conformational transition
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2022 ◽  
Vol 13 (1) ◽  
Author(s):  
Diane T. Takahashi ◽  
Danièle Gadelle ◽  
Keli Agama ◽  
Evgeny Kiselev ◽  
Hongliang Zhang ◽  
...  

AbstractEukaryotic topoisomerases I (TOP1) are ubiquitous enzymes removing DNA torsional stress. However, there is little data concerning the three-dimensional structure of TOP1 in the absence of DNA, nor how the DNA molecule can enter/exit its closed conformation. Here, we solved the structure of thermostable archaeal Caldiarchaeum subterraneum CsTOP1 in an apo-form. The enzyme displays an open conformation resulting from one substantial rotation between the capping (CAP) and the catalytic (CAT) modules. The junction between these two modules is a five-residue loop, the hinge, whose flexibility permits the opening/closing of the enzyme and the entry of DNA. We identified a highly conserved tyrosine near the hinge as mediating the transition from the open to closed conformation upon DNA binding. Directed mutagenesis confirmed the importance of the hinge flexibility, and linked the enzyme dynamics with sensitivity to camptothecin, a TOP1 inhibitor targeting the TOP1 enzyme catalytic site in the closed conformation.


Molecules ◽  
2021 ◽  
Vol 27 (1) ◽  
pp. 88
Author(s):  
Marco Giampà ◽  
María J. Amundarain ◽  
Maria Georgina Herrera ◽  
Nicolò Tonali ◽  
Veronica I. Dodero

The aggregation of proteins into amyloid fibers is linked to more than forty still incurable cellular and neurodegenerative diseases such as Parkinson’s disease (PD), multiple system atrophy, Alzheimer’s disease and type 2 diabetes, among others. The process of amyloid formation is a main feature of cell degeneration and disease pathogenesis. Despite being methodologically challenging, a complete understanding of the molecular mechanism of aggregation, especially in the early stages, is essential to find new biological targets for innovative therapies. Here, we reviewed selected examples on α-syn showing how complementary approaches, which employ different biophysical techniques and models, can better deal with a comprehensive study of amyloid aggregation. In addition to the monomer aggregation and conformational transition hypothesis, we reported new emerging theories regarding the self-aggregation of α-syn, such as the alpha-helix rich tetramer hypothesis, whose destabilization induce monomer aggregation; and the liquid-liquid phase separation hypothesis, which considers a phase separation of α-syn into liquid droplets as a primary event towards the evolution to aggregates. The final aim of this review is to show how multimodal methodologies provide a complete portrait of α-syn oligomerization and can be successfully extended to other protein aggregation diseases.


Author(s):  
Pierpaolo Pravatto ◽  
Davide Castaldo ◽  
Federico Gallina ◽  
Barbara Fresch ◽  
Stefano Corni ◽  
...  

Abstract The theory of stochastic processes impacts both physical and social sciences. At the molecular scale, stochastic dynamics is ubiquitous because of thermal fluctuations. The Fokker-Plank-Smoluchowski equation models the time evolution of the probability density of selected degrees of freedom in the diffusive regime and it is a workhorse of physical chemistry. In this paper, we report the development and implementation of a Variational Quantum Eigensolver procedure to solve the Fokker-Planck-Smoluchowski eigenvalue problem. We show that such an algorithm, typically adopted to address quantum chemistry problems, can be applied effectively to classical systems paving the way to new applications of quantum computers. We compute the conformational transition rate in a linear chain of rotors experiencing nearest-neighbor interaction. We provide a method to encode on the quantum computer the probability distribution for a given conformation of the chain and assess its scalability in terms of operations. Performance analysis on noisy quantum emulators and quantum devices (IBMQ Santiago) is provided for a small chain showing results in good agreement with the classical benchmark without further addition of any error mitigation technique.


2021 ◽  
Author(s):  
Sophia Gruber ◽  
Achim Loef ◽  
Adina Hausch ◽  
Res Joehr ◽  
Tobias Obser ◽  
...  

Von Willebrand factor (VWF) is a multimeric plasma glycoprotein that is critically involved in hemostasis. Biosynthesis of long VWF concatemers in the endoplasmic reticulum and the (trans-)Golgi is still not fully understood. We use the single-molecule force spectroscopy technique magnetic tweezers to analyze a previously hypothesized conformational change in the D'D3 domain crucial for VWF multimerization. We find that the interface formed by submodules C8-3, TIL3, and E3 wrapping around VWD3 can open and expose two previously buried cysteines that are known to be vital for multimerization. By characterizing the conformational change at varying levels of force, we are able to quantify the kinetics of the transition and the stability of the interface. We find a pronounced destabilization of the interface upon lowering the pH from 7.4 to 6.2 and 5.5. This is consistent with initiation of the conformational change that enables VWF multimerization at the D'D3 domain by a decrease in pH in the trans-Golgi network and Weibel-Palade bodies. Furthermore, we find a stabilization of the interface in the presence of coagulation factor VIII (FVIII), providing evidence for a previously hypothesized binding site in submodule C8-3. Our findings highlight the critical role of the D'D3 domain in VWF biosynthesis and function and we anticipate our methodology to be applicable to study other, similar conformational changes in VWF and beyond.


2021 ◽  
Author(s):  
Matthias Post ◽  
Benjamin Lickert ◽  
Georg Diez ◽  
Steffen Wolf ◽  
Gerhard Stock

Allosteric communication between distant protein sites represents a key mechanism of biomolecular regulation and signal transduction. Compared to other processes such as protein folding, however, the dynamical evolution of allosteric transitions is still not well understood. As example of allosteric coupling between distant protein regions, we consider the global open-closed motion of the two domains of T4 lysozyme, which is triggered by local motions in the hinge region. Combining extensive molecular dynamics simulations with machine learning of contact features, we identify a network of interresidue distances that move in a concerted manner. The cooperative process originates from a cogwheel-like motion of the hydrophobic core in the hinge region, which constitutes a flexible transmission network. Through rigid contacts and the protein backbone, the small local changes of the hydrophobic core are passed on to the distant terminal domains and lead to the emergence of a rare global conformational transition. As in an Ising-type model, the cooperativity of the allosteric transition can be explained via the interaction of local fluctuations.


2021 ◽  
Vol 12 ◽  
Author(s):  
Yassmin Abdelhamid ◽  
Meng Wang ◽  
Susannah L. Parkhill ◽  
Paul Brear ◽  
Xavier Chee ◽  
...  

Pseudomonas aeruginosa (PA) depends on the Entner-Doudoroff pathway (EDP) for glycolysis. The main enzymatic regulator in the lower half of the EDP is pyruvate kinase. PA contains genes that encode two isoforms of pyruvate kinase, denoted PykAPA and PykFPA. In other well-characterized organisms containing two pyruvate kinase isoforms (such as Escherichia coli) each isozyme is differentially regulated. The structure, function and regulation of PykAPA has been previously characterized in detail, so in this work, we set out to assess the biochemical and structural properties of the PykFPA isozyme. We show that pykFPA expression is induced in the presence of the diureide, allantoin. In spite of their relatively low amino acid sequence identity, PykAPA and PykFPA display broadly comparable kinetic parameters, and are allosterically regulated by a very similar set of metabolites. However, the x-ray crystal structure of PykFPA revealed significant differences compared with PykAPA. Notably, although the main allosteric regulator binding-site of PykFPA was empty, the “ring loop” covering the site adopted a partially closed conformation. Site-directed mutation of the proline residues flanking the ring loop yielded apparent “locked on” and “locked off” allosteric activation phenotypes, depending on the residue mutated. Analysis of PykFPA inter-protomer interactions supports a model in which the conformational transition(s) accompanying allosteric activation involve re-orientation of the A and B domains of the enzyme and subsequent closure of the active site.


Polymers ◽  
2021 ◽  
Vol 13 (22) ◽  
pp. 3929
Author(s):  
Mikhail Y. Laktionov ◽  
Ekaterina B. Zhulina ◽  
Ralf P. Richter ◽  
Oleg V. Borisov

To study conformational transition occuring upon inferior solvent strength in a brush formed by linear or dendritically branched macromolecules tethered to the inner surface of cylindrical or planar (slit-like) pore, a self-consistent field analytical approach is employed. Variations in the internal brush structure as a function of variable solvent strength and pore radius, and the onset of formation of a hollow channel in the pore center are analysed. The predictions of analytical theory are supported and complemented by numerical modelling by a self-consistent field Scheutjens–Fleer method. Scaling arguments are used to study microphase segregation under poor solvent conditions leading to formation of a laterally and longitudinally patterned structure in planar and cylindrical pores, respectively, and the effects of confinement on "octopus-like" clusters in the pores of different geometries.


2021 ◽  
Author(s):  
wenzhong liu ◽  
hualan li

Increased vascular permeability is a characteristic of Hantavirus illness, for which there is now no treatment. We employed the domain search method to investigate the Hantavirus protein in this present work. The results indicated that the membrane glycoprotein E protein (containing Gn-Gc) of Hantavirus had lipid phosphatase and C2-like domains. The E protein was a tensin phosphatase-like (PTEN) enzyme that could shuttle in the cytoplasm and cell membrane. In an acidic endosomal environment, Gn dissociates, exposing Gc's autophosphorylation region to complete autophosphorylation and activating the C2 domain. The C2 domain facilitates Gc's conformational transition, which is followed by Gc binding to the endosomal membrane. After being inserted into the endosomal membrane, the phosphatase domain of Gc phosphorylates PI(3,4,5)P3 on the endosomal membrane. Then converted PI(3,4,5)P3 to PI(4,5)P2 . PI(4,5)P2 bound to the N-terminal of Gc, completely anchoring the tetramer-shaped Gc to the endosomal membrane and forming a fusion hole. Then analogous to PTEN, phosphorylation of PI(3,4,5)P3 directly induced the disintegration of Gc tetramer. The enlargement of the fusion pore speeded up the fusion of the viral and endosomal membranes. Through the fusion hole, the virus's intracellular material was swiftly discharged into the cytoplasm. The C2 domain promoted the PKC signaling route during Hantavirus membrane fusion, whereas the phosphatase inhibited the PI3K signaling pathway. E protein's PTEN-like action impaired lipid metabolism and endothelial cell remodeling, increasing blood vessel permeability and resulting in renal and cardiac syndromes. Additionally, E protein inhibited the immune system and Akt-mediated eNOS activation, resulting in a cascade of consequences.


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