scholarly journals Gene duplication and subsequent diversification strongly affect phenotypic evolvability and robustness

2021 ◽  
Vol 8 (6) ◽  
pp. 201636
Author(s):  
V. Jouffrey ◽  
A. S. Leonard ◽  
S. E. Ahnert
Keyword(s):  
Gene Duplication ◽  
Structural Properties ◽  
Self Assembly ◽  
Quaternary Structure ◽  
Assembly Model ◽  
Positive Correlation ◽  
Inverse Effect ◽  
Deterministic Setting

We study the effects of non-determinism and gene duplication on the structure of genotype–phenotype (GP) maps by introducing a non-deterministic version of the Polyomino self-assembly model. This model has previously been used in a variety of contexts to model the assembly and evolution of protein quaternary structure. Firstly, we show the limit of the current deterministic paradigm which leads to built-in anti-correlation between evolvability and robustness at the genotypic level. We develop a set of metrics to measure structural properties of GP maps in a non-deterministic setting and use them to evaluate the effects of gene duplication and subsequent diversification. Our generalized versions of evolvability and robustness exhibit positive correlation for a subset of genotypes. This positive correlation is only possible because non-deterministic phenotypes can contribute to both robustness and evolvability. Secondly, we show that duplication increases robustness and reduces evolvability initially, but that the subsequent diversification that duplication enables has a stronger, inverse effect, greatly increasing evolvability and reducing robustness relative to their original values.

scholarly journals Duplication accelerates the evolution of structural complexity in protein quaternary structure

2020 ◽  
Author(s):  
Alexander S. Leonard ◽  
Sebastian E. Ahnert
Keyword(s):  
Gene Duplication ◽  
Lattice Model ◽  
Self Assembly ◽  
Large Scale ◽  
Quaternary Structure ◽  
Protein Complexes ◽  
Structural Complexity ◽  
Data Bank ◽  
Coarse Grained ◽  
Duplication Events

AbstractGene duplication, from single genes to whole genomes, has been observed in organisms across all taxa. Despite its prevalence, the evolutionary benefits of this mechanism are the subject of ongoing debate. Gene duplication can significantly alter the self-assembly of protein quaternary structures, impacting the dosage or interaction proclivity. Here we use a lattice model of self-assembly as a coarse-grained representation of protein complex assembly, and show that it can be used to examine potential evolutionary advantages of duplication. Duplication provides a unique mechanism for increasing the evolvability of protein complexes by enabling the transformation of symmetric homomeric interactions into heteromeric ones. This transformation is extensively observed in in silico evolutionary simulations of the lattice model, with duplication events significantly accelerating the rate at which structural complexity increases. These coarse-grained simulation results are corroborated with a large-scale analysis of complexes from the Protein Data Bank.

Capillary flows and self-assembly of porous hydrate structures

2012 ◽  
Vol 9 (1) ◽  
pp. 22-25
Author(s):  
S.V. Amel’kin ◽  
D.Ye. Igoshin
Keyword(s):  
Experimental Data ◽  
Aqueous Solution ◽  
Self Assembly ◽  
Capillary Flow ◽  
Secondary Crystallization ◽  
Assembly Model ◽  
Physical Processes ◽  
Good Correspondence ◽  
Solution Formation ◽  
Capillary Flows

A self-assembly model for porous hydrate structures is proposed, which takes into account the sequence of basic physical processes: hydrate growth on the surface of the aqueous solution, formation of islet structure, capillary flow, separation and transfer of secondary crystallization nuclei to the meniscus. The model was studied within the cellular automata method. A good correspondence between the results of the simulation and the experimental data is obtained.

scholarly journals DNA-Guided Assembly for Fibril Proteins

Mathematics ◽  
2021 ◽  
Vol 9 (4) ◽  
pp. 404
Author(s):  
Alexandru Amărioarei ◽  
Frankie Spencer ◽  
Gefry Barad ◽  
Ana-Maria Gheorghe ◽  
Corina Iţcuş ◽  
...  
Keyword(s):  
Computational Model ◽  
Structural Properties ◽  
Self Assembly ◽  
Structural Characteristics ◽  
Computational Modelling ◽  
Shape Reconstruction ◽  
Raw Material ◽  
Dna Assembly ◽  
Mesh Structure ◽  
Elementary Fibril

Current advances in computational modelling and simulation have led to the inclusion of computer scientists as partners in the process of engineering of new nanomaterials and nanodevices. This trend is now, more than ever, visible in the field of deoxyribonucleic acid (DNA)-based nanotechnology, as DNA’s intrinsic principle of self-assembly has been proven to be highly algorithmic and programmable. As a raw material, DNA is a rather unremarkable fabric. However, as a way to achieve patterns, dynamic behavior, or nano-shape reconstruction, DNA has been proven to be one of the most functional nanomaterials. It would thus be of great potential to pair up DNA’s highly functional assembly characteristics with the mechanic properties of other well-known bio-nanomaterials, such as graphene, cellulos, or fibroin. In the current study, we perform projections regarding the structural properties of a fibril mesh (or filter) for which assembly would be guided by the controlled aggregation of DNA scaffold subunits. The formation of such a 2D fibril mesh structure is ensured by the mechanistic assembly properties borrowed from the DNA assembly apparatus. For generating inexpensive pre-experimental assessments regarding the efficiency of various assembly strategies, we introduced in this study a computational model for the simulation of fibril mesh assembly dynamical systems. Our approach was based on providing solutions towards two main circumstances. First, we created a functional computational model that is restrictive enough to be able to numerically simulate the controlled aggregation of up to 1000s of elementary fibril elements yet rich enough to provide actionable insides on the structural characteristics for the generated assembly. Second, we used the provided numerical model in order to generate projections regarding effective ways of manipulating one of the the key structural properties of such generated filters, namely the average size of the openings (gaps) within these meshes, also known as the filter’s aperture. This work is a continuation of Amarioarei et al., 2018, where a preliminary version of this research was discussed.

The Rheological and Structural Properties of Fmoc-Peptide-Based Hydrogels: The Effect of Aromatic Molecular Architecture on Self-Assembly and Physical Characteristics

Langmuir ◽  
2012 ◽  
Vol 28 (4) ◽  
pp. 2015-2022 ◽  
Author(s):  
Ron Orbach ◽  
Iris Mironi-Harpaz ◽  
Lihi Adler-Abramovich ◽  
Estelle Mossou ◽  
Edward P. Mitchell ◽  
...  
Keyword(s):  
Structural Properties ◽  
Self Assembly ◽  
Physical Characteristics ◽  
Molecular Architecture

scholarly journals Cross-linking reveals laminin coiled-coil architecture

2016 ◽  
Vol 113 (47) ◽  
pp. 13384-13389 ◽  
Author(s):  
Gad Armony ◽  
Etai Jacob ◽  
Toot Moran ◽  
Yishai Levin ◽  
Tevie Mehlman ◽  
...  
Keyword(s):  
Extracellular Matrix ◽  
Self Assembly ◽  
Quaternary Structure ◽  
Coiled Coil ◽  
Surface Proteins ◽  
Cross Linking ◽  
Single Particle Reconstruction ◽  
Cross Links ◽  
Particle Reconstruction ◽  
Key Questions

Laminin, an ∼800-kDa heterotrimeric protein, is a major functional component of the extracellular matrix, contributing to tissue development and maintenance. The unique architecture of laminin is not currently amenable to determination at high resolution, as its flexible and narrow segments complicate both crystallization and single-particle reconstruction by electron microscopy. Therefore, we used cross-linking and MS, evaluated using computational methods, to address key questions regarding laminin quaternary structure. This approach was particularly well suited to the ∼750-Å coiled coil that mediates trimer assembly, and our results support revision of the subunit order typically presented in laminin schematics. Furthermore, information on the subunit register in the coiled coil and cross-links to downstream domains provide insights into the self-assembly required for interaction with other extracellular matrix and cell surface proteins.

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