Vibrio cholerae LMWPTP-2 display unique surface charge and grooves around the active site: Indicative of distinctive substrate specificity and scope to design specific inhibitor
Publication date: Available online 14 November 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Shramana Chatterjee, Seema Nath, Biplab Ghosh, Udayaditya SenAbstractLow molecular weight protein phosphotyrosine phosphatases (LMWPTPs) are ubiquitously found as small cytoplasmic enzymes which act on phospho-tyrosine containing proteins that are engaged in various cellular functions. Vibrio cholerae O395 contains two LMWPTPs having widely different sequence. Phylogenetic analysis based on a non redundant set of 100 LMWPTP sequences, designate that LMWPTP-2 from Vibrio choleraeO395 (VcLMWPTP-2...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 15, 2018 Category: Biochemistry Source Type: research

Allosteric regulation of pyruvate kinase from Mycobacterium tuberculosis by metabolites
Publication date: Available online 10 November 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Jan Snášel, Iva PichováAbstractMycobacterium tuberculosis (Mtb) causes both acute tuberculosis and latent, symptom-free infection that affects roughly one-third of the world's population. It is a globally important pathogen that poses multiple dangers. Mtb reprograms its metabolism in response to the host niche, and this adaptation contributes to its pathogenicity. Knowledge of the metabolic regulation mechanisms in Mtb is still limited. Pyruvate kinase, involved in the lat...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 11, 2018 Category: Biochemistry Source Type: research

Structural Stability of Human Butyrylcholinesterase under High Hydrostatic Pressure
Publication date: Available online 7 November 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Liina Kangur, Kõu Timpmann, Dominik Zeller, Patrick Masson, Judith Peters, Arvi FreibergAbstractHuman butyrylcholinesterase is a nonspecific enzyme of clinical, pharmacological and toxicological significance. Although the enzyme is relatively stable, its activity is affected by numerous factors, including pressure. In this work, hydrostatic pressure dependence of the intrinsic tryptophan fluorescence in native and salted human butyrylcholinesterase was studied up to the maximum pressure a...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 8, 2018 Category: Biochemistry Source Type: research

Editorial Board
Publication date: January 2019Source: Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Volume 1867, Issue 1Author(s): (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 2, 2018 Category: Biochemistry Source Type: research

Reviewer Acknowledgement
Publication date: January 2019Source: Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Volume 1867, Issue 1Author(s): (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 2, 2018 Category: Biochemistry Source Type: research

Analysis of cellular proteome changes in response to ZIKV NS2B-NS3 protease expression
This study sought to determine new host cell protein targets of ZIKV NS2B-NS3 (zNS2B-NS3). Plasmids encoding the protease domains of zNS2B-NS3pro and an inactive zNS2B-NS3(S135A) were transfected into HEK293T/17 cells and differentially expressed proteins were detected by 2D gel electrophoresis. A total of 18 protein spots were observed as differentially expressed between zNS2B-NS3pro and zNS2B-NS3(S135A), of which 7 were selected for identification by mass spectrometry. Four proteins (protein disulfide-isomerase A3 (PDIA3), heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1), voltage-dependent anion-selective chan...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 1, 2018 Category: Biochemistry Source Type: research

Pleiotropic effects of a cold shock protein homolog PprM on the proteome of Deinococcus radiodurans
Publication date: Available online 30 October 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Anaganti Narasimha, Mahesh Kumar Padwal, Pratiksha Dani, Bhakti BasuAbstractAn extremophile D. radiodurans encodes a non-cold shock inducible cold shock protein homolog DR_0907 (also known as PprM). The DR_0907 ORF was deleted by knockout mutagenesis and the resultant deletion mutant (ΔpprM D. radiodurans) displayed growth defect as well as gamma-radiation sensitivity (D10 values = ΔpprM D. radiodurans: 12.1 kGy versus wild type (WT) D. radiodurans: 14 kGy). 2D gel based comp...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - October 31, 2018 Category: Biochemistry Source Type: research

Inter and intra-subunit interactions at the subunit interface of chaperonin GroEL are essential for its stability and assembly
Publication date: Available online 26 October 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Sarita Puri, Tapan K. ChaudhuriAbstractChaperonin GroEL helps in the folding of substrate proteins under normal and stress conditions. Although it remains stable and functional during stress conditions, the quantitative estimation of stability parameters and the specific amino-acid residues playing a role in its stability are not known in sufficient detail. The reason for poor understanding is its large size, multimeric nature, and irreversible unfolding process. The X-ray crystal structure reve...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - October 27, 2018 Category: Biochemistry Source Type: research

Exploring the aggregation-prone regions from structural domains of human TDP-43
In this study, we attempted to delineate the aggregation-prone sequences of the structural domain of TDP-43. Here, we investigated the self-assembly of peptides of TDP-43 using aggregation prediction algorithms, Zipper DB and AMYLPRED2. The three aggregation-prone peptides identified were from N-terminal domain (24GTVLLSTV31), and RNA recognition motifs, RRM1 (128GEVLMVQV135) and RRM2 (247DLIIKGIS254). Furthermore, the amyloid fibril forming propensities of these peptides were analyzed through different biophysical techniques and molecular dynamics simulation. Our study shows the different aggregation ability of conserved ...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - October 24, 2018 Category: Biochemistry Source Type: research

Characterization of low-lying excited states of proteins by high-pressure NMR
Publication date: Available online 24 October 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Mike P. Williamson, Ryo KitaharaAbstractHydrostatic pressure alters the free energy of proteins by a few kJ mol−1, with the amount depending on their partial molar volumes. Because the folded ground state of a protein contains cavities, it is always a state of large partial molar volume. Therefore pressure always destabilises the ground state and increases the population of partially and completely unfolded states. This is a mild and reversible conformational change, which allows the study...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - October 24, 2018 Category: Biochemistry Source Type: research

Two Distinct Aggregation Pathways in Transthyretin Misfolding and Amyloid Formation
In this study, we report the effect of pH on TTR misfolding pathways and amyloid structures. Our combined solution and solid-state NMR studies revealed that TTR amyloid formation can proceed via at least two distinct misfolding pathways depending on the acidic conditions. Under mildly acidic conditions (pH 4.4), tetrameric native TTR appears to dissociate to monomers that maintain most of the native-like β-sheet structures. The amyloidogenic protein undergoes a conformational transition to largely unfolded states at more acidic conditions (pH 2.4), leading to amyloid with distinct molecular structures. Aggregation...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - October 24, 2018 Category: Biochemistry Source Type: research

Editorial Board
Publication date: December 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Volume 1866, Issue 12Author(s): (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - October 24, 2018 Category: Biochemistry Source Type: research

Rv3272 encodes a novel Family III CoA transferase that alters the cell wall lipid profile and protects mycobacteria from acidic and oxidative stress
Publication date: Available online 17 October 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Karade Sharanbasappa Shrimant, Shilpika Pandey, Ahmadullah Ansari, Swetarka Das, Sarita Tripathi, Ashish Arora, Sidharth Chopra, J. Venkatesh Pratap, Arunava DasguptaAbstractThe availability of complete genome sequence of Mycobacterium tuberculosis has provided an important tool to understand the mycobacterial biology with respect to host-pathogen interaction, which is an unmet need of the hour owing to continuous increasing drug resistance. Hypothetical proteins are often an overlooked pool tho...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - October 18, 2018 Category: Biochemistry Source Type: research

Evaluation of kinetic data: What the numbers tell us about PRMTs
Publication date: Available online 17 October 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Adam Frankel, Jennifer I. BrownAbstractProtein arginine N-methyltransferase (PRMT) kinetic parameters have been catalogued over the past fifteen years for eight of the nine mammalian enzyme family members. Like the majority of methyltransferases, these enzymes employ the highly ubiquitous cofactor S-adenosyl-l-methionine as a co-substrate to methylate arginine residues in peptidic substrates with an approximately 4-μM median KM. The median values for PRMT turnover number (kcat) and catalytic ...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - October 18, 2018 Category: Biochemistry Source Type: research

Dynamic light scattering study of base excision DNA repair proteins and their complexes
Publication date: Available online 12 October 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Inna A. Vasil’eva, Rashid O. Anarbaev, Nina A. Moor, Olga I. LavrikAbstractBase excision repair (BER) involves many enzymes acting in a coordinated fashion at the most common types of DNA damage. The coordination is facilitated by interactions between the enzymes and accessory proteins, X-ray repair cross-complementing protein 1 (XRCC1) and poly(ADP-ribose) polymerase 1 (PARP1). Here we use dynamic light scattering (DLS) technique to determine the hydrodynamic sizes of several BER enzymes ...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - October 14, 2018 Category: Biochemistry Source Type: research

The germinal Centre kinase Don3 is crucial for unconventional secretion of chitinase Cts1 in Ustilago maydis
Publication date: Available online 11 October 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Jörn Aschenbroich, Kai P. Hussnaetter, Peter Stoffels, Thorsten Langner, Sabrina Zander, Björn Sandrock, Michael Bölker, Michael Feldbrügge, Kerstin SchipperAbstractUnconventional secretion has emerged as an increasingly important cellular process in eukaryotic cells. The underlying translocation mechanisms are diverse and often little understood. We study unconventional secretion of chitinase Cts1 in the corn smut fungus Ustilago maydis. This protein participates in the cyto...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - October 12, 2018 Category: Biochemistry Source Type: research

Inhibition of amyloid fibril formation and disassembly of pre-formed fibrils by natural polyphenol rottlerin
Publication date: Available online 12 October 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Katarina Siposova, Tibor Kozar, Veronika Huntosova, Silvia Tomkova, Andrey MusatovAbstractNatural polyphenols, curcumin, rottlerin and EGCG were selected for initial computational modeling of protein-ligand interaction patterns. The docking calculations demonstrated that these polyphenols can easily adjust their conformational shape to fit well into the binding sites of amyloidogenic proteins. The experimental part of the study focused on the effect of rottlerin on fibrillation of three distinct...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - October 12, 2018 Category: Biochemistry Source Type: research

Exploring the Aggregation-prone regions from structural domains of. Human TDP-43
In this study, we attempted to delineate the aggregation-prone sequences of the structural domain of TDP-43. Here, we investigated the self-assembly of peptides of TDP-43 using aggregation prediction algorithms, Zipper DB and AMYLPRED2. The three aggregation-prone peptides identified were from N-terminal domain (24GTVLLSTV31), and RNA recognition motifs, RRM1 (128GEVLMVQV135) and RRM2 (247DLIIKGIS254). Furthermore, the amyloid fibril forming propensities of these peptides were analyzed through different biophysical techniques and molecular dynamics simulation. Our study shows the different aggregation ability of conserved ...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - October 12, 2018 Category: Biochemistry Source Type: research

Disruptive membrane interactions of alpha-synuclein aggregates
Publication date: Available online 11 October 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Aditya Iyer, Mireille M.A.E. ClaessensAbstractAlpha synuclein (αS) is a ~14 kDa intrinsically disordered protein. Decades of research have increased our knowledge on αS yet its physiological function remains largely elusive. The conversion of monomeric αS into oligomers and amyloid fibrils is believed to play a central role of the pathology of Parkinson's disease (PD). It is becoming increasingly clear that the interactions of αS with cellular membranes are important fo...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - October 12, 2018 Category: Biochemistry Source Type: research

The interaction of β2-glycoprotein I with lysophosphatidic acid in platelet aggregation and blood clotting
In this study, we investigated the interaction of β2-GPI with a negatively charged lysophosphatidic acid (LPA) on platelet aggregation and blood clotting. Two negatively charged lysophospholipids, LPA and lysophosphatidylserine, specifically inhibited the binding of β2-GPI to oxidized LDL in a concentration-dependent manner. Intrinsic tryptophan fluorescence studies demonstrated that emission intensity of β2-GPI decreases in an LPA-concentration-dependent manner without a shift in wavelength maxima. LPA specifically induced the aggregation of β2-GPI in phosphate-buffered saline, and incubated plasma and...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - October 10, 2018 Category: Biochemistry Source Type: research

A multiparametric analysis of the synergistic impact of anti-Parkinson's drugs on the fibrillation of human serum albumin
Publication date: Available online 9 October 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Tajalli Ilm Chandel, Nida Zaidi, Masihuz Zaman, Ishrat Jahan, Aiman Masroor, Ibrar Ahmad Siddique, Shahid M. Nayeem, Maroof Ali, Vladimir N. Uversky, Rizwan Hasan KhanAbstractProtein aggregation have been associated with several human neurodegenerative diseases, such as Parkinson's and Alzheimer's diseases. There are several small molecules that can reduce aggregation of proteins. The present study aimed to test the hypothesis that the application of more than one inhibitor either simultaneously ...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - October 10, 2018 Category: Biochemistry Source Type: research

Interaction of γ-conglutin from Lupinus albus with model phospholipid membranes: Investigations on structure, thermal stability and oligomerization status
Publication date: Available online 9 October 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Andrea Scirè, Maurizio Baldassarre, Fabio Tanfani, Jessica Capraro, Marcello Duranti, Alessio ScarafoniAbstractInteraction with model phospholipid membranes of lupin seed γ-conglutin, a glycaemia-lowering protein from Lupinus albus seeds, has been studied by means of Fourier-Transform infrared spectroscopy at p2H 7.0 and at p2H 4.5. The protein maintains the same secondary structure both at p2H 7.0 and at p2H 4.5, but at p2H 7.0 a higher 1H/2H exchange was observed, indicating a grea...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - October 10, 2018 Category: Biochemistry Source Type: research

Division of Rare Cancer Research
Publication date: Available online 9 October 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Tadashi Kondo (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - October 9, 2018 Category: Biochemistry Source Type: research

Engineering methionine γ-lyase from Citrobacter freundii for anticancer activity
Publication date: Available online 27 September 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Samanta Raboni, Svetlana Revtovich, Nicola Demitri, Barbara Giabbai, Paola Storici, Chiara Cocconcelli, Serena Faggiano, Elena Rosini, Loredano Pollegioni, Serena Galati, Annamaria Buschini, Elena Morozova, Vitalia Kulikova, Alexey Nikulin, Edi Gabellieri, Patrizia Cioni, Tatyana Demidkina, Andrea MozzarelliAbstractMethionine deprivation of cancer cells, which are deficient in methionine biosynthesis, has been envisioned as a therapeutic strategy to reduce cancer cell viability. Methionine &ga...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - October 5, 2018 Category: Biochemistry Source Type: research

GM1 locates to mature amyloid structures implicating a prominent role for glycolipid-protein interactions in Alzheimer pathology
Publication date: Available online 28 September 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Wojciech Michno, Patrick M. Wehrli, Henrik Zetterberg, Kaj Blennow, Jörg HanriederAbstractWhile the molecular mechanisms underlying Alzheimer's disease remain largely unknown, abnormal accumulation and deposition of beta amyloid (Aβ) peptide into plaques has been proposed as a critical pathological process driving disease progression. Over the last years, neuronal lipid species have been implicated in biological mechanisms underlying amyloid plaque pathology. While these processes co...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - October 5, 2018 Category: Biochemistry Source Type: research

Potential in vitro and ex vivo targeting of bZIP53 involved in stress response and seed maturation in Arabidopsis thaliana by five designed peptide inhibitors
Publication date: Available online 29 September 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Prateek Jain, Koushik Shah, Vikas RishiAbstractBasic leucine zipper (bZIP) transcription factors (TFs) are eukaryote-specific proteins that bind to DNA as a homodimer or heterodimer and regulate gene expression. They are involved in several biological processes in plants; therefore inhibiting bZIP-DNA binding activity by targeting protein-protein interface is an attractive proposition with aspects of both basic and applied biology. Here, we describe the equilibrium and kinetic interactions stu...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - October 5, 2018 Category: Biochemistry Source Type: research

Structural characterization of 1-deoxy-D-xylulose 5-phosphate Reductoisomerase from Vibrio vulnificus
In this study, we produced and structurally characterized V. vulnificus Dxr. The enzyme forms a dimeric assembly and contains a metal ion in the active site. Protein produced in Escherichia coli co-purifies with Mg2+ ions, however the Mg2+ cations may be substituted with Mn2+, as both of these metals may be utilized by Dxrs. These findings will provide a basis for the design of Dxr inhibitors that may find application as antimicrobial compounds.Graphical abstract (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - October 5, 2018 Category: Biochemistry Source Type: research

Predicting the location of the non-local Contacts in α-synuclein
Publication date: Available online 29 September 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Fernando Bergasa-Caceres, Herschel A. RabitzAbstractIn this paper, the Sequential Collapse Model (SCM) for protein folding pathways is applied to investigate the location of the non-local contacts in the intrinsically disordered state of α-synuclein, a protein implicated in the onset and spreading of several serious neurodegenerative diseases. The model relies on the entropic cost of forming protein loops due to self-crowding effects, and the protein sequence to determine contact locatio...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - October 5, 2018 Category: Biochemistry Source Type: research

Interplay between α-synuclein amyloid formation and membrane structure
This article is part of a Special Issue entitled: Lipid-protein interactions in amyloid formation.Graphical abstract (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - October 5, 2018 Category: Biochemistry Source Type: research

The deuridylylation activity of Herbaspirillum seropedicae GlnD protein is regulated by the glutamine:2-oxoglutarate ratio
Publication date: Available online 2 October 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Maurício T. Emori, Larissa F. Tomazini, Emanuel M. Souza, Fábio O. Pedrosa, Leda S. Chubatsu, Marco A.S. OliveiraAbstractThe nitrogen metabolism of Proteobacteria is controlled by the general Ntr system in response to nitrogen quality and availability. The PII proteins play an important role in this system by modulating the cellular metabolism through physical interaction with protein partners. Herbaspirillum seropedicae, a nitrogen-fixing bacterium, has two PII proteins paralogues,...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - October 5, 2018 Category: Biochemistry Source Type: research

Inorganic polyphosphate hydrolysis catalyzed by skeletal muscular actomyosin complexes is uncoupled with motility
Publication date: Available online 4 October 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Koji Ito, Mitsuru Seino, Yoshiya Miyasaka, Kuniyuki HatoriAbstractHydrolysis of the triphosphate moiety of ATP, catalyzed by myosin, induces alterations in the affinity of the myosin heads for actin filaments via conformational changes, thereby causing motility of the actomyosin complexes. To elucidate the contribution of the triphosphate group attached to adenosine, we examined the enzymatic activity of heavy meromyosin (HMM) with actin filaments for inorganic tripolyphosphate (3PP) using a Mala...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - October 5, 2018 Category: Biochemistry Source Type: research

Editorial Board
Publication date: November 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Volume 1866, Issue 11Author(s): (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - October 5, 2018 Category: Biochemistry Source Type: research

Probing the role of Arg97 in Heat shock protein 90 N-terminal domain from the parasite Leishmania braziliensis through site-directed mutagenesis on the human counterpart
Publication date: Available online 21 September 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Giusy Tassone, Stefano Mangani, Maurizio Botta, Cecilia PozziAbstractIn Brazil, the mucocutaneous form of leishmaniasis, caused by the parasite Leishmania braziliensis, is a widespread and very challenging disease responsible for disfiguration and, in the most severe cases, death. Heat shock protein 90 (Hsp90) is a ubiquitous molecular chaperone playing a pivotal role in the folding process of client proteins, and therefore its activity is fundamental for cell survival and proliferation. Since...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - September 22, 2018 Category: Biochemistry Source Type: research

Positional proteomics for identification of secreted proteoforms released by site-specific processing of membrane proteins
Publication date: Available online 20 September 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Stefan Niedermaier, Pitter F. HuesgenAbstractProteolytic processing shapes cellular interactions with the environment. As a pathway of unconventional protein secretion, ectodomain shedding releases soluble proteoforms of membrane-anchored proteins. This can trigger subsequent cleavage within the membrane stub and the release of additional soluble fragments to intra- and extracellular environments. Distinct membrane-bound proteases, or sheddases, may cleave the same membrane proteins at differe...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - September 21, 2018 Category: Biochemistry Source Type: research

Improved substrate specificity for D-galactose of L-arabinose isomerase for industrial application
Publication date: Available online 12 September 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Fina Amreta Laksmi, Shigeki Arai, Hirohito Tsurumaru, Yoshitaka Nakamura, Budi Saksono, Masao Tokunaga, Matsujiro IshibashiAbstractL-Arabinose isomerase isolated from Geobacillus stearothermophilus (GSAI) was modified to improve its substrate specificity for D-galactose for the production of D-tagatose, a potential reduced-energy sweetener. Among the selected residues, mutation at residue 18 produced a mutant strain, H18T, which exhibited increased activity for D-galactose compared with the wi...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - September 13, 2018 Category: Biochemistry Source Type: research

Peroxidase activity of cytochrome c in its compact state depends on dynamics of the heme region
Publication date: Available online 13 September 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Nataša Tomášková, Rastislav Varhač, Veronika Lysáková, Andrej Musatov, Erik SedlákAbstractCytochrome c (cyt c) is a small globular hemoprotein with the main function as an electron carrier in mitochondrial respiratory chain. Cyt c possesses also peroxidase-like activity in the native state despite its six-coordinated heme iron. In this work, we studied the effect of increasing urea concentration in the range from 0 M to 6 M at pH 7 (pH va...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - September 13, 2018 Category: Biochemistry Source Type: research

myo-Inositol dehydrogenase and scyllo-inositol dehydrogenase from Lactobacillus casei BL23 bind their substrates in very different orientations
Publication date: Available online 30 August 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Hari Babu Aamudalapalli, Drew Bertwistle, David R.J. Palmer, David A.R. SandersAbstractMany bacteria can use myo-inositol as the sole carbon source using enzymes encoded in the iol operon. The first step is catalyzed by the well-characterized myo-inositol dehydrogenase (mIDH), which oxidizes the axial hydroxyl group of the substrate to form scyllo-inosose. Some bacteria, including Lactobacillus casei, contain more than one apparent mIDH-encoding gene in the iol operon, but such redundant enzymes ...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - September 12, 2018 Category: Biochemistry Source Type: research

Genetic analysis of Hsp70 phosphorylation sites reveals a role in Candida albicans cell and colony morphogenesis
Publication date: Available online 10 September 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Ziva Weissman, Mariel Pinsky, Donald J. Wolfgeher, Stephen J. Kron, Andrew W. Truman, Daniel KornitzerAbstractHeat shock proteins are best known for their role as chaperonins involved in general proteostasis, but they can also participate in specific cellular regulatory pathways, e.g. via their post-translational modification. Hsp70/Ssa1 is a central cytoplasmic chaperonin in eukaryotes, which also participates in cell cycle regulation via its phosphorylation at a specific residue. Here we ana...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - September 11, 2018 Category: Biochemistry Source Type: research

Macromolecular crowding-induced molten globule states of the alkali pH-denatured proteins
Publication date: Available online 4 September 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Rajesh Kumar, Rajesh Kumar, Deepak Sharma, Mansi Garg, Vinay Kumar, Mukesh Chand AgarwalAbstractStructural and molecular properties extracted from circular dichroism (CD), tryptophan fluorescence and 1-anilino-8-napthalene sulfonate (ANS) binding experiments suggest that the high concentration of synthetic crowding agent (dextran 40, dextran 70 and ficoll 70) stabilizes and refolds the base-denatured ferricytochrome c (Ferricyt c) and lysozyme (Lyz) at pH 12.9 (±0.1) to molten globule ...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - September 5, 2018 Category: Biochemistry Source Type: research

Proteomic analyses Reveal GNG12 Regulates Cell Growth and Casein Synthesis by Activating the Leu-mediated mTORC1 Signaling Pathway
Publication date: Available online 4 September 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Chaochao Luo, Shengguo Zhao, Wenting Dai, Nan Zheng, Jiaqi WangAbstractIn cow mammary epithelial cells (CMECs), cell growth and casein synthesis are regulated by amino acids (AAs), and lysosomes are important organelles in this regulatory process, but the mechanisms remain unclear. Herein, lysosomal membrane proteins (LMPs) in CMECs in the presence (Leu+) and absence (Leu-) of leucine were quantitatively analysed using Sequential Windowed Acquisition of All Theoretical Fragment Ion (SWATH) mass...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - September 5, 2018 Category: Biochemistry Source Type: research

Lipid-apolipoprotein interactions in amyloid fibril formation and relevance to atherosclerosis
Publication date: Available online 1 September 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Geoffrey J. Howlett, Timothy M. Ryan, Michael D.W. GriffinAbstractThe apolipoprotein family is a set of highly conserved proteins characterized by the presence of amphipathic α-helical sequences that mediate lipid binding. Paradoxically, this family of proteins is also prominent among the proteins known to form amyloid fibrils, characterized by extensive cross-β structure. Several apolipoproteins including apolipoprotein (apo) A-I, apoA-II and apoC-II accumulate in amyloid deposits o...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - September 2, 2018 Category: Biochemistry Source Type: research

myo-inositol and scyllo-inositol dehydrogenase from Lactobacillus casei BL23 bind their substrates in very different orientations
Publication date: Available online 30 August 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Hari Babu Aamudalapalli, Drew Bertwistle, David R.J. Palmer, David A.R. SandersAbstractMany bacteria can use myo-inositol as the sole carbon using enzymes encoded in the iol operon. The first step is catalyzed by the well-characterized myo-inositol dehydrogenase (mIDH), which oxidizes the axial hydroxyl group of the substrate to form scyllo-inosose. Some bacteria, including Lactobacillus casei, contain more than one apparent mIDH-encoding gene in the iol operon, but such redundant enzymes have no...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - August 31, 2018 Category: Biochemistry Source Type: research

Structural and functional analysis of miraculin-like protein from Vitis vinifera
Publication date: Available online 27 August 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): So-ichiro Ohkura, Misaho Hori, Kazuki Saitoh, Takumi Okuzawa, Ikuko Okamoto, Nayuta Furukawa, Akiko Shimizu-IbukaAbstractThe so-called miraculin-like proteins (MLPs) are homologous to miraculin, a homodimeric protein with taste-modifying activity that converts sourness into sweetness. The identity between MLPs and miraculin generally ranges from 30% to 55%, and both MLPs and miraculin are categorized into the Kunitz-type soybean trypsin inhibitor (STI) family. MLP from grape (Vitis vinifera; vvML...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - August 28, 2018 Category: Biochemistry Source Type: research

Binding properties of sterol carrier protein 2 (SCP2) characterized using Laurdan
Publication date: Available online 27 August 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Alejo R. Gianotti, Raúl G. Ferreyra, Mario R. ErmácoraAbstractSterol carrier protein 2 (SCP2) binds lipids with high affinity and broad specificity. The overall hydrophobicity, fluidity, and dipolar dynamics of the binding site of SCP2 from Yarrowia lipolytica were characterized using the environmentally-sensitive fluorescent probe Laurdan. The study revealed a binding site with an overall polarity similar to that of dichloromethane and an internal phase comparable to that of phosph...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - August 28, 2018 Category: Biochemistry Source Type: research

Biochemical and biophysical characterization of 1,4-naphthoquinone as a dual inhibitor of two key enzymes of type II fatty acid biosynthesis from Moraxella catarrhalis
In this study, we report 1,4-naphthoquinone (NPQ) as a dual inhibitor of two key enzymes of FAS II pathway, namely FabD (Malonyl-CoA:ACP transacylase) and FabZ (β-hydroxyacyl-ACP dehydratase). Mode of inhibition of NPQ was found to be non-competitive for both enzymes with IC50 of 26.67 μΜ and 23.18 μΜ against McFabZ and McFabD respectively. Conformational changes in secondary and tertiary structures marked by the loss of helical contents were observed in both enzymes upon NPQ binding. The fluorescence quenching was found to be static with stable ground state complexes formation. ITC based studies have ...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - August 28, 2018 Category: Biochemistry Source Type: research

Metal ions-induced stability and function of bimetallic human arginase-I, a therapeutically important enzyme
Publication date: Available online 23 August 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Vineet Sadarangani, Safikur Rahman, Apurba Kumar SauAbstractRecent studies have highlighted the therapeutic importance of bimetallic human arginase-I against hyperargininemia and L-arginine auxotrophic cancers. The longer retention of catalytic activity of the Co2+-enzyme than that of the Mn2+ in human serum is associated with its enhanced therapeutic potential. To understand the basis of this and also to explore the role of a bimetallic center as well as the role of individual metal ions in the ...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - August 24, 2018 Category: Biochemistry Source Type: research

Editorial Board
Publication date: October 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Volume 1866, Issue 10Author(s): (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - August 23, 2018 Category: Biochemistry Source Type: research

Gel-based proteomics in disease research: Is it still valuable?
Publication date: Available online 15 August 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Yong-In Kim, Je-Yoel ChoAbstractGel electrophoresis had been the primary method in proteomics. In the early era of proteomics, gel electrophoresis was a dominant technique of sample preparation for mass spectrometry analysis. Particularly, two-dimensional electrophoresis provided high-resolution proteome separation, and was regarded as the standard methodology for the separation of wide-range proteomes. However, gel electrophoresis turned downwards due to the progress of other separations includi...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - August 21, 2018 Category: Biochemistry Source Type: research

Processing of high-titer prions for mass spectrometry inactivates prion infectivity
In this study we show that a straightforward denaturation and in-gel protease digestion protocol used to prepare prion-infected samples for mass spectroscopy leads to the loss of at least 7 logs of prion infectivity, yielding a final product that fails to transmit prion disease in vivo. We further show that the resultant sample remains suitable for mass spectrometry-based protein identifications. Thus, the procedure described can be used to prepare prion-infected samples for mass spectrometry analysis with greatly reduced biosafety concerns. (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - August 21, 2018 Category: Biochemistry Source Type: research

Ordered opening of LDL receptor binding domain of human apolipoprotein E3 revealed by hydrogen/deuterium exchange mass spectrometry and fluorescence spectroscopy
The objective of the study was to understand the mechanism of opening of the helix bundle. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) revealed that apoE3 NT domain adopts several disordered and unfolded regions, with H2 exhibiting relatively little protection against exchange-in compared to H1, H3, and H4. Site-directed fluorescence labeling indicated that H2 not only has the highest degree of solvent exposure but also the most flexibility in the helix bundle. It also indicated that the lipoprotein behavior of H1 was significnatly different from that of H2, H3 and H4. These results suggest that the opening of t...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - August 21, 2018 Category: Biochemistry Source Type: research