Cone snail analogs of the pituitary hormones oxytocin/vasopressin and their carrier protein neurophysin. Proteomic and transcriptomic identification of conopressins and conophysins
Publication date: Available online 10 February 2020Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Sanjeev Kumar, M. Vijayasarathy, M.A. Venkatesha, P. Sunita, P. BalaramAbstractTranscriptomic analysis of cone snail venom duct tissue has permitted the identification of diverse conopressin/conophysin precursor sequences from seven distinct conus species. Multiple precursor isoforms are present in C.monile, C.lividus and C.loroisii. Aqueous extracts of the venom duct tissue from C.monile yield a band, at ~ 15-20 kDa on SDS-PAGE. In-gel trypsin digestion, followed by mass spectrometry establi...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - February 11, 2020 Category: Biochemistry Source Type: research

Editorial Board
Publication date: April 2020Source: Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Volume 1868, Issue 4Author(s): (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - February 7, 2020 Category: Biochemistry Source Type: research

Production, thermodynamic characterization, and fruit juice quality improvement characteristics of an Exo-polygalacturonase from Penicillium janczewskii
In conclusion, the catalytic activity, thermal steadiness, and fruit juices clarification performance of Exo-PG manifests a great prospect for bio-industrial exploitation. (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - February 5, 2020 Category: Biochemistry Source Type: research

Targeted inhibition of Amyloidogenesis using a non-toxic, serum stable strategically designed cyclic peptide with therapeutic implications
Publication date: Available online 4 February 2020Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Ranit Pariary, Baijayanti Ghosh, Zuzana Bednarikova, Kyriakos Gabriel Varnava, Bhisma N. Ratha, Sreyan Raha, Dipita Bhattacharyya, Zuzana Gazova, Vijayalekshmi Sarojini, Atin K. Mandal, Anirban BhuniaAbstractAmyloidogenic disorders are currently rising as a global health issue, prompting more and more studies dedicated to the development of effective targeted therapeutics. The innate affinity of these amyloidogenic proteins towards the biomembranes adds further complexities to the systems. Our p...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - February 5, 2020 Category: Biochemistry Source Type: research

N-succinylamino acid racemases: Enzymatic properties and biotechnological applications
Publication date: Available online 23 January 2020Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Sergio Martínez-Rodríguez, Pablo Soriano-Maldonado, Jose Antonio GaviraAbstractThe N-succinylamino acid racemase/o-succinylbenzoate synthase (NSAR/OSBS) subfamily from the enolase superfamily contains different enzymes showing promiscuous N-substituted-amino acid racemase (NxAR) activity. These enzymes were originally named as N-acylamino acid racemases because of their industrial application. Nonetheless, they are pivotal in several enzymatic cascades due to their versatility to c...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - January 24, 2020 Category: Biochemistry Source Type: research

Kinetics aspects of Gamma-hydroxybutyrate dehydrogenase
Publication date: Available online 22 January 2020Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Esther S. Taxon, Lila P. Halbers, Stanley M. ParsonsAbstractTwo groups of metabolically related enzymes, the Group III family of Fe2+-dependent alcohol dehydrogenases (ADHs) and the separate subfamily of nucleoside diphosphates linked to x (nudix) hydrolases that activate Group III ADHs are under-characterized. Here we report the steady-state initial-velocity forward direction (alcohol → aldehyde) reaction of a Group III ADH, namely gamma-hydroxybutyrate dehydrogenase (GHBDH, UniProt: Q5910...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - January 23, 2020 Category: Biochemistry Source Type: research

Standard Gibbs energy of metabolic reactions: V. enolase reaction
Publication date: Available online 18 January 2020Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Thorsten Greinert, Kristina Vogel, Astrid-Ina Seifert, Riko Siewert, Irina V. Andreeva, Sergey P. Verevkin, Thomas Maskow, Gabriele Sadowski, Christoph HeldAbstractThe glycolytic pathway is one of the most important pathways for living organisms, due to its role in energy production and as supplier of precursors for biosynthesis in living cells. This work focuses on determination of the standard Gibbs energy of reaction ΔRg′0 of the enolase reaction, the ninth reaction in the glycoly...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - January 18, 2020 Category: Biochemistry Source Type: research

Changes in strand 6B and helix B during neuroserpin inhibition: Implication in severity of clinical phenotype
Publication date: Available online 16 January 2020Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Mohammad Farhan Ali, Abhinav Kaushik, Dinesh Gupta, Shoyab Ansari, Mohamad Aman JairajpuriAbstractNeuroserpin (NS) is predominantly expressed in brain and inhibits tissue-type plasminogen activator (tPA) with implications in brain development and memory. Nature of conformational change in pathological variants in strand 6B and helix B of NS that cause a relatively mild to severe epilepsy (and/or dementia) remains largely elusive. MD simulation with wild type (WT) NS, strand 6B and helix B varian...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - January 17, 2020 Category: Biochemistry Source Type: research

The alpha helix of the intermediate region in hGBP-1 acts as a coupler for enhanced GMP formation
Publication date: Available online 16 January 2020Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Sudeepa Rajan, Apurba Kumar SauAbstractThe interferon-gamma inducible large GTPase human guanylate binding protein-1 (hGBP-1) plays a key role in anti-pathogenic and anti-proliferative functions. This protein hydrolyzes GTP to both GDP and GMP (predominant product) through sequential phosphate cleavages, which makes it functionally distinct from other GTPases. Previous study on truncated variants of hGBP-1 suggested that the α-helix present in the intermediate region is essential for dimer...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - January 17, 2020 Category: Biochemistry Source Type: research

Editorial Board
Publication date: March 2020Source: Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Volume 1868, Issue 3Author(s): (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - January 17, 2020 Category: Biochemistry Source Type: research

Falcipain cysteine proteases of malaria parasites: An update
Publication date: Available online 9 January 2020Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Philip J. RosenthalAbstractBackgroundThe malaria parasite Plasmodium falciparum expresses four related papain-family cysteine proteases known as falcipains. These proteases play critical roles in the parasite life cycle, and as such are potential targets for new modes of antimalarial chemotherapy, as discussed in this review.Scope of reviewThis review summarizes available knowledge describing falcipain cysteine proteases of malaria parasites.Major conclusionsBased on available data the falcipains...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - January 11, 2020 Category: Biochemistry Source Type: research

Cysteinyl cathepsins in cardiovascular diseases
Publication date: Available online 9 January 2020Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Xian Zhang, Songyuan Luo, Minjie Wang, Guo-Ping ShiAbstractCysteinyl cathepsins are lysosomal/endosomal proteases that mediate bulk protein degradation in these intracellular acidic compartments. Yet, studies indicate that these proteases also appear in the nucleus, nuclear membrane, cytosol, plasma membrane, and extracellular space. Patients with cardiovascular diseases (CVD) show increased levels of cathepsins in the heart, aorta, and plasma. Plasma cathepsins often serve as biomarkers or risk ...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - January 9, 2020 Category: Biochemistry Source Type: research

High-resolution structure of intramolecularly proteolyzed human mucin-1 SEA domain
We report the first high-resolution X-ray structure of cleaved MUC1 SEA. Structural comparison with uncleaved SEA domains suggests that the number of residues evolutionarily inserted in the cleaved loop of MUC1 SEA precludes the formation of a properly hydrogen-bonded beta turn. By sequence analysis, we show that this conformational frustration is shared by all known cleaved SEA domains. In addition, alternative conformations of the uncleaved precursor could be modeled in which the scissile peptide bond is planar. The implications of these structures for autoproteolysis are discussed in the light of the previous research o...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - January 8, 2020 Category: Biochemistry Source Type: research

Selective pressure on an interfacial enzyme: Functional roles of a highly conserved asparagine residue in a cellulase
Publication date: Available online 3 January 2020Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Trine Holst Sørensen, Silke Flindt Badino, Michael Skovbo Windahl, Nanna Røjel, Brett McBrayer, Kim Borch, Peter Westh (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - January 5, 2020 Category: Biochemistry Source Type: research

Editorial Board
Publication date: February 2020Source: Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Volume 1868, Issue 2Author(s): (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - December 24, 2019 Category: Biochemistry Source Type: research

Analysis of uracil DNA glycosylase (UNG2) stimulation by replication protein A (RPA) at ssDNA-dsDNA junctions
Publication date: Available online 19 December 2019Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Brian P. WeiserAbstractReplication Protein A (RPA) is a single-stranded DNA binding protein that interacts with DNA repair proteins including Uracil DNA Glycosylase (UNG2). Here, I report DNA binding and activity assays using purified recombinant RPA and UNG2. Using synthetic DNA substrates, RPA was found to promote UNG2's interaction with ssDNA-dsDNA junctions regardless of the DNA strand polarity surrounding the junction. RPA stimulated UNG2's removal of uracil bases paired with adenine or gu...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - December 20, 2019 Category: Biochemistry Source Type: research

Regulation of Herbaspirillum seropedicae NifA by the GlnK PII signal transduction protein is mediated by effectors binding to allosteric sites
Publication date: Available online 19 December 2019Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Adriano Alves Stefanello, Marco Aurélio Schuler de Oliveira, Emanuel Maltempi de Souza, Fábio de Oliveira Pedrosa, Leda Satie Chubatsu, Luciano Fernandes Huergo, Ray Dixon, Rose Adele MonteiroAbstractHerbaspirillum seropedicae is a plant growth promoting bacterium that is able to fix nitrogen and to colonize the surface and internal tissues of important crops. Nitrogen fixation in H. seropedicae is regulated at the transcriptional level by the prokaryotic enhancer binding protein ...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - December 20, 2019 Category: Biochemistry Source Type: research

Recent advances in biocatalysis and biotransformations
Publication date: Available online 18 December 2019Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - December 18, 2019 Category: Biochemistry Source Type: research

Twenty-five years of nomenclature and classification of proteolytic enzymes
Publication date: Available online 12 December 2019Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Neil D. RawlingsAbstractProteolytic enzymes and their homologues have been classified into clans by comparing the tertiary structures of the peptidase domains, into families by comparing the protein sequences of the peptidase domains, and into protein-species by comparing various attributes including domain architecture, substrate preference, inhibitor interactions, subcellular location, and phylogeny. The results are compared with the earlier classification by Rawlings & Barrett (Rawlings ...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - December 13, 2019 Category: Biochemistry Source Type: research

The structure of a prokaryotic feruloyl-CoA hydratase-lyase from a lignin-degrading consortium with high oligomerization stability under extreme pHs
In this study, a prokaryotic FCHL derived from a lignin-degrading microbial consortium (named LM-FCHL) was cloned, successfully expressed in soluble form and purified. The crystal structure was solved and refined at 2.1 Å resolution. The LM-FCHL is a hexamer composed of a dimer of trimers, which showed to be quite stable under extreme pH conditions. Finally, small angle X-ray scattering corroborates the hexameric state in solution and indicates flexibility in the protein structure. The present study contributes to the field of lignin valorization to valuable molecules by establishing the biophysical and structural ...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - December 11, 2019 Category: Biochemistry Source Type: research

Small protease inhibitors in tick saliva and salivary glands and their role in tick-host-pathogen interactions
Publication date: Available online 7 December 2019Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Larissa Almeida Martins, Jan Kotál, Chaima Bensaoud, Jindřich Chmelař, Michail KotsyfakisAbstractTicks must durably suppress vertebrate host responses (hemostasis, inflammation, immunity) to avoid rejection and act as vectors of many pathogenic microorganisms that cause disease in humans and animals. Transcriptomics and proteomics studies have been used to study tick-host-pathogen interactions and have facilitated the systematic characterization of salivary composition and molecular dyn...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - December 7, 2019 Category: Biochemistry Source Type: research

Sterilization of epidermal growth factor with supercritical carbon dioxide and peracetic acid; analysis of changes at the amino acid and protein level
Publication date: Available online 29 November 2019Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): David M. Bednarski, Ellen E. Lantz, Cedric E. Bobst, Anthony R. Eisenhut, Stephen J. Eyles, Julien P. FeyAbstractAseptic processing and terminal sterilization become increasingly challenging as medical devices become more complex and include active biologics. Terminal sterilization is preferred for patient safety and production costs. We aimed to determine how sterilization using supercritical CO2 (scCO2) with low levels of peracetic acid (PAA) affects amino acids and human epidermal growth fac...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 29, 2019 Category: Biochemistry Source Type: research

Editorial Board
Publication date: January 2020Source: Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Volume 1868, Issue 1Author(s): (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 29, 2019 Category: Biochemistry Source Type: research

Reviewer Acknowledgement
Publication date: January 2020Source: Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Volume 1868, Issue 1Author(s): (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 29, 2019 Category: Biochemistry Source Type: research

Characterization of pyranose oxidase variants for bioelectrocatalytic applications
In this study, enzyme variants with improved electron acceptor turnover and reduced oxygen turnover were characterized as potential anode biocatalysts. Pre-steady-state kinetics of the oxidative half-reaction of ToPOx variants T166R, Q448H, L545C, and L547R with these alternative electron acceptors were evaluated using stopped-flow spectrophotometry. Higher kinetic constants were observed as compared to the wild-type ToPOx for some of the variants. Subsequently, the variants were immobilized on glassy carbon electrodes. Cyclic voltammetry measurements were performed to measure the electrochemical responses of these variant...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 28, 2019 Category: Biochemistry Source Type: research

On the relationship between structure and catalytic effectiveness in solid surface-immobilized enzymes: Advances in methodology and the quest for a single-molecule perspective
Publication date: Available online 25 November 2019Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Juan M. Bolivar, Bernd NidetzkyAbstractThe integration of enzymes with solid materials is important in many biotechnological applications, including the use of immobilized enzymes for biocatalytic synthesis. The development of functional enzyme-material composites is restrained by the lack of molecular-level insight into the behavior of enzymes in confined, surface-near environments. Here, we review recent advances in surface-sensitive spectroscopic techniques that push boundaries for the deter...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 26, 2019 Category: Biochemistry Source Type: research

New insights into human endometrial aminopeptidases in both implantation and menstruation
Publication date: Available online 23 November 2019Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Shigehiko Mizutani, Kunio Matsumoto, Yukio Kato, Eita Mizutani, Hidesuke Mizutani, Akira Iwase, Kiyosumi ShibataAbstractThe endometrium cycle involves proliferation of endometrial epithelial cells in preparation for implantation of fertilized ovum. With ovulation, the endometrium secretes nutrients such as peptides and amino acids into the endometrial cavity. The histological evidence of ovulation in normal menstrual cycle includes subnuclear glycogen vacuoles surrounded by placental leucine am...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 23, 2019 Category: Biochemistry Source Type: research

The substrate of the glucose-6-phosphate dehydrogenase of Pseudomonas aeruginosa provides structural stability
Publication date: Available online 22 November 2019Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Edaena Benítez-Rangel, Annia Rodríguez-Hernández, Roberto Velasco-GarcíaAbstractIn general, eukaryotic glucose-6-phosphate dehydrogenases (G6PDHs) are structurally stabilized by NADP+. Here we show by spectrofluorometric analysis, thermal and urea denaturation, and trypsin proteolysis, that a different mechanism stabilizes the enzyme from Pseudomonas aeruginosa (PaG6PDH) (EC 1.1.1.363). The spectrofluorometric analysis of the emission of 8-anilino-1-naphthalenesulfon...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 22, 2019 Category: Biochemistry Source Type: research

Protein knots provide mechano-resilience to an AAA+ protease-mediated proteolysis with profound ATP energy expenses
In this study, we directly monitored the ClpXP-mediated degradation of UCH variants by electrophoresis and quantitative imaging analyses. We demonstrated that untying of the 52 knot in UCHL1 via N-terminal truncation (UCHL1Δ11) significantly reduces its mechanostability. We further quantified the ATP expenditures of degrading different UCH variants by ClpXP. The unknotted UCHL1Δ11 underwent accelerated ClpXP-dependent proteolysis, with a 30-fold reduction in ATP consumption compared to the knotted wild type. Unlike all other known ClpXP substrates, UCHL5, which is the most resilient substrate known to date, sig...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 20, 2019 Category: Biochemistry Source Type: research

Metagenomics: Is it a powerful tool to obtain lipases for application in biocatalysis?
Publication date: Available online 20 November 2019Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Janaina Marques de Almeida, Robson Carlos Alnoch, Emanuel Maltempi de Souza, David Alexander Mitchell, Nadia KriegerAbstractIn recent years, metagenomic strategies have been widely used to isolate and identify new enzymes from uncultivable components of microbial communities. Among these enzymes, various lipases have been obtained from metagenomic libraries from different environments and characterized. Although many of these lipases have characteristics that could make them interesting for app...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 20, 2019 Category: Biochemistry Source Type: research

Energy migration captures membrane-induced oligomerization of the prion protein
Publication date: Available online 15 November 2019Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Aishwarya Agarwal, Debapriya Das, Tisya Banerjee, Samrat MukhopadhyayAbstractExcitation energy migration via homo-Förster resonance energy transfer (homo-FRET) can serve as an intermolecular proximity ruler within complex biomolecular assemblies. Here we present a unique case to demonstrate that energy migration can be a novel and sensitive readout to capture the membrane-mediated misfolding and oligomerization of the human prion protein (PrP), which is known to undergo an aberrant conform...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 17, 2019 Category: Biochemistry Source Type: research

Rat cathepsin K: Enzymatic specificity and regulation of its collagenolytic activity
Publication date: Available online 15 November 2019Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Fabien Lecaille, Thibault Chazeirat, Krzysztof K. Bojarski, Justine Renault, Ahlame Saidi, V. Gangadhara N.V. Prasad, Sergey Samsonov, Gilles LalmanachAbstractHuman cathepsin K (hCatK), which is highly expressed in osteoclasts, has the noteworthy ability to cleave type I and II collagens in their helical domain. Its collagenase potency depends strictly on the formation of an oligomeric complex with chondroitin 4-sulfate (C4-S). Accordingly, hCatK is a pivotal protease involved in bone resorptio...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 17, 2019 Category: Biochemistry Source Type: research

Unbiased libraries in protein directed evolution
Publication date: Available online 15 November 2019Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Victor Sayous, Paul Lubrano, Yanyan Li, Carlos G. Acevedo-RochaAbstractDirected evolution is a powerful approach to study the molecular basis of protein evolution and to engineer proteins for a wide range of applications in synthetic organic chemistry and biotechnology. There are many methods based on random or focused mutagenesis to engineer successfully any protein trait. Focused approaches such as site-directed and saturation mutagenesis have become methods of choice for improving protein ac...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 17, 2019 Category: Biochemistry Source Type: research

A novel enzymatic tool for transferring GalNAc moiety onto challenging acceptors
We present here a novel production method of this enzyme in the eukaryotic host of Pichia pastoris, followed by elegant one-step purification to homogeneity. The resulting recombinant enzyme has improved biochemical and catalytic properties compared to the fungal wild type. Its good production yield (11 mg/400 mL cultivation media) greatly expands the scope of synthetic applications. We further demonstrate the synthetic utility and broad acceptor specificity of recombinant PoHex in the glycosylation of a series of challenging acceptors with varying structural architectures, namely secondary and tertiary hydroxyl, aldox...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 17, 2019 Category: Biochemistry Source Type: research

Identification and application of threonine aldolase for synthesis of valuable α-amino, β-hydroxy-building blocks
Publication date: Available online 15 November 2019Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Mathieu Ligibel, Charles Moore, Robert Bruccoleri, Radka SnajdrovaAbstractChiral β-hydroxy α-amino acid structural motifs are interesting and common synthons present in multiple APIs and drug candidates. To access these chiral building blocks either multistep chemical syntheses are required or the application of threonine aldolases, which catalyze aldol reactions between an aldehyde and glycine. Bioinformatics tools have been utilized to identify the gene encoding threonine aldolase ...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 17, 2019 Category: Biochemistry Source Type: research

Biochemical properties and biotechnological applications of microbial enzymes involved in the degradation of polyester-type plastics
Publication date: Available online 16 November 2019Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Aneta K. Urbanek, Aleksandra M. Mirończuk, Alberto García-Martín, Ana Saborido, Isabel de la Mata, Miguel ArroyoAbstractApplication of polyester-degrading enzymes should be considered as an eco-friendly alternative to chemical recycling due to the huge plastic waste disposal nowadays. Many hydrolases from several fungi and bacteria have been discovered and successfully evaluated for their activity towards different aliphatic polyesters (PHA, PBS, PBSA, PCL, PLA), aromatic polyest...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 17, 2019 Category: Biochemistry Source Type: research

Xylanases from marine microorganisms: A brief overview on scope, sources, features and potential applications
Publication date: Available online 16 November 2019Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Fatemeh Izadpanah Qeshmi, Ahmad Homaei, Pedro Fernandes, Roohullah Hemmati, Bauke W. Dijkstra, Khosro KhajehAbstractGlobal economic growth often leads to depletion of raw materials and generation of greenhouse gases, as industry manufactures goods at ever increasing levels to keep up with the demand. The currently implemented production processes mostly rely on non-renewable resources, they suffer from high energy consumption, and generate waste that often has a negative environmental impact. E...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 17, 2019 Category: Biochemistry Source Type: research

Using enzyme cascades in biocatalysis: Highlight on transaminases and carboxylic acid reductases
Publication date: Available online 16 November 2019Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Rhys Cutlan, Simone De Rose, Michail N. Isupov, Jennifer A. Littlechild, Nicholas J. HarmerAbstractBiocatalysis, the use of enzymes in chemical transformations, is an important green chemistry tool. Cascade reactions combine different enzyme activities in a sequential set of reactions. Cascades can occur within a living (usually bacterial) cell; in vitro in ‘one pot’ systems where the desired enzymes are mixed together to carry out the multi-enzyme reaction; or using microfluidic sy...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 17, 2019 Category: Biochemistry Source Type: research

Quantitative proteomics indicate a strong correlation of mitotic phospho-/dephosphorylation with non-structured regions of substrates
In this study, we examined structural properties of mitotic phosphosites and neighboring residues to understand the role of heavy phosphorylation in non-structured domains. Quantitative mass spectrometry analysis of mitosis-arrested and non-arrested HeLa cells revealed>4100 and > 2200 residues either significantly phosphorylated or dephosphorylated, respectively, at mitotic entry. The calculated disorder scores of amino acid sequences of neighboring individual phosphosites revealed that>70% of dephosphorylated phosphosites exist in disordered regions, whereas 50% of phosphorylated sites exist in non-structured...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 13, 2019 Category: Biochemistry Source Type: research

Thermophilic nucleoside phosphorylases: Their properties, characteristics and applications
Publication date: Available online 2 November 2019Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Sarah Kamel, Isabel Thiele, Peter Neubauer, Anke WagnerAbstractNucleoside phosphorylases catalyze the reversible phosphorolysis of pyrimidine and purine nucleosides in the presence of phosphate. They are valuable catalysts in the synthesis of nucleosides and their analogues, which are often used as pharmaceuticals or their precursors. Thermostable nucleoside phosphorylases are promising biocatalysts, as they withstand harsh reaction conditions such as high pH or the addition of organic solvents....
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 3, 2019 Category: Biochemistry Source Type: research

Photochemical regeneration of flavoenzymes – An Old Yellow Enzyme case-study
Publication date: Available online 31 October 2019Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): M.C.R. Rauch, M. Pesic, M.M.E. Huijbers, M. Pabst, C.E. Paul, M. Pesic, I.W.C.E. Arends, F. HollmannAbstractDirect, NAD(P)H-independent regeneration of Old Yellow Enzymes represents an interesting approach for simplified reaction schemes for the stereoselective reduction of conjugated C=C-double bonds. Simply by illuminating the reaction mixtures with blue light in the presence of sacrificial electron donors enables to circumvent the costly and unstable nicotinamide cofactors and a corresponding...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 1, 2019 Category: Biochemistry Source Type: research

Chemoenzymatic synthesis of ultralow and low-molecular weight heparins
Publication date: Available online 31 October 2019Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Ting Wang, Li Liu, Josef VoglmeirAbstractHeparin is a naturally occurring glycosaminoglycan isolated from animal tissues and is medically used as an anticoagulant drug. Adulteration attempts of isolated heparin with chondroitin sulfate in the past resulted in great safety concerns. Also, increasing demands on batch-to-batch homogeneity for better evaluation and control of its pharmacodynamic and pharmacokinetic properties kindled the development of synthetic routes for the production of heparin ...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 1, 2019 Category: Biochemistry Source Type: research

Ubiquitin folds via a flip-twist-lock mechanism
Publication date: Available online 30 October 2019Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Manoj Mandal, Atanu Das, Chaitali MukhopadhyayAbstractTo perform specific functional activities, the majority of proteins should fold into their distinct three-dimensional conformations. However, the biologically active conformation of a protein is generally found to be marginally stable than the other conformations that the chain can adopt. How a protein finds its native conformation from its post-synthesis unfolded structure in a complex conformational landscape is the unsolved question that s...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - October 31, 2019 Category: Biochemistry Source Type: research

Sequential oxidation of 5-hydroxymethylfurfural to furan-2,5-dicarboxylic acid by an evolved aryl-alcohol oxidase
Publication date: Available online 30 October 2019Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Javier Viña-Gonzalez, Angel T. Martinez, Victor Guallar, Miguel AlcaldeAbstractFuran-2,5-dicarboxylic acid (FDCA) is a building block of biodegradable plastics that can be used to replace those derived from fossil carbon sources. In recent years, much interest has focused on the synthesis of FDCA from the bio-based 5-hydroxymethylfurfural (HMF) through a cascade of enzyme reactions. Aryl-alcohol oxidase (AAO) and 5-hydroxymethylfurfural oxidase (HMFO) are glucose-methanol-choline flavoenz...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - October 31, 2019 Category: Biochemistry Source Type: research

Use of nucleoside phosphorylases for the preparation of 5-modified pyrimidine ribonucleosides
Publication date: Available online 30 October 2019Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Cyril S. Alexeev, Mikhail S. Drenichev, Evgeniya O. Dorinova, Roman S. Esipov, Irina V. Kulikova, Sergey N. MikhailovAbstractEnzymatic transglycosylation, a transfer of the carbohydrate moiety from one heterocyclic base to another, is catalyzed by nucleoside phosphorylases (NPs) and is being actively developed and applied for the synthesis of biologically important nucleosides. Here, we report an efficient one-step synthesis of 5-substitited pyrimidine ribonucleosides starting from 7-methylguano...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - October 31, 2019 Category: Biochemistry Source Type: research

Roles of the N-terminal domain and remote substrate binding subsites in activity of the debranching barley limit dextrinase
Publication date: Available online 30 October 2019Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Susan Andersen, Birte Svensson, Marie Sofie MøllerAbstractBarley limit dextrinase (HvLD) of glycoside hydrolase family 13 is the sole enzyme hydrolysing α-1,6-glucosidic linkages from starch in the germinating seed. Surprisingly, HvLD shows 150- and 7-fold higher activity towards pullulan and β-limit dextrin, respectively, than amylopectin. This is investigated by mutational analysis of residues in the N-terminal CBM-21-like domain (Ser14Arg, His108Arg, Ser14Arg/His108Arg) and ...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - October 31, 2019 Category: Biochemistry Source Type: research

Biochemical and biophysical characterization of the smallest pyruvate kinase from Entamoeba histolytica
Publication date: Available online 30 October 2019Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Poonam Kumari, Danish Idrees, Pragyan Parimita Rath, Ramachandran Vijayan, Samudrala GourinathAbstractEntamoeba histolytica infection is highly prevalent in developing countries across the globe. The ATP synthesis in this pathogen is solely dependent on the glycolysis pathway where pyruvate kinase (Pyk) catalyzes the final reaction. Here, we have cloned, overexpressed and purified the pyruvate kinase (EhPyk) from E. histolytica. EhPyk is the shortest currently known Pyk till date as it contains ...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - October 31, 2019 Category: Biochemistry Source Type: research

Molecular characterization of an aggregation-prone variant of alpha-synuclein used to model synucleinopathies
Publication date: Available online 30 October 2019Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Caterina Masaracchia, Annekatrin König, Ariel A. Valiente-Gabioud, Pablo Peralta, Filippo Favretto, Timo Strohäker, Diana F. Lázaro, Markus Zweckstetter, Claudio O. Fernandez, Tiago F. OuteiroAbstractThe misfolding and aggregation of alpha-synuclein (aSyn) are thought to be central events in synucleinopathies. The physiological function of aSyn has been related to vesicle binding and trafficking, but the precise molecular mechanisms leading to aSyn pathogenicity are still obscur...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - October 31, 2019 Category: Biochemistry Source Type: research

Quantitative proteomics indicate a strong correlation of mitotic phospho−/dephosphorylation with non-structured regions of substrates
In this study, we examined structural properties of mitotic phosphosites and neighboring residues to understand the role of heavy phosphorylation in non-structured domains. Quantitative mass spectrometry analysis of mitosis-arrested and non-arrested HeLa cells revealed>4100 and > 2200 residues either significantly phosphorylated or dephosphorylated, respectively, at mitotic entry. The calculated disorder scores of amino acid sequences of neighboring individual phosphosites revealed that>70% of dephosphorylated phosphosites exist in disordered regions, whereas 50% of phosphorylated sites exist in non-structured...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - October 31, 2019 Category: Biochemistry Source Type: research

On the catalytic mechanism of bacteriophage endolysins: Opportunities for engineering
Publication date: Available online 31 October 2019Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Michael J. Love, Gayan S. Abeysekera, Andrew C. Muscroft-Taylor, Craig Billington, Renwick C.J. DobsonAbstractBacteriophage endolysins have the potential to be a long-term antibacterial replacement for antibiotics. The exogenous application of endolysins on some bacteria results in rapid cell lysis. The prospects for endolysins are furthered by the ability to engineer them; novel endolysins can be developed with optimised stability, specificity, and lytic function. But the success of endolysin e...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - October 31, 2019 Category: Biochemistry Source Type: research