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Article ; Online: A short recollection on the paper entitled "A common sense approach to peak picking in two-, three-, and four-dimensional spectra using automatic computer analysis of contour diagrams" by D.S. Garrett, R. Powers, A.M. Gronenborn, and G.M. Clore [J. Magn. Reson. 95 (1991) 214-220].

Garrett, Daniel S / Gronenborn, Angela M / Clore, G Marius

Journal of magnetic resonance (San Diego, Calif. : 1997)

2011 Volume 213, Issue 2, Page(s) 364–365

Abstract: The Contour Approach to Peak Picking was developed to aid in the analysis and interpretation and of multidimensional NMR spectra of large biomolecules. In essence, it comprises an interactive graphics software tool to computationally select resonance ... ...

Abstract	The Contour Approach to Peak Picking was developed to aid in the analysis and interpretation and of multidimensional NMR spectra of large biomolecules. In essence, it comprises an interactive graphics software tool to computationally select resonance positions in heteronuclear, 3- and 4D spectra.
MeSH term(s)	Magnetic Resonance Spectroscopy/methods
Language	English
Publishing date	2011-12
Publishing country	United States
Document type	Comment ; Journal Article
ZDB-ID	1469665-4
ISSN	1096-0856 ; 1557-8968 ; 1090-7807 ; 0022-2364
ISSN (online)	1096-0856 ; 1557-8968
ISSN	1090-7807 ; 0022-2364
DOI	10.1016/j.jmr.2011.08.009
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Commentary on the article: Purification and Characterization of the Ner Repressor of Bacteriophage Mu (1989) FEBS Lett. 244, 369-375 by G. Kukolj, P.P. Tolias and M.S. DuBow.

Allet, B / Payton, M / Mattaliano, R J / Gronenborn, A M / Clore, G M / Wingfield, P T

FEBS letters

1989 Volume 251, Issue 1-2, Page(s) 282

MeSH term(s)	Bacteriophages/genetics ; DNA-Binding Proteins/isolation & purification ; Repressor Proteins/isolation & purification ; Transcription Factors/isolation & purification ; Viral Proteins/isolation & purification ; Viral Regulatory and Accessory Proteins
Chemical Substances	DNA-Binding Proteins ; Repressor Proteins ; Transcription Factors ; Viral Proteins ; Viral Regulatory and Accessory Proteins ; phage repressor proteins
Language	English
Publishing date	1989-07-17
Publishing country	England
Document type	Journal Article
ZDB-ID	212746-5
ISSN	1873-3468 ; 0014-5793
ISSN (online)	1873-3468
ISSN	0014-5793
DOI	10.1016/0014-5793(89)81471-1
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Zs.B 282: Show issues

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Article ; Online: The measurement of relaxation rates of degenerate

Tugarinov, V / Clore, G M

Journal of magnetic resonance (San Diego, Calif. : 1997)

2021 Volume 330, Page(s) 107034

Abstract: A simple NMR experiment for the measurement of transverse relaxation rates of ... ...

Abstract	A simple NMR experiment for the measurement of transverse relaxation rates of degenerate
MeSH term(s)	Magnetic Resonance Imaging ; Magnetic Resonance Spectroscopy ; Nuclear Magnetic Resonance, Biomolecular ; Proteins
Chemical Substances	Proteins
Language	English
Publishing date	2021-07-14
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	1469665-4
ISSN	1096-0856 ; 1557-8968 ; 1090-7807 ; 0022-2364
ISSN (online)	1096-0856 ; 1557-8968
ISSN	1090-7807 ; 0022-2364
DOI	10.1016/j.jmr.2021.107034
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Probing the Interaction between HIV-1 Protease and the Homodimeric p66/p66' Reverse Transcriptase Precursor by Double Electron-Electron Resonance EPR Spectroscopy.

Schmidt, Thomas / Louis, John M / Clore, G Marius

Chembiochem : a European journal of chemical biology

2020 Volume 21, Issue 21, Page(s) 3051–3055

Abstract: Following excision from the Gag-Pol polyprotein, HIV-1 reverse transcriptase is released as an asymmetric homodimer comprising two p66 subunits that are structurally dissimilar but identical in amino acid sequence. Subsequent cleavage of the RNase H ... ...

Abstract	Following excision from the Gag-Pol polyprotein, HIV-1 reverse transcriptase is released as an asymmetric homodimer comprising two p66 subunits that are structurally dissimilar but identical in amino acid sequence. Subsequent cleavage of the RNase H domain from only one of the subunits, denoted p66', results in the formation of the mature p66/p51 enzyme in which catalytic activity resides in the p66 subunit, and the p51 subunit (derived from p66') provides a supporting structural scaffold. Here, we probe the interaction of the p66/p66' asymmetric reverse transcriptase precursor with HIV-1 protease by pulsed Q-band double electron-electron resonance EPR spectroscopy to measure distances between nitroxide labels introduced at surface-engineered cysteine residues. The data suggest that the flexible, exposed linker between the RNaseH and connection domains in the open state of the p66' subunit binds to the active site of protease in a configuration that is similar to that of extended peptide substrates.
MeSH term(s)	Electron Spin Resonance Spectroscopy ; HIV Protease/chemistry ; HIV Protease/metabolism ; HIV Reverse Transcriptase/chemistry ; HIV Reverse Transcriptase/metabolism ; Models, Molecular
Chemical Substances	reverse transcriptase, Human immunodeficiency virus 1 (EC 2.7.7.-) ; HIV Reverse Transcriptase (EC 2.7.7.49) ; HIV Protease (EC 3.4.23.-) ; p16 protease, Human immunodeficiency virus 1 (EC 3.4.23.-)
Language	English
Publishing date	2020-07-14
Publishing country	Germany
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural
ZDB-ID	2020469-3
ISSN	1439-7633 ; 1439-4227
ISSN (online)	1439-7633
ISSN	1439-4227
DOI	10.1002/cbic.202000263
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Article ; Online: Global Dynamics of a Protein on the Surface of Anisotropic Lipid Nanoparticles Derived from Relaxation-Based NMR Spectroscopy.

Ceccon, Alberto / Kubatova, Nina / Louis, John M / Clore, G Marius / Tugarinov, Vitali

The journal of physical chemistry. B

2022 Volume 126, Issue 30, Page(s) 5646–5654

Abstract: The global motions of ubiquitin, a model protein, on the surface of anisotropically tumbling 1-palmitoyl-2-oleoyl- ...

Abstract	The global motions of ubiquitin, a model protein, on the surface of anisotropically tumbling 1-palmitoyl-2-oleoyl-
MeSH term(s)	Lipid Bilayers/chemistry ; Liposomes ; Magnetic Resonance Spectroscopy/methods ; Nanoparticles ; Ubiquitins
Chemical Substances	Lipid Bilayers ; Lipid Nanoparticles ; Liposomes ; Ubiquitins
Language	English
Publishing date	2022-07-25
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.2c03519
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Article ; Online: Spatiotemporal distribution of community-acquired phenotypic extended-spectrum beta-lactamase

Smith, Matthew W / Carrel, Margaret / Shi, Qianyi / Hasegawa, Shinya / Clore, Gosia / Tang, Zhuo / Perencevich, Eli / Goto, Michihiko

Infection control and hospital epidemiology

2023 Volume 45, Issue 4, Page(s) 540–542

Abstract: Using data from the Veterans' Health Administration from 2010 to 2019, we examined the distribution and prevalence of community-acquired phenotypic extended-spectrum β-lactamase (ESBL) ...

Abstract	Using data from the Veterans' Health Administration from 2010 to 2019, we examined the distribution and prevalence of community-acquired phenotypic extended-spectrum β-lactamase (ESBL)
MeSH term(s)	Humans ; Escherichia coli ; Escherichia coli Infections/epidemiology ; Escherichia coli Infections/drug therapy ; beta-Lactamases ; Prevalence ; Cluster Analysis ; Community-Acquired Infections/epidemiology ; Community-Acquired Infections/drug therapy ; Anti-Bacterial Agents/therapeutic use
Chemical Substances	beta-Lactamases (EC 3.5.2.6) ; Anti-Bacterial Agents
Language	English
Publishing date	2023-12-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	639378-0
ISSN	1559-6834 ; 0195-9417 ; 0899-823X
ISSN (online)	1559-6834
ISSN	0195-9417 ; 0899-823X
DOI	10.1017/ice.2023.266
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Zs.A 1714: Show issues

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Article ; Online: Interaction of the bacterial division regulator MinE with lipid bicelles studied by NMR spectroscopy.

Cai, Mengli / Tugarinov, Vitali / Chaitanya Chiliveri, Sai / Huang, Ying / Schwieters, Charles D / Mizuuchi, Kyoshi / Clore, G Marius

The Journal of biological chemistry

2023 Volume 299, Issue 4, Page(s) 103037

Abstract: The bacterial MinE and MinD division regulatory proteins form a standing wave enabling MinC, which binds MinD, to inhibit FtsZ polymerization everywhere except at the midcell, thereby assuring correct positioning of the cytokinetic septum and even ... ...

Abstract	The bacterial MinE and MinD division regulatory proteins form a standing wave enabling MinC, which binds MinD, to inhibit FtsZ polymerization everywhere except at the midcell, thereby assuring correct positioning of the cytokinetic septum and even distribution of contents to daughter cells. The MinE dimer undergoes major structural rearrangements between a resting six-stranded state present in the cytoplasm, a membrane-bound state, and a four-stranded active state bound to MinD on the membrane, but it is unclear which MinE motifs interact with the membrane in these different states. Using NMR, we probe the structure and global dynamics of MinE bound to disc-shaped lipid bicelles. In the bicelle-bound state, helix α1 no longer sits on top of the six-stranded β-sheet, losing any contact with the protein core, but interacts directly with the bicelle surface; the structure of the protein core remains unperturbed and also interacts with the bicelle surface via helix α2. Binding may involve a previously identified excited state of free MinE in which helix α1 is disordered, thereby allowing it to target the membrane surface. Helix α1 and the protein core undergo nanosecond rigid body motions of differing amplitudes in the plane of the bicelle surface. Global dynamics on the sub-millisecond time scale between a ground state and a sparsely populated excited state are also observed and may represent a very early intermediate on the transition path between the resting six-stranded and active four-stranded conformations. In summary, our results provide insights into MinE structural rearrangements important during bacterial cell division.
MeSH term(s)	Bacterial Proteins/metabolism ; Cell Cycle Proteins/metabolism ; Lipids ; Magnetic Resonance Spectroscopy ; Bacteria/cytology ; Cell Division
Chemical Substances	Bacterial Proteins ; Cell Cycle Proteins ; Lipids
Language	English
Publishing date	2023-02-17
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2023.103037
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Uc I Zs.108: Show issues

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Article ; Online: XIPP: multi-dimensional NMR analysis software.

Garrett, Daniel S / Cai, Mengli / Clore, G Marius

Journal of biomolecular NMR

2019 Volume 74, Issue 1, Page(s) 9–25

Abstract: Here we present the XIPP (eXtensible Interactive Peak Picker) NMR software for analyzing multidimensional NMR data of proteins, DNA, RNA and protein-nucleic acid complexes. XIPP organizes experiments into pre-defined studies and replaces our original ... ...

Abstract	Here we present the XIPP (eXtensible Interactive Peak Picker) NMR software for analyzing multidimensional NMR data of proteins, DNA, RNA and protein-nucleic acid complexes. XIPP organizes experiments into pre-defined studies and replaces our original PIPP software suite which is no longer supported. Default study types exist for backbone assignment, sidechain assignment, NOE assignment and several relaxation series experiments, used in solution NMR studies. XIPP is written in Java and Jython. The default study types are defined in Jython which can be modified and extended to create new types of studies.
MeSH term(s)	Nuclear Magnetic Resonance, Biomolecular ; Programming Languages ; Software ; Spectrum Analysis
Language	English
Publishing date	2019-11-20
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1081696-3
ISSN	1573-5001 ; 0925-2738
ISSN (online)	1573-5001
ISSN	0925-2738
DOI	10.1007/s10858-019-00286-w
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Zs.A 4132: Show issues

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Article ; Online: A simple and cost-effective protocol for high-yield expression of deuterated and selectively isoleucine/leucine/valine methyl protonated proteins in Escherichia coli grown in shaker flasks.

Cai, Mengli / Huang, Ying / Lloyd, John / Craigie, Robert / Clore, G Marius

Journal of biomolecular NMR

2021 Volume 75, Issue 2-3, Page(s) 83–87

Abstract: A simple and cost-effective protocol is presented for expression of perdeuterated, Ile/Leu/ ... ...

Abstract	A simple and cost-effective protocol is presented for expression of perdeuterated, Ile/Leu/Val
MeSH term(s)	Amino Acids/metabolism ; Biochemistry/methods ; Bioreactors/microbiology ; Cost-Benefit Analysis ; Deuterium/metabolism ; Escherichia coli/growth & development ; Escherichia coli Proteins/metabolism ; Gene Expression ; Isoleucine/metabolism ; Leucine/metabolism ; Protons ; Valine/metabolism
Chemical Substances	Amino Acids ; Escherichia coli Proteins ; Protons ; Isoleucine (04Y7590D77) ; Deuterium (AR09D82C7G) ; Leucine (GMW67QNF9C) ; Valine (HG18B9YRS7)
Language	English
Publishing date	2021-02-04
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1081696-3
ISSN	1573-5001 ; 0925-2738
ISSN (online)	1573-5001
ISSN	0925-2738
DOI	10.1007/s10858-021-00357-x
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Article: Global Dynamics of a Protein on the Surface of Anisotropic Lipid Nanoparticles Derived from Relaxation-Based NMR Spectroscopy

Ceccon, Alberto / Kubatova, Nina / Louis, John M. / Clore, G. Marius / Tugarinov, Vitali

Journal of physical chemistry. 2022 July 25, v. 126, no. 30

2022

Abstract: The global motions of ubiquitin, a model protein, on the surface of anisotropically tumbling 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1′-rac-glycerol) (POPG):1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC) bicelles are described. The shapes of POPG: ... ...

Abstract	The global motions of ubiquitin, a model protein, on the surface of anisotropically tumbling 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1′-rac-glycerol) (POPG):1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC) bicelles are described. The shapes of POPG:DHPC bicelles prepared with high molar ratios q of POPG to DHPC can be approximated by prolate ellipsoids, with the ratio of ellipsoid dimensions and dimensions themselves increasing with higher values of q. Adaptation of the nuclear magnetic resonance (NMR) relaxation-based approach that we previously developed for interactions of ubiquitin with spherical POPG liposomes (Ceccon, A.J. Am. Chem. Soc.2016, 138, 5789−5792) allowed us to quantitatively analyze the variation in lifetime line broadening of NMR signals (ΔR₂) measured for ubiquitin in the presence of q = 2 POPG:DHPC bicelles and the associated transverse spin relaxation rates (R₂,B) of bicelle-bound ubiquitin. Ubiquitin, transiently bound to POPG:DHPC bicelles, undergoes internal rotation about an axis orthogonal to the surface of the bicelle and perpendicular to the principal axis of its rotational diffusion tensor on the low microsecond time scale (∼3 μs), while the rotation axis itself wobbles in a cone on a submicrosecond time scale (≤ 500 ns).
Keywords	anisotropy ; lipids ; nuclear magnetic resonance spectroscopy ; physical chemistry ; ubiquitin
Language	English
Dates of publication	2022-0725
Size	p. 5646-5654.
Publishing place	American Chemical Society
Document type	Article
ISSN	1520-5207
DOI	10.1021/acs.jpcb.2c03519
Database	NAL-Catalogue (AGRICOLA)

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