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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 - May 16, 2018 Category: Biochemistry Source Type: research

Revealing A-Raf functions through its interactome
Publication date: Available online 16 May 2018 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(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-RuiXu A-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 suggested that ...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - May 16, 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
Conclusion We found novel effects of SASP and its metabolites on SW982 cells by the combination of biotinylation of cell surface proteins and 2D-DIGE analysis. These data would help understanding of anti-rheumatic actions of SASP. Furthermore, the combination would be a useful method for the analysis of CS-proteins in various conditions. (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - May 10, 2018 Category: Biochemistry Source Type: research

A method for profiling the phosphorylation state of tyrosine protein kinases
Publication date: Available online 9 May 2018 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): Yuuki Uezato, Isamu Kameshita, Keiko Morisawa, Shuji Sakamoto, Eiji Kinoshita, Emiko Kinoshita-Kikuta, Tohru Koike, Yasunori Sugiyama Protein 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 kinase...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - May 10, 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...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - May 10, 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 2018 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): Emiko Kinoshita-Kikuta, Eiji Kinoshita, Sayaka Ueda, Yoko Ino, Yayoi Kimura, Hisashi Hirano, Tohru Koike The 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 detec...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - May 10, 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 - May 10, 2018 Category: Biochemistry Source Type: research

Applications of proteomics in pharmaceutical research and development
Publication date: Available online 9 May 2018 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): Hiroyuki Yokota The 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 used ...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - May 9, 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: Available online 5 May 2018 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): Alexandra Vasilyeva, Lyubov' Yurina, Maria Indeykina, Anna Bychkova, Anna Bugrova, Marina Biryukova, Alexey Kononikhin, Evgene Nikolaev, Mark Rosenfeld Plasma 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 FXIII-A2* is a...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - May 5, 2018 Category: Biochemistry Source Type: research

Role of methionine 71 in substrate recognition and structural integrity of bacterial peptidyl-tRNA hydrolase
Conclusion Our 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. Significance The 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 - May 5, 2018 Category: Biochemistry Source Type: research

Structure, dynamics, and biochemical characterization of ADF/cofilin Twinstar from Drosophila melanogastor
Conclusion On 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 Significance. This 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 - April 30, 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 - April 22, 2018 Category: Biochemistry Source Type: research

Special issue on “d-amino acids: biology in the mirror”
Publication date: Available online 19 April 2018 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): Loredano Pollegioni, Jean-Pierre Mothet, Molla Gianluca (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - April 20, 2018 Category: Biochemistry Source Type: research

Mechanism of irreversible inhibition of Mycobacterium tuberculosis shikimate kinase by ilimaquinone
Publication date: Available online 12 April 2018 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): Johayra Simithy, Ngolui Rene Fuanta, Judith V. Hobrath, Anna Kochanowska-Karamyan, Mark T. Hamann, Douglas C. Goodwin, Angela I. Calderón Ilimaquinone (IQ), a marine sponge metabolite, has been considered as a potential therapeutic agent for various diseases due to its broad range of biological activities. We show that IQ irreversibly inactivates Mycobacterium tuberculosis shikimate kinase (MtSK) through covalent modification of the protein. Inactivation occurred with an apparent second-o...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - April 12, 2018 Category: Biochemistry Source Type: research

Proteomic approach and expression analysis revealed the differential expression of predicted leptospiral proteases capable of ECM degradation
Publication date: Available online 12 April 2018 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): Dhandapani Gunasekaran, Thoduvayil Sikha, Sneha M. Pinto, M. Kiran Kumar, Krishna Patel, Manish Kumar, Vikram Kumar, Jebasingh Tennyson, P.K. Satheeshkumar, Harsha Gowda, T.S. Keshava Prasad, M.G. Madanan Leptospira, the causative agent of leptospirosis is known to have many proteases with potential to degrade extracellular matrix. However, a multipronged approach to identify, classify, characterize and elucidate their role has not been attempted. Our proteomic approach using high-resolution LC-...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - April 12, 2018 Category: Biochemistry Source Type: research

Synergistic stabilisation of NOsGC by cinaciguat and non-hydrolysable nucleotides: Evidence for sGC activator-induced communication between the heme-binding and catalytic domains
Publication date: Available online 11 April 2018 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): Anne Sömmer, Sönke Behrends Nitric oxide sensitive guanylyl cyclase (NOsGC) is a heterodimeric enzyme consisting of one α and one β subunit. Each subunit consists of four domains: the N-terminal heme-nitric oxide oxygen binding (HNOX) domain, a PAS domain, a coiled-coil domain and the C-terminal catalytic domain. Upon activation by the endogenous ligand NO or activating drugs, NOsGC catalyses the conversion of GTP to cGMP. Although several crystal structures of the isolated ...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - April 11, 2018 Category: Biochemistry Source Type: research

Identification of Isomeric Aspartate residues in βB2-crystallin from Aged Human Lens
Publication date: Available online 11 April 2018 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): Takumi Takata, Kento Murakami, Atsuhiko Toyama, Noriko Fujii Many post-translational modifications such as oxidation, deamidation and isomerization of amino acid residues occur in lens proteins with aging. One such modification, isomerization of aspartate in lens α-crystallin, has been well studied by amino acid enantiomer analysis and LC-MS/MS. LC-MS/MS can quickly and easily identify D- and L-amino acid-containing peptides without purification of lens protein mixtures. However, this meth...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - April 11, 2018 Category: Biochemistry Source Type: research

Detection of retromer assembly in Plasmodium falciparum by immunosensing coupled to Surface Plasmon Resonance
Publication date: Available online 11 April 2018 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): Mohd Shameel Iqbal, Asim Azhar Siddiqui, Chinmoy Banerjee, Shiladitya Nag, Somnath Mazumder, Rudranil De, Shubhra Jyoti Saha, Suresh Kumar Karri, Uday Bandyopadhyay Retromer complex plays a crucial role in intracellular protein trafficking and is conserved throughout the eukaryotes including malaria parasite, Plasmodium falciparum, where it is partially conserved. The assembly of retromer complex in RBC stages of malarial parasite is extremely difficult to explore because of its complicated phys...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - April 11, 2018 Category: Biochemistry Source Type: research

Similar structural stabilities of 3-isopropylmalate dehydrogenases from the obligatory piezophilic bacterium Shewanella benthica strain DB21MT-2 and its atmospheric congener S. oneidensis strain MR-1
In this study, we investigated the structural stability of these enzymes. At pH 7.6, SoIPMDH was slightly more stable against hydrostatic pressure than SbIPMDH, contrary to the physiological pressures of their normal environments. Pressure unfolding of these IPMDHs followed a two-state unfolding model between a native dimer and two unfolded monomers, and the dimer structure was pressure-tolerant up to 200 MPa, employing a midpoint pressure of 245.3 ± 0.1 MPa and a volume change of −225 ± 24 mL mol−1 for the most unstable mutant, SbIPMDH A266S. Thus, their pressure-dependent activ...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - April 7, 2018 Category: Biochemistry Source Type: research

Dimer-monomer equilibrium of human HSP27 is influenced by the in-cell macromolecular crowding environment and is controlled by fatty acids and heat
Publication date: Available online 7 April 2018 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): Satoshi B. Sato, Miwa Sugiura, Tatsuo Kurihara Small heat shock protein 27 (HSP27) is an essential element of the proteostasis network in human cells. The HSP27 monomer coexists with the dimer, which can bind unfolded client proteins. Here, we evaluated the in-cell dimer-monomer equilibrium and its relevance to the binding of client proteins in a normal human vascular endothelial cell line. When cells were treated with a membrane-permeable crosslinker, the protein existed primarily as a free mono...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - April 7, 2018 Category: Biochemistry Source Type: research

Effect of altered solution conditions on tau conformational dynamics: Plausible implication on order propensity and aggregation
Publication date: Available online 7 April 2018 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): Benita Jebarupa, Monita Muralidharan, Bindu Y. Srinivasu, Amit Kumar Mandal, Gopa Mitra Intrinsically disordered protein tau plays a central role in maintaining neuronal network by stabilizing microtubules in axon. Tau reportedly possesses random coil architecture, which is largely inert to alteration in solution conditions. However, the presence of transient compact conformers and residual structure has been evident from previous reports. Also, during Alzheimer's disease, misfolded tau detaches ...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - April 7, 2018 Category: Biochemistry Source Type: research

Rhodamine binds to silk fibroin and inhibits its self-aggregation
Publication date: Available online 2 April 2018 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): Laura Ragona, Oktay Gasymov, Aytaj J. Guliyeva, Rasim B. Aslanov, Serena Zanzoni, Chiara Botta, Henriette Molinari Amyloid structures are universal structures, widely diffuse in nature. Silk, capable of forming some of the strongest tensile materials on earth represents an important example of formation of functional amyloid fibrils, a process reminiscent of the oligomerization of peptides involved in neurodegenerative diseases. The stability of silk fibroin solutions in different conditions and ...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - April 2, 2018 Category: Biochemistry Source Type: research

Quantitation of myosin regulatory light chain phosphorylation in biological samples with multiple reaction monitoring mass spectrometry
Publication date: Available online 19 March 2018 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): Mona Chappellaz, Hayden Segboer, Annegret Ulke-Lemée, Cindy Sutherland, Huey-Miin Chen, Justin A. MacDonald The 20-kDa regulatory light chain of myosin II plays an important role in regulating smooth muscle contractile force. LC20 is phosphorylated canonically by myosin light chain kinase in a Ca2+/calmodulin-dependent manner at S19. The diphosphorylation of LC20 at T18 and S19 has been observed in smooth muscle tissues. Given that the phosphorylation of LC20 is positively correlated with...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - March 20, 2018 Category: Biochemistry Source Type: research

Inhibitor and peptide binding to calmodulin characterized by high pressure Fourier transform infrared spectroscopy and F örster resonance energy transfer
Publication date: Available online 17 March 2018 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): Süleyman Cinar, Claus Czeslik We compare the binding of an inhibitor with that of a natural peptide to Ca2+ saturated calmodulin (holo-CaM). As inhibitor we have chosen trifluoperazine (TFP) that is inducing a huge conformational change of holo-CaM from the open dumbbell-shaped to the closed globular conformation upon binding. On the other hand, melittin is used as model peptide, which is a well-known natural binding partner of holo-CaM. The experiments are carried out as a function of pres...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - March 19, 2018 Category: Biochemistry Source Type: research

d-Serine is a potential biomarker for clinical response in treatment of post-traumatic stress disorder using (R,S)-ketamine infusion and TIMBER psychotherapy: A pilot study
This article is part of a Special Issue entitled: d-Amino acids: biology in the mirror, edited by Dr. Loredano Pollegioni, Dr. Jean-Pierre Mothet and Dr. Molla Gianluca. (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - March 19, 2018 Category: Biochemistry Source Type: research

Kallikrein-related peptidase 6 can cleave human-muscle-type 6-phosphofructo-1-kinase into highly active shorter fragments
Conclusion KLK6 may be the key protease involved in the modification of PFK-M and trigger deregulated glycolytic flux in cancer cells. (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - March 19, 2018 Category: Biochemistry Source Type: research

The eS26 protein is involved in the formation of a nucleophosmin binding site on the human 40S ribosomal subunit
Publication date: Available online 18 March 2018 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): Anton V. Ivanov, Alexander V. Gopanenko, Alexey A. Malygin, Galina G. Karpova Human ribosomal protein eS26 is an indispensable component of the small (40S) ribosomal subunit and, along with other ribosomal proteins, is involved in interaction with mRNAs during translation. Here, we explored the behavior of the exogenous ribosomal protein eS26 modified at the C-terminus in the events related to translation in human cells using a doxycycline-inducible HEK293-derived cell line enabling the stable p...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - March 19, 2018 Category: Biochemistry Source Type: research

Salt-bridge dynamics in intrinsically disordered proteins: A trade-off between electrostatic interactions and structural flexibility
Publication date: Available online 14 March 2018 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): Sankar Basu, Parbati Biswas Intrinsically Disordered Proteins (IDPs) are enriched in charged and polar residues; and, therefore, electrostatic interactions play a predominant role in their dynamics. In order to remain multi-functional and exhibit their characteristic binding promiscuity, they need to retain considerable dynamic flexibility. At the same time, they also need to accommodate a large number of oppositely charged residues, which eventually lead to the formation of salt-bridges, impart...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - March 15, 2018 Category: Biochemistry Source Type: research

D-Amino acids in protein: The mirror of life as a molecular index of aging
Publication date: Available online 10 March 2018 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): Noriko Fujii, Takumi Takata, Norihiko Fujii, Kenzo Aki, Hiroaki Sakaue Proteins are composed exclusively of l-amino acids. Among elderly individuals, however, d-aspartic acid (d-Asp) residues have been found in eye lens and brain, as well as in other tissues. The presence of d-Asp may change the higher-order structure of a protein, which in turn may have a role in age-related disorders such as cataract and Alzheimer’s disease. d-Asp results from the spontaneous racemization of Asp residues...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - March 11, 2018 Category: Biochemistry Source Type: research

Enolase from Trypanosoma cruzi is inhibited by its interaction with metallocarboxypeptidase-1 and a putative acireductone dioxygenase
Publication date: Available online 10 March 2018 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): E. Quintero-Troconis, N. Buelvas, C. Carrasco-López, M.R. Domingo-Sananes, L. González-González, R. Ramírez-Molina, L. Osorio, A. Lobo-Rojas, A.J. Cáceres, P.A. Michels, H. Acosta, W. Quiñones, J.L. Concepción Purification of enolase (ENO) from the cytosol of Trypanosoma cruzi indicated that it may interact with at least five other proteins. Two of them were identified as metallocarboxypeptidase-1 (TcMCP-1) and a putative acireductone dioxygenase ...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - March 11, 2018 Category: Biochemistry Source Type: research

Human serine racemase is nitrosylated at multiple sites
Publication date: Available online 1 February 2018 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): Francesco Marchesani, Stefano Bruno, Gianluca Paredi, Samanta Raboni, Barbara Campanini, Andrea Mozzarelli Serine racemase is a pyridoxal 5′‑phosphate dependent enzyme responsible for the synthesis of d‑serine, a neuromodulator of the NMDA receptors. Its activity is modulated by several ligands, including ATP, divalent cations and protein interactors. The murine orthologue is inhibited by S-nitrosylation at Cys113, a residue adjacent to the ATP binding site. We found that the time co...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - March 10, 2018 Category: Biochemistry Source Type: research

Chromatographic separation of similar post-translationally modified metallothioneins reveals the changing conformations of apo-MT upon cysteine alkylation by high resolution LC-ESI-MS
Publication date: Available online 5 March 2018 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): Gordon W. Irvine, Martin J. Stillman Metallothioneins (MTs) are a class of small cysteine-rich proteins essential for Zn and Cu homeostasis, heavy metal detoxification, and cellular redox chemistry. Herein, we describe the separation and characterization of MTs differentially modified with N-ethylmaleimide (NEM) by liquid chromatography-mass spectrometry (LC-MS). The full-length recombinant MT isoform 1a as well as is isolated domain fragments were first alkylated, then separated on column with s...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - March 6, 2018 Category: Biochemistry Source Type: research

Structural studies of glyceraldehyde-3-phosphate dehydrogenase from Naegleria gruberi, the first one from phylum Percolozoa
Publication date: Available online 28 February 2018 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): Agnes Thiane Pereira Machado, Marcio Silva, Jorge Iulek Naegleria gruberi is a free life amoeba believed to have more than one billion years of existence; it is not pathogenic and had its genome sequenced, which revealed a high complexity in the metabolic pathways. This paper presents the experimental structure of GAPDH from N. gruberi, the first one belonging to the phylum Percolozoa, comparisons to structures from various species and molecular dynamics studies of some particular features. T...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - March 1, 2018 Category: Biochemistry Source Type: research

Capreomycin inhibits the initiation of amyloid fibrillation and suppresses amyloid induced cell toxicity
Publication date: Available online 26 February 2018 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): Mohammad Khursheed Siddiqi, Parvez Alam, Sumit Kumar Chaturvedi, Mohsin Vahid Khan, Saima Nusrat, Sadia Malik, Rizwan Hasan Khan Protein aggregation and amyloid fibrillation are responsible for several serious pathological conditions (like type II diabetes, Alzheimer's and Parkinson's diseases etc.) and protein drugs ineffectiveness. Therefore, a molecule that can inhibit the amyloid fibrillation and potentially clear amyloid fibrils is of great therapeutic value. In this manuscript, we inves...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - February 27, 2018 Category: Biochemistry Source Type: research

Functional effects of substitutions I92T and V95A in actin-binding period 3 of tropomyosin
Publication date: Available online 26 February 2018 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Author(s): Małgorzata Śliwinska, Katarzyna Robaszkiewicz, Marta Czajkowska, Wenjun Zheng, Joanna Moraczewska (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - February 27, 2018 Category: Biochemistry Source Type: research

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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