Insight into the interaction between PriB and DnaT on bacterial DNA replication restart: Significance of the residues on PriB dimer interface and highly acidic region on DnaT
In this study, we examined the contribution of the residues Ser20, His26 and Ser55, which are located on the PriB dimer interface. These residues are proximal to Glu39 and Arg44, which are important for PriB-DnaT interaction. Mutational analyses revealed that His26 and Ser20 of PriB are important for the interaction with DnaT, and that the Ser55 residue of PriB might have a role in negatively regulating the DnaT binding. These residues are involved in not only the interaction between PriB and DnaT but also the dissociation of single-stranded DNA (ssDNA) from the PriB−ssDNA complex due to DnaT binding. Moreover, NMR s...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - January 17, 2019 Category: Biochemistry Source Type: research

Sequence Specificity of Amylin-Insulin Interaction: A Fragment-based Insulin Fibrillation Inhibition Study
Publication date: Available online 17 January 2019Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Bhisma Narayan Ratha, Rajiv K. Kar, Sujan Kalita, Sourav Kalita, Sreyan Raha, Achintya Singha, Kanchan Garai, Bhubaneswar Mandal, Anirban BhuniaAbstractSubcutaneous insulin delivery serves as the major treatment for the ever-increasing spread of type II diabetes worldwide. However, long-term exposure to insulin results in local aggregates at the site of injection. This therapeutic concern accentuates the need to develop newer effective excipients to stabilize the insulin in pharmaceutical formul...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - January 17, 2019 Category: Biochemistry Source Type: research

Editorial Board
Publication date: March 2019Source: Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Volume 1867, Issue 3Author(s): (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - January 16, 2019 Category: Biochemistry Source Type: research

Modification by glyceraldehyde-3-phosphate prevents amyloid transformation of alpha-synuclein
Publication date: Available online 10 January 2019Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Kseniya Barinova, Marina Serebryakova, Evgeny Sheval, Elena Schmalhausen, Vladimir MuronetzAbstractNumerous investigations point to the relation between diabetes and neurodegenerative disorders. Alpha-synuclein is a protein involved in the development of synucleinopathies including Parkinson's disease. In the present work, alpha-synuclein was for the first time modified by the intermediate product of glycolysis, glyceraldehyde-3-phosphate (GA-3-P). The resulting product was compared with the alp...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - January 11, 2019 Category: Biochemistry Source Type: research

Transmembrane topology of mammalian ORMDL proteins in the endoplasmic reticulum as revealed by the substituted cysteine accessibility method (SCAM™)
Publication date: Available online 10 January 2019Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Deanna Davis, John Suemitsu, Binks WattenbergAbstractSphingolipids are diverse lipids with essential, and occasionally opposing, functions in the cell and therefore tight control over biosynthesis is vital. Mechanisms governing this regulation are not understood. Initial steps in sphingolipid biosynthesis take place on the cytosolic face of the endoplasmic reticulum (ER). Serine palmitoyltransferase (SPT) is an ER-resident enzyme catalyzing the first-committed step in sphingolipid biosynthesis. ...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - January 11, 2019 Category: Biochemistry Source Type: research

Thiopurine intolerance-causing mutations in NUDT15 induce temperature-dependent destabilization of the catalytic site
This study shows the action of pharmacogenetic variants in NUDT15 in a context of protein structure, which might open novel directions in personalized chemotherapy.Graphical abstract (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - January 11, 2019 Category: Biochemistry Source Type: research

In depth, thermodynamic analysis of Ca2+ binding to human cardiac troponin C: Extracting buffer-independent binding parameters
ConclusionsTaken together, the consistency of these data between buffer systems and the similarity between theoretical and experimental proton release is indicative of the reliability of the method used and the importance of extracting metal-buffer interactions in these studies.General significanceThe experimental approach described herein is clearly applicable to other metal ions and other EF-hand protein systems.Graphical abstract (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - January 11, 2019 Category: Biochemistry Source Type: research

Regulation of two GTPases Toc159 and Toc34 in the translocon of the outer envelope of chloroplasts
Publication date: Available online 3 January 2019Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Katharina Wiesemann, Stefan Simm, Oliver Mirus, Roman Ladig, Enrico SchleiffAbstractThe GTPases Toc159 and Toc34 of the translocon of the outer envelope of chloroplasts (TOC) are involved in recognition and transfer of precursor proteins at the cytosolic face of the organelle. Both proteins engage multiple interactions within the translocon during the translocation process, including dimeric states of their G-domains. The units of the Toc34 homodimer are involved in the recognition of the transit...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - January 4, 2019 Category: Biochemistry Source Type: research

Comparative proteomic analysis of salt-responsive proteins in canola roots by 2-DE and MALDI-TOF MS
Publication date: Available online 3 January 2019Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Maryam Kholghi, Mahmoud Toorchi, Ali Bandehagh, Anna Ostendorp, Steffen Ostendorp, Patrizia Hanhart, Julia KehrAbstractSalinity stress is a major abiotic stress that affects plant growth and limits crop production. Roots are the primary site of salinity perception, and salt sensitivity in roots limits the productivity of the entire plant. To better understand salt stress responses in canola, we performed a comparative proteomic analysis of roots from the salt-tolerant genotype Safi-7 and the salt...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - January 4, 2019 Category: Biochemistry Source Type: research

Comprehensive metabolomic and proteomic analysis in biochemical metabolic pathways of rice spikes under drought and submergence stress
In this study, T1 (drought duration: 10 d), T2 (submergence duration: 8 d) and CK (control) treatments were applied. This work aimed to study the changes in metabolic pathways of rice under drought and submergence stress during the panicle differentiation stage. The identification and analysis of differential metabolites and differentially expressed proteins functions indicate that drought and submergence mainly promoted the energy metabolism pathway, carbon fixation in photosynthetic organism pathway, carbohydrate metabolic process, and reactive oxygen species (ROS) metabolic process functions. Under drought stress, the i...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - January 4, 2019 Category: Biochemistry Source Type: research

Imaging individual protein aggregates to follow aggregation and determine the role of aggregates in neurodegenerative disease
Publication date: Available online 3 January 2019Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Suman De, David KlenermanAbstractProtein aggregates play a key role in the initiation and spreading of neurodegenerative disease but have been difficult to study due to their low abundance and heterogeneity, in both size and structure. Fluorescence based methods capable of detecting and characterising single aggregates have recently been developed and can be used to measure many important aggregate properties, and can be combined with sensitive assays to measure aggregate toxicity. Here we review...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - January 4, 2019 Category: Biochemistry Source Type: research

First evidence of changes in enzyme kinetics and stability of glucokinase affected by somatic cancer-associated variations
Publication date: March 2019Source: Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Volume 1867, Issue 3Author(s): Miroslav Těšínský, Daniela Šimčíková, Petr HenebergAbstractRecent investigation of somatic variations of allosterically regulated proteins in cancer genomes suggested that variations in glucokinase (GCK) might play a role in tumorigenesis. We hypothesized that somatic cancer-associated GCK variations include in part those with activating and/or stabilizing effects. We analyzed the enzyme kinetics and thermostability of recombinant proteins possessing t...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - January 1, 2019 Category: Biochemistry Source Type: research

Identification of serum biomarkers for premature ovarian failure
This study was undertaken to investigate the pathogenesis of POF using proteomic tools. Two-dimensional electrophoresis (2-DE) analysis was performed to screen for proteins differentially expressed in patients with POF. Using liquid chromatography-mass spectrometry / mass spectrometry (LC-MS / MS), we identified 11 significant proteins differentially expressed in the serum of POF patients: 5 proteins with expression increased more than two folds, 5 proteins with expression decreased more than two folds, and 1 protein expressed specifically in the serum of patients with POF. The results of the 2-DE analysis were further val...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - December 29, 2018 Category: Biochemistry Source Type: research

Editorial Board
Publication date: February 2019Source: Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Volume 1867, Issue 2Author(s): (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - December 26, 2018 Category: Biochemistry Source Type: research

First evidence of changes in enzyme kinetics and stability of the glucokinase affected by somatic cancer-associated variations
Publication date: Available online 24 December 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Miroslav Těšínský, Daniela Šimčíková, Petr HenebergAbstractRecent investigation of somatic variations of allosterically regulated proteins in cancer genomes suggested that variations in glucokinase (GCK) might play a role in tumorigenesis. We hypothesized that somatic cancer-associated GCK variations include in part those with activating and/or stabilizing effects. We analyzed the enzyme kinetics and thermostability of recombinant proteins possessing ...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - December 25, 2018 Category: Biochemistry Source Type: research

iTRAQ-based phosphoproteomic analysis reveals host cell's specific responses to Toxoplasma gondii at the phases of invasion and prior to egress
In this study, we assessed the host phosphoproteome data with isobaric tags for relative and absolute quantification (iTRAQ) method during the phases of T. gondii invasion (30 min post infection, PI) and prior to egress (28 h PI). Our iTRAQ analysis revealed a total of 665 phosphoproteins, among which the significantly regulated phosphoproteins in different between-group comparisons were further analyzed. Functional analysis of these significantly regulated phosphoproteins suggested that T. gondii modulated host cell processes through phosphorylation including cell cycle regulation, inducing apoptosis, blocking the syn...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - December 19, 2018 Category: Biochemistry Source Type: research

Redox-tuning of oxidizing disulfide oxidoreductase generates a potent disulfide isomerase
Publication date: Available online 18 December 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Shinya Sutoh, Yuko Uemura, Yuko Yamaguchi, Asako Kiyotou, Rena Sugihara, Makiko Nagayasu, Mihoko Kurokawa, Koreaki Ito, Naoki Tsunekawa, Michiko Nemoto, Kenji Inagaki, Takashi TamuraAbstractOxidative folding of extracellular proteins is pivotal for the biogenesis of bacterial virulence factors. Escherichia coli DsbA catalyzes disulfide bond formation in extracellular proteins and in multicomponent architectures on the cell surface. The present study assessed the significance of the redox proper...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - December 19, 2018 Category: Biochemistry Source Type: research

A One-Pot Analysis Approach to Simplify Measurements of Protein Stability and Folding Kinetics
Publication date: Available online 19 December 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Yi-Kai Liu, Huei-Yu Chen, Pin Ju Chueh, Pei-Fen LiuAbstractTo achieve a good understanding of the characteristics of a protein, it is important to study its stability and folding kinetics. Investigations of protein stability have been recently applied to drug-target identification, drug screening, and proteomic studies. The efficiency of the experiments performed to study protein stability and folding kinetics is now a crucial factor that needs to be optimized for these potential applications. ...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - December 19, 2018 Category: Biochemistry Source Type: research

A comprehensive analysis of the protein-ligand interactions in crystal structures of Mycobacterium tuberculosis EthR
Publication date: Available online 13 December 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Abdalkarim Tanina, Alexandre Wohlkönig, Sameh H. Soror, Marion Flipo, Baptiste Villemagne, Hugues Prevet, Benoit Déprez, Martin Moune, Hélène Perée, Franck Meyer, Alain R. Baulard, Nicolas Willand, René WintjensAbstractThe Mycobacterium tuberculosis EthR is a member of the TetR family of repressors, controlling the expression of EthA, a mono-oxygenase responsible for the bioactivation of the prodrug ethionamide. This protein was established as a promising...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - December 14, 2018 Category: Biochemistry Source Type: research

Thermal unfolding of calreticulin. Structural and thermodynamic characterization of the transition
Publication date: Available online 13 December 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): María B. Decca, Graciela A. Borioli, Edith S. Durand, Alejandro Moreschi, Marta E. Hallak, Guillermo G. MontichAbstractCalreticulin (CRT) is a calcium-binding protein that participates in several cellular processes including the control of protein folding and homeostasis of Ca2+. Its folding, stability and functions are strongly controlled by the presence of Ca2+. The oligomerization state of CRT is also relevant for its functions. We studied the thermal transitions of monomers and oligo...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - December 13, 2018 Category: Biochemistry Source Type: research

A conformational switch from a closed apo- to an open holo-form equips the acyl carrier protein for acyl chain accommodation
Publication date: Available online 10 December 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Richa Arya, Bhaskar Sharma, Chetna Dhembla, Ravi Kant Pal, Ashok Kumar Patel, Monica Sundd, Biplab Ghosh, Ravindra D. Makde, Suman KunduAbstractAcyl carrier proteins (ACPs) play crucial roles in the biosynthesis of fatty acids, non-ribosomal polypeptides and polyketides. The three-dimensional NMR structure of Leishmania major holo-LmACP, belonging to the type II pathway, has been reported previously, but the structure of its apo-form and its conformational differences with the holo-form remain ...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - December 11, 2018 Category: Biochemistry Source Type: research

Predicting eukaryotic protein secretion without signals
Publication date: Available online 4 December 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Henrik Nielsen, Eirini I. Petsalaki, Linlin Zhao, Kai StühlerAbstractPredicting unconventional protein secretion is a much harder problem than predicting signal peptide-based protein secretion, both due to the small number of examples and due to the heterogeneity and the limited knowledge of the pathways involved, especially in eukaryotes. However, the idea that secreted proteins share certain properties regardless of the secretion pathway used made it possible to construct the prediction m...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - December 5, 2018 Category: Biochemistry Source Type: research

Exosomal proteins constitute an essential part of the human adipose tissue secretome
In conclusion, the isolation of exosomes allows to further specify the functionality of adipokines and exoadipokines as part of the adipocyte secretome in signaling and interorgan crosstalk. (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 29, 2018 Category: Biochemistry Source Type: research

Proteomic profiling reveals key cancer progression modulators in shed microvesicles released from isogenic human primary and metastatic colorectal cancer cell lines
This study provides, for the first time, molecular insights into sMVs and CRC biology. (Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics)
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 29, 2018 Category: Biochemistry Source Type: research

Improved Expression, Purification and Characterization of VPR, a Cold active Subtilisin-like Serine Proteinase and the Effects of Calcium on Expression and Stability.
Publication date: Available online 28 November 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Kristinn R. Óskarsson, Magnús M. KristjánssonAbstractCloning into a pET 11a vector, followed by high-level expression of the cold adapted subtilase, VPR, utilizing the rhamnose titratable T7 system of Lemo21, resulted in a dramatic increase of soluble protein compared to the older system used. Expression optimization clearly shows the importance of calcium in the medium after induction, both for stability of the proteinase and cell health. Characterization of the purified e...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 28, 2018 Category: Biochemistry Source Type: research

Lysophospholipids induce fibrillation of the repeat domain of Pmel17 through intermediate core-shell structures
Publication date: Available online 22 November 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Jannik Nedergaard Pedersen, Zhiping Jiang, Gunna Christiansen, Jennifer C. Lee, Jan Skov Pedersen, Daniel E. OtzenAbstractLipids often play an important role in the initial steps of fibrillation. The melanosomal protein Pmel17 forms amyloid in vivo and contains a highly amyloidogenic Repeat domain (RPT), important for melanin biosynthesis. RPT fibrillation is influenced by two lysolipids, the anionic lysophosphatidylglycerol (LPG) and zwitterionic lysophosphatidylcholine (LPC), both present in ...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 23, 2018 Category: Biochemistry Source Type: research

Zinc Boosts EGCG's hIAPP Amyloid Inhibition both in solution and Membrane
In this study, a combination of Thioflavin- T fluorescence kinetics, transmission electron microscopy, isothermal titration calorimetery, circular dicrosim and nucelar magnetic resonance experiments were used to demonstrate a significant enhancement in EGCG's efficiency when complexed with Zn(II). We demonstrate that the Zn-EGCG complex is able to significantly suppress hIAPP's amyloid aggregation both in presence and absence of lipid membrane. Circular dichroism experiments indicate the formation and stabilization of a helical structure of hIAPP in presence of the EGCG:Zn(II) complex. Our results also reveal the ability o...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 22, 2018 Category: Biochemistry Source Type: research

Membrane-mimetic systems for biophysical studies of the amyloid-β peptide
Publication date: Available online 22 November 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Nicklas Österlund, Jinghui Luo, Sebastian K.T.S. Wärmländer, Astrid GräslundAbstractThe interplay between the amyloid-β (Aβ) peptide and cellular membranes have been proposed as an important mechanism for toxicity in Alzheimer's disease (AD). Membrane environments appear to influence Aβ aggregation and may stabilize intermediate Aβ oligomeric states that are considered to be neurotoxic. One important role for molecular biophysics within the field of A&bet...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 22, 2018 Category: Biochemistry Source Type: research

Mechanistic basis of Vitamin B12 and cobinamide salvaging by the Vibrio species
Publication date: Available online 18 November 2018Source: Biochimica et Biophysica Acta (BBA) - Proteins and ProteomicsAuthor(s): Shubhangi Agarwal, Sanjay Dey, Biplab Ghosh, Maitree Biswas, Jhimli DasguptaAbstractBiosynthesis of vitamin B12, which occurs through salvaging pathway or de novo synthesis, is essential for the survival and growth of bacteria. While the mechanism is known for many bacteria, it is elusive yet for diarrhea causing pathogenic bacteria Vibrio cholerae or the other Vibrio species. Sequence analysis using genome databases delineated that majority of the Vibrio species including V. cholerae contain g...
Source: Biochimica et Biophysica Acta (BBA) Proteins and Proteomics - November 19, 2018 Category: Biochemistry Source Type: research

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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