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

Minichaperone (GroEL191-345) mediated folding of MalZ proceeds by binding and release of native and functional intermediates
Publication date: September 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Volume 1866, Issue 9Author(s): Neha Jain, Timothy J. Knowles, Peter A. Lund, Tapan K. ChaudhuriAbstractThe isolated apical domain of GroEL consisting of residues 191–345 (known as “minichaperone”) binds and assists the folding of a wide variety of client proteins without GroES and ATP, but the mechanism of its action is still unknown. In order to probe into the matter, we have examined minichaperone-mediated folding of a large aggregation prone protein Maltodextrin-glucosidase (MalZ). The key objective w...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - July 11, 2018 Category: Biochemistry Source Type: research

Domain swapping dissection in Thermotoga maritima arginine binding protein: How structural flexibility may compensate destabilization
Publication date: September 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Volume 1866, Issue 9Author(s): Giovanni Smaldone, Rita Berisio, Nicole Balasco, Sabato D'Auria, Luigi Vitagliano, Alessia RuggieroAbstractThermotoga maritima Arginine Binding Protein (TmArgBP) is a valuable candidate for arginine biosensing in diagnostics. This protein is endowed with unusual structural properties that include an extraordinary thermal/chemical stability, a domain swapped structure that undergoes large tertiary and quaternary structural transition, and the ability to form non-canonical oligomeric species. ...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - July 11, 2018 Category: Biochemistry Source Type: research

Directed evolution and biophysical characterization of a full-length, soluble, human caveolin-1 variant
Publication date: September 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Volume 1866, Issue 9Author(s): Joshua N. Smith, Joshua M. Edgar, J. Mark Balk, Mariam Iftikhar, Jessica C. Fong, Tivoli J. Olsen, Dmitry A. Fishman, Sudipta Majumdar, Gregory A. WeissAbstractProtein engineering by directed evolution can alter proteins' structures, properties, and functions. However, membrane proteins, despite their importance to living organisms, remain relatively unexplored as targets for protein engineering and directed evolution. This gap in capabilities likely results from the tendency of membrane pro...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - July 11, 2018 Category: Biochemistry Source Type: research

Glycation induced conformational transitions in cystatin proceed to form biotoxic aggregates: A multidimensional analysis
Publication date: September 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Volume 1866, Issue 9Author(s): Sheraz Ahmad Bhat, Waseem Feeroze Bhat, Hussain Arif, Mohammad Afsar, Aamir Sohail, Md. Shahnawaz Khan, Md. Tabish Rehman, Rais Ahmad Khan, Bilqees BanoAbstractHyperglycaemic conditions facilitate the glycation of serum proteins which may have predisposition to aggregation and thus lead to complications. The current study investigates the glycation induced structural and functional modifications of chickpea cystatin (CPC) as well as biological toxicity of the modified protein forms, using CP...
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 10, 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 7, 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 7, 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 7, 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 6, 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 5, 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 5, 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 5, 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 5, 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 5, 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 5, 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 5, 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 5, 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 5, 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 5, 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 5, 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 5, 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 5, 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 5, 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 5, 2018 Category: Biochemistry Source Type: research