397 results match your criteria Biochimica Et Biophysica Acta-proteins And Proteomics[Journal]


Altered dynamics may drift pathological fibrillization in membraneless organelles.

Biochim Biophys Acta Proteins Proteom 2019 Apr 15. Epub 2019 Apr 15.

MTA-DE Laboratory of Protein Dynamics, University of Debrecen, Hungary. Electronic address:

Protein phase transition can generate non-membrane bound cellular compartments, which can convert from liquid-like to solid-like states. While the molecular driving forces of phase separation have been largely understood, much less is known about the mechanisms of material-state conversion. We apply a recently developed algorithm to describe the weak interaction network of multivalent motifs, and simulate the effect of pathological mutations. Read More

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http://dx.doi.org/10.1016/j.bbapap.2019.04.005DOI Listing

Mechanistic approaches to understand the prion-like propagation of aggregates of the human tau protein.

Biochim Biophys Acta Proteins Proteom 2019 Apr 12. Epub 2019 Apr 12.

National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India; Indian Institute of Science Education and Research, Pune 411008, India. Electronic address:

The dynamic nature of the tau protein under physiological conditions is likely to be critical for it to perform its diverse functions inside a cell. Under some conditions, this intrinsically disordered protein assembles into pathogenic aggregates that are self-perpetuating, toxic and infectious in nature. The role of liquid-liquid phase separation in the initiation of the aggregation reaction remains to be delineated. Read More

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http://dx.doi.org/10.1016/j.bbapap.2019.04.004DOI Listing

Analysis of the pathogenic I326T variant of human tRNA nucleotidyltransferase reveals reduced catalytic activity and thermal stability in vitro linked to a conformational change.

Biochim Biophys Acta Proteins Proteom 2019 Apr 5;1867(6):616-626. Epub 2019 Apr 5.

Department of Chemistry and Biochemistry and Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke St. W., Montréal H4B 1R6, Québec, Canada. Electronic address:

The I326T mutation in the TRNT1 gene encoding human tRNA nucleotidyltransferase (tRNA-NT) is linked to a relatively mild form of SIFD. Previous work indicated that the I326T variant was unable to incorporate AMP into tRNAs in vitro, however, expression of the mutant allele from a strong heterologous promoter supported in vivo CCA addition to both cytosolic and mitochondrial tRNAs in a yeast strain lacking tRNA-NT. To address this discrepancy, we determined the biochemical and biophysical characteristics of the I326T variant enzyme and the related variant, I326A. Read More

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http://dx.doi.org/10.1016/j.bbapap.2019.04.003DOI Listing

Inhibition of human 3-hydroxy-3-methylglutaryl CoA reductase by peptides leading to cholesterol homeostasis through SREBP2 pathway in HepG2 cells.

Biochim Biophys Acta Proteins Proteom 2019 Apr 4;1867(6):604-615. Epub 2019 Apr 4.

Department of Protein Chemistry and Technology, CSIR-Central Food Technological Research Institute, Mysuru, 570020, India; Academy of Scientific and Innovative Research, New Delhi, India. Electronic address:

In mammalian cells, human 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGCR), a rate-limiting endoplasmic reticulum (ER) bonded enzyme, plays a central role in the cholesterol homeostasis via the negative feedback mechanism. The present study indicates that the interactions of novel peptides with the catalytic domain of HMGCR, provides an alternative therapeutic candidate for reducing cholesterol. The potential natural origin of HMGCR peptide inhibitors were filtered from the peptide library using the molecular docking, which revealed three strong candidates for inhibition. Read More

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http://dx.doi.org/10.1016/j.bbapap.2019.04.002DOI Listing
April 2019
2 Reads

Characterization of a novel cytochrome c as the electron acceptor of XoxF-MDH in the thermoacidophilic methanotroph Methylacidiphilum fumariolicum SolV.

Biochim Biophys Acta Proteins Proteom 2019 Apr 4;1867(6):595-603. Epub 2019 Apr 4.

Department of Microbiology, IWWR, Radboud University, Heyendaalseweg, 135 6525, AJ, Nijmegen, the Netherlands. Electronic address:

Methanotrophs play a prominent role in the global carbon cycle, by oxidizing the potent greenhouse gas methane to CO. Methane is first converted into methanol by methane monooxygenase. This methanol is subsequently oxidized by either a calcium-dependent MxaF-type or a lanthanide-dependent XoxF-type methanol dehydrogenase (MDH). Read More

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http://dx.doi.org/10.1016/j.bbapap.2019.04.001DOI Listing

Lipid-protein interactions in amyloid formation.

Biochim Biophys Acta Proteins Proteom 2019 May;1867(5):455-457

Biochemistry and Structural Biology, Department of Chemistry, Lund University, P.O. Box 124, 22100 Lund, Sweden.

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https://linkinghub.elsevier.com/retrieve/pii/S15709639193005
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http://dx.doi.org/10.1016/j.bbapap.2019.03.006DOI Listing
May 2019
3 Reads

Impact of N-glycosylation site variants during human PrP aggregation and fibril nucleation.

Biochim Biophys Acta Proteins Proteom 2019 Mar 30. Epub 2019 Mar 30.

IFM-Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden. Electronic address:

Misfolding and aggregation of the human prion protein (PrP) cause neurodegenerative transmissible spongiform encephalopathies such as Creutzfeldt-Jakob disease. Mature native PrP is composed of 209 residues and is folded into a C-terminal globular domain (residues 125-209) comprising a small two-stranded β-sheet and three α-helices. The N-terminal domain (residues 23-124) is intrinsically disordered. Read More

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http://dx.doi.org/10.1016/j.bbapap.2019.03.010DOI Listing
March 2019
1 Read

Influence of crowding and surfaces on protein amyloidogenesis: A thermo-kinetic perspective.

Biochim Biophys Acta Proteins Proteom 2019 Mar 28. Epub 2019 Mar 28.

Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, India; Centre for Advanced Functional Materials (CAFM), Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, India. Electronic address:

The last few decades have irreversibly implicated protein self-assembly and aggregation leading to amyloid fibril formation in proteopathies that include several neurodegenerative diseases. Emerging studies recognize the importance of eliciting the pathways leading to protein aggregation in the context of the crowded intracellular environment rather than in conventional in vitro conditions. It is found that crowded environments can have acceleratory as well as inhibitory effects on protein aggregation, depending on the interplay of underlying factors on the crucial rate limiting steps. Read More

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http://dx.doi.org/10.1016/j.bbapap.2019.03.009DOI Listing
March 2019
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Simultaneous characterization of SNPs and N-glycans from multiple glycosylation sites of intact β-2-glycoprotein-1 (B2GP1) by ESI-qTOF-MS.

Biochim Biophys Acta Proteins Proteom 2019 Mar 20;1867(6):556-564. Epub 2019 Mar 20.

Organic Chemistry, Department of Chemistry, University of Hamburg, Martin-Luther-King Platz 6, 20146 Hamburg, Germany. Electronic address:

The highly glycosylated ß-2-glycoprotein-1 (B2GP1), also called apolipoprotein H, is a 50 kDa human plasma protein with four or five N-glycosylation sites. Glycosylation of B2GP1 can impact auto antibody recognition leading to the development of antiphospholipid syndrome (APS), which can result in miscarriages or thrombosis. Next to its glycosylation different genetic variants are known to increase the risk of suffering from APS. Read More

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http://dx.doi.org/10.1016/j.bbapap.2019.03.007DOI Listing
March 2019
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Novel X-ray sequences and crystal structures of Persian and Starry sturgeon methemoglobins: Highlighting the role of heme pocket waters in causing autoxidation.

Biochim Biophys Acta Proteins Proteom 2019 Mar 21;1867(6):586-594. Epub 2019 Mar 21.

Institute of Biochemistry and Biophysics, University of Tehran, P.O. Box 13145-1384, Tehran, Iran.

Although there is a high sequence similarity between mammalian and fish hemoglobin (Hb), the oxidation and heme loss rates can vary greatly between them such that fish Hbs oxidise much more rapidly than mammalian Hbs. There is to date no sequence or structural data for any sturgeon Hb to reveal the level of autoxidation in these fish. In this study, novel high resolution X-ray sequences and crystal structures of methemoglobin (Met-Hb) from two sturgeon fish including Persian sturgeon (Acipenser percisus) and Starry sturgeon (Acipenser stellatus) belonging to the Caspian sea has been determined. Read More

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http://dx.doi.org/10.1016/j.bbapap.2019.03.008DOI Listing
March 2019
4 Reads

An acidic loop within the human soluble CD23 protein may direct the interaction between sCD23 and the αβ integrin.

Biochim Biophys Acta Proteins Proteom 2019 Mar 20;1867(6):548-555. Epub 2019 Mar 20.

Nelson Mandela University, Faculty of Science, Department of Biochemistry and Microbiology, South Africa.

CD23 is involved in a myriad of immune reactions. It is not only a receptor for IgE, but also functions in the regulation of IgE synthesis, isotype switching in B cells, and induction of the inflammatory response. These effector functions of CD23 arise through its interaction with another leukocyte-specific cell surface receptor - the β integrin subfamily. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S15709639193004
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http://dx.doi.org/10.1016/j.bbapap.2019.03.004DOI Listing
March 2019
5 Reads

Functional characterization of PLP fold type IV transaminase with a mixed type of activity from Haliangium ochraceum.

Biochim Biophys Acta Proteins Proteom 2019 Mar 19;1867(6):575-585. Epub 2019 Mar 19.

Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russian Federation.

Pyridoxal-5'-phosphate (PLP)-dependent transaminases are industrially important enzymes catalyzing the stereoselective amination of ketones and keto acids. Transaminases of PLP fold type IV are characterized by (R)- or (S)-stereoselective transfer of amino groups, depending on the substrate profile of the enzyme. PLP fold type IV transaminases include branched-chain amino acid transaminases (BCATs), D-amino acid transaminases and (R)-amine:pyruvate transaminases. Read More

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http://dx.doi.org/10.1016/j.bbapap.2019.03.005DOI Listing
March 2019
2 Reads

Translocation of non-interacting heteropolymer protein chains in terms of single helical propensity and size.

Biochim Biophys Acta Proteins Proteom 2019 Mar 16;1867(6):565-574. Epub 2019 Mar 16.

Depto. Matemáticas y Mecánica, I.I.M.A.S., Universidad Nacional Autónoma de México, Apdo. Postal 20-726, 01000 Cd. México, Mexico; Posgrado en Nanociencias y Nanotecnología, Centro de Investigación y de Estudios Avanzados del IPN, Ap. Postal: 14-740, 07000 México, DF, Mexico. Electronic address:

In this work we present an analytical framework to calculate the average translocation time τ required for an ideal proteinogenic polypeptide chain to cross over a small pore on a membrane. Translocation is considered to proceed as a chain of non-interacting amino acid residues of sequence {X} diffuses through the pore against an energy barrier Δℱ, set by chain entropy and unfolding-folding energetics. We analyze the effect of sequence heterogeneity on the dynamics of translocation by means of helical propensity of amino acid residues. Read More

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http://dx.doi.org/10.1016/j.bbapap.2019.03.003DOI Listing

Structural and binding studies of phosphopantetheine adenylyl transferase from Acinetobacter baumannii.

Biochim Biophys Acta Proteins Proteom 2019 Mar 15;1867(6):537-547. Epub 2019 Mar 15.

Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India. Electronic address:

Phosphopantetheine adenylyltransferase (PPAT, EC. 2.7. Read More

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http://dx.doi.org/10.1016/j.bbapap.2019.03.002DOI Listing
March 2019
2.747 Impact Factor

Reprint of "Ganglioside lipids accelerate α-synuclein amyloid formation".

Biochim Biophys Acta Proteins Proteom 2019 May 13;1867(5):508-518. Epub 2019 Mar 13.

Departments of Physical-Chemistry, Lund University, Sweden. Electronic address:

The deposition of α-synuclein fibrils is one hallmark of Parkinson's disease. Here, we investigate how ganglioside lipids, present in high amounts in neurons and exosomes, influence the aggregation kinetics of α-synuclein. Gangliosides, as well as, other anionic lipid species with small or large headgroups were found to induce conformational changes of α-synuclein monomers and catalyse their aggregation at mildly acidic conditions. Read More

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http://dx.doi.org/10.1016/j.bbapap.2019.02.003DOI Listing

α-Synuclein misfolding and aggregation: Implications in Parkinson's disease pathogenesis.

Biochim Biophys Acta Proteins Proteom 2019 Mar 7. Epub 2019 Mar 7.

Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India. Electronic address:

α-Synuclein (α-Syn) has been extensively studied for its structural and biophysical properties owing to its pathophysiological role in Parkinson's disease (PD). Lewy bodies and Lewy neurites are the pathological hallmarks of PD and contain α-Syn aggregates as their major component. It was therefore hypothesized that α-Syn aggregation is actively associated with PD pathogenesis. Read More

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http://dx.doi.org/10.1016/j.bbapap.2019.03.001DOI Listing

Fungal Lanosterol 14α-demethylase: A target for next-generation antifungal design.

Biochim Biophys Acta Proteins Proteom 2019 Mar 6. Epub 2019 Mar 6.

Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand.

The cytochrome P450 enzyme lanosterol 14α-demethylase (LDM) is the target of the azole antifungals used widely in medicine and agriculture as prophylaxis or treatments of infections or diseases caused by fungal pathogens. These drugs and agrochemicals contain an imidazole, triazole or tetrazole substituent, with one of the nitrogens in the azole ring coordinating as the sixth axial ligand to the LDM heme iron. Structural studies show that this membrane bound enzyme contains a relatively rigid ligand binding pocket comprised of a deeply buried heme-containing active site together with a substrate entry channel and putative product exit channel that reach to the membrane. Read More

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http://dx.doi.org/10.1016/j.bbapap.2019.02.008DOI Listing
March 2019
1 Read

Modulation of p53 and prion protein aggregation by RNA.

Biochim Biophys Acta Proteins Proteom 2019 Feb 28. Epub 2019 Feb 28.

Instituto de Bioquímica Médica Leopoldo de Meis, Instituto Nacional de Ciência Tecnologia de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil. Electronic address:

Several RNA-binding proteins undergo reversible liquid-liquid phase transitions, which, in pathological conditions, might evolve into transitions to solid-state phases, giving rise to amyloid structures. Amyloidogenic and prion-like proteins, such as the tumor suppressor protein p53 and the mammalian prion protein (PrP), bind RNAs specifically or nonspecifically, resulting in changes in their propensity to undergo aggregation. Mutant p53 aggregation seems to play a crucial role in cancer through loss of function, negative dominance and gain of function. Read More

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http://dx.doi.org/10.1016/j.bbapap.2019.02.006DOI Listing
February 2019

Emergent functions of proteins in non-stoichiometric supramolecular assemblies.

Biochim Biophys Acta Proteins Proteom 2019 Feb 28. Epub 2019 Feb 28.

Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary; VIB Center for Structural Biology (CSB), Brussels, Belgium; Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Brussels, Belgium. Electronic address:

Proteins are the basic functional units of the cell, carrying out myriads of functions essential for life. There are countless reports in molecular cell biology addressing the functioning of proteins under physiological and pathological conditions, aiming to understand life at the atomistic-molecular level and thereby being able to develop remedies against diseases. The central theme in most of these studies is that the functional unit under study is the protein itself. Read More

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http://dx.doi.org/10.1016/j.bbapap.2019.02.007DOI Listing
February 2019

Ticket to a bubble ride: Cargo sorting into exosomes and extracellular vesicles.

Biochim Biophys Acta Proteins Proteom 2019 Feb 26. Epub 2019 Feb 26.

Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia. Electronic address:

Extracellular vesicles (EVs) are released by cells into the extracellular milieu to facilitate intercellular communication in both physiological and pathological condition. EVs contain selective repertoires of proteins, RNAs, lipids and metabolites that moderate signalling pathways in the recipient cells. The enrichment of a particular set of proteins or RNAs within the EVs highlights the existence of specific sorting mechanisms that orchestrate the selective packaging of the cargo. Read More

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http://dx.doi.org/10.1016/j.bbapap.2019.02.005DOI Listing
February 2019
1 Read

Inhibition of ricin A-chain (RTA) catalytic activity by a viral genome-linked protein (VPg).

Biochim Biophys Acta Proteins Proteom 2019 Feb 27. Epub 2019 Feb 27.

Department of Sciences, John Jay College of Criminal Justice, the City University of New York, New York 10019, NY, United States of America. Electronic address:

Ricin is a plant derived protein toxin produced by the castor bean plant (Ricinus communis). The Centers for Disease Control (CDC) classifies ricin as a Category B biological agent. Currently, there is neither an effective vaccine that can be used to protect against ricin exposure nor a therapeutic to reverse the effects once exposed. Read More

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http://dx.doi.org/10.1016/j.bbapap.2019.02.002DOI Listing
February 2019

Genetic code ambiguity modulates the activity of a C. albicans MAP kinase linked to cell wall remodeling.

Biochim Biophys Acta Proteins Proteom 2019 Feb 20. Epub 2019 Feb 20.

IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal; Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal. Electronic address:

The human fungal pathogen Candida albicans ambiguously decodes the universal leucine CUG codon predominantly as serine but also as leucine. C. albicans has a high capacity to survive and proliferate in adverse environments but the rate of leucine incorporation fluctuates in response to different stress conditions. Read More

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http://dx.doi.org/10.1016/j.bbapap.2019.02.004DOI Listing
February 2019
1 Read

Corrigendum to quantitative NMR study of heat-induced aggregation of eye-lens crystallin proteins under crowding conditions. BBAPAP Volume 1866/10 2018 1055-1061].

Biochim Biophys Acta Proteins Proteom 2019 Apr 14;1867(4):453-454. Epub 2019 Feb 14.

Institut für Physik, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle (Saale), Germany. Electronic address:

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http://dx.doi.org/10.1016/j.bbapap.2019.02.001DOI Listing

pH-Dependent fibril maturation of a Pmel17 repeat domain isoform revealed by tryptophan fluorescence.

Biochim Biophys Acta Proteins Proteom 2019 Feb 2. Epub 2019 Feb 2.

Laboratory of Protein Conformation and Dynamics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, United States. Electronic address:

The pre-melanosomal protein (Pmel17) aggregates within melanosomes to form functional amyloid fibrils that facilitate melanin polymerization. The repeat domain (RPT) of Pmel17 fibrillates under strict acidic melanosomal pH. Alternative splicing results in a shortened repeat domain (sRPT), which also forms amyloid fibrils. Read More

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http://dx.doi.org/10.1016/j.bbapap.2019.01.012DOI Listing
February 2019

Structure and function of the putative thioredoxin 1 from the thermophilic eubacterium Thermosipho africanus strain TCF52B.

Biochim Biophys Acta Proteins Proteom 2019 Apr 1;1867(4):426-433. Epub 2019 Feb 1.

Department of Chemistry, College of Arts and Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada. Electronic address:

The thioredoxin system is a ubiquitous oxidoreductase system that consists of the enzyme thioredoxin reductase (TrxR), its cofactor nicotinamide adenine dinucleotide phosphate (NAD(P)H) and the protein thioredoxin (Trx). The system has been comprehensively studied from many organisms, such as Escherichia coli (E. coli); however, structural and functional analysis of this system from thermophilic bacteria has not been as extensive. Read More

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http://dx.doi.org/10.1016/j.bbapap.2019.01.011DOI Listing

Secretome analysis of human bone marrow derived mesenchymal stromal cells.

Biochim Biophys Acta Proteins Proteom 2019 Apr 1;1867(4):434-441. Epub 2019 Feb 1.

Molecular Proteomics Laboratory, Biomedical Research Center (BMFZ), Heinrich-Heine-University, Düsseldorf, Germany. Electronic address:

As an essential cellular component of the bone marrow (BM) microenvironment mesenchymal stromal cells (MSC) play a pivotal role for the physiological regulation of hematopoiesis, in particular through the secretion of cytokines and chemokines. Mass spectrometry (MS) facilitates the identification and quantification of a large amount of secreted proteins (secretome), but can be hampered by the false-positive identification of contaminating proteins released from dead cells or derived from cell medium. To reduce the likelihood of contaminations we applied an approach combining secretome and proteome analysis to characterize the physiological secretome of BM derived human MSC. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S15709639193002
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http://dx.doi.org/10.1016/j.bbapap.2019.01.013DOI Listing
April 2019
6 Reads

Biophysical and structural characterization of the small heat shock protein HspA from Thermosynechococcus vulcanus in 2 M urea.

Biochim Biophys Acta Proteins Proteom 2019 Apr 31;1867(4):442-452. Epub 2019 Jan 31.

Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Technion City, Haifa 32000, Israel. Electronic address:

Small heat shock proteins (sHSPs) belong to the superfamily of molecular chaperones. They prevent aggregation of partially unfolded or misfolded client proteins, providing protection to organisms under stress conditions. Here, we report the biophysical and structural characterization of a small heat shock protein (HspA) from a thermophilic cyanobacterium Thermosynechococcus vulcanus in the presence of 2 M urea. Read More

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http://dx.doi.org/10.1016/j.bbapap.2018.12.011DOI Listing
April 2019
1 Read

Structural insights into amyloid structures of the C-terminal region of nucleophosmin 1 in type A mutation of acute myeloid leukemia.

Biochim Biophys Acta Proteins Proteom 2019 Jan 30. Epub 2019 Jan 30.

Department of Pharmacy, University of Naples "Federico II", Italy. Electronic address:

Acute myeloid leukemia (AML) is a clinically and a molecularly heterogeneous disease characterized by the accumulation of undifferentiated and uncontrolled proliferation of hematopoietic progenitor cells. The sub-group named "AML with gene mutations" includes mutations in nucleophosmin (NPM1) assumed as a distinct leukemic entity. NPM1 is an abundant multifunctional protein belonging to the nucleoplasmin family of nuclear chaperones. Read More

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http://dx.doi.org/10.1016/j.bbapap.2019.01.010DOI Listing
January 2019
2 Reads

Modulation of aggregation of silk fibroin by synergistic effect of the complex of curcumin and β-cyclodextrin.

Biochim Biophys Acta Proteins Proteom 2019 Apr 21;1867(4):416-425. Epub 2019 Jan 21.

Department of Textile Technology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.. Electronic address:

Amyloid aggregation has been associated with numerous human pathological diseases. A recent study has demonstrated that silk fibroin intermittently endorses amyloidogenesis in vivo. In the current study, we explored the propensity of silk fibroin to undergo amyloid-like aggregation and its prevention using an optimized concoction of curcumin with β-cyclodextrin. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S15709639193002
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http://dx.doi.org/10.1016/j.bbapap.2019.01.009DOI Listing
April 2019
5 Reads

Inter and intra-subunit interactions at the subunit interface of chaperonin GroEL are essential for its stability and assembly.

Biochim Biophys Acta Proteins Proteom 2019 Mar 26;1867(3):331-343. Epub 2018 Oct 26.

Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India. Electronic address:

Chaperonin 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. Read More

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http://dx.doi.org/10.1016/j.bbapap.2018.10.012DOI Listing
March 2019
1 Read

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.

Biochim Biophys Acta Proteins Proteom 2019 Apr 16;1867(4):367-375. Epub 2019 Jan 16.

Laboratory of Protein Structure, Function and Design, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan. Electronic address:

When the replisome collapses at a DNA damage site, a sequence-independent replication restart system is required. In Escherichia coli, PriA, PriB, and DnaT assemble in an orderly fashion at the stalled replication fork and achieve the reloading of the replisome. PriB-DnaT interaction is considered a significant step in the replication restart. Read More

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http://dx.doi.org/10.1016/j.bbapap.2019.01.008DOI Listing
April 2019
1 Read

Sequence specificity of amylin-insulin interaction: a fragment-based insulin fibrillation inhibition study.

Biochim Biophys Acta Proteins Proteom 2019 Apr 17;1867(4):405-415. Epub 2019 Jan 17.

Department of Biophysics, P-1/12 CIT Scheme VII (M), Kolkata 700054, India. Electronic address:

Subcutaneous 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 formulations. Read More

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http://dx.doi.org/10.1016/j.bbapap.2019.01.007DOI Listing
April 2019
3 Reads
2.747 Impact Factor

Modification by glyceraldehyde-3-phosphate prevents amyloid transformation of alpha-synuclein.

Biochim Biophys Acta Proteins Proteom 2019 Apr 10;1867(4):396-404. Epub 2019 Jan 10.

Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119234, Russia. Electronic address:

Numerous 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). Read More

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http://dx.doi.org/10.1016/j.bbapap.2019.01.003DOI Listing
April 2019
5 Reads

Transmembrane topology of mammalian ORMDL proteins in the endoplasmic reticulum as revealed by the substituted cysteine accessibility method (SCAM™).

Biochim Biophys Acta Proteins Proteom 2019 Apr 10;1867(4):382-395. Epub 2019 Jan 10.

Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA 23298, USA; Sanger Building, Room 2-032b, 1101 East Marshall Street, Richmond, VA 23298, USA. Electronic address:

Sphingolipids 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). Read More

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http://dx.doi.org/10.1016/j.bbapap.2019.01.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6391742PMC
April 2019
2 Reads

Thiopurine intolerance-causing mutations in NUDT15 induce temperature-dependent destabilization of the catalytic site.

Biochim Biophys Acta Proteins Proteom 2019 Apr 10;1867(4):376-381. Epub 2019 Jan 10.

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6 166 10, Czech Republic. Electronic address:

Germline mutations in NUDT15 cause thiopurine intolerance during treatment of leukemia or autoimmune diseases. Previously, it has been shown that the mutations affect the enzymatic activity of the NUDT15 hydrolase due to decreased protein stability in vivo. Here we provide structural insights into protein destabilization in R139C and V18I mutants using thermolysin-based proteolysis and H/D exchange followed by mass spectrometry. Read More

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http://dx.doi.org/10.1016/j.bbapap.2019.01.006DOI Listing
April 2019
3 Reads
2.747 Impact Factor

In depth, thermodynamic analysis of Ca binding to human cardiac troponin C: Extracting buffer-independent binding parameters.

Biochim Biophys Acta Proteins Proteom 2019 Apr 10;1867(4):359-366. Epub 2019 Jan 10.

Department of Chemistry, East Carolina University, 300 Science and Technology, Greenville, NC 27858, United States. Electronic address:

Background: Characterizing the thermodynamic parameters behind metal-biomolecule interactions is fundamental to understanding the roles metal ions play in biology. Isothermal Titration Calorimetry (ITC) is a "gold-standard" for obtaining these data. However, in addition to metal-protein binding, additional equilibria such as metal-buffer interactions must be taken into consideration prior to making meaningful comparisons between metal-binding systems. Read More

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http://dx.doi.org/10.1016/j.bbapap.2019.01.004DOI Listing
April 2019
4 Reads

Comprehensive metabolomic and proteomic analysis in biochemical metabolic pathways of rice spikes under drought and submergence stress.

Biochim Biophys Acta Proteins Proteom 2019 Mar 3;1867(3):237-247. Epub 2019 Jan 3.

Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Jiangxi 330045, China. Electronic address:

Drought and submergence are the main adverse factors affecting plant growth and yield formation in parts of China, especially in the Yangtze River region. 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. Read More

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http://dx.doi.org/10.1016/j.bbapap.2019.01.001DOI Listing

Comparative proteomic analysis of salt-responsive proteins in canola roots by 2-DE and MALDI-TOF MS.

Biochim Biophys Acta Proteins Proteom 2019 Mar 3;1867(3):227-236. Epub 2019 Jan 3.

Molecular Plant Genetics, Universität Hamburg, Biozentrum Klein Flottbek, Ohnhorststr. 18, 22609 Hamburg, Germany. Electronic address:

Salinity 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-sensitive genotype Zafar. Read More

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http://dx.doi.org/10.1016/j.bbapap.2018.12.009DOI Listing

Imaging individual protein aggregates to follow aggregation and determine the role of aggregates in neurodegenerative disease.

Biochim Biophys Acta Proteins Proteom 2019 Jan 3. Epub 2019 Jan 3.

Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; UK Dementia Research Institute, University of Cambridge, Cambridge CB2 0XY, United Kingdom. Electronic address:

Protein 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 these methods and discuss recent examples of their application to determine the molecular mechanism of aggregation and the detection of aggregates in cells and cerebrospinal fluid. Read More

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http://dx.doi.org/10.1016/j.bbapap.2018.12.010DOI Listing
January 2019

Regulation of two GTPases Toc159 and Toc34 in the translocon of the outer envelope of chloroplasts.

Biochim Biophys Acta Proteins Proteom 2019 Jan 3. Epub 2019 Jan 3.

Department of Molecular Cell Biology of Plants, Goethe University, Max-von-Laue Str. 9, D-60438 Frankfurt, Germany; Frankfurt Institute for Advanced Studies, Ruth-Moufang-Straße 1, D-60438 Frankfurt, Germany; Cluster of Excellence Frankfurt, Goethe University, D-60438 Frankfurt, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University, Max-von-Laue Str. 15, D-60438 Frankfurt, Germany. Electronic address:

The 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 peptide representing the translocation signal of precursor proteins. Read More

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http://dx.doi.org/10.1016/j.bbapap.2019.01.002DOI Listing
January 2019

Identification of serum biomarkers for premature ovarian failure.

Biochim Biophys Acta Proteins Proteom 2019 Mar 29;1867(3):219-226. Epub 2018 Dec 29.

Department of Biomedical Science, CHA University, Gyeonggi-Do 13488, Republic of Korea. Electronic address:

Premature ovarian failure (POF) is defined when a female achieves menopause before the age of 40. Although many conditions are known to be causative for POF, the most common one is idiopathic. This study was undertaken to investigate the pathogenesis of POF using proteomic tools. Read More

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http://dx.doi.org/10.1016/j.bbapap.2018.12.007DOI Listing
March 2019
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First evidence of changes in enzyme kinetics and stability of glucokinase affected by somatic cancer-associated variations.

Biochim Biophys Acta Proteins Proteom 2019 Mar 24;1867(3):213-218. Epub 2018 Dec 24.

Charles University, Third Faculty of Medicine, Prague, Czech Republic. Electronic address:

Recent 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 the likely activating variations and the variations present in the connecting loop I and provided the first experimental evidence of the effects of somatic cancer-associated GCK variations. Read More

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http://dx.doi.org/10.1016/j.bbapap.2018.12.008DOI Listing

A one-pot analysis approach to simplify measurements of protein stability and folding kinetics.

Biochim Biophys Acta Proteins Proteom 2019 Mar 19;1867(3):184-193. Epub 2018 Dec 19.

Department of Food Science and Biotechnology, National Chung Hsing University, 145 Xingda Rd., South Dist., Taichung City 402, Taiwan, ROC. Electronic address:

To 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. Read More

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http://dx.doi.org/10.1016/j.bbapap.2018.12.006DOI Listing

iTRAQ-based phosphoproteomic analysis reveals host cell's specific responses to Toxoplasma gondii at the phases of invasion and prior to egress.

Biochim Biophys Acta Proteins Proteom 2019 Mar 18;1867(3):202-212. Epub 2018 Dec 18.

Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China. Electronic address:

Protein phosphorylation plays a key role in host cell-T. gondii interaction. However, the phosphoproteome data of host cell at various phases of T. Read More

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http://dx.doi.org/10.1016/j.bbapap.2018.12.004DOI Listing

Redox-tuning of oxidizing disulfide oxidoreductase generates a potent disulfide isomerase.

Biochim Biophys Acta Proteins Proteom 2019 Mar 18;1867(3):194-201. Epub 2018 Dec 18.

Graduate School of Environmental and Life Sciences, Okayama University, 1-1-1, Tsushima-naka, Okayama 700-8530, Japan. Electronic address:

Oxidative 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 properties of DsbA by exploiting the plaque-forming ability of bacteriophage M13, which specifically recognizes F-pili during infection of the host cell. Read More

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http://dx.doi.org/10.1016/j.bbapap.2018.12.005DOI Listing
March 2019
3 Reads

A comprehensive analysis of the protein-ligand interactions in crystal structures of Mycobacterium tuberculosis EthR.

Biochim Biophys Acta Proteins Proteom 2019 Mar 13;1867(3):248-258. Epub 2018 Dec 13.

Unité Microbiologie, Bioorganique et Macromoléculaire (CP206/04), département R3D, Faculté de Pharmacie, Université Libre de Bruxelles, B-1050 Brussels, Belgium. Electronic address:

The 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 therapeutic target against tuberculosis, allowing, when inhibited by a drug-like molecule, to boost the action of ethionamide. Dozens of EthR crystal structures have been solved in complex with ligands. Read More

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http://dx.doi.org/10.1016/j.bbapap.2018.12.003DOI Listing
March 2019
7 Reads
2.747 Impact Factor

Thermal unfolding of calreticulin. Structural and thermodynamic characterization of the transition.

Biochim Biophys Acta Proteins Proteom 2019 Mar 13;1867(3):175-183. Epub 2018 Dec 13.

Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina; Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Universidad Nacional de Córdoba, Córdoba, Argentina. Electronic address:

Calreticulin (CRT) is a calcium-binding protein that participates in several cellular processes including the control of protein folding and homeostasis of Ca. Its folding, stability and functions are strongly controlled by the presence of Ca. The oligomerization state of CRT is also relevant for its functions. Read More

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http://dx.doi.org/10.1016/j.bbapap.2018.12.002DOI Listing
March 2019
1 Read

A conformational switch from a closed apo- to an open holo-form equips the acyl carrier protein for acyl chain accommodation.

Biochim Biophys Acta Proteins Proteom 2019 Mar 10;1867(3):163-174. Epub 2018 Dec 10.

Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India. Electronic address:

Acyl 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 to be explored. Here we report the crystal structures of apo-LmACP (wild-type and S37A mutant) at 2. Read More

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http://dx.doi.org/10.1016/j.bbapap.2018.12.001DOI Listing
March 2019
2 Reads

Predicting eukaryotic protein secretion without signals.

Biochim Biophys Acta Proteins Proteom 2018 Dec 4. Epub 2018 Dec 4.

Molecular Proteomics Laboratory, Institute of Molecular Medicine, Universitätsklinikum Düsseldorf, Düsseldorf, Germany.

Predicting 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 method SecretomeP in 2004. Here, we take a critical look at SecretomeP and its successors, and we also discuss whether multi-category subcellular location predictors can be used to predict unconventional protein secretion in eukaryotes. Read More

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http://dx.doi.org/10.1016/j.bbapap.2018.11.011DOI Listing
December 2018

Improved expression, purification and characterization of VPR, a cold active subtilisin-like serine proteinase and the effects of calcium on expression and stability.

Biochim Biophys Acta Proteins Proteom 2019 Feb 28;1867(2):152-162. Epub 2018 Nov 28.

Department of Biochemistry, Science Institute, University of Iceland, Reykjavík, Iceland. Electronic address:

Cloning 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 enzyme obtained in a redesigned purification protocol which removed apparent RNA contaminants, resulted in a significantly higher value for k than previously reported. Read More

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http://dx.doi.org/10.1016/j.bbapap.2018.11.010DOI Listing
February 2019
1 Read