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1

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

PubMed

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:24905822

Srivastava, Vineet Kumar; Tuteja, Narendra

2014-06-01

2

SEOS frame camera applications study  

NASA Technical Reports Server (NTRS)

A research and development satellite is discussed which will provide opportunities for observation of transient phenomena that fall within the fixed viewing circle of the spacecraft. The evaluation of possible applications for frame cameras, for SEOS, are studied. The computed lens characteristics for each camera are listed.

1974-01-01

3

CEOS SEO and GISS Meeting  

NASA Technical Reports Server (NTRS)

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.

Killough, Brian; Stover, Shelley

2008-01-01

4

A theoretical investigation of the diatomic dication SeO 2+ in the gas phase  

NASA Astrophysics Data System (ADS)

The present study was initiated by the recent observation of the novel molecular species SeO2+ in the gas phase by Franzreb and Williams at Arizona State University. Here we report a very detailed theoretical investigation of the low-lying electronic states of SeO2+. Our results show that the potential energy surfaces of the dicationic electronic states have high potential barriers with respect to dissociation, so this dication can exist in the gas phase as a long-lived metastable molecule. The potential energy curves are used to predict the double photoionization spectrum of SeO and to derive a set of spectroscopic parameters for the bound states of SeO2+.

Ghalila, H.; Lahmar, S.; Hochlaf, M.

2011-12-01

5

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

NASA Technical Reports Server (NTRS)

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.

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

1973-01-01

6

Synthesis, structure, and characterization of two new polar sodium tungsten selenites: Na2(WO3)3(SeO3)·2H2O and Na6(W6O19)(SeO3)2.  

PubMed

Two new quaternary sodium tungsten selenites, Na2(WO3)3(SeO3)·2H2O (P31c) and Na6(W6O19)(SeO3)2 (C2), have been synthesized and characterized. The former exhibits a hexagonal tungsten oxide layered structure, whereas the latter has a one-dimensional "ribbon" structure. The layers and "ribbons" consist of distorted WO6 and asymmetric SeO3 polyhedra. The layers in Na2(WO3)3(SeO3)·2H2O and the "ribbons" in Na6(W6O19)(SeO3)2 are separated by Na(+) cations. Powder second-harmonic-generation (SHG) measurements on Na2(WO3)3(SeO3)·2H2O and Na6(W6O19)(SeO3)2 using 1064 nm radiation reveal SHG efficiencies of approximately 450× and 20× ?-SiO2, respectively. Particle size versus SHG efficiency measurements indicate that the materials are type 1 non-phase-matchable. Converse piezoelectric measurements result in d33 values of approximately 23 and 12 pm/V, whereas pyroelectric measurements reveal coefficients of -0.41 and -1.10 ?C/m(2)·K at 60 °C for Na2(WO3)3(SeO3)·2H2O and Na6(W6O19)(SeO3)2, respectively. Frequency-dependent polarization measurements confirm that the materials are nonferroelectric; i.e., the macroscopic polarization is not reversible, or "switchable". IR and UV-vis spectroscopy, thermogravimetric and differential thermal analysis measurements, and electron localization function calculations were also done for the materials. Crystal data: Na2(WO3)3(SeO3)·2H2O, trigonal, space group P31c (No. 159), a = 7.2595(6) Å, b = 7.2595(6) Å, c = 12.4867(13) Å, V = 569.89(9) Å(3), Z = 2; Na6(W6O19)(SeO3)2, monoclinic, space group C2 (No. 5), a = 42.169(8) Å, b = 7.2690(15) Å, c = 6.7494(13) Å, ? = 98.48(3)°, V = 2046.2(7) Å(3), Z = 4. PMID:23425251

Nguyen, Sau Doan; Halasyamani, P Shiv

2013-03-01

7

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

NASA Astrophysics Data System (ADS)

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.

Nafisi, Shohreh; Manouchehri, Firouzeh; Montazeri, Maryam

2011-12-01

8

Optimized Karatsuba Squaring on 8-bit AVR Processors Hwajeong Seo1  

E-print Network

Optimized Karatsuba Squaring on 8-bit AVR Processors Hwajeong Seo1 , Zhe Liu2 , Jongseok Choi1-Precision Squaring, AVR, Karatsuba, Public Key Cryptography 1 Introduction The developments of embedded processors squaring results on AVR conducted. In this paper, we present Hybrid Karatsuba squaring on AVR, which finely

9

Rapid, room-temperature synthesis of amorphous selenium/protein composites using Capsicum annuum L extract  

NASA Astrophysics Data System (ADS)

We describe the formation of amorphous selenium (?-Se)/protein composites using Capsicum annuum L extract to reduce selenium ions (SeO32-) at room temperature. The reaction occurs rapidly and the process is simple and easy to handle. A protein with a molecular weight of 30 kDa extracted from Capsicum annuum L not only reduces the SeO32- ions to Se0, but also controls the nucleation and growth of Se0, and even participates in the formation of ?-Se/protein composites. The size and shell thickness of the ?-Se/protein composites increases with high Capsicum annuum L extract concentration, and decreases with low reaction solution pH. The results suggest that this eco-friendly, biogenic synthesis strategy could be widely used for preparing inorganic/organic biocomposites. In addition, we also discuss the possible mechanism of the reduction of SeO32- ions by Capsicum annuum L extract.

Li, Shikuo; Shen, Yuhua; Xie, Anjian; Yu, Xuerong; Zhang, Xiuzhen; Yang, Liangbao; Li, Chuanhao

2007-10-01

10

Seos - EARSEL'S Project on Science Education Through Earth Observation for High Schools  

NASA Astrophysics Data System (ADS)

SEOS is an initiative for using remote sensing in science education curricula in high schools funded under the 6th Framework Programme of the European Commission (EC). Eleven partners from several European countries, in cooperation with the European Space Agency (ESA) and teachers from European high schools, created e-learning tutorials for science students in high schools. The tutorials cover many disciplines such as physics, biology, geography, mathematics and engineering, emphasising the interdisciplinary character of remote sensing. They are the core element of the SEOS Learning Management System, allowing teachers to create their own courses, to distribute already available or new worksheets to the students for homework and to collect the results. Forums are available for teachers, students and other users to exchange information and discuss topics relevant for their study.

Reuter, R.

2011-09-01

11

Flickr SEO Tip Sheet Feinberg Office of Communications  

E-print Network

assigned by your camera. Descriptive names, including keywords, will help search engines connect interestedFlickr SEO Tip Sheet Feinberg Office of Communications You've just edited all your photos and phrases that are used in search when looking for content like yours. Look for high-volume keywords

Engman, David M.

12

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

NASA Astrophysics Data System (ADS)

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.

Lim, Ae Ran

2013-10-01

13

Existence of a Lifshitz point in incommensurate RbH3(SeO3)2  

Microsoft Academic Search

The temperature variation of the dielectric constant has been measured in RbH3(SeO3)2 at various bias electric fields. The results show a nonlinear variation of the transition temperature between the incommensurate and the commensurate phase with the applied electric field; this is consistent with the existence of a Lifshitz point at the critical field EL~=49 kV\\/cm.

A. Levstik; C. Filipi; P. Prelovek; R. Blinc; L. A. Shuvalov

1985-01-01

14

DMBC: SEO (Search Engine Optimization) search engines in a natural, non-promoted or advertised way.  

E-print Network

DMBC: SEO (Search Engine Optimization) SEO · e within search engines in a natural, non-promoted or advertised way. Search Engine Optimization is the practice of increasing the visibility of a websit previously searched for (and clicked on) your site vs. another content? More unique visitors = higher

Stowell, Michael

15

An empirical analysis of health care IPOs and SEOs.  

PubMed

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

Brau, James C; Holloway, Jonathan M

2009-01-01

16

Crystal structures of Na2SeO4·1.5H2O and Na2SeO4·10H2O  

PubMed Central

The crystal structures of Na2SeO4·1.5H2O (sodium selenate sesquihydrate) and Na2SeO4·10H2O (sodium selenate deca­hydrate) are isotypic with those of Na2CrO4·1.5H2O and Na2 XSeO4·10H2O (X = S, Cr), respectively. The asymmetric unit of the sesquihydrate contains two Na+ cations, one SeO4 tetra­hedron and one and a half water mol­ecules, the other half being generated by twofold rotation symmetry. The coordination polyhedra of the cations are a distorted monocapped octa­hedron and a square pyramid; these [NaOx] polyhedra are linked through common edges and corners into a three-dimensional framework structure, the voids of which are filled with the Se atoms of the SeO4 tetra­hedra. The structure is consolidated by O—H?O hydrogen bonds between coordinating water mol­ecules and framework O atoms. The asymmetric unit of the deca­hydrate consists of two Na+ cations, one SeO4 tetra­hedron and ten water mol­ecules. Both Na+ cations are octa­hedrally surrounded by water mol­ecules and by edge-sharing condensed into zigzag chains extending parallel to [001]. The SeO4 tetra­hedra and two uncoordinating water mol­ecules are situated between the chains and are connected to the chains through an intricate network of medium-strength O—H?O hydrogen bonds. PMID:25249853

Weil, Matthias; Bonneau, Barbara

2014-01-01

17

Crystal structures of Na2SeO4·1.5H2O and Na2SeO4·10H2O.  

PubMed

The crystal structures of Na2SeO4·1.5H2O (sodium selenate sesquihydrate) and Na2SeO4·10H2O (sodium selenate deca-hydrate) are isotypic with those of Na2CrO4·1.5H2O and Na2 XSeO4·10H2O (X = S, Cr), respectively. The asymmetric unit of the sesquihydrate contains two Na(+) cations, one SeO4 tetra-hedron and one and a half water mol-ecules, the other half being generated by twofold rotation symmetry. The coordination polyhedra of the cations are a distorted monocapped octa-hedron and a square pyramid; these [NaO x ] polyhedra are linked through common edges and corners into a three-dimensional framework structure, the voids of which are filled with the Se atoms of the SeO4 tetra-hedra. The structure is consolidated by O-H?O hydrogen bonds between coordinating water mol-ecules and framework O atoms. The asymmetric unit of the deca-hydrate consists of two Na(+) cations, one SeO4 tetra-hedron and ten water mol-ecules. Both Na(+) cations are octa-hedrally surrounded by water mol-ecules and by edge-sharing condensed into zigzag chains extending parallel to [001]. The SeO4 tetra-hedra and two uncoordinating water mol-ecules are situated between the chains and are connected to the chains through an intricate network of medium-strength O-H?O hydrogen bonds. PMID:25249853

Weil, Matthias; Bonneau, Barbara

2014-08-01

18

P-proteins in Arabidopsis are heteromeric structures involved in rapid sieve tube sealing  

PubMed Central

Structural phloem proteins (P-proteins) are characteristic components of the sieve elements in all dicotyledonous and many monocotyledonous angiosperms. Tobacco P-proteins were recently confirmed to be encoded by the widespread sieve element occlusion (SEO) gene family, and tobacco SEO proteins were shown to be directly involved in sieve tube sealing thus preventing the loss of photosynthate. Analysis of the two Arabidopsis SEO proteins (AtSEOa and AtSEOb) indicated that the corresponding P-protein subunits do not act in a redundant manner. However, there are still pending questions regarding the interaction properties and specific functions of AtSEOa and AtSEOb as well as the general function of structural P-proteins in Arabidopsis. In this study, we characterized the Arabidopsis P-proteins in more detail. We used in planta bimolecular fluorescence complementation assays to confirm the predicted heteromeric interactions between AtSEOa and AtSEOb. Arabidopsis mutants depleted for one or both AtSEO proteins lacked the typical P-protein structures normally found in sieve elements, underlining the identity of AtSEO proteins as P-proteins and furthermore providing the means to determine the role of Arabidopsis P-proteins in sieve tube sealing. We therefore developed an assay based on phloem exudation. Mutants with reduced AtSEO expression levels lost twice as much photosynthate following injury as comparable wild-type plants, confirming that Arabidopsis P-proteins are indeed involved in sieve tube sealing. PMID:23840197

Jekat, Stephan B.; Ernst, Antonia M.; von Bohl, Andreas; Zielonka, Sascia; Twyman, Richard M.; Noll, Gundula A.; Prüfer, Dirk

2013-01-01

19

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

NASA Astrophysics Data System (ADS)

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.

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

2015-01-01

20

Hydroxocobalamin association during cell culture results in pink therapeutic proteins  

PubMed Central

Process control of protein therapeutic manufacturing is central to ensuring the product is both safe and efficacious for patients. In this work, we investigate the cause of pink color variability in development lots of monoclonal antibody (mAb) and Fc-fusion proteins. Results show pink-colored product generated during manufacturing is due to association of hydroxocobalamin (OH-Cbl), a form of vitamin B12. OH-Cbl is not part of the product manufacturing process; however we found cyanocobalamin (CN-Cbl) in cell culture media converts to OH-Cbl in the presence of light. OH-Cbl can be released from mAb and Fc-fusion proteins by conversion with potassium cyanide to CN-Cbl, which does not bind. By exploiting the differential binding of CN-Cbl and OH-Cbl, we developed a rapid and specific assay to accurately measure B12 levels in purified protein. Analysis of multiple products and lots using this technique gives insight into color variability during manufacturing. PMID:23924851

Prentice, Kenneth M; Gillespie, Ronald; Lewis, Nathan; Fujimori, Kiyoshi; McCoy, Rebecca; Bach, Julia; Connell-Crowley, Lisa; Eakin, Catherine M

2013-01-01

21

The RCS of Wire-type Scattering Structures Dong-wook Seo1  

E-print Network

The RCS of Wire-type Scattering Structures Dong-wook Seo1 and Noh-Hoon Myung1 1 School works mainly utilized the method of moment (MoM) for predicting the radar cross section (RCS) of a large to minimize the calculation time. In this case, the total RCS of many wires is simply the product

Myung, Noh-Hoon

22

Japan, France Vying for Korea's Nuclear Project By Cho Jin-seo  

E-print Network

recently have sent high-ranking officials to South Korea, since it will play the key role in the selection, Japan, China, Russia, U.S., and South Korea, is the largest international collaborative scientificJapan, France Vying for Korea's Nuclear Project By Cho Jin-seo Staff Reporter France and Japan

23

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

E-print Network

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

Cordier, Frederic

24

Application and Research of SEO in the Development of Web2.0 Site  

Microsoft Academic Search

In order to activate the development of web2.0 site, SEO (search engine optimization) is discussed according to the problems the Web2.0 site now facing. With the problems, the paper put forward design Methods for Website optimization, and summed up the optimization strategies for Website design.

Chengling Zhao; Jiaojiao Lu; Fengfeng Duan

2009-01-01

25

Human SNPs resulting in premature stop codons and protein truncation  

PubMed Central

Single nucleotide polymorphisms (SNPs) constitute the most common type of genetic variation in humans. SNPs introducing premature termination codons (PTCs), herein called X-SNPs, can alter the stability and function of transcripts and proteins and thus are considered to be biologically important. Initial studies suggested a strong selection against such variations/mutations. In this study, we undertook a genome-wide systematic screening to identify human X-SNPs using the dbSNP database. Our results demonstrated the presence of 28 X-SNPs from 28 genes with known minor allele frequencies. Eight X-SNPs (28.6 per cent) were predicted to cause transcript degradation by nonsense-mediated mRNA decay. Seventeen X-SNPs (60.7 per cent) resulted in moderate to severe truncation at the C-terminus of the proteins (deletion of > 50 per cent of the amino acids). The majority of the X-SNPs (78.6 per cent) represent commonly occurring SNPs, by contrast with the rarely occurring disease-causing PTC mutations. Interestingly, X-SNPs displayed a non-uniform distribution across human populations: eight X-SNPs were reported to be prevalent across three different human populations, whereas six X-SNPs were found exclusively in one or two population(s). In conclusion, we have systematically investigated human SNPs introducing PTCs with respect to their possible biological consequences, distributions across different human populations and evolutionary aspects. We believe that the SNPs reported here are likely to affect gene/protein function, although their biological and evolutionary roles need to be further investigated. PMID:16595072

2006-01-01

26

New vanadium selenites: centrosymmetric Ca2(VO2)2(SeO3)3(H2O)2, Sr2(VO2)2(SeO3)3, and Ba(V2O5)(SeO3), and noncentrosymmetric and polar A4(VO2)2(SeO3)4(Se2O5) (A = Sr2+ or Pb2+).  

PubMed

Five new vanadium selenites, Ca(2)(VO(2))(2)(SeO(3))(3)(H(2)O)(2), Sr(2)(VO(2))(2)(SeO(3))(3), Ba(V(2)O(5))(SeO(3)), Sr(4)(VO(2))(2)(SeO(3))(4)(Se(2)O(5)), and Pb(4)(VO(2))(2)(SeO(3))(4)(Se(2)O(5)), have been synthesized and characterized. Their crystal structures were determined by single crystal X-ray diffraction. The compounds exhibit one- or two-dimensional structures consisting of corner- and edge-shared VO(4), VO(5), VO(6), and SeO(3) polyhedra. Of the reported materials, A(4)(VO(2))(2)(SeO(3))(4)(Se(2)O(5)) (A = Sr(2+) or Pb(2+)) are noncentrosymmetric (NCS) and polar. Powder second-harmonic generation (SHG) measurements revealed SHG efficiencies of approximately 130 and 150 × ?-SiO(2) for Sr(4)(VO(2))(2)(SeO(3))(4)(Se(2)O(5)) and Pb(4)(VO(2))(2)(SeO(3))(4)(Se(2)O(5)), respectively. Piezoelectric charge constants of 43 and 53 pm/V, and pyroelectric coefficients of -27 and -42 ?C/m(2)·K at 70 °C were obtained for Sr(4)(VO(2))(2)(SeO(3))(4)(Se(2)O(5)) and Pb(4)(VO(2))(2)(SeO(3))(4)(Se(2)O(5)), respectively. Frequency dependent polarization measurements confirmed that the materials are not ferroelectric, that is, the observed polarization cannot be reversed. In addition, the lone-pair on the Se(4+) cation may be considered as stereo-active consistent with calculations. For all of the reported materials, infrared, UV-vis, thermogravimetric, and differential thermal analysis measurements were performed. Crystal data: Ca(2)(VO(2))(2)(SeO(3))(3)(H(2)O)(2), orthorhombic, space group Pnma (No. 62), a = 7.827(4) Å, b = 16.764(5) Å, c = 9.679(5) Å, V = 1270.1(9) Å(3), and Z = 4; Sr(2)(VO(2))(2)(SeO(3))(3), monoclinic, space group P2(1)/c (No. 12), a = 14.739(13) Å, b = 9.788(8) Å, c = 8.440(7) Å, ? = 96.881(11)°, V = 1208.8(18) Å(3), and Z = 4; Ba(V(2)O(5))(SeO(3)), orthorhombic, space group Pnma (No. 62), a = 13.9287(7) Å, b = 5.3787(3) Å, c = 8.9853(5) Å, V = 673.16(6) Å(3), and Z = 4; Sr(4)(VO(2))(2)(SeO(3))(4)(Se(2)O(5)), orthorhombic, space group Fdd2 (No. 43), a = 25.161(3) Å, b = 12.1579(15) Å, c = 12.8592(16) Å, V = 3933.7(8) Å(3), and Z = 8; Pb(4)(VO(2))(2)(SeO(3))(4)(Se(2)O(5)), orthorhombic, space group Fdd2 (No. 43), a = 25.029(2) Å, b = 12.2147(10) Å, c = 13.0154(10) Å, V = 3979.1(6) Å(3), and Z = 8. PMID:22145697

Yeon, Jeongho; Kim, Sang-Hwan; Nguyen, Sau Doan; Lee, Hana; Halasyamani, P Shiv

2012-01-01

27

Copper(I)-mediated protein-protein interactions result from suboptimal interaction surfaces.  

PubMed

The homoeostasis of metal ions in cells is the result of the contribution of several cellular pathways that involve transient, often weak, protein-protein interactions. Metal transfer typically implies the formation of adducts where the metal itself acts as a bridge between proteins, by co-ordinating residues of both interacting partners. In the present study we address the interaction between the human copper(I)-chaperone HAH1 (human ATX1 homologue) and a metal-binding domain in one of its partners, namely the P-type copper-transporting ATPase, ATP7A (ATPase, Cu+ transporting, alpha polypeptide). The adduct was structurally characterized in solution, in the presence of copper(I), and through X-ray crystallography, upon replacing copper(I) with cadmium(II). Further insight was obtained through molecular modelling techniques and site-directed mutagenesis. It was found that the interaction involves a relatively small interface (less than 1000 A(2), 1 A=0.1 nm) with a low fraction of non-polar atoms. These observations provide a possible explanation for the low affinity of the two apoproteins. It appears that electrostatics is important in selecting which domain of the ATPase is able to form detectable amounts of the metal-mediated adduct with HAH1. PMID:19453293

Banci, Lucia; Bertini, Ivano; Calderone, Vito; Della-Malva, Nunzia; Felli, Isabella C; Neri, Sara; Pavelkova, Anna; Rosato, Antonio

2009-08-15

28

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)

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.

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

2013-11-01

29

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

NASA Astrophysics Data System (ADS)

Infrared reflection and transmission over a broad temperature range (10-300 K) have been measured on the anisotropic single-crystal Cu3(SeO3)2Cl. Two distinct space groups have previously been reported for Cu3(SeO3)2Cl 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)2Cl will be discussed in terms of our infrared spectra, group theoretical predictions, and comparisons to related compounds.

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

2013-03-01

30

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

NASA Astrophysics Data System (ADS)

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.

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

2013-03-01

31

Annotation of proteins of unknown function: initial enzyme results.  

PubMed

Working with a combination of ProMOL (a plugin for PyMOL that searches a library of enzymatic motifs for local structural homologs), BLAST and Pfam (servers that identify global sequence homologs), and Dali (a server that identifies global structural homologs), we have begun the process of assigning functional annotations to the approximately 3,500 structures in the Protein Data Bank that are currently classified as having "unknown function". Using a limited template library of 388 motifs, over 500 promising in silico matches have been identified by ProMOL, among which 65 exceptionally good matches have been identified. The characteristics of the exceptionally good matches are discussed. PMID:25630330

McKay, Talia; Hart, Kaitlin; Horn, Alison; Kessler, Haeja; Dodge, Greg; Bardhi, Keti; Bardhi, Kostandina; Mills, Jeffrey L; Bernstein, Herbert J; Craig, Paul A

2015-03-01

32

Combinatorial Algorithms for Protein Folding in Lattice Models: A Survey of Mathematical Results  

E-print Network

Combinatorial Algorithms for Protein Folding in Lattice Models: A Survey of Mathematical Results a comprehensive survey of combinatorial algorithms and theorems about lattice protein folding models obtained in the almost 15 years since the publication in 1995 of the first protein folding approximation algorithm

Istrail, Sorin

33

Protein crystal growth results from shuttle flight 51-F  

NASA Technical Reports Server (NTRS)

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.

Bugg, C. E.

1985-01-01

34

Silencing of Soybean Seed Storage Proteins Results in a Rebalanced Protein Composition Preserving Seed Protein Content without Major Collateral Changes in the Metabolome and Transcriptome[W][OA  

PubMed Central

The ontogeny of seed structure and the accumulation of seed storage substances is the result of a determinant genetic program. Using RNA interference, the synthesis of soybean (Glycine max) glycinin and conglycinin storage proteins has been suppressed. The storage protein knockdown (SP?) seeds are overtly identical to the wild type, maturing to similar size and weight, and in developmental ontogeny. The SP? seeds rebalance the proteome, maintaining wild-type levels of protein and storage triglycerides. The SP? soybeans were evaluated with systems biology techniques of proteomics, metabolomics, and transcriptomics using both microarray and next-generation sequencing transcript sequencing (RNA-Seq). Proteomic analysis shows that rebalancing of protein content largely results from the selective increase in the accumulation of only a few proteins. The rebalancing of protein composition occurs with small alterations to the seed’s transcriptome and metabolome. The selectivity of the rebalancing was further tested by introgressing into the SP? line a green fluorescent protein (GFP) glycinin allele mimic and quantifying the resulting accumulation of GFP. The GFP accumulation was similar to the parental GFP-expressing line, showing that the GFP glycinin gene mimic does not participate in proteome rebalancing. The results show that soybeans make large adjustments to the proteome during seed filling and compensate for the shortage of major proteins with the increased selective accumulation of other proteins that maintains a normal protein content. PMID:21398260

Schmidt, Monica A.; Barbazuk, W. Brad; Sandford, Michael; May, Greg; Song, Zhihong; Zhou, Wenxu; Nikolau, Basil J.; Herman, Eliot M.

2011-01-01

35

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

NASA Astrophysics Data System (ADS)

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.

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

2012-12-01

36

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

ERIC Educational Resources Information Center

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,…

Mulat, Tiruwork; Arcavi, Abraham

2009-01-01

37

Growth Energetics of Single-Wall Carbon Nanotubes with Carbon Monoxide Kwanyong Seo, Changwook Kim, and Bongsoo Kim*  

E-print Network

Growth Energetics of Single-Wall Carbon Nanotubes with Carbon Monoxide Kwanyong Seo, Changwook Kim energetics of single-wall carbon nanotubes (SWNTs) with gas-phase CO molecules is investigated. Our density-6 Though single-wall carbon nanotubes (SWNTs) have different electronic properties depending

Kim, Bongsoo

38

Skeletal muscle protein loss due to D-penicillamine results from reduced protein synthesis  

Microsoft Academic Search

Reports in the literature indicate that the trifunctional amino acid D-penicillamine (D-P) induces a variety of muscle abnormalities, although the mechanisms are unknown. We hypothesised that defects may also arise due to the effects of D-P on rates of protein synthesis, possibly via changes in muscle metal composition. Male Wistar rats were injected with D-P at doses of 50 and

Victor R. Preedy; Wassif S. Wassif; Dianne Baldwin; Jenny Jones; Gavin Falkous; Jaspaul S. Marway; David Mantle; David L. Scott

2001-01-01

39

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

PubMed Central

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

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

2013-01-01

40

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

... Money and Finance: Treasury Office of the Secretary of the Treasury TARP STANDARDS FOR COMPENSATION AND CORPORATE GOVERNANCE § 30.3 Q-3: How are the SEOs and most highly compensated employees identified for purposes of...

2010-07-01

41

The roughness of the protein energy landscape results in anomalous diffusion of the polypeptide backbone.  

PubMed

Although protein folding is often described by motion on a funnel-shaped overall topology of the energy landscape, the many local interactions that can occur result in considerable landscape roughness which slows folding by increasing internal friction. Recent experimental results have brought to light that this roughness also causes unusual diffusional behaviour of the backbone of an unfolded protein, i.e. the relative motion of protein sections cannot be described by the normal diffusion equation, but shows strongly subdiffusional behaviour with a nonlinear time dependence of the mean square displacement, ?r(2)(t)? ? t(?) (? ? 1). This results in significantly slower configurational equilibration than had been assumed hitherto. Analysis of the results also allows quantification of the energy landscape roughness, i.e. the root-mean-squared depth of local minima, yielding a value of 4-5kBT for a typical small protein. PMID:25412176

Volk, Martin; Milanesi, Lilia; Waltho, Jonathan P; Hunter, Christopher A; Beddard, Godfrey S

2014-12-10

42

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

NASA Astrophysics Data System (ADS)

A new bismuth oxo-selenite bromide Bi6(SeO3)3O5Br2 was synthesized and structurally characterized. The crystal structure belongs to the triclinic system (space group P1¯, Z=2, a=7.1253(7) Å, b=10.972(1) Å, c=12.117(1) Å, ?=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.

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

2012-12-01

43

Rational modification of protein stability by targeting surface sites leads to complicated results  

PubMed Central

The rational modification of protein stability is an important goal of protein design. Protein surface electrostatic interactions are not evolutionarily optimized for stability and are an attractive target for the rational redesign of proteins. We show that surface charge mutants can exert stabilizing effects in distinct and unanticipated ways, including ones that are not predicted by existing methods, even when only solvent-exposed sites are targeted. Individual mutation of three solvent-exposed lysines in the villin headpiece subdomain significantly stabilizes the protein, but the mechanism of stabilization is very different in each case. One mutation destabilizes native-state electrostatic interactions but has a larger destabilizing effect on the denatured state, a second removes the desolvation penalty paid by the charged residue, whereas the third introduces unanticipated native-state interactions but does not alter electrostatics. Our results show that even seemingly intuitive mutations can exert their effects through unforeseen and complex interactions. PMID:23798426

Xiao, Shifeng; Patsalo, Vadim; Shan, Bing; Bi, Yuan; Green, David F.; Raleigh, Daniel P.

2013-01-01

44

Dynamics of Nanoparticle-Protein Corona Complex Formation: Analytical Results from Population Balance Equations  

PubMed Central

Background Nanoparticle-protein corona complex formation involves absorption of protein molecules onto nanoparticle surfaces in a physiological environment. Understanding the corona formation process is crucial in predicting nanoparticle behavior in biological systems, including applications of nanotoxicology and development of nano drug delivery platforms. Method This paper extends the modeling work in to derive a mathematical model describing the dynamics of nanoparticle corona complex formation from population balance equations. We apply nonlinear dynamics techniques to derive analytical results for the composition of nanoparticle-protein corona complex, and validate our results through numerical simulations. Results The model presented in this paper exhibits two phases of corona complex dynamics. In the first phase, proteins rapidly bind to the free surface of nanoparticles, leading to a metastable composition. During the second phase, continuous association and dissociation of protein molecules with nanoparticles slowly changes the composition of the corona complex. Given sufficient time, composition of the corona complex reaches an equilibrium state of stable composition. We find analytical approximate formulae for metastable and stable compositions of corona complex. Our formulae are very well-structured to clearly identify important parameters determining corona composition. Conclusion The dynamics of biocorona formation constitute vital aspect of interactions between nanoparticles and living organisms. Our results further understanding of these dynamics through quantitation of experimental conditions, modeling results for in vitro systems to better predict behavior for in vivo systems. One potential application would involve a single cell culture medium related to a complex protein medium, such as blood or tissue fluid. PMID:23741371

Darabi Sahneh, Faryad; Scoglio, Caterina; Riviere, Jim

2013-01-01

45

Probity: A Protein Identification Algorithm with Accurate Assignment of the Statistical Significance of the Results  

E-print Network

Significance of the Results Jan Eriksson*, and David Fenyo1,§ Department of Chemistry, Swedish University result. We investigate the performance of the algorithm by simulation and show that the algorithm the risk that a particular identification result is false. Keywords: protein identification · algorithm

Chait, Brian T.

46

Enhanced sensitivity to conformation in various proteins. Vibrational circular dichroism results  

SciTech Connect

Vibrational circular dichroism (VCD) spectra of several globular proteins dissolved in D2O are presented and compared to conventional UV-CD results. It can be seen that, for the alpha, beta, and alpha + beta categories of Levitt and Chothia, VCD evidences much larger band shape variations, including sign alteration, than does UV-CD. A direct parallel is seen between the VCD of the alpha-helix found in model polypeptides and the amide I' VCD of myoglobin. Since all structural aspects of the protein contribute to the VCD on a roughly equal footing, a similar correlation of the chymotrypsin amide I' VCD with that of beta-sheet models is not as clear. In addition, the VCD of random-coil-type proteins is found to be clearly related to VCD results from random-coil polypeptides. Finally, simulations are presented to postulate the expected VCD for protein structures having conformations that lie between the limiting cases discussed here.

Pancoska, P.; Yasui, S.C.; Keiderling, T.A. (Univ. of Illinois, Chicago (USA))

1989-07-11

47

Body Characteristics, Dietary Protein and Body Weight Regulation. Reconciling Conflicting Results from Intervention and Observational Studies?  

PubMed Central

Background/Objectives Physiological evidence indicates that high-protein diets reduce caloric intake and increase thermogenic response, which may prevent weight gain and regain after weight loss. Clinical trials have shown such effects, whereas observational cohort studies suggest an association between greater protein intake and weight gain. In both types of studies the results are based on average weight changes, and show considerable diversity in both directions. This study investigates whether the discrepancy in the evidence could be due to recruitment of overweight and obese individuals into clinical trials. Subjects/Methods Data were available from the European Diet, Obesity and Genes (DiOGenes) post-weight-loss weight-maintenance trial and the Danish Diet, Cancer and Health (DCH) cohort. Participants of the DCH cohort were matched with participants from the DiOGenes trial on gender, diet, and body characteristics. Different subsets of the DCH-participants, comparable with the trial participants, were analyzed for weight maintenance according to the randomization status (high or low protein) of the matched trial participants. Results Trial participants were generally heavier, had larger waist circumference and larger fat mass than the participants in the entire DCH cohort. A better weight maintenance in the high-protein group compared to the low protein group was observed in the subgroups of the DCH cohort matching body characteristics of the trial participants. Conclusion This modified observational study, minimized the differences between the RCT and observational data with regard to dietary intake, participant characteristics and statistical analysis. Compared with low protein diet the high protein diet was associated with better weight maintenance when individuals with greater body mass index and waist circumference were analyzed. Selecting subsets of large-scale observational cohort studies with similar characteristics as participants in clinical trials may reconcile the otherwise conflicting results. PMID:24992329

Ankarfeldt, Mikkel Z.; Ängquist, Lars; Stocks, Tanja; Jakobsen, Marianne U.; Overvad, Kim; Halkjær, Jytte; Saris, Wim H. M.; Astrup, Arne; Sørensen, Thorkild I. A.

2014-01-01

48

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

PubMed Central

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

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

2013-01-01

49

Analyzing Proteomes and Protein Function Using Graphical Comparative Analysis of Tandem Mass Spectrometry Results  

Microsoft Academic Search

Although generating large amounts of proteomic data us- ing tandem mass spectrometry has become routine, there is currently no single set of comprehensive tools for the rigorous analysis of tandem mass spectrometry results given the large variety of possible experimental aims. Cur- rently available applications are typically designed for dis- playing proteins and posttranslational modifications from the point of view

K. Jill McAfee; Dexter T. Duncan; Michael Assink; Andrew J. Link

2006-01-01

50

Ingestion of Casein and Whey Proteins Result in Muscle Anabolism after Resistance Exercise  

Microsoft Academic Search

TIPTON, K. D., T. A. ELLIOTT, M. G. CREE, S. E. WOLF, A. P. SANFORD, and R. R. WOLFE. Ingestion of Casein and Whey Proteins Result in Muscle Anabolism after Resistance Exercise. Med. Sci. Sports Exerc., Vol. 36, No. 12, pp. 2073-2081, 2004. Purpose: Determination of the anabolic response to exercise and nutrition is important for individuals who may benefit

KEVIN D. TIPTON; TABATHA A. ELLIOTT; MELANIE G. CREE; STEVEN E. WOLF; ARTHUR P. SANFORD; ROBERT R. WOLFE

2004-01-01

51

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

NASA Astrophysics Data System (ADS)

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.

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

2013-11-01

52

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

PubMed Central

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

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

2009-01-01

53

Pokeweed antiviral protein alters splicing of HIV-1 RNAs, resulting in reduced virus production.  

PubMed

Processing of HIV-1 transcripts results in three populations in the cytoplasm of infected cells: full-length RNA, singly spliced, and multiply spliced RNAs. Rev, regulator of virion expression, is an essential regulatory protein of HIV-1 required for transporting unspliced and singly spliced viral transcripts from the nucleus to the cytoplasm. Export allows these RNAs to be translated and the full-length RNA to be packaged into virus particles. In our study, we investigate the activity of pokeweed antiviral protein (PAP), a glycosidase isolated from the pokeweed plant Phytolacca americana, on the processing of viral RNAs. We show that coexpression of PAP with a proviral clone alters the splicing ratio of HIV-1 RNAs. Specifically, PAP causes the accumulation of multiply spliced 2-kb RNAs at the expense of full-length 9-kb and singly spliced 4-kb RNAs. The change in splicing ratio is due to a decrease in activity of Rev. We show that PAP depurinates the rev open reading frame and that this damage to the viral RNA inhibits its translation. By decreasing Rev expression, PAP indirectly reduces the availability of full-length 9-kb RNA for packaging and translation of the encoded structural proteins required for synthesis of viral particles. The decline we observe in virus protein expression is not due to cellular toxicity as PAP did not diminish translation rate. Our results describing the reduced activity of a regulatory protein of HIV-1, with resulting change in virus mRNA ratios, provides new insight into the antiviral mechanism of PAP. PMID:24951553

Zhabokritsky, Alice; Mansouri, Sheila; Hudak, Katalin A

2014-08-01

54

Analyzing proteomes and protein function using graphical comparative analysis of tandem mass spectrometry results.  

PubMed

Although generating large amounts of proteomic data using tandem mass spectrometry has become routine, there is currently no single set of comprehensive tools for the rigorous analysis of tandem mass spectrometry results given the large variety of possible experimental aims. Currently available applications are typically designed for displaying proteins and posttranslational modifications from the point of view of the mass spectrometrist and are not versatile enough to allow investigators to develop biological models of protein function, protein structure, or cell state. In addition, storage and dissemination of mass spectrometry-based proteomic data are problems facing the scientific community. To address these issues, we have developed a relational database model that efficiently stores and manages large amounts of tandem mass spectrometry results. We have developed an integrated suite of multifunctional analysis software for interpreting, comparing, and displaying these results. Our system, Bioinformatic Graphical Comparative Analysis Tools (BIGCAT), allows sophisticated analysis of tandem mass spectrometry results in a biologically intuitive format and provides a solution to many data storage and dissemination issues. PMID:16707483

McAfee, K Jill; Duncan, Dexter T; Assink, Michael; Link, Andrew J

2006-08-01

55

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

NASA Astrophysics Data System (ADS)

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.

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

2012-03-01

56

Aging results in an unusual expression of Drosophila heat shock proteins  

SciTech Connect

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.

Fleming, J.E.; Walton, J.K.; Dubitsky, R.; Bensch, K.G. (Linus Pauling Institute of Science and Medicine, Palo Alto, CA (USA))

1988-06-01

57

Diurnal Rhythms Result in Significant Changes in the Cellular Protein Complement in the Cyanobacterium Cyanothece 51142  

SciTech Connect

Cyanothece sp. ATCC 51142 is a diazotrophic cyanobacterium notable for its ability to perform oxygenic photosynthesis and dinitrogen fixation in the same single cell. Previous transcriptional analysis revealed that the existence of these incompatible cellular processes largely depends on tightly synchronized expression programs involving ,30% of genes in the genome. To expand upon current knowledge, we have utilized sensitive proteomic approaches to examine the impact of diurnal rhythms on the protein complement in Cyanothece 51142. We found that 250 proteins accounting for,5% of the predicted ORFs from the Cyanothece 51142 genome and 20% of proteins detected under alternating light/dark conditions exhibited periodic oscillations in their abundances. Our results suggest that altered enzyme activities at different phases during the diurnal cycle can be attributed to changes in the abundance of related proteins and key compounds. The integration of global proteomics and transcriptomic data further revealed that post-transcriptional events are important for temporal regulation of processes such as photosynthesis in Cyanothece 51142. This analysis is the first comprehensive report on global quantitative proteomics in a unicellular diazotrophic cyanobacterium and uncovers novel findings about diurnal rhythms.

Stockel, Jana; Jacobs, Jon M.; Elvitigala, Thanura R.; Liberton, Michelle L.; Welsh, Eric A.; Polpitiya, Ashoka D.; Gritsenko, Marina A.; Nicora, Carrie D.; Koppenaal, David W.; Smith, Richard D.; Pakrasi, Himadri B.

2011-02-22

58

Upregulation of elastase proteins results in aortic dilatation in mucopolysaccharidosis I mice  

PubMed Central

Mucopolysaccharidosis I (MPS I), known as Hurler syndrome in the severe form, is a lysosomal storage disease due to ?-l-iduronidase (IDUA) deficiency. It results in fragmentation of elastin fibers in the aorta and heart valves via mechanisms that are unclear, but may result from the accumulation of the glycosaminoglycans heparan and dermatan sulfate. Elastin fragmentation causes aortic dilatation and valvular insufficiency, which can result in cardiovascular disease. The pathophysiology of aortic disease was evaluated in MPS I mice. MPS I mice have normal elastic fiber structure and aortic compliance at early ages, which suggests that elastin assembly is normal. Elastin fragmentation and aortic dilatation are severe at 6 months, which is temporally associated with marked increases in mRNA and enzyme activity for two elastin-degrading proteins, matrix metalloproteinase-12 (MMP-12) and cathepsin S. Upregulation of these genes likely involves activation of STAT proteins, which may be induced by structural stress to smooth muscle cells from accumulation of glycosaminoglycans in lysosomes. Neonatal intravenous injection of a retroviral vector normalized MMP-12 and cathepsin S mRNA levels and prevented aortic disease. We conclude that aortic dilatation in MPS I mice is likely due to degradation of elastin by MMP-12 and/or cathepsin S. This aspect of disease might be ameliorated by inhibition of the signal transduction pathways that upregulate expression of elastase proteins, or by inhibition of elastase activity. This could result in a treatment for patients with MPS I, and might reduce aortic aneurism formation in other disorders. PMID:18479957

Ma, Xiucui; Tittiger, Mindy; Knutsen, Russell H.; Kovacs, Attila; Schaller, Laura; Mecham, Robert P.; Ponder, Katherine P.

2013-01-01

59

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)

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.

Lim, Ae Ran; Jeong, Se-Young

2013-01-01

60

87Rb and 85Rb NQR study of phase transitions in RbH3(SeO3)2 J. Seliger, V. 017Dagar, R. Blinc  

E-print Network

dependence of the quadrupole coupling constants and the asymmetry parameters on going into the ferroelectric SeO3. Nous avons confirmé l'existence d'une phase incommensurable intermédiaire entre Tc et Tc + 4 K. Abstract. 2014 The temperature dependence of the nuclear quadrupole resonance spectra of 85Rb and 87Rb

Paris-Sud XI, Université de

61

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

PubMed

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. PMID:25528508

Rajamanickam, D; Dhatshanamurthi, P; Shanthi, M

2015-03-01

62

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

NASA Astrophysics Data System (ADS)

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.

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

2015-01-01

63

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

SciTech Connect

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.

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

1985-01-01

64

Protein  

MedlinePLUS

... gov . Nutrition for Everyone Nutrition Topics Share Compartir Protein What do you think about when you hear ... How much protein do I need? What is Protein? Proteins are part of every cell, tissue, and ...

65

Protein  

NSDL National Science Digital Library

Protein structure: Primary protein structure is a sequence of amino acids. Secondary protein structure occurs when the amino acids in the sequence are linked by hydrogen bonds. Tertiary protein structure occurs when certain attractions are present between alpha helices and pleated sheets. Quaternary protein structure is a protein consisting of more than one amino acid chain.

Darryl Leja (National Human Genome Research Institute REV)

2005-04-04

66

Altered protein prenylation in Sertoli cells is associated with adult infertility resulting from childhood mumps infection  

PubMed Central

Mumps commonly affects children 5–9 yr of age, and can lead to permanent adult sterility in certain cases. However, the etiology of this long-term effect remains unclear. Mumps infection results in progressive degeneration of the seminiferous epithelium and, occasionally, Sertoli cell–only syndrome. Thus, the remaining Sertoli cells may be critical to spermatogenesis recovery after orchitis healing. Here, we report that the protein farnesylation/geranylgeranylation balance is critical for patients’ fertility. The expression of geranylgeranyl diphosphate synthase 1 (GGPPS) was decreased due to elevated promoter methylation in the testes of infertile patients with mumps infection history. When we deleted GGPPS in mouse Sertoli cells, these cells remained intact, whereas the adjacent spermatogonia significantly decreased after the fifth postnatal day. The proinflammatory MAPK and NF-?B signaling pathways were constitutively activated in GGPPS?/? Sertoli cells due to the enhanced farnesylation of H-Ras. GGPPS?/? Sertoli cells secreted an array of cytokines to stimulate spermatogonia apoptosis, and chemokines to induce macrophage invasion into the seminiferous tubules. Invaded macrophages further blocked spermatogonia development, resulting in a long-term effect through to adulthood. Notably, this defect could be rescued by GGPP administration in EMCV-challenged mice. Our results suggest a novel mechanism by which mumps infection during childhood results in adult sterility. PMID:23825187

Wang, Xiu-Xing; Ying, Pu; Diao, Fan; Wang, Qiang; Ye, Dan; Jiang, Chen; Shen, Ning; Xu, Na; Chen, Wei-Bo; Lai, Shan-Shan; Jiang, Shan; Miao, Xiao-Li; Feng, Jin; Tao, Wei-Wei; Zhao, Ning-Wei; Yao, Bing; Xu, Zhi-Peng; Sun, Hai-Xiang; Sha, Jia-Hao; Huang, Xing-Xu; Shi, Qing-Hua; Tang, Hong

2013-01-01

67

Altered protein prenylation in Sertoli cells is associated with adult infertility resulting from childhood mumps infection.  

PubMed

Mumps commonly affects children 5-9 yr of age, and can lead to permanent adult sterility in certain cases. However, the etiology of this long-term effect remains unclear. Mumps infection results in progressive degeneration of the seminiferous epithelium and, occasionally, Sertoli cell-only syndrome. Thus, the remaining Sertoli cells may be critical to spermatogenesis recovery after orchitis healing. Here, we report that the protein farnesylation/geranylgeranylation balance is critical for patients' fertility. The expression of geranylgeranyl diphosphate synthase 1 (GGPPS) was decreased due to elevated promoter methylation in the testes of infertile patients with mumps infection history. When we deleted GGPPS in mouse Sertoli cells, these cells remained intact, whereas the adjacent spermatogonia significantly decreased after the fifth postnatal day. The proinflammatory MAPK and NF-?B signaling pathways were constitutively activated in GGPPS(-/-) Sertoli cells due to the enhanced farnesylation of H-Ras. GGPPS(-/-) Sertoli cells secreted an array of cytokines to stimulate spermatogonia apoptosis, and chemokines to induce macrophage invasion into the seminiferous tubules. Invaded macrophages further blocked spermatogonia development, resulting in a long-term effect through to adulthood. Notably, this defect could be rescued by GGPP administration in EMCV-challenged mice. Our results suggest a novel mechanism by which mumps infection during childhood results in adult sterility. PMID:23825187

Wang, Xiu-Xing; Ying, Pu; Diao, Fan; Wang, Qiang; Ye, Dan; Jiang, Chen; Shen, Ning; Xu, Na; Chen, Wei-Bo; Lai, Shan-Shan; Jiang, Shan; Miao, Xiao-Li; Feng, Jin; Tao, Wei-Wei; Zhao, Ning-Wei; Yao, Bing; Xu, Zhi-Peng; Sun, Hai-Xiang; Li, Jian-Min; Sha, Jia-Hao; Huang, Xing-Xu; Shi, Qing-Hua; Tang, Hong; Gao, Xiang; Li, Chao-Jun

2013-07-29

68

Crystallisation of alpha-crustacyanin, the lobster carapace astaxanthin-protein: results from EURECA  

NASA Astrophysics Data System (ADS)

Crystallisation of alpha-crustacyanin, the lobster carapace astaxanthin-protein was attempted under microgravity conditions in EURECA satellite using liquid-liquid diffusion with polyethyleneglycol (PEG) as precipitant; in a second reaction chamber phenol and dioxan were used as additives to prevent composite crystal growth. Crystals of alpha-crustacyanin grown under microgravity from PEG were larger than those grown terrestrially in the same apparatus under otherwise identical conditions. On retrieval, the crystals from PEG were shown to be composite and gave a powder diffraction pattern. The second reaction chamber showed leakage on retrieval and had also been subjected to rapid temperature variation during flight. Crystal fragments were nevertheless recovered but showed a powder diffraction pattern. It is concluded, certainly for liquid-liquid diffusion using PEG alone, that, for crustacyanin, although microgravity conditions resulted in an increase in dimensions of crystals, a measurable improvement in molecular ordering was not achieved.

Zagalsky, P. F.; Wright, C. E.; Parsons, M.

1995-08-01

69

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

SciTech Connect

Small angle neutron scattering (SANS) has been carried out to study the interaction of anionic silica nanoparticles (88 Å) 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.

Yadav, Indresh, E-mail: vkaswal@barc.gov.in; Aswal, V. K., E-mail: vkaswal@barc.gov.in [Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai-400085 (India); Kohlbrecher, J. [Laboratory for Neutron Scattering, Paul Scherrer Institute, CH-5232 PSI Villigen Switzerland (Switzerland)

2014-04-24

70

Experimental validation of FINDSITEcomb virtual ligand screening results for eight proteins yields novel nanomolar and micromolar binders  

PubMed Central

Background Identification of ligand-protein binding interactions is a critical step in drug discovery. Experimental screening of large chemical libraries, in spite of their specific role and importance in drug discovery, suffer from the disadvantages of being random, time-consuming and expensive. To accelerate the process, traditional structure- or ligand-based VLS approaches are combined with experimental high-throughput screening, HTS. Often a single protein or, at most, a protein family is considered. Large scale VLS benchmarking across diverse protein families is rarely done, and the reported success rate is very low. Here, we demonstrate the experimental HTS validation of a novel VLS approach, FINDSITEcomb, across a diverse set of medically-relevant proteins. Results For eight different proteins belonging to different fold-classes and from diverse organisms, the top 1% of FINDSITEcomb’s VLS predictions were tested, and depending on the protein target, 4%-47% of the predicted ligands were shown to bind with ?M or better affinities. In total, 47 small molecule binders were identified. Low nanomolar (nM) binders for dihydrofolate reductase and protein tyrosine phosphatases (PTPs) and micromolar binders for the other proteins were identified. Six novel molecules had cytotoxic activity (<10 ?g/ml) against the HCT-116 colon carcinoma cell line and one novel molecule had potent antibacterial activity. Conclusions We show that FINDSITEcomb is a promising new VLS approach that can assist drug discovery. PMID:24936211

2014-01-01

71

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)

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.

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

2012-08-01

72

Influence of protonation, tautomeric, and stereoisomeric states on protein-ligand docking results.  

PubMed

In this work, we present a systematical investigation of the influence of ligand protonation states, stereoisomers, and tautomers on results obtained with the two protein-ligand docking programs GOLD and PLANTS. These different states were generated with a fully automated tool, called SPORES (Structure PrOtonation and Recognition System). First, the most probable protonations, as defined by this rule based system, were compared to the ones stored in the well-known, manually revised CCDC/ASTEX data set. Then, to investigate the influence of the ligand protonation state on the docking results, different protonation states were created. Redocking and virtual screening experiments were conducted demonstrating that both docking programs have problems in identifying the correct protomer for each complex. Therefore, a preselection of plausible protomers or the improvement of the scoring functions concerning their ability to rank different molecules/states is needed. Additionally, ligand stereoisomers were tested for a subset of the CCDC/ASTEX set, showing similar problems regarding the ranking of these stereoisomers as the ranking of the protomers. PMID:19453150

ten Brink, Tim; Exner, Thomas E

2009-06-01

73

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)

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.

Killough, Brian D., Jr.

2008-01-01

74

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

NASA Astrophysics Data System (ADS)

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.

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

2012-12-01

75

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

NASA Astrophysics Data System (ADS)

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.

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

2014-01-01

76

39K and 77Se NMR study of the paraelectric-to-incommensurate phase transition of K2SeO4  

Microsoft Academic Search

The 39K quadrupole-coupling and chemical-shift tensors have been determined from the angular dependences of the 39K line shifts of the 39K+\\/-(1\\/2&lrarr2;-\\/+ 1) \\/ 2 central NMR transitions in the paraelectric (P) and incommensurate (I) phases of K2SeO4. The main effect of the P-I phase transition on these tensors is the appearance of nonzero off-diagonal elements Vab and Vbc which reflects

B. Topic; A. von Kienlin; A. Gölzhäuser; U. Haeberlen; R. Blinc

1988-01-01

77

17O and 39K quadrupole resonance study of the ferroelastic phase transition in KH3(SeO3)2  

Microsoft Academic Search

The 17O-proton nuclear double-resonance spectra of KH3(SeO3)2 have been measured above and below the ferroelastic transition and the quadrupole coupling has been determined for all three chemically nonequivalent oxygen sites in the unit cell. The 17O-proton magnetic dipolar coupling as well as the 17O quadrupole coupling data clearly show the presence of proton motion between two equilibrium sites in the

J. Seliger; V. Zagar; R. Blinc; A. Novak

1986-01-01

78

L:\\SEO\\SEOGN\\WORK-STUDY\\SWS\\SWS11\\EarningsChart.xls Hourly Rate 10 Hours 15 Hours 20 Hours 25 Hours 30 Hours  

E-print Network

,200 $5,250 $6,300 $15.00 $2,250 $3,375 $4,500 $5,625 $6,750 $16.00 $2,400 $3,600 $4,800 $6,000 $7,200 $17,200 $9,000 $10,800 $25.00 $3,750 $5,625 $7,500 $9,375 $11,250 #12;L:\\SEO\\SEOGN\\WORK-STUDY\\SWS\\SWS11

Guenther, Frank

79

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

SciTech Connect

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.

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

1987-05-01

80

Changes in structural characteristics of antioxidative soy protein hydrolysates resulting from scavenging of hydroxyl radicals.  

PubMed

Antioxidant activity of soy protein (SP) and its hydrolyzed peptides has been widely reported. During scavenging of radicals, these antioxidative compounds would be oxidatively modified, but their fate is not understood. The objective of this study was to evaluate the structural characteristics of SP hydrolysates (SPHs), compared to intact SP, when used to neutralize hydroxyl radicals (•OH). SPHs with degree of hydrolysis (DH) 1 to 5 were prepared with Alcalase. Antioxidant activity of SPHs was confirmed by lipid oxidation inhibition measured with thiobarbituric acid-reactive substances, ability to scavenge 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) radicals, and ferrous ion chelation capability. Oxidation of SPHs was initiated by reaction with •OH generated from 0.1 mM FeCl(3) , 20 mM H(2) O(2) , and 1.0 mM ascorbate. After oxidative stress, carbonyl content of SPHs increased by 2- to 3-fold and sulfhydryl groups decreased by up to 42% compared to nonoxidized samples (P < 0.05). Methionine, histidine, and lysine residues were significantly reduced as a result of inactivating •OH (P < 0.05). Attenuated total reflectance-Fourier transform infrared and circular dichroism spectroscopy suggested the conversion of helical structure to strands and turns. Oxidatively modified SPHs had a lower intrinsic fluorescence intensity but similar solubility when compared to nonoxidized samples. These structural changes due to •OH stress may impact the ingredient interaction and functionality of SPHs in food products. PMID:23331209

Zhao, Jing; Xiong, Youling L; McNear, Dave H

2013-02-01

81

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

PubMed Central

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 Å 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

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

82

Blocking of Monocyte Chemoattractant Protein-1 during Tubulointerstitial Nephritis Resulted in Delayed Neutrophil Clearance  

PubMed Central

The chemokine monocyte chemoattractant protein (MCP)-1 has been implicated in the monocyte/macrophage infiltration that occurs during tubulointerstitial nephritis (TIN). We investigated the role of MCP-1 in rats with TIN by administering a neutralizing anti-MCP-1 antibody (Ab). We observed significantly reduced macrophage infiltration and delayed neutrophil clearance in the kidneys of TIN model rats treated with the anti-MCP-1 Ab. To exclude the possibility that an observed immune complex could affect the resolution of apoptotic neutrophils via the Fc receptor, TIN model rats were treated with a peptide-based MCP-1 receptor antagonist (RA). The MCP-1 RA had effects similar to those of the anti-MCP-1 Ab. In addition, MCP-1 did not affect macrophage-mediated phagocytosis of neutrophils in vitro. Deposition of the anti-MCP-1 Ab in rat kidneys resulted from its binding to heparan sulfate-immobilized MCP-1, as demonstrated by the detection of MCP-1 in both pull-down and immunoprecipitation assays. We conclude that induction of chemokines, specifically MCP-1, in TIN corresponds with leukocyte infiltration and that the anti-MCP-1 Ab formed an immune complex with heparan sulfate-immobilized MCP-1 in the kidney. Antagonism of MCP-1 in TIN by Ab or RA may alter the pathological process, most likely through delayed removal of apoptotic neutrophils in the inflammatory loci. PMID:16127145

Li, Ping; Garcia, Gabriela E.; Xia, Yiyang; Wu, Wei; Gersch, Christine; Park, Pyong Woo; Truong, Luan; Wilson, Curtis B.; Johnson, Richard; Feng, Lili

2005-01-01

83

Synthesis, Crystal Structure and Thermal Decomposition of the New Cadmium Selenite Chloride, Cd4(SeO3)2OCl2  

PubMed Central

A synthetic study in the Cd-Se-O-Cl system led to formation of the new oxochloride compound Cd4(SeO3)2OCl2 via solid state reactions. The compound crystallizes in the orthorhombic space group Fmmm with cell parameters a?=?7.3610(3) Å, b?=?15.4936(2) Å, c?=?17.5603(3) Å, Z?=?8, S?=?0.969, F(000)?=?2800, R?=?0.0185, Rw?=?0.0384. Single crystal X-ray data were collected at 293 K. The crystal structure can be considered as layered and the building units are distorted [Cd(1)O6] octahedra, distorted [Cd(2)O8] cubes, irregular [Cd(3)O4Cl2] polyhedra and SeO3E trigonal pyramids. There are two crystallographically unique Cl atoms that both are half occupied. Thermogravimetric studies show that the compound starts to decompose at 500°C. The crystal structure of the new compound is closely related to the previously described compound Cd4(SeO3)2Cl4(H2O). PMID:24844633

Rabbani, Faiz; Ajaz, Humayun; Zimmermann, Iwan; Johnsson, Mats

2014-01-01

84

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

PubMed Central

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

2010-01-01

85

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

PubMed

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

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

2015-01-01

86

Prion Protein Repeat Expansion Results in Increased Aggregation and Reveals Phenotypic Variability  

Microsoft Academic Search

Mammalian prion diseases are fatal neurodegenerative disorders dependent on the prion protein PrP. Expansion of the oligopeptide repeats (ORE) found in PrP is associated with inherited prion diseases. Patients with ORE frequently harbor PrP aggregates, but other factors may contribute to pathology, as they often present with unexplained phenotypic variability. We created chimeric yeast-mammalian prion proteins to examine the influence

Elizabeth M. H. Tank; David A. Harris; Amar A. Desai; Heather L. True

2007-01-01

87

Multiple start codons and phosphorylation result in discrete Rad52 protein species  

PubMed Central

The sequence of the Saccharomyces cerevisiae RAD52 gene contains five potential translation start sites and protein-blot analysis typically detects multiple Rad52 species with different electrophoretic mobilities. Here we define the gene products encoded by RAD52. We show that the multiple Rad52 protein species are due to promiscuous choice of start codons as well as post-translational modification. Specifically, Rad52 is phosphorylated both in a cell cycle-independent and in a cell cycle-dependent manner. Furthermore, phosphorylation is dependent on the presence of the Rad52 C terminus, but not dependent on its interaction with Rad51. We also show that the Rad52 protein can be translated from the last three start sites and expression from any one of them is sufficient for spontaneous recombination and the repair of gamma-ray-induced double-strand breaks. PMID:16707661

de Mayolo, Adriana Antúnez; Lisby, Michael; Erdeniz, Naz; Thybo, Tanja; Mortensen, Uffe H.; Rothstein, Rodney

2006-01-01

88

Results of a screening programme to identify plants or plant extracts that inhibit ruminal protein degradation.  

PubMed

One aim of the EC Framework V project, 'Rumen-up' (QLK5-CT-2001-00 992), was to find plants or plant extracts that would inhibit the nutritionally wasteful degradation of protein in the rumen. A total of 500 samples were screened in vitro using 14C-labelled casein in a 30-min incubation with ruminal digesta. Eight were selected for further investigation using a batch fermentation system and soya protein and bovine serum albumin as proteolysis substrates; proteolysis was monitored over 12 h by the disappearance of soluble protein and the production of branched SCFA and NH3. Freeze-dried, ground foliage of Peltiphyllum peltatum, Helianthemum canum, Arbutus unedo, Arctostaphylos uva-ursi and Knautia arvensis inhibited proteolysis (P < 0.05), while Daucus carota, Clematis vitalba and Erica arborea had little effect. Inhibition by the first four samples appeared to be caused by the formation of insoluble tannin-protein complexes. The samples were rich in phenolics and inhibition was reversed by polyethyleneglycol. In contrast, K. arvensis contained low concentrations of phenolics and no tannins, had no effect in the 30-min assay, yet inhibited the degradation rate of soluble protein (by 14 %, P < 0.0001) and the production of branched SCFA (by 17 %, P < 0.05) without precipitating protein in the 12-h batch fermentation. The effects showed some resemblance to those obtained in parallel incubations containing 3 mum-monensin, suggesting that K. arvensis may be a plant-derived feed additive that can suppress growth and activity of key proteolytic ruminal micro-organisms in a manner similar to that already well known for monensin. PMID:17445338

Selje, N; Hoffmann, E M; Muetzel, S; Ningrat, R; Wallace, R J; Becker, K

2007-07-01

89

Diminished Self-Chaperoning Activity of the ?F508 Mutant of CFTR Results in Protein Misfolding  

PubMed Central

The absence of a functional ATP Binding Cassette (ABC) protein called the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) from apical membranes of epithelial cells is responsible for cystic fibrosis (CF). Over 90% of CF patients carry at least one mutant allele with deletion of phenylalanine at position 508 located in the N-terminal nucleotide binding domain (NBD1). Biochemical and cell biological studies show that the ?F508 mutant exhibits inefficient biosynthetic maturation and susceptibility to degradation probably due to misfolding of NBD1 and the resultant misassembly of other domains. However, little is known about the direct effect of the Phe508 deletion on the NBD1 folding, which is essential for rational design strategies of cystic fibrosis treatment. Here we show that the deletion of Phe508 alters the folding dynamics and kinetics of NBD1, thus possibly affecting the assembly of the complete CFTR. Using molecular dynamics simulations, we find that meta-stable intermediate states appearing on wild type and mutant folding pathways are populated differently and that their kinetic accessibilities are distinct. The structural basis of the increased misfolding propensity of the ?F508 NBD1 mutant is the perturbation of interactions in residue pairs Q493/P574 and F575/F578 found in loop S7-H6. As a proof-of-principle that the S7-H6 loop conformation can modulate the folding kinetics of NBD1, we virtually design rescue mutations in the identified critical interactions to force the S7-H6 loop into the wild type conformation. Two redesigned NBD1-?F508 variants exhibited significantly higher folding probabilities than the original NBD1-?F508, thereby partially rescuing folding ability of the NBD1-?F508 mutant. We propose that these observed defects in folding kinetics of mutant NBD1 may also be modulated by structures separate from the 508 site. The identified structural determinants of increased misfolding propensity of NBD1-?F508 are essential information in correcting this pathogenic mutant. PMID:18463704

Riordan, John R.; Dokholyan, Nikolay V.

2008-01-01

90

UU/UA Dinucleotide Frequency Reduction in Coding Regions Results in Increased mRNA Stability and Protein Expression  

PubMed Central

UU and UA dinucleotides are rare in mammalian genes and may offer natural selection against endoribonuclease-mediated mRNA decay. This study hypothesized that reducing UU and UA (UW) dinucleotides in the mRNA-coding sequence, including the codons and the dicodon boundaries, may promote resistance to mRNA decay, thereby increasing protein production. Indeed, protein expression from UW-reduced coding regions of enhanced green fluorescent protein (EGFP), luciferase, interferon-?, and hepatitis B surface antigen (HBsAg) was higher when compared to the wild-type protein expression. The steady-state level of UW-reduced EGFP mRNA was higher and the mRNA half-life was also longer. Ectopic expression of the endoribonuclease, RNase L, did not reduce the wild type or UW-reduced mRNA. A mutant form of the mRNA decay-promoting protein, tristetraprolin (TTP/ZFP36), which has a point mutation in the zinc-finger domain (C124R), was used. The wild-type EGFP mRNA but not the UW-reduced mRNA responded to the dominant negative action of the C124R ZFP36/TTP mutant. The results indicate the efficacy of the described rational approach to formulate a general scheme for boosting recombinant protein production in mammalian cells. PMID:22434136

Al-Saif, Maher; Khabar, Khalid SA

2012-01-01

91

Crystallisation of ?-crustacyanin, the lobster capapace astaxanthin-protein: Results from EURECA  

Microsoft Academic Search

Crystallisation of ?-crustacyanin, the lobster carapace astaxanthin-protein was attempted under microgravity conditions in EURECA satellite using liquid-liquid diffusion with polyethyleneglycol (PEG) as precipitant; in a second reaction chamber phenol and dioxan were used as additives to prevent composite crystal growth. Crystals of ?-crustacyanin grown under microgravity from PEG were larger than those grown terrestrially in the same apparatus under otherwise

P. F. Zagalsky; C. E. Wright; M. Parsons

1995-01-01

92

Diminished Self-Chaperoning Activity of the DF508 Mutant of CFTR Results in Protein Misfolding  

E-print Network

Chapel Hill, Chapel Hill, North Carolina, United States of America, 3 Cystic Fibrosis Research Center The absence of a functional ATP Binding Cassette (ABC) protein called the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) from apical membranes of epithelial cells is responsible for cystic fibrosis (CF

Dokholyan, Nikolay V.

93

Results.  

ERIC Educational Resources Information Center

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)

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

2001-01-01

94

Accumulation of mutant huntingtin fragments in aggresome-like inclusion bodies as a result of insufficient protein degradation.  

PubMed

The huntingtin exon 1 proteins with a polyglutamine repeat in the pathological range (51 or 83 glutamines), but not with a polyglutamine tract in the normal range (20 glutamines), form aggresome-like perinuclear inclusions in human 293 Tet-Off cells. These structures contain aggregated, ubiquitinated huntingtin exon 1 protein with a characteristic fibrillar morphology. Inclusion bodies with truncated huntingtin protein are formed at centrosomes and are surrounded by vimentin filaments. Inhibition of proteasome activity resulted in a twofold increase in the amount of ubiquitinated, SDS-resistant aggregates, indicating that inclusion bodies accumulate when the capacity of the ubiquitin-proteasome system to degrade aggregation-prone huntingtin protein is exhausted. Immunofluorescence and electron microscopy with immunogold labeling revealed that the 20S, 19S, and 11S subunits of the 26S proteasome, the molecular chaperones BiP/GRP78, Hsp70, and Hsp40, as well as the RNA-binding protein TIA-1, the potential chaperone 14-3-3, and alpha-synuclein colocalize with the perinuclear inclusions. In 293 Tet-Off cells, inclusion body formation also resulted in cell toxicity and dramatic ultrastructural changes such as indentations and disruption of the nuclear envelope. Concentration of mitochondria around the inclusions and cytoplasmic vacuolation were also observed. Together these findings support the hypothesis that the ATP-dependent ubiquitin-proteasome system is a potential target for therapeutic interventions in glutamine repeat disorders. PMID:11359930

Waelter, S; Boeddrich, A; Lurz, R; Scherzinger, E; Lueder, G; Lehrach, H; Wanker, E E

2001-05-01

95

A Deep Intronic Mutation in the Ankyrin-1 Gene Causes Diminished Protein Expression Resulting in Hemolytic Anemia in Mice  

PubMed Central

Linkage between transmembrane proteins and the spectrin-based cytoskeleton is necessary for membrane elasticity of red blood cells. Mutations of the proteins that mediate this linkage result in various types of hemolytic anemia. Here we report a novel N-ethyl-N-nitrosourea?induced mutation of ankyrin-1, named hema6, which causes hereditary spherocytosis in mice through a mild reduction of protein expression. The causal mutation was traced to a single nucleotide transition located deep into intron 13 of gene Ank1. In vitro minigene splicing assay revealed two abnormally spliced transcripts containing cryptic exons from fragments of Ank1 intron 13. The inclusion of cryptic exons introduced a premature termination codon, which leads to nonsense-mediated decay of the mutant transcripts in vivo. Hence, in homozygous mice, only wild-type ankyrin-1 is expressed, albeit at 70% of the level in wild-type mice. Heterozygotes display a similar hereditary spherocytosis phenotype stemming from intermediate protein expression level, indicating the haploinsufficiency of the mutation. Weakened linkage between integral transmembrane protein, band 3, and underlying cytoskeleton was observed in mutant mice as the result of reduced high-affinity binding sites provided by ankyrin-1. Hema6 is the only known mouse mutant of Ank1 allelic series that expresses full-length canonical ankyrin-1 at a reduced level, a fact that makes it particularly useful to study the functional impact of ankyrin-1 quantitative deficiency. PMID:23934996

Huang, Hua; Zhao, PengXiang; Arimatsu, Kei; Tabeta, Koichi; Yamazaki, Kazuhisa; Krieg, Lara; Fu, Emily; Zhang, Tian; Du, Xin

2013-01-01

96

Crystallisation of alpha-crustacyanin, the lobster carapace astaxanthin-protein: results from EURECA  

Microsoft Academic Search

Crystallisation of alpha-crustacyanin, the lobster carapace astaxanthin-protein was attempted under microgravity conditions in EURECA satellite using liquid-liquid diffusion with polyethyleneglycol (PEG) as precipitant; in a second reaction chamber phenol and dioxan were used as additives to prevent composite crystal growth. Crystals of alpha-crustacyanin grown under microgravity from PEG were larger than those grown terrestrially in the same apparatus under otherwise

P. F. Zagalsky; C. E. Wright; M. Parsons

1995-01-01

97

Inhibition of cellular protein phosphatases results in the disruption of p53-regulated homeostasis  

Microsoft Academic Search

Two important serine\\/threonine protein phosphatases (PP), PP1 and PP2A, are involved in many cellular processes including cell cycle regulation, cell signaling, and programmed cell death. A number of natural product toxins have been identified which selectively and potently inhibit PP1 and 2A. Two of these are the cyanobacteria-derived cyclic heptapeptide microcystin-LR, and the polyether fatty acid okadaic acid obtained from

Shawn Paul Clark

2005-01-01

98

Proteins  

NSDL National Science Digital Library

Paul Anderson explains the structure and importance of proteins. He describes how proteins are created from amino acids connected by dehydration synthesis. He shows the importance of chemical properties in the R-groups of individual amino acids in the polypeptide.

Paul Anderson

2013-03-12

99

Proteins.  

ERIC Educational Resources Information Center

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)

Doolittle, Russell F.

1985-01-01

100

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

NASA Astrophysics Data System (ADS)

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) Å, b = 9.6631 (6) Å, c = 9.2070 (5) Å, ß = 108.825 (4)°, Z = 4 and V = 730.83 (7) Å3. 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.

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

2013-05-01

101

Protein  

MedlinePLUS

... juvenile or insulin-dependent diabetes), proteins found in cow’s milk have been implicated in the development of ... O., et al., Removal of Bovine Insulin From Cow’s Milk Formula and Early Initiation of Beta-Cell ...

102

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

PubMed

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

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

2014-11-16

103

Expression of an insect ( Dendroides canadensis ) antifreeze protein in Arabidopsis thaliana results in a decrease in plant freezing temperature  

Microsoft Academic Search

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 expressed in transformed plants. Thermal hysteresis activity (indicating the presence of active AFPs) was present in protein extracts from plants expressing both proteins and was

Tao Huang; Jessie Nicodemus; Daniel G. Zarka; Michael F. Thomashow; Michael Wisniewski; John G. Duman

2002-01-01

104

Oxidative stress induced by potassium bromate exposure results in altered tight junction protein expression in renal proximal tubule cells.  

PubMed

Potassium bromate (KBrO(3)) is an oxidising agent that has been widely used in the food and cosmetic industries. It has shown to be both a nephrotoxin and a renal carcinogen in in vivo and in vitro models. Here, we investigated the effects of KBrO(3) in the human and rat proximal tubular cell lines RPTEC/TERT1 and NRK-52E. A genome-wide transcriptomic screen was carried out from cells exposed to a sub-lethal concentration of KBrO(3) for 6, 24 and 72 h. Pathway analysis identified "glutathione metabolism", "Nrf2-mediated oxidative stress" and "tight junction (TJ) signalling" as the most enriched pathways. TJ signalling was less impacted in the rat model, and further studies revealed low transepithelial electrical resistance (TEER) and an absence of several TJ proteins in NRK-52E cells. In RPTEC/TERT1 cells, KBrO(3) exposure caused a decrease in TEER and resulted in altered expression of several TJ proteins. N-Acetylcysteine co-incubation prevented these effects. These results demonstrate that oxidative stress has, in conjunction with the activation of the cytoprotective Nrf2 pathway, a dramatic effect on the expression of tight junction proteins. The further understanding of the cross-talk between these two pathways could have major implications for epithelial repair, carcinogenesis and metastasis. PMID:22760423

Limonciel, Alice; Wilmes, Anja; Aschauer, Lydia; Radford, Robert; Bloch, Katarzyna M; McMorrow, Tara; Pfaller, Walter; van Delft, Joost H; Slattery, Craig; Ryan, Michael P; Lock, Edward A; Jennings, Paul

2012-11-01

105

A new approach to immobilize poly(vinyl alcohol) on poly(dimethylsiloxane) resulting in low protein adsorption  

NASA Astrophysics Data System (ADS)

The hydrophobic characteristics of PDMS and non-specific protein adsorption are major drawbacks for its application in biosensing. Here we have combined surface oxidation by plasma and chemical binding of polyvinyl alcohol (PVA) to obtain long-term stability of hydrophilic PDMS surfaces. Mercaptopropyltrimethoxisilane and aminopropyltrimethoxisilane were used as adhesives between the plasma-oxidized PDMS surface and the PVA, immobilized at room temperature. This approach has allowed for fast, uniform, and very stable modification of the PDMS surface, which maintained a hydrophilic character for as long as 30 days. In addition, the modified hydrophilic surface presented minimized protein adsorption when compared to pristine PDMS. The results obtained in this work are important contributions to the growing field of integrated microfluidic biosensors.

Carneiro, Leandro B.; Ferreira, Jacqueline; Santos, Marcos J. L.; Monteiro, Johny P.; Girotto, Emerson M.

2011-10-01

106

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...

107

Upregulation of elastase proteins results in aortic dilatation in mucopolysaccharidosis I mice  

E-print Network

May 2008 Keywords: Hurler syndrome Lysosomal storage disease Elastin Aorta Gene therapy a b s t r a c t Mucopolysaccharidosis I (MPS I), known as Hurler syndrome in the severe form, is a lysosomal storage disease due to a- somal storage disease due to a-L-iduronidase (IDUA; EC 3.2.1.76) deficiency that results

Ponder, Katherine P.

108

RNA editing in wheat mitochondria results in the conservation of protein sequences  

Microsoft Academic Search

RNA editing is a process that results in the production of a messenger RNA with nucleotide sequences that differ from those of the template DNA1, and provides another mechanism for modulating gene expression. The phenomenon was initially described in the mitochondria of protozoa2, 3. Here we report that RNA editing is also required for the correct expression of plant mitochondria!

José M. Gualberto; Lorenzo Lamattina; Géraldine Bonnard; Jacques-Henry Weil; Jean-Michel Grienenberger

1989-01-01

109

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)

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.

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

2013-09-01

110

Heterogeneous N-terminal Acylation of Retinal Proteins Results from the Retina’s Unusual Lipid Metabolism†,§  

PubMed Central

Protein N-myristoylation occurs by a covalent attachment of a C14:0 fatty acid to the N-terminal Gly residue. This reaction is catalyzed by a N-myristoyltransferase that uses myristoyl-coenzyme A as substrate. But proteins in the retina also undergo heterogeneous N-acylation with C14:2, C14:1 and C12:0 fatty acids. The basis and the role of this retina-specific phenomenon are poorly understood. We studied guanylate cyclase-activating protein 1 (GCAP1) as an example of retina-specific heterogeneously N-acylated protein. The types and the abundance of fatty acids bound to bovine retinal GCAP1 were: C14:2, 37.0%; C14:0, 32.4%; C14:1, 22.3%; and C12:0, 8.3% as quantified by liquid chromatography coupled mass spectrometry. We also devised a method for N-acylating proteins in vitro and used it to modify GCAP1 with acyl moieties of different lengths. Analysis of these GCAPs both confirmed that N-terminal acylation of GCAP1 is critical for its high activity and proper Ca2+-dependent response and revealed comparable functionality for GCAP1 with acyl moieties of various lengths. We also tested the hypothesis that retinal heterogeneous N-acylation results from retinal enrichment of unusual N-myristoyltransferase substrates. Thus, acyl-coenzyme A esters were purified from both bovine retina and brain and analyzed by liquid chromatography coupled mass spectrometry. Substantial differences in acyl-coenzyme A profiles between the retina and brain were detected. Importantly, the ratios of uncommon N-acylation substrates; C14:2- and C14:1-coenyzme A to C14:0-coenzyme A were higher in the retina than in the brain. Thus, our results suggest that heterogeneous N-acylation, responsible for expansion of retinal proteome, reflects the unique character of retinal lipid metabolism. Additionally, we propose a new hypothesis explaining the physiological relevance of elevated retinal ratios of C14:2- and C14:1-coenzyme A to C14:0-coenzyme A. PMID:21449552

Bereta, Grzegorz; Palczewski, Krzysztof

2011-01-01

111

Enrichment of functional redox reactive proteins and identification by mass spectrometry results in several terminal Fe(III)-reducing candidate proteins in Shewanella oneidensis MR-1.  

PubMed

Identification of the proteins directly involved in microbial metal-reduction is important to understanding the biochemistry involved in heavy metal-reduction/immobilization and the ultimate cleanup of DOE contaminated sites. Although previous strategies for the identification of these proteins have traditionally required laborious protein purification/characterization of metal-reducing capability, activity is often lost before the final purification step, thus creating a significant knowledge gap. In the current study, subcellular fractions of Shewanella oneidensis MR-1 were enriched for Fe(III)-NTA reducing proteins in a single step using several orthogonal column matrices. The protein content of eluted fractions that demonstrated activity was determined by ultra-high pressure liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). A comparison of the proteins identified from active fractions in all separations produced 30 proteins that may act as the terminal electron-accepting protein for Fe(III)-reduction. These include MtrA, MtrB, MtrC and OmcA as well as a number of other proteins not previously associated with Fe(III)-reduction. This is the first report of such an approach where the laborious procedures for protein purification are not required for identification of metal-reducing proteins. Such work provides the basis for a similar approach with other cultured organisms as well as analysis of sediment and groundwater samples from biostimulation efforts at contaminated sites. PMID:17137661

Elias, Dwayne A; Yang, Feng; Mottaz, Heather M; Beliaev, Alexander S; Lipton, Mary S

2007-02-01

112

SeO2 ?  

NASA Astrophysics Data System (ADS)

This document is part of Subvolume A11 'Structure Types. Part 11: Space Groups (135) P42/mbc - (123) P4/mmm' of Volume 43 'Crystal Structures of Inorganic Compounds' of Landolt-Börnstein - Group III 'Condensed Matter'.

Villars, P.; Cenzual, K.; Gladyshevskii, R.; Shcherban, O.; Dubenskyy, V.; Kuprysyuk, V.; Savysyuk, I.; Zaremba, R.

113

Disruption of the Basal Body Protein POC1B Results in Autosomal-Recessive Cone-Rod Dystrophy  

PubMed Central

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

Roosing, Susanne; Lamers, Ideke J.C.; de Vrieze, Erik; van den Born, L. Ingeborgh; Lambertus, Stanley; Arts, Heleen H.; Boldt, Karsten; de Baere, Elfride; Klaver, Caroline C.W.; Coppieters, Frauke; Koolen, David A.; Lugtenberg, Dorien; Neveling, Kornelia; van Reeuwijk, Jeroen; Ueffing, Marius; van Beersum, Sylvia E.C.; Zonneveld-Vrieling, Marijke N.; 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.

2014-01-01

114

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

PubMed

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

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

115

Recombinant envelope protein (rgp90) ELISA for equine infectious anemia virus provides comparable results to the agar gel immunodiffusion.  

PubMed

Equine infectious anemia (EIA) is an important viral infection affecting horses worldwide. The course of infection is accompanied generally by three characteristic stages: acute, chronic and inapparent. There is no effective EIA vaccine or treatment, and the control of the disease is based currently on identification of EIAV inapparent carriers by laboratory tests. Recombinant envelope protein (rgp90) was expressed in Escherichia coli and evaluated via enzyme-linked immunosorbent assay (ELISA). There was an excellent agreement (95.42%) between the ELISA results using rgp90 and agar gel immunodiffusion test results. AGID is considered the "gold-standard" serologic test for equine infectious anemia (EIA). After 1160 serum samples were tested, the relative sensitivity and specificity of the ELISA were 96.1% and 96.4%, respectively. Moreover, analysis diagnostic accuracy of the ELISA was performed. The ELISA proved robust. Furthermore, good reproducibility was observed for the negative controls and, positive controls for all plates tested. PMID:22227617

Reis, Jenner K P; Diniz, Rejane S; Haddad, João P A; Ferraz, Isabella B F; Carvalho, Alex F; Kroon, Erna G; Ferreira, Paulo C P; Leite, Rômulo C

2012-03-01

116

Deficiency of a Protein-Repair Enzyme Results in the Accumulation of Altered Proteins, Retardation of Growth, and Fatal Seizures in Mice  

Microsoft Academic Search

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

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

1997-01-01

117

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

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

Abraham, Nader G.

118

Knockdown of DAPIT (Diabetes-associated Protein in Insulin-sensitive Tissue) Results in Loss of ATP Synthase in Mitochondria  

PubMed Central

It was found recently that a diabetes-associated protein in insulin-sensitive tissue (DAPIT) is associated with mitochondrial ATP synthase. Here, we report that the suppressed expression of DAPIT in DAPIT-knockdown HeLa cells causes loss of the population of ATP synthase in mitochondria. Consequently, DAPIT-knockdown cells show smaller mitochondrial ATP synthesis activity, slower growth in normal medium, and poorer viability in glucose-free medium than the control cells. The mRNA levels of ?- and ?-subunits of ATP synthase remain unchanged by DAPIT knockdown. These results indicate a critical role of DAPIT in maintaining the ATP synthase population in mitochondria and raise an intriguing possibility of active role of DAPIT in cellular energy metabolism. PMID:21345788

Ohsakaya, Shigenori; Fujikawa, Makoto; Hisabori, Toru; Yoshida, Masasuke

2011-01-01

119

Exchanging the Yellow Fever Virus Envelope Proteins with Modoc Virus prM and E Proteins Results in a Chimeric Virus That Is Neuroinvasive in SCID Mice  

Microsoft Academic Search

the chimeric precursor protein. The MOD E protein was shown to be N-linked glycosylated, whereas prM, as predicted from the genome sequence, did not contain N-linked carbohydrates. In Vero cells, the chimeric virus replicated with a similar efficiency as the parental viruses, although it formed smaller plaques than YF17D and MOD. In SCID mice that had been infected intraperitoneally with

Nathalie Charlier; Richard Molenkamp; Pieter Leyssen; Jan Paeshuyse; Christian Drosten; Marcus Panning; Erik De Clercq; Peter J. Bredenbeek; Johan Neyts

2004-01-01

120

Lateral gene transfer of a multigene region from cyanobacteria to dinoflagellates resulting in a novel plastid-targeted fusion protein.  

PubMed

The number of cases of lateral or horizontal gene transfer in eukaryotic genomes is growing steadily, but in most cases, neither the donor nor the recipient is known, and the biological implications of the transfer are not clear. We describe a relatively well-defined case of transfer from a cyanobacterial source to an ancestor of dinoflagellates that diverged before Oxyrrhis but after Perkinsus. This case is also exceptional in that 2 adjacent genes, a paralogue of the shikimate biosynthetic enzyme AroB and an O-methyltransferase (OMT) were transferred together and formed a fusion protein that was subsequently targeted to the dinoflagellate plastid. Moreover, this fusion subsequently reverted to 2 individual genes in the genus Karlodinium, but both proteins maintained plastid localization with the OMT moiety acquiring its own plastid-targeting peptide. The presence of shikimate biosynthetic enzymes in the plastid is not unprecedented as this is a plastid-based pathway in many eukaryotes, but this species of OMT has not been associated with the plastid previously. It appears that the OMT activity was drawn into the plastid simply by virtue of its attachment to the AroB paralogue resulting from their cotransfer and once in the plastid performed some essential function so that it remained plastid targeted after it separated from AroB. Gene fusion events are considered rare and likely stable, and such an event has recently been used to argue for a root of the eukaryotic tree. Our data, however, show that exact reversals of fusion events do take place, and hence gene fusion data are difficult to interpret without knowledge of the phylogeny of the organisms--therefore their use as phylogenetic markers must be considered carefully. PMID:16675503

Waller, Ross F; Slamovits, Claudio H; Keeling, Patrick J

2006-07-01

121

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...

122

Statins Exert the Pleiotropic Effects Through Small GTP-Binding Protein Dissociation Stimulator Upregulation With a Resultant Rac1 Degradation  

PubMed Central

Objective The pleiotropic effects of 3-hydroxy-3-methylglutaryl-coenzyme A reductase inhibitors (statins) independent of cholesterol-lowering effects are thought to be mediated through inhibition of the Rho/Rho-kinase pathway. However, we have previously demonstrated that the pleiotropic effects of regular-dose statins are mediated mainly through inhibition of the Rac1 signaling pathway rather than the Rho/Rho-kinase pathway, although the molecular mechanisms of the selective inhibition of the Rac1 signaling pathway by regular-dose statins remain to be elucidated. In this study, we tested our hypothesis that small GTP-binding protein GDP dissociation stimulator (SmgGDS) plays a crucial role in the molecular mechanisms of the Rac1 signaling pathway inhibition by statins in endothelial cells. Approach and Results In cultured human umbilical venous endothelial cells, statins concentration-dependently increased SmgGDS expression and decreased nuclear Rac1. Statins also enhanced SmgGDS expression in mouse aorta. In control mice, the protective effects of statins against angiotensin II–induced medial thickening of coronary arteries and fibrosis were noted, whereas in SmgGDS-deficient mice, the protective effects of statins were absent. When SmgGDS was knocked down by its small interfering RNA in human umbilical venous endothelial cells, statins were no longer able to induce Rac1 degradation or inhibit angiotensin II–induced production of reactive oxygen species. Finally, in normal healthy volunteers, statins significantly increased SmgGDS expression with a significant negative correlation between SmgGDS expression and oxidative stress markers, whereas no correlation was noted with total or low-density lipoprotein-cholesterol. Conclusions These results indicate that statins exert their pleiotropic effects through SmgGDS upregulation with a resultant Rac1 degradation and reduced oxidative stress in animals and humans. PMID:23640485

Tanaka, Shin-ichi; Fukumoto, Yoshihiro; Nochioka, Kotaro; Minami, Tatsuro; Kudo, Shun; Shiba, Nobuyuki; Takai, Yoshimi; Williams, Carol L.; Liao, James K.; Shimokawa, Hiroaki

2013-01-01

123

Multilateral in vivo and in vitro protective effects of the novel heat shock protein coinducer, bimoclomol: results of preclinical studies.  

PubMed

Bimoclomol, the recently developed non-toxic heat shock protein (HSP) coinducer, was shown to display multilateral protective activities against various forms of stress or injuries at the level of the cell, tissue or organism. The compound enhanced the transcription, translation and expression of the 70 kD heat shock protein (HSP-70) in myogenic and HeLa cell lines exposed to heat stress, and increased cell survival on exposure to otherwise lethal thermal injury. Bimoclomol increased contractility of the working mammalian heart, this effect was associated with the increased intracellular calcium transients due to increased probability of opening of ryanodine receptors in the sarcoplasmic reticulum (SR). In healthy tissues these cardiac effects were evident only at relatively high concentrations of the drug, while in the ischemic myocardium bimoclomol exerted significant cardioprotective and antiarrhythmic effects at submicromolar concentrations. It decreased ischemia-induced reduction of contractility and of cardiac output, and dramatically decreased the elevation of the ST-segment during ischemia as well as the occurrence of ventricular fibrillation upon reperfusion. Bimoclomol was also active in various pathological animal models subjected to acute or chronic stress. In the spontaneously hypertensive rats chronic pretreatment with bimoclomol restored sensitivity of aortic rings to acetylcholine; this effect was accompanied by accumulation of HSP-70 in the tissues. Bimoclomol pretreatment significantly diminished the consequences of vascular disorders associated with diabetes mellitus. Diabetic neuropathy, retinopathy, and nephropathy were prevented or diminished, while wound healing was enhanced by bimoclomol. Enhancement of wound healing by bimoclomol was observed after thermal injury as well as following ultraviolet (UV) irradiation. In addition to the beneficial effects on peripheral angiopathies, bimoclomol antagonized the increase in permeability of blood-brain barrier induced by subarachnoid hemorrhager or arachidonic acid. A general and very important feature of the above effects of bimoclomol was that the drug failed to cause alterations under physiological conditions (except the enhanced calcium release from cardiac sarcoplasmic reticulum). Bimoclomol was effective only under conditions of stress. Consistent with its HSP-coinducer property, bimoclomol alone had very little effect on HSP production. Its protective activity became apparent only in the presence of cell damage. Currently, bimoclomol reached the end of the Phase II clinical trial in a group of 410 patients with diabetic complications. Results of this trial will answer the question, whether a compound with promising in vitro and in vivo preclinical findings will produce the anticipated beneficial effects in humans. In the event of a positive outcome of this trial, the indications for bimoclomol will be substantially extended. PMID:11484067

Nánási, P P; Jednákovits, A

2001-01-01

124

Agents that Stabilize Mutated von Hippel Lindau Protein Result in Differential Post-Translational Modification and Subcellular Localization  

PubMed Central

Background von Hippel Lindau (VHL) disease is an autosomal dominant inherited disorder that results in multiple organ systems being affected. Treatment is mainly surgical, however, effective systemic therapies are needed. We developed and tested a cell-based screening tool to identify compounds that stabilize or upregulate full-length, point mutated VHL. Methods The 786-0 cell line was infected with full-length W117A mutated VHL linked to a C-terminal Venus fluorescent protein. This VHL-W117A-Venus line was used to screen the Prestwick drug library and was tested against the known proteasome inhibitors MG132 and bortezomib. Western blot validation and evaluation of downstream functional readouts, including HIF and GLUT1 levels, were performed. Results Bortezomib, MG132, and the Prestwick compounds 8-azaguanine, thiostrepton and thioguanosine were found to reliably upregulate VHL-W117A-Venus in 786-0 cells. 8-azaguanine was found to downregulate HIF2? levels, and was augmented by the presence of VHL W117A. VHL p30 band intensities varied as a function of compound used, suggesting alternate post-translational processing. In addition, nuclear-cytoplasmic localization of pVHL varied amongst the different compounds. Conclusion 786-0 cells containing VHL-W117A-Venus can be successfully used to identify compounds that upregulate VHL levels, and that have a differential effect on pVHL intracellular localization and posttranslational processing. Further screening efforts will broaden the number of pharmacophores available to develop therapeutic agents that will upregulate and refunctionalize mutated VHL. PMID:22357874

Ding, Zhiyong; German, Peter; Bai, Shanshan; Feng, Zhehui; Gao, Meng; Si, Wendy; Sobieski, Mary M.; Stephan, Clifford C.; Mills, Gordon B.; Jonasch, Eric

2014-01-01

125

Cross Talk between Adrenergic and Bradykinin B2 Receptors Results in Cooperative Regulation of Cyclic AMP Accumulation and Mitogen-Activated Protein Kinase Activity  

Microsoft Academic Search

Costimulation of G protein-coupled receptors (GPCRs) may result in cross talk interactions between their downstream signaling pathways. Stimulation of GPCRs may also lead to cross talk regulation of receptor tyrosine kinase signaling and thereby to activation of mitogen-activated protein kinase (MAPK). In COS-7 cells, we investigated the interactions between two particular mitogenic receptor pathways, the endogenously expressed -adrenergic receptor (-AR)

SABINE HANKE; BERND NURNBERG; DETLEF H. GROLL; CLAUS LIEBMANN

2001-01-01

126

Alterations in c-Myc phenotypes resulting from dynamin-related protein 1 (Drp1)-mediated mitochondrial fission  

PubMed Central

The c-Myc (Myc) oncoprotein regulates numerous phenotypes pertaining to cell mass, survival and metabolism. Glycolysis, oxidative phosphorylation (OXPHOS) and mitochondrial biogenesis are positively controlled by Myc, with myc?/? rat fibroblasts displaying atrophic mitochondria, structural and functional defects in electron transport chain (ETC) components, compromised OXPHOS and ATP depletion. However, while Myc influences mitochondrial structure and function, it is not clear to what extent the reverse is true. To test this, we induced a state of mitochondrial hyper-fission in rat fibroblasts by de-regulating Drp1, a dynamin-like GTPase that participates in the terminal fission process. The mitochondria from these cells showed reduced mass and interconnectivity, a paucity of cristae, a marked reduction in OXPHOS and structural and functional defects in ETC Complexes I and V. High rates of abortive mitochondrial fusion were observed, likely reflecting ongoing, but ultimately futile, attempts to normalize mitochondrial mass. Cellular consequences included reduction of cell volume, ATP depletion and activation of AMP-dependent protein kinase. In response to Myc deregulation, apoptosis was significantly impaired both in the absence and presence of serum, although this could be reversed by increasing ATP levels by pharmacologic means. The current work demonstrates that enforced mitochondrial fission closely recapitulates a state of Myc deficiency and that mitochondrial integrity and function can affect Myc-regulated cellular behaviors. The low intracellular ATP levels that are frequently seen in some tumors as a result of inadequate vascular perfusion could favor tumor survival by countering the pro-apoptotic tendencies of Myc overexpression. PMID:23764851

Sarin, M; Wang, Y; Zhang, F; Rothermund, K; Zhang, Y; Lu, J; Sims-Lucas, S; Beer-Stolz, D; Van Houten, B E; Vockley, J; Goetzman, E S; Anthony Graves, J; Prochownik, E V

2013-01-01

127

LAMBOT et al. (1979) found comparable results : the optimum crude protein concentration for growth and nitrogen utilisation is about 13.3 -12.2 and 11.4 per cent at body weights  

E-print Network

LAMBOT et al. (1979) found comparable results : the optimum crude protein concentration for growth for protein are expressed as digestible crude protein (DCP). #12;Energy value of feeds The content of SFU per= digestible crude protein, per cent of dry matter X! = digestible crude fat, per cent of dry matter X3

Paris-Sud XI, Université de

128

Parageorgbokiite, ?-Cu5O2(SeO3)2Cl2, a new mineral species from volcanic exhalations, Kamchatka Peninsula, Russia  

NASA Astrophysics Data System (ADS)

Parageorgbokiite, ?-Cu5O2(SeO3)2Cl2, has been found at the second cinder cone of the Great Fissure Tolbachik Eruption, Kamchatka Peninsula, Russia. Ralstonite, tolbachite, melanothallite, chalcocyanite, euchlorine, Fe oxides, tenorite, native gold, sophiite, Na, Ca, and Mg sulfates, cotunnite, and some copper oxoselenites are associated minerals. The estimated temperature of the mineral formation is 400-625°C. The color is green, with a vitreous luster; the streak is light green. The mineral is brittle, with the Mohs hardness ranging from 3 to 4. Cleavage is not observed. The calculated density is 4.70 g/cm3. Parageorgbokiite is biaxial (+); ? = 2.05(1), ? = 2.05(1), and ? = 2.08(1); 2 V (meas.) is ˜03, and 2 V (calc.) = 0(5)°. The optical orientation is X = a; other details remain unclear. The mineral is pleochroic, from grass green on X and Y to yellowish green on Z. The empirical formula calculated on the basis of O + Cl = 10 is Cu4.91Pb0.02O1.86(ScO3)2Cl2.14. The simplified formula is Cu5O2(ScO3)2Cl2. Parageorgbokiite pertains to a new structural type of inorganic compounds. Its name points out its dimorphism with georgbokiite, which was named in honor of G.B. Bokii, the prominent Russian crystal chemist (1909-2000).

Vergasova, L. P.; Krivovichev, S. V.; Filatov, S. K.; Britvin, S. N.; Burns, P. C.; Anan'ev, V. V.

2007-12-01

129

Frustration and Dzyaloshinsky-Moriya anisotropy in the kagome francisites Cu3Bi (SeO3)2 O2X (X = Br , Cl )  

NASA Astrophysics Data System (ADS)

We investigate the antiferromagnetic canting instability of the spin-1/2 kagome ferromagnet, as realized in the layered cuprates Cu3Bi (SeO3)2 O2X (X = Br , Cl ). While the local canting can be explained in terms of competing exchange interactions, the direction of the ferrimagnetic order parameter fluctuates strongly even at short distances on account of frustration which gives rise to an infinite ground state degeneracy at the classical level. In analogy with the kagome antiferromagnet, the accidental degeneracy is fully lifted only by nonlinear 1 /S corrections, rendering the selected uniform canted phase very fragile even for spins-1/2, as shown explicitly by coupled-cluster calculations. To account for the observed ordering, we show that the minimal description of these systems must include the microscopic Dzyaloshinsky-Moriya interactions, which we obtain from density-functional band-structure calculations. The model explains all qualitative properties of the kagome francisites, including the detailed nature of the ground state and the anisotropic response under a magnetic field. The predicted magnon excitation spectrum and quantitative features of the magnetization process call for further experimental investigations of these compounds.

Rousochatzakis, Ioannis; Richter, Johannes; Zinke, Ronald; Tsirlin, Alexander A.

2015-01-01

130

Bombyx mori Midgut Membrane Protein P252, Which Binds to Bacillus thuringiensis Cry1A, Is a Chlorophyllide-Binding Protein, and the Resulting Complex Has Antimicrobial Activity?  

PubMed Central

The epithelial cell membrane 252-kDa protein (P252) isolated in our laboratory from Bombyx mori midgut was shown to bind strongly with Cry1Aa, Cry1Ab, and Cry1Ac toxins of Bacillus thuringiensis (15). In the current paper, P252 was shown to bind with chlorophyllide (Chlide) to form red fluorescent protein (RFP) complex, termed Bm252RFP, with absorbance and fluorescence emission peaks at 600 nm and 620 nm, respectively. P252 at a concentration of 1 ?M is shown to bind with about 50 ?M Chlide in a positively cooperative reaction to form Bm252RFP under aerobic conditions and in the presence of light at 37°C. Various parameters influencing this reaction have been optimized for efficient in vitro chemical synthesis of Bm252RFP. Circular dichroism spectra revealed that P252 is composed of a ?-structure (39.8% ± 2.2%, based on 5 samples) with negligible contribution of ?-helix structure. When bound to Chlide, the ?-structure content in the complex is reduced to 21.6% ± 3.1% (n = 5). Since Chlide had no secondary structure, the observed reduction suggests significant conformational changes of P252 during the formation of Bm252RFP complex. Bm252RFP had antimicrobial activity against Escherichia coli, Serratia marcescens, B. thuringiensis, and Saccharomyces cerevisiae with 50% effective concentrations of 2.82, 2.94, 5.88 ?M, and 21.6 ?M, respectively. This is the first report ever to show clear, concrete binding characteristics of the midgut protein to form an RFP having significant antimicrobial activity. PMID:18192432

Pandian, Ganesh N.; Ishikawa, Toshiki; Togashi, Makoto; Shitomi, Yasuyuki; Haginoya, Kohsuke; Yamamoto, Shuhei; Nishiumi, Tadayuki; Hori, Hidetaka

2008-01-01

131

Bombyx mori midgut membrane protein P252, which binds to Bacillus thuringiensis Cry1A, is a chlorophyllide-binding protein, and the resulting complex has antimicrobial activity.  

PubMed

The epithelial cell membrane 252-kDa protein (P252) isolated in our laboratory from Bombyx mori midgut was shown to bind strongly with Cry1Aa, Cry1Ab, and Cry1Ac toxins of Bacillus thuringiensis (15). In the current paper, P252 was shown to bind with chlorophyllide (Chlide) to form red fluorescent protein (RFP) complex, termed Bm252RFP, with absorbance and fluorescence emission peaks at 600 nm and 620 nm, respectively. P252 at a concentration of 1 microM is shown to bind with about 50 microM Chlide in a positively cooperative reaction to form Bm252RFP under aerobic conditions and in the presence of light at 37 degrees C. Various parameters influencing this reaction have been optimized for efficient in vitro chemical synthesis of Bm252RFP. Circular dichroism spectra revealed that P252 is composed of a beta-structure (39.8% +/- 2.2%, based on 5 samples) with negligible contribution of alpha-helix structure. When bound to Chlide, the beta-structure content in the complex is reduced to 21.6% +/- 3.1% (n = 5). Since Chlide had no secondary structure, the observed reduction suggests significant conformational changes of P252 during the formation of Bm252RFP complex. Bm252RFP had antimicrobial activity against Escherichia coli, Serratia marcescens, B. thuringiensis, and Saccharomyces cerevisiae with 50% effective concentrations of 2.82, 2.94, 5.88 microM, and 21.6 microM, respectively. This is the first report ever to show clear, concrete binding characteristics of the midgut protein to form an RFP having significant antimicrobial activity. PMID:18192432

Pandian, Ganesh N; Ishikawa, Toshiki; Togashi, Makoto; Shitomi, Yasuyuki; Haginoya, Kohsuke; Yamamoto, Shuhei; Nishiumi, Tadayuki; Hori, Hidetaka

2008-03-01

132

Dietary Protein Intake and Coronary Heart Disease in a Large Community Based Cohort: Results from the Atherosclerosis Risk in Communities (ARIC) Study  

PubMed Central

Background Prospective data examining the relationship between dietary protein intake and incident coronary heart disease (CHD) are inconclusive. Most evidence is derived from homogenous populations such as health professionals. Large community-based analyses in more diverse samples are lacking. Methods We studied the association of protein type and major dietary protein sources and risk for incident CHD in 12,066 middle-aged adults (aged 45–64 at baseline, 1987–1989) from four U.S. communities enrolled in the Atherosclerosis Risk in Communities (ARIC) Study who were free of diabetes mellitus and cardiovascular disease at baseline. Dietary protein intake was assessed at baseline and after 6 years of follow-up by food frequency questionnaire. Our primary outcome was adjudicated coronary heart disease events or deaths with following up through December 31, 2010. Cox proportional hazard models with multivariable adjustment were used for statistical analyses. Results During a median follow-up of 22 years, there were 1,147 CHD events. In multivariable analyses total, animal and vegetable protein were not associated with an increased risk for CHD before or after adjustment. In food group analyses of major dietary protein sources, protein intake from red and processed meat, dairy products, fish, nuts, eggs, and legumes were not significantly associated with CHD risk. The hazard ratios [with 95% confidence intervals] for risk of CHD across quintiles of protein from poultry were 1.00 [ref], 0.83 [0.70–0.99], 0.93 [0.75–1.15], 0.88 [0.73–1.06], 0.79 [0.64–0.98], P for trend ?=?0.16). Replacement analyses evaluating the association of substituting one source of dietary protein for another or of decreasing protein intake at the expense of carbohydrates or total fats did not show any statistically significant association with CHD risk. Conclusion Based on a large community cohort we found no overall relationship between protein type and major dietary protein sources and risk for CHD. PMID:25303709

Haring, Bernhard; Gronroos, Noelle; Nettleton, Jennifer A.; Wyler von Ballmoos, Moritz C.; Selvin, Elizabeth; Alonso, Alvaro

2014-01-01

133

Long-term clinical results of microsomal triglyceride transfer protein inhibitor use in a patient with homozygous familial hypercholesterolemia.  

PubMed

We report the case of a 49-year-old woman with homozygous familial hypercholesterolemia and a complicated cardiovascular history, treated for 5 years with a microsomal triglyceride transfer protein inhibitor in addition to her other lipid-lowering therapy. PMID:25670368

Raper, Anna; Kolansky, Daniel M; Sachais, Bruce S; Meagher, Emma A; Baer, Amanda L; Cuchel, Marina

2015-01-01

134

Covalent Attachment of Cyclic TAT Peptides to GFP Results in Protein Delivery into Live Cells with Immediate Bioavailability.  

PubMed

The delivery of free molecules into the cytoplasm and nucleus by using arginine-rich cell-penetrating peptides (CPPs) has been limited to small cargoes, while large cargoes such as proteins are taken up and trapped in endocytic vesicles. Based on recent work, in which we showed that the transduction efficiency of arginine-rich CPPs can be greatly enhanced by cyclization, the aim was to use cyclic CPPs to transport full-length proteins, in this study green fluorescent protein (GFP), into the cytosol of living cells. Cyclic and linear CPP-GFP conjugates were obtained by using azido-functionalized CPPs and an alkyne-functionalized GFP. Our findings reveal that the cyclic-CPP-GFP conjugates are internalized into live cells with immediate bioavailability in the cytosol and the nucleus, whereas linear CPP analogues do not confer GFP transduction. This technology expands the application of cyclic CPPs to the efficient transport of functional full-length proteins into live cells. PMID:25521313

Nischan, Nicole; Herce, Henry D; Natale, Francesco; Bohlke, Nina; Budisa, Nediljko; Cardoso, M Cristina; Hackenberger, Christian P R

2015-02-01

135

Complementarity of Hydrophobic\\/Hydrophilic Properties In Protein---Ligand Complexes: A New Tool to Improve Docking Results  

Microsoft Academic Search

Computational techniques designed to predict the spatial structure of ligand---receptor complexes (molecular docking) are widely used in investigations of molecular details of protein functioning and in drug design. Here, a brief review of docking methods is given and recent advances in improvement of their accuracy and efficiency are discussed. Two acute problems of standard docking algorithms are considered: proper ranking

Timothy V. Pyrkov; Anton O. Chugunov; Nikolay A. Krylov; Dimitry E. Nolde; Roman G. Efremov

2009-01-01

136

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...

137

Polo-like Kinase 1 Activated by the Hepatitis B Virus X Protein Attenuates Both the DNA Damage Checkpoint and DNA Repair Resulting in Partial Polyploidy*  

PubMed Central

Hepatitis B virus X protein (pX), implicated in hepatocarcinogenesis, induces DNA damage because of re-replication and allows propagation of damaged DNA, resulting in partial polyploidy and oncogenic transformation. The mechanism by which pX allows cells with DNA damage to continue proliferating is unknown. Herein, we show pX activates Polo-like kinase 1 (Plk1) in the G2 phase, thereby attenuating the DNA damage checkpoint. Specifically, in the G2 phase of pX-expressing cells, the checkpoint kinase Chk1 was inactive despite DNA damage, and protein levels of claspin, an adaptor of ataxia telangiectasia-mutated and Rad3-related protein-mediated Chk1 phosphorylation, were reduced. Pharmacologic inhibition or knockdown of Plk1 restored claspin protein levels, Chk1 activation, and p53 stabilization. Also, protein levels of DNA repair protein Mre11 were decreased in the G2 phase of pX-expressing cells but not with Plk1 knockdown. Interestingly, in pX-expressing cells, Mre11 co-immunoprecipitated with transfected Plk1 Polo-box domain, and inhibition of Plk1 increased Mre11 stability in cycloheximide-treated cells. These results suggest that pX-activated Plk1 by down-regulating Mre11 attenuates DNA repair. Importantly, concurrent inhibition of Plk1, p53, and Mre11 increased the number of pX-expressing cells with DNA damage entering mitosis, relative to Plk1 inhibition alone. By contrast, inhibition or knockdown of Plk1 reduced pX-induced polyploidy while increasing apoptosis. We conclude Plk1, activated by pX, allows propagation of DNA damage by concurrently attenuating the DNA damage checkpoint and DNA repair, resulting in polyploidy. We propose this novel Plk1 mechanism initiates pX-mediated hepatocyte transformation. PMID:20624918

Studach, Leo; Wang, Wen-Horng; Weber, Gregory; Tang, Jiabin; Hullinger, Ronald L.; Malbrue, Raphael; Liu, Xiaoqi; Andrisani, Ourania

2010-01-01

138

Preconditioning Results in S-Nitrosylation of Proteins Involved in Regulation of Mitochondrial Energetics and Calcium Transport  

Microsoft Academic Search

Nitric oxide has been shown to be an important signaling messenger in ischemic preconditioning (IPC). Accordingly, we investigated whether protein S-nitrosylation occurs in IPC hearts and whether S-nitrosoglutathione (GSNO) elicits similar effects on S-nitrosylation and cardioprotection. Preceding 20 minutes of no-flow ischemia and reperfusion, hearts from C57BL\\/6J mice were perfused in the Langendorff mode and subjected to the following conditions:

Junhui Sun; Meghan Morgan; Rong-Fong Shen; Charles Steenbergen; Elizabeth Murphy

2009-01-01

139

Complementarity of Hydrophobic\\/Hydrophilic Properties In Protein—Ligand Complexes: A New Tool to Improve Docking Results  

Microsoft Academic Search

Computational techniques designed to predict the spatial structure of ligand—receptor complexes (molecular docking) are widely\\u000a used in investigations of molecular details of protein functioning and in drug design. Here, a brief review of docking methods\\u000a is given and recent advances in improvement of their accuracy and efficiency are discussed. Two acute problems of standard\\u000a docking algorithms are considered: proper ranking

Timothy V. Pyrkov; Anton O. Chugunov; Nikolay A. Krylov; Dimitry E. Nolde; Roman G. Efremov

140

Bioactive glass 45S5 powders: effect of synthesis route and resultant surface chemistry and crystallinity on protein adsorption from human plasma.  

PubMed

Despite its medical applications, the mechanisms responsible for the osseointegration of bioactive glass (45S5) have yet to be fully understood. Evidence suggests that the strongest predictor for osseointegration of bioactive glasses, and ceramics, with bone tissue as the formation of an apatitic calcium phosphate layer atop the implanted material, with osteoblasts being the main mediator for new bone formation. Most have tried to understand the formation of this apatitic calcium phosphate layer, and other bioresponses between the host and bioactive glass 45S5 using Simulated Body Fluid; a solution containing ion concentrations similar to that found in human plasma without the presence of proteins. However, it is likely that cell attachment is probably largely mediated via the adsorbed protein layer. Plasma protein adsorption at the tissue bioactive glass interface has been largely overlooked. Herein, we compare crystalline and amorphous bioactive glass 45S5, in both melt-derived as well as sol-gel forms. Thus, allowing for a detailed understanding of both the role of crystallinity and powder morphology on surface ions, and plasma protein adsorption. It was found that sol-gel 45S5 powders, regardless of crystallinity, adsorbed 3-5 times as much protein as the crystalline melt-derived counterpart, as well as a greater variety of plasma proteins. The devitrification of melt-cast 45S5 resulted in only small differences in the amount and variety of the adsorbed proteome. Surface properties, and not material crystallinity, play a role in directing protein adsorption phenomena for bioactive glasses given the differences found between crystalline melt-cast 45S5 and sol-gel derived 45S5. PMID:22669582

Bahniuk, Markian S; Pirayesh, Hamidreza; Singh, Harsh D; Nychka, John A; Unsworth, Larry D

2012-12-01

141

Cyclophilin A Binds to the Viral RNA and Replication Proteins, Resulting in Inhibition of Tombusviral Replicase Assembly  

PubMed Central

Replication of plus-stranded RNA viruses is greatly affected by numerous host-encoded proteins that act as restriction factors. Cyclophilins, which are a large family of cellular prolyl isomerases, have been found to inhibit Tomato bushy stunt tombusvirus (TBSV) replication in a Saccharomyces cerevisiae model based on genome-wide screens and global proteomics approaches. In this report, we further characterize single-domain cyclophilins, including the mammalian cyclophilin A and plant Roc1 and Roc2, which are orthologs of the yeast Cpr1p cyclophilin, a known inhibitor of TBSV replication in yeast. We found that recombinant CypA, Roc1, and Roc2 strongly inhibited TBSV replication in a cell-free replication assay. Additional in vitro studies revealed that CypA, Roc1, and Roc2 cyclophilins bound to the viral replication proteins, and CypA and Roc1 also bound to the viral RNA. These interactions led to inhibition of viral RNA recruitment, the assembly of the viral replicase complex, and viral RNA synthesis. A catalytically inactive mutant of CypA was also able to inhibit TBSV replication in vitro due to binding to the replication proteins and the viral RNA. Overexpression of CypA and its mutant in yeast or plant leaves led to inhibition of tombusvirus replication, confirming that CypA is a restriction factor for TBSV. Overall, the current work has revealed a regulatory role for the cytosolic single-domain Cpr1-like cyclophilins in RNA virus replication. PMID:24089553

Kovalev, Nikolay

2013-01-01

142

Differential regulation of amyloid precursor protein sorting with pathological mutations results in a distinct effect on amyloid-? production.  

PubMed

The deposition of amyloid-? (A?) peptide, which is generated from amyloid precursor protein (APP), is the pathological hallmark of Alzheimer's disease (AD). Three APP familial AD mutations (D678H, D678N, and H677R) located at the sixth and seventh amino acid of A? have distinct effect on A? aggregation, but their influence on the physiological and pathological roles of APP remain unclear. We found that the D678H mutation strongly enhances amyloidogenic cleavage of APP, thus increasing the production of A?. This enhancement of amyloidogenic cleavage is likely because of the acceleration of APPD678H sorting into the endosomal-lysosomal pathway. In contrast, the APPD678N and APPH677R mutants do not cause the same effects. Therefore, this study indicates a regulatory role of D678H in APP sorting and processing, and provides genetic evidence for the importance of APP sorting in AD pathogenesis. The internalization of amyloid precursor protein (APP) increases its opportunity to be processed by ?-secretase and to produce Amyloid-? (A?) that causes Alzheimer's disease (AD). We report a pathogenic APPD678H mutant that enhances APP internalization into the endosomal-lysosomal pathway and thus promotes the ?-secretase cleavage and A? production. This study provides genetic evidence for the importance of APP sorting in AD pathogenesis. PMID:25053581

Lin, Yen-Chen; Wang, Jia-Yi; Wang, Kai-Chen; Liao, Jhih-Ying; Cheng, Irene H

2014-11-01

143

The copper-transporting capacity of ATP7A mutants associated with Menkes disease is ameliorated by COMMD1 as a result of improved protein expression.  

PubMed

Menkes disease (MD) is an X-linked recessive disorder characterized by copper deficiency resulting in a diminished function of copper-dependent enzymes. Most MD patients die in early childhood, although mild forms of MD have also been described. A diversity of mutations in the gene encoding of the Golgi-resident copper-transporting P(1B)-type ATPase ATP7A underlies MD. To elucidate the molecular consequences of the ATP7A mutations, various mutations in ATP7A associated with distinct phenotypes of MD (L873R, C1000R, N1304S, and A1362D) were analyzed in detail. All mutants studied displayed changes in protein expression and intracellular localization parallel to a dramatic decline in their copper-transporting capacity compared to ATP7A the wild-type. We restored these observed defects in ATP7A mutant proteins by culturing the cells at 30°C, which improves the quality of protein folding, similar to that which as has recently has been demonstrated for misfolded ATP7B, a copper transporter homologous to ATP7A. Further, the effect of the canine copper toxicosis protein COMMD1 on ATP7A function was examined as COMMD1 has been shown to regulate the proteolysis of ATP7B proteins. Interestingly, in addition to adjusted growth temperature, binding of COMMD1 partially restored the expression, subcellular localization, and copper-exporting activities of the ATP7A mutants. However, no effect of pharmacological chaperones was observed. Together, the presented data might provide a new direction for developing therapies to improve the residual exporting activity of unstable ATP7A mutant proteins, and suggests a potential role for COMMD1 in this process. PMID:21667063

Vonk, Willianne I M; de Bie, Prim; Wichers, Catharina G K; van den Berghe, Peter V E; van der Plaats, Rozemarijn; Berger, Ruud; Wijmenga, Cisca; Klomp, Leo W J; van de Sluis, Bart

2012-01-01

144

Upregulation of N-acetylaspartic acid resulting nitric oxide toxicity induces aspartoacylase mutations and protein interaction to cause pathophysiology seen in Canavan disease.  

PubMed

Aspartoacylase (ASPA) converts N-acetylaspartic acid into aspartate and acetate. In Canavan disease (CD), N-acetylaspartic acid (NAA) is found to be increased and over 65 mutations including IVS4+1 G ? T, deletion of introns and exons have been reported in the ASPA gene. These changes lead to severe form or mild form of CD. The present study was aimed to understand mechanism in the cause of mutations in ASPA and pathophysiology seen in patients with CD. We have reported that elevated levels of NAA induce inducible nitric oxide (iNOS) to produce nitric oxide toxicity in CD. Nitric oxide toxicity has been shown to induce several mutations including base change G ? T and deletion and enhances protein interaction in several genes. Therefore we hypothesize that upregulation of NAA stimulates NOS and the resulting nitric oxide toxicity induces ASPA mutations and protein interaction to result pathophysiological abnormalities seen in patients with CD. PMID:20673702

Surendran, Sankar

2010-12-01

145

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

PubMed

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

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

146

Positive Selection Results in Frequent Reversible Amino Acid Replacements in the G Protein Gene of Human Respiratory Syncytial Virus  

PubMed Central

Human respiratory syncytial virus (HRSV) is the major cause of lower respiratory tract infections in children under 5 years of age and the elderly, causing annual disease outbreaks during the fall and winter. Multiple lineages of the HRSVA and HRSVB serotypes co-circulate within a single outbreak and display a strongly temporal pattern of genetic variation, with a replacement of dominant genotypes occurring during consecutive years. In the present study we utilized phylogenetic methods to detect and map sites subject to adaptive evolution in the G protein of HRSVA and HRSVB. A total of 29 and 23 amino acid sites were found to be putatively positively selected in HRSVA and HRSVB, respectively. Several of these sites defined genotypes and lineages within genotypes in both groups, and correlated well with epitopes previously described in group A. Remarkably, 18 of these positively selected tended to revert in time to a previous codon state, producing a “flip-flop” phylogenetic pattern. Such frequent evolutionary reversals in HRSV are indicative of a combination of frequent positive selection, reflecting the changing immune status of the human population, and a limited repertoire of functionally viable amino acids at specific amino acid sites. PMID:19119418

Botosso, Viviane F.; de A. Zanotto, Paolo M.; Ueda, Mirthes; Arruda, Eurico; Gilio, Alfredo E.; Vieira, Sandra E.; Stewien, Klaus E.; Peret, Teresa C. T.; Jamal, Leda F.; Pardini, Maria I. de M. C.; Pinho, João R. R.; Massad, Eduardo; Sant'Anna, Osvaldo A.; Holmes, Eddie C.; Durigon, Edison L.

2009-01-01

147

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)

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) Å, V = 1205.6(8) Å3, 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.

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

2013-04-01

148

Genetic divergence of rotavirus nonstructural protein 4 results in distinct serogroup-specific viroporin activity and intracellular punctate structure morphologies.  

PubMed

Nonstructural protein 4 (NSP4) viroporin activity is critical for the replication and assembly of serogroup A rotavirus (RVA); however, the dramatic primary sequence divergence of NSP4s across serogroups raises the possibility that viroporin activity is not a common feature among RVs. We tested for NSP4 viroporin activity from divergent strains, including RVA (EC and Ty-1), RVB (IDIR), and RVC (Cowden). Canonical viroporin motifs were identified in RVA, RVB, and RVC NSP4s, but the arrangement of basic residues and the amphipathic ?-helices was substantially different between serogroups. Using Escherichia coli and mammalian cell expression, we showed that each NSP4 tested had viroporin activity, but serogroup-specific viroporin phenotypes were identified. Only mammalian RVA and RVC NSP4s induced BL21-pLysS E. coli cell lysis, a classical viroporin activity assay. In contrast, RVA, RVB, and RVC NSP4 expression was universally cytotoxic to E. coli and disrupted reduction-oxidation activities, as measured by a new redox dye assay. In mammalian cells, RVB and RVC NSP4s were initially localized in the endoplasmic reticulum (ER) and trafficked into punctate structures that were mutually exclusive with RVA NSP4. The punctate structures partially localized to the ER-Golgi intermediate compartment (ERGIC) but primarily colocalized with punctate LC3, a marker for autophagosomes. Similar to RVA NSP4, expression of RVB and RVC NSP4s significantly elevated cytosolic calcium levels, demonstrating that despite strong primary sequence divergence, RV NSP4 has maintained viroporin activity across serogroups A to C. These data suggest that elevated cytosolic calcium is a common critical process for all rotavirus strains. PMID:22357281

Hyser, Joseph M; Utama, Budi; Crawford, Sue E; Estes, Mary K

2012-05-01

149

Genetic Divergence of Rotavirus Nonstructural Protein 4 Results in Distinct Serogroup-Specific Viroporin Activity and Intracellular Punctate Structure Morphologies  

PubMed Central

Nonstructural protein 4 (NSP4) viroporin activity is critical for the replication and assembly of serogroup A rotavirus (RVA); however, the dramatic primary sequence divergence of NSP4s across serogroups raises the possibility that viroporin activity is not a common feature among RVs. We tested for NSP4 viroporin activity from divergent strains, including RVA (EC and Ty-1), RVB (IDIR), and RVC (Cowden). Canonical viroporin motifs were identified in RVA, RVB, and RVC NSP4s, but the arrangement of basic residues and the amphipathic ?-helices was substantially different between serogroups. Using Escherichia coli and mammalian cell expression, we showed that each NSP4 tested had viroporin activity, but serogroup-specific viroporin phenotypes were identified. Only mammalian RVA and RVC NSP4s induced BL21-pLysS E. coli cell lysis, a classical viroporin activity assay. In contrast, RVA, RVB, and RVC NSP4 expression was universally cytotoxic to E. coli and disrupted reduction-oxidation activities, as measured by a new redox dye assay. In mammalian cells, RVB and RVC NSP4s were initially localized in the endoplasmic reticulum (ER) and trafficked into punctate structures that were mutually exclusive with RVA NSP4. The punctate structures partially localized to the ER-Golgi intermediate compartment (ERGIC) but primarily colocalized with punctate LC3, a marker for autophagosomes. Similar to RVA NSP4, expression of RVB and RVC NSP4s significantly elevated cytosolic calcium levels, demonstrating that despite strong primary sequence divergence, RV NSP4 has maintained viroporin activity across serogroups A to C. These data suggest that elevated cytosolic calcium is a common critical process for all rotavirus strains. PMID:22357281

Hyser, Joseph M.; Utama, Budi; Crawford, Sue E.

2012-01-01

150

Antisense-mediated suppression of C-hordein biosynthesis in the barley grain results in correlated changes in the transcriptome, protein profile, and amino acid composition.  

PubMed

Antisense- or RNAi-mediated suppression of the biosynthesis of nutritionally inferior storage proteins is a promising strategy for improving the amino acid profile of seeds. However, the potential pleiotropic effects of this on interconnected pathways and the agronomic quality traits need to be addressed. In the current study, a transcriptomic analysis of an antisense C-hordein line of barley was performed, using a grain-specific cDNA array. The C-hordein antisense line is characterized by marked changes in storage protein and amino acid profiles, while the seed weight is within the normal range and no external morphological irregularities were observed. The results of the transcriptome analysis showed excellent correlation with data on changes in the relative proportions of storage proteins and amino acid composition. The antisense line had a lower C-hordein level and down-regulated transcript encoding C-hordein. The production of the S-rich B/gamma- and D-hordeins was increased and significantly higher steady-state expression levels of the corresponding genes were observed. The increased synthesis of S-rich hordeins appeared to increase the demand for sulphur and the S-rich amino acids (cysteine and methionine), resulting in an up-regulation of key genes in the appropriate biosynthetic pathways. This study demonstrated the utility of the grain-specific cDNA microarray analysis to detect perturbations induced by antisense suppression of plant processes. PMID:18162630

Hansen, Michael; Lange, Mette; Friis, Carsten; Dionisio, Giuseppe; Holm, Preben Bach; Vincze, Eva

2007-01-01

151

Salidroside stimulates the accumulation of HIF-1? protein resulted in the induction of EPO expression: a signaling via blocking the degradation pathway in kidney and liver cells.  

PubMed

Rhodiolae Crenulatae Radix et Rhizoma (Rhodiola), the root and rhizome of Rhodiola crenulata (Hook. f. et Thoms.) H. Ohba, has been used as a traditional Chinese medicine (TCM) to increase the body resistance to mountain sickness in preventing hypoxia; however, the functional ingredient responsible for this adaptogenic effect has not been revealed. Here, we have identified salidroside, a glycoside predominantly found in Rhodiola, is the chemical in providing such anti-hypoxia effect. Cultured human embryonic kidney fibroblast (HEK293T) and human hepatocellular carcinoma (HepG2) were used to reveal the mechanism of this hematopoietic function mediated by salidroside. The application of salidroside in cultures induced the expression of erythropoietin (EPO) mRNA from its transcription regulatory element hypoxia response element (HRE), located on EPO gene. The application of salidroside stimulated the accumulation of hypoxia-inducible factor-1? (HIF-1?) protein, but not HIF-2? protein: the salidroside-induced HIF-1? protein was via the reduction of HIF-1? degradation but not the mRNA induction. The increased HIF-1? could account for the activation of EPO gene. These results supported the notion that hematopoietic function of Rhodiola was triggered, at least partially, by salidroside. PMID:22309741

Zheng, Ken Yu-Zhong; Zhang, Zhen-Xia; Guo, Ava Jiang-Yang; Bi, Cathy Wen-Chuang; Zhu, Kevin Yue; Xu, Sherry Li; Zhan, Janis Ya-Xian; Lau, David Tai-Wei; Dong, Tina Ting-Xia; Choi, Roy Chi-Yan; Tsim, Karl Wah-Keung

2012-03-15

152

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

SciTech Connect

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.

Luka, Zigmund; Pakhomova, Svetlana; Loukachevitch, Lioudmila V.; Newcomer, Marcia E.; Wagner, Conrad (Vanderbilt); (LSU)

2012-06-27

153

Improving docking results via reranking of ensembles of ligand poses in multiple X-ray protein conformations with MM-GBSA.  

PubMed

There is a tendency in the literature to be critical of scoring functions when docking programs perform poorly. The assumption is that existing scoring functions need to be enhanced or new ones developed in order to improve the performance of docking programs for tasks such as pose prediction and virtual screening. However, failures can result from either sampling or scoring (or a combination of the two), although less emphasis tends to be given to the former. In this work, we use the programs GOLD and Glide on a high-quality data set to explore whether failures in pose prediction and binding affinity estimation can be attributable more to sampling or scoring. We show that identification of the correct pose (docking power) can be improved by incorporating ligand strain into the scoring function or rescoring an ensemble of diverse docking poses with MM-GBSA in a postprocessing step. We explore the use of nondefault docking settings and find that enhancing ligand sampling also improves docking power, again suggesting that sampling is more limiting than scoring for the docking programs investigated in this work. In cross-docking calculations (docking a ligand to a noncognate receptor structure) we observe a significant reduction in the accuracy of pose ranking, as expected and has been reported by others; however, we demonstrate that these alternate poses may in fact be more complementary between the ligand and the rigid receptor conformation, emphasizing that treating the receptor rigidly is an artificial constraint on the docking problem. We simulate protein flexibility by the use of multiple crystallographic conformations of a protein and demonstrate that docking results can be improved with this level of protein sampling. This work indicates the need for better sampling in docking programs, especially for the receptor. This study also highlights the variable descriptive value of RMSD as the sole arbiter of pose replication quality. It is shown that ligand poses within 2 Å of the crystallographic one can show dramatic differences in calculated relative protein-ligand energies. MM-GBSA rescoring of distinct poses overcomes some of the sensitivities of pose ranking experienced by the docking scoring functions due to protein preparation and binding site definition. PMID:25266271

Greenidge, P A; Kramer, C; Mozziconacci, J-C; Sherman, W

2014-10-27

154

Comparison of AOD retrieved from Brewer spectrophotometer in SeoComparison of AOD retrieved from Brewer spectrophotometer in Seoulul JaJa--Ho Koo,Ho Koo, YunYun--Mi Kim,Mi Kim, Jhoon Kim, Hi Ku ChoJhoon Kim, Hi Ku Cho  

E-print Network

Comparison of AOD retrieved from Brewer spectrophotometer in SeoComparison of AOD retrieved from Brewer spectrophotometer in Seoulul JaJa--Ho Koo,Ho Koo, YunYun--Mi Kim,Mi Kim, Jhoon Kim, Hi Ku Cho-GAW Brewer Users Group Meeting : 28 Oct ­ 3 Nov 2007 Summary 1. AOD retrieved from Brewer spectrophotometer

Wang, Yuhang

155

Should the Amounts of Fat and Protein Be Taken into Consideration to Calculate the Lunch Prandial Insulin Bolus? Results from a Randomized Crossover Trial  

PubMed Central

Abstract Background Concerning continuous subcutaneous insulin infusion (CSII), there are controversial results related to changes in glycemic response according to the meal composition and bolus design. Our aim is to determine whether the presence of protein and fat in a meal could involve a different postprandial glycemic response than that obtained with only carbohydrates (CHs). Subjects and Methods This was a crossover, randomized clinical trial. Seventeen type 1 diabetes (T1D) patients on CSII wore a blinded continuous glucose monitoring system sensor for 3 days. They ingested two meals (meal 1 vs. meal 2) with the same CH content (50?g) but different fat (8.9?g vs. 37.4?g) and protein (3.3?g vs. 28.9?g) contents. A single-wave insulin bolus was used, and the interstitial glucose values were measured every 30?min for 3?h. We evaluated the different postprandial glycemic response between meal 1 and meal 2 by using mixed-effects models. Results The postmeal glucose increase was 22?mg/dL for meal 1 and 31?mg/dL for meal 2. In univariate analysis, at different times not statistically significant differences in glucose levels between meals occurred. In mixed-model analysis, a time×meal interaction was found, indicating a different response between treatments along the time. However, most of the patients remained in the normoglycemic range (70–180?mg/dL) during the 3-h postmeal period (84.4% for meal 1 and 93.1% for meal 2). Conclusions The presence of balanced amounts of protein and fat determined a different glycemic response from that obtained with only CH up to 3?h after eating. The clinical relevance of this finding remains to be elucidated. PMID:23259764

González-Rodriguez, María; Pazos-Couselo, Marcos; Gude, Francisco; Prieto-Tenreiro, Alma; Casanueva, Felipe

2013-01-01

156

DNA-binding and transcriptional activation properties of the EWS-FLI-1 fusion protein resulting from the t(11;22) translocation in Ewing sarcoma.  

PubMed Central

The 5' half of the EWS gene has recently been described to be fused to the 3' regions of genes encoding the DNA-binding domain of several transcriptional regulators, including ATF1, FLI-1, and ERG, in several human tumors. The most frequent occurrence of this situation results from the t(11;22)(q24;q12) chromosome translocation specific for Ewing sarcoma (ES) and related tumors which joins EWS sequences to the 3' half of FLI-1, which encodes a member of the Ets family of transcriptional regulators. We show here that this chimeric gene encodes an EWS-FLI-1 nuclear protein which binds DNA with the same sequence specificity as the wild-type parental FLI-1 protein. We further show that EWS-FLI-1 is an efficient sequence-specific transcriptional activator of model promoters containing FLI-1 (Ets)-binding sites, a property which is strictly dependent on the presence of its EWS domain. Comparison of the properties of the N-terminal activation domain of FLI-1 to those of the EWS domain of the fusion protein indicates that EWS-FLI-1 has altered transcriptional activation properties compared with FLI-1. These results suggest that EWS-FLI-1 contributes to the transformed phenotype of ES tumor cells by inducing the deregulated and/or unscheduled activation of genes normally responsive to FLI-1 or to other close members of the Ets family. ES and related tumors are characterized by an elevated level of c-myc expression. We show that EWS-FLI-1 is a transactivator of the c-myc promoter, suggesting that upregulation of c-myc expression is under control of EWS-FLI-1. Images PMID:8164678

Bailly, R A; Bosselut, R; Zucman, J; Cormier, F; Delattre, O; Roussel, M; Thomas, G; Ghysdael, J

1994-01-01

157

Search Engine Optimization: SEO Book  

NSDL National Science Digital Library

The strange and wondrous ways in which search engines gather their indexes is made a little clearer in this tutorial. Written by a web designer disappointed with how difficult his pages were to find with the standard search engines, this page gives insight into how Infoseek, Lycos, Alta Vista, Excite, Web Crawler, and Open Text catalog web pages. The search strategy of each engine is described, along with tips for how web designers can increase their site's chances of being among the hits returned when users enter relevant search criteria. Although indexing algorithms are constantly being updated, this site presents common-sense guidelines that web designers interested in reaching a wider audience will find useful.

Wall, Aaron

158

Knockdown of the Arabidopsis thaliana chloroplast protein disulfide isomerase 6 results in reduced levels of photoinhibition and increased D1 synthesis in high light.  

PubMed

A chloroplast protein disulfide isomerase (PDI) was previously proposed to regulate translation of the unicellular green alga Chlamydomonas reinhardtii chloroplast psbA mRNA, encoding the D1 protein, in response to light. Here we show that AtPDI6, one of 13 Arabidopsis thaliana PDI genes, also plays a role in the chloroplast. We found that AtPDI6 is targeted and localized to the chloroplast. Interestingly, AtPDI6 knockdown plants displayed higher resistance to photoinhibition than wild-type plants when exposed to a tenfold increase in light intensity. The AtPDI6 knockdown plants also displayed a higher rate of D1 synthesis under a similar light intensity. The increased resistance to photoinhibition may not be rationalized by changes in antenna or non-photochemical quenching. Thus, the increased D1 synthesis rate, which may result in a larger proportion of active D1 under light stress, may led to the decrease in photoinhibition. These results suggest that, although the D1 synthesis rates observed in wild-type plants under high light intensities are elevated, repair can potentially occur faster. The findings implicate AtPDI6 as an attenuator of D1 synthesis, modulating photoinhibition in a light-regulated manner. PMID:24684167

Wittenberg, Gal; Levitan, Alexander; Klein, Tamir; Dangoor, Inbal; Keren, Nir; Danon, Avihai

2014-06-01

159

Combination of a novel photosensitizer DTPP with 650 nm laser results in efficient apoptosis, arresting cell cycle and cytoskeleton protein changes in lung cancer A549 cells.  

PubMed

Photodynamic therapy (PDT) using photosensitized reaction to produce cytotoxicity was used for cancer therapy in recent years. To study the effectiveness of PDT mediated by a novel photosensitizer (PS), DTPP 5-(4'-(2?-dicarboxymethylamino)acetamidophenyl)-10, 15, 20-triphenylporphyrin, on lung cancer A549 cell lines in vitro, DTPP was employed in different concentrations (2, 4, 6, 8, 10, 12, 15, 20, 25, and 30 ?g/ml) and combined with 650 nm laser of different power densities (0.6, 1.2, 2.4, 4.8, 7.2, and 9.6 J/cm(2)) that resulted in obvious inhibition of cell proliferation and apoptosis. Results showed that cell survival rates have a dependent relationship with time and PS concentrations and no significant cytotoxicity was induced by DTPP itself. Apoptosis and cell cycle S arrest were observed; cytoskeleton morphologic observation revealed collapse, sparkling, and shrunken shapes. Apoptosis-related protein caspase-3 overexpression was detected while caspase-9, bcl-2, and cytoskeleton protein beta-catenin were in low levels of expression than the control. Cleavage of beta-catenin by caspase-3 or other proteases from the lysosome might be the main reason for the cytoskeleton collapse as beta-tubulin and actin were at a stable level 12 h after PDT. This paper gives a better understanding of the effectiveness of DTPP-mediated PDT in lung cancer A549 cells both with regard to dosimetry and apoptosis changes. PMID:24964751

Wang, H; Zhang, H M; Yin, H J; Wei, M Q; Sha, H; Liu, T J; Li, Y X

2015-01-01

160

Acid gelation properties of heated skim milk as a result of enzymatically induced changes in the micelle/serum distribution of the whey protein/kappa-casein aggregates.  

PubMed

Changes in the acid gelation properties of skim milk as a result of variations in the micelle/serum distribution of the heat-induced whey protein/kappa-casein aggregates, induced by the combination of heat treatment and limited renneting, were investigated. No dramatic change in the zeta potential or the isoelectric point of the casein micelles was suggested, whether the aggregates were all attached to the casein micelle or not. Fluorescence intensity measurement using 8-anilino-1-naphthalenesulfonic acid (ANS) showed that the heat-induced aggregates were highly hydrophobic. Dynamic oscillation viscosimetry showed that acid gelation using glucono-delta-lactone (GDL) started at a higher pH value in prerenneted milk. However, no change in the gelation profile of skim milk could be related to the proportion of aggregates bound to the surface of the casein micelles. The results support the idea of an early interaction between the serum aggregates and the casein micelles on acidification. PMID:18038987

Guyomarc'h, Fanny; Renan, Marie; Chatriot, Marc; Gamerre, Valérie; Famelart, Marie-Hélène

2007-12-26

161

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

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.

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

162

Disruption of the protein kinase N gene of drosophila melanogaster results in the recessive delorean allele (pkndln) with a negative impact on wing morphogenesis.  

PubMed

We describe the delorean mutation of the Drosophila melanogaster protein kinase N gene (pkn(dln)) with defects in wing morphology. Flies homozygous for the recessive pkn(dln) allele have a composite wing phenotype that exhibits changes in relative position and shape of the wing blade as well as loss of specific vein and bristle structures. The pkn(dln) allele is the result of a P-element insertion in the first intron of the pkn locus, and the delorean wing phenotype is contingent upon the interaction of insertion-bearing alleles in trans. The presence of the insertion results in production of a novel transcript that initiates from within the 3' end of the P-element. The delorean-specific transcript is predicted to produce a wild-type PKN protein. The delorean phenotype is not the result of a reduction in pkn expression, as it could not be recreated using a variety of wing-specific drivers of pkn-RNAi expression. Rather, it is the presence of the delorean-specific transcript that correlates with the mutant phenotype. We consider the delorean wing phenotype to be due to a pairing-dependent, recessive mutation that behaves as a dosage-sensitive, gain of function. Our analysis of genetic interactions with basket and nemo reflects an involvement of pkn and Jun-terminal kinase signaling in common processes during wing differentiation and places PKN as a potential effector of Rho1's involvement in the Jun-terminal kinase pathway. The delorean phenotype, with its associated defects in wing morphology, provides evidence of a role for PKN in adult morphogenetic processes. PMID:24531729

Sass, Georgette L; Ostrow, Bruce D

2014-04-01

163

Isoflurane anesthesia results in reversible ultrastructure and occludin tight junction protein expression changes in hippocampal blood-brain barrier in aged rats.  

PubMed

The underlying mechanism of isoflurane-induced cognitive dysfunction in older individuals is unknown. In this study, the effects of isoflurane exposure on the hippocampal blood-brain barrier (BBB) in aged rats were investigated because it was previously shown that BBB disruption involves in cognitive dysfunction. Twenty-month-old rats randomly received 1.5% isoflurane or vehicle gas as control. Hippocampal BBB ultrastructure was analyzed by transmission electron microscopy and expression of tight junction proteins was measured by western blot analysis. BBB permeability was detected with sodium fluorescein extravasation and further confirmed by immunoglobulin G immunohistochemistry. Spatial learning and memory were assessed by the Morris water maze test. Isoflurane anesthesia resulted in reversible time-dependent BBB ultrastructure morphological damage and significant decreases in expression of the tight junction proteins occludin, which contributed to sodium fluorescein and IgG leakage. Rats with isoflurane exposure also showed significant cognitive deficits in the Morris water maze test. This in vivo data indicate that occludin down-regulation may be one of the mediators of isoflurane-induced hippocampus BBB disruption, and may contribute to hippocampus-dependent cognitive impairment after isoflurane exposure in aged rats. PMID:25524410

Cao, Yiyun; Ni, Cheng; Li, Zhengqian; Li, Lunxu; Liu, Yajie; Wang, Chunyi; Zhong, Yanfeng; Cui, Dehua; Guo, Xiangyang

2015-02-01

164

An HLA-A2-restricted tyrosinase antigen on melanoma cells results from posttranslational modification and suggests a novel pathway for processing of membrane proteins  

PubMed Central

T lymphocytes recognize antigens consisting of peptides presented by class I and II major histocompatibility complex (MHC) molecules. The peptides identified so far have been predictable from the amino acid sequences of proteins. We have identified the natural peptide target of a CTL clone that recognizes the tyrosinase gene product on melanoma cells. The peptide results from posttranslational conversion of asparagine to aspartic acid. This change is of central importance for peptide recognition by melanoma-specific T cells, but has no impact on peptide binding to the MHC molecule. This posttranslational modification has not been previously described for any MHC-associated peptide and represents the first demonstration of posttranslational modification of a naturally processed class I-associated peptide. This observation is relevant to the identification and prediction of potential peptide antigens. The most likely mechanism for production of this peptide leads to the suggestion that antigenic peptides can be derived from proteins that are translated into the endoplasmic reticulum. PMID:8627164

1996-01-01

165

Secondary structure and shape of plasma sex steroid-binding protein--comparison with domain G of laminin results in a structural model of plasma sex steroid-binding protein.  

PubMed

We have analyzed the secondary structure, shape and dimensions of plasma sex steroid-binding protein (SBP) by CD, size-exclusion chromatography and electron microscopy. CD spectra show extrema at 186 nm and 216 nm characteristic for beta-sheet structures. Analysis with different algorithms indicates 15% alpha-helix, 43% beta-sheet and 10-16% beta-turn structures. An irreversible structural change is observed upon heating above 60 degrees C, which correlates with the loss of steroid-binding activity. As the SBP sequence shows similarity with domains of several multidomain proteins, including laminins, we evaluated the structure of domain G of laminin-1. The CD spectrum shows extrema at 200 nm and 216 nm. Deconvolution results in 13% alpha-helix, 32% beta-sheet and 15% beta-turn structures. Steroid-binding assays indicate that laminin and fragments thereof have no activity. Size-exclusion chromatography reveals that SBP has an extended shape and can be modeled as a cylinder with a length and diameter of 23 nm and 3 nm, respectively. This shape and the dimensions are in agreement with the appearance on electron micrographs. We propose a model for the structure of SBP in which two monomers assemble head to head with the steroid-binding site located in the center of the rod-like particle. PMID:9249045

Beck, K; Gruber, T M; Ridgway, C C; Hughes, W; Sui, L; Pétra, P H

1997-07-01

166

Directed evolution of single-chain Fv for cytoplasmic expression using the ?-galactosidase complementation assay results in proteins highly susceptible to protease degradation and aggregation  

Microsoft Academic Search

BACKGROUND: Antibody fragments are molecules widely used for diagnosis and therapy. A large amount of protein is frequently required for such applications. New approaches using folding reporter enzymes have recently been proposed to increase soluble expression of foreign proteins in Escherichia coli. To date, these methods have only been used to screen for proteins with better folding properties but have

Pascal Philibert; Pierre Martineau

2004-01-01

167

Overexpression of the Gene Encoding the Multidrug Resistance-Associated Protein Results in Increased ATP-Dependent Glutathione S-Conjugate Transport  

NASA Astrophysics Data System (ADS)

The multidrug resistance-associated protein (MRP) is a 180- to 195-kDa glycoprotein associated with multidrug resistance of human tumor cells. MRP is mainly located in the plasma membrane and it confers resistance by exporting natural product drugs out of the cell. Here we demonstrate that overexpression of the MRP gene in human cancer cells increases the ATP-dependent glutathione S-conjugate carrier activity in plasma membrane vesicles isolated from these cells. The glutathione S-conjugate export carrier is known to mediate excretion of bivalent anionic conjugates from mammalian cells and is thought to play a role in the elimination of conjugated xenobiotics. Our results suggest that MRP can cause multidrug resistance by promoting the export of drug modification products from cells and they shed light on the reported link between drug resistance and cellular glutathione and glutathione S-transferase levels.

Muller, Michael; Meijer, Coby; Zaman, Guido J. R.; Borst, Piet; Scheper, Rik J.; Mulder, Nanno H.; de Vries, Elisabeth G. E.; Jansen, Peter L. M.

1994-12-01

168

Homozygosity for a partial deletion of apoprotein A-V signal peptide results in intracellular missorting of the protein and chylomicronemia in a breast-fed infant.  

PubMed

Deficiency of apoprotein A-V (apoA-V) can cause hypertriglyceridemia. In an 11 months old boy presenting with a severe hypertriglyceridemia, a formerly unknown 24 nucleotide deletion in exon 2 of the APOA5 gene was detected. The homozygous mutation results in an eight amino acid loss in the signal peptide sequence (c.16_39del; p.Ala6_Ala13del). Screening of control persons proved that this deletion is a rare mutation. Hypertriglyceridemia in the patient was only found at the time when he was breast fed, while after weaning, triglyceride levels were close to normal. Under both dietary conditions, apoA-V protein was undetectable in plasma while post-heparin plasma lipoprotein lipase activity was normal. Expression analysis of normal and mutated protein by Western blot and immunofluorescence in apoA-V deficient primary hepatocytes revealed that, due to changes in the signal peptide, mutated apoA-V was intracellularly missorted to lipid droplets and not secreted. Wild type apoA-V, instead, was not targeted to lipid droplets but transported via endosomal compartments to the plasma membrane for secretion. It is concluded that the c.16_39del mutation in the APOA5 gene leads to hepatic missorting and impaired secretion, which consequently results in undetectable apoA-V plasma levels. The absence of apoA-V in plasma leads under conditions of fat-rich diets to severe chylomicronemia, suggestive for a modulatory role of apoA-V for lipoprotein lipase mediated intravascular triglyceride lipolysis. PMID:24529129

Albers, Kirstin; Schlein, Christian; Wenner, Kirsten; Lohse, Peter; Bartelt, Alexander; Heeren, Joerg; Santer, René; Merkel, Martin

2014-03-01

169

Polyoxopalladates encapsulating 8-coordinated metal ions, [MO8Pd(II)12L8]n- (M = Sc3+, Mn2+, Fe3+, Co2+, Ni2+, Cu2+, Zn2+, Lu3+; L = PhAsO3(2-), PhPO3(2-), SeO3(2-)).  

PubMed

A total of 16 discrete polyoxopalladates(II) [MO(8)Pd(II)(12)L(8)](n-), with a metal ion M encapsulated in a cuboid-shaped {Pd(12)O(8)L(8)} cage, have been synthesized: the phenylarsonate-capped series (1) L = PhAsO(3)(2-), M = Sc(3+) (ScPhAs), Mn(2+) (MnPhAs), Fe(3+) (FePhAs), Co(2+) (CoPhAs), Ni(2+) (NiPhAs), Cu(2+) (CuPhAs), Zn(2+) (ZnPhAs); the phenylphosphonate-capped series: (2) L = PhPO(3)(2-), M = Cu(2+) (CuPhP), Zn(2+) (ZnPhP); and the selenite-capped series (3) L = SeO(3)(2-), M = Mn(2+) (MnSe), Fe(3+) (FeSe), Co(2+) (CoSe), Ni(2+) (NiSe), Cu(2+), (CuSe), Zn(2+) (ZnSe), Lu(3+) (LuSe)). The polyanions were prepared in one-pot reactions in aqueous solution of [Pd(3)(CH(3)COO)(6)] with an appropriate salt of the metal ion M, as well as PhAsO(3)H(2), PhPO(3)H(2), and SeO(2), respectively, and then isolated as hydrated sodium salts Na(n)[MO(8)Pd(II)(12)L(8)]·yH(2)O (y = 10-37). The compounds were characterized in the solid state by IR spectroscopy, single-crystal XRD, elemental and thermogravimetric analyses. The solution stability of the diamagnetic polyanions ScPhAs, ZnPhAs, ZnPhP, ZnSe, and LuSe was confirmed by multinuclear ((77)Se, (31)P, (13)C, and (1)H) NMR spectroscopy. The polyoxopalladates ScPhAs, MnPhAs, CoPhAs, and CuPhAs were investigated by electrospray ionization mass spectrometry (ESI-MS) and tandem mass spectrometry (MS/MS). Electrochemical studies on the manganese- and iron-containing derivatives demonstrated that the redox properties of the Mn(2+), Fe(3+), and Pd(2+) centers in the polyanions are strikingly influenced by the nature of the capping group. These results have subsequently been verified by density functional theory (DFT) calculations. Interestingly, electron paramagnetic resonance (EPR) measurements suggest that the coordination geometry around Mn(2+) is dynamically distorted on the EPR time scale (?10(-11) s), whereas it appears as a static ensemble with cubic symmetry on the X-ray diffraction (XRD) time-scale (10(-15) s). The octacoordinated Cu(2+) cuboid is similarly distorted, in good agreement with DFT calculations. Interestingly, g(?) is smaller than g(?), which is quite unusual, needing further theoretical development. PMID:23194400

Barsukova-Stuckart, Maria; Izarova, Natalya V; Barrett, Ryan A; Wang, Zhenxing; van Tol, Johan; Kroto, Harold W; Dalal, Naresh S; Jiménez-Lozano, Pablo; Carbó, Jorge J; Poblet, Josep M; von Gernler, Marc S; Drewello, Thomas; de Oliveira, Pedro; Keita, Bineta; Kortz, Ulrich

2012-12-17

170

Inhibition of Protein Geranylgeranylation Specifically Interferes with CD40-Dependent B Cell Activation, Resulting in a Reduced Capacity To Induce T Cell Immunity.  

PubMed

Ab-independent effector functions of B cells, such as Ag presentation and cytokine production, have been shown to play an important role in a variety of immune-mediated conditions such as autoimmune diseases, transplant rejection, and graft-versus-host disease. Most current immunosuppressive treatments target T cells, are relatively unspecific, and result in profound immunosuppression that places patients at an increased risk of developing severe infections and cancer. Therapeutic strategies, which interfere with B cell activation, could therefore be a useful addition to the current immunosuppressive armamentarium. Using a transcriptomic approach, we identified upregulation of genes that belong to the mevalonate pathway as a key molecular event following CD40-mediated activation of B cells. Inhibition of 3-hydroxy-3-methylglutaryl CoA reductase, the rate-limiting enzyme of the mevalonate pathway, by lipophilic statins such as simvastatin and atorvastatin resulted in a specific inhibition of B cell activation via CD40 and impaired their ability to act as stimulatory APCs for allospecific T cells. Mechanistically, the inhibitory effect resulted from the inhibition of protein geranylgeranylation subsequent to the depletion of mevalonate, the metabolic precursor for geranylgeranyl. Thus, inhibition of geranylgeranylation either directly through geranylgeranyl transferase inhibitors or indirectly through statins represents a promising therapeutic approach for the treatment of diseases in which Ag presentation by B cells plays a role. PMID:25311809

Shimabukuro-Vornhagen, Alexander; Zoghi, Shahram; Liebig, Tanja M; Wennhold, Kerstin; Chemitz, Jens; Draube, Andreas; Kochanek, Matthias; Blaschke, Florian; Pallasch, Christian; Holtick, Udo; Scheid, Christof; Theurich, Sebastian; Hallek, Michael; von Bergwelt-Baildon, Michael S

2014-11-15

171

Disruption of Fyn SH3 Domain Interaction with a Proline-Rich Motif in Liver Kinase B1 Results in Activation of AMP-Activated Protein Kinase  

PubMed Central

Fyn-deficient mice display increased AMP-activated Protein Kinase (AMPK) activity as a result of Fyn-dependent regulation of Liver Kinase B1 (LKB1) in skeletal muscle. Mutation of Fyn-specific tyrosine sites in LKB1 results in LKB1 export into the cytoplasm and increased AMPK activation site phosphorylation. This study characterizes the structural elements responsible for the physical interaction between Fyn and LKB1. Effects of point mutations in the Fyn SH2/SH3 domains and in the LKB1 proline-rich motif on 1) Fyn and LKB1 binding, 2) LKB1 subcellular localization and 3) AMPK phosphorylation were investigated in C2C12 muscle cells. Additionally, novel LKB1 proline-rich motif mimicking cell permeable peptides were generated to disrupt Fyn/LKB1 binding and investigate the consequences on AMPK activity in both C2C12 cells and mouse skeletal muscle. Mutation of either Fyn SH3 domain or the proline-rich motif of LKB1 resulted in the disruption of Fyn/LKB1 binding, re-localization of 70% of LKB1 signal in the cytoplasm and a 2-fold increase in AMPK phosphorylation. In vivo disruption of the Fyn/LKB1 interaction using LKB1 proline-rich motif mimicking cell permeable peptides recapitulated Fyn pharmacological inhibition. We have pinpointed the structural elements within Fyn and LKB1 that are responsible for their binding, demonstrating the functionality of this interaction in regulating AMPK activity. PMID:24586906

Yamada, Eijiro; Bastie, Claire C.

2014-01-01

172

Disruption of Fyn SH3 domain interaction with a proline-rich motif in liver kinase B1 results in activation of AMP-activated protein kinase.  

PubMed

Fyn-deficient mice display increased AMP-activated Protein Kinase (AMPK) activity as a result of Fyn-dependent regulation of Liver Kinase B1 (LKB1) in skeletal muscle. Mutation of Fyn-specific tyrosine sites in LKB1 results in LKB1 export into the cytoplasm and increased AMPK activation site phosphorylation. This study characterizes the structural elements responsible for the physical interaction between Fyn and LKB1. Effects of point mutations in the Fyn SH2/SH3 domains and in the LKB1 proline-rich motif on 1) Fyn and LKB1 binding, 2) LKB1 subcellular localization and 3) AMPK phosphorylation were investigated in C2C12 muscle cells. Additionally, novel LKB1 proline-rich motif mimicking cell permeable peptides were generated to disrupt Fyn/LKB1 binding and investigate the consequences on AMPK activity in both C2C12 cells and mouse skeletal muscle. Mutation of either Fyn SH3 domain or the proline-rich motif of LKB1 resulted in the disruption of Fyn/LKB1 binding, re-localization of 70% of LKB1 signal in the cytoplasm and a 2-fold increase in AMPK phosphorylation. In vivo disruption of the Fyn/LKB1 interaction using LKB1 proline-rich motif mimicking cell permeable peptides recapitulated Fyn pharmacological inhibition. We have pinpointed the structural elements within Fyn and LKB1 that are responsible for their binding, demonstrating the functionality of this interaction in regulating AMPK activity. PMID:24586906

Yamada, Eijiro; Bastie, Claire C

2014-01-01

173

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

PubMed

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

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

2015-01-28

174

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

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

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

2014-09-01

175

Toxicity of human adenovirus E4orf4 protein in Saccharomyces cerevisiae results from interactions with the Cdc55 regulatory B subunit of PP2A.  

PubMed

The E4orf4 protein of human adenovirus induces p53-independent apoptosis, a process that may promote cell death and viral spread. When expressed alone, E4orf4 kills transformed cells but not normal human cells. The only clear target of E4orf4 in mammalian cells is the Balpha (B55) subunit of protein phosphatase 2A (PP2A), a member of one of three classes of regulatory B subunits. Here we report the effects of E4orf4 in Saccharomyces cerevisiae, which encodes two PP2A regulatory B subunits, CDC55 and RTS1, that share homology with mammalian B and B' subunits, respectively. E4orf4 expression was found to be toxic in yeast, resulting in the accumulation of cells in G2/M phase that failed to grow upon removal of E4orf4. E4orf4-expressing yeast also displayed an elongated cell morphology similar to cdc55 deletion strains. E4orf4 required CDC55 to elicit its effect, whereas RTS1 was dispensable. The recruitment of the PP2A holoenzyme by E4orf4 was entirely dependent on Cdc55. These studies indicate that E4orf4-induced apoptosis in mammalian cells and cell death in yeast require functional interactions with B-type subunits of PP2A. However, some inhibition of growth by E4orf4 was observed in the cdc55 strain and with an E4orf4 mutant that fails to interact with Cdc55, indicating that E4orf4 may possess a second Cdc55-independent function affecting cell growth. PMID:11536041

Roopchand, D E; Lee, J M; Shahinian, S; Paquette, D; Bussey, H; Branton, P E

2001-08-30

176

Moderate Hypoxia Followed by Reoxygenation Results in Blood-Brain Barrier Breakdown via Oxidative Stress-Dependent Tight-Junction Protein Disruption  

PubMed Central

Re-canalization of cerebral vessels in ischemic stroke is pivotal to rescue dysfunctional brain areas that are exposed to moderate hypoxia within the penumbra from irreversible cell death. Goal of the present study was to evaluate the effect of moderate hypoxia followed by reoxygenation (MHR) on the evolution of reactive oxygen species (ROS) and blood-brain barrier (BBB) integrity in brain endothelial cells (BEC). BBB integrity was assessed in BEC in vitro and in microvessels of the guinea pig whole brain in situ preparation. Probes were exposed to MHR (2 hours 67-70 mmHg O2, 3 hours reoxygenation, BEC) or towards occlusion of the arteria cerebri media (MCAO) with or without subsequent reperfusion in the whole brain preparation. In vitro BBB integrity was evaluated using trans-endothelial electrical resistance (TEER) and transwell permeability assays. ROS in BEC were evaluated using 2?,7?-dichlorodihydrofluorescein diacetate (DCF), MitoSox and immunostaining for nitrotyrosine. Tight-junction protein (TJ) integrity in BEC, stainings for nitrotyrosine and FITC-albumin extravasation in the guinea pig brain preparation were assessed by confocal microscopy. Diphenyleneiodonium (DPI) was used to investigate NADPH oxidase dependent ROS evolution and its effect on BBB parameters in BEC. MHR impaired TJ proteins zonula occludens 1 (ZO-1) and claudin 5 (Cl5), decreased TEER, and significantly increased cytosolic ROS in BEC. These events were blocked by the NADPH oxidase inhibitor DPI. MCAO with or without subsequent reoxygenation resulted in extravasation of FITC-albumin and ROS generation in the penumbra region of the guinea pig brain preparation and confirmed BBB damage. BEC integrity may be impaired through ROS in MHR on the level of TJ and the BBB is also functionally impaired in moderate hypoxic conditions followed by reperfusion in a complex guinea pig brain preparation. These findings suggest that the BBB is susceptible towards MHR and that ROS play a key role in this process. PMID:24324834

Zehendner, Christoph M.; Librizzi, Laura; Hedrich, Jana; Bauer, Nina M.; Angamo, Eskedar A.; de Curtis, Marco; Luhmann, Heiko J.

2013-01-01

177

Perturbation of N-linked oligosaccharide structure results in an altered incorporation of (³H)palmitate into specific proteins in Chinese hamster ovary cells  

Microsoft Academic Search

Increased (³H)palmitate incorporation into specific cellular proteins has been reported to occur in Chinese hamster ovary and yeast mutant cells. In this paper we report studies concerning the relationship between N-linked oligosaccharide structure and (³H)palmitate incorporation into proteins of Chinese hamster ovary (CHO) cells. We have compared the incorporation of (³H)palmitate into proteins of wild-type and four different mutant CHO

R. B. Wellner; P. C. Ghosh; B. Roecklein; H. C. Wu

1987-01-01

178

Gene transfer of master autophagy regulator TFEB results in clearance of toxic protein and correction of hepatic disease in alpha-1-anti-trypsin deficiency.  

PubMed

Alpha-1-anti-trypsin deficiency is the most common genetic cause of liver disease in children and liver transplantation is currently the only available treatment. Enhancement of liver autophagy increases degradation of mutant, hepatotoxic alpha-1-anti-trypsin (ATZ). We investigated the therapeutic potential of liver-directed gene transfer of transcription factor EB (TFEB), a master gene that regulates lysosomal function and autophagy, in PiZ transgenic mice, recapitulating the human hepatic disease. Hepatocyte TFEB gene transfer resulted in dramatic reduction of hepatic ATZ, liver apoptosis and fibrosis, which are key features of alpha-1-anti-trypsin deficiency. Correction of the liver phenotype resulted from increased ATZ polymer degradation mediated by enhancement of autophagy flux and reduced ATZ monomer by decreased hepatic NF?B activation and IL-6 that drives ATZ gene expression. In conclusion, TFEB gene transfer is a novel strategy for treatment of liver disease of alpha-1-anti-trypsin deficiency. This study may pave the way towards applications of TFEB gene transfer for treatment of a wide spectrum of human disorders due to intracellular accumulation of toxic proteins. PMID:23381957

Pastore, Nunzia; Blomenkamp, Keith; Annunziata, Fabio; Piccolo, Pasquale; Mithbaokar, Pratibha; Maria Sepe, Rosa; Vetrini, Francesco; Palmer, Donna; Ng, Philip; Polishchuk, Elena; Iacobacci, Simona; Polishchuk, Roman; Teckman, Jeffrey; Ballabio, Andrea; Brunetti-Pierri, Nicola

2013-03-01

179

Suppression of telomere-binding protein TPP1 resulted in telomere dysfunction and enhanced radiation sensitivity in telomerase-negative osteosarcoma cell line.  

PubMed

Mammalian telomeres are protected by the shelterin complex that contains the six core proteins POT1, TPP1, TIN2, TRF1, TRF2 and RAP1. TPP1, formerly known as TINT1, PTOP, and PIP1, is a key factor that regulates telomerase recruitment and activity. In addition to this, TPP1 is required to mediate the shelterin assembly and stabilize telomere. Previous work has found that TPP1 expression was elevated in radioresistant cells and that overexpression of TPP1 led to radioresistance and telomere lengthening in telomerase-positive cells. However, the exact effects and mechanism of TPP1 on radiosensitivity are yet to be precisely defined in the ALT cells. Here we report on the phenotypes of the conditional deletion of TPP1 from the human osteosarcoma U2OS cells using ALT pathway to extend the telomeres.TPP1 deletion resulted in telomere shortening, increased apoptosis and radiation sensitivity enhancement. Together, our findings show that TPP1 plays a vital role in telomere maintenance and protection and establish an intimate relationship between TPP1, telomere and cellular response to ionizing radiation, but likely has the specific mechanism yet to be defined. PMID:24513288

Qiang, Weiguang; Wu, Qinqin; Zhou, Fuxiang; Xie, Conghua; Wu, Changping; Zhou, Yunfeng

2014-03-01

180

Perturbations in the spi1p GTPase cycle of Schizosaccharomyces pombe through its GTPase-activating protein and guanine nucleotide exchange factor components result in similar phenotypic consequences.  

PubMed Central

spi1p of Schizosaccharomyces pombe is a structural homolog of the mammalian GTPase Ran. The distribution between the GTP- and GDP-bound forms of the protein is regulated by evolutionarily conserved gene products, rna1p and pim1p, functioning as GTPase-activating protein (GAP) and guanine nucleotide exchange factor (GEF), respectively. Antibodies to spi1p, pim1p, and rna1p were generated and used to demonstrate that pim1p is exclusively nuclear, while rna1p is cytoplasmic. A loss of pim1p GEF activity or an increase in the rna1p GAP activity correlates with a change in the localization of the GTPase from predominantly nuclear to uniformly distributed, suggesting that the two forms are topologically segregated and that the nucleotide-bound state of spi1p may dictate its intracellular localization. We demonstrate that the phenotype of cells overproducing the GAP resembles the previously reported phenotype of mutants with alterations in the GEF: the cells are arrested in the cell cycle as septated, binucleated cells with highly condensed chromatin, fragmented nuclear envelopes, and abnormally wide septa. Consistent with the expectation that either an increased dosage of the GAP or a mutation in the GEF would lead to an increase of the spi1p-GDP/spi1p-GTP ratio relative to that of wild-type cells, overexpression of the GAP together with a mutation in the GEF is synthetically lethal. The similar phenotypic consequences of altering the functioning of the nuclear GEF or the cytoplasmic GAP suggest that there is a single pool of the spi1p GTPase that shuttles between the nucleus and the cytoplasm. Phenotypically, rna1 null mutants, in which spi1p-GTP would be expected to accumulate, resemble pim1(ts) and rna1p-overproducing cells, in which spi1p-GDP would be expected to accumulate. Taken together, these results support the hypothesis that the balance between the GDP- and GTP-bound forms of spi1p mediates the host of nuclear processes that are adversely affected when the functioning of different components of this system is perturbed in various organisms. PMID:8887664

Matynia, A; Dimitrov, K; Mueller, U; He, X; Sazer, S

1996-01-01

181

Sequential Extraction Results in Improved Proteome Profiling of Medicinal Plant Pinellia ternata Tubers, Which Contain Large Amounts of High-Abundance Proteins  

PubMed Central

Pinellia ternata tuber is one of the well-known Chinese traditional medicines. In order to understand the pharmacological properties of tuber proteins, it is necessary to perform proteome analysis of P. ternata tubers. However, a few high-abundance proteins (HAPs), mainly mannose-binding lectin (agglutinin), exist in aggregates of various sizes in the tubers and seriously interfere with proteome profiling by two-dimensional electrophoresis (2-DE). Therefore, selective depletion of these HAPs is a prerequisite for enhanced proteome analysis of P. ternata tubers. Based on differential protein solubility, we developed a novel protocol involving two sequential extractions for depletion of some HAPs and prefractionation of tuber proteins prior to 2-DE. The first extraction using 10% acetic acid selectively extracted acid-soluble HAPs and the second extraction using the SDS-containing buffer extracted remaining acid-insoluble proteins. After application of the protocol, 2-DE profiles of P. ternata tuber proteins were greatly improved and more protein spots were detected, especially low-abundance proteins. Moreover, the subunit composition of P. ternata lectin was analyzed by electrophoresis. Native lectin consists of two hydrogen-bonded subunits (11 kDa and 25 kDa) and the 11 kDa subunit was a glycoprotein. Subsequently, major HAPs in the tubers were analyzed by mass spectrometry, with nine protein spots being identified as lectin isoforms. The methodology was easy to perform and required no specialized apparatus. It would be useful for proteome analysis of other tuber plants of Araceae. PMID:23185632

An, SuFang; Gong, FangPing; Wang, Wei

2012-01-01

182

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

PubMed Central

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

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

183

Theory and experimental results of transfer NOE experiments. II. The influence of residual mobility and relaxation centers inside the protein on the size of transfer NOEs  

NASA Astrophysics Data System (ADS)

Experimental evidence is presented for a strong dependence of transfer NOE values on the Larmor frequency for certain residues of a peptide in its complex with a protein. This dependency has been explained by residual mobility in these residues of the peptide when bound. As a consequence, effective correlation times exist for some proton-proton pairs that are at least one order of magnitude smaller than expected for a rigid complex. This is shown to be the main reason for the failure to observe certain transfer NOEs in such a complex when studied at proton frequencies of 400 MHz or less. Another factor that can reduce the size of transfer NOES is the possibility of leakage of magnetization toward relaxation centers inside the protein. We have observed several intermolecular NOE cross peaks demonstrating such an intermolecular exchange of magnetization. The influence of cross relaxation to relaxation centers in the protein on the buildup and magnitude of proton transfer NOES for the bound and the free ligand is described in a model of the ligand-protein system that consists of a set of Bloch equations in which chemical exchange, transfer of magnetization, and relaxation sinks in the protein have been included. Simulations have been done for the cases of fast and intermediate exchange on the spin-lattice relaxation time scale while in all cases bound and free ligand signals were assumed to be in fast exchange on the chemical-shift scale. It is found that the magnitude of intramolecular transfer NOEs is reduced by the presence of cross relaxation from the peptide into the protein, in particular when the protein has relaxation centers such as methyl groups and aromatic rings. It is shown that these effects can reduce the size of transfer NOE effects by an order of magnitude for those ligand protons that are directly in contact with the protein. The simulations for ligand protein concentration ratios of 2, 10, and 100 with various numbers of relaxation sinks in the protein show that concentration ratios and mixing times must be optimized in order to observe sizeable transfer NOES in 2D NMR experiments. The influence of these effects on the accuracy of distances determined via transfer NOEs is also discussed.

Nirmala, N. R.; Lippens, G. M.; Hallenga, K.

184

Mapping gene ontology to proteins based on protein-protein interaction data  

Microsoft Academic Search

Motivation: Gene Ontology (GO) consortium provides structural description of protein function that is used as a common language for gene annotation in many organ- isms. Large-scale techniques have generated many valuable protein-protein interaction datasets that are useful for the study of protein function. Combining both GO and protein- protein interaction data allows the prediction of function for unknown proteins. Result:

Minghua Deng; Zhidong Tu; Fengzhu Sun; Ting Chen

2004-01-01

185

Rheumatoid factor and anti-citrullinated protein antibody positivity, but not level, are associated with increased mortality in patients with rheumatoid arthritis: results from two large independent cohorts.  

PubMed

IntroductionTo investigate rheumatoid factor (RF) and anti-citrullinated protein antibody (ACPA) status and levels as predictors of mortality in two large cohorts of patients with early inflammatory arthritis (EIA).MethodsData from the Norfolk Arthritis Register (NOAR) and Leiden Early Arthritis Clinic (EAC) cohorts were used. At baseline, patients had demographic data and smoking status recorded; RF, ACPA and inflammatory markers were measured in the local laboratories. Patients were flagged with national death registers until death or censor date. Antibody status was stratified as negative, low or high positive by RF and ACPA levels individually. In addition, patients were grouped as seronegative, RF positive, ACPA positive or double antibody (RF and ACPA) positive. Cox regression models explored associations between antibody status and mortality adjusting for age, sex, smoking status, inflammatory markers and year of enrolment.Results4962 (NOAR:3053, EAC:1909) patients were included, 64% were female. Median age at onset was 56 (NOAR) and 54 (EAC) years. 35% and 42% of patients were ACPA/RF positive in NOAR and EAC respectively. When antibody status was stratified as negative, low or high positive, there were no consistent findings between the two cohorts. Double antibody positivity was associated with excess mortality in both cohorts compared to seronegative patients: NOAR and EAC respective adjusted HR (95% CI): 1.35 (1.09-1.68) and 1.58 (1.16-2.15).ConclusionsPatients with EIA who are seropositive for both RF and ACPA have increased mortality compared to those who are single positive or seronegative. Antibody level in seropositive patients was not consistently associated with excess mortality. PMID:25471696

Humphreys, Jennifer H; van Nies, Jessica; Chipping, Jackie; Marshall, Tarnya; Mil, Annette; Symmons, Deborah; Verstappen, Suzanne

2014-12-01

186

Switching to recombinant factor IX Fc fusion protein prophylaxis results in fewer infusions, decreased factor IX consumption and lower bleeding rates.  

PubMed

In the phase 3 B-LONG [Recombinant Factor IX Fc Fusion Protein (rFIXFc) in Subjects with Haemophilia B] study, rFIXFc dosed every 1-2 weeks was safe and efficacious in previously treated subjects with haemophilia B. To date, there are no evaluations of transitioning from conventional to long-acting factor IX (FIX) prophylaxis. This post-hoc analysis of B-LONG subjects compared prophylaxis with other FIX products and rFIXFc. Pre- and on-study data were analysed to assess dosing regimen, weekly FIX consumption and annualized bleeding rates (ABRs). Population pharmacokinetics models were used to generate FIX activity profiles with rFIXFc and recombinant FIX prophylaxis. Thirty-nine subjects, previously treated prophylactically, were evaluated. Prior to study, most subjects (69·2%) received twice-weekly FIX infusions; on study, subjects infused rFIXFc once every 1-2 weeks with c. 30-50% reductions in weekly consumption. On-study estimated mean ABRs were lower than pre-study estimated mean ABRs. Models predicted that rFIXFc administered 50 iu/kg weekly and 100 iu/kg every 10 d would maintain steady-state FIX trough levels ?1 iu/dl in 95·4% and 89·2% of subjects, respectively. These results indicate that patients receiving rFIXFc prophylaxis can markedly reduce infusion frequency and FIX consumption, have a greater likelihood of maintaining FIX activity >1 iu/dl and experience fewer bleeding episodes compared with prior FIX prophylaxis. PMID:25209873

Powell, Jerry; Shapiro, Amy; Ragni, Margaret; Negrier, Claude; Windyga, Jerzy; Ozelo, Margareth; Pasi, John; Baker, Ross; Potts, James; Li, Shuanglian; Mei, Baisong; Pierce, Glenn F; Robinson, Brian

2015-01-01

187

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...

188

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

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

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

189

Mutations in the Type II Protein Arginine Methyltransferase AtPRMT5 Result in Pleiotropic Developmental Defects in Arabidopsis1[C][OA  

PubMed Central

Human PROTEIN ARGININE METHYLTRANSFERASE5 (PRMT5) encodes a type II protein arginine (Arg) methyltransferase and its homologs in animals and yeast (Saccharomyces cerevisiae and Schizosaccharomyces pombe) are known to regulate RNA processing, signal transduction, and gene expression. However, PRMT5 homologs in higher plants have not yet been reported and the biological roles of these proteins in plant development remain elusive. Here, using conventional biochemical approaches, we purified a plant histone Arg methyltransferase from cauliflower (Brassica oleracea) that was nearly identical to AtPRMT5, an Arabidopsis (Arabidopsis thaliana) homolog of human PRMT5. AtPRMT5 methylated histone H4, H2A, and myelin basic protein in vitro. Western blot using symmetric dimethyl histone H4 Arg 3-specific antibody and thin-layer chromatography analysis demonstrated that AtPRMT5 is a type II enzyme. Mutations in AtPRMT5 caused pleiotropic developmental defects, including growth retardation, dark green and curled leaves, and FlOWERING LOCUS C (FLC)-dependent delayed flowering. Therefore, the type II protein Arg methyltransferase AtPRMT5 is involved in promotion of vegetative growth and FLC-dependent flowering time regulation in Arabidopsis. PMID:17573539

Pei, Yanxi; Niu, Lifang; Lu, Falong; Liu, Chunyan; Zhai, Jixian; Kong, Xiangfeng; Cao, Xiaofeng

2007-01-01

190

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

NASA Astrophysics Data System (ADS)

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) Å, V=3317(2) Å3, 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.

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

2013-08-01

191

Estimation of local cerebral protein synthesis rates with L-[1-11C]leucine and PET: methods, model, and results in animals and humans.  

PubMed

We have estimated the cerebral protein synthesis rates (CPSR) in a series of normal human volunteers and monkeys using L-[1-11C]leucine and positron emission tomography (PET) using a three-compartment model. The model structure, consisting of a tissue precursor, metabolite, and protein compartment, was validated with biochemical assay data obtained in rat studies. The CPSR values estimated in human hemispheres of about 0.5 nmol/min/g agree well with hemispheric estimates in monkeys. The sampling requirements (input function and scanning sequence) for accurate estimates of model parameters were investigated in a series of computer simulation studies. PMID:2786885

Hawkins, R A; Huang, S C; Barrio, J R; Keen, R E; Feng, D; Mazziotta, J C; Phelps, M E

1989-08-01

192

A single amino acid substitution in the hemagglutinin-neuraminidase protein of Newcastle disease virus results in increased fusion and decreased neuraminidase activities without changes in virus pathotype  

Technology Transfer Automated Retrieval System (TEKTRAN)

Newcastle disease virus (NDV) attachment to the host cell is mediated by the hemagglutinin-neuraminidase (HN), a multifunctional protein that has receptor recognition, neuraminidase and fusion promotion activities. The process that correlates receptor binding and fusion triggering is poorly understo...

193

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...

194

Fetal Wastage Syndrome due to Blood Protein\\/Platelet Defects: Results of Prevalence Studies and Treatment Outcome with Low-Dose Heparin and Low-Dose Aspirin  

Microsoft Academic Search

Fetal wastage syndrome is characterized by recurrent spontaneous abortion. Many syndromes are associated with recurrent fetal loss, including anatomical anomalies, endocrine\\/hormonal abnormalities, and coagulation defects, with coagulation defects accounting for ?30% of cases. Most procoagulant factor defects are due to inadequate fibrin-mediated implantation of the fertilized ovum into the decidua. However, blood protein\\/ platelet defects leading to hypercoagulability and thrombosis

Rodger L. Bick; H. Robert Laughlin; Brian M. Cohen; A. Jay Staub; James Madden; Ali Toofanian

1995-01-01

195

A serine-to-threonine substitution in the triazine herbicide-binding protein in potato cells results in atrazine resistance without impairing productivity.  

PubMed Central

A mutation of the psbA gene was identified in photoautotrophic potato (Solanum tuberosum L. cv Superior x U.S. Department of Agriculture line 66-142) cells selected for resistance to 6-chloro-N-ethyl-N'-(1-methylethyl)-1,3,5-triazine-2,4-diamine (atrazine). Photoaffinity labeling with 6-azido-N-ethyl-N'-(1-methylethyl)-1,3,5-triazine-2,4-diamine detected a thylakoid membrane protein with a M(r) of 32,000 in susceptible, but not in resistant, cells. This protein was identified as the secondary quinone acceptor of photosystem II (QB) protein. Atrazine resistance in selected cells was attributable to a mutation from AGT (serine) to ACT (threonine) in codon 264 of the psbA gene that encodes the QB protein. Although the mutant cells exhibited extreme levels of resistance to atrazine, no concomitant reductions in photosynthetic electron transport or cell growth rates compared to the unselected cells were detected. This is in contrast with the losses in productivity observed in atrazine-resistant mutants that contain a glycine-264 alteration. PMID:8022941

Smeda, R J; Hasegawa, P M; Goldsbrough, P B; Singh, N K; Weller, S C

1993-01-01

196

Conformational search of Proteins and Protein Loops  

E-print Network

. As discussed before the helix 3 (which corresponds to ?5 in holo proteins) is comparatively disrupted and similar results were observed during the MD simulations of Storch and Daggett. 23 During their MD simulations they observed that the helix ? 3 (69... movement of the N and C termini thereby resulting in closer contacts with protein core. Table 3.9: RMSD of helices for all apocytochrome proteins Proteins Helix 1 8 –13 (Å) Helix 2 32 – 36 (Å) Helix 3 69...

Venkataramani, Ranjitha

2008-02-26

197

Novel ENU-Induced Point Mutation in Scavenger Receptor Class B, Member 1, Results in Liver Specific Loss of SCARB1 Protein  

PubMed Central

Cardiovascular disease (CVD) is the largest cause of premature death in human populations throughout the world. Circulating plasma lipid levels, specifically high levels of LDL or low levels of HDL, are predictive of susceptibility to CVD. The scavenger receptor class B member 1 (SCARB1) is the primary receptor for the selective uptake of HDL cholesterol by liver and steroidogenic tissues. Hepatic SCARB1 influences plasma HDL-cholesterol levels and is vital for reverse cholesterol transport. Here we describe the mapping of a novel N-ethyl-N-nitrosourea (ENU) induced point mutation in the Scarb1 gene identified in a C57BL/6J background. The mutation is located in a highly conserved amino acid in the extracellular loop and leads to the conversion of an isoleucine to an asparagine (I179N). Homozygous mutant mice express normal Scarb1 mRNA levels and are fertile. SCARB1 protein levels are markedly reduced in liver (?90%), but not in steroidogenic tissues. This leads to ?70% increased plasma HDL levels due to reduced HDL cholesteryl ester selective uptake. Pdzk1 knockout mice have liver-specific reduction of SCARB1 protein as does this mutant; however, in vitro analysis of the mutation indicates that the regulation of SCARB1 protein in this mutant is independent of PDZK1. This new Scarb1 model may help further our understanding of post-translational and tissue-specific regulation of SCARB1 that may aid the important clinical goal of raising functional HDL. PMID:19654867

Stylianou, Ioannis M.; Svenson, Karen L.; VanOrman, Sara K.; Langle, Yanina; Millar, John S.; Paigen, Beverly; Rader, Daniel J.

2009-01-01

198

Differences in biological activity and structural protein VP1 phosphorylation of polyomavirus progeny resulting from infection of primary mouse kidney and primary mouse embryo cell cultures.  

PubMed Central

Both primary mouse kidney and primary mouse embryo cells in culture were used for polyomavirus progeny production. Examination of polyomavirus virion structural integrity revealed that mouse embryo cell progeny contained a threefold greater population of unstable particles when compared with mouse kidney cell progeny. Differences in biological activity between these two progeny virion types were also shown. Mouse kidney cell progeny compared with mouse embryo cell progeny exhibited a 10-fold greater ability to agglutinate guinea pig erythrocytes, a 3-fold lower ability to become internalized into monopinocytotic vesicles, and a 2-fold lower ability to initiate a productive infection based on positive nuclear immunofluorescence when mouse embryo host cell cultures were used. The mouse kidney progeny were also found to bind to host cells less specifically than the mouse embryo cell progeny. When these two progeny virion types were labeled in vivo with 32P and subjected to isoelectric focusing followed by sodium dodecyl sulfate-polyacrylamide gel electrophroesis in the second dimension, differences in the phosphorylation pattern of the major virus-encoded structural protein VP1 species were observed. It was revealed that species D and E of mouse kidney cell progeny were phosphorylated to the same degree, while mouse embryo cell progeny species E and F were phosphorylated equally. These data suggest that the host cells play a role in modulating the biological activity of the virus by affecting the degree and site-specific phosphorylation of the major capsid protein VP1 which may influence the recognition of virus attachment proteins for specific cellular receptors. Images PMID:3027379

Ludlow, J W; Consigli, R A

1987-01-01

199

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

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.

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

2014-09-15

200

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

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.

Dinh, Phat X.; Panda, Debasis; Das, Phani B.; Das, Subash C.; Das, Anshuman [School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska 68583-0900 (United States) [School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska 68583-0900 (United States); The Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, Nebraska 68583-0900 (United States); Pattnaik, Asit K., E-mail: apattnaik2@unl.edu [School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska 68583-0900 (United States); The Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, Nebraska 68583-0900 (United States)

2012-10-25

201

Probing local environments of tryptophan residues in proteins: comparison of 19F nuclear magnetic resonance results with the intrinsic fluorescence of soluble human tissue factor.  

PubMed

19F nuclear magnetic resonance (19F NMR) of 5-fluorotryptophan (5F-Trp) and tryptophan (Trp) fluorescence both provide information about local environment and solvent exposure of Trp residues. To compare the information provided by these spectroscopies, the four Trp residues in recombinant soluble human tissue factor (sTF) were replaced with 5F-Trp. 19F NMR assignments for the 5F-Trp residues (14, 25, 45, and 158) were based on comparison of the wild-type protein spectrum with the spectra of three single Trp-to-Phe replacement mutants. Previously we showed from fluorescence and absorption difference spectra of mutant versus wild-type sTF that the side chains of Trpl4 and Trp25 are buried, whereas those of Trp45 and Trp158 are partially exposed to bulk solvent (Hasselbacher et al., Biophys J 1995;69:20-29). 19F NMR paramagnetic broadening and solvent-induced isotope-shift experiments show that position 5 of the indole ring of 5F-Trp158 is exposed, whereas that of 5F-Trp45 is essentially inaccessible. Although 5F-Trp incorporation had no discernable effect on the procoagulant cofactor activity of either the wild-type or mutant proteins, 19F NMR chemical shifts showed that the single-Trp mutations are accompanied by subtle changes in the local environments of 5F-Trp residues residing in the same structural domain. PMID:10651284

Zemsky, J; Rusinova, E; Nemerson, Y; Luck, L A; Ross, J B

1999-12-01

202

Enterovirus 71 VP1 Activates Calmodulin-Dependent Protein Kinase II and Results in the Rearrangement of Vimentin in Human Astrocyte Cells  

PubMed Central

Enterovirus 71 (EV71) is one of the main causative agents of foot, hand and mouth disease. Its infection usually causes severe central nervous system diseases and complications in infected infants and young children. In the present study, we demonstrated that EV71 infection caused the rearrangement of vimentin in human astrocytoma cells. The rearranged vimentin, together with various EV71 components, formed aggresomes-like structures in the perinuclear region. Electron microscopy and viral RNA labeling indicated that the aggresomes were virus replication sites since most of the EV71 particles and the newly synthesized viral RNA were concentrated here. Further analysis revealed that the vimentin in the virus factories was serine-82 phosphorylated. More importantly, EV71 VP1 protein is responsible for the activation of calmodulin-dependent protein kinase II (CaMK-II) which phosphorylated the N-terminal domain of vimentin on serine 82. Phosphorylation of vimentin and the formation of aggresomes were required for the replication of EV71 since the latter was decreased markedly after phosphorylation was blocked by KN93, a CaMK-II inhibitor. Thus, as one of the consequences of CaMK-II activation, vimentin phosphorylation and rearrangement may support virus replication by playing a structural role for the formation of the replication factories. Collectively, this study identified the replication centers of EV71 in human astrocyte cells. This may help us understand the replication mechanism and pathogenesis of EV71 in human. PMID:24073199

Haolong, Cong; Du, Ning; Hongchao, Tian; Yang, Yang; Wei, Zhang; Hua, Zhang; Wenliang, Zhang; Lei, Song; Po, Tien

2013-01-01

203

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

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

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

2011-01-01

204

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)

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) Å, b=11.052(2) Å, c=10.666(2) Å and ?=93.897(3)°), P1bar (a=7.051(2) Å, b=7.198(2) Å, c=8.314(2) Å, ?=107.897(3)°, ?=102.687(3)° and ?=100.564(3)°) and C2/c (a=17.862(4) Å, b=6.931(1) Å, c=20.133(4) Å 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.

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

2013-10-01

205

A single amino acid substitution in the haemagglutinin-neuraminidase protein of Newcastle disease virus results in increased fusion promotion and decreased neuraminidase activities without changes in virus pathotype.  

PubMed

Attachment of Newcastle disease virus (NDV) to the host cell is mediated by the haemagglutinin-neuraminidase (HN), a multifunctional protein that has receptor recognition, neuraminidase (NA) and fusion promotion activities. The process that connects receptor binding and fusion triggering is poorly understood and amino acid residues important for the functions of the protein remain to be fully determined. During the process of generating an infectious clone of the Anhinga strain of NDV, we were able to rescue a NDV with highly increased fusogenic activity in vitro and decreased haemagglutinating activity, as compared with the wild-type parental strain. Sequencing of this recombinant virus showed a single mutation at amino acid position 192 of the HN protein (Ile?Met). In the present study, we characterized that single amino acid substitution (I192M) in three strains of NDV by assessing the NA activity and fusogenic potential of the mutated versus wild-type proteins in cell cultures. The original recombinant NDV harbouring the mutation in the HN gene was also used to characterize the phenotype of the virus in cell cultures, embryonated chicken eggs and day-old chickens. Mutation I192M results in low NA activity and highly increased cell fusion in vitro, without changes in the viral pathotype of recombinant viruses harbouring the mutation in vivo. The results obtained suggest that multiple regions of the HN-protein globular head are important for fusion promotion, and that wild-type levels of NA activity are not absolutely required for viral infection. PMID:21123551

Estevez, Carlos; King, Daniel J; Luo, Ming; Yu, Qingzhong

2011-03-01

206

Osteoprotegerin in relation to body weight, lipid parameters insulin sensitivity, adipocytokines, and C-reactive protein in obese and non-obese young individuals: results from both cross-sectional and interventional study  

Microsoft Academic Search

Objective: We analyzed the relation of osteoprotegerin (OPG) with insulin sensitivity, lipid profile, serum glutamic pyruvic transaminase (SGPT), adipocytokines, and C-reactive protein (CRP) in obese and non-obese subjects. Methods: In the study, 170 subjects (106 obese and 64 non-obese, sex ratio female\\/maleZ2.03) were included. Thirty-two obese subjects were reevaluated 6 months after the weight loss induced by bariatric surgery. Results:

M.-H. Gannage-Yared; Cesar Yaghi; Bassem Habre; Simon Khalife; Roger Noun; Myrna Germanos-Haddad; Viviane Trak-Smayra

2008-01-01

207

Reduced glutathione disrupts the intracellular trafficking of tyrosinase and tyrosinase-related protein-1 but not dopachrome tautomerase and Pmel17 to melanosomes, which results in the attenuation of melanization.  

PubMed

We previously reported that treatment of B16 melanotic melanoma cells with reduced glutathione (GSH) converts them to amelanotic cells without any significant down-regulation of tyrosinase activity. To characterize the cellular mechanism(s) involved, we determined the intracellular distribution of melanocyte-specific proteins, especially in melanin synthesis-specific organelles, termed melanosomes by subcellular fractionation followed by Western blotting and confocal laser microscopy (CFLM). In the melanosome-rich large granule fraction and in highly purified melanosome fractions, while GSH-induced amelanotic B16 cells have significantly diminished levels of protein/activity of tyrosinase and tyrosinase-related protein-1 compared with control melanized B16 cells, there was substantially no difference in the distribution and levels of dopachrome tautomerase and the processed isoform of Pmel17 (HMB45) between control melanized and GSH-induced amelanotic B16 cells. Analysis of merged images obtained by CFLM revealed that whereas tyrosinase, Pmel17 and dopachrome tautomerase colocalize with each other in the control melanized B16 cells, tyrosinase does not colocalize with Pmel17 or its processed isoform and with dopachrome tautomerase in GSH-induced amelanotic B16 cells. The sum of these findings suggests that reduced glutathione selectively disrupts the intracellular trafficking of tyrosinase and tyrosinase-related protein-1 but not dopachrome tautomerase and Pmel17 to melanosomes, which results in the attenuation of melanization, probably serving as a putative model for oculocutaneous albinism type 4. PMID:23764898

Nakajima, Hiroaki; Nagata, Takeshi; Koga, Shihiro; Imokawa, Genji

2014-01-01

208

Mobility of photosynthetic proteins.  

PubMed

The mobility of photosynthetic proteins represents an important factor that affects light-energy conversion in photosynthesis. The specific feature of photosynthetic proteins mobility can be currently measured in vivo using advanced microscopic methods, such as fluorescence recovery after photobleaching which allows the direct observation of photosynthetic proteins mobility on a single cell level. The heterogeneous organization of thylakoid membrane proteins results in heterogeneity in protein mobility. The thylakoid membrane contains both, protein-crowded compartments with immobile proteins and fluid areas (less crowded by proteins), allowing restricted diffusion of proteins. This heterogeneity represents an optimal balance as protein crowding is necessary for efficient light-energy conversion, and protein mobility plays an important role in the regulation of photosynthesis. The mobility is required for an optimal light-harvesting process (e.g., during state transitions), and also for transport of proteins during their synthesis or repair. Protein crowding is then a key limiting factor of thylakoid membrane protein mobility; the less thylakoid membranes are crowded by proteins, the higher protein mobility is observed. Mobility of photosynthetic proteins outside the thylakoid membrane (lumen and stroma/cytosol) is less understood. Cyanobacterial phycobilisomes attached to the stromal side of the thylakoid can move relatively fast. Therefore, it seems that stroma with their active enzymes of the Calvin-Benson cycle, are a more fluid compartment in comparison to the rather rigid thylakoid lumen. In conclusion, photosynthetic protein diffusion is generally slower in comparison to similarly sized proteins from other eukaryotic membranes or organelles. Mobility of photosynthetic proteins resembles restricted protein diffusion in bacteria, and has been rationalized by high protein crowding similar to that of thylakoids. PMID:23955784

Ka?a, Radek

2013-10-01

209

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 ...

210

[The results of application of the rapid quantitative assay for fatty acid-binding protein at the onset of acute coronary syndrome].  

PubMed

Fatty acid-binding protein (FABP) appearing in blood within a few hours of acute coronary syndrome (ACS) is a marker of myocardial necrosis. We estimated the diagnostic value of rapid immunochromatographic test for FABP in patients with ACS and compared it with other cardiomarkers: troponin 1 (Tn1), myoglobin and creatin phosphokinase-MB (CPK-MB). The study included 100 patients aged 61.3 +/- 12.9 yr hospitalized with ACS within 2 hr after beginning of anginous pain. FABP was detected by CardioFABP test, Tn1, myoglobin and CPK-MB by quantitative assays. Blood samples were taken 2, 6, and 24 hr after the onset of anginous pain. Acute myocardial infarction was diagnosed in 79 patients, unstable angina in 9, FC 3-4 angina of effort in 4, vasospastic angina in 1, non-coronary pathology in 7. Sensitivity of FABP, Tn1, myoglobin and CPK-MB 2 hr after onset of pain was 84.8; 34.2, 65.8; 22.8% respectively: it was 98.7: 92.4; 96.2; 82.3% in 6 hr and 56; 100; n/d; 86.7% in 24 hr. Specificity of FABP was 100% in all time intervals. It is concluded that FABP level determined by rapid qualitative assay within 2-6 hr after onset of ACS is a more sensitive cardiomarker than Tn1, myoglobin and CPK-MB for diagnostics of ACS. PMID:23659068

Kalinchenko, R M; Kopylov, F Iu; Syrkin, A L; Gitel', E P; Novikova, O V

2013-01-01

211

[Bilateral corneal ulceration as a result of caloric-protein malnutrition and vitamin A deficit in a patient with chronic alcoholism, chronic pancreatitis and cholecystostomy].  

PubMed

Since the discovery of vitamins, there has been an increasing interest at relating vitamins with particular diseases. In particular, for vitamin A its singular importance has been determined in multiple vital functions, and its relationship with diseases, both in deficit and in excess, is nowadays completely demonstrated. In developed countries, vitamin deficiency-related diseases have been greatly reduced; however, in some patients with particular features they must be kept in mind. This is the case of a 45 year-old man, with a history of chronic alcoholism, non insulin-dependent diabetes meIlitus and cholecystectomy with a high biliary drainage secondary to emphysematous cholecystitis and perivesicular abscess. He complains of bilateral ocular pain, photophobia, and decreased visual acuity besides a history of pasty, sticky and foul-smelling feces. He is admitted in the Ophthalmology Department and bilateral corneal ulceration is diagnosed. A consultation to the Nutrition Department is made because of cachexia. Severe caloric and mil protein hyponutrition is observed with a BMI of 18.2 and a 23% weight loss for the last 6 months, fat-soluble vitamins (A, D and E) deficit, mild fat malabsorption, and macrocytic and hypochromic anemia. The patient's diet is supplemented with a special hyperproteinic and hypercaloric diet for diabetics, deficient vitamins and pancreatic enzymes to improve absorption are administered, and glycemia is controlled with insulin. Four months later, the patient is assessed and has a BMI of 20, anemia has resolved and from an ophthalmologic viewpoint the course is favorable, the ulcers improve and visual acuity is almost completely recovered. In chronic alcoholic patients with a low dietary intake and clinical complications with nutritional repercussions (pancreatitis that produces malabsorption or cholecystectomy with biliary percutaneous drainage) we should not forget that micronutrients deficits may explain the etiology of other associated diseases, in the present case corneal ulceration. PMID:16045134

Benítez Cruz, S; Gómez Candela, C; Ruiz Martín, M; Cos Blanco, A I

2005-01-01

212

Vaccination with the Chlamydia trachomatis Major Outer Membrane Protein Can Elicit an Immune Response as Protective as That Resulting from Inoculation with Live Bacteria  

PubMed Central

BALB/c mice were vaccinated by the intramuscular (i.m.) and subcutaneous (s.c.) routes with a native preparation of the Chlamydia trachomatis mouse pneumonitis (MoPn) major outer membrane protein (MOMP), using Montanide ISA 720 and CpG-1826 as adjuvants. A negative control group was immunized with ovalbumin and the two adjuvants, and a positive control group was immunized intranasally (i.n.) with 104 inclusion-forming units (IFU) of C. trachomatis. Four weeks after the last i.m.-plus-s.c. immunization, mice were challenged in the ovarian bursa with 105 IFU of C. trachomatis MoPn. Six weeks after the genital challenge, animals were mated, and the pregnancies were monitored. After vaccination with MOMP, the mice developed strong Chlamydia-specific humoral and cellular immune responses. Following the genital challenge, of the mice vaccinated with the MOMP, only 15% (3/20) had positive vaginal cultures, while 85% (17/20) of the animals immunized with ovalbumin had positive cultures over the 6 weeks of observation (P < 0.05). Also, only 14% (3/21) of the animals inoculated i.n. with Chlamydia had positive vaginal cultures. After mating, 75% (15/20) of the mice vaccinated with MOMP carried embryos in both uterine horns. Of the animals vaccinated i.n. with the Chlamydia, 81% (17/21) had embryos in both uterine horns (P > 0.05). In contrast, only 10% (2/20) of the mice immunized with ovalbumin had embryos in both uterine horns (P < 0.05). In conclusion, immunization with a purified preparation of the MOMP is as effective as vaccination with viable C. trachomatis in eliciting a protective immune response against a genital challenge in mice. PMID:16299310

Pal, Sukumar; Peterson, Ellena M.; de la Maza, Luis M.

2005-01-01

213

Mutation in the matrix protein of Newcastle disease virus can result in decreased fusion glycoprotein incorporation into particles and decreased infectivity.  

PubMed Central

Virus particles produced in eggs by the group D ts mutants of Newcastle disease virus at permissive temperature display low infectious and hemolytic activities (M.E. Peeples and M. A. Bratt , J. Virol. 42:440-446, 1982). These lower activities correlate with a decreased incorporation of F1+2 (fusion glycoprotein) into virus particles, compared with that for wild type. The incorporation of F1+2 into virus particles of the group D mutants is also lower than that for wild type when grown in chicken embryo cells in culture at either permissive or nonpermissive temperature. The infectivity of virions from these mutants correlates with the amounts of F1+2 in the virus particles, below a certain concentration, indicating that the quantity of F1+2 in virus particles is a determining factor in the infectivity of those particles. In addition, one of these mutants, D1, produces an M (matrix protein) which migrates at a faster rate in sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Three of four revertants of D1 have coreverted to wild-type M electrophoretic mobility, associating M with the ts lesion and the other observed phenotypes. In each of these revertants, as well as in three revertants each from D2 and D3, there has been coreversion from the low specific infectious and hemolytic activities to greater, and often wild-type, activities. There is also a coreversion for F1+2 incorporation into virions. All of the revertants incorporate F1+2 into virions more efficiently than their mutant parents. The coreversions associate those phenotypes with the ts lesion and, in the case of D1, with the M lesion as well. Images PMID:6547186

Peeples, M E; Bratt, M A

1984-01-01

214

Consensus design of repeat proteins.  

PubMed

Consensus design is a valuable protein-engineering method that is based on statistical information derived from sequence alignments of homologous proteins. Recently, consensus design was adapted to repeat proteins. We discuss the potential of this novel repeat-based approach for the design of consensus repeat proteins and repeat protein libraries and summarize recent results from such experiments. PMID:14760739

Forrer, Patrik; Binz, H Kaspar; Stumpp, Michael T; Plückthun, Andreas

2004-02-01

215

Predicting Protein Phenotypes Based on Protein-Protein Interaction Network  

PubMed Central

Background Identifying associated phenotypes of proteins is a challenge of the modern genetics since the multifactorial trait often results from contributions of many proteins. Besides the high-through phenotype assays, the computational methods are alternative ways to identify the phenotypes of proteins. Methodology/Principal Findings Here, we proposed a new method for predicting protein phenotypes in yeast based on protein-protein interaction network. Instead of only the most likely phenotype, a series of possible phenotypes for the query protein were generated and ranked acording to the tethering potential score. As a result, the first order prediction accuracy of our method achieved 65.4% evaluated by Jackknife test of 1,267 proteins in budding yeast, much higher than the success rate (15.4%) of a random guess. And the likelihood of the first 3 predicted phenotypes including all the real phenotypes of the proteins was 70.6%. Conclusions/Significance The candidate phenotypes predicted by our method provided useful clues for the further validation. In addition, the method can be easily applied to the prediction of protein associated phenotypes in other organisms. PMID:21423698

Liu, Xiao-Jun; Cai, Yu-Dong

2011-01-01

216

Protein Analysis  

NSDL National Science Digital Library

This workbook allows the analysis of sample or imported protein sequences. The model can analyze protein sequences up to 500 amino acids long. The program analyzes five aspects of the protein sequence: the highest potential charge along the protein sequence, the amino acid composition of the protein sequence, the isoelectric point of the protein sequence at varying pHs, the hydrophobicity to predict surface and membrane spanning regions of the protein sequence and the protein structure using the Chau and Fassman algorithm.

John Jungck (Beloit College; Biology)

2007-05-22

217

Inherent limitations in protein-protein docking procedures  

Microsoft Academic Search

Motivation: The limited success rate of protein-protein docking procedures is generally attributed to structure differences between the bound and unbound states of the molecules. Herein we analyze a large dataset of protein-protein docking results and identify addi- tional parameters that affect the performance of docking procedures. Results: We find that the distinction between nearly correct models and decoys depends on

Noga Kowalsman; Miriam Eisenstein

2007-01-01

218

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

SciTech Connect

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.

Congiu, A.M.; Casu, S.; Ugazio, G. (Istituto di Genetica (Italy))

1989-10-01

219

Protein Crystallization  

NASA Technical Reports Server (NTRS)

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.

Chernov, Alexander A.

2005-01-01

220

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

PubMed

Abstract 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

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

2013-09-11

221

Protein Condensation  

NASA Astrophysics Data System (ADS)

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.

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

2007-09-01

222

Protein Condensation  

NASA Astrophysics Data System (ADS)

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.

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

2014-07-01

223

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. ...

224

RNA interference-based (RNAi) suppression of AtMPK6, an Arabidopsis mitogen-activated protein kinase, results in hypersensitivity to ozone and misregulation of AtMPK3.  

PubMed

The recent increase in tropospheric ozone (O(3)) concentrations promotes additional oxidative stress through the production of reactive oxygen species (ROS) in plant tissues, resulting in the activation of genes whose products enable the stressed cells to retain their integrity and function. This response is made possible by an integration of highly regulated signaling networks that mediate the perception of, and response to, this oxidative assault. In Arabidopsis thaliana, ROS-induced signaling has been shown to flow through a protein phosphorylation cascade involving the mitogen-activated protein kinases (MAPKs) AtMPK3 (MPK3) and AtMPK6 (MPK6). We found that RNAi-mediated silencing of MPK6 renders the plant more sensitive to ozone, as determined by visible leaf damage. The MPK6-RNAi genotype also displayed a more intense and prolonged activation of MPK3 compared to that of WT plants. An MPK3 loss-of-function genotype is similarly very sensitive to ozone, and displays an abnormally prolonged MPK6 activation profile, suggesting reciprocity in regulation between these two MAPKs. PMID:15964670

Miles, Godfrey P; Samuel, Marcus A; Zhang, Yuelin; Ellis, Brian E

2005-11-01

225

Effects of lactulose and lactitol on protein digestion and metabolism in conventional and germ free animal models: relevance of the results to their use in the treatment of portosystemic encephalopathy.  

PubMed Central

Protein digestion and metabolism have been studied in laboratory rats and miniature pigs to investigate the mechanisms of action of lactulose and lactitol when used in the treatment of patients with portosystemic encephalopathy. Lactulose (beta-D-galactopyranosyl-(1----4)-beta-D-fructofuranose) and lactitol (beta-D-galactopyranosyl-(1----4)-D-glucitol) increased the excretion of nitrogenous material in the faeces and decreased nitrogen excretion in the urine in a similar degree to that reported for human patients. In studies with germ free rats given lactulose no such effect was observed, suggesting that, for lactulose at least, these effects are mediated by the gut flora. Measurement of the alpha-, epsilon-diaminopimelic acid content of the faeces confirmed that the enhancement of faecal nitrogen was due to an increased contribution from bacteria. The similarity in the results for lactulose and lactitol suggests that, from the perspective of protein metabolism, lactitol acts in a similar way to lactulose in the treatment of portosystemic encephalopathy. PMID:2265782

Bird, S P; Hewitt, D; Ratcliffe, B; Gurr, M I

1990-01-01

226

Functional clustering of yeast proteins from the protein-protein interaction network  

Microsoft Academic Search

BACKGROUND: The abundant data available for protein interaction networks have not yet been fully understood. New types of analyses are needed to reveal organizational principles of these networks to investigate the details of functional and regulatory clusters of proteins. RESULTS: In the present work, individual clusters identified by an eigenmode analysis of the connectivity matrix of the protein-protein interaction network

Taner Z. Sen; Andrzej Kloczkowski; Robert L. Jernigan

2006-01-01

227

Photoswitchable cyan fluorescent protein for protein tracking.  

PubMed

In recent years diverse photolabeling techniques using green fluorescent protein (GFP)-like proteins have been reported, including photoactivatable PA-GFP, photoactivatable protein Kaede, the DsRed 'greening' technique and kindling fluorescent proteins. So far, only PA-GFP, which is monomeric and gives 100-fold fluorescence contrast, could be applied for protein tracking. Here we describe a dual-color monomeric protein, photoswitchable cyan fluorescent protein (PS-CFP). PS-CFP is capable of efficient photoconversion from cyan to green, changing both its excitation and emission spectra in response to 405-nm light irradiation. Complete photoactivation of PS-CFP results in a 1,500-fold increase in the green-to-cyan fluorescence ratio, making it the highest-contrast monomeric photoactivatable fluorescent protein described to date. We used PS-CFP as a photoswitchable tag to study trafficking of human dopamine transporter in living cells. At moderate excitation intensities, PS-CFP can be used as a pH-stable cyan label for protein tagging and fluorescence resonance energy transfer applications. PMID:15502815

Chudakov, Dmitriy M; Verkhusha, Vladislav V; Staroverov, Dmitry B; Souslova, Ekaterina A; Lukyanov, Sergey; Lukyanov, Konstantin A

2004-11-01

228

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

PubMed Central

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

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

2013-01-01

229

Protein solubility modeling  

NASA Technical Reports Server (NTRS)

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.

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

1999-01-01

230

Protein adsorption to hydrocephalus shunt catheters: CSF protein adsorption  

PubMed Central

OBJECTIVE—To assess the quantity and nature of the proteins that adsorb to hydrocephalus shunt catheters after implantation, and to determine whether sufficient could accumulate to obstruct the catheter.?DESIGN—Elution of proteins from 102 explanted shunt catheters, with protein assay and electrophoresis of the eluate, and scanning electron microscopy (SEM) of the catheters.?RESULTS—The amount of protein elutable was extremely low, and significant protein, apart from a thin film, was not found on SEM. Qualitative analysis disclosed that most of the adsorbed protein was albumin.?CONCLUSIONS—Protein deposition on hydrocephalus catheters does not occur in sufficient quantities to cause catheter obstruction.?? PMID:9598681

Brydon, H.; Keir, G.; Thompson, E.; Bayston, R.; Hayward, R.; Harkness, W.

1998-01-01

231

Myeloma Patient's Guide to Understanding Your Test Results  

MedlinePLUS

... test results. (continues on other side) n Serum Protein Electrophoresis (SPEP) Assesses the amount of abnormal (monoclonal) protein. n Urine Protein Electrophoresis (UPEP) Shows the amount of monoclonal protein ...

232

A novel intronic splice site deletion of the IL-2 receptor common gamma chain results in expression of a dysfunctional protein and T-cell-positive X-linked Severe combined immunodeficiency.  

PubMed

X-linked severe combined immunodeficiency is caused by mutations in the IL-2 receptor common gamma chain and classically presents in the first 6 months of life with predisposition to bacterial, viral and fungal infections. In most instances, affected individuals are lymphopenic with near complete absence of T cells and NK cells. We report a boy who presented at 12 months of age with Pneumocystis jiroveci pneumonia and a family history consistent with X-linked recessive inheritance. He had a normal lymphocyte count including the presence of T cells and a broad T-cell-receptor diversity, as well as normal surface expression of the common gamma chain (CD132) protein. He however had profound hypogammaglobulinaemia, and IL-2-induced STAT5 phosphorylation was absent. Sequencing of IL-2RG demonstrated a 12-base pair intronic deletion close to the canonical splice site of exon 5, which resulted in a variety of truncated IL2RG mRNA species. A review of the literature identified 4 other patients with T-cell-positive X-SCID, with the current patient being the first associated with an mRNA splicing defect. This case raises the question of how a dysfunctional protein incapable of mediating STAT5 phosphorylation might nonetheless support T-cell development. Possible explanations are that STAT5-mediated signal transduction may be less relevant to IL7-receptor-mediated T-cell development than are other IL7R-induced intracellular transduction pathways or that a low level of STAT5 phosphorylation, undetectable in the laboratory, may be sufficient to support some T-cell development. PMID:25443657

Gray, P E A; Logan, G J; Alexander, I E; Poulton, S; Roscioli, T; Ziegler, J

2015-02-01

233

Proteolytic cleavage of the reovirus sigma 3 protein results in enhanced double-stranded RNA-binding activity: identification of a repeated basic amino acid motif within the C-terminal binding region.  

PubMed Central

The reovirus capsid protein sigma 3 was examined for double-stranded RNA (dsRNA)-binding activity by Northwestern (RNA-protein) blot analysis. Treatment of virion-derived sigma 3 protein with Staphylococcus aureus V8 protease led to an increase in the dsRNA-binding activity associated with the C-terminal fragment of the protein. Recombinant C-terminal fragments of the sigma 3 protein were expressed in Escherichia coli from the S4 cDNA of reovirus serotype 1. These truncated sigma 3 proteins displayed proteolytic processing and dsRNA-binding activity similar to those observed for native, virion-derived sigma 3 protein as measured by Northwestern blot analysis. Construction of a modified pET3c vector, pET3Exo, allowed the production of 3'-terminal deletions of the S4 cDNA by using exonuclease III and rapid screening of the induced truncated sigma 3 proteins. An 85-amino-acid domain within the C-terminal portion of the sigma 3 protein which was responsible for dsRNA-binding activity was identified. The 85-amino-acid domain possessed a repeated basic amino acid motif which was conserved in all three serotypes of reovirus. Deletion of one of the basic motifs, predicted to be an amphipathic alpha-helix, destroyed dsRNA-binding activity. Images PMID:1501278

Miller, J E; Samuel, C E

1992-01-01

234

Protein- protein interaction detection system using fluorescent protein microdomains  

SciTech Connect

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.

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

2010-02-23

235

Results from tandem Phase 1 studies evaluating the safety, reactogenicity and immunogenicity of the vaccine candidate antigen Plasmodium falciparum FVO merozoite surface protein-1 (MSP142) administered intramuscularly with adjuvant system AS01  

PubMed Central

Background The development of an asexual blood stage vaccine against Plasmodium falciparum malaria based on the major merozoite surface protein-1 (MSP1) antigen is founded on the protective efficacy observed in preclinical studies and induction of invasion and growth inhibitory antibody responses. The 42 kDa C-terminus of MSP1 has been developed as the recombinant protein vaccine antigen, and the 3D7 allotype, formulated with the Adjuvant System AS02A, has been evaluated extensively in human clinical trials. In preclinical rabbit studies, the FVO allele of MSP142 has been shown to have improved immunogenicity over the 3D7 allele, in terms of antibody titres as well as growth inhibitory activity of antibodies against both the heterologous 3D7 and homologous FVO parasites. Methods Two Phase 1 clinical studies were conducted to examine the safety, reactogenicity and immunogenicity of the FVO allele of MSP142 in the adjuvant system AS01 administered intramuscularly at 0-, 1-, and 2-months: one in the USA and, after evaluation of safety data results, one in Western Kenya. The US study was an open-label, dose escalation study of 10 and 50 ?g doses of MSP142 in 26 adults, while the Kenya study, evaluating 30 volunteers, was a double-blind, randomized study of only the 50 ?g dose with a rabies vaccine comparator. Results In these studies it was demonstrated that this vaccine formulation has an acceptable safety profile and is immunogenic in malaria-naïve and malaria-experienced populations. High titres of anti-MSP1 antibodies were induced in both study populations, although there was a limited number of volunteers whose serum demonstrated significant inhibition of blood-stage parasites as measured by growth inhibition assay. In the US volunteers, the antibodies generated exhibited better cross-reactivity to heterologous MSP1 alleles than a MSP1-based vaccine (3D7 allele) previously tested at both study sites. Conclusions Given that the primary effector mechanism for blood stage vaccine targets is humoral, the antibody responses demonstrated to this vaccine candidate, both quantitative (total antibody titres) and qualitative (functional antibodies inhibiting parasite growth) warrant further consideration of its application in endemic settings. Trial registrations Clinical Trials NCT00666380 PMID:23342996

2013-01-01

236

Protein folds and functions  

Microsoft Academic Search

Background: The recent rapid increase in the number of available three-dimensional protein structures has further highlighted the necessity to understand the relationship between biological function and structure. Using structural classification schemes such as SCOP, CATH and DALI, it is now possible to explore global relationships between protein fold and function, something which was previously impractical.Results: Using a relational database of

Andrew CR Martin; Christine A Orengo; E Gail Hutchinson; Susan Jones; Maria Karmirantzou; Roman A Laskowski; John BO Mitchell; Chiara Taroni; Janet M Thornton

1998-01-01

237

Adaptation of Tick-Borne Encephalitis Virus to BHK-21 Cells Results in the Formation of Multiple Heparan Sulfate Binding Sites in the Envelope Protein and Attenuation In Vivo  

Microsoft Academic Search

Propagation of the flavivirus tick-borne encephalitis virus in BHK-21 cells selected for mutations within the large surface glycoprotein E that increased the net positive charge of the protein. In the course of 16 independent experiments, 12 different protein E mutation patterns were identified. These were located in all three of the structural domains and distributed over almost the entire upper

CHRISTIAN W. MANDL; HELGA KROSCHEWSKI; STEVEN L. ALLISON; REGINA KOFLER; HEIDEMARIE HOLZMANN; TAMARA MEIXNER; FRANZ X. HEINZ

2001-01-01

238

Lactose binding to human galectin-7 (p53-induced gene 1) induces long-range effects through the protein resulting in increased dimer stability and evidence for positive cooperativity  

PubMed Central

The product of p53-induced gene 1 is a member of the galectin family, i.e., galectin-7 (Gal-7). To move beyond structural data by X-ray diffraction, we initiated the study of the lectin by nuclear magnetic resonance (NMR) and circular dichroism spectroscopies, and molecular dynamics (MD) simulations. In concert, our results indicate that lactose binding to human Gal-7 induces long-range effects (minor conformational shifts and changes in structural dynamics) throughout the protein that result in stabilization of the dimer state, with evidence for positive cooperativity. Monte Carlo fits of 15N-Gal-7 HSQC titrations with lactose using a two-site model yield K1 = 0.9 ± 0.6 × 103 M?1 and K2 = 3.4 ± 0.8 × 103 M?1. Ligand binding-induced stabilization of the Gal-7 dimer was supported by several lines of evidence: MD-based calculations of interaction energies between ligand-loaded and ligand-free states, gel filtration data and hetero-FRET spectroscopy that indicate a highly reduced tendency for dimer dissociation in the presence of lactose, CD-based thermal denaturation showing that the transition temperature of the lectin is significantly increased in the presence of lactose, and saturation transfer difference (STD) NMR using a molecular probe of the monomer state whose presence is diminished in the presence of lactose. MD simulations with the half-loaded ligand-bound state also provided insight into how allosteric signaling may occur. Overall, our results reveal long-range effects on Gal-7 structure and dynamics, which factor into entropic contributions to ligand binding and allow further comparisons with other members of the galectin family. PMID:23376190

Ermakova, Elena; Miller, Michelle C; Nesmelova, Irina V; López-Merino, Lara; Berbís, Manuel Alvaro; Nesmelov, Yuri; Tkachev, Yaroslav V; Lagartera, Laura; Daragan, Vladimir A; André, Sabine; Cañada, F Javier; Jiménez-Barbero, Jesús; Solís, Dolores; Gabius, Hans-Joachim; Mayo, Kevin H

2013-01-01

239

Lactose binding to human galectin-7 (p53-induced gene 1) induces long-range effects through the protein resulting in increased dimer stability and evidence for positive cooperativity.  

PubMed

The product of p53-induced gene 1 is a member of the galectin family, i.e., galectin-7 (Gal-7). To move beyond structural data by X-ray diffraction, we initiated the study of the lectin by nuclear magnetic resonance (NMR) and circular dichroism spectroscopies, and molecular dynamics (MD) simulations. In concert, our results indicate that lactose binding to human Gal-7 induces long-range effects (minor conformational shifts and changes in structural dynamics) throughout the protein that result in stabilization of the dimer state, with evidence for positive cooperativity. Monte Carlo fits of (15)N-Gal-7 HSQC titrations with lactose using a two-site model yield K1 = 0.9 ± 0.6 × 10(3) M(-1) and K2 = 3.4 ± 0.8 × 10(3) M(-1). Ligand binding-induced stabilization of the Gal-7 dimer was supported by several lines of evidence: MD-based calculations of interaction energies between ligand-loaded and ligand-free states, gel filtration data and hetero-FRET spectroscopy that indicate a highly reduced tendency for dimer dissociation in the presence of lactose, CD-based thermal denaturation showing that the transition temperature of the lectin is significantly increased in the presence of lactose, and saturation transfer difference (STD) NMR using a molecular probe of the monomer state whose presence is diminished in the presence of lactose. MD simulations with the half-loaded ligand-bound state also provided insight into how allosteric signaling may occur. Overall, our results reveal long-range effects on Gal-7 structure and dynamics, which factor into entropic contributions to ligand binding and allow further comparisons with other members of the galectin family. PMID:23376190

Ermakova, Elena; Miller, Michelle C; Nesmelova, Irina V; López-Merino, Lara; Berbís, Manuel Alvaro; Nesmelov, Yuri; Tkachev, Yaroslav V; Lagartera, Laura; Daragan, Vladimir A; André, Sabine; Cañada, F Javier; Jiménez-Barbero, Jesús; Solís, Dolores; Gabius, Hans-Joachim; Mayo, Kevin H

2013-05-01

240

Protein Structure  

ERIC Educational Resources Information Center

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…

Asmus, Elaine Garbarino

2007-01-01

241

Protein Bracelets  

NSDL National Science Digital Library

In this activity, learners use beads, which represent amino acids, to create protein bracelets. Learners examine the relationship between amino acids and proteins. Learners also discover that different arrangements of amino acids create different kinds of proteins. Note: Have a bracelet already created so students can see what they are working to create.

Center, Arizona S.

2012-01-01

242

Co-immunization with an optimized plasmid-encoded immune stimulatory interleukin, high-mobility group box 1 protein, results in enhanced interferon-? secretion by antigen-specific CD8 T cells  

PubMed Central

DNA vaccination is a novel immunization strategy that has great potential for the development of vaccines and immune therapeutics. This strategy has been highly effective in mice, but is less immunogenic in non-human primates and in humans. Enhancing DNA vaccine potency remains a challenge. It is likely that antigen-presenting cells (APCs), and especially dendritic cells (DCs), play a significant role in the presentation of the vaccine antigen to the immune system. A new study reports the synergistic recruitment, expansion and activation of DCs in vivo by high-mobility group box 1 (HMGB1) protein. Such combinational strategies for delivering vaccine in a single, simple platform will hypothetically bolster the cellular immunity in vivo. Here, we combined plasmid encoding human immunodeficiency virus-1 (HIV-1) Gag and Env with an HMGB1 plasmid as a DNA adjuvant in BALB/c mice (by intramuscular immunization via electroporation), and humoral and cellular responses were measured. Co-administration of this potent immunostimulatory adjuvant strongly enhanced the cellular interferon-? (IFN-?) and humoral immune response compared with that obtained in mice immunized with vaccine only. Our results show that co-immunization with HMGB1 can have a strong adjuvant activity, driving strong cellular and humoral immunity that may be an effective immunological adjuvant in DNA vaccination against HIV-1. PMID:19740322

Muthumani, Gowtham; Laddy, Dominick J; Sundaram, Senthil G; Fagone, Paolo; Shedlock, Devon J; Kannan, Senthil; Wu, Ling; Chung, Christopher W; Lankaraman, Karthikbabu Mallil; Burns, John; Muthumani, Karuppiah; Weiner, David B

2009-01-01

243

Silencing of ANGPTL 3 (angiopoietin-like protein 3) in human hepatocytes results in decreased expression of gluconeogenic genes and reduced triacylglycerol-rich VLDL secretion upon insulin stimulation  

PubMed Central

Homozygosity of loss-of-function mutations in ANGPTL3 (angiopoietin-like protein 3)-gene results in FHBL2 (familial combined hypolipidaemia, OMIM #605019) characterized by the reduction of all major plasma lipoprotein classes, which includes VLDL (very-low-density lipoprotein), LDL (low-density lipoprotein), HDL (high-density lipoprotein) and low circulating NEFAs (non-esterified fatty acids), glucose and insulin levels. Thus complete lack of ANGPTL3 in humans not only affects lipid metabolism, but also affects whole-body insulin and glucose balance. We used wild-type and ANGPTL3-silenced IHHs (human immortalized hepatocytes) to investigate the effect of ANGPTL3 silencing on hepatocyte-specific VLDL secretion and glucose uptake. We demonstrate that both insulin and PPAR? (peroxisome-proliferator-activated receptor ?) agonist rosiglitazone down-regulate the secretion of ANGPTL3 and TAG (triacylglycerol)-enriched VLDL1-type particles in a dose-dependent manner. Silencing of ANGPTL3 improved glucose uptake in hepatocytes by 20–50% and influenced down-regulation of gluconeogenic genes, suggesting that silencing of ANGPTL3 improves insulin sensitivity. We further show that ANGPTL3-silenced cells display a more pronounced shift from the secretion of TAG-enriched VLDL1-type particles to secretion of lipid poor VLDL2-type particles during insulin stimulation. These data suggest liver-specific mechanisms involved in the reported insulin-sensitive phenotype of ANGPTL3-deficient humans, featuring lower plasma insulin and glucose levels. PMID:25495645

Tikka, Anna; Soronen, Jarkko; Laurila, Pirkka-Pekka; Metso, Jari; Ehnholm, Christian; Jauhiainen, Matti

2014-01-01

244

Hydrophobic folding units at protein-protein interfaces: implications to protein folding and to protein-protein association.  

PubMed Central

A hydrophobic folding unit cutting algorithm, originally developed for dissecting single-chain proteins, has been applied to a dataset of dissimilar two-chain protein-protein interfaces. Rather than consider each individual chain separately, the two-chain complex has been treated as a single chain. The two-chain parsing results presented in this work show hydrophobicity to be a critical attribute of two-state versus three-state protein-protein complexes. The hydrophobic folding units at the interfaces of two-state complexes suggest that the cooperative nature of the two-chain protein folding is the outcome of the hydrophobic effect, similar to its being the driving force in a single-chain folding. In analogy to the protein-folding process, the two-chain, two-state model complex may correspond to the formation of compact, hydrophobic nuclei. On the other hand, the three-state model complex involves binding of already folded monomers, similar to the association of the hydrophobic folding units within a single chain. The similarity between folding entities in protein cores and in two-state protein-protein interfaces, despite the absence of some chain connectivities in the latter, indicates that chain linkage does not necessarily affect the native conformation. This further substantiates the notion that tertiary, non-local interactions play a critical role in protein folding. These compact, hydrophobic, two-chain folding units, derived from structurally dissimilar protein-protein interfaces, provide a rich set of data useful in investigations of the role played by chain connectivity and by tertiary interactions in studies of binding and of folding. Since they are composed of non-contiguous pieces of protein backbones, they may also aid in defining folding nuclei. PMID:9232644

Tsai, C. J.; Nussinov, R.

1997-01-01

245

How many protein-protein interactions types exist in nature?  

PubMed

"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

Garma, Leonardo; Mukherjee, Srayanta; Mitra, Pralay; Zhang, Yang

2012-01-01

246

Predicting Permanent and Transient Protein-Protein Interfaces  

PubMed Central

Protein-protein interactions are involved in many diverse functions in a cell. To optimize functional roles of interactions, proteins interact with a spectrum of binding affinities. Interactions are conventionally classified into permanent and transient, where the former denotes tight binding between proteins that result in strong complexes, while the latter compose of relatively weak interactions that can dissociate after binding to regulate functional activity at specific time point. Knowing the type of interactions has significant implications for understanding the nature and function of protein-protein interactions. In this study, we constructed amino acid substitution models that capture mutation patterns at permanent and transient type of protein interfaces, which were found to be different with statistical significance. Using the substitution models, we developed a novel computational method that predicts permanent and transient protein binding interfaces in protein surfaces. Without knowledge of the interacting partner, the method employs a single query protein structure and a multiple sequence alignment of the sequence family. Using a large dataset of permanent and transient proteins, we show that our method performs very well in protein interface classification. A very high Area Under the Curve (AUC) value of 0.957 was observed when predicted protein binding sites were classified. Remarkably, near prefect accuracy was achieved with an AUC of 0.991 when actual binding sites were classified. The developed method will be also useful for protein design of permanent and transient protein binding interfaces. PMID:23239312

La, David; Kong, Misun; Hoffman, William; Choi, Youn Im; Kihara, Daisuke

2014-01-01

247

Molecular modelling of protein-protein/protein-solvent interactions  

NASA Astrophysics Data System (ADS)

The inner workings of individual cells are based on intricate networks of protein-protein interactions. However, each of these individual protein interactions requires a complex physical interaction between proteins and their aqueous environment at the atomic scale. In this thesis, molecular dynamics simulations are used in three theoretical studies to gain insight at the atomic scale about protein hydration, protein structure and tubulin-tubulin (protein-protein) interactions, as found in microtubules. Also presented, in a fourth project, is a molecular model of solvation coupled with the Amber molecular modelling package, to facilitate further studies without the need of explicitly modelled water. Basic properties of a minimally solvated protein were calculated through an extended study of myoglobin hydration with explicit solvent, directly investigating water and protein polarization. Results indicate a close correlation between polarization of both water and protein and the onset of protein function. The methodology of explicit solvent molecular dynamics was further used to study tubulin and microtubules. Extensive conformational sampling of the carboxy-terminal tails of 8-tubulin was performed via replica exchange molecular dynamics, allowing the characterisation of the flexibility, secondary structure and binding domains of the C-terminal tails through statistical analysis methods. Mechanical properties of tubulin and microtubules were calculated with adaptive biasing force molecular dynamics. The function of the M-loop in microtubule stability was demonstrated in these simulations. The flexibility of this loop allowed constant contacts between the protofilaments to be maintained during simulations while the smooth deformation provided a spring-like restoring force. Additionally, calculating the free energy profile between the straight and bent tubulin configurations was used to test the proposed conformational change in tubulin, thought to cause microtubule destabilization. No conformational change was observed but a nucleotide dependent 'softening' of the interaction was found instead, suggesting that an entropic force in a microtubule configuration could be the mechanism of microtubule collapse. Finally, to overcome much of the computational costs associated with explicit soIvent calculations, a new combination of molecular dynamics with the 3D-reference interaction site model (3D-RISM) of solvation was integrated into the Amber molecular dynamics package. Our implementation of 3D-RISM shows excellent agreement with explicit solvent free energy calculations. Several optimisation techniques, including a new multiple time step method, provide a nearly 100 fold performance increase, giving similar computational performance to explicit solvent.

Luchko, Tyler

248

Corresponding author: TaeWon Seo E-mail: taewon.seo1@gmail.com  

E-print Network

for parameter design, dynamic analysis, and optimization in biomimetic robot research. The proposed kinematic of a quadruped robot is important in gait planning, selection of kinematic pa- rameters, and dynamic analysis (2009) 246­254 Kinematic Analysis and Experimental Verification on the Locomotion of Gecko Woochul Nam1

Kim, Jongwon

249

The Halophile Protein Database  

PubMed Central

Halophilic archaea/bacteria adapt to different salt concentration, namely extreme, moderate and low. These type of adaptations may occur as a result of modification of protein structure and other changes in different cell organelles. Thus proteins may play an important role in the adaptation of halophilic archaea/bacteria to saline conditions. The Halophile protein database (HProtDB) is a systematic attempt to document the biochemical and biophysical properties of proteins from halophilic archaea/bacteria which may be involved in adaptation of these organisms to saline conditions. In this database, various physicochemical properties such as molecular weight, theoretical pI, amino acid composition, atomic composition, estimated half-life, instability index, aliphatic index and grand average of hydropathicity (Gravy) have been listed. These physicochemical properties play an important role in identifying the protein structure, bonding pattern and function of the specific proteins. This database is comprehensive, manually curated, non-redundant catalogue of proteins. The database currently contains 59 897 proteins properties extracted from 21 different strains of halophilic archaea/bacteria. The database can be accessed through link. Database URL: http://webapp.cabgrid.res.in/protein/ PMID:25468930

Sharma, Naveen; Farooqi, Mohammad Samir; Chaturvedi, Krishna Kumar; Lal, Shashi Bhushan; Grover, Monendra; Rai, Anil; Pandey, Pankaj

2014-01-01

250

Human Plasma Protein C  

PubMed Central

Protein C is a vitamin K-dependent protein, which exists in bovine plasma as a precursor of a serine protease. In this study, protein C was isolated to homogeneity from human plasma by barium citrate adsorption and elution, ammonium sulfate fractionation, DEAE-Sephadex chromatography, dextran sulfate agarose chromatography, and preparative polyacrylamide gel electrophoresis. Human protein C (Mr = 62,000) contains 23% carbohydrate and is composed of a light chain (Mr = 21,000) and a heavy chain (Mr = 41,000) held together by a disulfide bond(s). The light chain has an amino-terminal sequence of Ala-Asn-Ser-Phe-Leu- and the heavy chain has an aminoterminal sequence of Asp-Pro-Glu-Asp-Gln. The residues that are identical to bovine protein C are underlined. Incubation of human protein C with human ?-thrombin at an enzyme to substrate weight ratio of 1:50 resulted in the formation of activated protein C, an enzyme with serine amidase activity. In the activation reaction, the apparent molecular weight of the heavy chain decreased from 41,000 to 40,000 as determined by gel electrophoresis in the presence of sodium dodecyl sulfate. No apparent change in the molecular weight of the light chain was observed in the activation process. The heavy chain of human activated protein C also contains the active-site serine residue as evidenced by its ability to react with radiolabeled diisopropyl fluorophosphate. Human activated protein C markedly prolongs the kaolin-cephalin clotting time of human plasma, but not that of bovine plasma. The amidolytic and anticoagulant activities of human activated protein C were completely obviated by prior incubation of the enzyme with diisopropyl fluorophosphate. These results indicate that human protein C, like its bovine counterpart, exists in plasma as a zymogen and is converted to a serine protease by limited proteolysis with attendant anticoagulant activity. Images PMID:468991

Kisiel, Walter

1979-01-01

251

Unscrambling an egg: protein disaggregation by AAA+ proteins  

Microsoft Academic Search

A protein quality control system, consisting of molecular chaperones and proteases, controls the folding status of proteins and prevents the aggregation of misfolded proteins by either refolding or degrading aggregation-prone species. During severe stress conditions this protection system can be overwhelmed by high substrate load, resulting in the formation of protein aggregates. In such emergency situations, Hsp104\\/ClpB becomes a key

Jimena Weibezahn; Bernd Bukau; Axel Mogk

2004-01-01

252

Circulating concentrations of insulin-like growth factor-I, insulin-like growth factor-binding protein-3, genetic polymorphisms and mammographic density in premenopausal Mexican women: results from the ESMaestras cohort.  

PubMed

The insulin-like growth factor (IGF) axis plays an essential role in the development of the mammary gland. High circulating levels of IGF-I and of its major binding protein IGFBP3 have been related with increased mammographic density in Caucasian premenopausal women. Some common single nucleotide polymorphisms (SNPs) in genes of the IGF pathway have also been suggested to play a role in mammographic density. We conducted a cross-sectional study nested within the large Mexican ESMaestras cohort to investigate the relation between circulating levels of IGF-I, IGFBP-3, the IGF-I/IGFBP-3 ratio, five common SNPs in the IGF-1, IGFBP-3 and IGF-1R genes and mammographic density in 593 premenopausal Mexican women. Mean age at mammogram was 43.1 (standard deviation, SD = 3.7) years, and average body mass index (BMI) at recruitment was 28.5 kg/m(2). Mean percent mammographic density was 36.5% (SD: 17.1), with mean dense tissue area of 48.3 (SD: 33.3) cm(2) . Mean IGF-I and IGFBP-3 concentrations were 15.33 (SD: 5.52) nmol/l and 114.96 (SD: 21.34) nmol/l, respectively. No significant associations were seen between percent density and biomarker concentrations, but women with higher IGF-I and IGF-I/IGFBP-3 concentrations had lower absolute dense (p(trend) = 0.03 and 0.09, respectively) and nondense tissue areas (p(trend) < 0.001 for both parameters). However, these associations were null after adjustment by BMI. SNPs in specific genes were associated with circulating levels of growth factors, but not with mammographic density features. These results do not support the hypothesis of a strong association between circulating levels of growth hormones and mammographic density in Mexican premenopausal women. PMID:24037648

Rinaldi, S; Biessy, C; Hernandez, M; Lesueur, F; dos-Santos-Silva, I; Rice, M S; Lajous, M; Lopez-Ridaura, R; Torres-Mejía, G; Romieu, I

2014-03-15

253

Quantification of the influence of protein-protein interactions on adsorbed protein structure and bioactivity.  

PubMed

While protein-surface interactions have been widely studied, relatively little is understood at this time regarding how protein-surface interaction effects are influenced by protein-protein interactions and how these effects combine with the internal stability of a protein to influence its adsorbed-state structure and bioactivity. The objectives of this study were to develop a method to study these combined effects under widely varying protein-protein interaction conditions using hen egg-white lysozyme (HEWL) adsorbed on silica glass, poly(methyl methacrylate), and polyethylene as our model systems. In order to vary protein-protein interaction effects over a wide range, HEWL was first adsorbed to each surface type under widely varying protein solution concentrations for 2h to saturate the surface, followed by immersion in pure buffer solution for 15h to equilibrate the adsorbed protein layers in the absence of additionally adsorbing protein. Periodic measurements were made at selected time points of the areal density of the adsorbed protein layer as an indicator of the level of protein-protein interaction effects within the layer, and these values were then correlated with measurements of the adsorbed protein's secondary structure and bioactivity. The results from these studies indicate that protein-protein interaction effects help stabilize the structure of HEWL adsorbed on silica glass, have little influence on the structural behavior of HEWL on HDPE, and actually serve to destabilize HEWL's structure on PMMA. The bioactivity of HEWL on silica glass and HDPE was found to decrease in direct proportion to the degree of adsorption-induce protein unfolding. A direct correlation between bioactivity and the conformational state of adsorbed HEWL was less apparent on PMMA, thus suggesting that other factors influenced HEWL's bioactivity on this surface, such as the accessibility of HEWL's bioactive site being blocked by neighboring proteins or the surface itself. The developed methods provide an effective means to characterize the influence of protein-protein interaction effects and provide new molecular-level insights into how protein-protein interaction effects combine with protein-surface interaction and internal protein stability effects to influence the structure and bioactivity of adsorbed protein. PMID:23751416

Wei, Yang; Thyparambil, Aby A; Latour, Robert A

2013-10-01

254

Physicochemical mechanisms of protein regulation by phosphorylation  

PubMed Central

Phosphorylation offers a dynamic way to regulate protein activity and subcellular localization, which is achieved through its reversibility and fast kinetics. Adding or removing a dianionic phosphate group somewhere on a protein often changes the protein’s structural properties, its stability and dynamics. Moreover, the majority of signaling pathways involve an extensive set of protein–protein interactions, and phosphorylation can be used to regulate and modulate protein–protein binding. Losses of phosphorylation sites, as a result of disease mutations, might disrupt protein binding and deregulate signal transduction. In this paper we focus on the effects of phosphorylation on protein stability, dynamics, and binding. We describe several physico-chemical mechanisms of protein regulation through phosphorylation and pay particular attention to phosphorylation in protein complexes and phosphorylation in the context of disorder–order and order–disorder transitions. Finally we assess the role of multiple phosphorylation sites in a protein molecule, their possible cooperativity and function. PMID:25147561

Nishi, Hafumi; Shaytan, Alexey; Panchenko, Anna R.

2014-01-01

255

Transport Proteins  

NSDL National Science Digital Library

This Teaching Resource provides and describes two animated lessons that illustrate general properties of transport proteins. The lesson called “transport protein classes” depicts major classes and subclasses of transport proteins. The “transporters, mechanism of action” lesson explains how transporters and P class ATPase (adenosine triphosphatase) pumps function. These animations serve as valuable resources for any collegiate-level course that describes these important factors. Courses that might use them include introductory biology, biochemistry, cell biology, physiology, and biophysics.

Jack D. Thatcher (Lewisburg; West Virginia School of Osteopathic Medicine REV)

2013-04-16

256

A single immunization with a rhabdovirus-based vector expressing severe acute respiratory syndrome coronavirus (SARS-CoV) S protein results in the production of high levels of SARS-CoV-neutralizing antibodies  

PubMed Central

Foreign viral proteins expressed by rabies virus (RV) have been shown to induce potent humoral and cellular immune responses in immunized animals. In addition, highly attenuated and, therefore, very safe RV-based vectors have been constructed. Here, an RV-based vaccine vehicle was utilized as a novel vaccine against severe acute respiratory syndrome coronavirus (SARS-CoV). For this approach, the SARS-CoV nucleocapsid protein (N) or envelope spike protein (S) genes were cloned between the RV glycoprotein G and polymerase L genes. Recombinant vectors expressing SARS-CoV N or S protein were recovered and their immunogenicity was studied in mice. A single inoculation with the RV-based vaccine expressing SARS-CoV S protein induced a strong SARS-CoV-neutralizing antibody response. The ability of the RV-SARS-CoV S vector to confer immunity after a single inoculation makes this live vaccine a promising candidate for eradication of SARS-CoV in animal reservoirs, thereby reducing the risk of transmitting the infection to humans. PMID:15831955

Faber, Milosz; Lamirande, Elaine W.; Roberts, Anjeanette; Rice, Amy B.; Koprowski, Hilary; Dietzschold, Bernhard; Schnell, Matthias J.

2005-01-01

257

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

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

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

2013-01-01

258

Electronic transport via proteins.  

PubMed

A central vision in molecular electronics is the creation of devices with functional molecular components that may provide unique properties. Proteins are attractive candidates for this purpose, as they have specific physical (optical, electrical) and chemical (selective binding, self-assembly) functions and offer a myriad of possibilities for (bio-)chemical modification. This Progress Report focuses on proteins as potential building components for future bioelectronic devices as they are quite efficient electronic conductors, compared with saturated organic molecules. The report addresses several questions: how general is this behavior; how does protein conduction compare with that of saturated and conjugated molecules; and what mechanisms enable efficient conduction across these large molecules? To answer these questions results of nanometer-scale and macroscopic electronic transport measurements across a range of organic molecules and proteins are compiled and analyzed, from single/few molecules to large molecular ensembles, and the influence of measurement methods on the results is considered. Generalizing, it is found that proteins conduct better than saturated molecules, and somewhat poorer than conjugated molecules. Significantly, the presence of cofactors (redox-active or conjugated) in the protein enhances their conduction, but without an obvious advantage for natural electron transfer proteins. Most likely, the conduction mechanisms are hopping (at higher temperatures) and tunneling (below ca. 150-200 K). PMID:25256438

Amdursky, Nadav; Marchak, Debora; Sepunaru, Lior; Pecht, Israel; Sheves, Mordechai; Cahen, David

2014-11-12

259

Interfacial Protein-Protein Associations  

PubMed Central

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

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

2014-01-01

260

Interfacial protein-protein associations.  

PubMed

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 polyethylene 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

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

2014-01-13

261

Protein based Block Copolymers  

PubMed Central

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

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

2011-01-01

262

Phospholipid/protein cones.  

PubMed

The presence of protein in tubule-forming solutions of the diacetylenic phospholipid 1,2-bis(10,12-tricosadiynoyl)-sn-glycero-3-phosphocholine results in the formation of hollow cones rather than the expected hollow cylinders. Differential phase-contrast video microscopy reveals that cones grow from proteinaceous nodules in a fashion similar to cylindrical tubule growth from spherical vesicles. Spatially resolved electron-beam energy-dispersive X-ray fluorescence spectroscopy shows the protein to be associated with the cone wall. Small-angle X-ray scattering shows that, like the protein-free cylinders, the cones are multilamellar with essentially identical interlamellar spacing. PMID:12059207

Mishra, Bijaya K; Thomas, Britt N

2002-06-19

263

Activation of the Stem Cell-Derived Tyrosine Kinase\\/RON Receptor Tyrosine Kinase by Macrophage-Stimulating Protein Results in the Induction of Arginase Activity in Murine Peritoneal Macrophages1  

Microsoft Academic Search

Regulation of macrophage activities in response to inflammatory stimuli must be finely tuned to promote an effective immune response while, at the same time, preventing damage to the host. Our lab and others have previously shown that macrophage- stimulating protein (MSP), through activation of its receptor RON, negatively regulates NO production in response to IFN- and LPS by inhibiting the

Amy C. Morrison; Pamela H. Correll

264

Delayed formation of zero-valent selenium nanoparticles by Bacillus mycoides SeITE01 as a consequence of selenite reduction under aerobic conditions  

PubMed Central

Background Selenite (SeO32?) oxyanion shows severe toxicity to biota. Different bacterial strains exist that are capable of reducing SeO32? to non-toxic elemental selenium (Se0), with the formation of Se nanoparticles (SeNPs). These SeNPs might be exploited for technological applications due to their physico-chemical and biological characteristics. The present paper discusses the reduction of selenite to SeNPs by a strain of Bacillus sp., SeITE01, isolated from the rhizosphere of the Se-hyperaccumulator legume Astragalus bisulcatus. Results Use of 16S rRNA and GyrB gene sequence analysis positioned SeITE01 phylogenetically close to B. mycoides. On agarized medium, this strain showed rhizoid growth whilst, in liquid cultures, it was capable of reducing 0.5 and 2.0 mM SeO32? within 12 and 24 hours, respectively. The resultant Se0 aggregated to form nanoparticles and the amount of Se0 measured was equivalent to the amount of selenium originally added as selenite to the growth medium. A delay of more than 24 hours was observed between the depletion of SeO32 and the detection of SeNPs. Nearly spherical-shaped SeNPs were mostly found in the extracellular environment whilst rarely in the cytoplasmic compartment. Size of SeNPs ranged from 50 to 400 nm in diameter, with dimensions greatly influenced by the incubation times. Different SeITE01 protein fractions were assayed for SeO32? reductase capability, revealing that enzymatic activity was mainly associated with the membrane fraction. Reduction of SeO32? was also detected in the supernatant of bacterial cultures upon NADH addition. Conclusions The selenite reducing bacterial strain SeITE01 was attributed to the species Bacillus mycoides on the basis of phenotypic and molecular traits. Under aerobic conditions, the formation of SeNPs were observed both extracellularly or intracellullarly. Possible mechanisms of Se0 precipitation and SeNPs assembly are suggested. SeO32? is proposed to be enzimatically reduced to Se0 through redox reactions by proteins released from bacterial cells. Sulfhydryl groups on peptides excreted outside the cells may also react directly with selenite. Furthermore, membrane reductases and the intracellular synthesis of low molecular weight thiols such as bacillithiols may also play a role in SeO32? reduction. Formation of SeNPs seems to be the result of an Ostwald ripening mechanism. PMID:24606965

2014-01-01

265

This version: September 12, 2009 Liquidity, Investor Sentiment and Price  

E-print Network

1 This version: September 12, 2009 Liquidity, Investor Sentiment and Price Discount of SEOs stock liquidity and investor sentiment have interactive effect on SEO price discounts in Australia. Our results show that, in periods of deteriorating investor sentiment, the increase in SEO price discounts

Saskatchewan, University of

266

Mutations in the yeast RNA14 and RNA15 genes result in an abnormal mRNA decay rate; sequence analysis reveals an RNA-binding domain in the RNA15 protein.  

PubMed Central

In Saccharomyces cerevisiae, temperature-sensitive mutations in the genes RNA14 and RNA15 correlate with a reduction of mRNA stability and poly(A) tail length. Although mRNA transcription is not abolished in these mutants, the transcripts are rapidly deadenylated as in a strain carrying an RNA polymerase B(II) temperature-sensitive mutation. This suggests that the primary defect could be in the control of the poly(A) status of the mRNAs and that the fast decay rate may be due to the loss of this control. By complementation of their temperature-sensitive phenotype, we have cloned the wild-type genes. They are essential for cell viability and are unique in the haploid genome. The RNA14 gene, located on chromosome H, is transcribed as three mRNAs, one major and two minor, which are 2.2, 1.5, and 1.1 kb in length. The RNA15 gene gives rise to a single 1.2-kb transcript and maps to chromosome XVI. Sequence analysis indicates that RNA14 encodes a 636-amino-acid protein with a calculated molecular weight of 75,295. No homology was found between RNA14 and RNA15 or between RNA14 and other proteins contained in data banks. The RNA15 DNA sequence predicts a protein of 296 amino acids with a molecular weight of 32,770. Sequence comparison reveals an N-terminal putative RNA-binding domain in the RNA15-encoded protein, followed by a glutamine and asparagine stretch similar to the opa sequences. Both RNA14 and RNA15 wild-type genes, when cloned on a multicopy plasmid, are able to suppress the temperature-sensitive phenotype of strains bearing either the rna14 or the rna15 mutation, suggesting that the encoded proteins could interact with each other. Images PMID:1674817

Minvielle-Sebastia, L; Winsor, B; Bonneaud, N; Lacroute, F

1991-01-01

267

Exposure to the three structurally different PCB congeners (PCB 118, 153, and 126) results in decreased protein expression and altered steroidogenesis in the human adrenocortical carcinoma cell line H295R.  

PubMed

Polychlorinated biphenyls (PCB), synthetic, persistent organic pollutants (POP), are detected ubiquitously, in water, soil, air, and sediments, as well as in animals and humans. PCB are associated with range of adverse health effects, such as interference with the immune system and nervous system, reproductive abnormalities, fetotoxicity, carcinogenicity, and endocrine disruption. Our objective was to determine the effects of three structurally different PCB congeners, PCB118, PCB 126, and PCB 153, each at two concentrations, on the steroidogenic capacity and proteome of human adrenocortical carcinoma cell line cultures (H295R) . After 48 h of exposure, cell viability was monitored and estradiol, testosterone, cortisol and progesterone secretion measured to quantify steroidogenic capacity of the cells. Two-dimensional (2D) gel-based proteomics was used to screen for proteome alterations in H295R cells in response to the PCB. Exposure to PCB 118 increased estradiol and cortisol secretion, while exposure to PCB 153 elevated estradiol secretion. PCB 126 was the most potent congener, increasing estradiol, cortisol, and progesterone secretion in exposed H295R cells. Seventy-three of the 711 spots analyzed showed a significant difference in normalized spot volumes between controls (vehicle only) and at least one exposure group. Fourteen of these protein spots were identified by liquid chromatography with mass spectroscopy (LC-MS/MS). Exposure to three PCB congeners with different chemical structure perturbed steroidogenesis and protein expression in the H295R in vitro model. This study represents an initial analysis of the effects on proteins and hormones in the H295R cell model, and additional studies are required in order to obtain a more complete understanding of the pathways disturbed by PCB congeners in H295R cells. Overall, alterations in protein regulation and steroid hormone synthesis suggest that exposure to PCB disturbs several cellular processes, including protein synthesis, stress response, and apoptosis. PMID:24754389

Tremoen, Nina Hårdnes; Fowler, Paul A; Ropstad, Erik; Verhaegen, Steven; Krogenæs, Anette

2014-01-01

268

Understanding and predicting protein structure  

SciTech Connect

Protein structure prediction from sequence remains a premiere computational problem for modern molecular biology. Just as protein structure prediction may be divided into sub-problems of main-chain and side-chain placement, so the protein structure prediction track this year has been divided into sub-tracks of protein threading (organized by Daniel Fischer and Adam Godzik) and side-chain packing (organized by Su Chung and S. Subbiah). The result is an unusually rich tour through different levels of protein structure prediction, from coarse-grained prediction of the tertiary fold to the fine-grained atomic detail of individual side-chains. 8 refs.

Fischer, D. [Univ. of California, Los Angeles, CA (United States); Godzik, A. [Scripps Research Institute, La Jolla, CA (United States); Chung, S. [Uniformed Services Univ. of the Health Sciences, Bethesda, MD (United States)] [and others

1996-12-31

269

EDITORIAL: Precision proteins Precision proteins  

NASA Astrophysics Data System (ADS)

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

Demming, Anna

2010-06-01

270

Protein Phosphatases  

NSDL National Science Digital Library

This Teaching Resource provides lecture notes and slides for a class covering the structure and function of protein phosphatases and is part of the course "Cell Signaling Systems: A Course for Graduate Students." The lecture begins with a discussion of the importance of phosphatases in physiology, recognized by the award of a Nobel Prize in 1992, and then proceeds to describe the two types of protein phosphatases: serine/threonine and tyrosine phosphatases. The information covered includes the structure, regulation, and substrate specificity of protein phosphatases, with an emphasis on their importance in disease and clinical settings.

Stephen R. Salton (Mount Sinai School of Medicine;Department of Neuroscience REV)

2005-03-01

271

Studying protein-protein interactions using peptide arrays.  

PubMed

Screening of arrays and libraries of compounds is well-established as a high-throughput method for detecting and analyzing interactions in both biological and chemical systems. Arrays and libraries can be composed from various types of molecules, ranging from small organic compounds to DNA, proteins and peptides. The applications of libraries for detecting and characterizing biological interactions are wide and diverse, including for example epitope mapping, carbohydrate arrays, enzyme binding and protein-protein interactions. Here, we will focus on the use of peptide arrays to study protein-protein interactions. Characterization of protein-protein interactions is crucial for understanding cell functionality. Using peptides, it is possible to map the precise binding sites in such complexes. Peptide array libraries usually contain partly overlapping peptides derived from the sequence of one protein from the complex of interest. The peptides are attached to a solid support using various techniques such as SPOT-synthesis and photolithography. Then, the array is incubated with the partner protein from the complex of interest. Finally, the detection of the protein-bound peptides is carried out by using immunodetection assays. Peptide array screening is semi-quantitative, and quantitative studies with selected peptides in solution are required to validate and complement the screening results. These studies can improve our fundamental understanding of cellular processes by characterizing amino acid patterns of protein-protein interactions, which may even develop into prediction algorithms. The binding peptides can then serve as a basis for the design of drugs that inhibit or activate the target protein-protein interactions. In the current review, we will introduce the recent work on this subject performed in our and in other laboratories. We will discuss the applications, advantages and disadvantages of using peptide arrays as a tool to study protein-protein interactions. PMID:21243154

Katz, Chen; Levy-Beladev, Liron; Rotem-Bamberger, Shahar; Rito, Tiago; Rüdiger, Stefan G D; Friedler, Assaf

2011-05-01

272

Mechanism of protein decarbonylation  

PubMed Central

Ligand/receptor-stimulation of cells promotes protein carbonylation that is followed by the decarbonylation process, which might involve thiol-dependent reduction (Wong et al., Circ. Res. 102 301-318, 2008). The present study further investigated the properties of this protein decarbonylation mechanism. We found that the thiol-mediated reduction of protein carbonyls is dependent on heat-labile biologic components. Cysteine and glutathione were found to be efficient substrates for decarbonylation. Thiols decreased the protein carbonyl content, as detected by 2,4-dinitrophenylhydrazine, but not the levels of malondialdehyde or 4-hydroxynonenal protein adducts. Mass spectrometry identified proteins that undergo thiol-dependent decarbonylation, which include peroxiredoxins. Peroxiredoxins-2 and -6 were found to be carbonylated and subsequent decarbonylated in response to the ligand/receptor-stimulation of cells. siRNA knockdown of glutaredoxin inhibited the decarbonylation of peroxiredoxin. These results strengthen the concept that thiol-dependent decarbonylation defines the kinetics of protein carbonylation signaling. PMID:24044890

Wong, Chi-Ming; Marcocci, Lucia; Das, Dividutta; Wang, Xinhong; Luo, Haibei; Zungu-Edmondson, Makhosazane; Suzuki, Yuichiro J.

2013-01-01

273

Reclamation of Whey Protein with Carboxymethylcellulose1  

Microsoft Academic Search

Molecular complex formation between anionic hydrocolloids and proteins was used. to recover proteins from whey with carboxymethylcellulose. A predetermined amount of the hydrocolloid was mixed with acidified whey and the resulting complex removed by centrifugation. More than 90% of the protein was recovered in an acidic fraction (Fraction I) at pH 3.2. Following removal of this complex, addi- tional protein

P. M. T. Hansen; J. Hidalgo; I. A. Gould

1971-01-01

274

Protein Purification  

NSDL National Science Digital Library

This animation produced by WGBH and Digizyme, Inc. demonstrates how a protein of interest is isolated from other contents in a transformed bacterial cell—a process called purification—using a lab technique called hydrophobic interaction chromatography.

Foundation, Wgbh E.

2011-12-30

275

Environments of the four tryptophans in the extracellular domain of human tissue factor: comparison of results from absorption and fluorescence difference spectra of tryptophan replacement mutants with the crystal structure of the wild-type protein.  

PubMed Central

The local environments of the four tryptophan residues of the extracellular domain of human tissue factor (sTF) were assessed from difference absorption and fluorescence spectra. The difference spectra were derived by subtracting spectra from single Trp-to-Phe or Trp-to-Tyr replacement mutants from the corresponding spectrum of the wild-type protein. Each of the mutants was capable of enhancing the proteolytic activity of factor VIIa showing that the mutations did not introduce major structural changes, although the mutants were more susceptible to denaturation by guanidinium chloride. The difference spectra indicate that the Trp residues are buried to different extents within the protein matrix. This evaluation was compared with the x-ray crystal structure of sTF. There is excellent agreement between predictions from the difference spectra and the environments of the Trp residues observed in the x-ray crystal structure, demonstrating that difference absorption and particularly fluorescence spectra derived from functional single-Trp replacement mutants can be used to obtain information about the local environments of individual Trp residues in multi-tryptophan proteins. Images FIGURE 7 FIGURE 8 PMID:7669897

Hasselbacher, C A; Rusinova, E; Waxman, E; Rusinova, R; Kohanski, R A; Lam, W; Guha, A; Du, J; Lin, T C; Polikarpov, I

1995-01-01

276

Environments of the four tryptophans in the extracellular domain of human tissue factor: comparison of results from absorption and fluorescence difference spectra of tryptophan replacement mutants with the crystal structure of the wild-type protein.  

PubMed

The local environments of the four tryptophan residues of the extracellular domain of human tissue factor (sTF) were assessed from difference absorption and fluorescence spectra. The difference spectra were derived by subtracting spectra from single Trp-to-Phe or Trp-to-Tyr replacement mutants from the corresponding spectrum of the wild-type protein. Each of the mutants was capable of enhancing the proteolytic activity of factor VIIa showing that the mutations did not introduce major structural changes, although the mutants were more susceptible to denaturation by guanidinium chloride. The difference spectra indicate that the Trp residues are buried to different extents within the protein matrix. This evaluation was compared with the x-ray crystal structure of sTF. There is excellent agreement between predictions from the difference spectra and the environments of the Trp residues observed in the x-ray crystal structure, demonstrating that difference absorption and particularly fluorescence spectra derived from functional single-Trp replacement mutants can be used to obtain information about the local environments of individual Trp residues in multi-tryptophan proteins. PMID:7669897

Hasselbacher, C A; Rusinova, E; Waxman, E; Rusinova, R; Kohanski, R A; Lam, W; Guha, A; Du, J; Lin, T C; Polikarpov, I

1995-07-01

277

Dielectric response of hydrated proteins  

NASA Astrophysics Data System (ADS)

We study dipolar susceptibility of hydrated proteins, representing the average dipole moment induced at the hydrated protein by a uniform external field. This parameter shows remarkable variation among proteins. We find a negative value of the dipolar susceptibility for some proteins, which implies a dia-electric dipolar response and negative dielectrophoresis. Such proteins, even though carrying significant permanent dipole moments, repel from the electric field. This outcome is the result of a negative cross-correlation between the protein and water dipoles, compensating for the positive variance of the intrinsic protein dipole in the overall dipolar susceptibility. We therefore suggest that the dipolar response of proteins in solution is strongly affected by the coupling of the protein surface charge to the hydration water. The protein-water dipolar cross-correlations are long-ranged, extending approximately 2 nm from the protein surface into the bulk. A similar correlation length of about 1 nm is found for the electrostatic potential. The model is applied to the analysis of light absorption by protein solutions in the THz window of radiation. Here we also find significant deviations of the absorption coefficient from the predictions of traditional theories.

Matyushov, Dmitry

2013-03-01

278

PROTEIN DESIGN: Proteins from Scratch  

NSDL National Science Digital Library

Access to the article is free, however registration and sign-in are required. It is not easy to predict a protein's structure from its linear amino acid sequence, and the reverse problem--designing a protein that will assume a particular folded shape--is even harder. But on page 82 in this issue, Dahiyat and Mayo have succeeded in creating a zinc finger fold de novo, which forms the same shaped protein as the natural one but without the usual stabilizing zinc ion. In his Perspective, DeGrado explains why this problem has been so intractable and where we can go now that Dahiyat and Mayo have paved the way.

William F. DeGrado (University of Pennsylvania School of Medicine;Department of Biochemistry and Biophysics)

1997-10-03

279

Exploiting Amino Acid Composition for Predicting Protein-Protein Interactions  

PubMed Central

Background Computational prediction of protein interactions typically use protein domains as classifier features because they capture conserved information of interaction surfaces. However, approaches relying on domains as features cannot be applied to proteins without any domain information. In this paper, we explore the contribution of pure amino acid composition (AAC) for protein interaction prediction. This simple feature, which is based on normalized counts of single or pairs of amino acids, is applicable to proteins from any sequenced organism and can be used to compensate for the lack of domain information. Results AAC performed at par with protein interaction prediction based on domains on three yeast protein interaction datasets. Similar behavior was obtained using different classifiers, indicating that our results are a function of features and not of classifiers. In addition to yeast datasets, AAC performed comparably on worm and fly datasets. Prediction of interactions for the entire yeast proteome identified a large number of novel interactions, the majority of which co-localized or participated in the same processes. Our high confidence interaction network included both well-studied and uncharacterized proteins. Proteins with known function were involved in actin assembly and cell budding. Uncharacterized proteins interacted with proteins involved in reproduction and cell budding, thus providing putative biological roles for the uncharacterized proteins. Conclusion AAC is a simple, yet powerful feature for predicting protein interactions, and can be used alone or in conjunction with protein domains to predict new and validate existing interactions. More importantly, AAC alone performs at par with existing, but more complex, features indicating the presence of sequence-level information that is predictive of interaction, but which is not necessarily restricted to domains. PMID:19936254

Roy, Sushmita; Martinez, Diego; Platero, Harriett; Lane, Terran; Werner-Washburne, Margaret

2009-01-01

280

Binding Efficiency of Protein-Protein Complexes  

PubMed Central

We examine the relationship between binding affinity and interface size for reversible protein-protein interactions (PPI), using cytokines from the tumor necrosis factor (TNF) superfamily and their receptors as a test case. Using surface plasmon resonance, we measured single-site binding affinities for the large receptor TNFR1 binding to its ligands TNF? (KD = 1.4 ± 0.4 nM) and lymphotoxin-? (KD = 50 ± 10 nM), and also for the small receptor Fn14 binding to TWEAK (KD = 70 ± 10 nM). We additionally assembled data for all other TNF/TNFR family complexes for which reliable single site binding affinities have been reported. We used these values to calculate the binding efficiency – defined as binding energy per Å2 of surface area buried at the contact interface – for the nine of these complexes for which co-crystal structures are available, and compared the results to those for a set of 144 protein-protein complexes with published affinity values. The results show that the most efficient PPI complexes generate ~20 cal.mol?1/Å2 of binding energy. A minimum contact area of ~500 Å2 is required for a stable complex, required to generate sufficient interaction energy to pay the entropic cost of co-localizing two proteins from 1 M solution. The most compact and efficient TNF/TNFR complex was BAFF/BR3, which achieved ~80% of the maximum achievable binding efficiency. Other small receptors also gave high binding efficiencies, while the larger receptors generated only 44-49% of this limit despite interacting primarily through just a single small domain. The results provide new insight into how much binding energy can be generated by a PPI interface of a given size, and establish a quantitative method to predict how large a natural or engineered contact interface must be to achieve a given level of binding affinity. PMID:23088250

Day, Eric S.; Cote, Shaun M.; Whitty, Adrian

2012-01-01

281

Analysis and application of large-scale protein-protein interaction data sets  

Microsoft Academic Search

Protein-protein interactions play key roles in cells. Lots of experimental approaches andin silico methods have been developed to identify and predict large-scale protein-protein interactions. However, compared with the\\u000a traditionally experimental results, the high-throughput protein-protein interaction data often contain the false positives\\u000a in high probability. In order to fully utilize the large-scale data, it is necessary to develop bioinformatic methods for

Jingchun Sun; Jinlin Xu; Yixue Li; Tieliu Shi

2005-01-01

282

Protein crystal growth in microgravity  

NASA Technical Reports Server (NTRS)

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.

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

1989-01-01

283

Protein structure by mechanical triangulation  

NASA Astrophysics Data System (ADS)

Knowledge of protein structure is essential to understand protein function. High-resolution protein structure has so far been the domain of ensemble methods. Here, we develop a simple single-molecule technique to measure spatial position of selected residues within a folded and functional protein structure in solution. Construction and mechanical unfolding of cysteine-engineered polyproteins with controlled linkage topology allows measuring intramolecular distance with angstrom precision. We demonstrate the potential of this technique by determining the position of three residues in the structure of green fluorescent protein (GFP). Our results perfectly agree with the GFP crystal structure. Mechanical triangulation can find many applications where current bulk structural methods fail. mechanical protein unfolding | protein stability | single molecule force spectroscopy

Dietz, Hendrik; Rief, Matthias

2006-01-01

284

Unscrambling an egg: protein disaggregation by AAA+ proteins  

PubMed Central

A protein quality control system, consisting of molecular chaperones and proteases, controls the folding status of proteins and prevents the aggregation of misfolded proteins by either refolding or degrading aggregation-prone species. During severe stress conditions this protection system can be overwhelmed by high substrate load, resulting in the formation of protein aggregates. In such emergency situations, Hsp104/ClpB becomes a key player for cell survival, as it has the extraordinary capacity to rescue proteins from an aggregated state in cooperation with an Hsp70 chaperone system. The ring-forming Hsp104/ClpB chaperone belongs to the AAA+ protein superfamily, which in general drives the assembly and disassembly of protein complexes by ATP-dependent remodelling of protein substrates. A disaggregation activity was also recently attributed to other eubacterial AAA+ proteins, while such an activity has not yet been identified in mammalian cells. In this review, we report on new insights into the mechanism of protein disaggregation by AAA+ proteins, suggesting that these chaperones act as molecular crowbars or ratchets. PMID:14728719

Weibezahn, Jimena; Bukau, Bernd; Mogk, Axel

2004-01-01

285

Recombinant insulin-like growth factor-I (IGF-I) production in Super-CHO results in the expression of IGF-I receptor and IGF binding protein 3  

Microsoft Academic Search

Previously, we described the genetic construction Super- CHO, a cell line capable of autocrine growth under fully defined\\u000a protein-free conditions. Super-CHO cells constitutively express insulin growth factor-I (IGF-I) and transferrin in sufficient\\u000a amounts to support long-term, stable growth without the addition of exogenous growth factors, thus making it an ideal host\\u000a for the production of recombinant biopharmaceuticals. although IGF-I has

Noelle-Anne Sunstrom; Masood Baig; Louise Cheng; Derick Payet Sugyiono; Peter Gray

1998-01-01

286

Protein constituents of the eggshell: eggshell-specific matrix proteins  

Microsoft Academic Search

In this article, we review the results of recent proteomic and genomic analyses of eggshell matrix proteins and draw attention\\u000a to the impact of these data on current understanding of eggshell formation and function. Eggshell-specific matrix proteins\\u000a from avian (ovocleidins and ovocalyxins) and non-avian (paleovaterin) shells are discussed. Two possible roles for eggshell-specific\\u000a matrix proteins have been proposed; both reflect

Megan L. H. Rose; Maxwell T. Hincke

2009-01-01

287

Protein Complex Prediction in Large Ontology Attributed Protein-Protein Interaction Networks.  

PubMed

Protein complexes are important for unraveling the secrets of cellular organization and function. Many computational approaches have been developed to predict protein complexes in protein-protein interaction (PPI) networks. However, most existing approaches focus mainly on the topological structure of PPI networks, and largely ignore the gene ontology (GO) annotation information. In this article, we constructed ontology attributed PPI networks with PPI data and GO resource. After constructing ontology attributed networks, we proposed a novel approach called CSO (clustering based on network structure and ontology attribute similarity). Structural information and GO attribute information are complementary in ontology attributed networks. CSO can effectively take advantage of the correlation between frequent GO annotation sets and the dense subgraph for protein complex prediction. Our proposed CSO approach was applied to three different yeast PPI datasets and predicted many well-known protein complexes. The experimental results showed that CSO is valuable in predicting protein complexes and achieves state-of-the-art performance. PMID:23898017

Zhang, Yijia; Lin, Hongfei; Yang, Zhihao; Wang, Jian; Li, Yanpeng; Xu, Bo

2013-07-26

288

Cotton and Protein Interactions  

SciTech Connect

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.

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

2006-06-30

289

Immunohistochemical localization of S-100 protein and peripheral nerve myelin proteins (P2 protein, P0 protein) in granular cell tumors.  

PubMed Central

The presence and distribution of nervous-system-specific protein (S-100 protein), peripheral nerve myelin proteins (P2 protein and P0 protein) that have not been given any attention in the field of tumor pathology, and striated muscle-related proteins (myoglobin and myosin) were studied in 18 cases of granular cell tumor by the peroxidase-antiperoxidase method. The granular cells of all cases were negatively stained with anti-striated-muscle-related protein antiserums. On the other hand, they were positively stained with anti-S-100 protein, P2 protein, and P0 protein antiserums. The distribution of P2 protein and P0 protein corresponded with that of characteristic PAS-positive granules on serial sections. Angular bodies in the interstitial cells were also positively stained with anti-P2 protein antiserum and anti-P0 protein antiserum. These results further support the hypothesis that the granular cell tumor is derived from Schwann cells and also suggest that myelin proteins are major core proteins of the characteristic granules and angular bodies of interstitial cells. The biologic significance of these results in relation to myelinogenesis is also discussed. Images Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Figure 8 Figure 9 Figure 10 Figure 11 Figure 12 Figure 13 Figure 14 PMID:6192721

Mukai, M.

1983-01-01

290

Human Cancer Protein-Protein Interaction Network: A Structural Perspective  

PubMed Central

Protein-protein interaction networks provide a global picture of cellular function and biological processes. Some proteins act as hub proteins, highly connected to others, whereas some others have few interactions. The dysfunction of some interactions causes many diseases, including cancer. Proteins interact through their interfaces. Therefore, studying the interface properties of cancer-related proteins will help explain their role in the interaction networks. Similar or overlapping binding sites should be used repeatedly in single interface hub proteins, making them promiscuous. Alternatively, multi-interface hub proteins make use of several distinct binding sites to bind to different partners. We propose a methodology to integrate protein interfaces into cancer interaction networks (ciSPIN, cancer structural protein interface network). The interactions in the human protein interaction network are replaced by interfaces, coming from either known or predicted complexes. We provide a detailed analysis of cancer related human protein-protein interfaces and the topological properties of the cancer network. The results reveal that cancer-related proteins have smaller, more planar, more charged and less hydrophobic binding sites than non-cancer proteins, which may indicate low affinity and high specificity of the cancer-related interactions. We also classified the genes in ciSPIN according to phenotypes. Within phenotypes, for breast cancer, colorectal cancer and leukemia, interface properties were found to be discriminating from non-cancer interfaces with an accuracy of 71%, 67%, 61%, respectively. In addition, cancer-related proteins tend to interact with their partners through distinct interfaces, corresponding mostly to multi-interface hubs, which comprise 56% of cancer-related proteins, and constituting the nodes with higher essentiality in the network (76%). We illustrate the interface related affinity properties of two cancer-related hub proteins: Erbb3, a multi interface, and Raf1, a single interface hub. The results reveal that affinity of interactions of the multi-interface hub tends to be higher than that of the single-interface hub. These findings might be important in obtaining new targets in cancer as well as finding the details of specific binding regions of putative cancer drug candidates. PMID:20011507

Kar, Gozde; Gursoy, Attila; Keskin, Ozlem

2009-01-01

291

Tevatron results  

SciTech Connect

Recent results obtained by the CDF and D0 experiments at the Tevatron Run II are presented. A first part is dedicated to QCD physics where inclusive jet production, dijet azimuthal decorrelations and jet shapes measurements are reported. Electroweak physics is then discussed relating measurements of the W and Z bosons productions, of the forward-backward charge asymmetry in W production, of the W width and of the top quarks mass. The extensive Run II exploration program is finally approached reporting about searches for neutral supersymmetric Higgs bosons in multijet events and for sbottom quark from gluino decays.

Lefevre, R.; /Barcelona, Autonoma U.

2005-01-01

292

Conserved network motifs allow protein-protein interaction prediction  

Microsoft Academic Search

Motivation: High-throughput protein interaction detection methods are strongly affected by false positive and false neg- ative results. Focused experiments are needed to complement the large-scale methods by validating previously detected interactions but it is often difficult to decide which proteins to probe as interaction partners. Developing reliable computa- tional methods assisting this decision process is a pressing need in bioinformatics.

Istvan Albert; Reka Albert

2004-01-01

293

Recent Progress and Future Directions in Protein-Protein Docking  

Microsoft Academic Search

This article gives an overview of recent progress in protein-protein docking and it identies several direc- tions for future research. Recent results from the CAPRI blind docking experiments show that docking algorithms are steadily improving in both reliability and accuracy. Current docking algorithms employ a range of ecien t search and scoring strategies, including e.g. fast Fourier transform correlations, geomet-

David W. Ritchie

2008-01-01

294

Protein constituents of the eggshell: eggshell-specific matrix proteins.  

PubMed

In this article, we review the results of recent proteomic and genomic analyses of eggshell matrix proteins and draw attention to the impact of these data on current understanding of eggshell formation and function. Eggshell-specific matrix proteins from avian (ovocleidins and ovocalyxins) and non-avian (paleovaterin) shells are discussed. Two possible roles for eggshell-specific matrix proteins have been proposed; both reflect the protective function of the eggshell in avian reproduction: regulation of eggshell mineralization and antimicrobial defense. An emerging concept is the dual role (mineralization/antimicrobial protection) that certain eggshell matrix proteins can play. PMID:19452125

Rose, Megan L H; Hincke, Maxwell T

2009-08-01

295

A new protein structure representation for efficient protein function prediction.  

PubMed

Abstract One of the challenging problems in bioinformatics is the prediction of protein function. Protein function is the main key that can be used to classify different proteins. Protein function can be inferred experimentally with very small throughput or computationally with very high throughput. Computational methods are sequence based or structure based. Structure-based methods produce more accurate protein function prediction. In this article, we propose a new protein structure representation for efficient protein function prediction. The representation is based on three-dimensional patterns of protein residues. In the analysis, we used protein function based on enzyme activity through six mechanistically diverse enzyme superfamilies: amidohydrolase, crotonase, haloacid dehalogenase, isoprenoid synthase type I, and vicinal oxygen chelate. We applied three different classification methods, naïve Bayes, k-nearest neighbors, and random forest, to predict the enzyme superfamily of a given protein. The prediction accuracy using the proposed representation outperforms a recently introduced representation method that is based only on the distance patterns. The results show that the proposed representation achieved prediction accuracy up to 98%, with improvement of about 10% on average. PMID:25343279

Maghawry, Huda A; Mostafa, Mostafa G M; Gharib, Tarek F

2014-12-01

296

Unscrambling an egg: protein disaggregation by AAA+ proteins.  

PubMed

Aprotein quality control system, consisting of molecular chaperones and proteases, controls the folding status of proteins and prevents the aggregation of misfolded proteins by either refolding or degrading aggregation-prone species. During severe stress conditions this protection system can be overwhelmed by high substrate load, resulting in the formation of protein aggregates. In such emergency situations, Hsp104/ClpB becomes a key player for cell survival, as it has the extraordinary capacity to rescue proteins from an aggregated state in cooperation with an Hsp70 chaperone system. The ring-forming Hsp104/ClpB chaperone belongs to the AAA+ protein superfamily, which in general drives the assembly and disassembly of protein complexes by ATP-dependent remodelling of protein substrates. A disaggregation activity was also recently attributed to other eubacterial AAA+ proteins, while such an activity has not yet been identified in mammalian cells. In this review, we report on new insights into the mechanism of protein disaggregation by AAA+ proteins, suggesting that these chaperones act as molecular crowbars or ratchets. PMID:14728719

Weibezahn, Jimena; Bukau, Bernd; Mogk, Axel

2004-01-16

297

Solubilization and refolding of inclusion body proteins.  

PubMed

High-level expression of recombinant proteins in Escherichia coli often results in accumulation of protein molecules into aggregates known as inclusion bodies (IBs). Isolation of properly folded, bioactive protein from IBs is a cumbersome task and most of the times results in poor recovery. The process of recovering bioactive proteins from IBs consists of solubilization of IB aggregates using denaturants, followed by refolding of the solubilized protein. Here, we describe a simple protocol for screening of buffers for solubilization of IB proteins. Various IB aggregate solubilization methods including organic solvents have been described. PMID:25447870

Singh, Anupam; Upadhyay, Vaibhav; Panda, Amulya K

2015-01-01

298

Protein-Protein Interaction Detection: Methods and Analysis  

PubMed Central

Protein-protein interaction plays key role in predicting the protein function of target protein and drug ability of molecules. The majority of genes and proteins realize resulting phenotype functions as a set of interactions. The in vitro and in vivo methods like affinity purification, Y2H (yeast 2 hybrid), TAP (tandem affinity purification), and so forth have their own limitations like cost, time, and so forth, and the resultant data sets are noisy and have more false positives to annotate the function of drug molecules. Thus, in silico methods which include sequence-based approaches, structure-based approaches, chromosome proximity, gene fusion, in silico 2 hybrid, phylogenetic tree, phylogenetic profile, and gene expression-based approaches were developed. Elucidation of protein interaction networks also contributes greatly to the analysis of signal transduction pathways. Recent developments have also led to the construction of networks having all the protein-protein interactions using computational methods for signaling pathways and protein complex identification in specific diseases. PMID:24693427

Rao, V. Srinivasa; Srinivas, K.; Sujini, G. N.; Kumar, G. N. Sunand

2014-01-01

299

Protein Adsorption in Three Dimensions  

PubMed Central

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

Vogler, Erwin A.

2011-01-01

300

Protein adsorption in three dimensions.  

PubMed

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 C(B). This inflated interphase subsequently undergoes time-dependent (minutes-to-hours) decrease in volume V(I) by expulsion of either-or-both interphase water and initially adsorbed protein. Interphase protein concentration C(I) increases as V(I) decreases, resulting in slow reduction in interfacial energetics. Steady state is governed by a net partition coefficient P=(C(I)/C(B)). 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, adsorbent capacity 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 ?G(ads)(o) 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 adsorbing protein mol

Vogler, Erwin A

2012-02-01

301

Isotope-coded protein label.  

PubMed

A great variety of technologies using stable isotope labeling in combination with mass spectrometry have been described being tools to identify and relatively quantify proteins within complex mixtures. Here, we present a method, termed isotope-coded protein label (ICPL), which is capable of high-throughput quantitative proteome profiling on a global scale. Since ICPL is based on tagging stable isotope derivatives at the free amino groups of intact proteins, the method is applicable to any protein sample, including extracts from tissues or body fluids. All separation methods currently employed in proteome studies can be used to reduce complexity on the protein level. After enzymatic cleavage of the protein fractions, the ratios of peptides from different proteome states can be calculated by simple MS-based mass spectrometric analyses. Only peptides representing different expression levels in the different proteomic states are further analyzed by tandem-mass spectrometry to identify respective proteins. For quantification of proteins from multiplexed ICPL experiments, ICPLQuant was developed, a software package especially designed to cover the whole ICPL workflow. The ICPL method results in accurate and reproducible quantification of proteins and high sequence coverage, indispensable for a comprehensive detection of posttranslational modifications and discrimination of protein isoforms. PMID:22665300

Kellermann, Josef; Lottspeich, Friedrich

2012-01-01

302

Protein solubilization: A novel approach.  

PubMed

Formulation development presents significant challenges with respect to protein therapeutics. One component of these challenges is to attain high protein solubility (>50mg/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 4000 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

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

2014-11-15

303

Protein Immobilization Strategies for Protein Biochips  

Microsoft Academic Search

In the past few years, protein biochips have emerged as promising proteomic and diagnostic tools for obtaining information about protein functions and interactions. Important technological innovations have been made. However, considerable development is still required, especially regarding protein immobilization, in order to fully realize the potential of protein biochips. In fact, protein immobilization is the key to the success of

Federica Rusmini; Zhiyuan Zhong; Jan Feijen

2007-01-01

304

PROTEIN ENGINEERING KBK050 Protein Engineering  

E-print Network

PROTEIN ENGINEERING KBK050 Protein Engineering Poäng: 5.0 Betygskala: TH Kursansvarig: Leif Bülow proteiners struktur och funktion. Innehåll: I kursen behandlas hur proteiner kan muteras slumpmässigt och modifierat protein. Litteratur: Brown, T.A.: Gene Cloning, Chapman and Hall, 3rd ed. 1995; Brändén, C

305

DNA to Protein  

NSDL National Science Digital Library

Explore the relationship between the genetic code on the DNA strand and the resulting protein and rudimentary shape it forms. Through models of transcription and translation, you will discover this relationship and the resilience to mutations built into our genetic code. Start by exploring DNAÂs double helix with an interactive 3D model. Highlight base pairs, look at one or both strands, and turn hydrogen bonds on or off. Next, watch an animation of transcription, which creates RNA from DNA, and translation, which Âreads the RNA codons to create a protein.

Consortium, The C.

2012-01-13

306

Recombinant protein polymers in biomaterials.  

PubMed

Naturally occurring protein-based materials have been found that function as critical components in biomechanical response, fibers and adhesives. A relatively small but growing number of recombinant protein-based materials that mimic the desired features of their natural sources, such as collagens, elastins and silks, are considered as an alternative to conventional synthetic polymers. Advances in genetic engineering have facilitated the synthesis of repetitive protein polymers with precise control of molecular weights which are designed by using synthetic genes encoding tandem repeats of oligopeptide originating from a modular domain of natural proteins. Many repeat sequences as protein polymer building blocks adopt a well-defined secondary structure and undergo self-assembly to result in physically cross-linked networks or with chemical cross-linking so that further form three-dimensional architectures similar to natural counterparts. In this review, recombinant protein polymers currently developed will be presented that have emerged as promising class of next generation biomaterials. PMID:23276922

Kim, Wookhyun

2013-01-01

307

G Proteins in Reverse Mode  

PubMed Central

Active G protein-coupled receptors activate heterotrimeric G??? proteins by catalyzing the exchange of GDP by GTP at the G? subunit. A paradoxical attenuation of G protein-activated inwardly rectifying potassium channels (GIRK) upon stimulation of native cells with high concentrations of agonist is known. However, a deactivation of activated G proteins by active receptors has not been experimentally studied in intact cells. We monitored GIRK currents and Go protein activation by means of fluorescence resonance energy transfer (FRET) in parallel. The results suggested that GIRK currents were paradoxically attenuated due to an inactivation of Go proteins by active ?2A-adrenergic receptors. To study the mechanisms, G protein activation and receptor-G protein interactions were analyzed as a function of nucleotide type and nucleotide concentrations by means of FRET, while controlling intracellular nucleotides upon permeabilization of the cell membrane. Results suggested a receptor-catalyzed dissociation of GTP from activated heterotrimeric G???. Consequently, nucleotide-free G proteins were sequestrated in heterotrimeric conformation at the active receptor, thus attenuating downstream signaling in an agonist-dependent manner. PMID:20075078

Hommers, Leif G.; Klenk, Christoph; Dees, Christian; Bünemann, Moritz

2010-01-01

308

Increasing Stability Reduces Conformational Heterogeneity in a Protein Folding  

E-print Network

Increasing Stability Reduces Conformational Heterogeneity in a Protein Folding Intermediate, the results show that protein folding intermediates are ensembles of different structural forms direct experi- mental evidence in support of a basic tenet of energy landscape theory for protein folding

309

Water-protein interactions  

SciTech Connect

The interaction of macromolecules with solvent water is an important determinant of their properties, but this relationship has not yet been described satisfactorily. The following experiments focus on the process of protein hydration - the addition of water to dry protein to obtain the solution state. A detailed description of the sequence of hydration events is expected to produce a fuller understanding of the protein in dilute solution. This approach is analogous to the use of studies of protein unfolding for understanding the folded state. Heat capacity measurements (1) are of particular interest. These can be carried out over the full range of system composition, from dry protein to the dilute solution, and they serve to correlate information obtained by other techniques that can be applied only to solution or solid state but not both. The dependence of the heat capacity on water activity defines stages in the hydration process and suggests the following simple picture of it: water at the lowest activity, 0-0.07 h (g of water/g of protein), bound principally to ionizable groups; in the mid-range of water activity, 0.07 to 0.25 h, surface clusters form, probably centered on polar surface elements; these clusters are mobile, with heat capacity greater than bulk water, and grow with increased water activity until after the polar sites are saturated at 0.25 h. There is a condensation of water over the most weakly interacting portions of the surface, resulting in completion of a water monolayer containing approx. 300 molecules. From this hydration level, 0.38 h, to the dilute solution there are no changes in thermal properties of the protein.

Rupley, J.A.; Yang, P.H.; Tollin, G.

1980-10-01

310

Insulin action on skeletal muscle protein metabolism during catabolic states  

E-print Network

of muscle protein. Evidence of the ability of insulin to stimulate muscle protein synthesis in vivo was also-induced cytokines, resulted in a decrease in insulin action on protein synthesis or degradation. The effect; Inra/ Elsevier, Paris. insulin / skeletal muscle / protein synthesis / protein breakdown / catabolic

Paris-Sud XI, Université de

311

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

PubMed

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

Moosavi, Sobhan; Rahgozar, Masoud; Rahimi, Amir

2013-04-01

312

Protein Kinases  

NSDL National Science Digital Library

This Teaching Resource provides lecture notes and slides for a class covering the structure and function of protein kinases and is part of the course "Cell Signaling Systems: A Course for Graduate Students." The lecture begins with a discussion of the genomics and evolutionary relationships among kinases and then proceeds to describe the structure-function relationships of specific kinases, the molecular mechanisms underlying substrate specificity, and selected issues in regulation of kinase activity.

Avrom Caplan (Mount Sinai School of Medicine;Department of Pharmacology and Biological Chemistry REV)

2005-02-22

313

Protein Factory  

NSDL National Science Digital Library

In this activity, learners take on the role of various parts of the cell in order to model the process of protein synthesis. Each learner receives a card describing, step by step, what s/he should be doing. Learners play the roles of either RNA codons, an RNA polymerase, messenger RNA, a ribosome, or transfer RNA. This activity is designed for a large group of 30 learners, but could be used with smaller groups of at least 10 learners.

Salter, Irene

2012-04-09

314

Breakfast Proteins  

NSDL National Science Digital Library

In this activity, learners construct a cereal chain as a model of how proteins are made in the cell. Learners build their chain off of an initial template which represents a single copy of DNA and hand-written notes, replicating the process of transcription and translation. In this model, the letters of the chain correspond to the colors of the cereal (not the amino acids).

Yu, Julie

2009-01-01

315

Benchtop Detection of Proteins  

NASA Technical Reports Server (NTRS)

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.

Scardelletti, Maximilian C.; Varaljay, Vanessa

2007-01-01

316

Mapping Monomeric Threading to Protein–Protein Structure Prediction  

PubMed Central

The key step of template-based protein–protein structure prediction is the recognition of complexes from experimental structure libraries that have similar quaternary fold. Maintaining two monomer and dimer structure libraries is however laborious, and inappropriate library construction can degrade template recognition coverage. We propose a novel strategy SPRING to identify complexes by mapping monomeric threading alignments to protein–protein interactions based on the original oligomer entries in the PDB, which does not rely on library construction and increases the efficiency and quality of complex template recognitions. SPRING is tested on 1838 nonhomologous protein complexes which can recognize correct quaternary template structures with a TM score >0.5 in 1115 cases after excluding homologous proteins. The average TM score of the first model is 60% and 17% higher than that by HHsearch and COTH, respectively, while the number of targets with an interface RMSD <2.5 Å by SPRING is 134% and 167% higher than these competing methods. SPRING is controlled with ZDOCK on 77 docking benchmark proteins. Although the relative performance of SPRING and ZDOCK depends on the level of homology filters, a combination of the two methods can result in a significantly higher model quality than ZDOCK at all homology thresholds. These data demonstrate a new efficient approach to quaternary structure recognition that is ready to use for genome-scale modeling of protein–protein interactions due to the high speed and accuracy. PMID:23413988

Guerler, Aysam; Govindarajoo, Brandon; Zhang, Yang

2014-01-01

317

Repeated measures of body mass index and C-reactive protein in relation to all-cause mortality and cardiovascular disease: results from the consortium on health and ageing network of cohorts in Europe and the United States (CHANCES).  

PubMed

Obesity has been linked with elevated levels of C-reactive protein (CRP), and both have been associated with increased risk of mortality and cardiovascular disease (CVD). Previous studies have used a single 'baseline' measurement and such analyses cannot account for possible changes in these which may lead to a biased estimation of risk. Using four cohorts from CHANCES which had repeated measures in participants 50 years and older, multivariate time-dependent Cox proportional hazards was used to estimate hazard ratios (HR) and 95 % confidence intervals (CI) to examine the relationship between body mass index (BMI) and CRP with all-cause mortality and CVD. Being overweight (?25-<30 kg/m(2)) or moderately obese (?30-<35) tended to be associated with a lower risk of mortality compared to normal (?18.5-<25): ESTHER, HR (95 % CI) 0.69 (0.58-0.82) and 0.78 (0.63-0.97); Rotterdam, 0.86 (0.79-0.94) and 0.80 (0.72-0.89). A similar relationship was found, but only for overweight in Glostrup, HR (95 % CI) 0.88 (0.76-1.02); and moderately obese in Tromsø, HR (95 % CI) 0.79 (0.62-1.01). Associations were not evident between repeated measures of BMI and CVD. Conversely, increasing CRP concentrations, measured on more than one occasion, were associated with an increasing risk of mortality and CVD. Being overweight or moderately obese is associated with a lower risk of mortality, while CRP, independent of BMI, is positively associated with mortality and CVD risk. If inflammation links CRP and BMI, they may participate in distinct/independent pathways. Accounting for independent changes in risk factors over time may be crucial for unveiling their effects on mortality and disease morbidity. PMID:25421782

O'Doherty, Mark G; Jørgensen, Torben; Borglykke, Anders; Brenner, Hermann; Schöttker, Ben; Wilsgaard, Tom; Siganos, Galatios; Kavousi, Maryam; Hughes, Maria; Müezzinler, Aysel; Holleczek, Bernd; Franco, Oscar H; Hofman, Albert; Boffetta, Paolo; Trichopoulou, Antonia; Kee, Frank

2014-12-01

318

BIOCHEMISTRY: How Do Proteins Interact?  

NSDL National Science Digital Library

Access to the article is free, however registration and sign-in are required. New results provide support for the hypothesis that interactions between proteins involve selection from an ensemble of different conformations.

David D. Boehr (The Scripps Research Institute;Department of Molecular Biology and Skaggs Institute for Chemical Biology); Peter E. Wright (The Scripps Research Institute;Department of Molecular Biology and Skaggs Institute for Chemical Biology)

2008-06-13

319

Collective prediction of protein functions from protein-protein interaction networks  

PubMed Central

Background Automated assignment of functions to unknown proteins is one of the most important task in computational biology. The development of experimental methods for genome scale analysis of molecular interaction networks offers new ways to infer protein function from protein-protein interaction (PPI) network data. Existing techniques for collective classification (CC) usually increase accuracy for network data, wherein instances are interlinked with each other, using a large amount of labeled data for training. However, the labeled data are time-consuming and expensive to obtain. On the other hand, one can easily obtain large amount of unlabeled data. Thus, more sophisticated methods are needed to exploit the unlabeled data to increase prediction accuracy for protein function prediction. Results In this paper, we propose an effective Markov chain based CC algorithm (ICAM) to tackle the label deficiency problem in CC for interrelated proteins from PPI networks. Our idea is to model the problem using two distinct Markov chain classifiers to make separate predictions with regard to attribute features from protein data and relational features from relational information. The ICAM learning algorithm combines the results of the two classifiers to compute the ranks of labels to indicate the importance of a set of labels to an instance, and uses an ICA framework to iteratively refine the learning models for improving performance of protein function prediction from PPI networks in the paucity of labeled data. Conclusion Experimental results on the real-world Yeast protein-protein interaction datasets show that our proposed ICAM method is better than the other ICA-type methods given limited labeled training data. This approach can serve as a valuable tool for the study of protein function prediction from PPI networks. PMID:24564855

2014-01-01

320

Prediction of Protein-Protein Interaction Strength Using Domain Features with Supervised Regression  

PubMed Central

Proteins in living organisms express various important functions by interacting with other proteins and molecules. Therefore, many efforts have been made to investigate and predict protein-protein interactions (PPIs). Analysis of strengths of PPIs is also important because such strengths are involved in functionality of proteins. In this paper, we propose several feature space mappings from protein pairs using protein domain information to predict strengths of PPIs. Moreover, we perform computational experiments employing two machine learning methods, support vector regression (SVR) and relevance vector machine (RVM), for dataset obtained from biological experiments. The prediction results showed that both SVR and RVM with our proposed features outperformed the best existing method. PMID:25093200

Sakuma, Yusuke

2014-01-01

321

Identifying protein complexes based on density and modularity in protein-protein interaction network  

PubMed Central

Background Identifying protein complexes is crucial to understanding principles of cellular organization and functional mechanisms. As many evidences have indicated that the subgraphs with high density or with high modularity in PPI network usually correspond to protein complexes, protein complexes detection methods based on PPI network focused on subgraph's density or its modularity in PPI network. However, dense subgraphs may have low modularity and subgraph with high modularity may have low density, which results that protein complexes may be subgraphs with low modularity or with low density in the PPI network. As the density-based methods are difficult to mine protein complexes with low density, and the modularity-based methods are difficult to mine protein complexes with low modularity, both two methods have limitation for identifying protein complexes with various density and modularity. Results To identify protein complexes with various density and modularity, including those have low density but high modularity and those have low modularity but high density, we define a novel subgraph's fitness, f?, as f?= (density)?*(modularity)1-?, and propose a novel algorithm, named LF_PIN, to identify protein complexes by expanding seed edges to subgraphs with the local maximum fitness value. Experimental results of LF-PIN in S.cerevisiae show that compared with the results of fitness equal to density (? = 1) or equal to modularity (? = 0), the LF-PIN identifies known protein complexes more effectively when the fitness value is decided by both density and modularity (0results of seven competing protein complex detection methods (CMC, Core-Attachment, CPM, DPClus, HC-PIN, MCL, and NFC) in S.cerevisiae and E.coli, LF-PIN outperforms other seven methods in terms of matching with known complexes and functional enrichment. Moreover, LF-PIN has better performance in identifying protein complexes with low density or with low modularity. Conclusions By considering both the density and the modularity, LF-PIN outperforms other protein complexes detection methods that only consider density or modularity, especially in identifying known protein complexes with low density or low modularity. PMID:24565048

2013-01-01

322

Posttranslational modification of proteins during intermittent hypoxia  

Microsoft Academic Search

Post-translational modification (PTM) is one of the mechanisms by which protein function is regulated by chronic hypoxia. This article presents an overview of recent findings on PTM of proteins induced by chronic intermittent hypoxia (CIH) which is experienced by humans with sleep disordered breathing resulting in autonomic abnormalities. The analysis of PTM of proteins involves electrophoretic separation of tissue or

Ganesh K. Kumar; Nanduri R. Prabhakar

2008-01-01

323

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...

324

A surprising simplicity to protein folding  

Microsoft Academic Search

The polypeptide chains that make up proteins have thousands of atoms and hence millions of possible inter-atomic interactions. It might be supposed that the resulting complexity would make prediction of protein structure and protein-folding mechanisms nearly impossible. But the fundamental physics underlying folding may be much simpler than this complexity would lead us to expect: folding rates and mechanisms appear

David Baker

2000-01-01

325

Mercury-binding proteins of Mytilus edulis  

SciTech Connect

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.

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

1981-11-01

326

Protein-protein interaction networks (PPI) and complex diseases  

PubMed Central

The physical interaction of proteins which lead to compiling them into large densely connected networks is a noticeable subject to investigation. Protein interaction networks are useful because of making basic scientific abstraction and improving biological and biomedical applications. Based on principle roles of proteins in biological function, their interactions determine molecular and cellular mechanisms, which control healthy and diseased states in organisms. Therefore, such networks facilitate the understanding of pathogenic (and physiologic) mechanisms that trigger the onset and progression of diseases. Consequently, this knowledge can be translated into effective diagnostic and therapeutic strategies. Furthermore, the results of several studies have proved that the structure and dynamics of protein networks are disturbed in complex diseases such as cancer and autoimmune disorders. Based on such relationship, a novel paradigm is suggested in order to confirm that the protein interaction networks can be the target of therapy for treatment of complex multi-genic diseases rather than individual molecules with disrespect the network. PMID:25436094

Safari-Alighiarloo, Nahid; Taghizadeh, Mohammad; Rezaei-Tavirani, Mostafa; Goliaei, Bahram

2014-01-01

327

Electrostatic aspects of protein–protein interactions  

Microsoft Academic Search

Structural and mutational analyses reveal a central role for electrostatic interactions in protein–protein association. Experiment and theory both demonstrate that clusters of charged and polar residues that are located on protein–protein interfaces may enhance complex stability, although the total effect of electrostatics is generally net destabilizing. The past year also witnessed significant progress in our understanding of the effect of

Felix B Sheinerman; Raquel Norel; Barry Honig

2000-01-01

328

Moonlighting proteins: old proteins learning new tricks  

Microsoft Academic Search

Recently, several laboratories identifying proteins involved in the complex processes of replication, transcription and tumor suppression found that the ‘new’ protein they discovered had another, previously identified, function. A single protein with multiple functions might seem surprising, but there are actually many cases of proteins that ‘moonlight’, or have more than one role in an organism. As well as adding

Constance J. Jeffery

2003-01-01

329

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

E-print Network

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 ...

Kim, Do-Nyun

330

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

PubMed

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

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

2014-11-01

331

The Two-Hybrid System: A Method to Identify and Clone Genes for Proteins that Interact with a Protein of Interest  

Microsoft Academic Search

We describe a method that detects proteins capable of interacting with a known protein and that results in the immediate availability of the cloned genes for these interacting proteins. Plasmids are constructed to encode two hybrid proteins. One hybrid consists of the DNA-binding domain of the yeast transcriptional activator protein GAL4 fused to the known protein; the other hybrid consists

Cheng-Ting Chien; Paul L. Bartel; Rolf Sternglanz

1991-01-01

332

Solid-state protein formulations.  

PubMed

When formulated as liquid dosage forms, therapeutic proteins and peptides often show instability during handling as a result of chemical degradation. Solid formulations are frequently required to maintain protein stability during storage, transport and upon administration. Herein we highlight current strategies used to formulate pharmaceutical proteins in the solid form. An overview of the physical instabilities which can arise with proteins is first described. The key solidification techniques of crystallization, freeze-drying and particle forming technologies are then discussed. Examples of current commercial products that are formulated in the solid state are provided and include neutral protamine Hagedorn - insulin crystal suspensions, freeze-dried monoclonal antibodies and leuproride polylactide-co-glycolide microparticles. Finally, future perspectives in solid-state protein formulation are described. PMID:25565441

Angkawinitwong, Ukrit; Sharma, Garima; Khaw, Peng T; Brocchini, Steve; Williams, Gareth R

2015-01-01

333

Protein aggregation and lyophilization: Protein structural descriptors as predictors of aggregation propensity.  

PubMed

Lyophilization can induce aggregation in therapeutic proteins, but the relative importance of protein structure, formulation and processing conditions are poorly understood. To evaluate the contribution of protein structure to lyophilization-induced aggregation, fifteen proteins were co-lyophilized with each of five excipients. Extent of aggregation following lyophilization, measured using size-exclusion chromatography, was correlated with computational and biophysical protein structural descriptors via multiple linear regression. Descriptor selection was performed using exhaustive search and forward selection. The results demonstrate that, for a given excipient, extent of aggregation is highly correlated by eight to twelve structural descriptors. Leave-one-out cross validation showed that the correlations were able to successfully predict the aggregation for a protein "left out" of the data set. Selected descriptors varied with excipient, indicating both protein structure and excipient type contribute to lyophilization-induced aggregation. The results show some descriptors used to predict protein aggregation in solution are useful in predicting lyophilized protein aggregation. PMID:24516290

Roughton, Brock C; Iyer, Lavanya K; Bertelsen, Esben; Topp, Elizabeth M; Camarda, Kyle V

2013-11-11

334

Protein aggregation and lyophilization: Protein structural descriptors as predictors of aggregation propensity  

PubMed Central

Lyophilization can induce aggregation in therapeutic proteins, but the relative importance of protein structure, formulation and processing conditions are poorly understood. To evaluate the contribution of protein structure to lyophilization-induced aggregation, fifteen proteins were co-lyophilized with each of five excipients. Extent of aggregation following lyophilization, measured using size-exclusion chromatography, was correlated with computational and biophysical protein structural descriptors via multiple linear regression. Descriptor selection was performed using exhaustive search and forward selection. The results demonstrate that, for a given excipient, extent of aggregation is highly correlated by eight to twelve structural descriptors. Leave-one-out cross validation showed that the correlations were able to successfully predict the aggregation for a protein “left out” of the data set. Selected descriptors varied with excipient, indicating both protein structure and excipient type contribute to lyophilization-induced aggregation. The results show some descriptors used to predict protein aggregation in solution are useful in predicting lyophilized protein aggregation. PMID:24516290

Roughton, Brock C.; Iyer, Lavanya K.; Bertelsen, Esben; Topp, Elizabeth M.; Camarda, Kyle V.

2014-01-01

335

Contribution of sarcoplasmic proteins to myofibrillar proteins gelation.  

PubMed

Surimi, a refined protein extract, is produced by solubilizing myofibrillar proteins during the comminuting and salting stages of manufacturing. The resulting paste gels on heating to produce kamaboko or a range of analog shellfish such as crab claw, filament sticks, fish mushroom, and so on. The myosin molecule is the major myofibrillar protein in gelation. It is believed that washing steps during the traditional surimi process play an important role in enhancing the gel properties of the resultant kamaboko by removing water-soluble (sarcoplasmic, Sp-P) proteins. By contrast, some researchers claim that retaining Sp-P or adding it into the surimi gel network not only does not interfere with the action of myofibrillar proteins during the sol-gel transition step but also improves the gel characteristics of the resultant kamaboko. It seems that retention of Sp-P or their addition into raw surimi does enhance the textural properties of kamaboko gel perhaps by functioning as a proteinase inhibitor, particularly against trypsin and trypsin-like proteinases but this depends on the type of applied surimi process. Among different types of Sp-P, it has been claimed that some proteins such as endogenous transglutaminase (TGase) play a more important role than other Sp-P in bond formation, by catalyzing the cross-linking of myosin heavy chain (MHC) molecules during low-temperature setting of surimi, resulting a more elastic kamaboko gel. PMID:22224956

Jafarpour, Ali; Gorczyca, Elisabeth M

2012-02-01

336

Dynamics of protein conformations  

NASA Astrophysics Data System (ADS)

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.

Stepanova, Maria

2010-10-01

337

A method for investigating protein-protein interactions related to Salmonella Typhimurium pathogenesis  

PubMed Central

We successfully modified an existing method to investigate protein-protein interactions in the pathogenic bacterium Salmonella enterica serovar Typhimurium (S. Typhimurium). 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 and 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 eliminate the possibility of identifying background and non-specific proteins as interacting partners, especially those caused by non-specific binding to the stationary phase used for protein purification. In an initial demonstration of this approach, we tagged three Salmonella 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 for each bait protein, including the known binding partners such as HimA for HimD, as well as unexpected binding partners. Our results suggest that novel protein-protein interactions may be critical to pathogenesis by Salmonella. PMID:19206470

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

2009-01-01

338

Quantitative study of protein-protein interactions by quartz nanopipettes.  

PubMed

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. PMID:25060094

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

2014-09-01

339

Discover protein sequence signatures from protein-protein interaction data  

E-print Network

Background: The development of high-throughput technologies such as yeast two- hybrid systems and mass spectrometry technologies has made it possible to generate large protein-protein interaction ( PPI) datasets. Mining ...

Fang, Jianwen; Haasl, R. J.; Dong, Yinghua; Lushington, Gerald H.

2005-11-23

340

Contact Density Affects Protein Evolutionary Rate from Bacteria to Animals  

Microsoft Academic Search

The density of contacts or the fraction of buried sites in a protein structure is thought to be related to a protein’s designability,\\u000a and genes encoding more designable proteins should evolve faster than other genes. Several recent studies have tested this\\u000a hypothesis but have found conflicting results. Here, we investigate how a gene’s evolutionary rate is affected by its protein’s

Tong Zhou; D. Allan Drummond; Claus O. Wilke

2008-01-01

341

Dual targeting of peroxisomal proteins  

PubMed Central

Cellular compartmentalization into organelles serves to separate biological processes within the environment of a single cell. While some metabolic reactions are specific to a single organelle, others occur in more than one cellular compartment. Specific targeting of proteins to compartments inside of eukaryotic cells is mediated by defined sequence motifs. To achieve multiple targeting to different compartments cells use a variety of strategies. Here, we focus on mechanisms leading to dual targeting of peroxisomal proteins. In many instances, isoforms of peroxisomal proteins with distinct intracellular localization are encoded by separate genes. But also single genes can give rise to differentially localized proteins. Different isoforms can be generated by use of alternative transcriptional start sites, by differential splicing or ribosomal read-through of stop codons. In all these cases different peptide variants are produced, of which only one carries a peroxisomal targeting signal. Alternatively, peroxisomal proteins contain additional signals that compete for intracellular targeting. Dual localization of proteins residing in both the cytoplasm and in peroxisomes may also result from use of inefficient targeting signals. The recent observation that some bona fide cytoplasmic enzymes were also found in peroxisomes indicates that dual targeting of proteins to both the cytoplasm and the peroxisome might be more widespread. Although current knowledge of proteins exhibiting only partial peroxisomal targeting is far from being complete, we speculate that the metabolic capacity of peroxisomes might be larger than previously assumed. PMID:24151469

Ast, Julia; Stiebler, Alina C.; Freitag, Johannes; Bölker, Michael

2013-01-01

342

Protein compressibility, dynamics, and pressure.  

PubMed Central

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

Kharakoz, D P

2000-01-01

343

Nanobiomechanics of proteins and biomembrane  

PubMed Central

A review of the work done in the Laboratory of Biodynamics of Tokyo Institute of Technology in the last decade has been summarized in this article in relation to the results reported from other laboratories. The emphasis here is the application of nanomechanics based on the force mode of atomic force microscopy (AFM) to proteins and protein-based biological structures. Globular proteins were stretched in various ways to detect the localized rigidity inside of the molecule. When studied by this method, bovine carbonic anhydrase II (BCA II), calmodulin and OspA protein all showed the presence of localized rigid structures inside the molecules. Protein compression experiments were done on BCA II to obtain an estimate of the Young modulus and its change in the process of denaturation. Then, the AFM probe method was turned on to cell membranes and cytoplasmic components. Force curves accompanying the extraction process of membrane proteins from intact cells were analysed in relation to their interaction with the cytoskeletal components. By pushing the AFM probe further into the cytoplasm, mRNAs were recovered from a live cell with minimal damage, and multiplied using PCR technology for their identification. Altogether, the work introduced here forms the basis of nanomechanics of protein and protein-based biostructures and application of the nanomechanical technology to cell biology. PMID:18339603

Ikai, Atsushi

2008-01-01

344

Water at interface with proteins  

E-print Network

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.

Giancarlo Franzese; Valentino Bianco; Svilen Iskrov

2010-12-07

345

Dietary protein and bone health.  

PubMed

The effects of dietary protein on bone health are paradoxical and need to be considered in context of the age, health status and usual diet of the population. Over the last 80 years numerous studies have demonstrated that a high protein intake increases urinary Ca excretion and that on average 1 mg Ca is lost in urine for every 1 g rise in dietary protein. This relationship is primarily attributable to metabolism of S amino acids present in animal and some vegetable proteins, resulting in a greater acid load and buffering response by the skeleton. However, many of these early studies that demonstrated the calciuric effects of protein were limited by low subject numbers, methodological errors and the use of high doses of purified forms of protein. Furthermore, the cross-cultural and population studies that showed a positive association between animal-protein intake and hip fracture risk did not consider other lifestyle or dietary factors that may protect or increase the risk of fracture. The effects of protein on bone appear to be biphasic and may also depend on intake of Ca- and alkali-rich foods, such as fruit and vegetables. At low protein intakes insulin-like growth factor production is reduced, which in turn has a negative effect on Ca and phosphate metabolism, bone formation and muscle cell synthesis. Although growth and skeletal development is impaired at very low protein intakes, it is not known whether variations in protein quality affect the achievement of optimal peak bone mass in adolescents and young adults. Prospective studies in the elderly in the USA have shown that the greatest bone losses occur in elderly men and women with an average protein intake of 16-50 g/d. Although a low protein intake may be indicative of a generally poorer diet and state of health, there is a need to evaluate whether there is a lower threshold for protein intake in the elderly in Europe that may result in increased bone loss and risk of osteoporotic fracture. PMID:15018487

Ginty, Fiona

2003-11-01

346

IsothermalCalorimeter for determining protein-protein, protein-peptide, protein-ligand and protein-small molecule  

E-print Network

Facilities · IsothermalCalorimeter for determining protein-protein, protein-peptide, protein-ligand and protein-small molecule interactions. · UV-VisibleSpectrophotometerduoflows can be utilised to monitor secondary structure and tertiary structure of protein folding. · Automated

Hickman, Mark

347

Evolutionary Optimization of Protein Folding  

PubMed Central

Nature has shaped the make up of proteins since their appearance, 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 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

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

2013-01-01

348

Evolutionary optimization of protein folding.  

PubMed

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

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

2013-01-01

349

Solubility of commercial milk protein concentrates and milk protein isolates.  

PubMed

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?¹ region exhibited the highest discriminating power, with dominant bands at 1,173 and 968 cm?¹, 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

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

2011-12-01

350

Transfer and amplification of a mutant beta-tubulin gene results in colcemid dependence: use of the transformant to demonstrate regulation of beta-tubulin subunit levels by protein degradation.  

PubMed Central

Total genomic DNA from a temperature-sensitive, colcemid-resistant Chinese hamster ovary (CHO) cell mutant expressing an electrophoretic variant beta-tubulin was used to transform wild-type CHO cells to colcemid-resistant cells at 37 degrees C. Southern blot analysis of the transformant demonstrated the three- to fivefold amplification of one of many beta-tubulin sequences compared with that of the wild type or mutant, thereby identifying a functional tubulin gene in CHO cells. This amplification of one tubulin-coding sequence resulted in a threefold increase in two beta-tubulin mRNA species, suggesting that both species may be encoded by a single gene. Pulse-chase experiments showed that in the transformant, total beta-tubulin was synthesized and degraded faster than in the revertant or wild-type cells, so that the steady-state levels of beta-tubulin and alpha-tubulin were unchanged in the transformant compared with those of wild-type, mutant, or revertant cells. Increased ratios of mutant to wild-type beta-tubulin made the transformant dependent on microtubule-depolymerizing drugs for growth at 37 but not 34 degrees C and supersensitive to the microtubule-stabilizing drug taxol at 34 degrees C. Images PMID:3785170

Whitfield, C; Abraham, I; Ascherman, D; Gottesman, M M

1986-01-01

351

Integrated Analysis of Residue Coevolution and Protein Structures Capture Key Protein Sectors in HIV-1 Proteins  

PubMed Central

HIV type 1 (HIV-1) is characterized by its rapid genetic evolution, leading to challenges in anti-HIV therapy. However, the sequence variations in HIV-1 proteins are not randomly distributed due to a combination of functional constraints and genetic drift. In this study, we examined patterns of sequence variability for evidence of linked sequence changes (termed as coevolution or covariation) in 15 HIV-1 proteins. It shows that the percentage of charged residues in the coevolving residues is significantly higher than that in all the HIV-1 proteins. Most of the coevolving residues are spatially proximal in the protein structures and tend to form relatively compact and independent units in the tertiary structures, termed as “protein sectors”. These protein sectors are closely associated with anti-HIV drug resistance, T cell epitopes, and antibody binding sites. Finally, we explored candidate peptide inhibitors based on the protein sectors. Our results can establish an association between the coevolving residues and molecular functions of HIV-1 proteins, and then provide us with valuable knowledge of pathology of HIV-1 and therapeutics development. PMID:25671429

Zhao, Yuqi; Wang, Yanjie; Gao, Yuedong; Li, Gonghua; Huang, Jingfei

2015-01-01

352

Distinguishing Proteins From Arbitrary Amino Acid Sequences  

PubMed Central

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

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

2015-01-01

353

Distinguishing proteins from arbitrary amino Acid sequences.  

PubMed

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

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

2015-01-01

354

Improving accuracy of protein-protein interaction prediction by considering the converse problem for sequence representation  

PubMed Central

Background With the development of genome-sequencing technologies, protein sequences are readily obtained by translating the measured mRNAs. Therefore predicting protein-protein interactions from the sequences is of great demand. The reason lies in the fact that identifying protein-protein interactions is becoming a bottleneck for eventually understanding the functions of proteins, especially for those organisms barely characterized. Although a few methods have been proposed, the converse problem, if the features used extract sufficient and unbiased information from protein sequences, is almost untouched. Results In this study, we interrogate this problem theoretically by an optimization scheme. Motivated by the theoretical investigation, we find novel encoding methods for both protein sequences and protein pairs. Our new methods exploit sufficiently the information of protein sequences and reduce artificial bias and computational cost. Thus, it significantly outperforms the available methods regarding sensitivity, specificity, precision, and recall with cross-validation evaluation and reaches ~80% and ~90% accuracy in Escherichia coli and Saccharomyces cerevisiae respectively. Our findings here hold important implication for other sequence-based prediction tasks because representation of biological sequence is always the first step in computational biology. Conclusions By considering the converse problem, we propose new representation methods for both protein sequences and protein pairs. The results show that our method significantly improves the accuracy of protein-protein interaction predictions. PMID:22024143

2011-01-01

355

Nutritional quality of rice bran protein in comparison to animal and vegetable protein.  

PubMed

Rice bran protein (RBP) was prepared by alkali extraction and isoelectric precipitation from defatted rice bran. The protein quality of RPB was evaluated and compared to two vegetable proteins [soy protein (ISP) and rice endosperm protein (REP)] and two animal proteins [whey protein (WPI) and casein]. RPB contained 74.93% of protein and its pepsin digestibility and KOH solubility were 89.8% and 91.5%, respectively. In Sprague-Dawley rats, RBP showed protein efficiency ratio, net protein ratio, net protein utilisation, and biological value of 2.39, 3.77, 70.7, and 72.6, which were comparable to the qualities of animal proteins. The true digestibility of RBP (94.8%) was significantly higher than that of REP (90.8%), ISP (91.7%) and WPI (92.8%) and the same as that of casein. Protein digestibility corrected amino acid score (PDCAAS) of RBP was 0.90. These results suggest that rice bran protein appears to be a promising protein source with good biological values and digestibility. PMID:25442618

Han, Sung-Wook; Chee, Kyu-Man; Cho, Seong-Jun

2015-04-01

356

Detecting internally symmetric protein structures  

PubMed Central

Background Many functional proteins have a symmetric structure. Most of these are multimeric complexes, which are made of non-symmetric monomers arranged in a symmetric manner. However, there are also a large number of proteins that have a symmetric structure in the monomeric state. These internally symmetric proteins are interesting objects from the point of view of their folding, function, and evolution. Most algorithms that detect the internally symmetric proteins depend on finding repeating units of similar structure and do not use the symmetry information. Results We describe a new method, called SymD, for detecting symmetric protein structures. The SymD procedure works by comparing the structure to its own copy after the copy is circularly permuted by all possible number of residues. The procedure is relatively insensitive to symmetry-breaking insertions and deletions and amplifies positive signals from symmetry. It finds 70% to 80% of the TIM barrel fold domains in the ASTRAL 40 domain database and 100% of the beta-propellers as symmetric. More globally, 10% to 15% of the proteins in the ASTRAL 40 domain database may be considered symmetric according to this procedure depending on the precise cutoff value used to measure the degree of perfection of the symmetry. Symmetrical proteins occur in all structural classes and can have a closed, circular structure, a cylindrical barrel-like structure, or an open, helical structure. Conclusions SymD is a sensitive procedure for detecting internally symmetric protein structures. Using this procedure, we estimate that 10% to 15% of the known protein domains may be considered symmetric. We also report an initial, overall view of the types of symmetries and symmetric folds that occur in the protein domain structure universe. PMID:20525292

2010-01-01

357

Quinary structure modulates protein stability in cells.  

PubMed

Protein quinary interactions organize the cellular interior and its metabolism. Although the interactions stabilizing secondary, tertiary, and quaternary protein structure are well defined, details about the protein-matrix contacts that comprise quinary structure remain elusive. This gap exists because proteins function in the crowded cellular environment, but are traditionally studied in simple buffered solutions. We use NMR-detected H/D exchange to quantify quinary interactions between the B1 domain of protein G and the cytosol of Escherichia coli. We demonstrate that a surface mutation in this protein is 10-fold more destabilizing in cells than in buffer, a surprising result that firmly establishes the significance of quinary interactions. Remarkably, the energy involved in these interactions can be as large as the energies that stabilize specific protein complexes. These results will drive the critical task of implementing quinary structure into models for understanding the proteome. PMID:25624496

Monteith, William B; Cohen, Rachel D; Smith, Austin E; Guzman-Cisneros, Emilio; Pielak, Gary J

2015-02-10

358

Resource Seminar 2007: Introduction to Linux Eun-seo Choi  

E-print Network

Windows desktop or laptop. Then, you can keep working as if you locally logged in a linux server. Let's imagine a situation where you are wokring on your MS Windows laptop at home but want to finish up your Ge://www.straightrunning.com/XmingNotes/), or X-Win32 (http: //www.starnet.com/products/xwin32/). The first two are free; the latter is commercial

Choi, Eunseo

359

Seo 312 Reitoria /Tcnico-Administrativos Local: Auditrio da Reitoria  

E-print Network

DUARTE FILHO REITORIA-servidor 312 ADRIANA REGINA C.ESPINDOLA KOBIYAMA REITORIA-servidor 312 ADRIANE-servidor 312 ALINE MARIA VIEIRA DA COSTA REITORIA-servidor 312 ALITA DIANA CORREA KUCHLER REITORIA-servidor 312

Floeter, Sergio Ricardo

360

updated 10/08/10 seo5 Graduate Student Activities  

E-print Network

Chair's Asst 368.6252 kar18@case.edu SOM E653 Nutrition http://www.case.edu/med/nutrition/phd_nutrition, WRB5136 Blood Club (Cancer Center) Fridays, noon, BRB105 Neurodegeneration Journal Club Fridays, noon

Yang, Sichun

361

Seo 103 CCB/DOCENTES Local : Sala do Conselho -CCB  

E-print Network

ADAIR ROBERTO SOARES DOS SANTOS CCB-professor 103 ADEMIR NEVES CCB-professor 103 ADJA BALBINO DE AMORIM ANA CLAUDIA RODRIGUES CCB-professor 103 ANA LUCIA SEVERO RODRIGUES CCB-professor 103 ANA LUIZA BRITTO

Floeter, Sergio Ricardo

362

Protein in diet  

MedlinePLUS

... basic structure of protein is a chain of amino acids. You need protein in your diet to help ... Protein foods are broken down into parts called amino acids during digestion. The human body needs a number ...

363

Protein conformational modifications and kinetics of water-protein interactions in milk protein concentrate powder upon aging: effect on solubility.  

PubMed

Protein conformational modifications and water-protein interactions are two major factors believed to induce instability of protein and eventually affect the solubility of milk protein concentrate (MPC) powder. To test these hypotheses, MPC was stored at different water activities (a(w) 0.0-0.85) and temperatures (25 and 45 degrees C) for up to 12 weeks. Samples were examined periodically to determine solubility, change in protein conformation by Fourier transform infrared (FTIR) spectroscopy and principal component analysis (PCA), and water status (interaction of water with the protein molecule/surface) by measuring the transverse relaxation time (T(2)) with proton nuclear magnetic resonance ((1)H NMR). The solubility of MPC decreased significantly with aging, and this process was enhanced by increasing water activity (a(w)) and storage temperature. Minor changes in protein secondary structure were observed with FTIR, which indicated some degree of unfolding of protein molecules. PCA of the FTIR data was able to discriminate samples according to moisture content and storage period. Partial least-squares (PLS) analysis showed some correlation between FTIR spectral feature and solubility. The NMR T(2) results indicated the presence of three distinct populations of water molecules, and the proton signal intensity and T(2) values of proton fractions varied with storage conditions (humidity, temperature) and aging. Results suggest that protein/protein interactions may be initiated by unfolding of protein molecules that eventually affects solubility. PMID:20536137

Haque, Enamul; Bhandari, Bhesh R; Gidley, Michael J; Deeth, Hilton C; Møller, Sandie M; Whittaker, Andrew K

2010-07-14

364

PINT: Protein-protein Interactions Thermodynamic Database  

Microsoft Academic Search

The first release of Protein-protein Interactions Thermodynamic Database (PINT) contains .1500 data of several thermodynamic parameters along with sequence and structural information, experi- mental conditions and literature information. Each entry contains numerical data for the free energy change, dissociation constant, association constant, enthalpy change, heat capacity change and so on of the interacting proteins upon binding, which are important for

M. D. Shaji Kumar; M. Michael Gromiha

2006-01-01

365

Side-Chain Conformational Changes upon Protein-Protein Association  

PubMed Central

Conformational changes upon protein-protein association are the key element of the binding mechanism. The study presents a systematic large-scale analysis of such conformational changes in the side chains. The results indicate that short and long side chains have different propensities for the conformational changes. Long side chains with three or more dihedral angles are often subject to large conformational transition. Shorter residues with one or two dihedral angles typically undergo local conformational changes not leading to a conformational transition. The relationship between the local readjustments and the equilibrium fluctuations of a side chain around its unbound conformation is suggested. Most of the side chains undergo larger changes in the dihedral angle most distant from the backbone. The frequencies of the core-to-surface interface transitions of six nonpolar residues and Tyr are larger than the frequencies of the opposite, surface-to-core transitions. The binding increases both polar and nonpolar interface areas. However, the increase of the nonpolar area is larger for all considered classes of protein complexes, suggesting that the protein association perturbs the unbound interfaces to increase the hydrophobic contribution to the binding free energy. To test modeling approaches to side-chain flexibility in protein docking, conformational changes in the X-ray set were compared with those in the docking decoys sets. The results lead to a better understanding of the conformational changes in proteins and suggest directions for efficient conformational sampling in docking protocols. PMID:21354429

Ruvinsky, Anatoly M.; Kirys, Tatsiana; Tuzikov, Alexander V.; Vakser, Ilya A.

2011-01-01

366

Encounter complexes and dimensionality reduction in protein-protein association.  

PubMed

An outstanding challenge has been to understand the mechanism whereby proteins associate. We report here the results of exhaustively sampling the conformational space in protein-protein association using a physics-based energy function. The agreement between experimental intermolecular paramagnetic relaxation enhancement (PRE) data and the PRE profiles calculated from the docked structures shows that the method captures both specific and non-specific encounter complexes. To explore the energy landscape in the vicinity of the native structure, the nonlinear manifold describing the relative orientation of two solid bodies is projected onto a Euclidean space in which the shape of low energy regions is studied by principal component analysis. Results show that the energy surface is canyon-like, with a smooth funnel within a two dimensional subspace capturing over 75% of the total motion. Thus, proteins tend to associate along preferred pathways, similar to sliding of a protein along DNA in the process of protein-DNA recognition. DOI: http://dx.doi.org/10.7554/eLife.01370.001. PMID:24714491

Kozakov, Dima; Li, Keyong; Hall, David R; Beglov, Dmitri; Zheng, Jiefu; Vakili, Pirooz; Schueler-Furman, Ora; Paschalidis, Ioannis Ch; Clore, G Marius; Vajda, Sandor

2014-01-01

367

Encounter complexes and dimensionality reduction in protein–protein association  

PubMed Central

An outstanding challenge has been to understand the mechanism whereby proteins associate. We report here the results of exhaustively sampling the conformational space in protein–protein association using a physics-based energy function. The agreement between experimental intermolecular paramagnetic relaxation enhancement (PRE) data and the PRE profiles calculated from the docked structures shows that the method captures both specific and non-specific encounter complexes. To explore the energy landscape in the vicinity of the native structure, the nonlinear manifold describing the relative orientation of two solid bodies is projected onto a Euclidean space in which the shape of low energy regions is studied by principal component analysis. Results show that the energy surface is canyon-like, with a smooth funnel within a two dimensional subspace capturing over 75% of the total motion. Thus, proteins tend to associate along preferred pathways, similar to sliding of a protein along DNA in the process of protein-DNA recognition. DOI: http://dx.doi.org/10.7554/eLife.01370.001 PMID:24714491

Kozakov, Dima; Li, Keyong; Hall, David R; Beglov, Dmitri; Zheng, Jiefu; Vakili, Pirooz; Schueler-Furman, Ora; Paschalidis, Ioannis Ch; Clore, G Marius; Vajda, Sandor

2014-01-01

368

Hash subgraph pairwise kernel for protein-protein interaction extraction.  

PubMed

Extracting protein-protein interaction (PPI) from biomedical literature is an important task in biomedical text mining (BioTM). In this paper, we propose a hash subgraph pairwise (HSP) kernel-based approach for this task. The key to the novel kernel is to use the hierarchical hash labels to express the structural information of subgraphs in a linear time. We apply the graph kernel to compute dependency graphs representing the sentence structure for protein-protein interaction extraction task, which can efficiently make use of full graph structural information, and particularly capture the contiguous topological and label information ignored before. We evaluate the proposed approach on five publicly available PPI corpora. The experimental results show that our approach significantly outperforms all-path kernel approach on all five corpora and achieves state-of-the-art performance. PMID:22595237

Zhang, Yijia; Lin, Hongfei; Yang, Zhihao; Wang, Jian; Li, Yanpeng

2012-01-01

369

Theoretical Perspectives on Protein Folding  

E-print Network

Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing the folding mechanisms of globular proteins. The experimental data and theoretical methods have revealed the multifaceted character of proteins. Proteins exhibit universal features that can be determined using only the number of amino acid residues (N) and polymer concepts. The sizes of proteins in the denatured and folded states, cooperativity of the folding transition, dispersions in the melting temperatures at the residue level, and time scales of folding are to a large extent determined by N. The consequences of finite N especially on how individual residues order upon folding depends on the topology of the folded states. Such intricate details can be predicted using the Molecular Transfer Model that combines simulations with measured transfer free energies of protein building blocks from water to the desired concentration of the denaturant. By watching one molecule fold at a time, using single molecule methods, the validity of the theoretically anticipated heterogeneity in the folding routes, and the N-dependent time scales for the three stages in the approach to the native state have been established. Despite the successes of theory, of which only a few examples are documented here, we conclude that much remains to be done to solve the "protein folding problem" in the broadest sense.

D. Thirumalai; Edward P. O'Brien; Greg Morrison; Changbong Hyeon

2010-07-18

370

Photoaffinity labeling of plasma proteins.  

PubMed

Photoaffinity labeling is a powerful technique for identifying a target protein. A high degree of labeling specificity can be achieved with this method in comparison to chemical labeling. Human serum albumin (HSA) and ?1-acid glycoprotein (AGP) are two plasma proteins that bind a variety of endogenous and exogenous substances. The ligand binding mechanism of these two proteins is complex. Fatty acids, which are known to be transported in plasma by HSA, cause conformational changes and participate in allosteric ligand binding to HSA. HSA undergoes an N-B transition, a conformational change at alkaline pH, that has been reported to result in increased ligand binding. Attempts have been made to investigate the impact of fatty acids and the N-B transition on ligand binding in HSA using ketoprofen and flunitrazepam as photolabeling agents. Meanwhile, plasma AGP is a mixture of genetic variants of the protein. The photolabeling of AGP with flunitrazepam has been utilized to shed light on the topology of the protein ligand binding site. Furthermore, a review of photoaffinity labeling performed on other major plasma proteins will also be discussed. Using a photoreactive natural ligand as a photolabeling agent to identify target protein in the plasma would reduce non-specific labeling. PMID:24217326

Chuang, Victor Tuan Giam; Otagiri, Masaki

2013-01-01

371

Evolutionary Monte Carlo for protein folding simulations Faming Lianga)  

E-print Network

Evolutionary Monte Carlo for protein folding simulations Faming Lianga) Department of Statistics to simulations of protein folding on simple lattice models, and to finding the ground state of a protein. In all structures in protein folding. The numerical results show that it is drastically superior to other methods

Liang, Faming

372

A fast indexing approach for protein structure comparison  

Microsoft Academic Search

BACKGROUND: Protein structure comparison is a fundamental task in structural biology. While the number of known protein structures has grown rapidly over the last decade, searching a large database of protein structures is still relatively slow using existing methods. There is a need for new techniques which can rapidly compare protein structures, whilst maintaining high matching accuracy. RESULTS: We have

Lei Zhang; James Bailey; Arun S. Konagurthu; Kotagiri Ramamohanarao

2010-01-01

373

Topology analysis and visualization of Potyvirus protein-protein interaction network.  

PubMed

BackgroundOne of the central interests of Virology is the identification of host factors that contribute to virus infection. Despite tremendous efforts, the list of factors identified remains limited. With omics techniques, the focus has changed from identifying and thoroughly characterizing individual host factors to the simultaneous analysis of thousands of interactions, framing them on the context of protein-protein interaction networks and of transcriptional regulatory networks. This new perspective is allowing the identification of direct and indirect viral targets. Such information is available for several members of the Potyviridae family, one of the largest and more important families of plant viruses.ResultsAfter collecting information on virus protein-protein interactions from different potyviruses, we have processed it and used it for inferring a protein-protein interaction network. All proteins are connected into a single network component. Some proteins show a high degree and are highly connected while others are much less connected, with the network showing a significant degree of dissortativeness. We have attempted to integrate this virus protein-protein interaction network into the largest protein-protein interaction network of Arabidopsis thaliana, a susceptible laboratory host. To make the interpretation of data and results easier, we have developed a new approach for visualizing and analyzing the dynamic spread on the host network of the local perturbations induced by viral proteins. We found that local perturbations can reach the entire host protein-protein interaction network, although the efficiency of this spread depends on the particular viral proteins. By comparing the spread dynamics among viral proteins, we found that some proteins spread their effects fast and efficiently by attacking hubs in the host network while other proteins exert more local effects.ConclusionsOur findings confirm that potyvirus protein-protein interaction networks are highly connected, with some proteins playing the role of hubs. Several topological parameters depend linearly on the protein degree. Some viral proteins focus their effect in only host hubs while others diversify its effect among several proteins at the first step. Future new data will help to refine our model and to improve our predictions. PMID:25409737

Bosque, Gabriel; Folch-Fortuny, Abel; Picó, Jesús; Ferrer, Alberto; Elena, Santiago F

2014-11-20

374

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

PubMed Central

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

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

2013-01-01

375

PDZ Domain Proteins: Plug and Play!  

NSDL National Science Digital Library

PDZ domains (an acronym from PSD-95, Dlg, and ZO-1) are protein modules found in many cytoplasmic proteins (more than 400 in humans); they are discussed in this STKE Review. They are associated with a wide range of other protein-protein interaction domains (for example, WW, PTB, LRR, SH3) or with domains that exhibit particular enzymatic activities (such as guanosine triphosphatases, serine-threonine kinases, phosphatases), and they participate in various intracellular protein networks. PDZ domains bind to very diverse carboxyl-termini of protein partners in a specific (and sometimes reversible) manner, which enables the formation of supramolecular networks. Scaffolding of proteins by PDZ domain proteins usually occurs at specific sites within the cell (such as the plasma membrane or the Golgi apparatus) and is frequently involved in localizing proteins to specialized subcellular compartments of polarized cells, such as the presynaptic terminals and postsynaptic densities of neurons and the basolateral or apical membranes of epithelial cells. Genetic models in invertebrates and vertebrates that are now available for some PDZ proteins illuminate the large set of biological processes in which this protein family is involved, from the establishment and maintenance of the cytoarchitecture to signaling events. Accordingly, defects of PDZ proteins that play a central role in tissue homeostasis result in pathological conditions including cancer and developmental abnormalities. The simplicity of PDZ domain interactions has enabled the design of pharmacological inhibitors of potential therapeutic interest.

Claire Nourry (Marseille;Laboratory of Molecular Pharmacology REV); Seth G. N. Grant (University of Edinburgh;Centre for Neuroscience Research REV); Jean-Paul Borg (Marseille;Laboratory of Molecular Pharmacology REV)

2003-04-22

376

Dephosphorylation of chicken cardiac myofibril C-protein by protein phosphatases 1 and 2A  

SciTech Connect

C-Protein, which is a regulatory component of cardiac muscle myofibrils, is phosphorylated in response to US -adrenergic agonists by a cAMP-dependent mechanism and dephosphorylated in response to cholinergic agonists. It is believed that the cAMP-dependent phosphorylation is due to cAMP-dependent protein kinase. The protein phosphatase(s) involved in the dephosphorylation of C-protein has not been determined. In this study, chicken cardiac C-protein was phosphorylated with the cAMP-dependent protein kinase to about 3 mol phosphate/mol C-protein. Incubation of (TSP)C-protein with the catalytic subunit of protein phosphatase 1 or 2A rapidly removed 30-40% of TS(P). Phosphopeptide maps and phosphoamino acid analysis revealed that the major site(s) dephosphorylated by either phosphatase was a phosphothreonine residue(s) located on the same tryptic peptide and on the same CNBr fragment. Increasing the incubation period or the phosphatase concentration did not result in any further dephosphorylation of C-protein by phosphatase 1, but phosphatase 2A completely dephosphorylated C-protein. Preliminary studies showed that the major protein phosphatase associated with the myofibril was phosphatase 2A. These results indicate the phosphatase 2A may be important in the regulation of the phosphorylation state of C-protein.

Thysseril, T.J.; Hegazy, M.G.; Schlender, K.K.

1987-05-01

377

Mechanisms of m-cresol induced protein aggregation studied using a model protein cytochrome c†  

PubMed Central

Multi-dose protein formulations require an effective antimicrobial preservative (AP) to inhibit microbial growth during long-term storage of unused formulations. m-cresol is one such AP, but has been shown to cause protein aggregation. However, the fundamental physical mechanisms underlying such AP-induced protein aggregation are not understood. In this study, we used a model protein cytochrome c to identify the protein unfolding that triggers protein aggregation. m-cresol induced cytochrome c aggregation at preservative concentrations that are commonly used to inhibit microbial growth. Addition of m-cresol decreased the temperature at which the protein aggregated and increased the aggregation rate. However, m-cresol did not perturb the tertiary or secondary structure of cytochrome c. Instead, it populated an “invisible” partially unfolded intermediate where a local protein region around the methionine residue at position 80 was unfolded. Stabilizing the Met80 region drastically decreased the protein aggregation, which conclusively shows that this local protein region acts as an aggregation “hot-spot”. Based on these results, we propose that APs induce protein aggregation by partial rather than global unfolding. Because of the availability of site-specific probes to monitor different levels of protein unfolding, cytochrome c provided a unique advantage in characterizing the partial protein unfolding that triggers protein aggregation. PMID:21229618

Singh, Surinder M.; Hutchings, Regina L.; Mallela, Krishna M.G.

2014-01-01

378

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

SciTech Connect

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. .

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

379

Large-scale mapping of human protein–protein interactions by mass spectrometry  

PubMed Central

Mapping protein–protein interactions is an invaluable tool for understanding protein function. Here, we report the first large-scale study of protein–protein interactions in human cells using a mass spectrometry-based approach. The study maps protein interactions for 338 bait proteins that were selected based on known or suspected disease and functional associations. Large-scale immunoprecipitation of Flag-tagged versions of these proteins followed by LC-ESI-MS/MS analysis resulted in the identification of 24 540 potential protein interactions. False positives and redundant hits were filtered out using empirical criteria and a calculated interaction confidence score, producing a data set of 6463 interactions between 2235 distinct proteins. This data set was further cross-validated using previously published and predicted human protein interactions. In-depth mining of the data set shows that it represents a valuable source of novel protein–protein interactions with relevance to human diseases. In addition, via our preliminary analysis, we report many novel protein interactions and pathway associations. PMID:17353931

Ewing, Rob M; Chu, Peter; Elisma, Fred; Li, Hongyan; Taylor, Paul; Climie, Shane; McBroom-Cerajewski, Linda; Robinson, Mark D; O'Connor, Liam; Li, Michael; Taylor, Rod; Dharsee, Moyez; Ho, Yuen; Heilbut, Adrian; Moore, Lynda; Zhang, Shudong; Ornatsky, Olga; Bukhman, Yury V; Ethier, Martin; Sheng, Yinglun; Vasilescu, Julian; Abu-Farha, Mohamed; Lambert, Jean-Philippe; Duewel, Henry S; Stewart, Ian I; Kuehl, Bonnie; Hogue, Kelly; Colwill, Karen; Gladwish, Katharine; Muskat, Brenda; Kinach, Robert; Adams, Sally-Lin; Moran, Michael F; Morin, Gregg B; Topaloglou, Thodoros; Figeys, Daniel

2007-01-01

380

Engineering A-kinase Anchoring Protein (AKAP)-selective Regulatory Subunits of Protein Kinase A (PKA) through  

E-print Network

Engineering A-kinase Anchoring Protein (AKAP)-selective Regulatory Subunits of Protein Kinase proteins (AKAPs). Results: A structure-based phage-directed evolution strategy has yielded modified PKA regulatory type II subunits with AKAP- selective binding properties. Conclusion: Engineered RSelect proteins

Scott, John D.

381

Macromolecular mechanisms of protein translocation.  

PubMed

When macromolecules such as proteins are forced to translocate through a narrow pore, their conformational entropy is reduced, resulting in a free energy barrier. This free energy barrier is additionally modulated by protein-pore interactions. Furthermore, the driving force of the translocation such as the electrochemical potential gradient and electroosmotic flow navigates the transport of the protein through the free energy landscape. Depending on the specifics of the protein-pore system and the driving force, the details of the translocation process and their statistical properties such as the average translocation time can vary significantly. Nevertheless, there are a few fundamental physical concepts that underly the ubiquitous phenomenon of polymer translocation, which are reviewed here. PMID:24370256

Muthukumar, M

2014-03-01

382

A Least Square Method Based Model for Identifying Protein Complexes in Protein-Protein Interaction Network  

PubMed Central

Protein complex formed by a group of physical interacting proteins plays a crucial role in cell activities. Great effort has been made to computationally identify protein complexes from protein-protein interaction (PPI) network. However, the accuracy of the prediction is still far from being satisfactory, because the topological structures of protein complexes in the PPI network are too complicated. This paper proposes a novel optimization framework to detect complexes from PPI network, named PLSMC. The method is on the basis of the fact that if two proteins are in a common complex, they are likely to be interacting. PLSMC employs this relation to determine complexes by a penalized least squares method. PLSMC is applied to several public yeast PPI networks, and compared with several state-of-the-art methods. The results indicate that PLSMC outperforms other methods. In particular, complexes predicted by PLSMC can match known complexes with a higher accuracy than other methods. Furthermore, the predicted complexes have high functional homogeneity. PMID:25405206

Dai, Qiguo; Guo, Maozu; Guo, Yingjie; Liu, Xiaoyan; Liu, Yang; Teng, Zhixia

2014-01-01

383

Protein complex prediction in large ontology attributed protein-protein interaction networks.  

PubMed

Protein complexes are important for unraveling the secrets of cellular organization and function. Many computational approaches have been developed to predict protein complexes in protein-protein interaction (PPI) networks. However, most existing approaches focus mainly on the topological structure of PPI networks, and largely ignore the gene ontology (GO) annotation information. In this paper, we constructed ontology attributed PPI networks with PPI data and GO resource. After constructing ontology attributed networks, we proposed a novel approach called CSO (clustering based on network structure and ontology attribute similarity). Structural information and GO attribute information are complementary in ontology attributed networks. CSO can effectively take advantage of the correlation between frequent GO annotation sets and the dense subgraph for protein complex prediction. Our proposed CSO approach was applied to four different yeast PPI data sets and predicted many well-known protein complexes. The experimental results showed that CSO was valuable in predicting protein complexes and achieved state-of-the-art performance. PMID:24091405

Zhang, Yijia; Lin, Hongfei; Yang, Zhihao; Wang, Jian; Li, Yanpeng; Xu, Bo

2013-01-01

384

Protein sensing with engineered protein nanopores*  

PubMed Central

The use of nanopores is a powerful new frontier in single-molecule sciences. Nanopores have been used effectively in exploring various biophysical features of small polypeptides and proteins, such as their folding state and structure, ligand interactions, and enzymatic activity. In particular, the ?-hemolysin protein pore (?HL) has been used extensively for the detection, characterization and analysis of polypeptides, because this protein nanopore is highly robust, versatile and tractable under various experimental conditions. Inspired by the mechanisms of protein translocation across the outer membrane translocases of mitochondria, we have shown the ability to use nanopore-probe techniques in controlling a single protein using engineered ?HL pores. Here, we provide a detailed protocol for the preparation of ?HL protein nanopores. Moreover, we demonstrate that placing attractive electrostatic traps is instrumental in tackling single-molecule stochastic sensing of folded proteins. PMID:22528256

Mohammad, Mohammad M.; Movileanu, Liviu

2013-01-01

385

Origins of Protein Functions in Cells  

NASA Technical Reports Server (NTRS)

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.

Seelig, Burchard; Pohorille, Andrzej

2011-01-01

386

Nonlinear features in protein circuitry  

NASA Astrophysics Data System (ADS)

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.

Liu, Bo; Yan, Shiwei

2011-07-01

387

Prion protein and aging  

PubMed Central

The cellular prion protein (PrPC) has been widely investigated ever since its conformational isoform, the prion (or PrPSc), was identified as the etiological agent of prion disorders. The high homology shared by the PrPC-encoding gene among mammals, its high turnover rate and expression in every tissue strongly suggest that PrPC may possess key physiological functions. Therefore, defining PrPC roles, properties and fate in the physiology of mammalian cells would be fundamental to understand its pathological involvement in prion diseases. Since the incidence of these neurodegenerative disorders is enhanced in aging, understanding PrPC functions in this life phase may be of crucial importance. Indeed, a large body of evidence suggests that PrPC plays a neuroprotective and antioxidant role. Moreover, it has been suggested that PrPC is involved in Alzheimer disease, another neurodegenerative pathology that develops predominantly in the aging population. In prion diseases, PrPC function is likely lost upon protein aggregation occurring in the course of the disease. Additionally, the aging process may alter PrPC biochemical properties, thus influencing its propensity to convert into PrPSc. Both phenomena may contribute to the disease development and progression. In Alzheimer disease, PrPC has a controversial role because its presence seems to mediate ?-amyloid toxicity, while its down-regulation correlates with neuronal death. The role of PrPC in aging has been investigated from different perspectives, often leading to contrasting results. The putative protein functions in aging have been studied in relation to memory, behavior and myelin maintenance. In aging mice, PrPC changes in subcellular localization and post-translational modifications have been explored in an attempt to relate them to different protein roles and propensity to convert into PrPSc. Here we provide an overview of the most relevant studies attempting to delineate PrPC functions and fate in aging. PMID:25364751

Gasperini, Lisa; Legname, Giuseppe

2014-01-01

388

Why do proteins aggregate? “Intrinsically insoluble proteins” and “dark mediators” revealed by studies on “insoluble proteins” solubilized in pure water  

PubMed Central

In 2008, I reviewed and proposed a model for our discovery in 2005 that unrefoldable and insoluble proteins could in fact be solubilized in unsalted water. Since then, this discovery has offered us and other groups a powerful tool to characterize insoluble proteins, and we have further addressed several fundamental and disease-relevant issues associated with this discovery. Here I review these results, which are conceptualized into several novel scenarios. 1) Unlike 'misfolded proteins', which still retain the capacity to fold into well-defined structures but are misled to 'off-pathway' aggregation, unrefoldable and insoluble proteins completely lack this ability and will unavoidably aggregate in vivo with ~150 mM ions, thus designated as 'intrinsically insoluble proteins (IIPs)' here. IIPs may largely account for the 'wastefully synthesized' DRiPs identified in human cells. 2) The fact that IIPs including membrane proteins are all soluble in unsalted water, but get aggregated upon being exposed to ions, logically suggests that ions existing in the background play a central role in mediating protein aggregation, thus acting as 'dark mediators'. Our study with 14 salts confirms that IIPs lack the capacity to fold into any well-defined structures. We uncover that salts modulate protein dynamics and anions bind proteins with high selectivity and affinity, which is surprisingly masked by pre-existing ions. Accordingly, I modified my previous model. 3) Insoluble proteins interact with lipids to different degrees. Remarkably, an ALS-causing P56S mutation transforms the ?-sandwich MSP domain into a helical integral membrane protein. Consequently, the number of membrane-interacting proteins might be much larger than currently recognized. To attack biological membranes may represent a common mechanism by which aggregated proteins initiate human diseases. 4) Our discovery also implies a solution to the 'chicken-and-egg paradox' for the origin of primitive membranes embedded with integral membrane proteins, if proteins originally emerged in unsalted prebiotic media. PMID:24555050

Song, Jianxing

2013-01-01

389

Enriched Protein-Protein Interactions from Biomedical Text  

E-print Network

Enriched Protein-Protein Interactions from Biomedical Text Barry Haddow, Michael Matthews University of Edinburgh 13th March 2007 Barry Haddow, Michael Matthews Enriched Protein-Protein Interactions from Biomedical Text #12;Overview The TXM Project Protein-Protein Interactions Enriched Protein-Protein

Edinburgh, University of

390

Winter 2011 Evaluating Protein-Protein Docking Web Servers  

E-print Network

protein docking web servers: PIPER, GRAMM-X, 3D Garden, SmoothDock and PatchDock. I #12;will also performNina Ly Winter 2011 Evaluating Protein-Protein Docking Web Servers Proteins are involved in many of protein-protein and protein-ligand complexes by a procedure called docking. The goal of protein docking

391

Protein–protein binding affinities by pulse proteolysis: Application to TEM-1/BLIP protein complexes  

PubMed Central

Efficient methods for quantifying dissociation constants have become increasingly important for high-throughput mutagenesis studies in the postgenomic era. However, experimentally determining binding affinity is often laborious, requires large amounts of purified protein, and utilizes specialized equipment. Recently, pulse proteolysis has been shown to be a robust and simple method to determine the dissociation constants for a protein–ligand pair based on the increase in thermodynamic stability upon ligand binding. Here, we extend this technique to determine binding affinities for a protein–protein complex involving the ?-lactamase TEM-1 and various ?-lactamase inhibitor protein (BLIP) mutants. Interaction with BLIP results in an increase in the denaturation curve midpoint, Cm, of TEM-1, which correlates with the rank order of binding affinities for several BLIP mutants. Hence, pulse proteolysis is a simple, effective method to assay for mutations that modulate binding affinity in protein–protein complexes. From a small set (n = 4) of TEM-1/BLIP mutant complexes, a linear relationship between energy of stabilization (dissociation constant) and ?Cm was observed. From this “calibration curve,” accurate dissociation constants for two additional BLIP mutants were calculated directly from proteolysis-derived ?Cm values. Therefore, in addition to qualitative information, armed with knowledge of the dissociation constants from the WT protein and a limited number of mutants, accurate quantitation of binding affinities can be determined for additional mutants from pulse proteolysis. Minimal sample requirements and the suitability of impure protein preparations are important advantages that make pulse proteolysis a powerful tool for high-throughput mutagenesis binding studies. PMID:20669180

Hanes, Melinda S; Ratcliff, Kathleen; Marqusee, Susan; Handel, Tracy M

2010-01-01

392

PREFACE: Protein protein interactions: principles and predictions  

NASA Astrophysics Data System (ADS)

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.

Nussinov, Ruth; Tsai, Chung-Jung

2005-06-01

393

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...

394

SIGNAL TRANSDUCTION: Proteins in Motion  

NSDL National Science Digital Library

Access to the article is free, however registration and sign-in are required. Some membrane receptors undergo conformational changes after binding their ligand, generating a signal transduction cascade that results in a change in gene expression. But how the motion of proteins is translated into altered signaling is not known. In their Perspective, Gerstein and Chothia describe how transmembrane helices in a bacterial membrane receptor slide over each other in a piston-like motion (Ottemann et al.). They discuss how these results fit with current models of transmembrane conformational changes and signaling and whether these findings are likely to be applicable to other types of transmembrane proteins.

Mark Gerstein (Yale University;Molecular Biophysics and Biochemistry Department); Cyrus Chothia (Medical Research Council;Laboratory of Molecular Biology)

1999-09-10

395

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 ...

396

Heterotrimeric G Protein Cycle  

NSDL National Science Digital Library

This animation shows the basic heterotrimeric G protein cycle and allows the user to then add three different regulators of the cycle, an RGS (regulator of G protein signaling) protein, a GDI (guanine nucleotide dissociation inhibitor) protein, or a guanine nucleotide exchange factor (GEF).

Anita Preininger (Vanderbilt University Medical Center; Department of Pharmacology)

2004-02-03

397

Theory of protein folding  

Microsoft Academic Search

Protein folding should be complex. Proteins organize themselves into specific three-dimensional structures, through a myriad of conformational changes. The classical view of protein folding describes this process as a nearly sequential series of discrete intermediates. In contrast, the energy landscape theory of folding considers folding as the progressive organization of an ensemble of partially folded structures through which the protein

José Nelson Onuchic; Peter G. Wolynes

2004-01-01

398

Protein sequence comparison and protein evolution  

SciTech Connect

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.

Pearson, W.R. [Univ. of Virginia, Charlottesville, VA (United States). Dept. of Biochemistry

1995-12-31

399

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

PubMed Central

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

2012-01-01

400

Quantitative study of protein-protein interactions by quartz nanopipettes  

NASA Astrophysics Data System (ADS)

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

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

2014-08-01

401

Protein N-Myristoylation Plays a Critical Role in the Endoplasmic Reticulum Morphological Change Induced by Overexpression of Protein Lunapark, an Integral Membrane Protein of the Endoplasmic Reticulum  

PubMed Central

N-myristoylation of eukaryotic cellular proteins has been recognized as a modification that occurs mainly on cytoplasmic proteins. In this study, we examined the membrane localization, membrane integration, and intracellular localization of four recently identified human N-myristoylated proteins with predicted transmembrane domains. As a result, it was found that protein Lunapark, the human ortholog of yeast protein Lnp1p that has recently been found to be involved in network formation of the endoplasmic reticulum (ER), is an N-myristoylated polytopic integral membrane protein. Analysis of tumor necrosis factor-fusion proteins with each of the two putative transmembrane domains and their flanking regions of protein Lunapark revealed that transmembrane domain 1 and 2 functioned as type II signal anchor sequence and stop transfer sequence, respectively, and together generated a double-spanning integral membrane protein with an N-/C-terminal cytoplasmic orientation. Immunofluorescence staining of HEK293T cells transfected with a cDNA encoding protein Lunapark tagged with FLAG-tag at its C-terminus revealed that overexpressed protein Lunapark localized mainly to the peripheral ER and induced the formation of large polygonal tubular structures. Morphological changes in the ER induced by overexpressed protein Lunapark were significantly inhibited by the inhibition of protein N-myristoylation by means of replacing Gly2 with Ala. These results indicated that protein N-myristoylation plays a critical role in the ER morphological change induced by overexpression of protein Lunapark. PMID:24223779

Moriya, Koko; Nagatoshi, Kei; Noriyasu, Yoshimi; Okamura, Tsuyoshi; Takamitsu, Emi; Suzuki, Takashi; Utsumi, Toshihiko

2013-01-01

402

The Protein Model Portal  

Microsoft Academic Search

Structural Genomics has been successful in determining the structures of many unique proteins in a high throughput manner.\\u000a Still, the number of known protein sequences is much larger than the number of experimentally solved protein structures. Homology\\u000a (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins.\\u000a Thereby, experimental structure determination efforts and

Konstantin Arnold; Florian Kiefer; Jürgen Kopp; James N. D. Battey; Michael Podvinec; John D. Westbrook; Helen M. Berman; Lorenza Bordoli; Torsten Schwede

2009-01-01

403

Protein Sequence, Structure, Stability and Functionality  

E-print Network

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 o