Kinetics of competitive Cd2+ binding pathways: the realistic structure of intrinsically disordered, partially metallated metallothioneins

Metallomics ◽  
2019 ◽  
Vol 11 (5) ◽  
pp. 894-905 ◽  
Author(s):  
Daisy L. Wong ◽  
Natalie C. Korkola ◽  
Martin J. Stillman
Keyword(s):  
Cluster Structure ◽  
Intrinsically Disordered ◽  
Domain Protein ◽  
Kinetics Of ◽  
Realistic Structure

The metallation of metallothionein can proceed via two different intermediate structures: a beaded structure that forms quickly (top) and a slow-forming cluster structure (bottom) before forming the fully metallated two-domain protein.

scholarly journals Thermodynamics and kinetics of the amyloid-β peptide revealed by Markov state models based on MD data in agreement with experiment

2021 ◽  
Author(s):  
Arghadwip Paul ◽  
Suman Samantray ◽  
Marco Anteghini ◽  
Mohammed Khaled ◽  
Birgit Strodel
Keyword(s):  
Amyloid Β ◽  
Md Simulations ◽  
Amyloid Β Peptide ◽  
Intrinsically Disordered ◽  
Thermodynamics And Kinetics ◽  
Markov State ◽  
Markov State Models ◽  
State Models ◽  
Kinetics Of

The convergence of MD simulations is tested using varying measures for the intrinsically disordered amyloid-β peptide (Aβ). Markov state models show that 20–30 μs of MD is needed to reliably reproduce the thermodynamics and kinetics of Aβ.

The microtubule- and PP1-binding activities of Drosophila melanogaster Spc105 control the kinetics of SAC satisfaction.

2021 ◽  
Author(s):  
Margaux R. Audett ◽  
Erin L. Johnson ◽  
Jessica M. McGory ◽  
Dylan M. Barcelos ◽  
Evelin Oroszne Szalai ◽  
...  
Keyword(s):  
Protein Binding ◽  
Protein Phosphatase ◽  
Spindle Assembly Checkpoint ◽  
Protein Phosphatase 1 ◽  
Intrinsically Disordered ◽  
Regulatory Circuit ◽  
Cell Assays ◽  
Kinetics Of

KNL1 is a large intrinsically disordered kinetochore (KT) protein that recruits spindle assembly checkpoint (SAC) components to mediate SAC signaling. The N-terminal region (NTR) of KNL1 possesses two activities that have been implicated in SAC silencing: microtubule (MT) binding and protein phosphatase 1 (PP1) recruitment. The NTR of D. melanogaster KNL1 (Spc105) has never been shown to bind MTs nor to recruit PP1. Furthermore, the phospho-regulatory mechanisms known to control SAC protein binding to KNL1 orthologues is absent in D. melanogaster. Here, these apparent discrepancies are resolved using in vitro and cell based-assays. A phospho-regulatory circuit, which utilizes Aurora B kinase (ABK), promotes SAC protein binding to the central disordered region of Spc105 while the NTR binds directly to MTs in vitro and recruits PP1-87B to KTs in vivo. Live-cell assays employing an optogenetic oligomerization tag, and deletion/chimera mutants are used to define the interplay of MT- and PP1-binding by Spc105 and the relative contributions of both activities to the kinetics of SAC satisfaction. [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text]

scholarly journals Aggregation kinetics and cluster structure of amino-PEG covered gold nanoparticles

RSC Advances ◽  
2016 ◽  
Vol 6 (32) ◽  
pp. 27151-27157 ◽  
Author(s):  
D. Zámbó ◽  
Sz. Pothorszky ◽  
D. F. Brougham ◽  
A. Deák
Keyword(s):  
Gold Nanoparticles ◽  
Self Assembly ◽  
Cluster Structure ◽  
Aggregation Kinetics ◽  
Kinetics Of

Perturbation induced directed self-assembly of amino PEGylated gold nanoparticles: kinetics of aggregation and cluster structure.

scholarly journals The ubiquitin E3 ligase POSH regulates calcium homeostasis through spatial control of Herp

2007 ◽  
Vol 177 (1) ◽  
pp. 51-61 ◽  
Author(s):  
Shmuel Tuvia ◽  
Daniel Taglicht ◽  
Omri Erez ◽  
Iris Alroy ◽  
Iris Alchanati ◽  
...  
Keyword(s):  
Calcium Homeostasis ◽  
Critical Role ◽  
Dominant Negative ◽  
Spatial Control ◽  
Ubiquitin E3 Ligase ◽  
Lysine Residues ◽  
Domain Protein ◽  
Golgi Network ◽  
Kinetics Of

The ubiquitin (Ub) domain protein Herp plays a crucial role in the maintenance of calcium homeostasis during endoplasmic reticulum (ER) stress. We now show that Herp is a substrate as well as an activator of the E3 Ub ligase POSH. Herp-mediated POSH activation requires the Ubl domain and exclusively promotes lysine-63–linked polyubiquitination. Confocal microscopy demonstrates that Herp resides mostly in the trans-Golgi network, but, shortly after calcium perturbation by thapsigargin (Tpg), it appears mainly in the ER. Substitution of all lysine residues within the Ubl domain abolishes lysine-63–linked polyubiquitination of Herp in vitro and calcium-induced Herp relocalization that is also abrogated by the overexpression of a dominant-negative POSHV14A. A correlation exists between the kinetics of Tpg-induced Herp relocalization and POSH-dependent polyubiquitination. Finally, the overexpression of POSH attenuates, whereas the inhibition of POSH by the expression of POSHV14A or by RNA interference enhances Tpg-induced calcium burst. Altogether, these results establish a critical role for POSH-mediated ubiquitination in the maintenance of calcium homeostasis through the spatial control of Herp.

scholarly journals Intrinsically disordered linkers control tethered kinases via effective concentration

2020 ◽  
Author(s):  
Mateusz Dyla ◽  
Magnus Kjaergaard
Keyword(s):  
Effective Concentration ◽  
Scaffolding Proteins ◽  
Know How ◽  
Intrinsically Disordered ◽  
Steady State Kinetics ◽  
Interaction Domains ◽  
Substrate Usage ◽  
Kinase Specificity ◽  
Complex Architecture ◽  
Kinetics Of

AbstractKinase specificity is crucial to the fidelity of signalling pathways, yet many pathways use the same kinases to achieve widely different effects. Specificity arises in part from the enzymatic domain, but also from the physical tethering of kinases to their substrates. Such tethering can occur via protein interaction domains in the kinase or via anchoring and scaffolding proteins, and can drastically increase the kinetics of phosphorylation. However, we do not know how such intra-complex reactions depend on the link between enzyme and substrate. Here we show that the kinetics of tethered kinases follow a Michaelis-Menten like dependence on effective concentration. We find that phosphorylation kinetics scale with the length of the intrinsically disordered linkers that join the enzyme and substrate, but that the scaling differs between substrates. Steady-state kinetics can only partially predict rates of tethered reactions as product release may obscure the rate of phospho-transfer. Our results suggest that changes in signalling complex architecture not only enhance the rates of phosphorylation reactions, but may also alter the relative substrate usage. This suggests a mechanism for how scaffolding proteins can allosterically modify the output from a signalling pathway.

scholarly journals An intrinsically disordered region of methyl-CpG binding domain protein 2 (MBD2) recruits the histone deacetylase core of the NuRD complex

2015 ◽  
Vol 43 (6) ◽  
pp. 3100-3113 ◽  
Author(s):  
Megha A. Desai ◽  
Heather D. Webb ◽  
Leander M. Sinanan ◽  
J. Neel Scarsdale ◽  
Ninad M. Walavalkar ◽  
...  
Keyword(s):  
Histone Deacetylase ◽  
Binding Domain ◽  
Nurd Complex ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Region ◽  
Domain Protein

scholarly journals Intrinsically disordered linkers control tethered kinases via effective concentration

2020 ◽  
Vol 117 (35) ◽  
pp. 21413-21419 ◽  
Author(s):  
Mateusz Dyla ◽  
Magnus Kjaergaard
Keyword(s):  
Effective Concentration ◽  
Scaffolding Proteins ◽  
Signaling Complex ◽  
Intrinsically Disordered ◽  
Steady State Kinetics ◽  
Interaction Domains ◽  
Substrate Usage ◽  
Kinase Specificity ◽  
Complex Architecture ◽  
Kinetics Of

Kinase specificity is crucial to the fidelity of signaling pathways, yet many pathways use the same kinases to achieve widely different effects. Specificity arises in part from the enzymatic domain but also from the physical tethering of kinases to their substrates. Such tethering can occur via protein interaction domains in the kinase or via anchoring and scaffolding proteins and can drastically increase the kinetics of phosphorylation. However, we do not know how such intracomplex reactions depend on the link between enzyme and substrate. Here we show that the kinetics of tethered kinases follow a Michaelis–Menten-like dependence on effective concentration. We find that phosphorylation kinetics scale with the length of the intrinsically disordered linkers that join the enzyme and substrate but that the scaling differs between substrates. Steady-state kinetics can only partially predict rates of tethered reactions as product release may obscure the rate of phosphotransfer. Our results suggest that changes in signaling complex architecture not only enhance the rates of phosphorylation reactions but may also alter the relative substrate usage. This suggests a mechanism for how scaffolding proteins can allosterically modify the output from a signaling pathway.

scholarly journals Parallel and sequential pathways of molecular recognition of a tandem-repeat protein and its intrinsically disordered binding partner

2021 ◽  
Author(s):  
Ben M. Smith ◽  
Pamela J. E. Rowling ◽  
Chris M. Dobson ◽  
Laura S. Itzhaki
Keyword(s):  
Molecular Recognition ◽  
Crystal Structures ◽  
Site Directed Mutagenesis ◽  
Dissociation Pathway ◽  
Reporter System ◽  
Dissociation Kinetics ◽  
Repeat Protein ◽  
Intrinsically Disordered ◽  
Kinetic Rate Constants ◽  
Kinetics Of

The Wnt signalling pathway plays an important role in cell proliferation, differentiation and fate decisions in embryonic development and in the maintenance of adult tissues, and the twelve Armadillo (ARM) repeat-containing protein β-catenin acts as the signal transducer in this pathway. Here we investigate the interaction between β-catenin and the intrinsically disordered transcription factor TCF7L2, comprising a very long nanomolar-affinity interface of approximately 4800 Å2 that spans ten of the twelve ARM repeats of β-catenin. First, a fluorescence reporter system for the interaction was engineered and used to determine the kinetic rate constants for the association and dissociation. The association kinetics of TCF7L2 and β-catenin was monophasic and rapid (7.3 ± 0.1 ×107 M-1s-1), whereas dissociation was biphasic and slow (5.7 ± 0.4 ×10−4 s-1, 15.2 ± 2.8 ×10−4 s-1). This reporter system was then combined with site-directed mutagenesis to investigate the striking variability in the conformation adopted by TCF7L2 in the three different crystal structures of the TCF7L2-β-catenin complex. We found that mutation of the N- and C-terminal subdomains of TCF7L2 that adopt relatively fixed conformations in the crystal structures has a large effect on the dissociation kinetics, whereas mutation of the labile sub-domain connecting them has negligible effect. These results point to a two-site avidity mechanism of binding with the linker region forming a “fuzzy” complex involving transient contacts that are not site-specific. Strikingly, two mutations in the N-terminal subdomain that have the largest effects on the dissociation kinetics showed two additional phases, indicating partial flux through an alternative dissociation pathway that is inaccessible to the wild type. The results presented here provide insights into the kinetics of molecular recognition of a long intrinsically disordered region with an elongated repeat-protein surface, a process found to involve parallel routes with sequential steps in each.

scholarly journals The intrinsically disordered structural platform of the plant defence hub protein RPM1-interacting protein 4 provides insights into its mode of action in the host-pathogen interface and evolution of the nitrate-induced domain protein family

FEBS Journal ◽  
2014 ◽  
Vol 281 (17) ◽  
pp. 3955-3979 ◽  
Author(s):  
Xiaolin Sun ◽  
David R. Greenwood ◽  
Matthew D. Templeton ◽  
David S. Libich ◽  
Tony K. McGhie ◽  
...  
Keyword(s):  
Mode Of Action ◽  
Plant Defence ◽  
Protein Family ◽  
Interacting Protein ◽  
Intrinsically Disordered ◽  
Host Pathogen ◽  
Domain Protein
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