New Approaches Towards Visualization of Biological Samples by the Means of Liquid Phase TEM DOI

Evgeniya Pechnikova,

Hongyu Sun,

Alejandro Rozene

et al.

Microscopy and Microanalysis, Journal Year: 2024, Volume and Issue: 30(Supplement_1)

Published: July 1, 2024

Language: Английский

Identifying protein conformational states in the Protein Data Bank: Toward unlocking the potential of integrative dynamics studies DOI Creative Commons
Joseph I. J. Ellaway, Stephen Anyango, Sreenath Nair

et al.

Structural Dynamics, Journal Year: 2024, Volume and Issue: 11(3)

Published: May 1, 2024

Studying protein dynamics and conformational heterogeneity is crucial for understanding biomolecular systems treating disease. Despite the deposition of over 215 000 macromolecular structures in Protein Data Bank advent AI-based structure prediction tools such as AlphaFold2, RoseTTAFold, ESMFold, static representations are typically produced, which fail to fully capture motion. Here, we discuss importance integrating experimental with computational clustering explore landscapes that manifest function. We describe method developed by Europe - Knowledge Base identify distinct states, demonstrate resource's primary use cases, through examples, need further efforts annotate conformations functional information. Such initiatives will be unlocking potential data, expediting drug discovery research, deepening our mechanisms.

Language: Английский

Citations

9
EnsembleFlex: Protein Structure Ensemble Analysis Made Easy DOI
Melanie Schneider,

José Antonio Márquez,

Andrew R. Leach

et al.

Published: Jan. 1, 2025

Language: Английский

Citations

0
Quantum Mechanics Paradox in Protein Structure Prediction: Intrinsically Linked to Sequence yet Independent of it DOI Creative Commons
Sarfaraz K. Niazi

Deleted Journal, Journal Year: 2025, Volume and Issue: unknown, P. 100039 - 100039

Published: April 1, 2025

Language: Английский

Citations

0
Structure and Stabilities of Solution and Gas Phase Protein Complexes DOI Creative Commons
R. Rider,

Carter Lantz,

Liqi Fan

et al.

Journal of the American Society for Mass Spectrometry, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 21, 2024

Collision-induced unfolding (CIU) has provided new levels of understanding the stabilities and structure(s) for gas phase protein complex ions formed by electrospray ionization (ESI). Variable-temperature (vT-ESI) data provide complementary information about temperature-induced folding/unfolding (TIU) reactions solution ions. Results obtained using CIU TIU versus Such comparisons may most direct experimental approach to answer a long-standing question from Fred McLafferty: "For how long, under what conditions, extent, can structure be retained without solvent?" Answers this require greater (i) structure(s), stabilities, dynamics proteins/protein complexes in prior ESI; (ii) effects water removal droplet fission "freeze-drying" evaporation nanodroplet; (iii) potential structural changes that occur as traverse heated capillary, final stage transition solvent-free Here, we employ vT-ESI coupled with ion mobility-mass spectrometry (IM-MS) means more detailed answers above-mentioned questions. Apo- metalated-metallothionein-2A (MT), cysteine-rich metal binding protein, various proteoforms transthyretin (TTR), homotetrameric (56 kDa) retinol thyroxine transporter were studied examine distinct features across two different types complexes. The results work shed light on capabilities CIU, TIU, average charge state (Zavg) probing rugged energy landscape native proteins highlights cofactors (metal ions)

Language: Английский

Citations

1
New Approaches Towards Visualization of Biological Samples by the Means of Liquid Phase TEM DOI

Evgeniya Pechnikova,

Hongyu Sun,

Alejandro Rozene

et al.

Microscopy and Microanalysis, Journal Year: 2024, Volume and Issue: 30(Supplement_1)

Published: July 1, 2024

Language: Английский

Citations

0