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  1. Article: Copper-chelating peptide from salmon by-product proteolysate

    Vo, Tam D.L / Pham, Khoa Trong

    International journal of food engineering. 2020 Apr. 14, v. 16, no. 4

    2020  

    Abstract: The aims of this study included evaluation of copper-binding capacity (CBC) and amino acid composition of salmon by-product proteolysate and its peptide fractions, optimization of hydrolysis condition, and identification of copper-binding peptides from ... ...

    Abstract The aims of this study included evaluation of copper-binding capacity (CBC) and amino acid composition of salmon by-product proteolysate and its peptide fractions, optimization of hydrolysis condition, and identification of copper-binding peptides from the proteolysate. The result was that under the ideal hydrolysis (Neutrase, temperature of 45 °C, pH 7, enzyme:substrate (E:S) proportion of 72.24 U/g protein and hydrolysis time of 8.02 h), the proteolysate had the indispensable amino acid content at approximately 38.7% and also displayed the maximal CBC of 15163.6 µg Cu²⁺/g protein. Besides, four peptide fractions of 10–30 kDa, 3–10 kDa, 1–3 kDa, and <1 kDa were recovered using ultrafiltration, among which the <1 kDa fraction had the highest CBC of 10852.00 ± 895.06 µgCu²⁺/g protein. A copper-binding peptide, Phe-Ile-Asp-Asp-Asp-Ala-Phe-Ile-Arg (1110 Da), was identified from this fraction using tandem mass spectrometry (MS/MS). As a whole, the proteolysate/peptides could be used for copper enhancement that could shield human body from copper inadequacy disorders.
    Keywords amino acid composition ; byproducts ; copper ; enzymes ; humans ; hydrolysis ; pH ; peptides ; salmon ; tandem mass spectrometry ; temperature ; ultrafiltration
    Language English
    Dates of publication 2020-0414
    Publishing place De Gruyter
    Document type Article
    ZDB-ID 2207267-6
    ISSN 1556-3758 ; 2194-5764
    ISSN (online) 1556-3758
    ISSN 2194-5764
    DOI 10.1515/ijfe-2019-0280
    Database NAL-Catalogue (AGRICOLA)

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  2. Article: DNA-facilitated target search by nucleoproteins: Extension of a biosensor-surface plasmon resonance method

    Vo, Tam D. / Schneider, Amelia L. / Poon, Gregory M.K. / Wilson, W. David

    Analytical biochemistry. 2021 Sept. 15, v. 629

    2021  

    Abstract: To extend the value of biosensor-SPR in the characterization of DNA recognition by nucleoproteins, we report a comparative analysis of DNA-facilitated target search by two ETS-family transcription factors: Elk1 and ETV6. ETS domains represent an ... ...

    Abstract To extend the value of biosensor-SPR in the characterization of DNA recognition by nucleoproteins, we report a comparative analysis of DNA-facilitated target search by two ETS-family transcription factors: Elk1 and ETV6. ETS domains represent an attractive system for developing biosensor-based techniques due to a broad range of physicochemical properties encoded within a highly conserved DNA-binding motif. Building on a biosensor approach in which the protein is quantitatively sequestered and presented to immobilized cognate DNA as nonspecific complexes, we assessed the impact of intrinsic cognate and nonspecific affinities on long-range (intersegmental) target search. The equilibrium constants of DNA-facilitated binding were sensitive to the intrinsic binding properties of the proteins such that their relative specificity for cognate DNA were reinforced when binding occurred by transfer vs. without nonspecific DNA. Direct measurement of association and dissociation kinetics revealed ionic features of the activated complex that evidenced DNA-facilitated dissociation, even though Elk1 and ETV6 harbor only a single DNA-binding surface. At salt concentrations that masked the effects of nonspecific pre-binding at equilibrium, the dissociation kinetics of cognate binding were nevertheless distinct from conditions under which nonspecific DNA was absent. These results further strengthen the significance of long-range DNA-facilitated translocation in the physiologic environment.
    Keywords DNA ; biosensors ; dissociation ; nucleoproteins
    Language English
    Dates of publication 2021-0915
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 1110-1
    ISSN 1096-0309 ; 0003-2697
    ISSN (online) 1096-0309
    ISSN 0003-2697
    DOI 10.1016/j.ab.2021.114298
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    In stock of ZB MED Bonn / Germany

    Z 70/124: Show issues

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  3. Article ; Online: Salt bridge dynamics in protein/DNA recognition: a comparative analysis of Elk1 and ETV6.

    Vo, Tam D / Schneider, Amelia L / Wilson, W David / Poon, Gregory M K

    Physical chemistry chemical physics : PCCP

    2021  Volume 23, Issue 24, Page(s) 13490–13502

    Abstract: Electrostatic protein/DNA interactions arise from the neutralization of the DNA phosphodiester backbone as well as coupled exchanges by charged protein residues as salt bridges or with mobile ions. Much focus has been and continues to be paid to ... ...

    Abstract Electrostatic protein/DNA interactions arise from the neutralization of the DNA phosphodiester backbone as well as coupled exchanges by charged protein residues as salt bridges or with mobile ions. Much focus has been and continues to be paid to interfacial ion pairs with DNA. The role of extra-interfacial ionic interactions, particularly as dynamic drivers of DNA sequence selectivity, remain poorly known. The ETS family of transcription factors represents an attractive model for addressing this knowledge gap given their diverse ionic composition in primary structures that fold to a tightly conserved DNA-binding motif. To probe the importance of extra-interfacial salt bridges in DNA recognition, we compared the salt-dependent binding by Elk1 with ETV6, two ETS homologs differing markedly in ionic composition. While both proteins exhibit salt-dependent binding with cognate DNA that corresponds to interfacial phosphate contacts, their nonspecific binding diverges from cognate binding as well as each other. Molecular dynamics simulations in explicit solvent, which generated ionic interactions in agreement with the experimental binding data, revealed distinct salt-bridge dynamics in the nonspecific complexes formed by the two proteins. Impaired DNA contact by ETV6 resulted in fewer backbone contacts in the nonspecific complex, while Elk1 exhibited a redistribution of extra-interfacial salt bridges via residues that are non-conserved between the two ETS relatives. Thus, primary structure variation in ionic residues can encode highly differentiated specificity mechanisms in a highly conserved DNA-binding motif.
    MeSH term(s) DNA/chemistry ; Density Functional Theory ; Humans ; Molecular Dynamics Simulation ; Proto-Oncogene Proteins c-ets/chemistry ; Repressor Proteins/chemistry ; ets-Domain Protein Elk-1/chemistry ; ETS Translocation Variant 6 Protein
    Chemical Substances ELK1 protein, human ; Proto-Oncogene Proteins c-ets ; Repressor Proteins ; ets-Domain Protein Elk-1 ; DNA (9007-49-2)
    Language English
    Publishing date 2021-06-13
    Publishing country England
    Document type Comparative Study ; Journal Article
    ZDB-ID 1476244-4
    ISSN 1463-9084 ; 1463-9076
    ISSN (online) 1463-9084
    ISSN 1463-9076
    DOI 10.1039/d1cp01568k
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: DNA-facilitated target search by nucleoproteins: Extension of a biosensor-surface plasmon resonance method.

    Vo, Tam D / Schneider, Amelia L / Poon, Gregory M K / Wilson, W David

    Analytical biochemistry

    2021  Volume 629, Page(s) 114298

    Abstract: To extend the value of biosensor-SPR in the characterization of DNA recognition by nucleoproteins, we report a comparative analysis of DNA-facilitated target search by two ETS-family transcription factors: Elk1 and ETV6. ETS domains represent an ... ...

    Abstract To extend the value of biosensor-SPR in the characterization of DNA recognition by nucleoproteins, we report a comparative analysis of DNA-facilitated target search by two ETS-family transcription factors: Elk1 and ETV6. ETS domains represent an attractive system for developing biosensor-based techniques due to a broad range of physicochemical properties encoded within a highly conserved DNA-binding motif. Building on a biosensor approach in which the protein is quantitatively sequestered and presented to immobilized cognate DNA as nonspecific complexes, we assessed the impact of intrinsic cognate and nonspecific affinities on long-range (intersegmental) target search. The equilibrium constants of DNA-facilitated binding were sensitive to the intrinsic binding properties of the proteins such that their relative specificity for cognate DNA were reinforced when binding occurred by transfer vs. without nonspecific DNA. Direct measurement of association and dissociation kinetics revealed ionic features of the activated complex that evidenced DNA-facilitated dissociation, even though Elk1 and ETV6 harbor only a single DNA-binding surface. At salt concentrations that masked the effects of nonspecific pre-binding at equilibrium, the dissociation kinetics of cognate binding were nevertheless distinct from conditions under which nonspecific DNA was absent. These results further strengthen the significance of long-range DNA-facilitated translocation in the physiologic environment.
    MeSH term(s) Binding Sites ; Biosensing Techniques ; DNA/analysis ; Escherichia coli/genetics ; Nucleoproteins/chemistry ; Nucleoproteins/genetics ; Protein Binding ; Proto-Oncogene Proteins c-ets/chemistry ; Repressor Proteins/chemistry ; Surface Plasmon Resonance ; ets-Domain Protein Elk-1/chemistry ; ETS Translocation Variant 6 Protein
    Chemical Substances Nucleoproteins ; Proto-Oncogene Proteins c-ets ; Repressor Proteins ; ets-Domain Protein Elk-1 ; DNA (9007-49-2)
    Language English
    Publishing date 2021-07-10
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1110-1
    ISSN 1096-0309 ; 0003-2697
    ISSN (online) 1096-0309
    ISSN 0003-2697
    DOI 10.1016/j.ab.2021.114298
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 389: Show issues Location:
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    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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