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Article ; Online: Movement and specificity in a modular DNA binding protein.

Liptak, Cary / Loria, J Patrick

Structure (London, England : 1993)

2015 Volume 23, Issue 6, Page(s) 973–974

Abstract: The single-stranded DNA (ssDNA) binding protein RPA binds to and protects ssDNA while simultaneously recruiting numerous replication and repair proteins essential for genome integrity. In this issue of Structure, Brosey et al. (2015) show that the ... ...

Abstract	The single-stranded DNA (ssDNA) binding protein RPA binds to and protects ssDNA while simultaneously recruiting numerous replication and repair proteins essential for genome integrity. In this issue of Structure, Brosey et al. (2015) show that the flexibility and interactions of the modular domains of RPA are altered by ssDNA binding and suggest that these changes in configurational freedom are important for the many functions of RPA.
MeSH term(s)	DNA/metabolism ; Models, Molecular ; Replication Protein A/chemistry ; Replication Protein A/metabolism
Chemical Substances	Replication Protein A ; DNA (9007-49-2)
Language	English
Publishing date	2015-05-28
Publishing country	United States
Document type	Journal Article ; Comment
ZDB-ID	1213087-4
ISSN	1878-4186 ; 0969-2126
ISSN (online)	1878-4186
ISSN	0969-2126
DOI	10.1016/j.str.2015.05.004
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Article: Tag and Capture Flow Hydrogen Exchange Mass Spectrometry with a Fluorous-Immobilized Probe

Marcsisin, Sean R / Bradner James E / Engen John R / Liptak Cary / Marineau Jason

Analytical chemistry. 2015 June 16, v. 87, no. 12

2015

Abstract: Analysis of complex mixtures of proteins by hydrogen exchange (HX) mass spectrometry (MS) is limited by oneâs ability to resolve the protein(s) of interest from the proteins that are not of interest. One strategy for overcoming this problem is to tag ... ...

Abstract	Analysis of complex mixtures of proteins by hydrogen exchange (HX) mass spectrometry (MS) is limited by oneâs ability to resolve the protein(s) of interest from the proteins that are not of interest. One strategy for overcoming this problem is to tag the target protein(s) to allow for rapid removal from the mixture for subsequent analysis. Here we illustrate a new solution involving fluorous conjugation of a retrievable probe. The appended fluorous tag allows for facile immobilization on a fluorous surface. When a target protein is passed over the immobilized probe molecule, it can be efficiently captured and then exposed to a flowing stream of deuterated buffer for hydrogen exchange. The utility of this method is illustrated for a model system of the Elongin BC protein complex bound to a peptide from HIV Vif. Efficient capture is demonstrated, and deuteration when immobilized was identical to deuteration in conventional solution-phase hydrogen exchange MS. Protein captured from a crude bacterial cell lysate could also be deuterated without the need for separate purification steps before HX MS. The advantages and disadvantages of the method are discussed in light of miniaturization and automation.
Keywords	automation ; bacteria ; Human immunodeficiency virus ; hydrogen ; mass spectrometry ; proteins
Language	English
Dates of publication	2015-0616
Size	p. 6349-6356.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021%2Facs.analchem.5b01220
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Article ; Online: Tag and Capture Flow Hydrogen Exchange Mass Spectrometry with a Fluorous-Immobilized Probe.

Marcsisin, Sean R / Liptak, Cary / Marineau, Jason / Bradner, James E / Engen, John R

Analytical chemistry

2015 Volume 87, Issue 12, Page(s) 6349–6356

Abstract: Analysis of complex mixtures of proteins by hydrogen exchange (HX) mass spectrometry (MS) is limited by one's ability to resolve the protein(s) of interest from the proteins that are not of interest. One strategy for overcoming this problem is to tag the ...

Abstract	Analysis of complex mixtures of proteins by hydrogen exchange (HX) mass spectrometry (MS) is limited by one's ability to resolve the protein(s) of interest from the proteins that are not of interest. One strategy for overcoming this problem is to tag the target protein(s) to allow for rapid removal from the mixture for subsequent analysis. Here we illustrate a new solution involving fluorous conjugation of a retrievable probe. The appended fluorous tag allows for facile immobilization on a fluorous surface. When a target protein is passed over the immobilized probe molecule, it can be efficiently captured and then exposed to a flowing stream of deuterated buffer for hydrogen exchange. The utility of this method is illustrated for a model system of the Elongin BC protein complex bound to a peptide from HIV Vif. Efficient capture is demonstrated, and deuteration when immobilized was identical to deuteration in conventional solution-phase hydrogen exchange MS. Protein captured from a crude bacterial cell lysate could also be deuterated without the need for separate purification steps before HX MS. The advantages and disadvantages of the method are discussed in light of miniaturization and automation.
MeSH term(s)	Fluorocarbons/chemistry ; Hydrocarbons, Fluorinated ; Hydrogen/chemistry ; Mass Spectrometry ; Molecular Probe Techniques ; Proteins/analysis ; Solutions
Chemical Substances	Fluorocarbons ; Hydrocarbons, Fluorinated ; Proteins ; Solutions ; Hydrogen (7YNJ3PO35Z)
Language	English
Publishing date	2015-05-29
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.5b01220
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Article ; Online: I260Q DNA polymerase β highlights precatalytic conformational rearrangements critical for fidelity.

Liptak, Cary / Mahmoud, Mariam M / Eckenroth, Brian E / Moreno, Marcus V / East, Kyle / Alnajjar, Khadijeh S / Huang, Ji / Towle-Weicksel, Jamie B / Doublié, Sylvie / Loria, J Patrick / Sweasy, Joann B

Nucleic acids research

2018 Volume 46, Issue 20, Page(s) 10740–10756

Abstract: DNA polymerase β (pol β) fills single nucleotide gaps in DNA during base excision repair and non-homologous end-joining. Pol β must select the correct nucleotide from among a pool of four nucleotides with similar structures and properties in order to ... ...

Abstract	DNA polymerase β (pol β) fills single nucleotide gaps in DNA during base excision repair and non-homologous end-joining. Pol β must select the correct nucleotide from among a pool of four nucleotides with similar structures and properties in order to maintain genomic stability during DNA repair. Here, we use a combination of X-ray crystallography, fluorescence resonance energy transfer and nuclear magnetic resonance to show that pol β's ability to access the appropriate conformations both before and upon binding to nucleotide substrates is integral to its fidelity. Importantly, we also demonstrate that the inability of the I260Q mutator variant of pol β to properly navigate this conformational landscape results in error-prone DNA synthesis. Our work reveals that precatalytic conformational rearrangements themselves are an important underlying mechanism of substrate selection by DNA pol β.
MeSH term(s)	Amino Acid Substitution/genetics ; Catalysis ; Codon, Nonsense ; Crystallography, X-Ray ; DNA/chemistry ; DNA/metabolism ; DNA Polymerase beta/chemistry ; DNA Polymerase beta/genetics ; DNA Polymerase beta/metabolism ; DNA Repair/genetics ; DNA Replication/genetics ; Fluorescence Resonance Energy Transfer ; Genomic Instability/genetics ; Glutamic Acid/genetics ; Isoenzymes/chemistry ; Isoenzymes/genetics ; Isoenzymes/metabolism ; Isoleucine/genetics ; Models, Molecular ; Nucleic Acid Conformation ; Nucleotides/chemistry ; Nucleotides/metabolism ; Protein Binding ; Substrate Specificity/genetics ; Templates, Genetic
Chemical Substances	Codon, Nonsense ; Isoenzymes ; Nucleotides ; Isoleucine (04Y7590D77) ; Glutamic Acid (3KX376GY7L) ; DNA (9007-49-2) ; DNA Polymerase beta (EC 2.7.7.-)
Language	English
Publishing date	2018-10-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gky825
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Article ; Online: A multiplex immunoassay gives different results than singleplex immunoassays which may bias epidemiologic associations.

de Koning, Lawrence / Liptak, Cary / Shkreta, Aida / Bradwin, Gary / Hu, Frank B / Pradhan, Aruna Das / Rifai, Nader / Kellogg, Mark D

Clinical biochemistry

2012 Volume 45, Issue 10-11, Page(s) 848–851

Abstract: Objectives: Multiplex immunoassays are increasingly used in epidemiologic studies to measure inflammatory factors, however there are few published evaluations of this technology. Our objective was to compare a common multiplex immunoassay to singleplex ... ...

Abstract	Objectives: Multiplex immunoassays are increasingly used in epidemiologic studies to measure inflammatory factors, however there are few published evaluations of this technology. Our objective was to compare a common multiplex immunoassay to singleplex immunoassays for measuring inflammatory factors, and to examine how combining data from each affects an epidemiologic association. Design and methods: Plasma IL-1 beta, IFN-gamma, IL-6, and TNF-alpha were measured in 100 samples using a multiplex kit from Mesoscale Discovery (MSD) and singleplex ELISAs from R&D Systems. Separate samples (n=80) were collected to compare multiplex and singleplex assays from MSD. We simulated the effect of combining MSD multiplex and R&D singleplex data on the association between sugar sweetened beverage (SSB) intake and IL-6 in the Health Professionals Follow-up Study (HPFS; n=1314). Results: Compared to R&D ELISAs, the MSD multiplex proportionally and significantly overestimated IL-1 beta (slope=1.2), and IFN-gamma (slope=2.9) but underestimated IL-6 (slope=0.5). Correlations were ≥ 0.81 except for TNF-alpha (r=0.31). Compared to MSD singleplex, the MSD multiplex proportionally underestimated IFN-gamma (slope=0.7) and TNF-alpha (slope=0.5). Correlations were ≥ 0.96. The association between sugar sweetened beverage intake and IL-6 in the HPFS (+0.16 pg/mL per serving/day, p=0.02, all singleplex) was gradually attenuated as multiplex data made an increasing contribution to the data-set. (+0.09 pg/mL [-45%], p=0.02, all multiplex) Conclusions: A multiplex immunoassay for inflammatory factors yielded significantly different results than singleplex immunoassays-including those from the same company. Correlations were not consistently high, except among assays from the same company. Such differences may distort epidemiologic relationships if data from both methods are merged.
MeSH term(s)	Beverages ; Bias ; Enzyme-Linked Immunosorbent Assay/instrumentation ; Enzyme-Linked Immunosorbent Assay/methods ; Humans ; Immunoassay/instrumentation ; Immunoassay/methods ; Interferon-gamma/blood ; Interleukin-1beta/blood ; Interleukin-6/blood ; Reproducibility of Results ; Sweetening Agents/administration & dosage ; Tumor Necrosis Factor-alpha/blood
Chemical Substances	Interleukin-1beta ; Interleukin-6 ; Sweetening Agents ; Tumor Necrosis Factor-alpha ; Interferon-gamma (82115-62-6)
Language	English
Publishing date	2012-07
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	390372-2
ISSN	1873-2933 ; 0009-9120
ISSN (online)	1873-2933
ISSN	0009-9120
DOI	10.1016/j.clinbiochem.2012.04.006
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Article ; Online: Acute effects of ingestion of a novel whey-derived extract on vascular endothelial function in overweight, middle-aged men and women.

Ballard, Kevin D / Kupchak, Brian R / Volk, Brittanie M / Mah, Eunice / Shkreta, Aida / Liptak, Cary / Ptolemy, Adam S / Kellogg, Mark S / Bruno, Richard S / Seip, Richard L / Maresh, Carl M / Kraemer, William J / Volek, Jeff S

The British journal of nutrition

2013 Volume 109, Issue 5, Page(s) 882–893

Abstract: Whey protein intake reduces CVD risk, but little is known whether whey-derived bioactive peptides regulate vascular endothelial function (VEF). We determined the impact of a whey-derived extract (NOP-47) on VEF in individuals with an increased ... ...

Abstract	Whey protein intake reduces CVD risk, but little is known whether whey-derived bioactive peptides regulate vascular endothelial function (VEF). We determined the impact of a whey-derived extract (NOP-47) on VEF in individuals with an increased cardiovascular risk profile. Men and women with impaired brachial artery flow-mediated dilation (FMD) (n 21, age 55 (sem 1·3) years, BMI 27·8 (sem 0·6) kg/m2, FMD 3·7 (sem 0·4) %) completed a randomised, cross-over study to examine whether ingestion of NOP-47 (5 g) improves postprandial VEF. Brachial artery FMD, plasma amino acids, insulin, and endothelium-derived vasodilators and vasoconstrictors were measured for 2 h after ingestion of NOP-47 or placebo. Acute NOP-47 ingestion increased FMD at 30 min (4·6 (sem 0·5) %) and 120 min (5·1 (sem 0·5) %) post-ingestion (P< 0·05, time × trial interaction), and FMD responses at 120 min were significantly greater in the NOP-47 trial compared with placebo (4·3 (sem 0·5) %). Plasma amino acids increased at 30 min following NOP-47 ingestion (P< 0·05). Serum insulin increased at 15, 30 and 60 min (P< 0·001) following NOP-47 ingestion. No changes were observed between the trials for plasma NO∙ and prostacyclin metabolites or endothelin-1. Ingestion of a rapidly absorbed extract derived from whey protein improved endothelium-dependent dilation in older adults by a mechanism independent of changes in circulating vasoactive compounds. Future investigation is warranted in individuals at an increased CVD risk to further elucidate potential health benefits and the underlying mechanisms of extracts derived from whey.
MeSH term(s)	Amino Acids/blood ; Body Mass Index ; Brachial Artery/physiopathology ; Cross-Over Studies ; Double-Blind Method ; Endothelium, Vascular/drug effects ; Endothelium, Vascular/physiopathology ; Female ; Health Promotion ; Humans ; Insulin/blood ; Male ; Middle Aged ; Milk Proteins/administration & dosage ; Overweight/physiopathology ; Placebos ; Protein Hydrolysates/administration & dosage ; Vasodilation/drug effects ; Whey Proteins
Chemical Substances	Amino Acids ; Insulin ; Milk Proteins ; Placebos ; Protein Hydrolysates ; Whey Proteins
Language	English
Publishing date	2013-03-14
Publishing country	England
Document type	Journal Article ; Randomized Controlled Trial ; Research Support, Non-U.S. Gov't
ZDB-ID	280396-3
ISSN	1475-2662 ; 0007-1145
ISSN (online)	1475-2662
ISSN	0007-1145
DOI	10.1017/S0007114512002061
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Article: Acute effects of ingestion of a novel whey-derived extract on vascular endothelial function in overweight, middle-aged men and women

British journal of nutrition. 2013 Mar. 14, v. 109, no. 5

2013

Abstract	Whey protein intake reduces CVD risk, but little is known whether whey-derived bioactive peptides regulate vascular endothelial function (VEF). We determined the impact of a whey-derived extract (NOP-47) on VEF in individuals with an increased cardiovascular risk profile. Men and women with impaired brachial artery flow-mediated dilation (FMD) (n 21, age 55 (sem 1·3) years, BMI 27·8 (sem 0·6) kg/m2, FMD 3·7 (sem 0·4) %) completed a randomised, cross-over study to examine whether ingestion of NOP-47 (5 g) improves postprandial VEF. Brachial artery FMD, plasma amino acids, insulin, and endothelium-derived vasodilators and vasoconstrictors were measured for 2 h after ingestion of NOP-47 or placebo. Acute NOP-47 ingestion increased FMD at 30 min (4·6 (sem 0·5) %) and 120 min (5·1 (sem 0·5) %) post-ingestion (P< 0·05, time × trial interaction), and FMD responses at 120 min were significantly greater in the NOP-47 trial compared with placebo (4·3 (sem 0·5) %). Plasma amino acids increased at 30 min following NOP-47 ingestion (P< 0·05). Serum insulin increased at 15, 30 and 60 min (P< 0·001) following NOP-47 ingestion. No changes were observed between the trials for plasma NO∙ and prostacyclin metabolites or endothelin-1. Ingestion of a rapidly absorbed extract derived from whey protein improved endothelium-dependent dilation in older adults by a mechanism independent of changes in circulating vasoactive compounds. Future investigation is warranted in individuals at an increased CVD risk to further elucidate potential health benefits and the underlying mechanisms of extracts derived from whey.
Keywords	acute effects ; amino acids ; blood serum ; body mass index ; cross-over studies ; elderly ; endothelins ; insulin ; men ; metabolites ; middle-aged adults ; nutrition risk assessment ; overweight ; placebos ; prostacyclin ; protein intake ; risk profile ; vasoconstrictor agents ; vasodilator agents ; whey ; whey protein ; women
Language	English
Dates of publication	2013-0314
Size	p. 882-893.
Publishing place	Cambridge University Press
Document type	Article
ZDB-ID	280396-3
ISSN	1475-2662 ; 0007-1145
ISSN (online)	1475-2662
ISSN	0007-1145
DOI	10.1017/S0007114512002061
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Movement and specificity in a modular DNA binding protein.

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Article: Tag and Capture Flow Hydrogen Exchange Mass Spectrometry with a Fluorous-Immobilized Probe

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Article ; Online: Tag and Capture Flow Hydrogen Exchange Mass Spectrometry with a Fluorous-Immobilized Probe.

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Article ; Online: I260Q DNA polymerase β highlights precatalytic conformational rearrangements critical for fidelity.

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Article ; Online: A multiplex immunoassay gives different results than singleplex immunoassays which may bias epidemiologic associations.

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Article ; Online: Acute effects of ingestion of a novel whey-derived extract on vascular endothelial function in overweight, middle-aged men and women.

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Article: Acute effects of ingestion of a novel whey-derived extract on vascular endothelial function in overweight, middle-aged men and women

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