scholarly journals Computational studies on eukaryotic transmembrane β-barrel proteins

2018 ◽  
Author(s):  
Ahmed F. Roumia ◽  
Margarita C. Theodoropoulou ◽  
Konstantinos D. Tsirigos ◽  
Pantelis G. Bagos
Keyword(s):  
Computational Analysis ◽  
Markov Models ◽  
Outer Membrane Proteins ◽  
Computational Studies ◽  
Cellular Functions ◽  
Pfam Database ◽  
Eukaryotic Proteins ◽  
Transport Of Ions ◽  
First Time

Transmembrane β-barrel proteins perform multiple cellular functions such as passive transport of ions and allowing the flux of molecules. Also, they act as enzymes, transporters, receptors and virulence factors. Even though, in the last few years, several families of eukaryotic β-barrel outer membrane proteins (OMPs) have been discovered, the computational characterization of these families is far from complete. The PFAM database includes only very few characteristic profiles for these families and, in most cases, the profile Hidden Markov Models where trained using both prokaryotic and eukaryotic proteins. Here, we present, for the first time, a comprehensive computational analysis of eukaryotic transmembrane β- barrels. Ten characteristic pHMMs were build that can discriminate eukaryotic β-barrels from other classes of β-barrel proteins (globular and bacterial) and are, also, capable of discriminating between mitochondrial and chloroplastic ones. Specifically, we built six new pHMMs for the chloroplastic β-barrel families not included in the PFAM database and, also, updated the profile for MDM10 family (PF12519) and divided the porin family (PF01459) into two separated families VDAC and TOM40. We hope that all the pHMMs presented here will be used for the detection and characterization of eukaryotic OMPs in newly discovered proteomes.

scholarly journals Computational studies on eukaryotic transmembrane β-barrel proteins

2018 ◽  
Author(s):  
Ahmed F. Roumia ◽  
Margarita C. Theodoropoulou ◽  
Konstantinos D. Tsirigos ◽  
Pantelis G. Bagos
Keyword(s):  
Computational Analysis ◽  
Markov Models ◽  
Outer Membrane Proteins ◽  
Computational Studies ◽  
Cellular Functions ◽  
Pfam Database ◽  
Eukaryotic Proteins ◽  
Transport Of Ions ◽  
First Time

Transmembrane β-barrel proteins perform multiple cellular functions such as passive transport of ions and allowing the flux of molecules. Also, they act as enzymes, transporters, receptors and virulence factors. Even though, in the last few years, several families of eukaryotic β-barrel outer membrane proteins (OMPs) have been discovered, the computational characterization of these families is far from complete. The PFAM database includes only very few characteristic profiles for these families and, in most cases, the profile Hidden Markov Models where trained using both prokaryotic and eukaryotic proteins. Here, we present, for the first time, a comprehensive computational analysis of eukaryotic transmembrane β- barrels. Ten characteristic pHMMs were build that can discriminate eukaryotic β-barrels from other classes of β-barrel proteins (globular and bacterial) and are, also, capable of discriminating between mitochondrial and chloroplastic ones. Specifically, we built six new pHMMs for the chloroplastic β-barrel families not included in the PFAM database and, also, updated the profile for MDM10 family (PF12519) and divided the porin family (PF01459) into two separated families VDAC and TOM40. We hope that all the pHMMs presented here will be used for the detection and characterization of eukaryotic OMPs in newly discovered proteomes.

scholarly journals Structural characterization of NORAD reveals a stabilizing role of spacers and two new repeat units.

2021 ◽  
Author(s):  
Uciel Chorostecki ◽  
Ester Saus ◽  
Toni Gabaldon
Keyword(s):  
Modular Organization ◽  
Cellular Functions ◽  
Repeat Units ◽  
Non Coding Rna ◽  
High Sequence Conservation ◽  
Non Coding Rnas ◽  
First Time ◽  
Computational Predictions

Long non-coding RNAs (lncRNAs) can perform a variety of key cellular functions by interacting with proteins and other RNAs. Recent studies have shown that the function of lncRNAS are largely mediated by their structures. However, our structural knowledge for most lncRNAS is limited to sequence-based computational predictions. Non-coding RNA activated by DNA damage (NORAD) is an atypical lncRNA due to its abundant expression and high sequence conservation. NORAD regulates genomic stability by interacting with proteins and microRNAs. Previous sequence-based characterization has identified a modular organization of NORAD composed of several NORAD repeat units (NRUs). These units comprise the protein-binding elements and are separated by regular spacers of unknown function. Here, we experimentally determine for the first time the secondary structure of NORAD using the nextPARS approach. Our results suggest that the spacer regions provide structural stability to NRUs. Furthermore, we uncover two previously-unreported NRUs, and determine the core structural motifs conserved across NRUs. Overall, these findings will help to elucidate the function and evolution of NORAD.

scholarly journals Reviving the Coordination Chemistry of Sulfonium Cations

2021 ◽  
Author(s):  
Ruiping Li ◽  
Nitsan Barel ◽  
Vasudevan Subramaniyan ◽  
Orit Cohen ◽  
Francoise Tibika ◽  
...  
Keyword(s):  
Coordination Chemistry ◽  
Computational Analysis ◽  
Acid Catalysis ◽  
Phosphine Ligands ◽  
Pincer Complexes ◽  
Full Characterization ◽  
Sulfonium Ions ◽  
The Stability ◽  
First Time

ABSTRACT: More than a century old, sulfonium ions are still intriguing species in the landscape of organic chemistry. On one hand they have found broad applications in organic synthesis and material science, but on the other hand, while isoelectronic to the ubiquitous tertiary phosphine ligands, their own coordination chemistry has been neglected for the last three decades. Here we report the synthesis and full characterization of the first Rh(I) and Pt(II) complexes of sul-fonium. Moreover, for the first time, the coordinating ability of an aromatic sulfonium has been established. A thorough computational analysis of the exceptionally short S-Rh bonds obtained attests for the strongly π-accepting nature of sul-fonium cations and places them among the best π-acceptor ligands available today. Our calculations also show that when embedded within a pincer framework their π-acidity is enhanced. Therefore, in addition to the stability and modularity that these frameworks offer, our pincer complexes might open the way for sulfonium cations to become powerful tools in π-acid catalysis.

TBE in Sweden

2020 ◽  
Keyword(s):  
Genetic Characterization ◽  
Immunoglobulin M ◽  
Enzyme Linked Immunosorbent Assay ◽  
Second Phase ◽  
Serum Samples ◽  
Tick Borne Encephalitis ◽  
Specific Immunoglobulin ◽  
Tick Borne Encephalitis Virus ◽  
First Time

Tick-borne encephalitis virus (TBEV) was isolated for the first time in Sweden in 1958 (from ticks and from 1 tick-borne encephalitis [TBE] patient).1 In 2003, Haglund and colleagues reported the isolation and antigenic and genetic characterization of 14 TBEV strains from Swedish patients (samples collected 1991–1994).2 The first serum sample, from which TBEV was isolated, was obtained 2–10 days after onset of disease and found to be negative for anti-TBEV immunoglobulin M (IgM) by enzyme-linked immunosorbent assay (ELISA), whereas TBEV-specific IgM (and TBEV-specific immunoglobulin G/cerebrospinal fluid [IgG/CSF] activity) was demonstrated in later serum samples taken during the second phase of the disease.

Chemical Constituents and Antibacterial Activity of Cissus Aralioides.

2020 ◽  
Vol 17 ◽  
Author(s):  
Balogun Olaoye Solomon ◽  
Ajayi Olukayode Solomon ◽  
Owolabi Temitayo Abidemi ◽  
Oladimeji Abdulkarbir Oladele ◽  
Liu Zhiqiang
Keyword(s):  
Plant Extract ◽  
Chemical Constituents ◽  
Ethyl Acetate Fraction ◽  
Antibacterial Activities ◽  
Sub Saharan Africa ◽  
Chromatographic Purification ◽  
Whole Plant ◽  
Sub Saharan ◽  
First Time

: Cissus aralioides is a medicinal plant used in sub-Saharan Africa for treatment of infectious diseases; however the chemical constituents of the plant have not been investigated. Thus, in this study, attempt was made at identifying predominant phytochemical constituents of the plant through chromatographic purification and silylation of the plant extract, and subsequent characterization using spectroscopic and GC-MS techniques. The minimum inhibitory concentration (MICs) for the antibacterial activities of the plant extract, chromatographic fractions and isolated compounds were also examined. Chromatographic purification of the ethyl acetate fraction from the whole plant afforded three compounds: β-sitosterol (1), stigmasterol (2) and friedelin (3). The phytosterols (1 and 2) were obtained together as a mixture. The GC-MS analysis of silylated extract indicated alcohols, fatty acids and sugars as predominant classes, with composition of 24.62, 36.90 and 26.52% respectively. Results of MICs indicated that friedelin and other chromatographic fractions had values (0.0626-1.0 mg/mL) comparable with the standard antibiotics used. Characterization of natural products from C. aralioides is being reported for the first time in this study.

Green Synthesis and Spectroscopic Studies of Ag-rGO Nanocomposites for Highly Selective Mercury (II) Sensing

2018 ◽  
Vol 9 (1) ◽  
pp. 101-108 ◽  
Author(s):  
Shubhangi J. Mane-Gavade ◽  
Sandip R. Sabale ◽  
Xiao-Ying Yu ◽  
Gurunath H. Nikam ◽  
Bhaskar V. Tamhankar
Keyword(s):  
Green Synthesis ◽  
Color Change ◽  
Limit Of Detection ◽  
Aqueous Media ◽  
Suitable Condition ◽  
Cost Effective ◽  
Spectroscopic Studies ◽  
Calibration Plot ◽  
First Time

Introduction: Herein we report the green synthesis and characterization of silverreduced graphene oxide nanocomposites (Ag-rGO) using Acacia nilotica gum for the first time. Experimental: We demonstrate the Hg2+ ions sensing ability of the Ag-rGO nanocomposites form aqueous medium. The developed colorimetric sensor method is simple, fast and selective for the detection of Hg2+ ions in aqueous media in presence of other associated ions. A significant color change was noticed with naked eye upon Hg2+ addition. The color change was not observed for cations including Sr2+, Ni2+, Cd2+, Pb2+, Mg2+, Ca2+, Fe2+, Ba2+ and Mn2+indicating that only Hg2+ shows a strong interaction with Ag-rGO nanocomposites. Under the most suitable condition, the calibration plot (A0-A) against concentration of Hg2+ was linear in the range of 0.1-1.0 ppm with a correlation coefficient (R2) value 0.9998. Results & Conclusion The concentration of Hg2+ was quantitatively determined with the Limit of Detection (LOD) of 0.85 ppm. Also, this method shows excellent selectivity towards Hg2+ over nine other cations tested. Moreover, the method offers a new cost effective, rapid and simple approach for the detection of Hg2+ in water samples.

scholarly journals Waste-Based One-Part Alkali Activated Materials

Materials ◽  
2021 ◽  
Vol 14 (11) ◽  
pp. 2911
Author(s):  
Margarida Gonçalves ◽  
Inês Silveirinha Vilarinho ◽  
Marinélia Capela ◽  
Ana Caetano ◽  
Rui Miguel Novais ◽  
...  
Keyword(s):  
Compressive Strength ◽  
Microstructural Analysis ◽  
Construction Materials ◽  
Sodium Metasilicate ◽  
High Compressive Strength ◽  
Hardened State ◽  
First Time ◽  
Furnace Slag ◽  
Alkali Activated

Ordinary Portland Cement is the most widely used binder in the construction sector; however, a very high carbon footprint is associated with its production process. Consequently, more sustainable alternative construction materials are being investigated, namely, one-part alkali activated materials (AAMs). In this work, waste-based one-part AAMs binders were developed using only a blast furnace slag, as the solid precursor, and sodium metasilicate, as the solid activator. For the first time, mortars in which the commercial sand was replaced by two exhausted sands from biomass boilers (CA and CT) were developed. Firstly, the characterization of the slag and sands (aggregates) was performed. After, the AAMs fresh and hardened state properties were evaluated, being the characterization complemented by FTIR and microstructural analysis. The binder and the mortars prepared with commercial sand presented high compressive strength values after 28 days of curing-56 MPa and 79 MPa, respectively. The mortars developed with exhausted sands exhibit outstanding compressive strength values, 86 and 70 MPa for CT and CA, respectively, and the other material’s properties were not affected. Consequently, this work proved that high compressive strength waste-based one-part AAMs mortars can be produced and that it is feasible to use another waste as aggregate in the mortar’s formulations: the exhausted sands from biomass boilers.

scholarly journals Isolation and characterization of a new cold-active protease from psychrotrophic bacteria of Western Himalayan glacial soil

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Saleem Farooq ◽  
Ruqeya Nazir ◽  
Shabir Ahmad Ganai ◽  
Bashir Ahmad Ganai
Keyword(s):  
Specific Activity ◽  
Temperature Range ◽  
Psychrotrophic Bacteria ◽  
Isolation And Characterization ◽  
Cold Active ◽  
Active Protease ◽  
Quantitative Screening ◽  
First Time ◽  
Low K

AbstractAs an approach to the exploration of cold-active enzymes, in this study, we isolated a cold-active protease produced by psychrotrophic bacteria from glacial soils of Thajwas Glacier, Himalayas. The isolated strain BO1, identified as Bacillus pumilus, grew well within a temperature range of 4–30 °C. After its qualitative and quantitative screening, the cold-active protease (Apr-BO1) was purified. The Apr-BO1 had a molecular mass of 38 kDa and showed maximum (37.02 U/mg) specific activity at 20 °C, with casein as substrate. It was stable and active between the temperature range of 5–35 °C and pH 6.0–12.0, with an optimum temperature of 20 °C at pH 9.0. The Apr-BO1 had low Km value of 1.0 mg/ml and Vmax 10.0 µmol/ml/min. Moreover, it displayed better tolerance to organic solvents, surfactants, metal ions and reducing agents than most alkaline proteases. The results exhibited that it effectively removed the stains even in a cold wash and could be considered a decent detergent additive. Furthermore, through protein modelling, the structure of this protease was generated from template, subtilisin E of Bacillus subtilis (PDB ID: 3WHI), and different methods checked its quality. For the first time, this study reported the protein sequence for psychrotrophic Apr-BO1 and brought forth its novelty among other cold-active proteases.

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