Advances in hydrogen/deuterium exchange mass spectrometry and the pursuit of challenging biological systems

EI James, TA Murphree, C Vorauer, JR Engen… - Chemical …, 2021 - ACS Publications
Solution-phase hydrogen/deuterium exchange (HDX) coupled to mass spectrometry (MS) is
a widespread tool for structural analysis across academia and the biopharmaceutical …

Periplasmic chaperones: outer membrane biogenesis and envelope stress

AN Combs, TJ Silhavy - Annual Review of Microbiology, 2024 - annualreviews.org
Envelope biogenesis and homeostasis in gram-negative bacteria are exceptionally intricate
processes that require a multitude of periplasmic chaperones to ensure cellular survival …

Bacteroides fragilis ubiquitin homologue drives intraspecies bacterial competition in the gut microbiome

K Jiang, W Li, M Tong, J Xu, Z Chen, Y Yang… - Nature …, 2024 - nature.com
Interbacterial antagonism and associated defensive strategies are both essential during
bacterial competition. The human gut symbiont Bacteroides fragilis secretes a ubiquitin …

FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices

E Lerner, A Barth, J Hendrix, B Ambrose, V Birkedal… - Elife, 2021 - elifesciences.org
Single-molecule FRET (smFRET) has become a mainstream technique for studying
biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by …

Outer membrane protein assembly mediated by BAM-SurA complexes

KL Fenn, JE Horne, JA Crossley, N Böhringer… - Nature …, 2024 - nature.com
The outer membrane is a formidable barrier that protects Gram-negative bacteria against
environmental threats. Its integrity requires the correct folding and insertion of outer …

PyXlinkViewer: A flexible tool for visualization of protein chemical crosslinking data within the PyMOL molecular graphics system

B Schiffrin, SE Radford, DJ Brockwell… - Protein …, 2020 - Wiley Online Library
Chemical crosslinking‐mass spectrometry (XL‐MS) is a valuable technique for gaining
insights into protein structure and the organization of macromolecular complexes. XL‐MS …

ATP-independent chaperones

R Mitra, K Wu, C Lee… - Annual Review of …, 2022 - annualreviews.org
The folding of proteins into their native structure is crucial for the functioning of all biological
processes. Molecular chaperones are guardians of the proteome that assist in protein …

Deep learning-driven insights into super protein complexes for outer membrane protein biogenesis in bacteria

M Gao, DN An, J Skolnick - Elife, 2022 - elifesciences.org
To reach their final destinations, outer membrane proteins (OMPs) of gram-negative bacteria
undertake an eventful journey beginning in the cytosol. Multiple molecular machines …

Machine learning-boosted docking enables the efficient structure-based virtual screening of giga-scale enumerated chemical libraries

T Sivula, L Yetukuri, T Kalliokoski… - Journal of Chemical …, 2023 - ACS Publications
The emergence of ultra-large screening libraries, filled to the brim with billions of readily
available compounds, poses a growing challenge for docking-based virtual screening …

Dynamic interplay between the periplasmic chaperone SurA and the BAM complex in outer membrane protein folding

B Schiffrin, JM Machin, TK Karamanos… - Communications …, 2022 - nature.com
Correct folding of outer membrane proteins (OMPs) into the outer membrane of Gram-
negative bacteria depends on delivery of unfolded OMPs to the β-barrel assembly …