Jacek; Jarmuszkiewicz, Wieslawa

    2014-01-01

    STAT (signal transducers and activators of transcription) proteins are one of the important mediators of phosphotyrosine-regulated signaling in metazoan cells. We described the presence of STAT protein in a unicellular, free-living amoebae with a simple life cycle, Acanthamoeba castellanii. A. castellanii is the only, studied to date, Amoebozoan that does not belong to Mycetozoa but possesses STATs. A sequence of the A. castellanii STAT protein includes domains similar to those of the Dictyostelium STAT proteins: a coiled coil (characteristic for Dictyostelium STAT coiled coil), a STAT DNA-binding domain and a Src-homology domain. The search for protein sequences homologous to A. castellanii STAT revealed 17 additional sequences from lower eukaryotes. Interestingly, all of these sequences come from Amoebozoa organisms that belong to either Mycetozoa (slime molds) or Centramoebida. We showed that there are four separated clades within the slime mold STAT proteins. The A. castellanii STAT protein branches next to a group of STATc proteins from Mycetozoa. We also demonstrate that Amoebozoa form a distinct monophyletic lineage within the STAT protein world that is well separated from the other groups. PMID:25338074

  17. Protein-Phospholipid Interactions in Nonclassical Protein Secretion: Problem and Methods of Study

    PubMed Central

    Prudovsky, Igor; Kumar, Thallapuranam Krishnaswamy Suresh; Sterling, Sarah; Neivandt, David

    2013-01-01

    Extracellular proteins devoid of signal peptides use nonclassical secretion mechanisms for their export. These mechanisms are independent of the endoplasmic reticulum and Golgi. Some nonclassically released proteins, particularly fibroblast growth factors (FGF) 1 and 2, are exported as a result of their direct translocation through the cell membrane. This process requires specific interactions of released proteins with membrane phospholipids. In this review written by a cell biologist, a structural biologist and two membrane engineers, we discuss the following subjects: (i) Phenomenon of nonclassical protein release and its biological significance; (ii) Composition of the FGF1 multiprotein release complex (MRC); (iii) The relationship between FGF1 export and acidic phospholipid externalization; (iv) Interactions of FGF1 MRC components with acidic phospholipids; (v) Methods to study the transmembrane translocation of proteins; (vi) Membrane models to study nonclassical protein release. PMID:23396106

  18. Protein kinase A dependent membrane protein phosphorylation and chloride conductance in endosomal vesicles from kidney cortex

    SciTech Connect

    Reenstra, W.W.; Bae, H.R.; Verkman, A.S. Univ. of California, San Francisco ); Sabolic, I. Harvard Medical School, Charlestown, MA )

    1992-01-14

    Regulation of Cl conductance by protein kinase A action, cell-free measurements of Cl transport and membrane protein phosphorylation were carried out in apical endocytic vesicles from rabbit kidney proximal tubule. Cl transport was measured by a stopped-flow quenching assay in endosomes labeled in vivo with the fluorescent Cl indicator 6-methoxy-N-(3-sulfopropyl)quinolinium. Phosphorylation was studied in a purified endosomal preparation by SDS-PAGE and autoradiography of membrane proteins labeled by ({gamma}-{sup 32}P)ATP. These results suggest that, in a cell-free system, protein kinase A increases Cl conductance in endosomes from kidney proximal tubule by a phosphorylation mechanism. The labeled protein has a size similar to that of the 64-kDa putative kidney Cl channel reported by Landry et al. but is much smaller than the {approximately}170-kDa cystic fibrosis transmembrane conductance regulatory protein.

  19. SAFE Software and FED Database to Uncover Protein-Protein Interactions using Gene Fusion Analysis

    PubMed Central

    Tsagrasoulis, Dimosthenis; Danos, Vasilis; Kissa, Maria; Trimpalis, Philip; Koumandou, V. Lila; Karagouni, Amalia D.; Tsakalidis, Athanasios; Kossida, Sophia

    2012-01-01

    Domain Fusion Analysis takes advantage of the fact that certain proteins in a given proteome A, are found to have statistically significant similarity with two separate proteins in another proteome B. In other words, the result of a fusion event between two separate proteins in proteome B is a specific full-length protein in proteome A. In such a case, it can be safely concluded that the protein pair has a common biological function or even interacts physically. In this paper, we present the Fusion Events Database (FED), a database for the maintenance and retrieval of fusion data both in prokaryotic and eukaryotic organisms and the Software for the Analysis of Fusion Events (SAFE), a computational platform implemented for the automated detection, filtering and visualization of fusion events (both available at: http://www.bioacademy.gr/bioinformatics/projects/ProteinFusion/index.htm). Finally, we analyze the proteomes of three microorganisms using these tools in order to demonstrate their functionality. PMID:22267904

  20. Antimicrobial proteins: From old proteins, new tricks.

    PubMed

    Smith, Valerie J; Dyrynda, Elisabeth A

    2015-12-01

    This review describes the main types of antimicrobial peptides (AMPs) synthesised by crustaceans, primarily those identified in shrimp, crayfish, crab and lobster. It includes an overview of their range of microbicidal activities and the current landscape of our understanding of their gene expression patterns in different body tissues. It further summarises how their expression might change following various types of immune challenges. The review further considers proteins or protein fragments from crustaceans that have antimicrobial properties but are more usually associated with other biological functions, or are derived from such proteins. It discusses how these unconventional AMPs might be generated at, or delivered to, sites of infection and how they might contribute to crustacean host defence in vivo. It also highlights recent work that is starting to reveal the extent of multi-functionality displayed by some decapod AMPs, particularly their participation in other aspects of host protection. Examples of such activities include proteinase inhibition, phagocytosis, antiviral activity and haematopoiesis. PMID:26320628