534 results match your criteria Biochimica et biophysica acta. Proteins and proteomics[Journal]


Utility of d-serine monitoring in kidney disease.

Biochim Biophys Acta Proteins Proteom 2020 May 22:140449. Epub 2020 May 22.

Department of Nephrology, Osaka University Graduate School of Medicine, Japan.

d-Serine, a long-term undetected enantiomer of serine, is now showing its potential as a biomarker for kidney diseases. The intra-body dynamics of d-serine, currently defined by blood levels and urinary excretion dynamics, are useful for a comprehensive assessment of kidney function and disease activity. Thus, widespread adoption of d-serine as a biomarker can resolve the long-standing clinical challenge of the early detection and prognostic prediction of kidney diseases. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140449DOI Listing

Regulation of the α-ketoglutarate dehydrogenasecomplex during hibernation in a small mammal, the Richardson's ground squirrel (Urocitellus richardsonii).

Biochim Biophys Acta Proteins Proteom 2020 May 20:140448. Epub 2020 May 20.

Institute of Biochemistry & Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, Canada, K1S 5B6. Electronic address:

The citric acid cycle (CAC) is a central metabolic pathway that links carbohydrate, lipid, and amino acid metabolism in the mitochondria and, hence, is a crucial target for metabolic regulation. The α-ketoglutarate dehydrogenase complex (KGDC) is the rate-limiting step of the CAC, the three enzymes of the complex catalyzing the transformation of α-ketoglutarate to succinyl-CoA with the release of CO and reduction of NAD to NADH. During hibernation, the metabolic rate of small mammals is suppressed, in part due to reduced body temperature but also active controls that suppress aerobic metabolism. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140448DOI Listing

TGFβ1-Smad3 signaling mediates the formation of a stable serine racemase dimer in microglia.

Biochim Biophys Acta Proteins Proteom 2020 May 19:140447. Epub 2020 May 19.

Departamento de Neurología, Facultad de Medicina, Universidad Católica de Chile, Av. Libertador Bernardo O'Higgins 340, Santiago, Chile. Electronic address:

d-serine is synthesized by serine racemase (SR), a fold type II class of pyridoxal-5'-phosphate (PLP)-dependent enzyme. Whereas X-ray crystallography reveals that SR can be monomeric, reversible dimers having the highest racemase activity, or stable SR dimers resistant to both denaturation and reductive treatment, showing reduced racemase activity have been detected in microglia and astrocytes; the latter especially in oxidative or inflammatory environments. The microglial inflammatory environment depends largely on the TGFβ1-mediated regulation of inflammatory cytokines such as TNFα and IL1β. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140447DOI Listing

Asp isomerization increases aggregation of α-crystallin and decreases its chaperone activity in human lens of various ages.

Biochim Biophys Acta Proteins Proteom 2020 May 19:140446. Epub 2020 May 19.

Rexxam Co., Ltd., Nishi-ku, Nagoya, Aichi 541-0054, Japan.

α-Crystallin, comprising 40-50 subunits of αA- and αB-subunits, is a long-lived major soluble chaperone protein in lens. During aging, α-crystallin forms aggregates of high molecular weight (HMW) protein and eventually becomes water-insoluble (WI). Isomerization of Asp in α-crystallin has been proposed as a trigger of protein aggregation, ultimately leading to cataract formation. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140446DOI Listing

A comprehensive study of construction and analysis of competitive endogenous RNA networks in lung adenocarcinoma.

Biochim Biophys Acta Proteins Proteom 2020 May 11;1868(8):140444. Epub 2020 May 11.

Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China. Electronic address:

Background: Long noncoding RNAs (lncRNAs) have gain increasing attention in lung adenocarcinoma. In this study, we aimed at constructing and analyzing the lncRNAs and the related proteins based competitive endogenous RNA (ceRNA) network.

Methods: RNA expression data of lung adenocarcinoma were extracted from the TCGA database. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140444DOI Listing

The aging lysosome: An essential catalyst for late-onset neurodegenerative diseases.

Authors:
Ralph A Nixon

Biochim Biophys Acta Proteins Proteom 2020 May 13:140443. Epub 2020 May 13.

Center for Dementia Research, Nathan S. Kline Institute, 140 Old Orangeburg Road, Orangeburg, NY 10962, USA; Departments of Psychiatry, New York University Langone Medical Center, 550 First Ave, New York, NY 10016, USA; Cell Biology, New York University Langone Medical Center, 550 First Ave, New York, NY 10016, USA; NYU Neuroscience Institute, New York University Langone Medical Center, 550 First Ave, New York, NY 10016, USA. Electronic address:

Lysosomes figure prominently in theories of aging as the proteolytic system most responsible for eliminating growing burdens of damaged proteins and organelles in aging neurons and other long lived cells. Newer evidence shows that diverse experimental measures known to extend lifespan in invertebrate aging models share the property of boosting lysosomal clearance of substrates through the autophagy pathway. Maintaining an optimal level of lysosome acidification is particularly crucial for these anti-aging effects. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140443DOI Listing

Coumarin as a structural component of substrates and probes for serine and cysteine proteases.

Biochim Biophys Acta Proteins Proteom 2020 May 13;1868(9):140445. Epub 2020 May 13.

Pharmaceutical Institute, Department of Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany. Electronic address:

Coumarins represent well-established structures to introduce fluorescence into tool compounds for biochemical investigations. They are valued for their small size, chemical stability and accessibility as well as their tunable photochemical properties. As components of fluorophore/quencher pairs or FRET donor/acceptor pairs, coumarins have frequently been applied in substrate mapping approaches for serine and cysteine proteases. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140445DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7219385PMC

Physicochemical and structural properties of lunasin revealed by spectroscopic, chromatographic and molecular dynamics approaches.

Biochim Biophys Acta Proteins Proteom 2020 May 4;1868(8):140440. Epub 2020 May 4.

Laboratório de Biotecnologia Farmacêutica, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil; Programa de Pós-Graduação em Nanobiossistemas (PPGIM-NANOBIOS), Universidade Federal do Rio de Janeiro, Duque de Caxias, RJ, Brazil; Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil. Electronic address:

Lunasin is a 43-amino acid peptide from seeds and grains with bioavailability in humans and potent chemotherapeutic action against several cancer cell lines. Here, we investigate new information about the physicochemical and structural properties of lunasin using circular dichroism (CD), fluorescence spectroscopy, electrospray ionization-ion mobility spectrometry-mass spectrometry (ESI-IMS-MS), size exclusion chromatography (SEC), molecular dynamics (MD), and bioinformatics. CD analysis and disorder prediction obtained by PONDR indicate that lunasin has a mostly unordered structure. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140440DOI Listing

Biochemical characterization of d-aspartate oxidase from Caenorhabditis elegans: its potential use in the determination of free d-glutamate in biological samples.

Biochim Biophys Acta Proteins Proteom 2020 May 3;1868(8):140442. Epub 2020 May 3.

Laboratory of Biomolecular Sciences, Graduate School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan. Electronic address:

d-Aspartate oxidase (DDO) is a flavin adenine dinucleotide (FAD)-containing flavoprotein that stereospecifically acts on acidic d-amino acids (i.e., free d-aspartate and d-glutamate). Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140442DOI Listing

Nucleotide-dependent dynamics of the Dengue NS3 helicase.

Biochim Biophys Acta Proteins Proteom 2020 May 1;1868(8):140441. Epub 2020 May 1.

Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Inorgánica, Analítica y Química Física. Argentina; CONICET- Universidad de Buenos Aires. Instituto de Química-Física de los Materiales, Medio Ambiente y Energía (INQUIMAE). Buenos Aires, Argentina. Electronic address:

Dengue represents a substantial public health burden, particularly in low-resource countries. Non-structural protein 3 (NS3) is a multifunctional protein critical in the virus life cycle and has been identified as a promising anti-viral drug target. Despite recent crystallographic studies of the NS3 helicase domain, only subtle structural nucleotide-dependent differences have been identified, such that its coupled ATPase and helicase activities remain mechanistically unclear. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140441DOI Listing

Solid-state vibrational circular dichroism studies on the conformation of an amino acid molecule in crystalline state.

Biochim Biophys Acta Proteins Proteom 2020 May 1;1868(8):140439. Epub 2020 May 1.

Graduate School of Engineering Science, Yokohama National University, 240-8501 Yokohama, Japan. Electronic address:

The present article reviews the results of solid-state vibrational circular dichroism (SD-VCD) measurements on the crystals of amino acids. The investigated series were Ala, Ile, Leu, Phe, Ser, Val, and Thr. Spectra were recorded for the samples containing both D- and L-enantiomers. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140439DOI Listing

Seryl-tRNA synthetase specificity for tRNA in Bacterial Sec biosynthesis.

Biochim Biophys Acta Proteins Proteom 2020 Apr 21;1868(8):140438. Epub 2020 Apr 21.

Physics Institute of Sao Carlos, University of Sao Paulo, Trabalhador São Carlense Av., 400. São Carlos, SP CEP 13566-590, Brazil; Department of Genetics and Evolution, Federal University of São Carlos - UFSCar, 13565-905 São Carlos, 16 SP, Brazil. Electronic address:

tRNA synthetases are responsible for decoding the molecular information, from codons to amino acids. Seryl-tRNA synthetase (SerRS), besides the five isoacceptors of tRNA, recognizes tRNA for the incorporation of selenocysteine (Sec, U) into selenoproteins. The selenocysteine synthesis pathway is known and is dependent on several protein-protein and protein-RNA interactions. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140438DOI Listing

Functional characterization of the different oligomeric forms of human surfactant protein SP-D.

Biochim Biophys Acta Proteins Proteom 2020 Apr 20;1868(8):140436. Epub 2020 Apr 20.

Division of Neonatology and Pulmonary Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA. Electronic address:

Surfactant Protein D (SP-D) is a collectin protein that participates in the innate immune defense of the lungs. SP-D mediates the clearance of invading microorganisms by opsonization, aggregation or direct killing, which are lately removed by macrophages. SP-D is found as a mixture of trimers, hexamers, dodecamers and higher order oligomers, "fuzzy balls". Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140436DOI Listing

High-resolution structure of a modular hyperthermostable endo-β-1,4-mannanase from Thermotoga petrophila: The ancillary immunoglobulin-like module is a thermostabilizing domain.

Biochim Biophys Acta Proteins Proteom 2020 Apr 21;1868(8):140437. Epub 2020 Apr 21.

Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, SP, Brazil. Electronic address:

The endo-β-1,4-mannanase from the hyperthermostable bacterium Thermotoga petrophila (TpMan) is an enzyme that catalyzes the hydrolysis of mannan and heteromannan polysaccharides. Of the three domains that comprise TpMan, the N-terminal GH5 catalytic domain and the C-terminal carbohydrate-binding domain are connected through a central ancillary domain of unknown structure and function. In this study, we report the partial crystal structure of the TpMan at 1. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140437DOI Listing

Cathepsin B in neurodegeneration of Alzheimer's disease, traumatic brain injury, and related brain disorders.

Biochim Biophys Acta Proteins Proteom 2020 Apr 17;1868(8):140428. Epub 2020 Apr 17.

American Life Sciences Pharmaceuticals, Inc., La Jolla, CA, United States of America.

Investigations of Alzheimer's disease (AD), traumatic brain injury (TBI), and related brain disorders have provided extensive evidence for involvement of cathepsin B, a lysosomal cysteine protease, in mediating the behavioral deficits and neuropathology of these neurodegenerative diseases. This review integrates findings of cathepsin B regulation in clinical biomarker studies, animal model genetic and inhibitor evaluations, structural studies, and lysosomal cell biological mechanisms in AD, TBI, and related brain disorders. The results together indicate the role of cathepsin B in the behavioral deficits and neuropathology of these disorders. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140428DOI Listing

Separation of D-amino acid-containing peptide phenylseptin using 3,3'-phenyl-1,1'-binaphthyl-18-crown-6-ether columns.

Biochim Biophys Acta Proteins Proteom 2020 Apr 13;1868(8):140429. Epub 2020 Apr 13.

Graduate School of Science and Engineering, Ehime University, Japan.

Several D-amino acid-containing peptides (DAACPs) with antimicrobial, cardio-excitatory, or neuronal activities have been found in several species. Here, we demonstrated the chiral separation of the antimicrobial peptide diastereomers, D-phenylseptin and L-phenylseptin using (S) and (R) 3,3'-phenyl-1,1'-binaphthyl-18-crown-6-ether columns (CR-I (+) and CR-I (-), respectively) and also investigated the underlying mechanism. First, using D-amino acid-containing tripeptide Phe-Phe-Phe-OH, we found that CR-I (+) could be used to recognize diastereomeric tripeptides containing an L-amino acid as the first residue. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140429DOI Listing

Discovery of strong inhibitory properties of a monoclonal antibody of PKA and use of the antibody and a competitive photoluminescent orthosteric probe for analysis of the protein kinase.

Biochim Biophys Acta Proteins Proteom 2020 Apr 10;1868(8):140427. Epub 2020 Apr 10.

Institute of Chemistry, University of Tartu, 14A Ravila St., 50411 Tartu, Estonia. Electronic address:

We show that the antibody, clone mAb(D38C6), of the α isoform of the catalytic subunit of PKA (PKAcα) inhibits the kinase-catalyzed phosphorylation with low-nanomolar inhibitory potency (K = 2.4 nM). This property of the antibody was established by its capacity to displace a synthetic small-molecule active site-binding (orthosteric) photoluminescent ARC-Lum(Fluo) probe from the complex with PKAcα. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140427DOI Listing

The GLP-1 analog exendin-4 modulates HSP72 expression and ERK1/2 activity in BTC6 mouse pancreatic cells.

Biochim Biophys Acta Proteins Proteom 2020 Jul 7;1868(7):140426. Epub 2020 Apr 7.

Biochemistry and Molecular Biology Department, Dasman Diabetes Institute, Kuwait. Electronic address:

Lipotoxicity, an important factor in the pathogenesis of diabetes, leads to defective β-cell proliferation and increased apoptosis. Glucagon-like peptide-1 (GLP-1) analogs, which are used to treat type 2 diabetes, reduce endoplasmic reticulum stress and inflammation in pancreatic β-cells and improve their survival. However, their effects on the heat shock response (HSR) have not been elucidated yet. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140426DOI Listing
July 2020
2.747 Impact Factor

Tumor cell- and microenvironment-specific roles of cysteine cathepsins in mouse models of human cancers.

Biochim Biophys Acta Proteins Proteom 2020 Jul 2;1868(7):140423. Epub 2020 Apr 2.

Institute of Molecular Medicine and Cell Research, Medical Faculty, University of Freiburg, Freiburg, Germany; German Cancer Research Center (DKFZ), Heidelberg, German Cancer Consortium (DKTK), Partner Site, Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany. Electronic address:

The human genome encodes for 11 papain-like endolysosomal cysteine peptidases, collectively known as the cysteine cathepsins. Based on their biochemical properties and with the help of experiments in cell culture, the cysteine cathepsins have acquired a reputation as promotors of progression and metastasis of various cancer entities. However, tumors are known to be complex tissues in which non-cancerous cells are also critical for tumorigenesis. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140423DOI Listing

Deep learning based prediction of species-specific protein S-glutathionylation sites.

Biochim Biophys Acta Proteins Proteom 2020 Jul 29;1868(7):140422. Epub 2020 Mar 29.

School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China. Electronic address:

As a widespread and reversible post-translational modification of proteins, S-glutathionylation specifically generates the mixed disulfides between cysteine residues and glutathione, which regulates various biological processes including oxidative stress, nitrosative stress and signal transduction. The identification of proteins and specific sites that undergo S-glutathionylation is crucial for understanding the underlying mechanisms and regulatory effects of S-glutathionylation. Experimental identification of S-glutathionylation sites is laborious and time-consuming, whereas computational predictions are more attractive due to their high speed and convenience. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140422DOI Listing
July 2020
2.747 Impact Factor

Corrigendum to "Structural and functional characterization of the phosphoglucomutase from Xanthomonas citri subsp. Citri".

Biochim Biophys Acta Proteins Proteom 2020 Jul 29;1868(7):140408. Epub 2020 Mar 29.

Laboratório de Bioquímica e Biologia Molecular Aplicada - LBBMA, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil.

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http://dx.doi.org/10.1016/j.bbapap.2020.140408DOI Listing

Thermodynamic insights into the role of aromatic residues in chitooligosaccharide binding to the transglycosylating chitinase-D from Serratia proteamaculans.

Biochim Biophys Acta Proteins Proteom 2020 Jul 26;1868(7):140414. Epub 2020 Mar 26.

Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432 Ås, Norway. Electronic address:

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http://dx.doi.org/10.1016/j.bbapap.2020.140414DOI Listing

A muscle-specific calpain, CAPN3, forms a homotrimer.

Biochim Biophys Acta Proteins Proteom 2020 Jul 19;1868(7):140411. Epub 2020 Mar 19.

From Calpain Project, Department of Advanced Science for Biomolecules, Tokyo Metropolitan Institute of Medical Science (TMiMS), 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan. Electronic address:

Calpain-3 (CAPN3), a 94-kDa member of the calpain protease family, is abundant in skeletal muscle. Mutations in the CAPN3 gene cause limb girdle muscular dystrophy type 2A, indicating that CAPN3 plays important roles in muscle physiology. CAPN3 has several unique features. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140411DOI Listing

Inhibition of matrix metalloproteinase expression and cellular invasion by NF-κB inhibitors of microbial origin.

Biochim Biophys Acta Proteins Proteom 2020 Jun 14;1868(6):140412. Epub 2020 Mar 14.

Department of Molecular Target Medicine, Aichi Medical University, Nagakute 480-1195, Japan.

Matrix metalloproteinases (MMPs) are zinc-dependent extracellular matrix remodeling endopeptidases. MMPs cleave various matrix proteins such as collagen, elastin, gelatin and casein. MMPs are often implicated in pathological processes, such as cancer progression including metastasis. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140412DOI Listing

Surprising differences in the respiratory protein of insects: A spectroscopic study of haemoglobin from the European honeybee and the malaria mosquito.

Biochim Biophys Acta Proteins Proteom 2020 Jun 13;1868(6):140413. Epub 2020 Mar 13.

BIMEF Laboratory, Department of Chemistry, University of Antwerp, Belgium. Electronic address:

Only recently it was discovered that haemoglobin (Hb) belongs to the standard gene repertoire of insects, although their tracheal system is used for respiration. A classical oxygen-carrying function of Hb is only obvious for hexapods living in hypoxic environments. In other insect species, including the common fruit fly Drosophila melanogaster, the physiological role of Hb is yet unclear. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140413DOI Listing

Molecular recognition of fibroblast activation protein for diagnostic and therapeutic applications.

Biochim Biophys Acta Proteins Proteom 2020 Jul 6;1868(7):140409. Epub 2020 Apr 6.

Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 542/2, 166 10 Praha 6, Czech Republic; Department of Biochemistry, Faculty of Science, Charles University, Hlavova 8, 12843 Praha 2, Czech Republic. Electronic address:

Fibroblast activation protein (FAP) is a non-classical serine protease expressed predominantly in conditions accompanied by tissue remodeling, particularly cancer. Due to its plasma membrane localization, FAP represents a promising molecular target for tumor imaging and treatment. The unique enzymatic activity of FAP facilitates development of diagnostic and therapeutic tools based on molecular recognition of FAP by substrates and small-molecule inhibitors, in addition to conventional antibody-based strategies. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140409DOI Listing

Age-related isomerization of Asp in human immunoglobulin G kappa chain.

Biochim Biophys Acta Proteins Proteom 2020 Jun 10;1868(6):140410. Epub 2020 Mar 10.

Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka, Japan. Electronic address:

Isomerization of aspartate (Asp) is a common non-enzymatic posttranslational modification. Isomerized residues accumulate in proteins associated with age-related human disorders such as cataract and are well known to affect protein structure and function. We previously detected d-Asp-containing peptides in human serum. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140410DOI Listing

Corrigendum to "Capreomycin inhibits the initiation of amyloid fibrillation and suppresses amyloid induced cell toxicity" [Biochim. Biophy. Acta 1866 (2018) 549-557].

Biochim Biophys Acta Proteins Proteom 2020 Jun 6;1868(6):140407. Epub 2020 Mar 6.

Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, Uttar Pradesh, India.. Electronic address:

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http://dx.doi.org/10.1016/j.bbapap.2020.140407DOI Listing

Review and comparative analysis of machine learning-based phage virion protein identification methods.

Biochim Biophys Acta Proteins Proteom 2020 Jun 2;1868(6):140406. Epub 2020 Mar 2.

Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China; Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China. Electronic address:

Phage virion protein (PVP) identification plays key role in elucidating relationships between phages and hosts. Moreover, PVP identification can facilitate the design of related biochemical entities. Recently, several machine learning approaches have emerged for this purpose and have shown their potential capacities. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140406DOI Listing

Structural and mechanistic insights into the Keap1-Nrf2 system as a route to drug discovery.

Biochim Biophys Acta Proteins Proteom 2020 Jul 28;1868(7):140405. Epub 2020 Feb 28.

Department of Pharmacology, University of Cambridge, Tennis Court Road, CB2 1PD, United Kingdom. Electronic address:

The proteins Keap1 and Nrf2 together act as a cytoprotective mechanism that enables cells to overcome electrophilic and oxidative stress. Research has shown that manipulating this system by modulating the Keap1-Nrf2 interaction either through inhibition at the binding interface or via the covalent modification of Keap1 could provide a powerful therapeutic strategy for a range of diseases. However, despite intensive investigation of the system and significant progress in the development of inhibitory small molecules, there is still much to learn about the pathways associated with the Keap1-Nrf2 system and the structural details underpinning its mechanism of action. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140405DOI Listing

Thermodynamics, cooperativity and stability of the tetracycline repressor (TetR) upon tetracycline binding.

Biochim Biophys Acta Proteins Proteom 2020 Jun 27;1868(6):140404. Epub 2020 Feb 27.

Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Straße 4, 17489 Greifswald, Germany. Electronic address:

Allosteric regulation of the Tet repressor (TetR) homodimer relies on tetracycline binding that abolishes the affinity for the DNA operator. Previously, interpretation of circular dichroism data called for unfolding of the α-helical DNA-binding domains in absence of binding to DNA or tetracycline. Our small angle X-ray scattering of TetR(D) in solution contradicts this unfolding as a physiological process. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140404DOI Listing
June 2020
2.747 Impact Factor

Combinatorial degradomics: Precision tools to unveil proteolytic processes in biological systems.

Biochim Biophys Acta Proteins Proteom 2020 Jun 20;1868(6):140392. Epub 2020 Feb 20.

Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark. Electronic address:

The biological activity of a protein is regulated at many levels ranging from control of transcription and translation to post-translational modifications (PTM). Proteolytic processing is an irreversible PTM generating novel isoforms of a mature protein termed proteoforms. Proteoform dynamics is a major focus of current proteome research, since it has been associated with many pathological conditions. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140392DOI Listing

Conformational analysis of the riboflavin-responsive ETF:QO-p.Pro456Leu variant associated with mild multiple acyl-CoA dehydrogenase deficiency.

Biochim Biophys Acta Proteins Proteom 2020 Jun 19;1868(6):140393. Epub 2020 Feb 19.

Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal. Electronic address:

Multiple-CoA dehydrogenase deficiency (MADD) is an inborn disorder of fatty acid and amino acid metabolism caused by mutations in the genes encoding for human electron transfer flavoprotein (ETF) and its partner electron transfer flavoprotein:ubiquinone oxidoreductase (ETF:QO). Albeit a rare disease, extensive newborn screening programs contributed to a wider coverage of MADD genotypes. However, the impact of non-lethal mutations on ETF:QO function remains scarcely understood from a structural perspective. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140393DOI Listing

Cone snail analogs of the pituitary hormones oxytocin/vasopressin and their carrier protein neurophysin. Proteomic and transcriptomic identification of conopressins and conophysins.

Biochim Biophys Acta Proteins Proteom 2020 May 10;1868(5):140391. Epub 2020 Feb 10.

National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India; Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India. Electronic address:

Transcriptomic analysis of cone snail venom duct tissue has permitted the identification of diverse conopressin/conophysin precursor sequences from seven distinct Conus species. Multiple precursor isoforms are present in C.monile, C. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140391DOI Listing
May 2020
2.747 Impact Factor

Production, thermodynamic characterization, and fruit juice quality improvement characteristics of an Exo-polygalacturonase from Penicillium janczewskii.

Biochim Biophys Acta Proteins Proteom 2020 May 4;1868(5):140379. Epub 2020 Feb 4.

School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China. Electronic address:

Exo-polygalacturonase (Exo-PG), an extracellular pectinolytic enzyme with great potential in the food industry, was produced from Penicillium janczewskii under solid-state fermentation using wheat bran as a lignocellulosic substrate. Optimization of various fermentation process variables revealed that a moisture level of 70%, d-mannitol (carbon source), yeast extract (nitrogen source) and ZnSO/NiCl as metal salt inducers generated the maximum yield of Exo-PG. After ammonium sulfate precipitation (70% saturation level), the enzyme was characterized in terms of various kinetic (i. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140379DOI Listing

Targeted inhibition of amyloidogenesis using a non-toxic, serum stable strategically designed cyclic peptide with therapeutic implications.

Biochim Biophys Acta Proteins Proteom 2020 May 4;1868(5):140378. Epub 2020 Feb 4.

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

Amyloidogenic disorders are currently rising as a global health issue, prompting more and more studies dedicated to the development of effective targeted therapeutics. The innate affinity of these amyloidogenic proteins towards the biomembranes adds further complexities to the systems. Our previous studies have shown that biologically active peptides can effectively target amyloidogenesis serving as an efficient therapeutic alternative in several amyloidogenic disorders. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140378DOI Listing
May 2020
2.747 Impact Factor

N-succinylamino acid racemases: Enzymatic properties and biotechnological applications.

Biochim Biophys Acta Proteins Proteom 2020 04 23;1868(4):140377. Epub 2020 Jan 23.

Laboratorio de Estudios Cristalográficos, CSIC, 18100 Granada, Spain.

The N-succinylamino acid racemase/o-succinylbenzoate synthase (NSAR/OSBS) subfamily from the enolase superfamily contains different enzymes showing promiscuous N-substituted-amino acid racemase (NxAR) activity. These enzymes were originally named as N-acylamino acid racemases because of their industrial application. Nonetheless, they are pivotal in several enzymatic cascades due to their versatility to catalyze a wide substrate spectrum, allowing the production of optically pure d- or l-amino acids from cheap precursors. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140377DOI Listing

Kinetics aspects of Gamma-hydroxybutyrate dehydrogenase.

Biochim Biophys Acta Proteins Proteom 2020 May 22;1868(5):140376. Epub 2020 Jan 22.

Department of Chemistry and Biochemistry, Department of Biomolecular Science and Engineering, University of California, Santa Barbara, California, United States. Electronic address:

Two groups of metabolically related enzymes, the Group III family of Fe-dependent alcohol dehydrogenases (ADHs) and the separate subfamily of nucleoside diphosphates linked to x (nudix) hydrolases that activate Group III ADHs are under-characterized. Here we report the steady-state initial-velocity forward direction (alcohol → aldehyde) reaction of a Group III ADH, namely gamma-hydroxybutyrate dehydrogenase (GHBDH, UniProt: Q59104), cloned from Cupriavidus necator as a fusion protein. We also report the effects of nudix hydrolases on the GHBDH reaction. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140376DOI Listing

Genetic analysis of Hsp70 phosphorylation sites reveals a role in Candida albicans cell and colony morphogenesis.

Biochim Biophys Acta Proteins Proteom 2020 03 10;1868(3):140135. Epub 2018 Sep 10.

Department of Molecular Microbiology, B. Rappaport Faculty of Medicine, Technion - I.I.T. and the Rappaport Institute for Research in the Medical Sciences, Haifa 31096, Israel. Electronic address:

Heat shock proteins are best known for their role as chaperonins involved in general proteostasis, but they can also participate in specific cellular regulatory pathways, e.g. via their post-translational modification. Read More

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http://dx.doi.org/10.1016/j.bbapap.2018.09.001DOI Listing
March 2020
2.747 Impact Factor

Standard Gibbs energy of metabolic reactions: V. Enolase reaction.

Biochim Biophys Acta Proteins Proteom 2020 04 18;1868(4):140365. Epub 2020 Jan 18.

Laboratory of Thermodynamics, Department of Biochemical and Chemical Engineering, Technische Universitaet Dortmund, Emil-Figge-Str. 70, 44227 Dortmund, Germany. Electronic address:

The glycolytic pathway is one of the most important pathways for living organisms, due to its role in energy production and as supplier of precursors for biosynthesis in living cells. This work focuses on determination of the standard Gibbs energy of reaction Δg' of the enolase reaction, the ninth reaction in the glycolysis pathway. Exact Δg' values are required to predict the thermodynamic feasibility of single metabolic reactions or even of metabolic reaction sequences under cytosolic conditions. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140365DOI Listing

Changes in strand 6B and helix B during neuroserpin inhibition: Implication in severity of clinical phenotype.

Biochim Biophys Acta Proteins Proteom 2020 04 16;1868(4):140363. Epub 2020 Jan 16.

Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia (A Central University), New Delhi 110025, India. Electronic address:

Neuroserpin (NS) is predominantly expressed in brain and inhibits tissue-type plasminogen activator (tPA) with implications in brain development and memory. Nature of conformational change in pathological variants in strand 6B and helix B of NS that cause a relatively mild to severe epilepsy (and/or dementia) remains largely elusive. MD simulation with wild type (WT) NS, strand 6B and helix B variants indicated that substitution in this region affects the conformation of the strands 5B, 5A and reactive centre loop. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140363DOI Listing

The alpha helix of the intermediate region in hGBP-1 acts as a coupler for enhanced GMP formation.

Biochim Biophys Acta Proteins Proteom 2020 May 16;1868(5):140364. Epub 2020 Jan 16.

National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India. Electronic address:

The interferon-gamma inducible large GTPase human guanylate binding protein-1 (hGBP-1) plays a key role in anti-pathogenic and anti-proliferative functions. This protein hydrolyzes GTP to both GDP and GMP (predominant product) through sequential phosphate cleavages, which makes it functionally distinct from other GTPases. Previous study on truncated variants of hGBP-1 suggested that the α-helix present in the intermediate region is essential for dimerization and thus for GMP formation. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140364DOI Listing

Falcipain cysteine proteases of malaria parasites: An update.

Biochim Biophys Acta Proteins Proteom 2020 03 9;1868(3):140362. Epub 2020 Jan 9.

Dept. of Medicine, University of California, San Francisco, CA, USA. Electronic address:

Background: The malaria parasite Plasmodium falciparum expresses four related papain-family cysteine proteases known as falcipains. These proteases play critical roles in the parasite life cycle, and as such are potential targets for new modes of antimalarial chemotherapy, as discussed in this review.

Scope Of Review: This review summarizes available knowledge describing falcipain cysteine proteases of malaria parasites. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140362DOI Listing

Cysteinyl cathepsins in cardiovascular diseases.

Biochim Biophys Acta Proteins Proteom 2020 04 9;1868(4):140360. Epub 2020 Jan 9.

Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115. Electronic address:

Cysteinyl cathepsins are lysosomal/endosomal proteases that mediate bulk protein degradation in these intracellular acidic compartments. Yet, studies indicate that these proteases also appear in the nucleus, nuclear membrane, cytosol, plasma membrane, and extracellular space. Patients with cardiovascular diseases (CVD) show increased levels of cathepsins in the heart, aorta, and plasma. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140360DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7029168PMC

High-resolution structure of intramolecularly proteolyzed human mucin-1 SEA domain.

Biochim Biophys Acta Proteins Proteom 2020 03 7;1868(3):140361. Epub 2020 Jan 7.

Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Argentina; Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes,Argentina. Electronic address:

SEA domains are ubiquitous in large proteins associated with highly glycosylated environments. Certain SEA domains undergo intramolecular proteolysis involving a nucleophilic attack of a serine hydroxyl group on the preceding glycine carbonyl. The mucin-1 (MUC1) SEA domain has been extensively investigated as a model of intramolecular proteolysis. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140361DOI Listing

Selective pressure on an interfacial enzyme: Functional roles of a highly conserved asparagine residue in a cellulase.

Biochim Biophys Acta Proteins Proteom 2020 03 3;1868(3):140359. Epub 2020 Jan 3.

Technical University of Denmark, DTU Bioengineering, Building 224, DK-2800 Kgs. Lyngby, Denmark. Electronic address:

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http://dx.doi.org/10.1016/j.bbapap.2019.140359DOI Listing

Regulation of Herbaspirillum seropedicae NifA by the GlnK PII signal transduction protein is mediated by effectors binding to allosteric sites.

Biochim Biophys Acta Proteins Proteom 2020 03 19;1868(3):140348. Epub 2019 Dec 19.

Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CEP 81530-900 Curitiba, PR, Brazil. Electronic address:

Herbaspirillum seropedicae is a plant growth promoting bacterium that is able to fix nitrogen and to colonize the surface and internal tissues of important crops. Nitrogen fixation in H. seropedicae is regulated at the transcriptional level by the prokaryotic enhancer binding protein NifA. Read More

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http://dx.doi.org/10.1016/j.bbapap.2019.140348DOI Listing

Analysis of uracil DNA glycosylase (UNG2) stimulation by replication protein A (RPA) at ssDNA-dsDNA junctions.

Authors:
Brian P Weiser

Biochim Biophys Acta Proteins Proteom 2020 03 19;1868(3):140347. Epub 2019 Dec 19.

Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA. Electronic address:

Replication Protein A (RPA) is a single-stranded DNA binding protein that interacts with DNA repair proteins including Uracil DNA Glycosylase (UNG2). Here, I report DNA binding and activity assays using purified recombinant RPA and UNG2. Using synthetic DNA substrates, RPA was found to promote UNG2's interaction with ssDNA-dsDNA junctions regardless of the DNA strand polarity surrounding the junction. Read More

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http://dx.doi.org/10.1016/j.bbapap.2019.140347DOI Listing

Recent advances in biocatalysis and biotransformations.

Authors:

Biochim Biophys Acta Proteins Proteom 2020 03 18;1868(3):140346. Epub 2019 Dec 18.

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http://dx.doi.org/10.1016/j.bbapap.2019.140346DOI Listing