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Article ; Online: Sisyphus observed: Unraveling the high ATP usage of an RNA chaperone.

Duran, Elizabeth C / Walter, Nils G

2021 Volume 296, Page(s) 100265

Abstract: DEAD-box proteins are nonprocessive RNA helicases that can function as RNA chaperones by coupling ATP binding and hydrolysis to structural reorganization of RNA. Here, Jarmoskaite et al. quantify the ATP utilization of an RNA chaperone during refolding ... ...

Abstract	DEAD-box proteins are nonprocessive RNA helicases that can function as RNA chaperones by coupling ATP binding and hydrolysis to structural reorganization of RNA. Here, Jarmoskaite et al. quantify the ATP utilization of an RNA chaperone during refolding of a misfolded ribozyme substrate. Strikingly, 100 ATP hydrolysis events are needed per successfully refolded ribozyme, suggesting that each round of unfolding requires ten ATP molecules, since 90% of substrate unfolding cycles only lead back to the kinetically favored misfolded state. This near-Sisyphean effort reveals a potentially conserved model for RNA reorganization by RNA chaperones.
MeSH term(s)	Adenosine Triphosphate/metabolism ; DEAD-box RNA Helicases/metabolism ; Molecular Chaperones/metabolism ; RNA/metabolism
Chemical Substances	Molecular Chaperones ; RNA (63231-63-0) ; Adenosine Triphosphate (8L70Q75FXE) ; DEAD-box RNA Helicases (EC 3.6.4.13)
Language	English
Publishing date	2021-02-11
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.2021.100265
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Article ; Online: What is hot ….

Batalla-Duran, Elizabeth

Thorax

2017 Volume 72, Issue 5, Page(s) 488

Language	English
Publishing date	2017-05
Publishing country	England
Document type	Journal Article
ZDB-ID	204353-1
ISSN	1468-3296 ; 0040-6376
ISSN (online)	1468-3296
ISSN	0040-6376
DOI	10.1136/thoraxjnl-2017-210255
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Article ; Online: Examination of the nucleotide-linked assembly mechanism of E. coli ClpA.

Duran, Elizabeth C / Lucius, Aaron L

Protein science : a publication of the Protein Society

2019 Volume 28, Issue 7, Page(s) 1312–1323

Abstract: Escherichia coli ClpA is a AAA+ (ATPase Associated with diverse cellular Activities) chaperone that catalyzes the ATP-dependent unfolding and translocation of substrate proteins targeted for degradation by a protease, ClpP. ClpA hexamers associate with ... ...

Abstract	Escherichia coli ClpA is a AAA+ (ATPase Associated with diverse cellular Activities) chaperone that catalyzes the ATP-dependent unfolding and translocation of substrate proteins targeted for degradation by a protease, ClpP. ClpA hexamers associate with one or both ends of ClpP tetradecamers to form ClpAP complexes. Each ClpA protomer contains two nucleotide-binding sites, NBD1 and NBD2, and self-assembly into hexamers is thermodynamically linked to nucleotide binding. Despite a number of studies aimed at characterizing ClpA and ClpAP-catalyzed substrate unfolding and degradation, respectively, to date the field is unable to quantify the concentration of ClpA hexamers available to interact with ClpP for any given nucleotide and total ClpA concentration. In this work, sedimentation velocity studies are used to quantitatively examine the self-assembly of a ClpA Walker B variant in the presence of ATP. In addition to the hexamerization, we observe the formation of a previously unreported ClpA dodecamer in the presence of ATP. Further, we report apparent equilibrium constants for the formation of each ClpA oligomer obtained from direct boundary modeling of the sedimentation velocity data. The energetics of nucleotide binding to NBD1 and NBD2 are revealed by examining the dependence of the apparent association equilibrium constants on free nucleotide concentration.
MeSH term(s)	Adenosine Triphosphate/chemistry ; Adenosine Triphosphate/metabolism ; Endopeptidase Clp/chemistry ; Endopeptidase Clp/metabolism ; Escherichia coli/chemistry ; Escherichia coli/metabolism ; Escherichia coli Proteins/chemistry ; Escherichia coli Proteins/metabolism ; Nucleotides/chemistry ; Nucleotides/metabolism
Chemical Substances	Escherichia coli Proteins ; Nucleotides ; Adenosine Triphosphate (8L70Q75FXE) ; ClpA protease, E coli (EC 3.4.21.53) ; Endopeptidase Clp (EC 3.4.21.92)
Language	English
Publishing date	2019-06-03
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1106283-6
ISSN	1469-896X ; 0961-8368
ISSN (online)	1469-896X
ISSN	0961-8368
DOI	10.1002/pro.3638
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Zs.A 3407: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Utilizing functional cell-free extracts to dissect ribonucleoprotein complex biology at single-molecule resolution.

Duran, Elizabeth / Schmidt, Andreas / Welty, Robb / Jalihal, Ameya P / Pitchiaya, Sethuramasundaram / Walter, Nils G

Wiley interdisciplinary reviews. RNA

2023 Volume 14, Issue 5, Page(s) e1787

Abstract: Cellular machineries that drive and regulate gene expression often rely on the coordinated assembly and interaction of a multitude of proteins and RNA together called ribonucleoprotein complexes (RNPs). As such, it is challenging to fully reconstitute ... ...

Abstract	Cellular machineries that drive and regulate gene expression often rely on the coordinated assembly and interaction of a multitude of proteins and RNA together called ribonucleoprotein complexes (RNPs). As such, it is challenging to fully reconstitute these cellular machines recombinantly and gain mechanistic understanding of how they operate and are regulated within the complex environment that is the cell. One strategy for overcoming this challenge is to perform single molecule fluorescence microscopy studies within crude or recombinantly supplemented cell extracts. This strategy enables elucidation of the interaction and kinetic behavior of specific fluorescently labeled biomolecules within RNPs under conditions that approximate native cellular environments. In this review, we describe single molecule fluorescence microcopy approaches that dissect RNP-driven processes within cellular extracts, highlighting general strategies used in these methods. We further survey biological advances in the areas of pre-mRNA splicing and transcription regulation that have been facilitated through this approach. Finally, we conclude with a summary of practical considerations for the implementation of the featured approaches to facilitate their broader future implementation in dissecting the mechanisms of RNP-driven cellular processes. This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.
MeSH term(s)	Cell Extracts ; Ribonucleoproteins/metabolism ; RNA/metabolism ; RNA Splicing ; Biology
Chemical Substances	Cell Extracts ; Ribonucleoproteins ; RNA (63231-63-0)
Language	English
Publishing date	2023-04-12
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2634714-3
ISSN	1757-7012 ; 1757-7004
ISSN (online)	1757-7012
ISSN	1757-7004
DOI	10.1002/wrna.1787
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Zs.A 6953: Show issues

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Article ; Online: ATP hydrolysis inactivating Walker B mutation perturbs E. coli ClpA self-assembly energetics in the absence of nucleotide.

Duran, Elizabeth C / Lucius, Aaron L

Biophysical chemistry

2018 Volume 242, Page(s) 6–14

Abstract: E. coli ClpA is an AAA+ (ATPase Associated with diverse cellular Activities) chaperone that catalyzes the ATP-dependent unfolding and translocation of substrate proteins for the purposes of proper proteome maintenance. Biologically active ClpA hexamers ... ...

Abstract	E. coli ClpA is an AAA+ (ATPase Associated with diverse cellular Activities) chaperone that catalyzes the ATP-dependent unfolding and translocation of substrate proteins for the purposes of proper proteome maintenance. Biologically active ClpA hexamers contain two nucleotide binding domains (NBD) per protomer, D1 and D2. Despite extensive study, complete understanding of how the twelve NBDs within a ClpA hexamer coordinate ATP binding and hydrolysis to polypeptide translocation is currently lacking. To examine nucleotide binding and coordination at D1 and D2, ClpA Walker B variants deficient in ATP hydrolysis at one or both NBDs have been employed in various studies. In the presence of ATP, it is widely assumed that ClpA Walker B variants are entirely hexameric. However, a thermodynamically rigorous examination of the self-assembly mechanism has not been obtained. Differences in the assembly due to the mutation can be misattributed to the active NBD, leading to potential misinterpretations of kinetic studies. Here we use sedimentation velocity studies to quantitatively examine the self-assembly mechanism of ClpA Walker B variants deficient in ATP hydrolysis at D1, D2, and both NBDs. We found that the Walker B mutations had clear, if modest, effects on the assembly. Most notably, the Walker B mutation stabilizes the population of a larger oligomer in the absence of nucleotide, that is not present for analogous concentrations of wild type ClpA. Our results indicate that Walker B mutants, widely used in studies of AAA+ family proteins, require additional characterization as the mutation affects not only ATP hydrolysis, but also the ligand linked assembly of these complexes. This linkage must be considered in investigations of unfolding or other ATP dependent functions.
MeSH term(s)	Adenosine Triphosphate/metabolism ; Endopeptidase Clp/chemistry ; Endopeptidase Clp/genetics ; Endopeptidase Clp/metabolism ; Escherichia coli/enzymology ; Escherichia coli Proteins/chemistry ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; Kinetics ; Mutagenesis, Site-Directed ; Nucleotides/chemistry ; Recombinant Proteins/biosynthesis ; Recombinant Proteins/chemistry ; Recombinant Proteins/isolation & purification ; Thermodynamics ; Ultracentrifugation
Chemical Substances	Escherichia coli Proteins ; Nucleotides ; Recombinant Proteins ; Adenosine Triphosphate (8L70Q75FXE) ; ClpA protease, E coli (EC 3.4.21.53) ; Endopeptidase Clp (EC 3.4.21.92)
Language	English
Publishing date	2018-08-27
Publishing country	Netherlands
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	185052-0
ISSN	1873-4200 ; 0301-4622
ISSN (online)	1873-4200
ISSN	0301-4622
DOI	10.1016/j.bpc.2018.08.005
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Zs.A 1147: Show issues

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Article ; Online: Defining and Improving Outcomes Measurement for Virtual Care: Report from the VHA State-of-the-Art Conference on Virtual Care.

Connolly, Samantha L / Sherman, Scott E / Dardashti, Navid / Duran, Elizabeth / Bosworth, Hayden B / Charness, Michael E / Newton, Terry J / Reddy, Ashok / Wong, Edwin S / Zullig, Leah L / Gutierrez, Jeydith

Journal of general internal medicine

2024 Volume 39, Issue Suppl 1, Page(s) 29–35

Abstract: Virtual care, including synchronous and asynchronous telehealth, remote patient monitoring, and the collection and interpretation of patient-generated health data (PGHD), has the potential to transform healthcare delivery and increase access to care. The ...

Abstract	Virtual care, including synchronous and asynchronous telehealth, remote patient monitoring, and the collection and interpretation of patient-generated health data (PGHD), has the potential to transform healthcare delivery and increase access to care. The Veterans Health Administration (VHA) Office of Health Services Research and Development (HSR&D) convened a State-of-the-Art (SOTA) Conference on Virtual Care to identify future virtual care research priorities. Participants were divided into three workgroups focused on virtual care access, engagement, and outcomes. In this article, we report the findings of the Outcomes Workgroup. The group identified virtual care outcome areas with sufficient evidence, areas in need of additional research, and areas that are particularly well-suited to be studied within VHA. Following a rigorous process of literature review and consensus, the group focused on four questions: (1) What outcomes of virtual care should we be measuring and how should we measure them?; (2) how do we choose the "right" care modality for the "right" patient?; (3) what are potential consequences of virtual care on patient safety?; and (4) how can PGHD be used to benefit provider decision-making and patient self-management?. The current article outlines key conclusions that emerged following discussion of these questions, including recommendations for future research.
MeSH term(s)	Humans ; Delivery of Health Care ; Consensus ; Telemedicine
Language	English
Publishing date	2024-01-22
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	639008-0
ISSN	1525-1497 ; 0884-8734
ISSN (online)	1525-1497
ISSN	0884-8734
DOI	10.1007/s11606-023-08464-1
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Zs.A 2205: Show issues

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Article ; Online: Escherichia coli DnaK Allosterically Modulates ClpB between High- and Low-Peptide Affinity States.

Durie, Clarissa L / Duran, Elizabeth C / Lucius, Aaron L

Biochemistry

2018 Volume 57, Issue 26, Page(s) 3665–3675

Abstract: ClpB and DnaKJE provide protection to Escherichia coli cells during extreme environmental stress. Together, this co-chaperone system can resolve protein aggregates, restoring misfolded proteins to their native form and function in solubilizing damaged ... ...

Abstract	ClpB and DnaKJE provide protection to Escherichia coli cells during extreme environmental stress. Together, this co-chaperone system can resolve protein aggregates, restoring misfolded proteins to their native form and function in solubilizing damaged proteins for removal by the cell's proteolytic systems. DnaK is the component of the KJE system that directly interacts with ClpB. There are many hypotheses for how DnaK affects ClpB-catalyzed disaggregation, each with some experimental support. Here, we build on our recent work characterizing the molecular mechanism of ClpB-catalyzed polypeptide translocation by developing a stopped-flow FRET assay that allows us to detect ClpB's movement on model polypeptide substrates in the absence or presence of DnaK. We find that DnaK induces ClpB to dissociate from the polypeptide substrate. We propose that DnaK acts as a peptide release factor, binding ClpB and causing the ClpB conformation to change to a low-peptide affinity state. Such a role for DnaK would allow ClpB to rebind to another portion of an aggregate and continue nonprocessive translocation to disrupt the aggregate.
MeSH term(s)	Allosteric Regulation ; Endopeptidase Clp/metabolism ; Escherichia coli/metabolism ; Escherichia coli Proteins/metabolism ; Fluorescence Resonance Energy Transfer ; HSP70 Heat-Shock Proteins/metabolism ; Heat-Shock Proteins/metabolism ; Peptides/metabolism ; Protein Binding ; Substrate Specificity
Chemical Substances	Escherichia coli Proteins ; HSP70 Heat-Shock Proteins ; Heat-Shock Proteins ; Peptides ; Endopeptidase Clp (EC 3.4.21.92) ; dnaK protein, E coli (EC 3.6.1.-) ; ClpB protein, E coli (EC 3.6.1.3)
Language	English
Publishing date	2018-06-11
Publishing country	United States
Document type	Journal Article ; 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.8b00045
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Article ; Online: Correction to Ultra-photostable DNA FluoroCubes: Mechanism of Photostability and Compatibility with FRET and Dark Quenching.

Blanchard, Aaron T / Li, Zi / Duran, Elizabeth C / Scull, Catherine E / Hoff, J Damon / Wright, Keenan R / Pan, Victor / Walter, Nils G

Nano letters

2022 Volume 22, Issue 19, Page(s) 8032

Language	English
Publishing date	2022-09-21
Publishing country	United States
Document type	Published Erratum
ISSN	1530-6992
ISSN (online)	1530-6992
DOI	10.1021/acs.nanolett.2c03349
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Article ; Online: Ultra-photostable DNA FluoroCubes: Mechanism of Photostability and Compatibility with FRET and Dark Quenching.

Blanchard, Aaron T / Li, Zi / Duran, Elizabeth C / Scull, Catherine E / Hoff, J Damon / Wright, Keenan R / Pan, Victor / Walter, Nils G

Nano letters

2022 Volume 22, Issue 15, Page(s) 6235–6244

Abstract: DNA-based FluoroCubes were recently developed as a solution to photobleaching, a ubiquitous limitation of fluorescence microscopy (Niekamp; ... Stuurman; ... ...

Abstract	DNA-based FluoroCubes were recently developed as a solution to photobleaching, a ubiquitous limitation of fluorescence microscopy (Niekamp; Stuurman; Vale
MeSH term(s)	DNA ; Fluorescence Resonance Energy Transfer/methods ; Fluorescent Dyes ; Microscopy, Fluorescence/methods ; Photobleaching
Chemical Substances	Fluorescent Dyes ; DNA (9007-49-2)
Language	English
Publishing date	2022-07-26
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
ISSN	1530-6992
ISSN (online)	1530-6992
DOI	10.1021/acs.nanolett.2c01757
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Article ; Online: Neighborhood Deprivation, Race and Ethnicity, and Prostate Cancer Outcomes Across California Health Care Systems.

Wadhwa, Ananta / Roscoe, Charlotte / Duran, Elizabeth A / Kwan, Lorna / Haroldsen, Candace L / Shelton, Jeremy B / Cullen, Jennifer / Knudsen, Beatrice S / Rettig, Mathew B / Pyarajan, Saiju / Nickols, Nicholas G / Maxwell, Kara N / Yamoah, Kosj / Rose, Brent S / Rebbeck, Timothy R / Iyer, Hari S / Garraway, Isla P

JAMA network open

2024 Volume 7, Issue 3, Page(s) e242852

Abstract: Importance: Non-Hispanic Black (hereafter, Black) individuals experience worse prostate cancer outcomes due to socioeconomic and racial inequities of access to care. Few studies have empirically evaluated these disparities across different health care ... ...

Abstract	Importance: Non-Hispanic Black (hereafter, Black) individuals experience worse prostate cancer outcomes due to socioeconomic and racial inequities of access to care. Few studies have empirically evaluated these disparities across different health care systems. Objective: To describe the racial and ethnic and neighborhood socioeconomic status (nSES) disparities among residents of the same communities who receive prostate cancer care in the US Department of Veterans Affairs (VA) health care system vs other settings. Design, setting, and participants: This cohort study obtained data from the VA Central Cancer Registry for veterans with prostate cancer who received care within the VA Greater Los Angeles Healthcare System (VA cohort) and from the California Cancer Registry (CCR) for nonveterans who received care outside the VA setting (CCR cohort). The cohorts consisted of all males with incident prostate cancer who were living within the same US Census tracts. These individuals received care between 2000 and 2018 and were followed up until death from any cause or censoring on December 31, 2018. Data analyses were conducted between September 2022 and December 2023. Exposures: Health care setting, self-identified race and ethnicity (SIRE), and nSES. Main outcomes and measures: The primary outcome was all-cause mortality (ACM). Cox proportional hazards regression models were used to estimate hazard ratios for associations of SIRE and nSES with prostate cancer outcomes in the VA and CCR cohorts. Results: Included in the analysis were 49 461 males with prostate cancer. Of these, 1881 males were in the VA cohort (mean [SD] age, 65.3 [7.7] years; 833 Black individuals [44.3%], 694 non-Hispanic White [hereafter, White] individuals [36.9%], and 354 individuals [18.8%] of other or unknown race). A total of 47 580 individuals were in the CCR cohort (mean [SD] age, 67.0 [9.6] years; 8183 Black individuals [17.2%], 26 206 White individuals [55.1%], and 13 191 individuals [27.8%] of other or unknown race). In the VA cohort, there were no racial disparities observed for metastasis, ACM, or prostate cancer-specific mortality (PCSM). However, in the CCR cohort, the racial disparities were observed for metastasis (adjusted odds ratio [AOR], 1.36; 95% CI, 1.22-1.52), ACM (adjusted hazard ratio [AHR], 1.13; 95% CI, 1.04-1.24), and PCSM (AHR, 1.15; 95% CI, 1.05-1.25). Heterogeneity was observed for the racial disparity in ACM in the VA vs CCR cohorts (AHR, 0.90 [95% CI, 0.76-1.06] vs 1.13 [95% CI, 1.04-1.24]; P = .01). No evidence of nSES disparities was observed for any prostate cancer outcomes in the VA cohort. However, in the CCR cohort, heterogeneity was observed for nSES disparities with ACM (AHR, 0.82; 95% CI, 0.80-0.84; P = .002) and PCSM (AHR, 0.86; 95% CI, 0.82-0.89; P = .007). Conclusions and relevance: Results of this study suggest that racial and nSES disparities were wider among patients seeking care outside of the VA health care system. Health systems-related interventions that address access barriers may mitigate racial and socioeconomic disparities in prostate cancer.
MeSH term(s)	United States/epidemiology ; Male ; Humans ; Aged ; Cohort Studies ; Ethnicity ; Prostatic Neoplasms/therapy ; Prostate ; Los Angeles
Language	English
Publishing date	2024-03-04
Publishing country	United States
Document type	Journal Article
ISSN	2574-3805
ISSN (online)	2574-3805
DOI	10.1001/jamanetworkopen.2024.2852
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