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


Interaction of TGFβ3 ligand with its receptors type II (TβRII) and type I (TβRI): A unique mechanism of protein-protein association.

Biochim Biophys Acta Proteins Proteom 2020 Jul 8:140485. Epub 2020 Jul 8.

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

The proper orchestration of transforming growth factor beta (TGFβ) mediated signal transduction depends upon a delicate set of interactions between specific ligands and their receptors. Here we present an in-depth profiling of the binding mechanism of TGFβ3 ligand with its type II and type I receptors (TβRII and TβRI) using isothermal titration calorimetry (ITC). Studies were carried out in acidic pH as it has great physiological relevance for TGFβ3 activity. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140485DOI Listing

d-serine regulation of the timing and architecture of the inspiratory burst in neonatal mice.

Biochim Biophys Acta Proteins Proteom 2020 Jul 8:140484. Epub 2020 Jul 8.

Facultad de Química y Biología, Departamento de Biología, Universidad de Santiago de Chile, USACH, PO 9170022, Santiago, Chile. Electronic address:

d-serine, released from mouse medullary astrocytes in response to increased CO levels, boosts the respiratory frequency to adapt breathing to physiological demands. We analyzed in mouse neonates, the influence of d-serine upon inspiratory/expiratory durations and the architecture of the inspiratory burst, assessed by pwelch's power spectrum density (PSD) and continuous wavelet transform (CWT) analyses. Suction electrode recordings were performed in slices from the ventral respiratory column (VRC), site of generation of the respiratory rhythm, and in brainstem-spinal cord (en bloc) preparations, from the C5 ventral roots, containing phrenic fibers that in vivo innervate and drive the diaphragm, the main inspiratory muscle. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140484DOI Listing

Analysis of Hashimoto's thyroiditis on fine needle aspiration samples by MALDI-Imaging.

Biochim Biophys Acta Proteins Proteom 2020 Jul 6:140481. Epub 2020 Jul 6.

Pathology, Department of Medicine and Surgery, University of Milano-Bicocca, San Gerardo Hospital, ASST, Monza, Italy. Electronic address:

Matrix-Assisted Laser Desorption/Ionization (MALDI)- Mass Spectrometry imaging (MSI) has been applied in various diseases aimed to biomarkers discovery. In this study diagnosis and prognosis of Hashimoto Thyroiditis (HT) in cytopathology by MALDI-MSI has been investigated. Specimens from a routine series of subjects who underwent UltraSound-guided thyroid Fine Needle Aspirations (FNAs) were used. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140481DOI Listing

d-Alanine: Distribution, origin, physiological relevance, and implications in disease.

Biochim Biophys Acta Proteins Proteom 2020 Jul 5:140482. Epub 2020 Jul 5.

Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, United States. Electronic address:

d-Alanine (d-Ala) is an unusual endogenous amino acid present in invertebrates and vertebrates. Compared to its l-isomer, the characterization of d-Ala is challenging because of the need for chiral resolution and the low amounts of the d-enantiomer present. With recent improvements in measurement capabilities, research on d-Ala, along with other d-amino acids, has been growing, especially as the functional significance of d-Ala in the mammalian nervous and endocrine systems is becoming known. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140482DOI Listing

Characterization of an NAD(P)-dependent meso-diaminopimelate dehydrogenase from Thermosyntropha lipolytica.

Biochim Biophys Acta Proteins Proteom 2020 Jun 26:140476. Epub 2020 Jun 26.

Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046, Japan. Electronic address:

meso-Diaminopimelate dehydrogenase (meso-DAPDH) catalyzes the reversible NADP-dependent oxidative deamination of meso-2,6-diaminopimelate (meso-DAP) to produce L-2-amino-6-oxopimelate. meso-DAPDH is divided into two major clusters, types I and II, based on substrate specificity and structural characteristic. Here, we describe a novel type II meso-DAPDH from Thermosyntropha lipolytica (TlDAPDH). Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140476DOI Listing

Post-translational modifications contribute to neoepitopes in Type-1 diabetes: Challenges for inducing antigen-specific tolerance.

Biochim Biophys Acta Proteins Proteom 2020 Jun 26;1868(10):140478. Epub 2020 Jun 26.

Department of Microbiology and Immunology, University of Illinois-College of Medicine, Chicago, IL, United States of America. Electronic address:

Type-1 Diabetes (T1D) is the major autoimmune disease affecting the juvenile population in which insulin-producing pancreatic β-cells are destroyed by self-reactive T-cells and B-cells. Emerging studies have identified the presence of autoantibodies and altered T-cell reactivity against several autoantigens in individuals who are at risk of developing T1D even before the clinical onset of diabetes. Whilst these findings could lead to the development of predictive biomarkers for early diagnosis, growing evidence on the generation of neoepitopes, epitope spreading and diverse antigen repertoire in T1D poses a major challenge for developing approaches to induce antigen-specific tolerance. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140478DOI Listing

Tyr-nitration in maize CDKA;1 results in lower affinity for ATP binding.

Biochim Biophys Acta Proteins Proteom 2020 Jun 26;1868(10):140479. Epub 2020 Jun 26.

Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química y Fisicoquímica Biológicas "Profesor Alejandro C. Paladini" (IQUIFIB), Facultad de Farmacia y Bioquímica, Buenos Aires, Argentina. Electronic address:

Cyclin-dependent kinase A (CDKA) is a key component for cell cycle progression. The catalytic kinase activity depends on the protein's ability to form an active complex with cyclins and on phosphoregulatory mechanisms. Cell cycle arrest and plant growth impairment under abiotic stress have been linked to different molecular processes triggered by increased levels of reactive oxygen and nitrogen species (ROS and RNS). Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140479DOI Listing

Influence of the conformations of αA-crystallin peptides on the isomerization rates of aspartic acid residues.

Biochim Biophys Acta Proteins Proteom 2020 Jun 26;1868(10):140480. Epub 2020 Jun 26.

Graduate School of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi 468-8503, Japan; Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan; Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan. Electronic address:

The isomerization rate of aspartic acid (Asp) residue is known to be affected by the three-dimensional structures of peptides and proteins. Although the isomerized Asp residues were experimentally observed, structural features which affect the isomerization cannot be elucidated sufficiently because of protein denaturation and aggregation. In this study, molecular dynamics (MD) simulations were conducted on three αA-crystallin peptides (T6, T10, and T18), each containing a single Asp residue with different isomerization rate (T18 > T6 > T10) to clarify the structural factors of Asp isomerization tendency. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140480DOI Listing

Predicting protein subcellular location with network embedding and enrichment features.

Biochim Biophys Acta Proteins Proteom 2020 Jun 25;1868(10):140477. Epub 2020 Jun 25.

School of Life Sciences, Shanghai University, Shanghai 200444, People's Republic of China. Electronic address:

The subcellular location of a protein is highly related to its function. Identifying the location of a given protein is an essential step for investigating its related problems. Traditional experimental methods can produce solid determination. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140477DOI Listing

Criticality in the conformational phase transition among self-similar groups in intrinsically disordered proteins: Probed by salt-bridge dynamics.

Biochim Biophys Acta Proteins Proteom 2020 Jun 21;1868(10):140474. Epub 2020 Jun 21.

Department of Microbiology, Asutosh College (affiliated to University of Calcutta), Kolkata 700026, India. Electronic address:

Intrinsically disordered proteins (IDP) serve as one of the key components in the global proteome. In contrast to globular proteins, they harbor an enormous amount of physical flexibility enforcing them to be retained in conformational ensembles rather than stable folds. Previous studies in an aligned direction have revealed the importance of transient dynamical phenomena like that of salt-bridge formation in IDPs to support their physical flexibility and have further highlighted their functional relevance. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140474DOI Listing

Insights into predicting diabetic nephropathy using urinary biomarkers.

Biochim Biophys Acta Proteins Proteom 2020 Jun 20;1868(10):140475. Epub 2020 Jun 20.

College of Life Science and Oceanography, Shenzhen University, Shenzhen 518060, PR China. Electronic address:

Diabetic nephropathy (DN) is a serious complication of diabetes caused by changes in the structure and function of the kidneys. It is important to detect diagnostic biomarkers of DN at an early stage, in which the drug can slow the loss of kidney function and prevent disease progression. In recent years, a variety of biological markers related to DN have been discovered, which is of great significance for predicting the occurrence and development of diseases. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140475DOI Listing

The effect of L-theanine and S-ketamine on d-serine cellular uptake.

Biochim Biophys Acta Proteins Proteom 2020 Jun 20;1868(10):140473. Epub 2020 Jun 20.

Department of Pharmacodynamics, Semmelweis University, 4 Nagyvárad tér, Budapest H-1089, Hungary. Electronic address:

Decreased extracellular level of d-Serine (D-Ser), a co-agonist of the N-methyl-d-aspartate (NMDA) receptors was connected to receptor hypofunction in the brain and the related deficit of cognitive functions. Extracellular D-Ser concentration is modulated by ASCT neutral amino acid transporters. L-Theanine (L-Tea), a neutral amino acid component of green tea was reported to improve cognitive functions. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140473DOI Listing

New insights on the influence of free d-aspartate metabolism in the mammalian brain during prenatal and postnatal life.

Biochim Biophys Acta Proteins Proteom 2020 Jun 16:140471. Epub 2020 Jun 16.

CEINGE Biotecnologie Avanzate, 80145 Naples, Italy; Department of Environmental, Biological and Pharmaceutical Science and Technologies, Università degli Studi della Campania "Luigi Vanvitelli", 81100 Caserta, Italy.

Free d-aspartate is abundant in the mammalian embryonic brain. However, following the postnatal onset of the catabolic d-aspartate oxidase (DDO) activity, cerebral d-aspartate levels drastically decrease, remaining constantly low throughout life. d-Aspartate stimulates both glutamatergic NMDA receptors (NMDARs) and metabotropic Glu5 receptors. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140471DOI Listing
June 2020
2.747 Impact Factor

Application of mass spectrometry based proteomics to understand diabetes: A special focus on interactomics.

Biochim Biophys Acta Proteins Proteom 2020 Jun 15;1868(10):140469. Epub 2020 Jun 15.

National Centre for Cell Science, Ganeshkhind, Pune 411007, MH, India. Electronic address:

Diabetes, a multifactorial disorder is characterized by elevated blood glucose levels resulting from changes in lifestyle, genetic and epigenetic changes or aberrations in proteome. In addition, alterations in post-translational modifications (PTMs) and protein-protein interactions (PPIs) also contribute to the development of diabetes pathogenesis. Recent advances in omics technologies have broadened the perspective for systematic investigation of proteome alterations in understanding the pathogenesis of diabetes. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140469DOI Listing

Biochemical characterization of mouse d-aspartate oxidase.

Biochim Biophys Acta Proteins Proteom 2020 Jun 14;1868(10):140472. Epub 2020 Jun 14.

"The Protein Factory 2.0", Dipartimento di Biotecnologie e Scienze della Vita, Università degli studi dell'Insubria, via J. H. Dunant 3, 21100 Varese, Italy; International Research Center on D-amino acids DAAIR, via Lepetit 34, 21040, Gerenzano (VA), Italy. Electronic address:

D-amino acids research field has recently gained an increased interest since these atypical molecules have been discovered to play a plethora of different roles. In the mammalian central nervous system, d-aspartate (D-Asp) is critically involved in the regulation of glutamatergic neurotransmission by acting as an agonist of NMDA receptor. Accordingly, alterations in its metabolism have been related to different pathologies. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140472DOI Listing
June 2020
2.747 Impact Factor

ESAT-6 regulates autophagous response through SOD-2 and as a result induces intracellular survival of Mycobacterium bovis BCG.

Biochim Biophys Acta Proteins Proteom 2020 Jun 11;1868(10):140470. Epub 2020 Jun 11.

Division of Microbiology and Academy of Scientific and Innovative Research, CSIR-Central, Drug Research Institute, Lucknow 226031, India. Electronic address:

Mycobacterium is known for subverting the host defense machinery, and one such mechanism is the inhibition of autophagy. Here, we have demonstrated that Mycobacterium tuberculosis (MTB) secretes a virulence factor; an early secretory antigenic target protein (ESAT-6) into the phagosome, which induces the expression and activity of mitochondrial superoxide dismutase (SOD-2) of macrophages. Using a series of experiments, and Mycobacterium bovis BCG as a model strain (where ESAT-6 protein is not expressed), we have delineated that the protein regulates SOD-2 of macrophages. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140470DOI Listing

The extended N-terminus of Mycobacterium smegmatis RecX potentiates its ability to antagonize RecA functions.

Biochim Biophys Acta Proteins Proteom 2020 Jun 9;1868(10):140468. Epub 2020 Jun 9.

Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, India. Electronic address:

The members of the RecX family of proteins have a unique capacity to regulate the catalytic activities of RecA/Rad51 proteins in both prokaryotic and eukaryotic organisms. However, our understanding of the functional roles of RecX in pathogenic and non-pathogenic mycobacteria has been limited by insufficient knowledge of the molecular mechanisms of its activity and regulation. Moreover, the significance of a unique 14 amino acid N-terminal extension in Mycobacterium smegmatis RecX (MsRecX) to its function remains unknown. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140468DOI Listing

Cathepsin regulation on microglial function.

Biochim Biophys Acta Proteins Proteom 2020 Sep 9;1868(9):140465. Epub 2020 Jun 9.

Department of Pharmacology, Faculty of Pharmacy, Yasuda Women's University, Hiroshima 731-0153, Japan. Electronic address:

Microglia, the resident mononuclear phagocyte population in the brain, have long been implicated in the pathology of neurodegenerative age-associated disorders. However, activated microglia have now been identified as homeostatic keepers in the brain, because they are involved in the initiation and resolution of neuropathology. The complex roles of activated microglia appear to be linked to change from inflammatory and neurotoxic to anti-inflammatory and neuroprotective phenotypes. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140465DOI Listing
September 2020

Characterization of soluble folate receptors (folate binding proteins) in humans. Biological roles and clinical potentials in infection and malignancy.

Biochim Biophys Acta Proteins Proteom 2020 Jun 9;1868(10):140466. Epub 2020 Jun 9.

Department of Clinical Biochemistry, Nordsjællands Hospital - Hillerød, University Hospital Copenhagen, Dyrehavevej 29, DK 3400 Hillerød, Denmark. Electronic address:

This review surveys soluble Folate Receptors (FOLRs) in humans. FOLR1 and FOLR2 are equipped with cellular glycosylphosphatidylinositol (GPI) anchors. FOLR1 is secreted from epithelia with or without a micelle-encapsulated GPI-anchor into milk and other body fluids/secretions, e. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140466DOI Listing

Degradation of thymic humoral factor γ2 in human, rat and mouse blood: An experimental and theoretical study.

Biochim Biophys Acta Proteins Proteom 2020 Sep 5;1868(9):140467. Epub 2020 Jun 5.

School of Biochemistry and Immunology, Trinity College, Dublin 2, Ireland. Electronic address:

The degradation of the immunomodulatory octapeptide, thymic humoral factor γ2 (THF-γ2, thymoctonan) has been studied in whole blood samples from human, rat and mouse. The peptide, Leu-Glu-Asp-Gly-Pro-Lys-Phe-Leu, was shown to be rapidly degraded by peptidases. The half-life of the intact peptide was less than 6 min at 37 °C in blood from the three species tested. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140467DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7274130PMC
September 2020

d-Amino acid oxidase deficiency is caused by a large deletion in the Dao gene in LEA rats.

Biochim Biophys Acta Proteins Proteom 2020 Sep 5;1868(9):140463. Epub 2020 Jun 5.

Department of Laboratory Animal Medicine, Research Institute, National Center for Global Health and Medicine (NCGM), 1-21-1 Toyama, Shinjuku, Tokyo 162-8655, Japan; Section of Animal Models, Department of Infectious Diseases, Research Institute, National Center for Global Health and Medicine (NCGM), 1-21-1 Toyama, Shinjuku, Tokyo 162-8655, Japan. Electronic address:

d-Amino acids, enantiomers of l-amino acids, are increasingly recognized as physiologically active molecules as well as potential biomarkers for diseases. d-Amino acid oxidase (DAO) catalyzes the oxidative deamination of d-amino acids and is present in a wide variety of organisms from yeasts to humans. Previous studies indicated that LEA rats lacked DAO activity, and levels of d-Ser and d-Ala were markedly increased in their tissues, suggesting a mutated locus responsible for the lack of Dao activity (ldao) existed in the LEA genome. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140463DOI Listing
September 2020

Distinct residual and disordered structures of alpha-synuclein analyzed by amide-proton exchange and NMR signal intensity.

Biochim Biophys Acta Proteins Proteom 2020 Sep 2;1868(9):140464. Epub 2020 Jun 2.

Faculty of Pharmaceutical Sciences, Teikyo Heisei University, Nakano, Tokyo 164-8530, Japan; Institute for Protein Research, Osaka University, Yamadaoka, Suita, Osaka 565-0871, Japan. Electronic address:

The residual solution structures of two alpha-synuclein mutants, A30P and A53T, observed in family members of patients with Parkinson's disease were compared with that of wild-type by NMR. The A53T substitution had been shown to accelerate fibril formation of alpha-synuclein, whereas the A30P mutation has the negative and positive effects on the formation of the fibril and spherical oligomer, respectively. The remaining structure was analyzed via amide-proton exchange and signal intensity measurements using NMR. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140464DOI Listing
September 2020

The NADP-dependent malic enzyme MaeB is a central metabolic hub controlled by the acetyl-CoA to CoASH ratio.

Biochim Biophys Acta Proteins Proteom 2020 Sep 30;1868(9):140462. Epub 2020 May 30.

Interfaculty Institute of Microbiology and Infection Medicine, Eberhard Karls University Tübingen, Germany.

Malic enzymes participate in key metabolic processes, the MaeB-like malic enzymes carry a catalytic inactive phosphotransacetylase domain whose function remains elusive. Here we show that acetyl-CoA directly binds and inhibits MaeB-like enzymes with a saturable profile under physiological relevant acetyl-CoA concentrations. A MaeB-like enzyme from the nitrogen-fixing bacterium Azospirillum brasilense, namely AbMaeB1, binds both acetyl-CoA and unesterified CoASH in a way that inhibition of AbMaeB1 by acetyl-CoA is relieved by increasing CoASH concentrations. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140462DOI Listing
September 2020

Enzymatic properties and physiological function of glutamate racemase from Thermus thermophilus.

Biochim Biophys Acta Proteins Proteom 2020 Sep 28;1868(9):140461. Epub 2020 May 28.

Institute of Environmental Microbiology, Kyowa Kako Co., 2-15-5 Tadao, Machida, Tokyo 194-0035, Japan. Electronic address:

d-Amino acids are physiologically important components of peptidoglycan in the bacterial cell wall, maintaining cell structure and aiding adaptation to environmental changes through peptidoglycan remodelling. Therefore, the biosynthesis of d-amino acids is essential for bacteria to adapt to different environmental conditions. The peptidoglycan of the extremely thermophilic bacterium Thermus thermophilus contains d-alanine (d-Ala) and d-glutamate (d-Glu), but its d-amino acid metabolism remains poorly understood. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140461DOI Listing
September 2020

Mechanism of eukaryotic serine racemase-catalyzed serine dehydration.

Biochim Biophys Acta Proteins Proteom 2020 Sep 29;1868(9):140460. Epub 2020 May 29.

Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furou-chou, Chikusa, Nagoya, Aichi 464-8601, Japan. Electronic address:

Eukaryotic serine racemase (SR) is a pyridoxal 5'-phosphate enzyme belonging to the Fold-type II group, which catalyzes serine racemization and is responsible for the synthesis of D-Ser, a co-agonist of the N-methyl-d-aspartate receptor. In addition to racemization, SR catalyzes the dehydration of D- and L-Ser to pyruvate and ammonia. The bifuctionality of SR is thought to be important for D-Ser homeostasis. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140460DOI Listing
September 2020

Genetic variants entail type 2 diabetes as an innate immune disorder.

Biochim Biophys Acta Proteins Proteom 2020 Sep 29;1868(9):140458. Epub 2020 May 29.

Academy of Scientific and Innovative Research, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110020, India; Systems Genomics Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India. Electronic address:

Type 2 Diabetes (T2D) is characterized by alteration in the circulatory levels of key inflammatory proteins, where our body strives to eliminate the perturbing factor through inflammation as a final resort to restore homeostasis. Plasma proteins play a crucial role to orchestrate this immune response. Over the past two decades, rigorous genetic efforts taken to comprehend T2D physiology have been partially successful and have left behind a dearth of knowledge of its causality. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140458DOI Listing
September 2020

Computational studies on nonenzymatic succinimide-formation mechanisms of the aspartic acid residues catalyzed by two water molecules.

Biochim Biophys Acta Proteins Proteom 2020 Sep 29;1868(9):140459. Epub 2020 May 29.

Graduate School of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi 468-8503, Japan; Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan; Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan. Electronic address:

In the biological proteins, aspartic acid (Asp) residues are prone to nonenzymatic isomerization via a succinimide (Suc) intermediate. Asp-residue isomerization causes the aggregation and the insolubilization of proteins, and is considered to be involved in various age-related diseases. Although Suc intermediate was considered to be formed by nucleophilic attack of the main-chain amide nitrogen of N-terminal side adjacent residue to the side-chain carboxyl carbon of Asp residue, previous studies have shown that the nucleophilic attack is more likely to proceed via iminol tautomer when the water molecules act as catalysts. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140459DOI Listing
September 2020

Differential cleavage of viral polypeptides by allotypic variants of granzyme B skews immunity to mouse cytomegalovirus.

Biochim Biophys Acta Proteins Proteom 2020 Sep 27;1868(9):140457. Epub 2020 May 27.

Rosie Lew Cancer Immunology Program, Peter MacCallum Cancer Centre, 305 Grattan Street Melbourne 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne 3050, Australia. Electronic address:

We investigated the molecular basis for the remarkably different survival outcomes of mice expressing different alloforms of the pro-apoptotic serine protease granzyme B to mouse cytomegalovirus infection. Whereas C57BL/6 mice homozygous for granzyme B (GzmB) raise cytotoxic T lymphocytes that efficiently kill infected cells, those of C57BL/6 mice congenic for the outbred allele (GzmB) fail to kill MCMV-infected cells and died from uncontrolled hepatocyte infection and acute liver failure. We identified subtle differences in how GzmB and GzmB activate cell death signalling - both alloforms predominantly activated pro-caspases directly, and cleaved pro-apoptotic Bid poorly. Read More

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http://dx.doi.org/10.1016/j.bbapap.2020.140457DOI Listing
September 2020

Utility of d-serine monitoring in kidney disease.

Biochim Biophys Acta Proteins Proteom 2020 Sep 22;1868(9):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
September 2020

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 Sep 20;1868(9):140448. Epub 2020 May 20.

Institute of Biochemistry & Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada. 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
September 2020
2.747 Impact Factor

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

Biochim Biophys Acta Proteins Proteom 2020 Sep 20;1868(9):140447. Epub 2020 May 20.

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
September 2020

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

Biochim Biophys Acta Proteins Proteom 2020 Sep 19;1868(9):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
September 2020

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

Biochim Biophys Acta Proteins Proteom 2020 Aug 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 Sep 13;1868(9):140443. Epub 2020 May 13.

Center for Dementia Research, Nathan S. Kline Institute, 140 Old Orangeburg Road, Orangeburg, NY 10962, USA; Department of Psychiatry, New York University Langone Medical Center, 550 First Ave, New York, NY 10016, USA; Department of Cell Biology, New York University Langone Medical Center, 550 First Ave, New York, NY 10016, USA; Department of 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
September 2020

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

Biochim Biophys Acta Proteins Proteom 2020 Sep 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
September 2020

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

Biochim Biophys Acta Proteins Proteom 2020 Aug 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 Aug 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 Aug 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 Aug 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 Aug 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 Aug 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 Aug 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 Aug 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
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7261628PMC

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 Aug 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 Aug 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 07 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 07 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 07 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 07 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 07 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