A strategy for refining the calculation of contacts in protein-RNA complexes DOI
Luana Luiza Bastos, Rafael Pereira Lemos, Diego Mariano

et al.

Published: Dec. 2, 2024

Protein-RNA interactions are essential for several biological processes, including gene expression. However, traditional methods studying these use superficial criteria to perform this analysis, which can lead false positives. This study presents a new strategy modeling protein-RNA contacts. We classify RNA atoms and integrate previously used protein contacts, developing the proposed approach that detects broader range of interactions. compare our proposal an existing benchmark observe method identifies more contacts provides detailed insights into different types interactions, such as aromatic stacking hydrogen bonding. envision could improve development interaction databases deepen understanding complexes.

Language: Английский

Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry DOI Creative Commons
Yuming Jiang, Rex Devasahayam Arokia Balaya, Dina Schuster

et al.

ACS Measurement Science Au, Journal Year: 2024, Volume and Issue: 4(4), P. 338 - 417

Published: June 4, 2024

Proteomics is the large scale study of protein structure and function from biological systems through identification quantification."Shotgun proteomics" or "bottom-up prevailing strategy, in which proteins are hydrolyzed into peptides that analyzed by mass spectrometry.Proteomics studies can be applied to diverse ranging simple proteoforms, protein-protein interactions, structural alterations, absolute relative quantification, post-translational modifications, stability.To enable this range different experiments, there strategies for proteome analysis.The nuances how proteomic workflows differ may challenging understand new practitioners.Here, we provide a comprehensive overview proteomics methods.We cover biochemistry basics extraction interpretation orthogonal validation.We expect Review will serve as handbook researchers who field bottom-up proteomics.

Language: Английский

Citations

25
Comprehensive Overview of Bottom-up Proteomics using Mass Spectrometry DOI Creative Commons
Yuming Jiang, Rex Devasahayam Arokia Balaya, Dina Schuster

et al.

arXiv (Cornell University), Journal Year: 2023, Volume and Issue: unknown

Published: Jan. 1, 2023

Proteomics is the large scale study of protein structure and function from biological systems through identification quantification. "Shotgun proteomics" or "bottom-up prevailing strategy, in which proteins are hydrolyzed into peptides that analyzed by mass spectrometry. studies can be applied to diverse ranging simple proteoforms, protein-protein interactions, structural alterations, absolute relative quantification, post-translational modifications, stability. To enable this range different experiments, there strategies for proteome analysis. The nuances how proteomic workflows differ may challenging understand new practitioners. Here, we provide a comprehensive overview proteomics methods aid novice experienced researcher. We cover biochemistry basics extraction interpretation orthogonal validation. expect work serve as basic resource practitioners field shotgun bottom-up proteomics.

Language: Английский

Citations

2
A special issue ofEssays in Biochemistryon structural mass spectrometry DOI Creative Commons
Hannah M. Britt, Rebecca Beveridge, Antonio N. Calabrese

et al.

Essays in Biochemistry, Journal Year: 2023, Volume and Issue: 67(2), P. 147 - 149

Published: March 1, 2023

Abstract Mass spectrometry (MS) is now established as an analytical tool to interrogate the structure and dynamics of proteins their assemblies. An array MS-based technologies has been developed, with each providing unique information pertaining protein structure, forming heart integrative structural biology studies. This special issue includes a collection review articles that discuss both emerging MS methodologies, along examples how these are being deployed function. Combined, this highlights immense potential toolkit in study molecular mechanisms underpinning cellular homeostasis disease.

Language: Английский

Citations

1
Multi-adductomics: Advancing mass spectrometry techniques for comprehensive exposome characterization DOI
Mu‐Rong Chao, Yuan-Jhe Chang, Marcus S. Cooke

et al.

TrAC Trends in Analytical Chemistry, Journal Year: 2024, Volume and Issue: 180, P. 117900 - 117900

Published: Aug. 5, 2024

Language: Английский

Citations

0
A strategy for refining the calculation of contacts in protein-RNA complexes DOI
Luana Luiza Bastos, Rafael Pereira Lemos, Diego Mariano

et al.

Published: Dec. 2, 2024

Protein-RNA interactions are essential for several biological processes, including gene expression. However, traditional methods studying these use superficial criteria to perform this analysis, which can lead false positives. This study presents a new strategy modeling protein-RNA contacts. We classify RNA atoms and integrate previously used protein contacts, developing the proposed approach that detects broader range of interactions. compare our proposal an existing benchmark observe method identifies more contacts provides detailed insights into different types interactions, such as aromatic stacking hydrogen bonding. envision could improve development interaction databases deepen understanding complexes.

Language: Английский

Citations

0