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

Modification of quaternary structure of Candida albicans GlcN-6-P synthase and its desensitization to inhibition by UDP-GlcNAc by site-directed mutagenesis
Publication date: Available online 18 August 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Karolina Kwiatkowska-Semrau, Marek Wojciechowski, Iwona Gabriel, Sara Crucho, Sławomir MilewskiAbstractSite-directed mutagenesis of the CaGFA1 gene encoding glucosamine-6-phosphate synthase from Candida albicans was performed. Desensitization of the enzyme to inhibition by UDPGlcNAc was achieved upon T487I and H492F substitutions at the UDP-GlcNAc binding site, exchange of D524, S525 and S527 for Ala at the dimer:dimer interface and construction of the tail-lock array (L434R and L460A) at the C-...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - August 18, 2018 Category: Biochemistry Source Type: research

Target deconvolution from phenotype-based drug discovery by using chemical proteomics approaches
Publication date: Available online 15 August 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Kazuishi Kubota, Masanori Funabashi, Yuji OguraAbstractPhenotype-based drug discovery is a key strategy for small molecule drug screening, and the molecular target identification of small molecules, termed “target deconvolution,” is critical albeit challenging. In this review, we classify approaches for target deconvolution, including both direct and indirect approaches, summarize their underlying principles, and provide examples of current chemical proteomics strategies including aff...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - August 15, 2018 Category: Biochemistry Source Type: research

Gel-based proteomics in disease research: Is it still valuable?1
Publication date: Available online 15 August 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Yong-In Kim, Je-Yoel ChoAbstractGel electrophoresis has been the primary method in proteomics. In the early era of proteomics, gel electrophoresis was a dominant technique of sample preparation for mass spectrometry (MS) analysis. Particularly, two-dimensional electrophoresis (2-DE) 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 separat...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - August 15, 2018 Category: Biochemistry Source Type: research

Ganglioside lipids accelerate α-synuclein amyloid formation
Publication date: Available online 2 August 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Ricardo Gaspar, Jon Pallbo, Ulrich Weininger, Sara Linse, Emma SparrAbstractThe deposition of α-synuclein fibrils is one hallmark of Parkinson's disease. Here, we investigate how ganglioside lipids, present in high amounts in neurons and exosomes, influence the aggregation kinetics of α-synuclein. Gangliosides, as well as, other anionic lipid species with small or large headgroups were found to induce conformational changes of α-synuclein monomers and catalyse their aggregation a...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - August 3, 2018 Category: Biochemistry Source Type: research

Erratum to Residue-specific mobility changes in soluble oligomers of the prion protein define regions involved in aggregation, BBAPAP (2018) 982–988
Publication date: Available online 1 August 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): John Paul Glaves, Carol L. Ladner-Keay, Trent C. Bjorndahl, David S. Wishart, Brian D. Sykes (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - August 2, 2018 Category: Biochemistry Source Type: research

Quantitative NMR study of heat-induced aggregation of eye-lens crystallin proteins under crowding conditions
Publication date: Available online 31 July 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Maria Camilles, Susanne Link, Jochen Balbach, Kay Saalwächter, Alexey KrushelnitskyAbstractThe eye lens contains a highly concentrated, polydisperse mixture of crystallins, and a loss in transparency during cataract formation is attributed to the aggregation of these proteins. Most biochemical and biophysical studies of crystallins have been performed in diluted samples because of various physical limitations of the respective method at physiological concentrations of up to 200–400 mg/...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - July 31, 2018 Category: Biochemistry Source Type: research

Characterization of the interaction interface and conformational dynamics of human TGIF1 homeodomain upon the binding of consensus DNA
Publication date: Available online 23 July 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Shuangli Li, Rui Hu, Haijie Yao, Dong Long, Fan Luo, Xin Zhou, Xu Zhang, Maili Liu, Jiang Zhu, Yunhuang YangAbstractThe TG interacting factor-1 homeodomain (TGIF1-HD) binds with the consensus DNA motif 5’-TGTCA-3′ in gene promoters through its three-amino acid loop extension (TALE) type homeodomain, and then recruits co-regulators to regulate gene expression. Although the solution NMR structure of human TGIF1-HD has been reported previously, little is known about its DNA binding mechani...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - July 24, 2018 Category: Biochemistry Source Type: research

Comparative proteomic analysis of mouse models of pathological and physiological cardiac hypertrophy, with selection of biomarkers of pathological hypertrophy by integrative Proteogenomics
Publication date: Available online 24 July 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Hye Kyeong Kwon, Hyobin Jeong, Daehee Hwang, Zee-Yong ParkAbstractTo determine fundamental characteristics of pathological cardiac hypertrophy, protein expression profiles in two widely accepted models of cardiac hypertrophy (swimming-trained mouse for physiological hypertrophy and pressure-overload-induced mouse for pathological hypertrophy) were compared using a label-free quantitative proteomics approach. Among 3955 proteins (19,235 peptides, false-discovery rate 
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - July 24, 2018 Category: Biochemistry Source Type: research

A rapid separation and characterization of mucins from mouse submandibular glands by supported molecular matrix electrophoresis
In this study, we describe a simple enrichment of mucins without trypsinization for SMME analysis. The enrichment was developed using a porcine submandibular gland and then was applied to study and compare mouse submandibular glands between young and aged mice. From mouse submandibular glands, hyaluronic acid and some mucins were observed by SMME. One of the mucins was identified as MUC10 by proteomic analysis of the band on the SMME membrane and immunostaining using anti-MUC10 antibody. A major O-glycan of MUC10 was determined to be NeuAcα2-3Galβ1-3GalNAc. Furthermore, our experiments revealed that the concentr...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - July 11, 2018 Category: Biochemistry Source Type: research

Prognostic significance of G6PD expression and localization in lung adenocarcinoma
In this study, aiming at the discovery of predictive markers for tumor invasion, we performed protein profiling between LCN1-sus and LCN1-co cells using two-dimensional gel electrophoresis. Twenty-six protein spots with>1.2-fold quantitative differences between LCN1-sus and LCN1-co cells were detected. Among the identified proteins, we focused on and immunohistochemically investigated G6PD in lung cancer. G6PD expression was significantly associated with a higher pathological TNM stage (p = 0.0024), lymph node metastasis (p = 0.0187), poorer differentiation (p = 0.0046), pleural invasion (p = 0.0197), va...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - July 11, 2018 Category: Biochemistry Source Type: research

Effects of salazosulfapyridine on the profile of cell surface proteins, revealed by biotinylation of cell surface proteins and 2-dimentional electrophoresis
Publication date: Available online 9 May 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Kazuki Omoteyama, Toshiyuki Sato, Mitsumi Arito, Masaaki Sato, Naoya Suematsu, Manae S. Kurokawa, Tomohiro KatoAbstractObjectiveWe investigated effects of salazosulfapyridine (SASP) on the protein profile of cell surface (CS)-proteins of SW982, a human synovial sarcoma cell line, using biotinylation of CS-proteins and 2-dimensional fluorescence difference gel electrophoresis (2D-DIGE).MethodsSW982 cells were treated with SASP and its metabolites, sulfapyridine (SP) and 5-aminosalicylic acid (5ASA). T...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - July 11, 2018 Category: Biochemistry Source Type: research

A method for profiling the phosphorylation state of tyrosine protein kinases
Publication date: Available online 9 May 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Yuuki Uezato, Isamu Kameshita, Keiko Morisawa, Shuji Sakamoto, Eiji Kinoshita, Emiko Kinoshita-Kikuta, Tohru Koike, Yasunori SugiyamaAbstractProtein kinases are known to be implicated in various biological phenomena and diseases through their involvement in protein phosphorylation. Therefore, analysis of the activity of protein kinases by examination of their phosphorylation state is important to elucidate their mechanisms. However, a method for analyzing the phosphorylation state of entire protein k...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - July 11, 2018 Category: Biochemistry Source Type: research

Applications of proteomics in pharmaceutical research and development
Publication date: Available online 9 May 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Hiroyuki YokotaAbstractThe significance of proteomics in the pharmaceutical industry has increased since overcoming initial difficulties. This review discusses recent proteomics publications from pharmaceutical companies to identify new trends in proteomics applications to research and development. Applications of proteomics such as chemical proteomics, protein expression profiling, targeted protein quantitation, analysis of protein-protein interactions and post-translational modification are widely ...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - July 11, 2018 Category: Biochemistry Source Type: research

Increase in constitutively active MEK1 species by introduction of MEK1 mutations identified in cancers
Publication date: Available online 9 May 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Emiko Kinoshita-Kikuta, Eiji Kinoshita, Sayaka Ueda, Yoko Ino, Yayoi Kimura, Hisashi Hirano, Tohru KoikeAbstractThe kinase MEK1 is an essential component of the mitogen-activated protein kinase cascades. Somatic mutations that have been identified in the MEK1-coding gene generally enhance kinase activity. Consequently, MEK1 has attracted much interest as a target for cancer therapy to block the aberrant activity. By using Phos-tag affinity electrophoresis, we found that the introduction of mutations ...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - July 11, 2018 Category: Biochemistry Source Type: research

Phosphoproteomic identification and functional characterization of protein kinase substrates by 2D-DIGE and Phos-tag PAGE
Publication date: Available online 5 June 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Kou Motani, Hidetaka KosakoAbstractProtein phosphorylation is one of the most common post-translational modifications in eukaryotes and can regulate diverse properties of proteins. Protein kinases are encoded by more than 500 genes in higher eukaryotes and play central roles in various cellular signaling pathways. Consequently, genetic abnormalities of protein kinases have been implicated in many diseases. To fully understand the complex phosphorylation-mediated signaling networks, it is important t...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - July 11, 2018 Category: Biochemistry Source Type: research

Bioenergetic and proteomic profiling to screen small molecule inhibitors that target cancer metabolisms
In this study, we constructed a screening system that focuses on bioenergetic profiles (specifically oxygen consumption rate and extracellular acidification rate) and characteristic proteomic changes. Thus, small molecules that target cancer-specific metabolism were investigated. We screened the chemical library of RIKEN Natural Products Depository (NPDepo) and found that unantimycin A, which was recently isolated from the fraction library of microbial metabolites, and NPL40330, which is derived from a chemical library, inhibit mitochondrial respiration. Furthermore, we developed an in vitro reconstitution assay method for...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - July 11, 2018 Category: Biochemistry Source Type: research

Development and validation of an improved diced electrophoresis gel assay cutter-plate system for enzymomics studies
Publication date: Available online 19 June 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Toru Komatsu, Masahiro Shimoda, Yukiko Kawamura, Yasuteru Urano, Tetsuo NaganoAbstractDiced electrophoresis gel (DEG) assay is a methodology to identify enzymes with a specified activity in complex cell or tissue lysates by means of two-dimensional separation using isoelectric focusing and native PAGE, followed by dicing of the gel into small pieces that are assayed separately, and digestion and peptide fingerprinting to identify the protein(s) of interest in positive wells. The existing hand-made ...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - July 11, 2018 Category: Biochemistry Source Type: research

Solution structure and dynamics of glia maturation factor from Caenorhabditis elegans
ConclusionWe have presented the first solution structure of GMF from C. elegans, which highlights the structural differences between the Site-2 of CeGMF and mammalian GMF isoforms. Further, we have seen the differences in structure, dynamics, and thermal stability of GMF and ADF/cofilin.General Significance.This study provides a useful insight to structural and dynamics factors that define the specificity of GMF towards Arp2/3 complex. (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - July 11, 2018 Category: Biochemistry Source Type: research

Cancer biomarker development and two-dimensional difference gel electrophoresis (2D-DIGE)
Publication date: Available online 7 July 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Tadashi KondoAbstractCancer results from the accumulation of genomic alterations. As the genome is functionally translated to the proteome and regulates tumor cell behavior, proteomics studies are expected to further the current understanding of the molecular mechanisms underlying carcinogenesis and cancer progression. Biomarkers are potential tools to classify cancers for therapy, predict responses to treatments, and support treatment-related decision-making. Biomarker development has been actively...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - July 11, 2018 Category: Biochemistry Source Type: research

Ligand binding complexes in lipocalins: Underestimation of the stoichiometry parameter (n)
Publication date: Available online 7 July 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Ben J. Glasgow, Adil R. AbduragimovAbstractThe stoichiometry of a ligand binding reaction to a protein is given by a parameter (n). The value of this parameter may indicate the presence of protein monomer or dimers in the binding complex. Members of the lipocalin superfamily show variation in the stoichiometry of binding to ligands. In some cases the stoichiometry parameter (n) has been variously reported for the same protein as mono- and multimerization of the complex. Prime examples include retino...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - July 11, 2018 Category: Biochemistry Source Type: research

Effect of polyols on the structure and aggregation of recombinant human γ-Synuclein, an intrinsically disordered protein
Publication date: Available online 9 July 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Sneha Roy, Rajiv BhatAbstractPolyol osmolytes accumulated in cells under stress are known to promote stability in globular proteins with respect to their increasing hydroxyl groups but their effect on the structure, stability and aggregation of intrinsically disordered proteins (IDPs) is still elusive. The lack of a natively folded structure in intrinsically disordered proteins under physiological conditions results in their aggregation and fibrillation that gives rise to a number of diseases. We ha...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - July 11, 2018 Category: Biochemistry Source Type: research

Editorial Board
Publication date: August 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Volume 1866, Issue 8Author(s): (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - July 11, 2018 Category: Biochemistry Source Type: research

Proteomic approaches unravel the intricacy of secreted proteins of Leishmania: An updated review
Publication date: August 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Volume 1866, Issue 8Author(s): Gaurav Garg, Kuljit Singh, Vahab AliAbstractLeishmaniasis, a parasitic protozoan disease, is still a worldwide concern due to persistent issues with chemotherapy, rapid emerging drug resistance; and non- availability of approved vaccine for the control of disease. Therefore, the search of parasite specific proteins to identify new anti-leishmanial drug targets and vaccine candidates is an urgent priority. In this context, proteins that are secreted, in vitro during parasite growth under defined...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - July 11, 2018 Category: Biochemistry Source Type: research

Revealing A-Raf functions through its interactome
Publication date: August 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Volume 1866, Issue 8Author(s): Xin-Yu Zhang, Hui Guo, Bing Han, Xu-Min Zhang, Ying Huang, Yang Yang, Ying Liu, Xiao-Xi Guo, Qian Hao, Su An, Tian-Rui XuAbstractA-Raf is a member of the Raf kinase family. Unlike B-Raf and C-Raf, the functions of A-Raf remain obscure. To gain more insight into the biological functions of A-Raf, we investigated the A-Raf interactome using proteomics. We found 132 proteins that interact with A-Raf and confirmed the interaction of 12 of these proteins with A-Raf by western blotting. Our data sugg...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - July 11, 2018 Category: Biochemistry Source Type: research

In vitro activity characterization of the tomato SnRK1 complex proteins
In this study, the phylogenetic placement and in vitro kinase activity of a second tomato SnRK1 α-subunit, SlSnRK1.2, were characterized. Interestingly, in the phylogenetic analysis of SnRK1 sequences from monocots and dicots SlSnRK1.2 clusters only with other Solanaceae SnRK1.2 sequences, suggesting possible functional divergence of these kinases from other SnRK1 kinases. For analysis of kinase activity, SlSnRK1.2 was able to autophosphorylate, phosphorylate the complex β-subunits, and phosphorylate the SnRK1 AMARA peptide substrate, all with drastically lower overall kinase activity compared to SlSnRK1.1. Acti...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - July 11, 2018 Category: Biochemistry Source Type: research

Role of methionine 71 in substrate recognition and structural integrity of bacterial peptidyl-tRNA hydrolase
ConclusionOur results indicate that the interactions of M71 with N14 and H24 play an important role in optimal positioning of their side-chains relative to the peptidyl-tRNA substrate. Overall, these interactions of M71 are important for the activity, stability, and compactness of the protein.SignificanceThe work presented provides original and new structural and dynamics information that significantly enhances our understanding of the network of interactions that govern this enzyme's activity and selectivity. (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - July 11, 2018 Category: Biochemistry Source Type: research

Oxidation-induced modifications of the catalytic subunits of plasma fibrin-stabilizing factor at the different stages of its activation identified by mass spectrometry
Publication date: August 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Volume 1866, Issue 8Author(s): Alexandra Vasilyeva, Lyubov' Yurina, Maria Indeykina, Anna Bychkova, Anna Bugrova, Marina Biryukova, Alexey Kononikhin, Evgene Nikolaev, Mark RosenfeldAbstractPlasma fibrin-stabilizing factor (pFXIII) is a heterotetrameric proenzyme composed of two catalytic A subunits (FXIII-A2) and two inhibitory/carrier B subunits (FXIII-B2). The main function of the protein is the formation of cross-links between the polypeptide chains of the fibrin clot. The conversion of pFXIII into the enzymatic form FXI...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - July 11, 2018 Category: Biochemistry Source Type: research

Structure, dynamics, and biochemical characterization of ADF/cofilin Twinstar from Drosophilamelanogaster
ConclusionOn the basis of structure, dynamics, and biochemical activity, Twinstar can be taken to execute its biochemical role by facilitating directional growth and maintenance of length of actin filaments.General significanceThis study characterizes the structure, backbone dynamics, and biochemical activities of Twinstar of Drosophila, which provides an insight into the regulation of actin dynamics in the member of phylum insecta. (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - July 11, 2018 Category: Biochemistry Source Type: research

Dynamics-based community analysis and perturbation response scanning of allosteric interaction networks in the TRAP1 chaperone structures dissect molecular linkage between conformational asymmetry and sequential ATP hydrolysis
This study has revealed that key effector sites that orchestrate allosteric interactions occupy the ATP binding region and N-terminal interface of the buckled protomer, whereas the main sensors of allosteric signals that drive functional conformational changes during ATPase cycle are consolidated near the client binding region of the straight protomer, channeling the energy of ATP hydrolysis for client remodeling. The community decomposition analysis of the interaction networks and reconstruction of allosteric communication pathways in the TRAP1 structures have quantified mechanism of allosteric regulation, revealing contr...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - July 11, 2018 Category: Biochemistry Source Type: research

Residue-specific mobility changes in soluble oligomers of the prion protein define regions involved in aggregation
Publication date: September 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Volume 1866, Issue 9Author(s): John Paul Glaves, Carol L. Ladner-Keay, Trent C. Bjorndahl, David S. Wishart, Brian D. SykesAbstractPrion (PrP) diseases are neurodegenerative diseases characterized by the formation of β-sheet rich, insoluble and protease resistant protein deposits (called PrPSc) that occur throughout the brain. Formation of synthetic or in vitro PrPSc can occur through on-pathway toxic oligomers. Similarly, toxic and infectious oligomers identified in cell and animal models of prion disease indicate t...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - July 11, 2018 Category: Biochemistry Source Type: research

Editorial Board
Publication date: September 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Volume 1866, Issue 9Author(s): (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - July 11, 2018 Category: Biochemistry Source Type: research

Locating macromolecules and determining structures inside bacterial cells using electron cryotomography
Publication date: September 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Volume 1866, Issue 9Author(s): Charlotte E. Melia, Tanmay A.M. BharatAbstractElectron cryotomography (cryo-ET) is an imaging technique uniquely suited to the study of bacterial ultrastructure and cell biology. Recent years have seen a surge in structural and cell biology research on bacteria using cryo-ET. This research has driven major technical developments in the field, with applications emerging to address a wide range of biological questions. In this review, we explore the diversity of cryo-ET approaches used for str...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - July 11, 2018 Category: Biochemistry Source Type: research

A dynamic loop provides dual control over the catalytic and membrane binding activity of a bacterial serine hydrolase
Publication date: September 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Volume 1866, Issue 9Author(s): Mackenzie A. Smith, Whitney K. Phillips, Perry L. Rabin, R. Jeremy JohnsonAbstractThe bacterial acyl protein thioesterase (APT) homologue FTT258 from the gram-negative pathogen Francisella tularensis exists in equilibrium between a closed and open state. Interconversion between these two states is dependent on structural rearrangement of a dynamic loop overlapping its active site. The dynamics and structural properties of this loop provide a simple model for how the catalytic activity of FTT...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - July 11, 2018 Category: Biochemistry Source Type: research

The role of extended Fe4S4 cluster ligands in mediating sulfite reductase hemoprotein activity
Publication date: September 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Volume 1866, Issue 9Author(s): Marisa R. Cepeda, Lauren McGarry, Joseph M. Pennington, J. Krzystek, M. Elizabeth StroupeAbstractThe siroheme-containing subunit from the multimeric hemoflavoprotein NADPH-dependent sulfite reductase (SiR/SiRHP) catalyzes the six electron-reduction of SO32− to S2−. Siroheme is an iron-containing isobacteriochlorin that is found in sulfite and homologous siroheme-containing nitrite reductases. Siroheme does not work alone but is covalently coupled to a Fe4S4 cluster through one of...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - July 11, 2018 Category: Biochemistry Source Type: research