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A novel neuropilin-1 –binding sequence in the human T-cell lymphotropic virus type 1 envelope glycoprotein
Publication date: Available online 16 February 2018 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): Hideki Kusunoki, Toshiyuki Tanaka, Toshiyuki Kohno, Kazuhiko Matsuhashi, Kazuo Hosoda, Kaori Wakamatsu, Isao Hamaguchi Entry of human T-cell lymphotropic virus type 1 (HTLV-1) into host cells is mainly mediated by interactions between the viral envelope glycoprotein surface unit (SU) and three host receptors: glucose transporter type 1, heparin/heparan sulfate proteoglycan, and neuropilin-1 (Nrp1). Here, we analyzed the interaction between HTLV-1 SU and Nrp1 using nuclear magnetic resonance a...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - February 17, 2018 Category: Biochemistry Source Type: research

A novel β-glucosidase isolated from the microbial metagenome of Lake Poraquê (Amazon, Brazil)
Publication date: Available online 16 February 2018 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): Danyelle Toyama, Mariana Abrahão Bueno de Morais, Felipe Cardoso Ramos, Letícia Maria Zanphorlin, Celisa Caldana Costa Tonoli, Augusto Furio Balula, Fernando Pellon de Miranda, Vitor Medeiros Almeida, Sandro Roberto Marana, Roberto Ruller, Mario Tyago Murakami, Flavio Henrique-Silva The Amazon region holds most of the biological richness of Brazil. Despite their ecological and biotechnological importance, studies related to microorganisms from this region are limited. Metagenomi...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - February 17, 2018 Category: Biochemistry Source Type: research

In vitro studies of disease-linked variants of human tRNA nucleotidyltransferase reveal decreased thermal stability and altered catalytic activity
Publication date: Available online 16 February 2018 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): M. Leibovitch, P.J. Hanic-Joyce, P.B.M. Joyce Mutations in the human TRNT1 gene encoding tRNA nucleotidyltransferase (tRNA-NT), an essential enzyme responsible for addition of the CCA (cytidine-cytidine-adenosine) sequence to the 3′-termini of tRNAs, have been linked to disease phenotypes including congenital sideroblastic anemia with B-cell immunodeficiency, periodic fevers and developmental delay (SIFD) or retinitis pigmentosa with erythrocyte microcytosis. The effects of these diseas...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - February 17, 2018 Category: Biochemistry Source Type: research

Influences of conformations of peptides on stereoinversions and/or isomerizations of aspartic acid residues
This article is part of a Special Issue entitled: D-Amino acids: biology in the mirror, edited by Dr. Loredano Pollegioni, Dr. Jean-Pierre Mothet and Dr. Molla Gianluca. Graphical abstract (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - February 13, 2018 Category: Biochemistry Source Type: research

The role of d-allo-isoleucine in the deposition of the anti-Leishmania peptide bombinin H4 as revealed by 31P solid-state NMR, VCD spectroscopy, and MD simulation
This article is part of a Special Issue entitled: d-Amino acids: biology in the mirror, edited by Dr. Loredano Pollegioni, Dr. Jean-Pierre Mothet and Dr. Molla Gianluca. Graphical abstract (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - February 13, 2018 Category: Biochemistry Source Type: research

d-Amino acids in molecular evolution in space – Absolute asymmetric photolysis and synthesis of amino acids by circularly polarized light
This article is part of a Special Issue entitled: d-Amino acids: biology in the mirror, edited by Dr. Loredano Pollegioni, Dr. Jean-Pierre Mothet and Dr. Molla Gianluca. (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - February 13, 2018 Category: Biochemistry Source Type: research

Corrigendum to “LMD proteomics provides evidence for hippocampus field-specific motor protein abundance changes with relevance to Alzheimer's disease” [BBAPAP 1865 (6) (2017) 703–714]
Publication date: Available online 9 February 2018 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): A. Schrötter, A. Oberhaus, K. Kolbe, S. Seger, T. Mastalski, F. El Magraoui, E. Hoffmann-Posorske, M. Bohnert, J. Deckert, C. Braun, M. Graw, C. Schmitz, T. Arzberger, C. Loosse, H. Heinsen, H.E. Meyer, T. Müller (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - February 13, 2018 Category: Biochemistry Source Type: research

The chaperonin CCT promotes the formation of fibrillar aggregates of γ-tubulin
Publication date: April 2018 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Volume 1866, Issue 4 Author(s): Luis Pouchucq, Pablo Lobos-Ruiz, Gissela Araya, José María Valpuesta, Octavio Monasterio The type II chaperonin CCT is involved in the prevention of the pathogenesis of numerous human misfolding disorders, as it sequesters misfolded proteins, blocks their aggregation and helps them to achieve their native state. In addition, it has been reported that CCT can prevent the toxicity of non-client amyloidogenic proteins by the induction of non-toxic aggregates, leading to new insight ...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - February 13, 2018 Category: Biochemistry Source Type: research

Structure and function of a highly active Bile Salt Hydrolase (BSH) from Enterococcus faecalis and Post-translational Processing of BSH enzymes
We report the three-dimensional structure of a BSH enzyme from the Gram-positive bacteria Enterococcus faecalis (EfBSH) which has manifold higher hydrolase activity compared to other known BSHs and displays unique allosteric catalytic property. The structural analysis revealed reduced secondary structure content compared to other known BSH structures, particularly devoid of an anti-parallel β-sheet in the assembly loop and part of a β-strand is converted to increase the length of a substrate binding loop 2. The analysis of the substrate binding pocket showed reduced volume owing to altered loop conformations and ...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - January 8, 2018 Category: Biochemistry Source Type: research

Tandem mass tags labeled quantitative proteomics to study the effect of tobacco smoke exposure on the rat lung
Conclusions These findings make a crucial contribution to the search for a comprehensive understanding of TSE-induced RSD's pathogenesis, and furthermore provide guidance for the diagnosis and treatment of TSE-induced RSD. (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - January 4, 2018 Category: Biochemistry Source Type: research

Exploring interfacial water trapping in protein-ligand complexes with multithermal titration calorimetry
Publication date: Available online 4 January 2018 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): Iris N. Serratos, Cesar Millán-Pacheco, Georgina Garza-Ramos, Gerardo Pérez-Hernández, Rafael A. Zubillaga In this work, we examine the hypothesis about how trapped water molecules at the interface between triosephosphate isomerase (TIM) and either of two phosphorylated inhibitors, 2-phosphoglycolate (2PG) or phosphoglycolohydroxamate (PGH), can explain the anomalous highly negative binding heat capacities (ΔC p,b ) of both complexes, TIM–2PG and TIM–PGH. ...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - January 4, 2018 Category: Biochemistry Source Type: research

Comparison of the activation energy barrier for succinimide formation from α- and β-aspartic acid residues obtained from density functional theory calculations
In this study, we computationally investigated the cyclization of α- and β-Asp residues to form succinimide with dihydrogen phosphate ion as a catalyst (H2PO4 −). We performed the study using B3LYP/6–31+G(d,p) density functional theory calculations. The comparison of the activation barriers of both residues is discussed. All the calculations were performed using model compounds in which an α/β-Asp-Gly sequence is capped with acetyl and methylamino groups on the N- and C-termini, respectively. Moreover, H2PO4 − catalyzes all the steps of the succinimide formation (cyclization-dehydrat...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - January 3, 2018 Category: Biochemistry Source Type: research

Detection and quantification of D-amino acid residues in peptides and proteins using acid hydrolysis
This article is part of a Special Issue entitled: D-Amino acids: biology in the mirror, edited by Dr. Loredano Pollegioni, Dr. Jean-Pierre Mothet and Dr. Molla Gianluca. Graphical abstract (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - December 29, 2017 Category: Biochemistry Source Type: research

Rat d-aspartate oxidase is more similar to the human enzyme than the mouse enzyme
This article is part of a Special Issue entitled: D-Amino acids: biology in the mirror, edited by Dr. Loredano Pollegioni, Dr. Jean-Pierre Mothet and Dr. Molla Gianluca. (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - December 29, 2017 Category: Biochemistry Source Type: research

Structural evidence for a fatty acid-independent myotoxic mechanism for a phospholipase A2-like toxin
Publication date: Available online 27 December 2017 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): Guilherme H.M. Salvador, Juliana I. dos Santos, Rafael J. Borges, Marcos R.M. Fontes The myotoxic mechanism for PLA2-like toxins has been proposed recently to be initiated by an allosteric change induced by a fatty acid binding to the protein, leading to the alignment of the membrane docking site (MDoS) and membrane disrupting site (MDiS). Previous structural studies performed by us demonstrated that MjTX-II, a PLA2-like toxin isolated from Bothrops moojeni, presents a different mode of ligan...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - December 27, 2017 Category: Biochemistry Source Type: research

Crystal structure of d-glycero- α-d-manno-heptose-1-phosphate guanylyltransferase from Yersinia pseudotuberculosis
In this study, HddC from the synthesized HddC gene of Y. pseudotuberculosis has been expressed, purified, crystallized. Synchrotron X-ray data from a selenomethionine-substituted HddC crystal were also collected and its structure was determined at 2.0Å resolution. Structure analyses revealed that it belongs to the glycosyltransferase A type superfamily members with the signature motif GXGXR for nucleotide binding. Despite of remarkable structural similarity, HddC uses GTP for catalysis instead of CTP and UTP which are used for other major family members, cytidylyltransferase and uridylyltransferase, respectively. We ...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - December 23, 2017 Category: Biochemistry Source Type: research

Properties and mechanism of d-glucosaminate-6-phosphate ammonia-lyase: An aminotransferase family enzyme with d-amino acid specificity
Publication date: Available online 23 December 2017 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): Robert S. Phillips, Samuel C. Ting, Ange G. Tetsadjio, Kaitlin L. Anderson, Kyle M. Friez, Katherine A. Miller, Timothy R. Hoover Salmonella enterica serovar Typhimurium utilizes a wide range of growth substrates, some of which are relatively novel. One of these unusual substrates is d-glucosaminate, which is metabolized by the enzymes encoded in the dga operon. d-Glucosaminate is transported and converted to d-glucosaminate-6-phosphate (G6P) by a phosphotransferase system, composed of DgaABC...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - December 23, 2017 Category: Biochemistry Source Type: research

Human d-amino acid oxidase: The inactive G183R variant
Publication date: Available online 21 December 2017 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): Giulia Murtas, Laura Caldinelli, Pamela Cappelletti, Silvia Sacchi, Loredano Pollegioni In the brain, the enzyme d-amino acid oxidase (DAAO) catalyzes the oxidative deamination of d-serine, a main positive modulator of the N-methyl-d-aspartate subtype of glutamate receptors (NMDAR). Dysregulation in d-serine signaling is implicated in the NMDAR dysfunctions observed in various brain diseases, such as amyotrophic lateral sclerosis, Alzheimer's disease, schizophrenia. A strain of ddY mice lacki...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - December 22, 2017 Category: Biochemistry Source Type: research

Peptide deformylases from Vibrio parahaemolyticus phage and bacteria display similar deformylase activity and inhibitor binding clefts
In this study, we characterize the bacteriophage Vp16 PDF enzyme, as representative member of the newly identified C-terminally truncated viral PDFs. We show here that conditions classically used for bacterial PDFs lead to an enzyme exhibiting weak activity. Nonetheless, our integrated biophysical and biochemical approaches reveal specific effects of pH and metals on Vp16 PDF stability and activity. A novel purification protocol taking in account these data allowed strong improvement of Vp16 PDF specific activity to values similar to those of bacterial PDFs. We next show that Vp16 PDF is as sensitive to the natural inhibit...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - December 21, 2017 Category: Biochemistry Source Type: research

Quantitative proteomics analysis reveals alterations of lysine acetylation in mouse testis in response to heat shock and X-ray exposure
In this study, we employed quantitative proteomic techniques and bioinformatics tools to analyze the alterations of acetylome profile of mouse testis after heat shock and X-irradiation. Overall, we identified 1139 lysine acetylation sites in 587 proteins in which 1020 lysine acetylation sites were quantified. The Gene Ontology analysis showed that the major acetylated protein groups were involved in generation of precursor metabolites and metabolic processes, and were localized predominantly in cytosolic and mitochondrial. Compared to the control group, 36 sites of 28 acetylated proteins have changed after heat shock, and ...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - December 16, 2017 Category: Biochemistry Source Type: research

Proteome-wide lysine acetylation identification in developing Rice (Oryza sativa) seeds and protein co-modification by acetylation, Succinylation, ubiquitination, and phosphorylation
In this report, we identified 1003 lysine acetylation sites in 692 proteins of developing rice seeds, which greatly extended the number of known acetylated sites in plants. Seven distinguished motifs were detected flanking acetylated lysine. Functional annotation analyses indicated diverse biological processes and pathways engaged in lysine acetylation. Remarkably, we found that several key enzymes in storage starch synthesis pathway and the main storage proteins were heavily acetylated. A comprehensive comparison of the rice acetylome, succinylome, ubiquitome and phosphorylome with available published data was conducted. ...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - December 16, 2017 Category: Biochemistry Source Type: research

Crystal structure of UDP-N-acetylglucosamine-enolpyruvate reductase (MurB) from Mycobacterium tuberculosis
Publication date: Available online 5 December 2017 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): Kandasamy Eniyan, Sudhaker Dharavath, Ramachandran Vijayan, Urmi Bajpai, Samudrala Gourinath The biosynthesis of UDP-N-acetylmuramic acid (UDP-MurNAc) by reduction of UDP-N-acetylglucosamine-enolpyruvate (UDP-GlcNAc-EP) in an NADPH and FAD-dependent reaction in bacteria is one of the key steps in peptidoglycan biosynthesis catalyzed by UDP-N-acetylglucosamine-enolpyruvate reductase (MurB). Here, we present the crystal structure of Mycobacterium tuberculosis MurB (MtbMurB) with FAD as the prost...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - December 16, 2017 Category: Biochemistry Source Type: research

Free energy calculations on the stability of the 14-3-3 ζ protein
Publication date: Available online 5 December 2017 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): Zuzana Jandova, Zuzana Trosanova, Veronika Weissova, Chris Oostenbrink, Jozef Hritz Mutations of cysteine are often introduced to e.g. avoid formation of non-physiological inter-molecular disulfide bridges in in-vitro experiments, or to maintain specificity in labeling experiments. Alanine or serine is typically preferred, which usually do not alter the overall protein stability, when the original cysteine was surface exposed. However, selecting the optimal mutation for cysteines in the hydrop...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - December 16, 2017 Category: Biochemistry Source Type: research

L. donovani XPRT: Molecular characterization and evaluation of inhibitors
Publication date: Available online 9 December 2017 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): Bhumi Patel, Dhaval Patel, Krupali Parmar, Rupal Chauhan, Desh Deepak Singh, Anju Pappachan Among all PRT enzymes of purine salvage pathway in Leishmania, XPRT (Xanthine phosphoribosyl transferase) is unique in its substrate specificity and their non-existence in human. It is an interesting protein not only for drug designing but also to understand the molecular determinants of its substrate specificity. Analysis of the 3D model of L. donovani XPRT (Ld-XPRT) revealed that Ile 209, Glu 215 and ...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - December 16, 2017 Category: Biochemistry Source Type: research

Active-site mutations improved the transglycosylation activity of Stenotrophomonas maltophilia chitinase A
Publication date: Available online 9 December 2017 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): Bhoopal Bhuvanachandra, Jogi Madhuprakash, Appa Rao Podile Transglycosylation (TG) by family 18 chitinases is of special interest due to the many biological applications of long-chain chitooligosaccharides (CHOS). In the current study, the TG activity of chitinase A from Stenotrophomonas maltophilia (StmChiA) was improved through structure-guided mutations within and around the active site. Three independent mutants were created, targeting Trp residues from the −3 and −1 subsites a...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - December 16, 2017 Category: Biochemistry Source Type: research

Structural and thermodynamic characterization of endo-1,3- β-glucanase: Insights into the substrate recognition mechanism
Publication date: Available online 12 December 2017 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): Masayuki Oda, Satomi Inaba, Narutoshi Kamiya, Gert-Jan Bekker, Bunzo Mikami Endo-1,3-β-glucanase from Cellulosimicrobium cellulans is composed of a catalytic domain and a carbohydrate-binding module. We have determined the X-ray crystal structure of the catalytic domain at a high resolution of 1.66Å. The overall fold is a sandwich-like β-jelly roll architecture like the enzymes in the glycoside hydrolase family 16. The substrate-binding cleft has a length and a width of ~28 an...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - December 16, 2017 Category: Biochemistry Source Type: research

Quantitative proteomics study of host response to virulent and attenuated pseudorabies virus infection in mouse brain
This study may provide new clues for molecular mechanisms for PRV infection and spread. (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - December 16, 2017 Category: Biochemistry Source Type: research

Functional diversification of sea lamprey globins in evolution and development
Publication date: February 2018 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Volume 1866, Issue 2 Author(s): Angela Fago, Kim Rohlfing, Elin E. Petersen, Agnieszka Jendroszek, Thorsten Burmester Agnathans have a globin repertoire that markedly differs from that of jawed (gnathostome) vertebrates. The sea lamprey (Petromyzon marinus) harbors at least 18 hemoglobin, two myoglobin, two globin X, and one cytoglobin genes. However, agnathan hemoglobins and myoglobins are not orthologous to their cognates in jawed vertebrates. Thus, blood-based O2 transport and muscle-based O2 storage proteins emerged t...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - December 16, 2017 Category: Biochemistry Source Type: research

Analysis of substrate binding in individual active sites of bifunctional human ATIC
Publication date: February 2018 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Volume 1866, Issue 2 Author(s): Danuta Witkowska, Heather L. Cox, Tara C. Hall, Gemma C. Wildsmith, Darren C. Machin, Michael E. Webb Aminoimidazolecarboxamide ribonucleotide formyl transferase (AICARFT): Inosine monophosphate cyclohydrolase (IMPCH, collectively called ATIC) is a bifunctional enzyme that catalyses the penultimate and final steps in the purine de novo biosynthesis pathway. The bifunctional protein is dimeric and each monomer contains two different active sites both of which are capable of binding nucleotid...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - December 16, 2017 Category: Biochemistry Source Type: research

Monomerization and aggregation of β-Lactoglobulin under adverse condition: A fluorescence correlation spectroscopic investigation
Publication date: Available online 15 November 2017 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): Bhaswati Sengupta, Nilimesh Das, Pratik Sen β-lactoglobulin is one of the major components of bovine milk and it remains in a dimeric form under physiological conditions. The present contribution elucidates the structural change of β-lactoglobulin at pH7.4 under the action of guanidine hydrochloride (GnHCl) and heat at the single molecular level. The only free cysteine (Cys-121) of β-lactoglobulin has been tagged with 7-Diethylamino-3-(4-maleimidophenyl)-4-methylcoumarin (CPM) ...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 16, 2017 Category: Biochemistry Source Type: research

Structural insights of RmXyn10A – A prebiotic-producing GH10 xylanase with a non-conserved aglycone binding region
In this study, the structure of RmXyn10A was investigated, the catalytic module by homology modelling and site-directed mutagenesis and the arrangement of its five domains by small-angle X-ray scattering (SAXS). Substrate specificity was explored in silico by manual docking and molecular dynamic simulations. It has been shown in the literature that the glycone subsites of GH10 xylanases are well conserved and our results suggest that RmXyn10A is no exception. The aglycone subsites are less investigated, and the modelled structure of RmXyn10A suggests that loop β6α6 in the aglycone part of the active site contain...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 14, 2017 Category: Biochemistry Source Type: research

The N-terminal domains of Bacillus subtilis CopA do not form a stable complex in the absence of their inter-domain linker
Publication date: Available online 14 November 2017 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): Liang Zhou, Kristine L. Kay, Oliver Hecht, Geoffrey R. Moore, Nick E. Le Brun Copper-transporting P-type ATPases, which play important roles in trafficking Cu(I) across membranes for the biogenesis of copper proteins or for copper detoxification, contain a variable number of soluble metal-binding domains at their N-termini. It is increasingly apparent that these play an important role in regulating copper transport in a Cu(I)-responsive manner, but how they do this is unknown. CopA, a Cu(I)-t...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 14, 2017 Category: Biochemistry Source Type: research

Simple strategies to enhance discovery of acetylation post-translational modifications by quadrupole-orbitrap LC-MS/MS
Publication date: February 2018 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Volume 1866, Issue 2 Author(s): Andrew J. Manning, Jiyoung Lee, Donald J. Wolfgeher, Stephen J. Kron, Jean T. Greenberg Enzyme-dependent post-translational modifications (PTMs) mediate the cellular regulation of proteins and can be discovered using proteomics. However, even where the peptides of interest can be enriched for analysis with state-of-the-art LC-MS/MS tools and informatics, only a fraction of peptide ions can be identified confidently. Thus, many PTM sites remain undiscovered and unconfirmed. In this minirevie...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 14, 2017 Category: Biochemistry Source Type: research

In silico analysis of cytochrome P450 monooxygenases in chronic granulomatous infectious fungus Sporothrix schenckii: Special focus on CYP51
This article is part of a Special Issue entitled: Cytochrome P450 biodiversity and biotechnology, edited by Erika Plettner, Gianfranco Gilardi, Luet Wong, Vlada Urlacher, Jared Goldstone. Graphical abstract (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 13, 2017 Category: Biochemistry Source Type: research

CYP106A2 —A versatile biocatalyst with high potential for biotechnological production of selectively hydroxylated steroid and terpenoid compounds
This article is part of a Special Issue entitled: Cytochrome P450 biodiversity and biotechnology, edited by Erika Plettner, Gianfranco Gilardi, Luet Wong, Vlada Urlacher, Jared Goldstone. (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 13, 2017 Category: Biochemistry Source Type: research

Preface: Cytochrome P450
Publication date: January 2018 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Volume 1866, Issue 1 Author(s): Erika Plettner (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 13, 2017 Category: Biochemistry Source Type: research

An artificially constructed dimer through deformation of a short zinc-binding loop
Publication date: Available online 6 November 2017 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): Jimin Park, Mi-Sun Kim, Keehyung Joo, Jooyoung Lee, Dong Hae Shin We have analyzed the crystal structure of the dimeric form of d-glycero-d-manno-heptose-1,7-bisphosphate phosphatase from Burkholderia thailandensis (BtGmhB), catalyzing the removal of the phosphate at the 7 position of d-glycero-d-manno-heptose-1,7-bisphosphate. The crystal structure of BtGmhB revealed a dimeric form caused by a disruption of a short zinc-binding loop. The dimeric BtGmhB structure was induced by triggering the ...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 11, 2017 Category: Biochemistry Source Type: research

New insights into the structural and functional involvement of the gate loop in AcrB export activity
Publication date: Available online 8 November 2017 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): Abdessamad Ababou AcrB is a major multidrug exporter in Escherichia coli and other Gram-negative bacteria. Its gate loop, located between the proximal and the distal pockets, have been reported to play important role in the export of many antibiotics. This loop location, rigidity and interactions with substrates have led recent reports to suggest that AcrB export mechanism operates in a sequential manner. First the substrate binds the proximal pocket in the access monomer, then it moves to bin...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 11, 2017 Category: Biochemistry Source Type: research

How nature tunes isoenzyme activity in the multifunctional catalytic globin Dehaloperoxidase from Amphitrite ornata
Publication date: Available online 9 November 2017 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): Leiah M. Carey, Roman Gavenko, Dimitri A. Svistunenko, Reza A. Ghiladi The coelomic hemoglobin of Amphitrite ornata, termed dehaloperoxidase (DHP), is the first known multifunctional catalytic globin to possess biologically-relevant peroxidase and peroxygenase activities. Although the two isoenzymes of DHP, A and B, differ in sequence by only 5 amino acids out of 137 residues, DHP B consistently exhibits a greater activity than isoenzyme A. To delineate the contributions of each amino acid sub...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 11, 2017 Category: Biochemistry Source Type: research

Review of NAD(P)H-dependent oxidoreductases: Properties, engineering and application
Publication date: Available online 10 November 2017 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): Lara Sellés Vidal, Ciarán L. Kelly, Paweł M. Mordaka, John T. Heap NAD(P)H-dependent oxidoreductases catalyze the reduction or oxidation of a substrate coupled to the oxidation or reduction, respectively, of a nicotinamide adenine dinucleotide cofactor NAD(P)H or NAD(P)+. NAD(P)H-dependent oxidoreductases catalyze a large variety of reactions and play a pivotal role in many central metabolic pathways. Due to the high activity, regiospecificity and stereospecificity with which t...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 11, 2017 Category: Biochemistry Source Type: research

Molecular modeling of biomolecules by paramagnetic NMR and computational hybrid methods
This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman. (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - October 13, 2017 Category: Biochemistry Source Type: research

Computational membrane biophysics: From ion channel interactions with drugs to cellular function
This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman. (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - October 13, 2017 Category: Biochemistry Source Type: research

Biophysics in Canada
Publication date: November 2017 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Volume 1865, Issue 11, Part B Author(s): John Baenziger, Lewis Kay, Albert Berghuis, Peter Tieleman (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - October 13, 2017 Category: Biochemistry Source Type: research

PAK4 crystal structures suggest unusual kinase conformational movements
In this study, we observe unusual conformational ‘hinging’ for protein kinases. Hinging, the opening and closing of the kinase sub-domains to allow nucleotide binding and release, is critical for proper kinase regulation and for targeted drug discovery. We determine new crystal structures of PAK4, an important Rho-effector kinase, and conduct analyses of these and previously determined structures. We find that PAK4 crystal structures can be classified into specific conformational groups, and that these groups are associated with previously unobserved hinging motions and an unusual conformation for the kinase hy...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - October 7, 2017 Category: Biochemistry Source Type: research

The physical forces mediating self-association and phase-separation in the C-terminal domain of TDP-43
In this study, we used nuclear magnetic resonance spectroscopy and optical methods to demonstrate that an α-helical component in the centre (residues 320–340) of the C-terminal domain is related to the protein's self-association and LLPS. Systematically analysing ALS-related TDP-43 mutants (G298S, M337V, and Q331K) in different buffer conditions at different temperatures, we prove that this phase separation is driven by hydrophobic interactions but is inhibited by electrostatic repulsion. Based on these findings, we rationally introduced a mutant, W334G, and demonstrate that this mutant disrupts LLPS without di...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - October 4, 2017 Category: Biochemistry Source Type: research

(machine-)learning to analyze in vivo microscopy: Support vector machines
This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman. (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - September 30, 2017 Category: Biochemistry Source Type: research

Peroxidase-like activity of cytochrome b5 is triggered upon hemichrome formation in alkaline pH
Publication date: Available online 27 September 2017 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): K. Samhan-Arias Alejandro, Luisa B. Maia, M. Cordas Cristina, Moura Isabel, Gutierrez-Merino Carlos, J.G. Moura José In alkaline media (pH12) a catalytic peroxidase activity of cytochrome b 5 was found associated to a different conformational state. Upon incubation at this pH, cytochrome b 5 electronic absorption spectrum was altered, with disappearance of characteristic bands of cytochrome b 5 at pH7.0. The appearance of new electronic absorption bands and EPR measurements support th...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - September 28, 2017 Category: Biochemistry Source Type: research

Utilizing tagged paramagnetic shift reagents to monitor protein dynamics by NMR
This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman. (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - September 23, 2017 Category: Biochemistry Source Type: research

Reversible association of proteins into sub-visible amorphous aggregates using short solubility controlling peptide tags
Publication date: Available online 22 September 2017 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): Md. Golam Kabir, Mohammad Monirul Islam, Yutaka Kuroda Careful analysis of sub-visible amorphous aggregates, where proteins associate non- covalently in either native or denatured states without forming a specific quaternary structure, may shed insight into the mechanisms of protein aggregation and solubility. Here we report a biophysical and biochemical analysis of our model protein, a bovine pancreatic trypsin inhibitor variant (BPTI-19A), whose oligomerization were controlled by attaching...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - September 23, 2017 Category: Biochemistry Source Type: research

Crystal structure of l-glutamate N-acetyltransferase ArgA from Mycobacterium tuberculosis
Publication date: Available online 22 September 2017 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): Xiuna Yang, Lijie Wu, Yajun Ran, Ao Xu, Bing Zhang, Xiaolin Yang, Rongguang Zhang, Zihe Rao, Jun Li l-arginine is used as a source of both carbon and nitrogen in Mycobacterium tuberculosis (Mtb) and its biosynthesis is essential for the pathogen's survival. MtbArgA (Rv2747) catalyzes the initial step in l-arginine biosynthesis by transferring an acetyl group from acetyl coenzyme A (AcCoA) to l-glutamate. MtbArgA is a class III N-acetylglutamate synthase (NAGS) with no structural information....
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - September 23, 2017 Category: Biochemistry Source Type: research