63 results match your criteria Bioscience biotechnology and biochemistry[Journal]


Allosteric Regulation of Chromatin-Modifying Enzymes.

Biochemistry 2019 Jan 29;58(1):15-23. Epub 2018 Oct 29.

Department of Biological Sciences , Korea Advanced Institute of Science and Technology , Daejeon 34141 , South Korea.

Dynamic changes in chromatin structure are crucial for diverse biological processes. Given the complexity of the epigenetic landscape, understanding the specificity of chromatin modification has been a major interest in the epigenetics field. Recent progress in biochemical and structural analyses in the field of chromatin biology has revealed that recognition of allosteric effectors and the subsequent conformational change(s) are central to the regulation of catalytic activities and functions of chromatin-modifying enzymes. Read More

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http://pubs.acs.org/doi/10.1021/acs.biochem.8b00894
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http://dx.doi.org/10.1021/acs.biochem.8b00894DOI Listing
January 2019
7 Reads

Photoirradiation Generates an Ultrastable 8-Formyl FAD Semiquinone Radical with Unusual Properties in Formate Oxidase.

Biochemistry 2018 Oct 27;57(40):5818-5826. Epub 2018 Sep 27.

School of Chemical and Biomolecular Engineering , Georgia Institute of Technology , Atlanta , Georgia 30332-0100 , United States.

Formate oxidase (FOX) was previously shown to contain a noncovalently bound 8-formyl FAD (8-fFAD) cofactor. However, both the absorption spectra and the kinetic parameters previously reported for FOX are inconsistent with more recent reports. The ultraviolet-visible (UV-vis) absorption spectrum reported in early studies closely resembles the spectra observed for protein-bound 8-formyl flavin semiquinone species, thus suggesting FOX may be photosensitive. Read More

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http://pubs.acs.org/doi/10.1021/acs.biochem.8b00571
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http://dx.doi.org/10.1021/acs.biochem.8b00571DOI Listing
October 2018
4 Reads

Structure of the K82 Capsular Polysaccharide from Acinetobacter baumannii LUH5534 Containing a d-Galactose 4,6-Pyruvic Acid Acetal.

Biochemistry (Mosc) 2018 Jul;83(7):831-835

School of Molecular Bioscience, The University of Sydney, Sydney, NSW 2006, Australia.

Type K82 capsular polysaccharide (CPS) was isolated from Acinetobacter baumannii LUH5534. The structure of a linear tetrasaccharide repeating unit of the CPS was established by sugar analysis along with one- and two-dimensional H and C NMR spectroscopy. Proteins encoded by the KL82 capsule gene cluster in the genome of LUH5534 were assigned to roles in the synthesis of the K82 CPS. Read More

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http://dx.doi.org/10.1134/S0006297918070064DOI Listing
July 2018
1 Read

Tyr51: Key Determinant of the Low Thermostability of the Colwellia psychrerythraea Cold-Shock Protein.

Biochemistry 2018 07 18;57(26):3625-3640. Epub 2018 May 18.

Department of Bioscience and Biotechnology , Konkuk University , Seoul 05029 , Republic of Korea.

Cold-shock proteins (Csps) are expressed at lower-than-optimum temperatures, and they function as RNA chaperones; however, no structural studies on psychrophilic Csps have been reported. Here, we aimed to investigate the structure and dynamics of the Csp of psychrophile Colwellia psychrerythraea 34H, ( Cp-Csp). Although Cp-Csp shares sequence homology, common folding patterns, and motifs, including a five β-stranded barrel, with its thermophilic counterparts, its thermostability (37 °C) was markedly lower than those of other Csps. Read More

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http://pubs.acs.org/doi/10.1021/acs.biochem.8b00144
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http://dx.doi.org/10.1021/acs.biochem.8b00144DOI Listing
July 2018
6 Reads

Tissue Inhibitor of Metalloprotease-2 (TIMP-2): Bioprocess Development, Physicochemical, Biochemical, and Biological Characterization of Highly Expressed Recombinant Protein.

Biochemistry 2017 Dec 28;56(49):6423-6433. Epub 2017 Nov 28.

Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute , Bethesda, Maryland 20892, United States.

Tissue inhibitor of metalloprotease-2 (TIMP-2) is a secreted 21 kDa multifunctional protein first described as an endogenous inhibitor of matrix metalloproteinases (MMPs) that prevents breakdown of the extracellular matrix often observed in chronic diseases. TIMP-2 diminishes the level of growth factor-mediated cell proliferation in vitro, as well as neoangiogenesis and tumor growth in vivo independent of its MMP inhibitory activity. These physiological properties make TIMP-2 an excellent candidate for further preclinical development as a biologic therapy of cancer. Read More

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http://dx.doi.org/10.1021/acs.biochem.7b00700DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6322544PMC
December 2017
1 Read

Gene Regulation and Signal Transduction in the ICE-CBF-COR Signaling Pathway during Cold Stress in Plants.

Biochemistry (Mosc) 2017 Oct;82(10):1103-1117

College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, 110866, China.

Low temperature is an abiotic stress that adversely affects the growth and production of plants. Resistance and adaptation of plants to cold stress is dependent upon the activation of molecular networks and pathways involved in signal transduction and the regulation of cold-stress related genes. Because it has numerous and complex genes, regulation factors, and pathways, research on the ICE-CBF-COR signaling pathway is the most studied and detailed, which is thought to be rather important for cold resistance of plants. Read More

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http://dx.doi.org/10.1134/S0006297917100030DOI Listing
October 2017
5 Reads

CrMAPK3 regulates the expression of iron-deficiency-responsive genes in Chlamydomonas reinhardtii.

BMC Biochem 2017 05 16;18(1). Epub 2017 May 16.

Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Haikou, 571101, China.

Background: Under iron-deficient conditions, Chlamydomonas exhibits high affinity for iron absorption. Nevertheless, the response, transmission, and regulation of downstream gene expression in algae cells have not to be investigated. Considering that the MAPK pathway is essential for abiotic stress responses, we determined whether this pathway is involved in iron deficiency signal transduction in Chlamydomonas. Read More

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http://dx.doi.org/10.1186/s12858-017-0081-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5434638PMC
May 2017
35 Reads

Conformational Changes in Active and Inactive States of Human PP2Cα Characterized by Hydrogen/Deuterium Exchange-Mass Spectrometry.

Biochemistry 2017 05 12;56(21):2676-2689. Epub 2017 May 12.

Bioprocess Measurement Group, Biomolecular Measurement Division, National Institute of Standards and Technology , Gaithersburg, Maryland 20899, United States.

PPM serine/threonine protein phosphatases function in signaling pathways and require millimolar concentrations of Mn or Mg ions for activity. Whereas the crystal structure of human PP2Cα displayed two tightly bound Mn ions in the active site, recent investigations of PPM phosphatases have characterized the binding of a third, catalytically essential metal ion. The binding of the third Mg to PP2Cα was reported to have millimolar affinity and to be entropically driven, suggesting it may be structurally and catalytically important. Read More

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http://dx.doi.org/10.1021/acs.biochem.6b01220DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5593270PMC
May 2017
8 Reads

Neutron and Atomic Resolution X-ray Structures of a Lytic Polysaccharide Monooxygenase Reveal Copper-Mediated Dioxygen Binding and Evidence for N-Terminal Deprotonation.

Biochemistry 2017 05 11;56(20):2529-2532. Epub 2017 May 11.

Protein Crystallography Station, Bioscience Division, Los Alamos National Laboratory , Los Alamos, New Mexico 87545, United States.

A 1.1 Å resolution, room-temperature X-ray structure and a 2.1 Å resolution neutron structure of a chitin-degrading lytic polysaccharide monooxygenase domain from the bacterium Jonesia denitrificans (JdLPMO10A) show a putative dioxygen species equatorially bound to the active site copper. Read More

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http://dx.doi.org/10.1021/acs.biochem.7b00019DOI Listing
May 2017
32 Reads

Inhibition of α-Synuclein Fibril Elongation by Hsp70 Is Governed by a Kinetic Binding Competition between α-Synuclein Species.

Biochemistry 2017 03 23;56(9):1177-1180. Epub 2017 Feb 23.

Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Unit BIFI-IQFR (CSIC), University of Zaragoza , 50018 Zaragoza, Spain.

The Hsp70 family of chaperones plays an essential role in suppressing protein aggregation in the cell. Here we investigate the factors controlling the intrinsic ability of human Hsp70 to inhibit the elongation of amyloid fibrils formed by the Parkinson's disease-related protein α-synuclein. Using kinetic analysis, we show that Hsp70 binds preferentially to α-synuclein fibrils as a consequence of variations in the association and dissociation rate constants of binding to the different aggregated states of the protein. Read More

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http://dx.doi.org/10.1021/acs.biochem.6b01178DOI Listing
March 2017
21 Reads

Short Carboxylic Acid-Carboxylate Hydrogen Bonds Can Have Fully Localized Protons.

Biochemistry 2017 Jan 30;56(2):391-402. Epub 2016 Dec 30.

Department of Biochemistry and Redox Biology Center, University of Nebraska , Lincoln, Nebraska 68588, United States.

Short hydrogen bonds (H-bonds) have been proposed to play key functional roles in several proteins. The location of the proton in short H-bonds is of central importance, as proton delocalization is a defining feature of low-barrier hydrogen bonds (LBHBs). Experimentally determining proton location in H-bonds is challenging. Read More

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http://dx.doi.org/10.1021/acs.biochem.6b00906DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5805389PMC
January 2017
19 Reads

Structural Basis for Excision of 5-Formylcytosine by Thymine DNA Glycosylase.

Biochemistry 2016 Nov 2;55(45):6205-6208. Epub 2016 Nov 2.

Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine , Baltimore, Maryland 21201, United States.

Thymine DNA glycosylase (TDG) is a base excision repair enzyme with key functions in epigenetic regulation. Performing a critical step in a pathway for active DNA demethylation, TDG removes 5-formylcytosine and 5-carboxylcytosine, oxidized derivatives of 5-methylcytosine that are generated by TET (ten-eleven translocation) enzymes. We determined a crystal structure of TDG bound to DNA with a noncleavable (2'-fluoroarabino) analogue of 5-formyldeoxycytidine flipped into its active site, revealing how it recognizes and hydrolytically excises fC. Read More

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http://dx.doi.org/10.1021/acs.biochem.6b00982DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5148694PMC
November 2016
1 Read

Crystal Structures of SgcE6 and SgcC, the Two-Component Monooxygenase That Catalyzes Hydroxylation of a Carrier Protein-Tethered Substrate during the Biosynthesis of the Enediyne Antitumor Antibiotic C-1027 in Streptomyces globisporus.

Biochemistry 2016 09 1;55(36):5142-54. Epub 2016 Sep 1.

Department of Chemistry, The Scripps Research Institute , Jupiter, Florida 33458, United States.

C-1027 is a chromoprotein enediyne antitumor antibiotic produced by Streptomyces globisporus. In the last step of biosynthesis of the (S)-3-chloro-5-hydroxy-β-tyrosine moiety of the C-1027 enediyne chromophore, SgcE6 and SgcC compose a two-component monooxygenase that hydroxylates the C-5 position of (S)-3-chloro-β-tyrosine. This two-component monooxygenase is remarkable for two reasons. Read More

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http://dx.doi.org/10.1021/acs.biochem.6b00713DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5024704PMC
September 2016
16 Reads

Hyperstabilization of Tetrameric Bacillus sp. TB-90 Urate Oxidase by Introducing Disulfide Bonds through Structural Plasticity.

Biochemistry 2016 Feb 15;55(4):724-32. Epub 2016 Jan 15.

Tsuruga Institute for Biotechnology, Toyobo Company Ltd. , Tsuruga, Fukui 914-0047, Japan.

Bacillus sp. TB-90 urate oxidase (BTUO) is one of the most thermostable homotetrameric enzymes. We previously reported [Hibi, T. Read More

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http://dx.doi.org/10.1021/acs.biochem.5b01119DOI Listing
February 2016
37 Reads

Diol Dehydratase-Reactivase Is Essential for Recycling of Coenzyme B12 in Diol Dehydratase.

Biochemistry 2016 Jan 24;55(1):69-78. Epub 2015 Dec 24.

Department of Bioscience and Biotechnology, Graduate School of Natural Science and Technology, Okayama University , Tsushima-naka, Kita-ku, Okayama 700-8530, Japan.

Holoenzymes of adenosylcobalamin-dependent diol and glycerol dehydratases undergo mechanism-based inactivation by glycerol and O2 inactivation in the absence of substrate, which accompanies irreversible cleavage of the coenzyme Co-C bond. The inactivated holodiol dehydratase and the inactive enzyme·cyanocobalamin complex were (re)activated by incubation with NADH, ATP, and Mg(2+) (or Mn(2+)) in crude extracts of Klebsiella oxytoca, suggesting the presence of a reactivating system in the extract. The reducing system with NADH could be replaced by FMNH2. Read More

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http://dx.doi.org/10.1021/acs.biochem.5b01023DOI Listing
January 2016
5 Reads

Structure-Free Validation of Residual Dipolar Coupling and Paramagnetic Relaxation Enhancement Measurements of Disordered Proteins.

Biochemistry 2015 Nov 11;54(46):6876-86. Epub 2015 Nov 11.

Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, U.K.

Residual dipolar couplings (RDCs) and paramagnetic relaxation enhancements (PREs) have emerged as valuable parameters for defining the structures and dynamics of disordered proteins by nuclear magnetic resonance (NMR) spectroscopy. Procedures for their measurement, however, may lead to conformational perturbations because of the presence of the alignment media necessary for recording RDCs, or of the paramagnetic groups that must be introduced for measuring PREs. We discuss here experimental methods for quantifying these effects by considering the case of the 40-residue isoform of the amyloid β peptide (Aβ40), which is associated with Alzheimer's disease. Read More

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http://www-vendruscolo.ch.cam.ac.uk/newby2015b.pdf
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http://pubs.acs.org/doi/10.1021/acs.biochem.5b00670
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http://dx.doi.org/10.1021/acs.biochem.5b00670DOI Listing
November 2015
8 Reads

ATP Hydrolysis in the RecA-DNA Filament Promotes Structural Changes at the Protein-DNA Interface.

Biochemistry 2015 Aug 27;54(30):4579-82. Epub 2015 Jul 27.

‡Department of Chemical and Biological Engineering, Physical Chemistry, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden.

To address the mechanistic roles of ATP hydrolysis in RecA-promoted strand exchange reaction in homologous recombination, quantum mechanical calculations are performed on key parts of the RecA-DNA complex. We find that ATP hydrolysis may induce changes at the protein-DNA interface, resulting in the rearrangement of the hydrogen bond network connecting the ATP and the DNA binding sites. Read More

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http://dx.doi.org/10.1021/acs.biochem.5b00614DOI Listing
August 2015
2 Reads

Identification, Characterization, and Three-Dimensional Structure of the Novel Circular Bacteriocin, Enterocin NKR-5-3B, from Enterococcus faecium.

Biochemistry 2015 Aug 31;54(31):4863-76. Epub 2015 Jul 31.

†Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan.

Enterocin NKR-5-3B, one of the multiple bacteriocins produced by Enterococcus faecium NKR-5-3, is a 64-amino acid novel circular bacteriocin that displays broad-spectrum antimicrobial activity. Here we report the identification, characterization, and three-dimensional nuclear magnetic resonance solution structure determination of enterocin NKR-5-3B. Enterocin NKR-5-3B is characterized by four helical segments that enclose a compact hydrophobic core, which together with its circular backbone impart high stability and structural integrity. Read More

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http://dx.doi.org/10.1021/acs.biochem.5b00196DOI Listing
August 2015
11 Reads

Peptoid-Substituted Hybrid Antimicrobial Peptide Derived from Papiliocin and Magainin 2 with Enhanced Bacterial Selectivity and Anti-inflammatory Activity.

Biochemistry 2015 Jun 17;54(25):3921-31. Epub 2015 Jun 17.

†Department of Bioscience and Biotechnology, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701, Korea.

Antimicrobial peptides (AMPs) are important components of the host innate immune system. Papiliocin is a 37-residue AMP purified from larvae of the swallowtail butterfly Papilio xuthus. Magainin 2 is a 23-residue AMP purified from the skin of the African clawed frog Xenopus laevis. Read More

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http://dx.doi.org/10.1021/acs.biochem.5b00392DOI Listing
June 2015
21 Reads

Investigating the Structural Variability and Binding Modes of the Glioma Targeting NFL-TBS.40-63 Peptide on Tubulin.

Biochemistry 2015 Jun 4;54(23):3660-9. Epub 2015 Jun 4.

†Laboratoire de Biochimie Théorique, UPR 9080 CNRS Institut de Biologie Physico-Chimique,13 rue Pierre et Marie Curie, 75005 Paris, France.

NFL-TBS.40-63 is a 24 amino acid peptide corresponding to the tubulin-binding site located on the light neurofilament subunit, which selectively enters glioblastoma cells, where it disrupts their microtubule network and inhibits their proliferation. We investigated its structural variability and binding modes on a tubulin heterodimer using a combination of NMR experiments, docking, and molecular dynamics (MD) simulations. Read More

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http://dx.doi.org/10.1021/acs.biochem.5b00146DOI Listing
June 2015
6 Reads

Structure and backbone dynamics of vanadate-bound PRL-3: comparison of 15N nuclear magnetic resonance relaxation profiles of free and vanadate-bound PRL-3.

Biochemistry 2014 Jul 14;53(29):4814-25. Epub 2014 Jul 14.

Department of Bioscience and Biotechnology and BioMolecular Informatics Center, Konkuk University , Seoul 143-701, South Korea.

Phosphatases of regenerating liver (PRLs) constitute a novel class of small, prenylated phosphatases with oncogenic activity. PRL-3 is particularly important in cancer metastasis and represents a potential therapeutic target. The flexibility of the WPD loop as well as the P-loop of protein tyrosine phosphatases is closely related to their catalytic activity. Read More

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http://dx.doi.org/10.1021/bi5003844DOI Listing
July 2014
21 Reads

Catalytic roles of substrate-binding residues in coenzyme B12-dependent ethanolamine ammonia-lyase.

Biochemistry 2014 Apr 15;53(16):2661-71. Epub 2014 Apr 15.

Department of Bioscience and Biotechnology, Graduate School of Natural Science and Technology, Okayama University , Tsushima-naka, Kita-ku, Okayama 700-8530, Japan.

Ethanolamine ammonia-lyase (EAL) catalyzes the adenosylcobalamin-dependent conversion of ethanolamine to acetaldehyde and ammonia. 1-OH of the substrate is hydrogen-bonded with Gluα287, Argα160, and Asnα193 and 2-NH2 with Gluα287, Glnα162, and Aspα362. The active site somewhat resembles that of diol dehydratase. Read More

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http://dx.doi.org/10.1021/bi500223kDOI Listing
April 2014
3 Reads

Relationship between structural flexibility and function in the C-terminal region of the heparin-binding domain of VEGF165.

Biochemistry 2013 Dec 27;52(49):8823-32. Epub 2013 Nov 27.

Department of Bioscience and Biotechnology and Bio/Molecular Informatics Center, Institute of KU Biotechnology, Konkuk University , Seoul 143-701, Korea.

Vascular endothelial growth factor (VEGF) is an angiogenic protein with neurotrophic and neuroprotective effects. Previously, we reported that triamterene (Trm) inhibits VEGF-amyloid β (Aβ) interactions without affecting other biological activities of VEGF or Aβ [Jeong, K.-W. Read More

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http://dx.doi.org/10.1021/bi4011682DOI Listing
December 2013
37 Reads

Essential roles of nucleotide-switch and metal-coordinating residues for chaperone function of diol dehydratase-reactivase.

Biochemistry 2013 Dec 14;52(48):8677-86. Epub 2013 Nov 14.

Department of Bioscience and Biotechnology, Graduate School of Natural Science and Technology, Okayama University , Tsushima-naka, Kita-ku, Okayama 700-8530, Japan.

Diol dehydratase-reactivase (DD-R) is a molecular chaperone that reactivates inactivated holodiol dehydratase (DD) by cofactor exchange. Its ADP-bound and ATP-bound forms are high-affinity and low-affinity forms for DD, respectively. Among DD-Rs mutated at the nucleotide-binding site, neither the Dα8N nor Dα413N mutant was effective as a reactivase. Read More

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http://dx.doi.org/10.1021/bi401290jDOI Listing
December 2013
1 Read

Structural and dynamic features of cold-shock proteins of Listeria monocytogenes, a psychrophilic bacterium.

Biochemistry 2013 Apr 1;52(14):2492-504. Epub 2013 Apr 1.

Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University, Seoul 143-701, South Korea.

Cold-shock proteins (Csps), proteins expressed when the ambient temperature drops below the growth-supporting temperature, bind to single-stranded nucleic acids and act as RNA chaperones to regulate translation. Listeria monocytogenes is a psychrophilic food-borne pathogen that is problematic for the food industry. Structures of Csps from psychrophilic bacteria have not yet been studied. Read More

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http://pubs.acs.org/doi/10.1021/bi301641b
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http://dx.doi.org/10.1021/bi301641bDOI Listing
April 2013
2 Reads

Structure and activity of PA5508, a hexameric glutamine synthetase homologue.

Biochemistry 2012 Dec 12;51(51):10121-3. Epub 2012 Dec 12.

Institute for Bioscience and Biotechnology Research, University of Maryland, MD, USA.

The structure of PA5508 from Pseudomonas aeruginosa, a glutamine synthetase (GS) homologue, has been determined at 2.5 Å. Surprisingly, PA5508 forms single hexameric rings rather than the stacked double rings that are characteristic of GS. Read More

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http://dx.doi.org/10.1021/bi3014856DOI Listing
December 2012

Structure of aminodeoxychorismate synthase from Stenotrophomonas maltophilia.

Biochemistry 2012 Dec 11;51(51):10208-17. Epub 2012 Dec 11.

Institute for Bioscience and Biotechnology Research, University of Maryland, MD, USA.

PabB, aminodeoxychorismate synthase, is the chorismic acid binding component of the heterodimeric PabA-PabB complex that converts chorismic acid to 4-amino-4-deoxychorismate, a precursor of p-aminobenzoate and folic acid in microorganisms. The second component, a glutamine amidotransferase subunit, PabA, generates ammonia that is channeled to the PabB active site where it attacks C4 of a chorismate-derived intermediate that is covalently bound, through C2, to an active site lysine residue. The presence of a PIKGT motif was, until recently, believed to allow discrimination of PabB enzymes from the closely related enzyme anthranilate synthase, which typically contains a PIAGT active site motif and does not form a covalent enzyme-substrate intermediate with chorismate. Read More

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http://dx.doi.org/10.1021/bi301243vDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3532939PMC
December 2012
3 Reads

Dynamics of a heparin-binding domain of VEGF(165) complexed with its inhibitor triamterene.

Biochemistry 2011 Jun 13;50(22):4843-54. Epub 2011 May 13.

Department of Bioscience and Biotechnology and Bio/Molecular Informatics Center, Konkuk University, Seoul 143-701, Korea.

Vascular endothelial growth factor (VEGF), which has neurotrophic and neuroprotective effects in addition to its major role in angiogenesis, interacts with Aβ and accumulates in the senile plaques of Alzheimer's disease (AD) patients' brains. It is known that Aβ binds to the heparin-binding domain (HBD) of the 165-amino acid VEGF variant, VEGF(165). In this study, we showed that triamterene (Trm) inhibits VEGF--Aβ interaction without affecting other biological activities of VEGF or Aβ. Read More

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http://dx.doi.org/10.1021/bi2000752DOI Listing
June 2011
2 Reads

Temperature- and time-dependent changes in the structure and composition of glycolipids during the growth of the green sulfur photosynthetic bacterium Chlorobaculum tepidum.

Biochemistry 2011 May 4;50(21):4504-12. Epub 2011 May 4.

Department of Bioscience and Biotechnology, Faculty of Science and Engineering, Ritsumeikan University, Kusatsu, Shiga, Japan.

The green sulfur photosynthetic bacterium Chlorobaculum (Cba.) tepidum (previously known as Chlorobium tepidum), which grows at an optimal temperature of around 45 °C, biosynthesized unique disaccharide rhamnosylgalactosyldiacylglyceride (RGDG) having a methylene-bridged palmitoleyl (17:Cyc) and a palmitoyl group (16:0) as the two acyl chains in a molecule [RGDG(17:Cyc,16:0)], together with the corresponding monosaccharide monogalactosyldiacylglyceride (MGDG). Here, we report changes in the structure and composition of the glycolipids that are dependent upon the temperature and period of cultivation. Read More

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http://dx.doi.org/10.1021/bi2002339DOI Listing
May 2011
4 Reads

Biochemical and physiological characterization of a BLUF protein-EAL protein complex involved in blue light-dependent degradation of cyclic diguanylate in the purple bacterium Rhodopseudomonas palustris.

Biochemistry 2010 Dec 23;49(50):10647-55. Epub 2010 Nov 23.

Graduate School of Bioscience and Biotechnology, Tokyo Institute ofTechnology, Yokohama 226-8501, Japan.

Organisms adapt their physiologies in response to the quality and quantity of environmental light. Members of a recently identified photoreceptor protein family, BLUF domain proteins, use a flavin chromophore to sense blue light. Herein, we report that PapB, which contains a BLUF domain, controls the biofilm formation of the purple photosynthetic bacterium Rhodopseudomonas palustris. Read More

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http://pubs.acs.org/doi/abs/10.1021/bi101448t
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http://dx.doi.org/10.1021/bi101448tDOI Listing
December 2010
9 Reads

Assessing energetic contributions to binding from a disordered region in a protein-protein interaction .

Biochemistry 2010 Nov;49(43):9256-68

W. M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA.

Many functional proteins are at least partially disordered prior to binding. Although the structural transitions upon binding of disordered protein regions can influence the affinity and specificity of protein complexes, their precise energetic contributions to binding are unknown. Here, we use a model protein-protein interaction system in which a locally disordered region has been modified by directed evolution to quantitatively assess the thermodynamic and structural contributions to binding of disorder-to-order transitions. Read More

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http://dx.doi.org/10.1021/bi1008968DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2964404PMC
November 2010
4 Reads

A biosensor study indicating that entropy, electrostatics, and receptor glycosylation drive the binding interaction between interleukin-7 and its receptor.

Authors:
Scott T R Walsh

Biochemistry 2010 Oct 15;49(40):8766-78. Epub 2010 Sep 15.

Department of Cell Biology and Molecular Genetics, Institute for Bioscience and Biotechnology Research, W. M. Keck Laboratory for Structural Biology, University of Maryland, 9600 Gudelsky Drive, Rockville, Maryland 20850, USA.

The interaction between interleukin-7 (IL-7) and its α-receptor, IL-7Rα, plays fundamental roles in the development, survival, and homeostasis of B- and T-cells. N-Linked glycosylation of human IL-7Rα enhances its binding affinity for human IL-7 300-fold versus that of the nonglycosylated receptor through an allosteric mechanism. The N-glycans of IL-7Rα do not participate directly in the binding interface with IL-7. Read More

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http://dx.doi.org/10.1021/bi101050hDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3005950PMC
October 2010
2 Reads

Coenzyme B12-dependent diol dehydratase is a potassium ion-requiring calcium metalloenzyme: evidence that the substrate-coordinated metal ion is calcium.

Biochemistry 2010 Aug;49(33):7210-7

Department of Bioscience and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan.

The X-ray analyses of coenzyme B(12)-dependent diol dehydratase revealed two kinds of electron densities that correspond to metal ions in the active site. One is directly coordinated by substrate [Shibata, N., et al. Read More

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http://dx.doi.org/10.1021/bi100561mDOI Listing
August 2010
1 Read

Structural changes of horse heart ferricytochrome C induced by changes of ionic strength and anion binding.

Biochemistry 2008 May 12;47(18):5250-7. Epub 2008 Apr 12.

Department of Bioscience and Biotechnology, Drexel University, Philadelphia, Pennsylvania 19104, USA.

To test the validity of the notion that changes in ionic strength and ion binding do not cause any major functionally relevant structural changes in cytochrome c, we measured the absorption and electronic circular dichroism (ECD) of horse heart ferricytochrome c for the Soret and 695 nm charge-transfer band as a function of dihydrogen phosphate and sodium acetate concentrations. This band is known to probe the integrity of the functionally pivotal Fe3+-M80 linkage. Spectral changes indicate that an ionic strength increase (via an increasing acetate ion concentration) affects only a subset of conformational substates of the Fe-M80 interface, probed by the 695 nm charge-transfer band, without a substantial modification of the heme environment. Read More

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http://dx.doi.org/10.1021/bi702492nDOI Listing
May 2008
3 Reads

Histidine-alpha143 assists 1,2-hydroxyl group migration and protects radical intermediates in coenzyme B12-dependent diol dehydratase.

Biochemistry 2008 Mar 9;47(10):3162-73. Epub 2008 Feb 9.

Department of Bioscience and Biotechnology, Faculty of Engineering, Okayama University, Tsushima-Naka, Okayama 700-8530, Japan.

Diol dehydratase of Klebsiella oxytoca contains an essential histidine residue. Its X-ray structure revealed that the migrating hydroxyl group on C2 of substrate is hydrogen-bonded to Hisalpha143. Mutant enzymes in which Hisalpha143 was mutated to another amino acid residue were expressed in Escherichia coli, purified, and examined for enzymatic activity. Read More

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http://dx.doi.org/10.1021/bi7018095DOI Listing
March 2008
1 Read

Quantitative structure--activity relationship analysis and molecular dynamics simulation to functionally validate nonsynonymous polymorphisms of human ABC transporter ABCB1 (P-glycoprotein/MDR1).

Biochemistry 2007 Jul 9;46(26):7678-93. Epub 2007 Jun 9.

Department of Biomolecular Engineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan.

Several preclinical and clinical studies suggest the importance of naturally occurring polymorphisms of drug transporters in the individual difference of drug response. To functionally validate the nonsynonymous polymorphisms of ABCB1 (P-glycoprotein/MDR1) in vitro, we generated SNP variant forms (i.e. Read More

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http://dx.doi.org/10.1021/bi700330bDOI Listing
July 2007
8 Reads

Dynamics of light-induced conformational changes of the phoborhodopsin/transducer complex formed in the n-dodecyl beta-D-maltoside micelle.

Biochemistry 2007 May 14;46(18):5349-57. Epub 2007 Apr 14.

Nano-biotechnology Research Center and Department of Bioscience, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo, Japan.

A complex of photoreceptor phoborhodopsin (ppR; also called sensory rhodopsin II) and its cognate halobacterial transducer II (pHtrII) existing in the plasma membrane mediates the light signal to the cytoplasm in the earliest step of negative phototaxis in Natronomonas pharaonis. We have investigated the dynamics of the light-induced conformational changes of the ppR/pHtrII(1-159) complex formed in the presence of 0.1% n-dodecyl beta-d-maltoside (DDM) by a fluorescence resonance energy transfer (FRET) based method. Read More

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http://pubs.acs.org/doi/abs/10.1021/bi602482s
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http://dx.doi.org/10.1021/bi602482sDOI Listing
May 2007
14 Reads

Solution structure and cell selectivity of piscidin 1 and its analogues.

Biochemistry 2007 Mar 1;46(12):3653-63. Epub 2007 Mar 1.

Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, IBST, Konkuk University, Kwangjin-gu, Seoul 143-701, Korea.

Piscidin 1 (Pis-1) is a novel cytotoxic peptide with a cationic alpha-helical structure that was isolated from the mast cells of hybrid striped bass [Silphaduang, U., and Noga, E. J. Read More

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http://dx.doi.org/10.1021/bi062233uDOI Listing
March 2007
4 Reads

P-Glycoprotein (P-gp) expressed in a confluent monolayer of hMDR1-MDCKII cells has more than one efflux pathway with cooperative binding sites.

Biochemistry 2006 Dec 30;45(51):15505-19. Epub 2006 Nov 30.

Department of Bioscience and Biotechnology, Drexel University, Philadelphia, Pennsylvania 19104, USA.

The multidrug resistance transporter P-glycoprotein (P-gp) effluxes a wide range of substrates and can be affected by a wide range of inhibitors or modulators. Many studies have presented classifications for these binding interactions, within either the context of equilibrium binding or the Michaelis-Menten enzyme analysis of the ATPase activity of P-gp. Our approach is to study P-gp transport and its inhibition using a physiologically relevant confluent monolayer of hMDR1-MDCKII cells. Read More

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http://pubs.acs.org/doi/abs/10.1021/bi060593b
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http://dx.doi.org/10.1021/bi060593bDOI Listing
December 2006
1 Read

Denatured and reversibly cationized p53 readily enters cells and simultaneously folds to the functional protein in the cells.

Biochemistry 2006 May;45(19):6124-32

Department of Bioscience and Biotechnology, Faculty of Engineering, Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan.

Cationization is a powerful strategy for internalizing a protein into living cells. On the other hand, a reversibly cationized denatured protein through disulfide bonds is not only soluble in water but also able to fold to the native conformation in vitro. When these advantages in cationization were combined, we developed a novel method to deliver a denatured protein into cells and simultaneously let it fold to express its function within cells. Read More

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http://dx.doi.org/10.1021/bi052642aDOI Listing
May 2006
6 Reads
4 Citations
3.020 Impact Factor

Interaction of the nucleotide binding domains and regulation of the ATPase activity of the human retina specific ABC transporter, ABCR.

Biochemistry 2006 Mar;45(11):3813-23

Department of Bioscience Technologies, Program in Biotechnology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA.

We report here a novel regulation of the ATPase activity of the human retina specific ATP binding cassette transporter (ABC), ABCR, by nucleotide binding domain interactions. We also present evidence that recombinant nucleotide binding domains of ABCR interact in vitro in the complete absence of transmembrane domains (TMDs). Although similar domain-domain interactions have been described in other ABC transporters, the roles of such interactions on the enzymatic mechanisms of these transporters have not been demonstrated experimentally. Read More

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http://dx.doi.org/10.1021/bi052059uDOI Listing

Integrin-supported fast rate intracellular delivery of plasmid DNA by extracellular matrix protein embedded calcium phosphate complexes.

Biochemistry 2005 Sep;44(37):12273-8

Department of Biomolecular Engineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.

Extracellular matrix (ECM) proteins, such as collagen and fibronectin, play vital roles in development and maintenance of hard tissue (bone or tooth) and are, consequently, thoroughly investigated for construction of biomimetic scaffolds in combination with calcium phosphate (CaP) material (the major component of hard tissue) for bone or dental tissue engineering. Realizing the natural affinity of ECM components toward inorganic constituents of hard tissue, we successfully constructed the nanohybrids of DNA/CaP particles with either collagen 1 or fibronectin, which finally possessed the capability of specific recognition of integrin receptor for being swiftly internalized across the plasma membrane, leading to remarkably high transgene expression in mammalian cells. This new approach with precise receptor-specific delivery as well as 10- to 50-fold enhanced efficiency level compared to the classical one, has immediate applications for basic research and large scale production of recombinant therapeutic proteins and looks promising for gene therapy. Read More

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http://dx.doi.org/10.1021/bi050595gDOI Listing
September 2005

Crystal structure of a ribonuclease P protein Ph1601p from Pyrococcus horikoshii OT3: an archaeal homologue of human nuclear ribonuclease P protein Rpp21.

Biochemistry 2005 Sep;44(36):12086-93

Laboratory of Biochemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka 812-8581, Japan.

Ribonuclease P (RNase P) is a ribonucleoprotein complex involved in the removal of 5' leader sequences from tRNA precursors (pre-tRNA). The human protein Rpp21 is essential for human RNase P activity in tRNA processing in vitro. The crystal structure of Ph1601p from the hyperthermophilic archaeon Pyrococcus horikoshii OT3, the archaeal homologue of Rpp21, was determined using the multiple anomalous dispersion (MAD) method with the aid of anomalous scattering in zinc and selenium at 1. Read More

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http://pubs.acs.org/doi/abs/10.1021/bi050738z
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http://dx.doi.org/10.1021/bi050738zDOI Listing
September 2005
2 Reads

Identification of the 1,2-propanediol-1-yl radical as an intermediate in adenosylcobalamin-dependent diol dehydratase reaction.

Biochemistry 2005 Feb;44(6):2113-8

Department of Bioscience and Biotechnology, Faculty of Engineering, Okayama University, Tsushima-Naka, Okayama 700-8530, Japan.

The reaction catalyzed by adenosylcobalamin-dependent diol dehydratase proceeds by a radical mechanism. A radical pair consisting of the Co(II) of cob(II)alamin and an organic radical intermediate formed during catalysis gives EPR spectra. The high-field doublet and the low-field broad signals arise from the weak interaction of an organic radical with the low-spin Co(II) of cob(II)alamin. Read More

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http://dx.doi.org/10.1021/bi0481850DOI Listing
February 2005
4 Reads

Functional analysis of genetic mutations in nucleotide binding domain 2 of the human retina specific ABC transporter.

Biochemistry 2003 Sep;42(36):10683-96

Program in Biotechnology, Department of Bioscience Technologies, Jefferson College of Health Professions, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA.

The rod outer segment (ROS) ABC transporter (ABCR) plays an important role in the outer segment of retinal rod cells, where it functions as a transporter of all-trans retinal, most probably as the complex lipid, retinylidene-phosphatidyl-ethanolamine. We report here a quantitative analysis of the structural and functional effects of genetic mutations, associated with several macular degenerations, in the second nucleotide-binding domain of ABCR (NBD2). We have analyzed the ATP binding, kinetics of ATP hydrolysis, and structural changes. Read More

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http://dx.doi.org/10.1021/bi034481lDOI Listing
September 2003
17 Reads

Crystal structures of the ribonuclease MC1 mutants N71T and N71S in complex with 5'-GMP: structural basis for alterations in substrate specificity.

Biochemistry 2003 May;42(18):5270-8

Laboratory of Biochemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka 812-8581, Japan.

Ribonuclease MC1 (RNase MC1), isolated from bitter gourd seeds, is a uridine specific RNase belonging to the RNase T2 family. Mutations of Asn71 in RNase MC1 to the amino acids Thr (N71T) and Ser (N71S) in guanosine preferential RNases altered the substrate specificity from uridine specific to guanosine specific, as shown by the transphosphorylation of diribonucleoside monophosphates [Numata, T., et al. Read More

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http://dx.doi.org/10.1021/bi034103gDOI Listing
May 2003
2 Reads

Guanine binding site of the Nicotiana glutinosa ribonuclease NW revealed by X-ray crystallography.

Biochemistry 2002 Dec;41(51):15195-202

Laboratory of Biochemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka 812-8581, Japan.

Ribonuclease NW (RNase NW), the wound-inducible RNase in Nicotiana glutinosa leaves, preferentially cleaves guanylic acid. We expressed the cDNA encoding RNase NW in the methylotrophic yeast Pichia pastoris using the expression vector pPIC9K, and the resulting recombinant RNase NW (ryRNaseNW) secreted into medium was purified to apparent homogeneity using column chromatography. The crystal structure of ryRNase NW bound to 5'-GMP was determined at 1. Read More

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December 2002
2 Reads

Calcium-dependent catalytic activity of a novel phytase from Bacillus amyloliquefaciens DS11.

Biochemistry 2001 Aug;40(32):9669-76

Microbial Genomic Laboratory, Korea Research Institute of Bioscience and Biotechnology, Yusong, Taejon,

The thermostable phytase from Bacillus amyloliquefaciens DS11 hydrolyzes phytate (myo-inositol hexakisphosphate, IP6) to less phosphorylated myo-inositol phosphates in the presence of Ca2+. In this report, we discuss the unique Ca2+-dependent catalytic properties of the phytase and its specific substrate requirement. Initial rate kinetic studies of the phytase indicate that the enzyme activity follows a rapid equilibrium ordered mechanism in which binding of Ca2+ to the active site is necessary for the essential activation of the enzyme. Read More

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Incorporation of nonnatural amino acids into proteins by using various four-base codons in an Escherichia coli in vitro translation system.

Biochemistry 2001 Sep;40(37):11060-4

Department of Bioscience and Biotechnology, Faculty of Engineering, Okayama University, 3-1-1 Tsushimanaka, Okayama 700-8530, Japan.

Incorporation of nonnatural amino acids into proteins is a powerful technique in protein research. Amber suppression has been used to this end, but this strategy does not allow multiple incorporation of nonnatural amino acids into single proteins. In this article, we developed an alternative strategy for nonnatural mutagenesis by using four-base codons. Read More

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September 2001
1 Read

Preparation of potent cytotoxic ribonucleases by cationization: enhanced cellular uptake and decreased interaction with ribonuclease inhibitor by chemical modification of carboxyl groups.

Biochemistry 2001 Jun;40(25):7518-24

Department of Bioscience and Biotechnology, Faculty of Engineering, Okayama University, Okayama 700-8530, Japan.

Carboxyl groups of bovine RNase A were amidated with ethylenediamine (to convert negative charges of carboxylate anions to positive ones), 2-aminoethanol (to eliminate negative charges), and taurine (to keep negative charges), respectively, by a carbodiimide reaction. Human RNase 1 was also modified with ethylenediamine. Surprisingly, the modified RNases were all cytotoxic toward 3T3-SV-40 cells despite their decreased ribonucleolytic activity. Read More

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