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Book: Structural studies of protein nucleic acid interaction

Steitz, Thomas A.

the sources of sequence specific binding

1993

Title variant	protein-nucleic sequence-specific
Author's details	Thomas A. Steitz
Keywords	DNA-Binding Proteins ; RNA-Binding Proteins ; Molecular Sequence Data ; Zinc Fingers ; Nucleic Acid Conformation ; Protein Conformation ; Transcription Factors ; Nuclear Magnetic Resonance ; Crystallography ; DNS-Bindungsproteine
Subject	DNA-Bindungsproteine ; DNS-bindendes Protein ; DNA-bindendes Protein ; DNS-bindende Proteine ; DNS-Bindeproteine ; DNS-Proteinkomplex ; Protein-DNS-Komplex
Language	English
Size	VII, 79 S.: Ill., graph. Darst.
Publisher	Cambridge Univ. Press
Publishing place	Cambridge u.a.
Publishing country	Great Britain
Document type	Book
HBZ-ID	HT004550980
ISBN	0-521-41489-X ; 978-0-521-41489-0
Database	Catalogue ZB MED Medicine, Health

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1994 A 1389	order for loan	Magazin

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Article ; Online: Molecular dynamics analysis of Mg

Joseph, Newlyn N / Roy, Raktim N / Steitz, Thomas A

Journal of computational chemistry

2020 Volume 41, Issue 14, Page(s) 1345–1352

Abstract: Pistol ribozymes comprise a class of small, self-cleaving RNAs discovered via comparative genomic analysis. Prior work in the field has probed the kinetics of the cleavage reaction, as well as the influence of various metal ion cofactors that accelerate ... ...

Abstract	Pistol ribozymes comprise a class of small, self-cleaving RNAs discovered via comparative genomic analysis. Prior work in the field has probed the kinetics of the cleavage reaction, as well as the influence of various metal ion cofactors that accelerate the process. In the current study, we performed unbiased and unconstrained molecular dynamics simulations from two current high-resolution pistol crystal structures, and we analyzed trajectory data within the context of the currently accepted ribozyme mechanistic framework. Root-mean-squared deviations, radial distribution functions, and distributions of nucleophilic angle-of-attack reveal insights into the potential roles of three magnesium ions with respect to catalysis and overall conformational stability of the molecule. A series of simulation trajectories containing in silico mutations reveal the relatively flexible and partially interchangeable roles of two particular magnesium ions within solvated hydrogen-bonding distances from the catalytic center.
MeSH term(s)	Biocatalysis ; Ions/chemistry ; Ions/metabolism ; Magnesium/chemistry ; Magnesium/metabolism ; Molecular Dynamics Simulation ; RNA, Catalytic/chemistry ; RNA, Catalytic/metabolism
Chemical Substances	Ions ; RNA, Catalytic ; Magnesium (I38ZP9992A)
Language	English
Publishing date	2020-02-24
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1479181-X
ISSN	1096-987X ; 0192-8651
ISSN (online)	1096-987X
ISSN	0192-8651
DOI	10.1002/jcc.26179
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Article ; Online: Perspectives on the ribosome.

Steitz, Thomas A / Moore, Peter B

Philosophical transactions of the Royal Society of London. Series B, Biological sciences

2017 Volume 372, Issue 1716

Language	English
Publishing date	2017--19
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	208382-6
ISSN	1471-2970 ; 0080-4622 ; 0264-3839 ; 0962-8436
ISSN (online)	1471-2970
ISSN	0080-4622 ; 0264-3839 ; 0962-8436
DOI	10.1098/rstb.2016.0537
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Article ; Online: POINT: Pipeline for Offline Conversion and Integration of Geocodes and Neighborhood Data.

Guo, Kevin / McCoy, Allison B / Reese, Thomas J / Wright, Adam / Rosenbloom, Samuel Trent / Liu, Siru / Russo, Elise M / Steitz, Bryan D

Applied clinical informatics

2023 Volume 14, Issue 5, Page(s) 833–842

Abstract: Objectives: Geocoding, the process of converting addresses into precise geographic coordinates, allows researchers and health systems to obtain neighborhood-level estimates of social determinants of health. This information supports opportunities to ... ...

Abstract	Objectives: Geocoding, the process of converting addresses into precise geographic coordinates, allows researchers and health systems to obtain neighborhood-level estimates of social determinants of health. This information supports opportunities to personalize care and interventions for individual patients based on the environments where they live. We developed an integrated offline geocoding pipeline to streamline the process of obtaining address-based variables, which can be integrated into existing data processing pipelines. Methods: POINT is a web-based, containerized, application for geocoding addresses that can be deployed offline and made available to multiple users across an organization. Our application supports use through both a graphical user interface and application programming interface to query geographic variables, by census tract, without exposing sensitive patient data. We evaluated our application's performance using two datasets: one consisting of 1 million nationally representative addresses sampled from Open Addresses, and the other consisting of 3,096 previously geocoded patient addresses. Results: A total of 99.4 and 99.8% of addresses in the Open Addresses and patient addresses datasets, respectively, were geocoded successfully. Census tract assignment was concordant with reference in greater than 90% of addresses for both datasets. Among successful geocodes, median (interquartile range) distances from reference coordinates were 52.5 (26.5-119.4) and 14.5 (10.9-24.6) m for the two datasets. Conclusion: POINT successfully geocodes more addresses and yields similar accuracy to existing solutions, including the U.S. Census Bureau's official geocoder. Addresses are considered protected health information and cannot be shared with common online geocoding services. POINT is an offline solution that enables scalability to multiple users and integrates downstream mapping to neighborhood-level variables with a pipeline that allows users to incorporate additional datasets as they become available. As health systems and researchers continue to explore and improve health equity, it is essential to quickly and accurately obtain neighborhood variables in a Health Insurance Portability and Accountability Act (HIPAA)-compliant way.
MeSH term(s)	Humans ; Geographic Information Systems ; Geographic Mapping ; Residence Characteristics ; Software
Language	English
Publishing date	2023-08-04
Publishing country	Germany
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	1869-0327
ISSN (online)	1869-0327
DOI	10.1055/a-2148-6414
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Article ; Online: Development and Validation of a Machine Learning Algorithm Using Clinical Pages to Predict Imminent Clinical Deterioration.

Steitz, Bryan D / McCoy, Allison B / Reese, Thomas J / Liu, Siru / Weavind, Liza / Shipley, Kipp / Russo, Elise / Wright, Adam

Journal of general internal medicine

2023 Volume 39, Issue 1, Page(s) 27–35

Abstract: Background: Early detection of clinical deterioration among hospitalized patients is a clinical priority for patient safety and quality of care. Current automated approaches for identifying these patients perform poorly at identifying imminent events.!## ...

Abstract	Background: Early detection of clinical deterioration among hospitalized patients is a clinical priority for patient safety and quality of care. Current automated approaches for identifying these patients perform poorly at identifying imminent events. Objective: Develop a machine learning algorithm using pager messages sent between clinical team members to predict imminent clinical deterioration. Design: We conducted a large observational study using long short-term memory machine learning models on the content and frequency of clinical pages. Participants: We included all hospitalizations between January 1, 2018 and December 31, 2020 at Vanderbilt University Medical Center that included at least one page message to physicians. Exclusion criteria included patients receiving palliative care, hospitalizations with a planned intensive care stay, and hospitalizations in the top 2% longest length of stay. Main measures: Model classification performance to identify in-hospital cardiac arrest, transfer to intensive care, or Rapid Response activation in the next 3-, 6-, and 12-hours. We compared model performance against three common early warning scores: Modified Early Warning Score, National Early Warning Score, and the Epic Deterioration Index. Key results: There were 87,783 patients (mean [SD] age 54.0 [18.8] years; 45,835 [52.2%] women) who experienced 136,778 hospitalizations. 6214 hospitalized patients experienced a deterioration event. The machine learning model accurately identified 62% of deterioration events within 3-hours prior to the event and 47% of events within 12-hours. Across each time horizon, the model surpassed performance of the best early warning score including area under the receiver operating characteristic curve at 6-hours (0.856 vs. 0.781), sensitivity at 6-hours (0.590 vs. 0.505), specificity at 6-hours (0.900 vs. 0.878), and F-score at 6-hours (0.291 vs. 0.220). Conclusions: Machine learning applied to the content and frequency of clinical pages improves prediction of imminent deterioration. Using clinical pages to monitor patient acuity supports improved detection of imminent deterioration without requiring changes to clinical workflow or nursing documentation.
MeSH term(s)	Humans ; Female ; Middle Aged ; Male ; Clinical Deterioration ; Hospitalization ; Critical Care ; ROC Curve ; Algorithms ; Machine Learning ; Retrospective Studies
Language	English
Publishing date	2023-08-01
Publishing country	United States
Document type	Observational Study ; Journal Article
ZDB-ID	639008-0
ISSN	1525-1497 ; 0884-8734
ISSN (online)	1525-1497
ISSN	0884-8734
DOI	10.1007/s11606-023-08349-3
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Article ; Online: A structure-based kinetic model of transcription.

Zuo, Yuhong / Steitz, Thomas A

Transcription

2017 Volume 8, Issue 1, Page(s) 1–8

Abstract: During transcription, RNA polymerase moves downstream along the DNA template and maintains a transcription bubble. Several recent structural studies of transcription complexes with a complete transcription bubble provide new insights into how RNAP ... ...

Abstract	During transcription, RNA polymerase moves downstream along the DNA template and maintains a transcription bubble. Several recent structural studies of transcription complexes with a complete transcription bubble provide new insights into how RNAP couples the nucleotide addition reaction to its directional movement.
MeSH term(s)	DNA/chemistry ; DNA/genetics ; DNA-Directed RNA Polymerases/chemistry ; DNA-Directed RNA Polymerases/metabolism ; Models, Molecular ; Transcription, Genetic
Chemical Substances	DNA (9007-49-2) ; DNA-Directed RNA Polymerases (EC 2.7.7.6)
Language	English
Publishing date	2017
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2646974-1
ISSN	2154-1272 ; 2154-1264
ISSN (online)	2154-1272
ISSN	2154-1264
DOI	10.1080/21541264.2016.1234821
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Article ; Online: Structural Insights into Transcription Initiation from

Zuo, Yuhong / De, Swastik / Feng, Yingang / Steitz, Thomas A

iScience

2020 Volume 23, Issue 9, Page(s) 101445

Abstract: In bacteria, the dissociable σ subunit of the RNA polymerase (RNAP) is responsible for initiating RNA synthesis from specific DNA sites. As nascent RNA grows, downstream DNA unwinds and is pulled into the RNAP, causing stress accumulation and initiation ... ...

Abstract	In bacteria, the dissociable σ subunit of the RNA polymerase (RNAP) is responsible for initiating RNA synthesis from specific DNA sites. As nascent RNA grows, downstream DNA unwinds and is pulled into the RNAP, causing stress accumulation and initiation complex destabilization. Processive transcription elongation requires at least partial separation of the σ factor from the RNAP core enzyme. Here, we present a series of transcription complexes captured between the early initiation and elongation phases via in-crystal RNA synthesis and cleavage. Crystal structures of these complexes indicate that stress accumulation during transcription initiation is not due to clashing of the growing nascent RNA with the σ
Language	English
Publishing date	2020-08-11
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2020.101445
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Article ; Online: Structural insights into NusG regulating transcription elongation.

Liu, Bin / Steitz, Thomas A

Nucleic acids research

2016 Volume 45, Issue 2, Page(s) 968–974

Abstract: NusG is an essential transcription factor that plays multiple key regulatory roles in transcription elongation, termination and coupling translation and transcription. The core role of NusG is to enhance transcription elongation and RNA polymerase ... ...

Abstract	NusG is an essential transcription factor that plays multiple key regulatory roles in transcription elongation, termination and coupling translation and transcription. The core role of NusG is to enhance transcription elongation and RNA polymerase processivity. Here, we present the structure of Escherichia coli RNA polymerase complexed with NusG. The structure shows that the NusG N-terminal domain (NGN) binds at the central cleft of RNA polymerase surrounded by the β' clamp helices, the β protrusion, and the β lobe domains to close the promoter DNA binding channel and constrain the β' clamp domain, but with an orientation that is different from the one observed in the archaeal β' clamp-Spt4/5 complex. The structure also allows us to construct a reliable model of the complete NusG-associated transcription elongation complex, suggesting that the NGN domain binds at the upstream fork junction of the transcription elongation complex, similar to σ2 in the transcription initiation complex, to stabilize the junction, and therefore enhances transcription processivity.
MeSH term(s)	Escherichia coli/genetics ; Escherichia coli/metabolism ; Escherichia coli Proteins/chemistry ; Escherichia coli Proteins/metabolism ; Gene Expression Regulation, Bacterial ; Models, Biological ; Models, Molecular ; Molecular Conformation ; Peptide Elongation Factors/chemistry ; Peptide Elongation Factors/metabolism ; Protein Binding ; Protein Interaction Domains and Motifs ; Structure-Activity Relationship ; Transcription Elongation, Genetic ; Transcription Factors/chemistry ; Transcription Factors/metabolism
Chemical Substances	Escherichia coli Proteins ; NusG protein, E coli ; Peptide Elongation Factors ; Transcription Factors
Language	English
Publishing date	2016-11-29
Publishing country	England
Document type	Journal Article
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/gkw1159
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Zs.A 1067: Show issues

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ab Jg. 2022: Lesesaal (EG)

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Article ; Online: From the structure and function of the ribosome to new antibiotics (Nobel Lecture).

Steitz, Thomas A

Angewandte Chemie (International ed. in English)

2010 Volume 49, Issue 26, Page(s) 4381–4398

MeSH term(s)	Anti-Bacterial Agents/chemistry ; Anti-Bacterial Agents/pharmacology ; Biochemistry/history ; Crystallography, X-Ray ; History, 21st Century ; Nobel Prize ; Protein Structure, Tertiary ; Protein Subunits/antagonists & inhibitors ; Protein Subunits/metabolism ; RNA, Ribosomal, 23S/chemistry ; Ribosomes/chemistry ; Substrate Specificity ; United States
Chemical Substances	Anti-Bacterial Agents ; Protein Subunits ; RNA, Ribosomal, 23S
Language	English
Publishing date	2010-06-14
Publishing country	Germany
Document type	Autobiography ; Biography ; Historical Article ; Lectures ; Portraits ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2011836-3
ISSN	1521-3773 ; 1433-7851
ISSN (online)	1521-3773
ISSN	1433-7851
DOI	10.1002/anie.201000708
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Article ; Online: Conceptualizing clinical decision support as complex interventions: a meta-analysis of comparative effectiveness trials.

Reese, Thomas J / Liu, Siru / Steitz, Bryan / McCoy, Allison / Russo, Elise / Koh, Brian / Ancker, Jessica / Wright, Adam

Journal of the American Medical Informatics Association : JAMIA

2022 Volume 29, Issue 10, Page(s) 1744–1756

Abstract: Objectives: Complex interventions with multiple components and behavior change strategies are increasingly implemented as a form of clinical decision support (CDS) using native electronic health record functionality. Objectives of this study were, ... ...

Abstract	Objectives: Complex interventions with multiple components and behavior change strategies are increasingly implemented as a form of clinical decision support (CDS) using native electronic health record functionality. Objectives of this study were, therefore, to (1) identify the proportion of randomized controlled trials with CDS interventions that were complex, (2) describe common gaps in the reporting of complexity in CDS research, and (3) determine the impact of increased complexity on CDS effectiveness. Materials and methods: To assess CDS complexity and identify reporting gaps for characterizing CDS interventions, we used the Preferred Reporting Items for Systematic Reviews and Meta-Analyses reporting tool for complex interventions. We evaluated the effect of increased complexity using random-effects meta-analysis. Results: Most included studies evaluated a complex CDS intervention (76%). No studies described use of analytical frameworks or causal pathways. Two studies discussed use of theory but only one fully described the rationale and put it in context of a behavior change. A small but positive effect (standardized mean difference, 0.147; 95% CI, 0.039-0.255; P < .01) in favor of increasing intervention complexity was observed. Discussion: While most CDS studies should classify interventions as complex, opportunities persist for documenting and providing resources in a manner that would enable CDS interventions to be replicated and adapted. Unless reporting of the design, implementation, and evaluation of CDS interventions improves, only slight benefits can be expected. Conclusion: Conceptualizing CDS as complex interventions may help convey the careful attention that is needed to ensure these interventions are contextually and theoretically informed.
MeSH term(s)	Decision Support Systems, Clinical ; Randomized Controlled Trials as Topic
Language	English
Publishing date	2022-06-02
Publishing country	England
Document type	Journal Article ; Meta-Analysis ; Research Support, N.I.H., Extramural
ZDB-ID	1205156-1
ISSN	1527-974X ; 1067-5027
ISSN (online)	1527-974X
ISSN	1067-5027
DOI	10.1093/jamia/ocac089
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