scholarly journals Molecular Diversity and Network Complexity in Growing Protocells

Life ◽  
2019 ◽  
Vol 9 (2) ◽  
pp. 53
Author(s):  
Atsushi Kamimura ◽  
Kunihiko Kaneko
Keyword(s):  
Molecular Species ◽  
Catalytic Reaction ◽  
Molecular Diversity ◽  
Reaction Network ◽  
Cellular Growth ◽  
Reaction Networks ◽  
Cell Reproduction ◽  
A Cell ◽  
Molecular Components ◽  
Cellular Components

A great variety of molecular components is encapsulated in cells. Each of these components is replicated for cell reproduction. To address the essential role of the huge diversity of cellular components, we studied a model of protocells that convert resources into catalysts with the aid of a catalytic reaction network. As the resources were limited, the diversity in the intracellular components was found to be increased to allow the use of diverse resources for cellular growth. A scaling relation was demonstrated between resource abundances and molecular diversity. In the present study, we examined how the molecular species diversify and how complex catalytic reaction networks develop through an evolutionary course. At some generations, molecular species first appear as parasites that do not contribute to the replication of other molecules. Later, the species turn into host species that contribute to the replication of other species, with further diversification of molecular species. Thus, a complex joint network evolves with this successive increase in species. The present study sheds new light on the origin of molecular diversity and complex reaction networks at the primitive stage of a cell.

scholarly journals Molecular Diversity and Network Complexity in Growing Protocells

2019 ◽  
Author(s):  
Atsushi Kamimura ◽  
Kunihiko Kaneko
Keyword(s):  
Catalytic Reaction ◽  
Host Species ◽  
Molecular Diversity ◽  
Reaction Network ◽  
Cellular Growth ◽  
Cell Reproduction ◽  
A Cell ◽  
Molecular Components ◽  
Growth Scaling ◽  
Cellular Components

AbstractA great variety of molecular components is encapsulated in cells. Each of these components is replicated for cell reproduction. To address an essential role of the huge diversity of cellular components, we study a model of protocells that convert resources into catalysts with the aid of a catalytic reaction network. As the resources are limited, it is shown that diversity in intracellular components is increased to allow the use of diverse resources for cellular growth. Scaling relation is demonstrated between resource abundances and molecular diversity. We then study how the molecule species diversify and complex catalytic reaction networks develop through the evolutionary course. It is shown that molecule species first appear, at some generations, as parasitic ones that do not contribute to replication of other molecules. Later, the species turn to be host species that support the replication of other species. With this successive increase of host species, a complex joint network evolves. The present study sheds new light on the origin of molecular diversity and complex reaction network at the primitive stage of a cell.

scholarly journals Activated Self-Resolution and Error-Correction in Catalytic Reaction Networks

2021 ◽  
Author(s):  
Fredrik Schaufelberger ◽  
Olof Ramstrom
Keyword(s):  
Dynamic System ◽  
Error Correction ◽  
Small Molecule ◽  
Catalytic Reaction ◽  
Reaction Network ◽  
Reaction Networks ◽  
Complex Reaction ◽  
Catalytic Systems ◽  
Systems Chemistry ◽  
Mbh Reaction

<p>To understand the emergence of function in complex reaction networks is a primary goal of systems chemistry and origin-of-life studies. Especially challenging is the establishment of systems that simultaneously exhibit several functionality parameters that can be independently tuned. In this work, a multifunctional complex reaction network of nucleophilic small molecule catalysts for the Morita-Baylis-Hillman (MBH) reaction is demonstrated. The dynamic system exhibited triggered self-resolution, preferentially amplifying a specific catalyst/product set out of a many potential alternatives. By utilizing selective reversibility of the products of the reaction set, systemic thermodynamically driven error-correction could also be introduced. To achieve this, a dynamic covalent MBH reaction based on adducts with internal H-transfer capabilities was developed, displaying rate accelerations of retro-MBH reactions up to 104 times. This study demonstrates how efficient self-sorting of catalytic systems can be achieved through an interplay of several complex emergent functionalities.</p>

scholarly journals Activated Self-Resolution and Error-Correction in Catalytic Reaction Networks

2021 ◽  
Author(s):  
Fredrik Schaufelberger ◽  
Olof Ramstrom
Keyword(s):  
Dynamic System ◽  
Error Correction ◽  
Small Molecule ◽  
Catalytic Reaction ◽  
Reaction Network ◽  
Reaction Networks ◽  
Complex Reaction ◽  
Catalytic Systems ◽  
Systems Chemistry ◽  
Mbh Reaction

<p>To understand the emergence of function in complex reaction networks is a primary goal of systems chemistry and origin-of-life studies. Especially challenging is the establishment of systems that simultaneously exhibit several functionality parameters that can be independently tuned. In this work, a multifunctional complex reaction network of nucleophilic small molecule catalysts for the Morita-Baylis-Hillman (MBH) reaction is demonstrated. The dynamic system exhibited triggered self-resolution, preferentially amplifying a specific catalyst/product set out of a many potential alternatives. By utilizing selective reversibility of the products of the reaction set, systemic thermodynamically driven error-correction could also be introduced. To achieve this, a dynamic covalent MBH reaction based on adducts with internal H-transfer capabilities was developed, displaying rate accelerations of retro-MBH reactions up to 104 times. This study demonstrates how efficient self-sorting of catalytic systems can be achieved through an interplay of several complex emergent functionalities.</p>

scholarly journals Gazing into the Metaboverse: Automated exploration and contextualization of metabolic data

2020 ◽  
Author(s):  
Jordan A. Berg ◽  
Youjia Zhou ◽  
T. Cameron Waller ◽  
Yeyun Ouyang ◽  
Sara M. Nowinski ◽  
...  
Keyword(s):  
Reaction Network ◽  
Reaction Networks ◽  
Metabolic Reaction ◽  
Automated Extraction ◽  
Reaction Systems ◽  
High Magnitude ◽  
Downstream Effects ◽  
A Cell ◽  
Metabolic Data ◽  
Omic Data

AbstractMetabolism and its component reactions are complex, each with variable inputs, outputs, and modifiers. The harmony between these factors consequently determines the health and stability of a cell or an organism. Perturbations to any reaction or set of reactions can have rippling downstream effects, which can be challenging to trace across the total reaction network, particularly when the effects occur between complex interconnected pathways. Researchers have primarily utilized reductionist approaches to understand metabolic reaction systems; however, these simplistic methods often limit the scope of the analysis. Even systems-centric omics approaches can be limited when only a handful of high magnitude signals in the data are prioritized for interpretation. To address these challenges, we developed Metaboverse, an interactive tool for the exploration and automated extraction of potential regulatory events, patterns, and trends from multi-omic data within the context of the metabolic network and other reaction networks. This framework will be foundational in increasing our ability to holistically understand static, temporal, and multi-condition metabolic events and perturbations as well as gene-metabolite intra-cooperativity. Metaboverse is freely available under a GPL-3.0 license at https://github.com/Metaboverse/.

Chemical Organization Theory Applied to Virus Dynamics (Theorie chemischer Organisationen angewendet auf Infektionsmodelle)

2006 ◽  
Vol 48 (3) ◽  
Author(s):  
Naoki Matsumaru ◽  
Florian Centler ◽  
Pietro Speroni di Fenizio ◽  
Peter Dittrich
Keyword(s):  
Immune Response ◽  
Molecular Species ◽  
Organization Theory ◽  
Reaction Network ◽  
Reaction Networks ◽  
Virus Dynamics ◽  
Abstract Level ◽  
Level I ◽  
New Perspective

SummaryChemical organization theory has been proposed to provide a new perspective to study complex dynamical reaction networks. It decomposes a reaction network into overlapping sub-networks called organizations. An organization is an algebraically closed and self-maintaining set of molecular species. The set of organizations form a hierarchical “organizational structure”, which is here a lattice. In order to evaluate the usefulness of this approach we apply the theory to five models of immune response to HIV infection. We found four different lattices of organizations, which can be used as a first classification of the models. Furthermore, each organization found can be assigned to a functional state of the system. And finally, the lattice of organizations can be used to explain a treatment strategy on a more abstract level, i. e., as a movement from one organization into another.

Protein Flexibility Catalyzes a Cell Signaling Reaction of the Ras-GAP Complex

2019 ◽  
Author(s):  
Keiei Kumon ◽  
Masahiro Higashi ◽  
Shinji Saito ◽  
Shigehiko Hayashi
Keyword(s):  
Cell Signaling ◽  
Conformational Changes ◽  
Catalytic Reaction ◽  
Protein Complex ◽  
Enzyme Mechanism ◽  
Activation Free Energy ◽  
Chemical Catalysis ◽  
Simple Chemical ◽  
A Cell ◽  
Enzyme Molecules

Many enzyme molecules exhibit characteristic global and slow dynamics which furnish them with allostery realizing remarkable molecular functionalities more than simple chemical catalysis. However, molecular mechanism of a catalytic reaction associated with the molecular flexibility of enzymes is not well-understood. Here we report a hybrid molecular simulation study on GTPase activity of a Ras-GAP protein complex for cell signaling termination. We unveiled that extensive conformational changes of the protein complex and exclusion of internal water molecules are induced upon the transition state (TS) formation in the catalytic reaction and significantly lower the reaction activation free energy. We also revealed that tumor-related mutations perturb those conformational changes upon the TS formation, leading to reduction of the catalytic activity. The findings of the remarkably dynamic protein conformation directly linking to the catalytic reaction have broad implications for understanding of enzyme mechanism and for developments of allosteric drugs and novel catalysts.

Proteomic Characterization of Protein-Protein Interactions

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Veenstra TD ◽  
Keyword(s):  
Protein Interactions ◽  
Disease Diagnosis ◽  
Cell System ◽  
Protein Protein Interactions ◽  
Novel Technologies ◽  
Cell Functions ◽  
Single Protein ◽  
A Cell ◽  
Molecular Components

Identifying all the molecular components within a living cell is the first step into understanding how it functions. To further understand how a cell functions requires identifying the interactions that occur between these components. This fact is especially relevant for proteins. No protein within a human cell functions on its own without interacting with another biomolecule - usually another protein. While Protein-Protein Interactions (PPI) have historically been determined by examining a single protein per study, novel technologies developed over the past couple of decades are enabling high-throughput methods that aim to describe entire protein networks within cells. In this review, some of the technologies that have led to these developments are described along with applications of these techniques. Ultimately the goal of these technologies is to map out the entire circuitry of PPI within human cells to be able to predict the global consequences of perturbations to the cell system. This predictive capability will have major impacts on the future of both disease diagnosis and treatment.

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