scholarly journals Conformational Ensemble and Biological Role of the TCTP Intrinsically Disordered Region: Influence of Calcium and Phosphorylation

2018 ◽  
Vol 430 (11) ◽  
pp. 1621-1639 ◽  
Author(s):  
Florian Malard ◽  
Nadine Assrir ◽  
Mouad Alami ◽  
Samir Messaoudi ◽  
Ewen Lescop ◽  
...  
Keyword(s):  
Biological Role ◽  
Conformational Ensemble ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Region

scholarly journals Light-dependent THRUMIN1 phosphorylation regulates its association with actin filaments and 14-3-3 proteins

2021 ◽  
Author(s):  
Matthew E Dwyer ◽  
Roger P. Hangarter
Keyword(s):  
Aspartic Acid ◽  
Actin Filaments ◽  
Chloroplast Movement ◽  
Cell Surfaces ◽  
Intrinsically Disordered ◽  
C Terminus ◽  
Intrinsically Disordered Region ◽  
Chloroplast Movements ◽  
Cell Layers

Light-dependent chloroplast movements in leaf cells contribute to the optimization of photosynthesis. Low light conditions induce chloroplast accumulation along periclinal cell surfaces, providing greater access to the available light, whereas high light induces movement of chloroplasts to anticlinal cell surfaces providing photodamage protection and allowing more light to reach underlying cell layers. The THRUMIN1 protein is required for normal chloroplast movements in Arabidopsis thaliana and has been shown to localize at the plasma membrane and to undergo rapid light-dependent interactions with actin filaments through the N-terminal intrinsically disordered region. A predicted WASP-Homology 2 (WH2) domain was found in the intrinsically disordered region but mutations in this domain did not disrupt localization of THRUMIN1:YFP to actin filaments. A series of other protein truncations and site-directed mutations of known and putative phosphorylation sites indicated that a phosphomimetic mutation (serine to aspartic acid) at position 170 disrupted localization of THRUMIN1 with actin filaments. However, the phosphomimetic mutant rescued the thrumin1-2 mutant phenotype for chloroplast movement and raises questions about the role of THRUMIN1's interaction with actin. Mutation of serine 146 to aspartic acid also resulted in cytoplasmic localization of THRUMIN1:YFP in Nicotiana benthamiana. Mutations to a group of putative zinc-binding cysteine clusters implicates the C-terminus of THRUMIN1 in chloroplast movement. Phosphorylation-dependent association of THRUMIN1 with 14-3-3 KAPPA and OMEGA were also identified. Together, these studies provide new insights into the mechanistic role of THRUMIN1 in light-dependent chloroplast movements.

scholarly journals An intrinsically disordered region of RPN10 plays a key role in restricting ubiquitin chain elongation in RPN10 monoubiquitination

2015 ◽  
Vol 469 (3) ◽  
pp. 455-467 ◽  
Author(s):  
Pilar Puig-Sàrries ◽  
Marie-José Bijlmakers ◽  
Alice Zuin ◽  
Anne Bichmann ◽  
Miquel Pons ◽  
...  
Keyword(s):  
Protein Domain ◽  
Chain Elongation ◽  
Ubiquitin Chain ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Region ◽  
Regulatory Particle ◽  
Unstructured Protein

The proteasomal ubiquitin receptor Rpn10 (regulatory particle non-ATPase 10) is monoubiquitinated by Rsp5 (reverses SPT-phenotype protein 5). We show that a disordered region flanking the ubiquitin-interacting motif of Rpn10 is required for restricting polyubiquitination in the process of Rpn10 monoubiquitination. A novel role of an unstructured protein domain in controlling ubiquitin chain elongation is proposed.

scholarly journals Multivalent interactions between eIF4G1, Pub1 and Pab1 drive the formation of protein condensates

2020 ◽  
Author(s):  
Belén Chaves-Arquero ◽  
Santiago Martínez-Lumbreras ◽  
Nathalie Sibille ◽  
Sergio Camero ◽  
Pau Bernadó ◽  
...  
Keyword(s):  
Translation Initiation ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Dynamic Network ◽  
Conformational Ensemble ◽  
Aromatic Residues ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Region ◽  
Α Helix ◽  
Micrometer Size

SummaryYeast eIF4G1 interacts with RNA binding proteins (RBPs) like Pab1 and Pub1 affecting its function in translation initiation and stress granules formation. We present an NMR and SAXS study of the intrinsically disordered region of eIF4G1, eIF4G11-249, and its interactions with Pub1 and Pab1. The conformational ensemble of eIF4G11-249 shows an α-helix within the BOX3 conserved element and a dynamic network of fuzzy π-π and π-cation interactions involving arginine and aromatic residues. The Pab1 RRM2 domain interacts with eIF4G1 BOX3, the canonical interaction site, but also with BOX2, a conserved element of unknown function to date. In contrast, the Pub1 RRM3 domain interacts with the RNA1-1 and BOX1 regions of eIF4G1. Mixtures of Pub1, Pab1 and eIF4G1 form micrometer-size protein condensates that require the presence of the eIF4G1 BOX1 element. These homotypic interactions suggest a double key mechanism of eIF4G1 regulation, important for understanding the architecture of stress granule cores.

Association/dissociation Mechanisms of Intrinsically Disordered Region of Protein Beyond Conformational Selection and Induced Fit

2019 ◽  
Author(s):  
Duy Phuoc Tran ◽  
Akio Kitao
Keyword(s):  
Free Energy ◽  
Transcriptional Activation ◽  
Binding Free Energy ◽  
Energy Structure ◽  
Induced Fit ◽  
Hydrogen Bond Formation ◽  
Conformational Selection ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Region ◽  
Dissociation Mechanisms

<p>We investigate association and dissociation mechanisms of a typical intrinsically disordered region (IDR), transcriptional activation subdomain of tumor repressor protein p53 (TAD-p53) with murine double-minute clone 2 protein (MDM2). Using the combination of cycles of association and dissociation parallel cascade molecular dynamics, multiple standard MD, and Markov state model, we are successful in obtaining the lowest free energy structure of MDM2/TAD-p53 complex as the structure very close to that in crystal without prior knowledge. This method also reproduces the experimentally measured standard binding free energy, and association and dissociation rate constants solely with the accumulated MD simulation cost of 11.675 μs, in spite of the fact that actual dissociation occurs in the order of a second. Although there exist a few complex intermediates with similar free energies, TAD-p53 first binds MDM2 as the second lowest free energy intermediate dominantly (> 90% in flux), taking a form similar to one of the intermediate structures in its monomeric state. The mechanism of this step has a feature of conformational selection. In the second step, dehydration of the interface, formation of π-π stackings of the side-chains, and main-chain relaxation/hydrogen bond formation to complete α-helix take place, showing features of induced fit. In addition, dehydration (dewetting) is a key process for the final relaxation around the complex interface. These results demonstrate a more fine-grained view of the IDR association/dissociation beyond classical views of protein conformational change upon binding.</p>

From Organizations of Processes to Organisms and Other Biological Individuals

2018 ◽  
Author(s):  
Argyris Arnellos
Keyword(s):  
Multicellular Organism ◽  
Collaborative Networks ◽  
Biological Role ◽  
Regulatory Processes ◽  
Different Types ◽  
Organizational Framework

The emphasis on the collaborative dimension of life overlooks the importance of biological individuals (conceived of as integrated, self-maintaining organizations) in the build-up of more complex collaborative networks in the course of evolution. This chapter proposes a process-based organizational ontology for biology, according to which the essential features of unicellular organismicality are captured by a self-maintaining organization of processes integrated by means of a special type of collaboration (realized through regulatory processes entailing an indispensable interdependence) between its constitutive and its interactive aspects. This ontology is then used to describe different types of collaborations among cells and to suggest the type that yields a multicellular organism. The proposed organizational framework enables us to critically assess hypercollaborative views of life, especially issues related to the distinction between biological individuals and organisms and between life and non-life, without however underestimating the central biological role of collaboration.

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