scholarly journals Highly Dynamic Polynuclear Metal Cluster Revealed in a Single Metallothionein Molecule

Research ◽  
2021 ◽  
Vol 2021 ◽  
pp. 1-11
Author(s):  
Guodong Yuan ◽  
Felipe Curtolo ◽  
Yibing Deng ◽  
Tao Wu ◽  
Fang Tian ◽  
...  
Keyword(s):  
Single Molecule ◽  
Metal Binding ◽  
Metal Cluster ◽  
Dynamic Structure ◽  
Ring Structure ◽  
Bond Rupture ◽  
Conformational Substates ◽  
Intrinsically Disordered ◽  
Transient Nature ◽  
The Individual

Human metallothionein (MT) is a small-size yet efficient metal-binding protein, playing an essential role in metal homeostasis and heavy metal detoxification. MT contains two domains, each forming a polynuclear metal cluster with an exquisite hexatomic ring structure. The apoprotein is intrinsically disordered, which may strongly influence the clusters and the metal-thiolate (M-S) bonds, leading to a highly dynamic structure. However, these features are challenging to identify due to the transient nature of these species. The individual signal from dynamic conformations with different states of the cluster and M-S bond will be averaged and blurred in classic ensemble measurement. To circumvent these problems, we combined a single-molecule approach and multiscale molecular simulations to investigate the rupture mechanism and chemical stability of the metal cluster by a single MT molecule, focusing on the Zn4S11 cluster in the α domain upon unfolding. Unusual multiple unfolding pathways and intermediates are observed for both domains, corresponding to different combinations of M-S bond rupture. None of the pathways is clearly preferred suggesting that unfolding proceeds from the distribution of protein conformational substates with similar M-S bond strengths. Simulations indicate that the metal cluster may rearrange, forming and breaking metal-thiolate bonds even when MT is folded independently of large protein backbone reconfiguration. Thus, a highly dynamic polynuclear metal cluster with multiple conformational states is revealed in MT, responsible for the binding promiscuity and diverse cellular functions of this metal-carrier protein.

scholarly journals The structural heterogeneity of α-synuclein is governed by several distinct subpopulations with interconversion times slower than milliseconds

2020 ◽  
Author(s):  
Jiaxing Chen ◽  
Sofia Zaer ◽  
Paz Drori ◽  
Joanna Zamel ◽  
Khalil Joron ◽  
...  
Keyword(s):  
Single Molecule ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Intrinsically Disordered Protein ◽  
Structural Heterogeneity ◽  
Conformational Space ◽  
Conformational Ensemble ◽  
Time Resolved ◽  
Intrinsically Disordered ◽  
Transient Nature

AbstractThe intrinsically disordered protein, α-synuclein, implicated in synaptic vesicle homeostasis and neurotransmitter release, is also associated with several neurodegenerative diseases. The different roles of α-synuclein are characterized by distinct structural states (membrane-bound, dimer, tetramer, oligomer, and fibril), which are originated from its various monomeric conformations. The pathological states, determined by the ensemble of α-synuclein monomer conformations and dynamic pathways of interconversion between dominant states, remain elusive due to their transient nature. Here, we use inter-dye distance distributions from bulk time-resolved Förster resonance energy transfer as restraints in discrete molecular dynamics simulations to map the conformational space of the α-synuclein monomer. We further confirm the generated conformational ensemble in orthogonal experiments utilizing far-UV circular dichroism and cross-linking mass spectrometry. Single-molecule protein-induced fluorescence enhancement measurements show that within this conformational ensemble, some of the conformations of α-synuclein are surprisingly stable, exhibiting conformational transitions slower than milliseconds. Our comprehensive analysis of the conformational ensemble reveals essential structural properties and potential conformations that promote its various functions in membrane interaction or oligomer and fibril formation.

Preparation and Characterization of Chitosan/Alginate Polyelectrolyte Complex Prepared by Using Calcium Tripolyphosphate Ionic Gelator

2016 ◽  
Vol 857 ◽  
pp. 447-451
Author(s):  
Nur Syairah Muhamad Rahim ◽  
Norlaily Ahmad ◽  
Dzaraini Kamarun
Keyword(s):  
Single Molecule ◽  
Polyelectrolyte Complex ◽  
Sodium Tripolyphosphate ◽  
Hybrid Compound ◽  
Polyelectrolyte Complexes ◽  
Sem Image ◽  
Degradation Temperature ◽  
Prepared Material ◽  
True Hybrid ◽  
The Individual

The formation of polyelectrolyte complexes (PECs) between chitosan and alginate has been widely investigated for many pharmaceutical and biomedical uses. Ionotropic gelation resulted from the crosslinking of polyelectrolytes (PEs) in the presence of ionic crosslinkers to form hydrogels. The most widely used ionic crosslinker for chitosan is sodium tripolyphosphate (NaTPP); and Ca2+ ions for alginates. The use of these cross-linkers to prepare PECs of chitosan and alginates resulted in hydrogels of similar moieties: chitosan-chitosan and alginate-alginate rather than the sought for hybrid chitosan-alginate PECs. Calcium tripolyphosphate (CaTPP) is a single molecule ionic gelator of chitosan and alginate that have the capability of producing the true hybrid compound of chitosan/alginate polyelectrolyte complex. This paper reported the synthesis of calcium tripolyphosphate and the preparation of a hybrid chitosan/alginate PECs using this newly identified ionic gelator. The newly-synthesized ionic gelator was characterized using ICP-OES; the PECs thereof prepared were characterized using TGA and SEM. The degradation temperature of the prepared PECs is higher than the degradation temperatures of the individual chitosan and alginates. SEM image of the prepared PECs showed rougher surfaces compared to the images of the individual chitosan and alginate compound. Both TGA and SEM revealed the possibility of the newly prepared material to be of the PECs sought for.

scholarly journals Individual growth of Heleobia piscium in natural populations (Gastropoda: Cochliopidae) from the multiple use natural Reserve Isla Martin Garcia, Buenos Aires, Argentina

2008 ◽  
Vol 68 (3) ◽  
pp. 617-621 ◽  
Author(s):  
SM. Martin
Keyword(s):  
Buenos Aires ◽  
Natural Populations ◽  
Dynamic Structure ◽  
Reproductive Period ◽  
Individual Growth ◽  
Growth Equation ◽  
Multiple Use ◽  
Natural Reserve ◽  
Drainage Channels ◽  
The Individual

The present work analyses the individual growth of Heleobia piscium in natural conditions in coastal drainage channels of the Multiple Use Natural Reserve Isla Martín García, Buenos Aires, Argentina. Isla Martín García is located in the Upper Río de la Plata, to the south of the mouth of the Uruguay river (34° 11' 25" S and 58° 15' 38" W). Monthly collections were made from July 2005 to July 2006 in the eastern part of the island (Arena Beach). The population of H. piscium showed a complex and dynamic structure of sizes during a long period of the annual cycle. Two cohorts could be detected. The Bertalanffy growth equation was: Lt = 6 (1-e -1.85 (t+0.38)) and Lt = 3.9 (1-e -0.19 (t+4.84)) for cohorts 1 and 2, respectively. The pattern of population growth displayed a staggered model, where the greatest growth is observed during the summer. The reproductive period occurred during six months, from the beginning of summer to middle of fall. Based on only one reproductive effort, this pattern is not similar to that of other cogeneric species already studied.

scholarly journals Planar Boronic Graphene and Nitrogenized Graphene Heterostructure for Protein Stretch and Confinement

Biomolecules ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1756
Author(s):  
Xuchang Su ◽  
Zhi He ◽  
Lijun Meng ◽  
Hong Liang ◽  
Ruhong Zhou
Keyword(s):  
Single Molecule ◽  
Intrinsically Disordered Proteins ◽  
Electron Tunneling ◽  
Amyloid Β ◽  
Protein Sequencing ◽  
Disordered Proteins ◽  
Force Microscopy ◽  
Intrinsically Disordered ◽  
Atomic Force ◽  
Dynamics Simulations

Single-molecule techniques such as electron tunneling and atomic force microscopy have attracted growing interests in protein sequencing. For these methods, it is critical to refine and stabilize the protein sample to a “suitable mode” before applying a high-fidelity measurement. Here, we show that a planar heterostructure comprising boronic graphene (BC3) and nitrogenized graphene (C3N) sandwiched stripe (BC3/C3N/BC3) is capable of the effective stretching and confinement of three types of intrinsically disordered proteins (IDPs), including amyloid-β (1–42), polyglutamine (Q42), and α-Synuclein (61–95). Our molecular dynamics simulations demonstrate that the protein molecules interact more strongly with the C3N stripe than the BC3 one, which leads to their capture, elongation, and confinement along the center C3N stripe of the heterostructure. The conformational fluctuations of IDPs are substantially reduced after being stretched. This design may serve as a platform for single-molecule protein analysis with reduced thermal noise.

scholarly journals History of Personality and Personality in History: On the 20th Anniversary of the Publication of the Monograph by A.V. Tolstykh "The Experience of Concrete Historical Psychology of Personality"

2020 ◽  
Vol 16 (4) ◽  
pp. 118-121
Author(s):  
V.A. Ilyin
Keyword(s):  
Personality Development ◽  
Early Death ◽  
Dynamic Structure ◽  
Psychological Phenomena ◽  
Three Phase ◽  
Depth Study ◽  
History Of ◽  
20Th Anniversary ◽  
The Individual ◽  
Original Concept

The article presents the main provisions of the original concept of personality development by A.V. Tolstykh, relatively little known today due to the early death of this prominent representative of the cultural-historical tradition in psychology. It is shown that within the framework of A.V. Tolstykh, the process of personality development is a three-phase dynamic structure aimed at integrating the individual with the mankind as a full-fledged subject of ancestral life — “historical, cultural, social”. The article describes the methodology based on a polydisciplinary approach to the study of psychological phenomena used by A.V. Tolstykh which allowed him to successfully solve a number of fundamental problems associated with the study of the phenomenology of personality and, thereby, make a real contribution to the development of cultural-historical psychology. We argue that the monograph by A.V. Tolstykh is an essential and even unique textbook for an in-depth study of personality development, both within the framework of the cultural-historical concept itself, and in a wide personal and socio-psychological context.

scholarly journals Transcription initiation at a consensus bacterial promoter proceeds via a 'bind-unwind-load-and-lock' mechanism

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Abhishek Mazumder ◽  
Richard H Ebright ◽  
Achillefs Kapanidis
Keyword(s):  
Single Molecule ◽  
Conformational Changes ◽  
Transcription Initiation ◽  
Core Promoter ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Extensive Study ◽  
Active Centre ◽  
Transient Nature ◽  
Promoter Dna

Transcription initiation starts with unwinding of promoter DNA by RNA polymerase (RNAP) to form a catalytically competent RNAP-promoter complex (RPO). Despite extensive study, the mechanism of promoter unwinding has remained unclear, in part due to the transient nature of intermediates on path to RPo. Here, using single-molecule unwinding-induced fluorescence enhancement to monitor promoter unwinding, and single-molecule fluorescence resonance energy transfer to monitor RNAP clamp conformation, we analyze RPo formation at a consensus bacterial core promoter. We find that the RNAP clamp is closed during promoter binding, remains closed during promoter unwinding, and then closes further, locking the unwound DNA in the RNAP active-centre cleft. Our work defines a new, 'bind-unwind-load-and-lock' model for the series of conformational changes occurring during promoter unwinding at a consensus bacterial promoter and provides the tools needed to examine the process in other organisms and at other promoters.

scholarly journals Tuning levels of low-complexity domain interactions to modulate endogenous oncogenic transcription

2021 ◽  
Author(s):  
Shasha Chong ◽  
Thomas G. W. Graham ◽  
Claire Dugast-Darzacq ◽  
Gina M. Dailey ◽  
Xavier Darzacq ◽  
...  
Keyword(s):  
Single Molecule ◽  
Target Genes ◽  
Gene Activation ◽  
Low Complexity ◽  
Intrinsically Disordered ◽  
Human Genes ◽  
Domain Interactions ◽  
Bona Fide ◽  
Liquid Liquid Phase Separation

Gene activation by mammalian transcription factors (TFs) requires dynamic, multivalent, and selective interactions of their intrinsically disordered low-complexity domains (LCDs), but how such interactions mediate transcription remains unclear. It has been proposed that extensive LCD-LCD interactions culminating in liquid-liquid phase separation (LLPS) of TFs is the dominant mechanism underlying transactivation. Here, we investigated how tuning the amount and localization of LCD-LCD interactions in vivo affects transcription of endogenous human genes. Quantitative single-cell and single-molecule imaging reveals that the oncogenic TF EWS/FLI1 requires a finely tuned range of LCD-LCD interactions to efficiently activate target genes. Modest or more dramatic increases in LCD-LCD interactions toward putative LLPS repress EWS/FLI1-driven transcription in patient cells. Likewise, ectopically creating LCD-LCD interactions to sequester EWS/FLI1 into a bona fide LLPS compartment, the nucleolus, inhibits EWS/FLI1-driven transcription and oncogenic transformation. Our findings reveal fundamental principles underlying LCD-mediated transcription and suggest mislocalizing specific LCD-LCD interactions as a novel therapeutic strategy for targeting disease-causing TFs.

scholarly journals Transcription factor clusters regulate genes in eukaryotic cells

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Adam JM Wollman ◽  
Sviatlana Shashkova ◽  
Erik G Hedlund ◽  
Rosmarie Friemann ◽  
Stefan Hohmann ◽  
...  
Keyword(s):  
Single Molecule ◽  
Functional Unit ◽  
Yeast Genome ◽  
Gene Promoters ◽  
Intrinsically Disordered ◽  
Extracellular Signal ◽  
Genome Model ◽  
Nuclear Targets

Transcription is regulated through binding factors to gene promoters to activate or repress expression, however, the mechanisms by which factors find targets remain unclear. Using single-molecule fluorescence microscopy, we determined in vivo stoichiometry and spatiotemporal dynamics of a GFP tagged repressor, Mig1, from a paradigm signaling pathway of Saccharomyces cerevisiae. We find the repressor operates in clusters, which upon extracellular signal detection, translocate from the cytoplasm, bind to nuclear targets and turnover. Simulations of Mig1 configuration within a 3D yeast genome model combined with a promoter-specific, fluorescent translation reporter confirmed clusters are the functional unit of gene regulation. In vitro and structural analysis on reconstituted Mig1 suggests that clusters are stabilized by depletion forces between intrinsically disordered sequences. We observed similar clusters of a co-regulatory activator from a different pathway, supporting a generalized cluster model for transcription factors that reduces promoter search times through intersegment transfer while stabilizing gene expression.

scholarly journals A functional role for intrinsic disorder in the tau-tubulin complex

2016 ◽  
Vol 113 (50) ◽  
pp. 14336-14341 ◽  
Author(s):  
Ana M. Melo ◽  
Juliana Coraor ◽  
Garrett Alpha-Cobb ◽  
Shana Elbaum-Garfinkle ◽  
Abhinav Nath ◽  
...  
Keyword(s):  
Single Molecule ◽  
Solution Structure ◽  
Dynamic Instability ◽  
Resonance Energy ◽  
Intrinsically Disordered Protein ◽  
Conformational Ensemble ◽  
Binding Region ◽  
Global Features ◽  
Microtubule Binding ◽  
Intrinsically Disordered

Tau is an intrinsically disordered protein with an important role in maintaining the dynamic instability of neuronal microtubules. Despite intensive study, a detailed understanding of the functional mechanism of tau is lacking. Here, we address this deficiency by using intramolecular single-molecule Förster Resonance Energy Transfer (smFRET) to characterize the conformational ensemble of tau bound to soluble tubulin heterodimers. Tau adopts an open conformation on binding tubulin, in which the long-range contacts between both termini and the microtubule binding region that characterize its compact solution structure are diminished. Moreover, the individual repeats within the microtubule binding region that directly interface with tubulin expand to accommodate tubulin binding, despite a lack of extension in the overall dimensions of this region. These results suggest that the disordered nature of tau provides the significant flexibility required to allow for local changes in conformation while preserving global features. The tubulin-associated conformational ensemble is distinct from its aggregation-prone one, highlighting differences between functional and dysfunctional states of tau. Using constraints derived from our measurements, we construct a model of tubulin-bound tau, which draws attention to the importance of the role of tau’s conformational plasticity in function.

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