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Article ; Online: Elucidation of Cryptic and Allosteric Pockets within the SARS-CoV-2 Main Protease.

Sztain, Terra / Amaro, Rommie / McCammon, J Andrew

Journal of chemical information and modeling

2021 Volume 61, Issue 7, Page(s) 3495–3501

Abstract: The SARS-CoV-2 pandemic has rapidly spread across the globe, posing an urgent health concern. Many quests to computationally identify treatments against the virus rely ... ...

Abstract	The SARS-CoV-2 pandemic has rapidly spread across the globe, posing an urgent health concern. Many quests to computationally identify treatments against the virus rely on
MeSH term(s)	COVID-19 ; Catalytic Domain ; Humans ; Molecular Docking Simulation ; Peptide Hydrolases ; Protease Inhibitors ; SARS-CoV-2 ; Viral Proteins
Chemical Substances	Protease Inhibitors ; Viral Proteins ; Peptide Hydrolases (EC 3.4.-)
Language	English
Publishing date	2021-05-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	190019-5
ISSN	1549-960X ; 0095-2338
ISSN (online)	1549-960X
ISSN	0095-2338
DOI	10.1021/acs.jcim.1c00140
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Elucidation of cryptic and allosteric pockets within the SARS-CoV-2 protease.

Sztain, Terra / Amaro, Rommie / McCammon, J Andrew

bioRxiv : the preprint server for biology

2020

Abstract: The SARS-CoV-2 pandemic has rapidly spread across the globe, posing an urgent health concern. Many quests to computationally identify treatments against the virus rely ... ...

Abstract	The SARS-CoV-2 pandemic has rapidly spread across the globe, posing an urgent health concern. Many quests to computationally identify treatments against the virus rely on
Keywords	covid19
Language	English
Publishing date	2020-07-24
Publishing country	United States
Document type	Preprint
DOI	10.1101/2020.07.23.218784
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Protein-protein interaction based substrate control in the

Bartholow, Thomas G / Sztain, Terra / Young, Megan A / Davis, Tony D / Abagyan, Ruben / Burkart, Michael D

RSC chemical biology

2021 Volume 2, Issue 5, Page(s) 1466–1473

Abstract: Lipoic acid is an essential cofactor produced in all organisms by diverting octanoic acid derived as an intermediate of type II fatty acid biosynthesis. In bacteria, octanoic acid is transferred from the acyl carrier protein (ACP) to the lipoylated ... ...

Abstract	Lipoic acid is an essential cofactor produced in all organisms by diverting octanoic acid derived as an intermediate of type II fatty acid biosynthesis. In bacteria, octanoic acid is transferred from the acyl carrier protein (ACP) to the lipoylated target protein by the octanoyltransferase LipB. LipB has a well-documented substrate selectivity, indicating a mechanism of octanoic acid recognition. The present study reveals the precise protein-protein interactions (PPIs) responsible for this selectivity in
Language	English
Publishing date	2021-07-28
Publishing country	England
Document type	Journal Article
ISSN	2633-0679
ISSN (online)	2633-0679
DOI	10.1039/d1cb00125f
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Control of Unsaturation in

Bartholow, Thomas G / Sztain, Terra / Young, Megan A / Lee, D John / Davis, Tony D / Abagyan, Ruben / Burkart, Michael D

Biochemistry

2022 Volume 61, Issue 7, Page(s) 608–615

Abstract: Carrier protein-dependent biosynthesis provides a thiotemplated format for the production of natural products. Within these pathways, many reactions display exquisite substrate selectivity, a regulatory framework proposed to be controlled by protein- ... ...

Abstract	Carrier protein-dependent biosynthesis provides a thiotemplated format for the production of natural products. Within these pathways, many reactions display exquisite substrate selectivity, a regulatory framework proposed to be controlled by protein-protein interactions (PPIs). In
MeSH term(s)	Acyl Carrier Protein/metabolism ; Escherichia coli/enzymology ; Fatty Acid Synthase, Type II/metabolism ; Fatty Acids/biosynthesis ; Fatty Acids, Unsaturated/metabolism ; Hydro-Lyases/metabolism
Chemical Substances	Acyl Carrier Protein ; Fatty Acids ; Fatty Acids, Unsaturated ; Hydro-Lyases (EC 4.2.1.-) ; 3-hydroxyacyl-(acyl-carrier-protein) dehydratase (EC 4.2.1.59) ; Fatty Acid Synthase, Type II (EC 6.-)
Language	English
Publishing date	2022-03-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021/acs.biochem.2c00094
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Article ; Online: Elucidation of cryptic and allosteric pockets within the SARS-CoV-2 protease

Sztain, Terra / Amaro, Rommie E / McCammon, James Andrew

bioRxiv

Abstract: The SARS-CoV-2 pandemic has rapidly spread across the globe, posing an urgent health concern. Many quests to computationally identify treatments against the virus rely on ... in silico ... small molecule docking to experimentally determined structures of ... ...

Abstract	The SARS-CoV-2 pandemic has rapidly spread across the globe, posing an urgent health concern. Many quests to computationally identify treatments against the virus rely on in silico small molecule docking to experimentally determined structures of viral proteins. One limit to these approaches is that protein dynamics are often unaccounted for, leading to overlooking transient, druggable conformational states. Using Gaussian accelerated molecular dynamics to enhance sampling of conformational space, we identified cryptic pockets within the SARS-CoV-2 main protease, including some within regions far from the active site and assed their druggability. These pockets can aid in virtual screening efforts to identify a protease inhibitor for the treatment of COVID-19.
Keywords	covid19
Language	English
Publishing date	2020-07-24
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2020.07.23.218784
Database	COVID19

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Article ; Online: Interface Engineering of Carrier-Protein-Dependent Metabolic Pathways.

Sztain, Terra / Corpuz, Joshua C / Bartholow, Thomas G / Sanlley Hernandez, Javier O / Jiang, Ziran / Mellor, Desirae A / Heberlig, Graham W / La Clair, James J / McCammon, J Andrew / Burkart, Michael D

ACS chemical biology

2023 Volume 18, Issue 9, Page(s) 2014–2022

Abstract: Carrier-protein-dependent metabolic pathways biosynthesize fatty acids, polyketides, and non-ribosomal peptides, producing metabolites with important pharmaceutical, environmental, and industrial properties. Recent findings demonstrate that these ... ...

Abstract	Carrier-protein-dependent metabolic pathways biosynthesize fatty acids, polyketides, and non-ribosomal peptides, producing metabolites with important pharmaceutical, environmental, and industrial properties. Recent findings demonstrate that these pathways rely on selective communication mechanisms involving protein-protein interactions (PPIs) that guide enzyme reactivity and timing. While rational design of these PPIs could enable pathway design and modification, this goal remains a challenge due to the complex nature of protein interfaces. Computational methods offer an encouraging avenue, though many score functions fail to predict experimental observables, leading to low success rates. Here, we improve upon the Rosetta score function, leveraging experimental data through iterative rounds of computational prediction and mutagenesis, to design a hybrid fatty acid-non-ribosomal peptide initiation pathway. By increasing the weight of the electrostatic score term, the computational protocol proved to be more predictive, requiring fewer rounds of iteration to identify mutants with high in vitro activity. This allowed efficient design of new PPIs between a non-ribosomal peptide synthetase adenylation domain, PltF, and a fatty acid synthase acyl carrier protein, AcpP, as validated by activity and structural studies. This method provides a promising platform for customized pathway design, establishing a standard for carrier-protein-dependent pathway engineering through PPI optimization.
MeSH term(s)	Carrier Proteins ; Acyl Carrier Protein ; Excipients ; Fatty Acid Synthases ; Fatty Acids ; Metabolic Networks and Pathways
Chemical Substances	Carrier Proteins ; Acyl Carrier Protein ; Excipients ; Fatty Acid Synthases (EC 2.3.1.85) ; Fatty Acids
Language	English
Publishing date	2023-09-06
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1554-8937
ISSN (online)	1554-8937
DOI	10.1021/acschembio.3c00238
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Elucidation of transient protein-protein interactions within carrier protein-dependent biosynthesis.

Bartholow, Thomas G / Sztain, Terra / Patel, Ashay / Lee, D John / Young, Megan A / Abagyan, Ruben / Burkart, Michael D

Communications biology

2021 Volume 4, Issue 1, Page(s) 340

Abstract: Fatty acid biosynthesis (FAB) is an essential and highly conserved metabolic pathway. In bacteria, this process is mediated by an elaborate network of protein•protein interactions (PPIs) involving a small, dynamic acyl carrier protein that interacts with ...

Abstract	Fatty acid biosynthesis (FAB) is an essential and highly conserved metabolic pathway. In bacteria, this process is mediated by an elaborate network of protein•protein interactions (PPIs) involving a small, dynamic acyl carrier protein that interacts with dozens of other partner proteins (PPs). These PPIs have remained poorly characterized due to their dynamic and transient nature. Using a combination of solution-phase NMR spectroscopy and protein-protein docking simulations, we report a comprehensive residue-by-residue comparison of the PPIs formed during FAB in Escherichia coli. This technique describes and compares the molecular basis of six discrete binding events responsible for E. coli FAB and offers insights into a method to characterize these events and those in related carrier protein-dependent pathways.
MeSH term(s)	3-Oxoacyl-(Acyl-Carrier-Protein) Synthase/metabolism ; Acetyltransferases/metabolism ; Acyl Carrier Protein/metabolism ; Alcohol Oxidoreductases/metabolism ; Binding Sites ; Enoyl-(Acyl-Carrier-Protein) Reductase (NADH)/metabolism ; Escherichia coli/enzymology ; Escherichia coli Proteins/metabolism ; Fatty Acid Synthase, Type II/metabolism ; Fatty Acids/biosynthesis ; Lysophospholipase/metabolism ; Molecular Docking Simulation ; Periplasmic Proteins/metabolism ; Protein Binding ; Protein Interaction Domains and Motifs ; Proton Magnetic Resonance Spectroscopy
Chemical Substances	Acyl Carrier Protein ; Escherichia coli Proteins ; Fatty Acids ; Periplasmic Proteins ; acpP protein, E coli ; Alcohol Oxidoreductases (EC 1.1.-) ; acetoacetyl-CoA reductase (EC 1.1.1.36) ; Enoyl-(Acyl-Carrier-Protein) Reductase (NADH) (EC 1.3.1.9) ; fabI protein, E coli (EC 1.3.1.9) ; Acetyltransferases (EC 2.3.1.-) ; fabF protein, E coli (EC 2.3.1.179) ; 3-Oxoacyl-(Acyl-Carrier-Protein) Synthase (EC 2.3.1.41) ; FabB protein, E coli (EC 2.3.1.41) ; Lysophospholipase (EC 3.1.1.5) ; tesA protein, E coli (EC 3.1.2.-) ; Fatty Acid Synthase, Type II (EC 6.-)
Language	English
Publishing date	2021-03-16
Publishing country	England
Document type	Comparative Study ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-021-01838-3
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Article: Shifting the Hydrolysis Equilibrium of Substrate Loaded Acyl Carrier Proteins

Sztain, Terra / Bartholow, Thomas G / McCammon, J. Andrew / Burkart, Michael D

Biochemistry. 2019 Aug. 09, v. 58, no. 34

2019

Abstract: Acyl carrier proteins (ACP)s transport intermediates through many primary and secondary metabolic pathways. Studying the effect of substrate identity on ACP structure has been hindered by the lability of the thioester bond that attaches acyl substrates ... ...

Abstract	Acyl carrier proteins (ACP)s transport intermediates through many primary and secondary metabolic pathways. Studying the effect of substrate identity on ACP structure has been hindered by the lability of the thioester bond that attaches acyl substrates to the 4′-phosphopantetheine cofactor of ACP. Here we show that an acyl acyl-carrier protein synthetase (AasS) can be used in real time to shift the hydrolysis equilibrium toward favoring acyl-ACP during solution NMR spectroscopy. Only 0.005 molar equivalents of AasS enables 1 week of stability to palmitoyl-AcpP from Escherichia coli. 2D NMR spectra enabled with this method revealed that the tethered palmitic acid perturbs nearly every secondary structural region of AcpP. This technique will allow previously unachievable structural studies of unstable acyl-ACP species, contributing to the understanding of these complex biosynthetic pathways.
Keywords	Escherichia coli ; biochemical pathways ; hydrolysis ; nuclear magnetic resonance spectroscopy ; palmitic acid ; thioesters
Language	English
Dates of publication	2019-0809
Size	p. 3557-3560.
Publishing place	American Chemical Society
Document type	Article
Note	NAL-light
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021/acs.biochem.9b00612
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Shifting the Hydrolysis Equilibrium of Substrate Loaded Acyl Carrier Proteins.

Sztain, Terra / Bartholow, Thomas G / McCammon, J Andrew / Burkart, Michael D

Biochemistry

2019 Volume 58, Issue 34, Page(s) 3557–3560

Abstract	Acyl carrier proteins (ACP)s transport intermediates through many primary and secondary metabolic pathways. Studying the effect of substrate identity on ACP structure has been hindered by the lability of the thioester bond that attaches acyl substrates to the 4'-phosphopantetheine cofactor of ACP. Here we show that an acyl acyl-carrier protein synthetase (AasS) can be used in real time to shift the hydrolysis equilibrium toward favoring acyl-ACP during solution NMR spectroscopy. Only 0.005 molar equivalents of AasS enables 1 week of stability to palmitoyl-AcpP from
MeSH term(s)	Acyl Carrier Protein/metabolism ; Escherichia coli/metabolism ; Hydrolysis ; Pantetheine/analogs & derivatives ; Pantetheine/metabolism ; Protein Conformation
Chemical Substances	Acyl Carrier Protein ; Pantetheine (496-65-1) ; 4'-phosphopantetheine (NM39WU8OFM)
Language	English
Publishing date	2019-08-14
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021/acs.biochem.9b00612
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Article ; Online: Elucidation of transient protein-protein interactions within carrier protein-dependent biosynthesis

Thomas G. Bartholow / Terra Sztain / Ashay Patel / D. John Lee / Megan A. Young / Ruben Abagyan / Michael D. Burkart

Communications Biology, Vol 4, Iss 1, Pp 1-

2021 Volume 10

Abstract: Using structural and computational analysis, Bartholow et al. perform a comprehensive residue-by-residue comparison of the protein-protein interactions in de novo fatty acid biosynthesis that occurs in E. coli. This study provides insights into molecular ...

Abstract	Using structural and computational analysis, Bartholow et al. perform a comprehensive residue-by-residue comparison of the protein-protein interactions in de novo fatty acid biosynthesis that occurs in E. coli. This study provides insights into molecular events that occur in carrier protein-dependent pathways.
Keywords	Biology (General) ; QH301-705.5
Language	English
Publishing date	2021-03-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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