Opportunities and obstacles for deep learning in biology and medicine

T Ching, DS Himmelstein… - Journal of the …, 2018 - royalsocietypublishing.org
Deep learning describes a class of machine learning algorithms that are capable of
combining raw inputs into layers of intermediate features. These algorithms have recently …

Structure, dynamics and function of the 26S proteasome

Y Mao - Macromolecular protein complexes III: structure and …, 2021 - Springer
The 26S proteasome is the most complex ATP-dependent protease machinery, of~ 2.5 MDa
mass, ubiquitously found in all eukaryotes. It selectively degrades ubiquitin-conjugated …

Structural mechanism for NEK7-licensed activation of NLRP3 inflammasome

H Sharif, L Wang, WL Wang, VG Magupalli, L Andreeva… - Nature, 2019 - nature.com
The NLRP3 inflammasome can be activated by stimuli that include nigericin, uric acid
crystals, amyloid-β fibrils and extracellular ATP. The mitotic kinase NEK7 licenses the …

Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome

Y Dong, S Zhang, Z Wu, X Li, WL Wang, Y Zhu… - Nature, 2019 - nature.com
The proteasome is an ATP-dependent, 2.5-megadalton molecular machine that is
responsible for selective protein degradation in eukaryotic cells. Here we present cryo …

USP14-regulated allostery of the human proteasome by time-resolved cryo-EM

S Zhang, S Zou, D Yin, L Zhao, D Finley, Z Wu, Y Mao - Nature, 2022 - nature.com
Proteasomal degradation of ubiquitylated proteins is tightly regulated at multiple levels,–. A
primary regulatory checkpoint is the removal of ubiquitin chains from substrates by the …

Structural basis for dynamic regulation of the human 26S proteasome

S Chen, J Wu, Y Lu, YB Ma, BH Lee… - Proceedings of the …, 2016 - National Acad Sciences
The proteasome is the major engine of protein degradation in all eukaryotic cells. At the
heart of this machine is a heterohexameric ring of AAA (ATPases associated with diverse …

Emerging themes in CryoEM─ Single particle analysis image processing

JL Vilas, JM Carazo, COS Sorzano - Chemical Reviews, 2022 - ACS Publications
Cryo-electron microscopy (CryoEM) has become a vital technique in structural biology. It is
an interdisciplinary field that takes advantage of advances in biochemistry, physics, and …

Structural mechanism for nucleotide-driven remodeling of the AAA-ATPase unfoldase in the activated human 26S proteasome

Y Zhu, WL Wang, D Yu, Q Ouyang, Y Lu… - Nature communications, 2018 - nature.com
The proteasome is a sophisticated ATP-dependent molecular machine responsible for
protein degradation in all known eukaryotic cells. It remains elusive how conformational …

Determining subunit-subunit interaction from statistics of cryo-EM images: observation of nearest-neighbor coupling in a circadian clock protein complex

X Han, D Zhang, L Hong, D Yu, Z Wu, T Yang… - Nature …, 2023 - nature.com
Biological processes are typically actuated by dynamic multi-subunit molecular complexes.
However, interactions between subunits, which govern the functions of these complexes, are …

Cryo-EM structure of the DNA-PK holoenzyme

H Sharif, Y Li, Y Dong, L Dong… - Proceedings of the …, 2017 - National Acad Sciences
DNA-dependent protein kinase (DNA-PK) is a large protein complex central to the
nonhomologous end joining (NHEJ) DNA-repair pathway. It comprises the DNA-PK catalytic …