scholarly journals Entropic stabilization of a deubiquitinase provides conformational plasticity and slow unfolding kinetics beneficial for functioning on the proteasome

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Yun-Tzai Cloud Lee ◽  
Chia-Yun Chang ◽  
Szu-Yu Chen ◽  
Yun-Ru Pan ◽  
Meng-Ru Ho ◽  
...  
Keyword(s):  
Conformational Plasticity ◽  
Unfolding Kinetics ◽  
Entropic Stabilization

scholarly journals Conformational Plasticity in Human Heme-Based Dioxygenases

2020 ◽  
Author(s):  
Khoa N. Pham ◽  
Ariel Lewis-Ballester ◽  
Syun-Ru Yeh
Keyword(s):  
Conformational Plasticity

scholarly journals Conformational Plasticity of Hepatitis B Core Protein Spikes Promotes Peptide Binding Independent of the Secretion Phenotype

2021 ◽  
Vol 9 (5) ◽  
pp. 956
Author(s):  
Cihan Makbul ◽  
Vladimir Khayenko ◽  
Hans Michael Maric ◽  
Bettina Böttcher
Keyword(s):  
Hepatitis B ◽  
Core Protein ◽  
Peptide Binding ◽  
Surface Proteins ◽  
Binding Motif ◽  
Virus Particles ◽  
Enveloped Virus ◽  
Conformational Plasticity ◽  
Viral Maturation ◽  
Hepatitis B Core Protein

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.

Conformational Plasticity of the Gerstmann–Sträussler–Scheinker Disease Peptide as Indicated by Its Multiple Aggregation Pathways

2008 ◽  
Vol 381 (5) ◽  
pp. 1349-1361 ◽  
Author(s):  
Antonino Natalello ◽  
Valery V. Prokorov ◽  
Fabrizio Tagliavini ◽  
Michela Morbin ◽  
Gianluigi Forloni ◽  
...  
Keyword(s):  
Conformational Plasticity

scholarly journals Conformational plasticity of the Ebola virus matrix protein

2014 ◽  
Vol 23 (11) ◽  
pp. 1519-1527 ◽  
Author(s):  
Jens Radzimanowski ◽  
Gregory Effantin ◽  
Winfried Weissenhorn
Keyword(s):  
Matrix Protein ◽  
Ebola Virus ◽  
Conformational Plasticity

Folding/Unfolding Kinetics of Apomyoglobin

2005 ◽  
Vol 39 (6) ◽  
pp. 884-891
Author(s):  
E. N. Baryshnikova ◽  
B. S. Melnik ◽  
G. V. Semisotnov ◽  
V. E. Bychkova
Keyword(s):  
Unfolding Kinetics ◽  
Kinetics Of

scholarly journals Kinetic Analysis of the Effect of Poliovirus Receptor on Viral Uncoating: the Receptor as a Catalyst

2001 ◽  
Vol 75 (11) ◽  
pp. 4984-4989 ◽  
Author(s):  
Simon K. Tsang ◽  
Brian M. McDermott ◽  
Vincent R. Racaniello ◽  
James M. Hogle
Keyword(s):  
Activation Energy ◽  
Transition State ◽  
Kinetic Analysis ◽  
Transition State Theory ◽  
State Theory ◽  
Viral Receptor ◽  
Poliovirus Receptor ◽  
Entropic Stabilization ◽  
Entropic Effects

ABSTRACT We examined the role of soluble poliovirus receptor on the transition of native poliovirus (160S or N particle) to an infectious intermediate (135S or A particle). The viral receptor behaves as a classic transition state theory catalyst, facilitating the N-to-A conversion by lowering the activation energy for the process by 50 kcal/mol. In contrast to earlier studies which demonstrated that capsid-binding drugs inhibit thermally mediated N-to-A conversion through entropic stabilization alone, capsid-binding drugs are shown to inhibit receptor-mediated N-to-A conversion through a combination of enthalpic and entropic effects.

scholarly journals Structural Basis for Dodecameric Assembly States and Conformational Plasticity of the Full-Length AAA+ ATPases Rvb1·Rvb2

Structure ◽  
2015 ◽  
Vol 23 (3) ◽  
pp. 483-495 ◽  
Author(s):  
Kristina Lakomek ◽  
Gabriele Stoehr ◽  
Alessandro Tosi ◽  
Monika Schmailzl ◽  
Karl-Peter Hopfner
Keyword(s):  
Full Length ◽  
Structural Basis ◽  
Conformational Plasticity ◽  
Aaa Atpases

scholarly journals Design and Properties of Ligand-Conjugated Guanine Oligonucleotides for Recovery of Mutated G-Quadruplexes

Molecules ◽  
2018 ◽  
Vol 23 (12) ◽  
pp. 3228
Author(s):  
Shuntaro Takahashi ◽  
Boris Chelobanov ◽  
Ki Kim ◽  
Byeang Kim ◽  
Dmitry Stetsenko ◽  
...  
Keyword(s):  
Cancer Progression ◽  
Polyaromatic Hydrocarbons ◽  
Fine Tuning ◽  
Vascular Endothelial ◽  
Quadruplex Dna ◽  
Guanine Quadruplex ◽  
Anthracene Derivatives ◽  
Novel Strategy ◽  
Endothelial Growth Factor ◽  
Unfolding Kinetics

The formation of a guanine quadruplex DNA structure (G4) is known to repress the expression of certain cancer-related genes. Consequently, a mutated G4 sequence can affect quadruplex formation and induce cancer progression. In this study, we developed an oligonucleotide derivative consisting of a ligand-containing guanine tract that replaces the mutated G4 guanine tract at the promoter of the vascular endothelial growth factor (VEGF) gene. A ligand moiety consisting of three types of polyaromatic hydrocarbons, pyrene, anthracene, and perylene, was attached to either the 3′ or 5′ end of the guanine tract. Each of the ligand-conjugated guanine tracts, with the exception of anthracene derivatives, combined with other intact guanine tracts to form an intermolecular G4 on the mutated VEGF promoter. This intermolecular G4, exhibiting parallel topology and high thermal stability, enabled VEGF G4 formation to be recovered from the mutated sequence. Stability of the intramolecular G4 increased with the size of the conjugated ligand. However, suppression of intermolecular G4 replication was uniquely dependent on whether the ligand was attached to the 3′ or 5′ end of the guanine tract. These results indicate that binding to either the top or bottom guanine quartet affects unfolding kinetics due to polarization in DNA polymerase processivity. Our findings provide a novel strategy for recovering G4 formation in case of damage, and fine-tuning processes such as replication and transcription.

scholarly journals Temperature Dependence of the Folding and Unfolding Kinetics of the GCN4 Leucine Zipper via 13Cα-NMR

2001 ◽  
Vol 80 (2) ◽  
pp. 939-951 ◽  
Author(s):  
Marilyn Emerson Holtzer ◽  
G. Larry Bretthorst ◽  
D. André d’Avignon ◽  
Ruth Hogue Angeletti ◽  
Lisa Mints ◽  
...  
Keyword(s):  
Temperature Dependence ◽  
Leucine Zipper ◽  
Unfolding Kinetics ◽  
Kinetics Of
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