LIVIVO - Search results -

Search results

Result 1 - 10 of total 170

Search options

Article ; Online: A FRET-Based Assay and Computational Tools to Quantify Enzymatic Rates and Explore the Mechanisms of RNA Deadenylases in Heterogeneous Environments.

Irwin, Rose / Harkness, Robert W / Forman-Kay, Julie D

Methods in molecular biology (Clifton, N.J.)

2023 Volume 2723, Page(s) 69–91

Abstract: We developed a medium-throughput assay that can measure the time-dependent distribution of RNA products generated as a deadenylase degrades a polyadenosine (poly(A)) RNA tract, thereby providing insight into the mechanism of deadenylation. Importantly, ... ...

Abstract	We developed a medium-throughput assay that can measure the time-dependent distribution of RNA products generated as a deadenylase degrades a polyadenosine (poly(A)) RNA tract, thereby providing insight into the mechanism of deadenylation. Importantly, this assay can be performed in both homogeneous and heterogeneous environments without relying on gel electrophoresis of RNA products or coupled enzymatic reactions that indirectly report on the RNA distribution through the detection of freed adenosine monophosphate. In parallel, we have established an open-source, Python-based command-line software package, deadenylationkinetics, that can be used to numerically simulate and/or fit the datasets afforded by our assay with different deadenylation mechanisms to determine the most likely case and estimate the associated rate constants. In this chapter, we detail the implementation of our method and the quantification of poly(A) RNA binding and degradation kinetics in application to a truncated version of CNOT7 from the CCR4-NOT deadenylation complex, which serves as a model deadenylase with enhanced activity.
MeSH term(s)	RNA ; RNA, Messenger/genetics ; Fluorescence Resonance Energy Transfer ; Adenosine Monophosphate ; Ribonucleases/metabolism ; Exoribonucleases/metabolism ; RNA Stability
Chemical Substances	RNA (63231-63-0) ; RNA, Messenger ; Adenosine Monophosphate (415SHH325A) ; Ribonucleases (EC 3.1.-) ; Exoribonucleases (EC 3.1.-)
Language	English
Publishing date	2023-10-12
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-3481-3_5
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Aberrant phase separation: linking IDR mutations to disease.

Ahmed, Rashik / Forman-Kay, Julie D

Cell research

2023 Volume 33, Issue 8, Page(s) 583–584

MeSH term(s)	Mutation ; Humans ; Disease/genetics
Language	English
Publishing date	2023-04-02
Publishing country	England
Document type	Journal Article
ZDB-ID	1319303-x
ISSN	1748-7838 ; 1001-0602
ISSN (online)	1748-7838
ISSN	1001-0602
DOI	10.1038/s41422-023-00804-4
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Cologne/Königswinter

Zs.A 5283: 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)

Order via subito

Details ▾

Article ; Online: NMR insights into dynamic, multivalent interactions of intrinsically disordered regions: from discrete complexes to condensates.

Ahmed, Rashik / Forman-Kay, Julie D

Essays in biochemistry

2022

Abstract: The spatial and temporal organization of interactions between proteins underlie the regulation of most cellular processes. The requirement for such interactions to be specific predisposes a view that protein-protein interactions are relatively static and ...

Abstract	The spatial and temporal organization of interactions between proteins underlie the regulation of most cellular processes. The requirement for such interactions to be specific predisposes a view that protein-protein interactions are relatively static and are formed through the stable complementarity of the interacting partners. A growing body of reports indicate, however, that many interactions lead to fuzzy complexes with an ensemble of conformations in dynamic exchange accounting for the observed binding. Here, we discuss how NMR has facilitated the characterization of these discrete, dynamic complexes and how such characterization has aided the understanding of dynamic, condensed phases of phase-separating proteins with exchanging multivalent interactions.
Language	English
Publishing date	2022-11-23
Publishing country	England
Document type	Journal Article
ISSN	1744-1358 ; 0071-1365
ISSN (online)	1744-1358
ISSN	0071-1365
DOI	10.1042/EBC20220056
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: An Interpretable Machine-Learning Algorithm to Predict Disordered Protein Phase Separation Based on Biophysical Interactions.

Cai, Hao / Vernon, Robert M / Forman-Kay, Julie D

Biomolecules

2022 Volume 12, Issue 8

Abstract: Protein phase separation is increasingly understood to be an important mechanism of biological organization and biomaterial formation. Intrinsically disordered protein regions (IDRs) are often significant drivers of protein phase separation. A number of ... ...

Abstract	Protein phase separation is increasingly understood to be an important mechanism of biological organization and biomaterial formation. Intrinsically disordered protein regions (IDRs) are often significant drivers of protein phase separation. A number of protein phase-separation-prediction algorithms are available, with many being specific for particular classes of proteins and others providing results that are not amenable to the interpretation of the contributing biophysical interactions. Here, we describe LLPhyScore, a new predictor of IDR-driven phase separation, based on a broad set of physical interactions or features. LLPhyScore uses sequence-based statistics from the RCSB PDB database of folded structures for these interactions, and is trained on a manually curated set of phase-separation-driving proteins with different negative training sets including the PDB and human proteome. Competitive training for a variety of physical chemical interactions shows the greatest contribution of solvent contacts, disorder, hydrogen bonds, pi-pi contacts, and kinked beta-structures to the score, with electrostatics, cation-pi contacts, and the absence of a helical secondary structure also contributing. LLPhyScore has strong phase-separation-prediction recall statistics and enables a breakdown of the contribution from each physical feature to a sequence's phase-separation propensity, while recognizing the interdependence of many of these features. The tool should be a valuable resource for guiding experiments and providing hypotheses for protein function in normal and pathological states, as well as for understanding how specificity emerges in defining individual biomolecular condensates.
MeSH term(s)	Algorithms ; Humans ; Intrinsically Disordered Proteins/chemistry ; Machine Learning ; Static Electricity
Chemical Substances	Intrinsically Disordered Proteins
Language	English
Publishing date	2022-08-17
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2701262-1
ISSN	2218-273X ; 2218-273X
ISSN (online)	2218-273X
ISSN	2218-273X
DOI	10.3390/biom12081131
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: Systematic identification of conditionally folded intrinsically disordered regions by AlphaFold2.

Alderson, T Reid / Pritišanac, Iva / Kolarić, Đesika / Moses, Alan M / Forman-Kay, Julie D

Proceedings of the National Academy of Sciences of the United States of America

2023 Volume 120, Issue 44, Page(s) e2304302120

Abstract: The AlphaFold Protein Structure Database contains predicted structures for millions of proteins. For the majority of human proteins that contain intrinsically disordered regions (IDRs), which do not adopt a stable structure, it is generally assumed that ... ...

Abstract	The AlphaFold Protein Structure Database contains predicted structures for millions of proteins. For the majority of human proteins that contain intrinsically disordered regions (IDRs), which do not adopt a stable structure, it is generally assumed that these regions have low AlphaFold2 confidence scores that reflect low-confidence structural predictions. Here, we show that AlphaFold2 assigns confident structures to nearly 15% of human IDRs. By comparison to experimental NMR data for a subset of IDRs that are known to conditionally fold (i.e., upon binding or under other specific conditions), we find that AlphaFold2 often predicts the structure of the conditionally folded state. Based on databases of IDRs that are known to conditionally fold, we estimate that AlphaFold2 can identify conditionally folding IDRs at a precision as high as 88% at a 10% false positive rate, which is remarkable considering that conditionally folded IDR structures were minimally represented in its training data. We find that human disease mutations are nearly fivefold enriched in conditionally folded IDRs over IDRs in general and that up to 80% of IDRs in prokaryotes are predicted to conditionally fold, compared to less than 20% of eukaryotic IDRs. These results indicate that a large majority of IDRs in the proteomes of human and other eukaryotes function in the absence of conditional folding, but the regions that do acquire folds are more sensitive to mutations. We emphasize that the AlphaFold2 predictions do not reveal functionally relevant structural plasticity within IDRs and cannot offer realistic ensemble representations of conditionally folded IDRs.
MeSH term(s)	Humans ; Intrinsically Disordered Proteins/chemistry ; Eukaryota/metabolism ; Protein Conformation
Chemical Substances	Intrinsically Disordered Proteins
Language	English
Publishing date	2023-10-25
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2304302120
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 1148: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Exploration of O-GlcNAc transferase glycosylation sites reveals a target sequence compositional bias.

Chong, P Andrew / Nosella, Michael L / Vanama, Manasvi / Ruiz-Arduengo, Roxana / Forman-Kay, Julie D

The Journal of biological chemistry

2023 Volume 299, Issue 5, Page(s) 104629

Abstract: O-GlcNAc transferase (OGT) is an essential glycosylating enzyme that catalyzes the addition of N-acetylglucosamine to serine or threonine residues of nuclear and cytoplasmic proteins. The enzyme glycosylates a broad range of peptide sequences and the ... ...

Abstract	O-GlcNAc transferase (OGT) is an essential glycosylating enzyme that catalyzes the addition of N-acetylglucosamine to serine or threonine residues of nuclear and cytoplasmic proteins. The enzyme glycosylates a broad range of peptide sequences and the prediction of glycosylation sites has proven challenging. The lack of an experimentally verified set of polypeptide sequences that are not glycosylated by OGT has made prediction of legitimate glycosylation sites more difficult. Here, we tested a number of intrinsically disordered protein regions as substrates of OGT to establish a set of sequences that are not glycosylated by OGT. The negative data set suggests an amino acid compositional bias for OGT targets. This compositional bias was validated by modifying the amino acid composition of the protein fused in sarcoma (FUS) to enhance glycosylation. NMR experiments demonstrate that the tetratricopeptide repeat region of OGT can bind FUS and that glycosylation-promoting mutations enhance binding. These results provide evidence that the tetratricopeptide repeat region recognizes disordered segments of substrates with particular compositions to promote glycosylation, providing insight into the broad specificity of OGT.
MeSH term(s)	Amino Acids/metabolism ; Glycosylation ; Mutation ; N-Acetylglucosaminyltransferases/metabolism ; Humans ; Adaptor Proteins, Signal Transducing/chemistry ; Adaptor Proteins, Signal Transducing/genetics ; Adaptor Proteins, Signal Transducing/metabolism ; Computational Biology ; Magnetic Resonance Imaging
Chemical Substances	Amino Acids ; N-Acetylglucosaminyltransferases (EC 2.4.1.-) ; O-GlcNAc transferase (EC 2.4.1.-) ; GOPC protein, human ; Adaptor Proteins, Signal Transducing ; EWSR1 protein, human ; TAF15 protein, human
Language	English
Publishing date	2023-03-22
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2023.104629
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Uc I Zs.108: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Intrinsic disorder: A term to define the specific physicochemical characteristic of protein conformational heterogeneity.

Lemke, Edward A / Babu, M Madan / Kriwacki, Richard W / Mittag, Tanja / Pappu, Rohit V / Wright, Peter E / Forman-Kay, Julie D

Molecular cell

2024 Volume 84, Issue 7, Page(s) 1188–1190

Abstract: In his commentary in this issue of Molecular Cell, ...

Abstract	In his commentary in this issue of Molecular Cell,
MeSH term(s)	Intrinsically Disordered Proteins/metabolism ; Protein Conformation
Chemical Substances	Intrinsically Disordered Proteins
Language	English
Publishing date	2024-04-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2024.02.024
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Cologne/Königswinter

Zs.A 5055: 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)

Order via subito

Details ▾

Article ; Online: Phosphorylation-dependent regulation of messenger RNA transcription, processing and translation within biomolecular condensates.

Nosella, Michael L / Forman-Kay, Julie D

Current opinion in cell biology

2021 Volume 69, Page(s) 30–40

Abstract: Regulation of messenger RNA (mRNA) transcription, processing and translation occurs in the context of biomolecular condensates. How the physical properties of condensates connect with their biological regulatory functions is an ongoing area of interest, ... ...

Abstract	Regulation of messenger RNA (mRNA) transcription, processing and translation occurs in the context of biomolecular condensates. How the physical properties of condensates connect with their biological regulatory functions is an ongoing area of interest, particularly for RNA metabolic pathways. Phosphorylation has emerged as an important mechanism for regulating protein phase separation propensities and localization patterns into different condensates, affecting compositions and dynamics. Key factors in transcription, mRNA processing and translation exhibit such phosphorylation-dependent changes in their roles within condensates, including their catalytic activities. Phosphorylation is increasingly understood to regulate the exchange of proteins through functionally linked condensates to fulfil their mRNA metabolic functions.
MeSH term(s)	Humans ; Phosphorylation ; Protein Biosynthesis ; Proteins/metabolism ; RNA, Messenger/genetics
Chemical Substances	Proteins ; RNA, Messenger
Language	English
Publishing date	2021-01-13
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1026381-0
ISSN	1879-0410 ; 0955-0674
ISSN (online)	1879-0410
ISSN	0955-0674
DOI	10.1016/j.ceb.2020.12.007
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Cologne/Königswinter

Zs.A 2963: 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)

Order via subito

Details ▾

Article ; Online: Transitions in the framework of condensate biology

Seydoux, Geraldine / Zhang, Mingjie / Forman-Kay, Julie D. / McStay, Brian / Liu, Kathy Fange / Li, Pilong

Molecular Cell. 2023 Apr., v. 83, no. 7 p.1016-1021

2023

Abstract: As phase separation is found in an increasing variety of biological contexts, additional challenges have arisen in understanding the underlying principles of condensate formation and function. We spoke with researchers across disciplines about their ... ...

Abstract	As phase separation is found in an increasing variety of biological contexts, additional challenges have arisen in understanding the underlying principles of condensate formation and function. We spoke with researchers across disciplines about their views on the ever-changing landscape of biomolecular condensates.
Keywords	condensates ; landscapes ; separation
Language	English
Dates of publication	2023-04
Size	p. 1016-1021.
Publishing place	Elsevier Inc.
Document type	Article ; Online
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2023.03.014
Database	NAL-Catalogue (AGRICOLA)

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Bonn / Germany

Z 2005/501: Show issues

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾

Article ; Online: Surface electrostatics dictate RNA-binding protein CAPRIN1 condensate concentration and hydrodynamic properties.

Toyama, Yuki / Rangadurai, Atul Kaushik / Forman-Kay, Julie D / Kay, Lewis E

The Journal of biological chemistry

2022 Volume 299, Issue 1, Page(s) 102776

Abstract: Biomolecular condensates concentrate proteins, nucleic acids, and small molecules and play an essential role in many biological processes. Their formation is tuned by a balance between energetically favorable and unfavorable contacts, with charge-charge ... ...

Abstract	Biomolecular condensates concentrate proteins, nucleic acids, and small molecules and play an essential role in many biological processes. Their formation is tuned by a balance between energetically favorable and unfavorable contacts, with charge-charge interactions playing a central role in some systems. The positively charged intrinsically disordered carboxy-terminal region of the RNA-binding protein CAPRIN1 is one such example, phase separating upon addition of negatively charged ATP or high concentrations of sodium chloride (NaCl). Using solution NMR spectroscopy, we measured residue-specific near-surface electrostatic potentials (ϕ
MeSH term(s)	Adenosine Triphosphate ; Hydrodynamics ; Intrinsically Disordered Proteins/chemistry ; RNA-Binding Proteins/chemistry ; Sodium Chloride/metabolism ; Static Electricity
Chemical Substances	Adenosine Triphosphate (8L70Q75FXE) ; Intrinsically Disordered Proteins ; RNA-Binding Proteins ; Sodium Chloride (451W47IQ8X)
Language	English
Publishing date	2022-12-07
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2022.102776
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Uc I Zs.108: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

To top

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

Full text online

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

Full text online

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

Full text online

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

Full text online

More links

Kategorien

In stock of ZB MED Bonn / Germany

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito