scholarly journals Conformational Plasticity of the Clpap Aaa+ Protease Couples Protein Unfolding and Proteolysis

2021 ◽  
Vol 120 (3) ◽  
pp. 99a
Author(s):  
Alexandrea N. Rizo ◽  
Kyle Eric Lopez ◽  
James Shorter ◽  
Daniel R. Southworth
2019 ◽  
Author(s):  
Kyle E. Lopez ◽  
Alexandrea N. Rizo ◽  
Eric Tse ◽  
JiaBei Lin ◽  
Nathaniel W. Scull ◽  
...  

AbstractThe ClpAP complex functions as a “bacterial proteasome” that simultaneously unfolds and degrades proteins targeted for destruction. ClpA utilizes two AAA+ domains per protomer to power substrate unfolding and translocation into the ClpP proteolytic chamber. To understand this mechanism, we determined high-resolution structures of wildtype E. coli ClpAP in distinct substrate-bound states. ClpA forms a spiral with substrate contacts across both AAA+ domains, while protomers at the seam undergo nucleotide-specific rearrangements indicating a conserved rotary mechanism. ClpA IGL loops extend flexibly to bind the planar, heptameric ClpP surface and support a large ClpA-P rotation that re-orients the translocation channel. The symmetry mismatch is maintained at the spiral seam through bind and release states of the IGL loops, which appear precisely coupled to substrate translocation. Thus, ClpA rotates around the apical surface of ClpP to processively translocate substrate into the protease.


2020 ◽  
Vol 27 (5) ◽  
pp. 406-416 ◽  
Author(s):  
Kyle E. Lopez ◽  
Alexandrea N. Rizo ◽  
Eric Tse ◽  
JiaBei Lin ◽  
Nathaniel W. Scull ◽  
...  

Author(s):  
Khoa N. Pham ◽  
Ariel Lewis-Ballester ◽  
Syun-Ru Yeh

2021 ◽  
Vol 9 (5) ◽  
pp. 956
Author(s):  
Cihan Makbul ◽  
Vladimir Khayenko ◽  
Hans Michael Maric ◽  
Bettina Böttcher

Hepatitis B virus is a major human pathogen, which forms enveloped virus particles. During viral maturation, membrane-bound hepatitis B surface proteins package hepatitis B core protein capsids. This process is intercepted by certain peptides with an “LLGRMKG” motif that binds to the capsids at the tips of dimeric spikes. With microcalorimetry, electron cryo microscopy and peptide microarray-based screens, we have characterized the structural and thermodynamic properties of peptide binding to hepatitis B core protein capsids with different secretion phenotypes. The peptide “GSLLGRMKGA” binds weakly to hepatitis B core protein capsids and mutant capsids with a premature (F97L) or low-secretion phenotype (L60V and P5T). With electron cryo microscopy, we provide novel structures for L60V and P5T and demonstrate that binding occurs at the tips of the spikes at the dimer interface, splaying the helices apart independent of the secretion phenotype. Peptide array screening identifies “SLLGRM” as the core binding motif. This shortened motif binds only to one of the two spikes in the asymmetric unit of the capsid and induces a much smaller conformational change. Altogether, these comprehensive studies suggest that the tips of the spikes act as an autonomous binding platform that is unaffected by mutations that affect secretion phenotypes.


Nanoscale ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 5422-5434 ◽  
Author(s):  
David Winogradoff ◽  
Shalini John ◽  
Aleksei Aksimentiev

Molecular dynamics simulations reveal how anionic surfactant SDS and heat unfold full-length proteins.


2008 ◽  
Vol 130 (25) ◽  
pp. 7898-7907 ◽  
Author(s):  
Angel Orte ◽  
Timothy D. Craggs ◽  
Samuel S. White ◽  
Sophie E. Jackson ◽  
David Klenerman

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