scholarly journals Chiral Dualism as an Instrument of Hierarchical Structure Formation in Molecular Biology

Symmetry ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 587 ◽  
Author(s):  
Vsevolod A. Tverdislov ◽  
Ekaterina V. Malyshko
Keyword(s):  
Molecular Biology ◽  
Degrees Of Freedom ◽  
Organic Molecules ◽  
Conformational Dynamics ◽  
Research Community ◽  
Self Organization ◽  
Structural Basis ◽  
Chiral Asymmetry ◽  
Sign Alternation

The origin of chiral asymmetry in biology has attracted the attention of the research community throughout the years. In this paper we discuss the role of chirality and chirality sign alternation (L–D–L–D in proteins and D–L–D–L in DNA) in promoting self-organization in biology, starting at the level of single molecules and continuing to the level of supramolecular assemblies. In addition, we also discuss chiral assemblies in solutions of homochiral organic molecules. Sign-alternating chiral hierarchies created by proteins and nucleic acids are suggested to create the structural basis for the existence of selected mechanical degrees of freedom required for conformational dynamics in enzymes and macromolecular machines.

scholarly journals Molecular determinant of substrate binding and specificity of cytochrome P450 2J2

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Liang Xu ◽  
Liao Y. Chen
Keyword(s):  
Arachidonic Acid ◽  
Cytochrome P450 ◽  
Active Site ◽  
Structural Model ◽  
Substrate Binding ◽  
Conformational Dynamics ◽  
Structural Basis ◽  
Molecular Determinant ◽  
Dynamics Simulations

AbstractCytochrome P450 2J2 (CYP2J2) is responsible for the epoxidation of endogenous arachidonic acid, and is involved in the metabolism of exogenous drugs. To date, no crystal structure of CYP2J2 is available, and the proposed structural basis for the substrate recognition and specificity in CYP2J2 varies with the structural models developed using different computational protocols. In this study, we developed a new structural model of CYP2J2, and explored its sensitivity to substrate binding by molecular dynamics simulations of the interactions with chemically similar fluorescent probes. Our results showed that the induced-fit binding of these probes led to the preferred active poses ready for the catalysis by CYP2J2. Divergent conformational dynamics of CYP2J2 due to the binding of each probe were observed. However, a stable hydrophobic clamp composed of residues I127, F310, A311, V380, and I487 was identified to restrict any substrate access to the active site of CYP2J2. Molecular docking of a series of compounds including amiodarone, astemizole, danazol, ebastine, ketoconazole, terfenadine, terfenadone, and arachidonic acid to CYP2J2 confirmed the role of those residues in determining substrate binding and specificity of CYP2J2. In addition to the flexibility of CYP2J2, the present work also identified other factors such as electrostatic potential in the vicinity of the active site, and substrate strain energy and property that have implications for the interpretation of CYP2J2 metabolism.

scholarly journals Chiral Dualism as a Unifying Principle in Molecular Biophysics

Biophysica ◽  
2021 ◽  
Vol 1 (1) ◽  
pp. 22-37
Author(s):  
Ekaterina V. Malyshko ◽  
Ekaterina V. Semenova ◽  
Olga E. Bagrova ◽  
Alina R. Murtazina ◽  
Vsevolod A. Tverdislov
Keyword(s):  
Potential Role ◽  
The Self ◽  
Self Organization ◽  
Biological Macromolecules ◽  
Essential Factor ◽  
Macromolecular Assemblies ◽  
Chiral Asymmetry ◽  
Systemic Factor ◽  
Physical And Chemical

The origin and potential role of chiral asymmetry remain one of the most exciting issues in biology. In this paper we review the chirality of biological macromolecules, starting at the level of single molecules and continuing to the level of supramolecular assemblies. We discuss the physical and chemical consequences of the presence of chirality and their role in the self-organization and formation of structural hierarchies in cells. Homochirality may serve as an essential factor that invokes mechanisms required to control the formation of discrete structural hierarchies in macromolecules and macromolecular assemblies. Symmetry is of fundamental importance not only for all molecular biology as a systemic factor of its organization but also for pharmacology, as well as a systemic factor of drug stereospecificity.

On the Use of Quantum Thermal Bath in Unimolecular Fragmentation Simulations

2019 ◽  
Author(s):  
Riccardo Spezia ◽  
Hichem Dammak
Keyword(s):  
Degrees Of Freedom ◽  
Molecular Simulations ◽  
Zero Point ◽  
Thermal Bath ◽  
Unimolecular Dissociation ◽  
Point Energy ◽  
Rotational Degrees Of Freedom ◽  
The Difference ◽  
Nuclear Effects

<div> <div> <div> <p>In the present work we have investigated the possibility of using the Quantum Thermal Bath (QTB) method in molecular simulations of unimolecular dissociation processes. Notably, QTB is aimed in introducing quantum nuclear effects with a com- putational time which is basically the same as in newtonian simulations. At this end we have considered the model fragmentation of CH4 for which an analytical function is present in the literature. Moreover, based on the same model a microcanonical algorithm which monitor zero-point energy of products, and eventually modifies tra- jectories, was recently proposed. We have thus compared classical and quantum rate constant with these different models. QTB seems to correctly reproduce some quantum features, in particular the difference between classical and quantum activation energies, making it a promising method to study unimolecular fragmentation of much complex systems with molecular simulations. The role of QTB thermostat on rotational degrees of freedom is also analyzed and discussed. </p> </div> </div> </div>

Synergetic Theory of Document in Evolution of Document Science

2018 ◽  
pp. 1060-1068
Author(s):  
Galina A. Dvoenosova ◽  
Keyword(s):  
Social Role ◽  
Scientific Study ◽  
Self Organization ◽  
Universal Theory ◽  
Social Self ◽  
Social Goal ◽  
The Social ◽  
Synergetic Theory ◽  
First Time

The article assesses synergetic theory of document as a new development in document science. In information society the social role of document grows, as information involves all members of society in the process of documentation. The transformation of document under the influence of modern information technologies increases its interest to representatives of different sciences. Interdisciplinary nature of document as an object of research leads to an ambiguous interpretation of its nature and social role. The article expresses and contends the author's views on this issue. In her opinion, social role of document is incidental to its being a main social tool regulating the life of civilized society. Thus, the study aims to create a scientific theory of document, explaining its nature and social role as a tool of social (goal-oriented) action and social self-organization. Substantiation of this idea is based on application of synergetics (i.e., universal theory of self-organization) to scientific study of document. In the synergetic paradigm, social and historical development is seen as the change of phases of chaos and order, and document is considered a main tool that regulates social relations. Unlike other theories of document, synergetic theory studies document not as a carrier and means of information transfer, but as a unique social phenomenon and universal social tool. For the first time, the study of document steps out of traditional frameworks of office, archive, and library. The document is placed on the scales with society as a global social system with its functional subsystems of politics, economy, culture, and personality. For the first time, the methods of social sciences and modern sociological theories are applied to scientific study of document. This methodology provided a basis for theoretical vindication of nature and social role of document as a tool of social (goal-oriented) action and social self-organization. The study frames a synergetic theory of document with methodological foundations and basic concepts, synergetic model of document, laws of development and effectiveness of document in the social continuum. At the present stage of development of science, it can be considered the highest form of theoretical knowledge of document and its scientific explanatory theory.

A Brief Statement on the Future of Public Scholarship and the Research Methods Landscape

2019 ◽  
pp. 700-707
Author(s):  
Patricia Leavy
Keyword(s):  
Research Methods ◽  
Teaching Practices ◽  
Knowledge Building ◽  
Research Community ◽  
The State ◽  
Public Scholarship ◽  
Institutional Structures ◽  
The Future ◽  
Book Editor

The book editor offers some final comments about the state of the field and promise for the future. Leavy suggests researchers consider using the language of “shapes” to talk about the forms their research takes and to highlight the ongoing role of the research community in shaping knowledge-building practices. She reviews the challenges and rewards of taking your work public. Leavy concludes by noting that institutional structures need to evolve their rewards criteria in order to meet the demands of practicing contemporary research and suggests that professors update their teaching practices to bring the audiences of research into the forefront of discussions of methodology.

scholarly journals Dzyaloshinskii–Moriya interaction in noncentrosymmetric superlattices

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Woo Seung Ham ◽  
Abdul-Muizz Pradipto ◽  
Kay Yakushiji ◽  
Kwangsu Kim ◽  
Sonny H. Rhim ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Degrees Of Freedom ◽  
Orbit Coupling ◽  
Inversion Symmetry ◽  
Spin Orbit Coupling ◽  
Spin Orbit ◽  
Band Formation ◽  
Research Activities ◽  
Moriya Interaction

AbstractDzyaloshinskii–Moriya interaction (DMI) is considered as one of the most important energies for specific chiral textures such as magnetic skyrmions. The keys of generating DMI are the absence of structural inversion symmetry and exchange energy with spin–orbit coupling. Therefore, a vast majority of research activities about DMI are mainly limited to heavy metal/ferromagnet bilayer systems, only focusing on their interfaces. Here, we report an asymmetric band formation in a superlattices (SL) which arises from inversion symmetry breaking in stacking order of atomic layers, implying the role of bulk-like contribution. Such bulk DMI is more than 300% larger than simple sum of interfacial contribution. Moreover, the asymmetric band is largely affected by strong spin–orbit coupling, showing crucial role of a heavy metal even in the non-interfacial origin of DMI. Our work provides more degrees of freedom to design chiral magnets for spintronics applications.

scholarly journals A Superfluid Perspective on Neutron Star Dynamics

Universe ◽  
2021 ◽  
Vol 7 (1) ◽  
pp. 17
Author(s):  
Nils Andersson
Keyword(s):  
Neutron Star ◽  
Degrees Of Freedom ◽  
Temperature Scale ◽  
Fluid System ◽  
Fluid Core ◽  
State Of Matter ◽  
Entrainment Effect ◽  
Neutron Component ◽  
The Impact

As mature neutron stars are cold (on the relevant temperature scale), one has to carefully consider the state of matter in their interior. The outer kilometre or so is expected to freeze to form an elastic crust of increasingly neutron-rich nuclei, coexisting with a superfluid neutron component, while the star’s fluid core contains a mixed superfluid/superconductor. The dynamics of the star depend heavily on the parameters associated with the different phases. The presence of superfluidity brings new degrees of freedom—in essence we are dealing with a complex multi-fluid system—and additional features: bulk rotation is supported by a dense array of quantised vortices, which introduce dissipation via mutual friction, and the motion of the superfluid is affected by the so-called entrainment effect. This brief survey provides an introduction to—along with a commentary on our current understanding of—these dynamical aspects, paying particular attention to the role of entrainment, and outlines the impact of superfluidity on neutron-star seismology.

scholarly journals Tethering-induced destabilization and ATP-binding for tandem RRM domains of ALS-causing TDP-43 and hnRNPA1

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mei Dang ◽  
Yifan Li ◽  
Jianxing Song
Keyword(s):  
Conformational Dynamics ◽  
Md Simulations ◽  
Atp Binding ◽  
Rna Recognition Motif ◽  
Rna Recognition ◽  
Nucleic Acid Binding ◽  
General Role ◽  
Nmr Characterization ◽  
Lateral Sclerosis

AbstractTDP-43 and hnRNPA1 contain tandemly-tethered RNA-recognition-motif (RRM) domains, which not only functionally bind an array of nucleic acids, but also participate in aggregation/fibrillation, a pathological hallmark of various human diseases including amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), alzheimer's disease (AD) and Multisystem proteinopathy (MSP). Here, by DSF, NMR and MD simulations we systematically characterized stability, ATP-binding and conformational dynamics of TDP-43 and hnRNPA1 RRM domains in both tethered and isolated forms. The results reveal three key findings: (1) upon tethering TDP-43 RRM domains become dramatically coupled and destabilized with Tm reduced to only 49 °C. (2) ATP specifically binds TDP-43 and hnRNPA1 RRM domains, in which ATP occupies the similar pockets within the conserved nucleic-acid-binding surfaces, with the affinity slightly higher to the tethered than isolated forms. (3) MD simulations indicate that the tethered RRM domains of TDP-43 and hnRNPA1 have higher conformational dynamics than the isolated forms. Two RRM domains become coupled as shown by NMR characterization and analysis of inter-domain correlation motions. The study explains the long-standing puzzle that the tethered TDP-43 RRM1–RRM2 is particularly prone to aggregation/fibrillation, and underscores the general role of ATP in inhibiting aggregation/fibrillation of RRM-containing proteins. The results also rationalize the observation that the risk of aggregation-causing diseases increases with aging.

scholarly journals Higher spins from exotic dualisations

2021 ◽  
Vol 2021 (3) ◽  
Author(s):  
Nicolas Boulanger ◽  
Victor Lekeu
Keyword(s):  
Infinite Number ◽  
Arbitrary Number ◽  
Degrees Of Freedom ◽  
Young Tableaux ◽  
Spacetime Dimension ◽  
Massless Field ◽  
Free Level ◽  
Higher Spins

Abstract At the free level, a given massless field can be described by an infinite number of different potentials related to each other by dualities. In terms of Young tableaux, dualities replace any number of columns of height hi by columns of height D − 2 − hi, where D is the spacetime dimension: in particular, applying this operation to empty columns gives rise to potentials containing an arbitrary number of groups of D − 2 extra antisymmetric indices. Using the method of parent actions, action principles including these potentials, but also extra fields, can be derived from the usual ones. In this paper, we revisit this off-shell duality and clarify the counting of degrees of freedom and the role of the extra fields. Among others, we consider the examples of the double dual graviton in D = 5 and two cases, one topological and one dynamical, of exotic dualities leading to spin three fields in D = 3.

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