scholarly journals Energy Bilocalization Effect and the Emergence of Molecular Functions in Proteins

2021 ◽  
Vol 8 ◽  
Author(s):  
Yann Chalopin ◽  
Julien Sparfel
Keyword(s):  
Natural Selection ◽  
Physical Theory ◽  
Dynamical Behavior ◽  
Molecular Structures ◽  
Information Storage ◽  
Spike Protein ◽  
Biological Functions ◽  
Genetic Sequence ◽  
Structural Irregularities ◽  
Thermal Vibrations

Proteins are among the most complex molecular structures, which have evolved to develop broad functions, such as energy conversion and transport, information storage and processing, communication, and regulation of chemical reactions. However, the mechanisms by which these dynamical entities coordinate themselves to perform biological tasks remain hotly debated. Here, a physical theory is presented to explain how functional dynamical behavior possibly emerge in complex/macro molecules, thanks to the effect that we term bilocalization of thermal vibrations. More specifically, our approach allows us to understand how structural irregularities lead to a partitioning of the energy of the vibrations into two distinct sets of molecular domains, corresponding to slow and fast motions. This shape-encoded spectral allocation, associated to the genetic sequence, provides a close access to a wide reservoir of dynamical patterns, and eventually allows the emergence of biological functions by natural selection. To illustrate our approach, the SPIKE protein structure of SARS-COV2 is considered.

scholarly journals Evolutionary stalling and a limit on the power of natural selection to improve a cellular module

2020 ◽  
Vol 117 (31) ◽  
pp. 18582-18590 ◽  
Author(s):  
Sandeep Venkataram ◽  
Ross Monasky ◽  
Shohreh H. Sikaroodi ◽  
Sergey Kryazhimskiy ◽  
Betul Kacar
Keyword(s):  
Escherichia Coli ◽  
Natural Selection ◽  
Adaptive Evolution ◽  
Genetic Load ◽  
Performance Theory ◽  
Biological Functions ◽  
Beneficial Mutations ◽  
Translation Machinery ◽  
Adaptive Mutations ◽  
Organismal Fitness

Cells consist of molecular modules which perform vital biological functions. Cellular modules are key units of adaptive evolution because organismal fitness depends on their performance. Theory shows that in rapidly evolving populations, such as those of many microbes, adaptation is driven primarily by common beneficial mutations with large effects, while other mutations behave as if they are effectively neutral. As a consequence, if a module can be improved only by rare and/or weak beneficial mutations, its adaptive evolution would stall. However, such evolutionary stalling has not been empirically demonstrated, and it is unclear to what extent stalling may limit the power of natural selection to improve modules. Here we empirically characterize how natural selection improves the translation machinery (TM), an essential cellular module. We experimentally evolved populations ofEscherichia coliwith genetically perturbed TMs for 1,000 generations. Populations with severe TM defects initially adapted via mutations in the TM, but TM adaptation stalled within about 300 generations. We estimate that the genetic load in our populations incurred by residual TM defects ranges from 0.5 to 19%. Finally, we found evidence that both epistasis and the depletion of the pool of beneficial mutations contributed to evolutionary stalling. Our results suggest that cellular modules may not be fully optimized by natural selection despite the availability of adaptive mutations.

A Taxonomy of Functions

1996 ◽  
Vol 26 (4) ◽  
pp. 493-514 ◽  
Author(s):  
Denis M. Walsh ◽  
André Ariew
Keyword(s):  
Natural Selection ◽  
The Other ◽  
Evolutionary Significance ◽  
System Call ◽  
Biological Functions ◽  
Function Concept ◽  
Causal Contribution ◽  
Function Concepts ◽  
Evolutionary Function

There are two general approaches to characterising biological functions. One originates with Cummins. According to this approach, the function of a part of a system is just its causal contribution to some specified activity of the system. Call this the ‘C-function’ (or ‘Cummins function’) concept. The other approach ties the function of a trait to some aspect of its evolutionary significance. Call this the ‘E-function’ (or ‘evolutionary function’) concept. According to the latter view, a trait's function is determined by the forces of natural selection. The C-function and E-function concepts are clearly quite different, but there is an important relation between them which heretofore has gone unnoticed. The purpose of this paper is to outline that relation.This is not the first paper to discuss the relation of C-function and E-function. Previous attempts all follow either one of two strategies. The first proposes that the two concepts are ‘unified.’ The other proposes that they are radically distinct and apply to wholly different fields within biology.

scholarly journals Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica

2021 ◽  
Author(s):  
Jose Arturo Molina-Mora
Keyword(s):  
Immune Response ◽  
Molecular Docking ◽  
Natural Selection ◽  
Costa Rica ◽  
In Silico ◽  
Spike Protein ◽  
Evolutionary Models ◽  
Bioinformatics Pipeline ◽  
Predominant Genotype ◽  
Adaptive Selection

Emerging mutations and genotypes of the SARS-CoV-2 virus, responsible for the COVID-19 pandemic, have been reported globally. In Costa Rica during the year 2020, a predominant genotype carrying the mutation T1117I in the spike (S:T1117I) was previously identified. To investigate the possible effects of this mutation on the function of the spike, i.e. the biology of the virus, different bioinformatic pipelines based on phylogeny, natural selection and co-evolutionary models, molecular docking and epitopes prediction were implemented. Results of the phylogeny of sequences carrying the S:T1117I worldwide showed a polyphyletic group, with the emergency of local lineages. In Costa Rica, the mutation is found in the lineage B.1.1.389 and it is suggested to be a product of positive/adaptive selection. Different changes in the function of the spike protein and more stable interaction with a ligand (nelfinavir drug) were found. Only one epitope out 742 in the spike was affected by the mutation, with some different properties, but suggesting scarce changes in the immune response and no influence on the vaccine effectiveness. Jointly, these results suggest a partial benefit of the mutation for the spread of the virus with this genotype during the year 2020 in Costa Rica, although possibly not strong enough with the introduction of new lineages during early 2021 which became predominant later. In addition, the bioinformatics pipeline offers an integrative and exhaustive in silico strategy to eventually study other mutations of interest for the SARS-CoV-2 virus and other pathogens.

scholarly journals Deciphering the O-Glycosylation of HKU1 Spike Protein With the Dual-Functional Hydrophilic Interaction Chromatography Materials

2021 ◽  
Vol 9 ◽  
Author(s):  
Yun Cui ◽  
Xuefang Dong ◽  
Xiaofei Zhang ◽  
Cheng Chen ◽  
Dongmei Fu ◽  
...  
Keyword(s):  
Protein S ◽  
Host Cells ◽  
Spike Protein ◽  
Biological Functions ◽  
Hydrophilic Interaction ◽  
Protein Surface ◽  
Enrichment Method ◽  
Dual Functional ◽  
Glycosylation Sites ◽  
Comprehensive Study

HKU1 is a human beta coronavirus and infects host cells via highly glycosylated spike protein (S). The N-glycosylation of HKU1 S has been reported. However, little is known about its O-glycosylation, which hinders the in-depth understanding of its biological functions. Herein, a comprehensive study of O-glycosylation of HKU1 S was carried out based on dual-functional histidine-bonded silica (HBS) materials. The enrichment method for O-glycopeptides with HBS was developed and validated using standard proteins. The application of the developed method to the HKU1 S1 subunit resulted in 46 novel O-glycosylation sites, among which 55.6% were predicted to be exposed on the outer protein surface. Moreover, the O-linked glycans and their abundance on each HKU1 S1 site were analyzed. The obtained O-glycosylation dataset will provide valuable insights into the structure of HKU1 S.

scholarly journals Evolutionary Stalling and a Limit on the Power of Natural Selection to Improve a Cellular Module

2019 ◽  
Author(s):  
Sandeep Venkataram ◽  
Ross Monasky ◽  
Shohreh H Sikaroodi ◽  
Sergey Kryazhimskiy ◽  
Betül Kaçar
Keyword(s):  
Escherichia Coli ◽  
Natural Selection ◽  
Adaptive Evolution ◽  
Genetic Load ◽  
Performance Theory ◽  
Biological Functions ◽  
Beneficial Mutations ◽  
Translation Machinery ◽  
Adaptive Mutations ◽  
Organismal Fitness

AbstractCells consist of molecular modules which perform vital biological functions. Cellular modules are key units of adaptive evolution because organismal fitness depends on their performance. Theory shows that in rapidly evolving populations, such as those of many microbes, adaptation is driven primarily by common beneficial mutations with large effects, while other mutations behave as if they are effectively neutral. As a consequence, if a module can be improved only by rare and/or weak beneficial mutations, its adaptive evolution would stall. However, such evolutionary stalling has not been empirically demonstrated, and it is unclear to what extent stalling may limit the power of natural selection to improve modules. Here, we empirically characterize how natural selection improves the translation machinery (TM), an essential cellular module. We experimentally evolved populations of Escherichia coli with genetically perturbed TMs for 1,000 generations. Populations with severe TM defects initially adapted via mutations in the TM, but TM adaptation stalled within about 300 generations. We estimate that the genetic load in our populations incurred by residual TM defects ranges from 0.5 to 19%. Finally, we found evidence that both epistasis and the depletion of the pool of beneficial mutations contributed to evolutionary stalling. Our results suggest that cellular modules may not be fully optimized by natural selection despite the availability of adaptive mutations.

scholarly journals RNA Methylations in Cardiovascular Diseases, Molecular Structure, Biological Functions and Regulatory Roles in Cardiovascular Diseases

2021 ◽  
Vol 12 ◽  
Author(s):  
Wanwan Zhou ◽  
Changhui Wang ◽  
Jun Chang ◽  
Yurong Huang ◽  
Qiuyun Xue ◽  
...  
Keyword(s):  
Cardiovascular Diseases ◽  
Rna Processing ◽  
Nuclear Export ◽  
Molecular Structures ◽  
Molecular Characteristics ◽  
Biological Functions ◽  
Non Coding Rna ◽  
Therapeutic Measures ◽  
New Research ◽  
Almost All

Cardiovascular diseases (CVDs) are the leading cause of morbidity and mortality in the world. Despite considerable progress in the diagnosis, treatment and prognosis of CVDs, new diagnostic biomarkers and new therapeutic measures are urgently needed to reduce the mortality of CVDs and improve the therapeutic effect. RNA methylations regulate almost all aspects of RNA processing, such as RNA nuclear export, translation, splicing and non-coding RNA processing. In view of the importance of RNA methylations in the pathogenesis of diseases, this work reviews the molecular structures, biological functions of five kinds of RNA methylations (m6A, m5C, m1a, m6am and m7G) and their effects on CVDs, including pulmonary hypertension, hypertension, vascular calcification, cardiac hypertrophy, heart failure. In CVDs, m6A “writers” catalyze the installation of m6A on RNAs, while “erasers” remove these modifications. Finally, the “readers” of m6A further influence the mRNA splicing, nuclear export, translation and degradation. M5C, m1A, m6Am and m7G are new types of RNA methylations, their roles in CVDs need to be further explored. RNA methylations have become a new research hotspot and the roles in CVDs is gradually emerging, the review of the molecular characteristics, biological functions and effects of RNA methylation on CVDs will contribute to the elucidation of the pathological mechanisms of CVDs and the discovery of new diagnostic markers and therapeutic targets of CVDs.

Hegel's Organizational Account of Biological Functions

2020 ◽  
pp. 1-19
Author(s):  
Edgar Maraguat
Keyword(s):  
Natural Selection ◽  
Biological Function ◽  
The Other ◽  
Proper Function ◽  
Biological Functions ◽  
Real Work ◽  
Organizational Account ◽  
Philosophical Debates ◽  
Self Production

Abstract Two concepts have polarized the philosophical debates on functions since the 1970s. One is Millikan's concept of ‘proper function’, meant to capture the aetiology of biological organs and artefacts. The other is Cummins's concept of ‘dispositional function’, designed to account for the real work that functional devices perform within a system. In this paper I locate Hegel's concept of biological function in the context of those debates. Admittedly, Hegel's concept is ‘etiological’, since in his account the existence of purposive organs is explained by appeal to their purpose, yet, against Millikan's concept, Hegel's does not presuppose the phenomenon of natural selection nor derives the function of tokens from the function of types. So, my aim is, first, to present Hegel's approach to biological functions as one neither purely etiological nor purely dispositional. It will appear rather as an example of an organizational account (as those advocated today by McLaughlin, Mossio and others), that attributes function according to present performances (unlike etiological accounts) and emphasizes the role of functional parts in their self-production within the system they belong to (unlike dispositional accounts). Finally, I briefly discuss how Hegel's concept performs against common objections to organizational accounts.

Nanotechnology can provide therapeutic agent by targeting molecular structures of SARS-CoV-2 (COVID-19): A Mini-Review

2021 ◽  
Vol 18 ◽  
Author(s):  
Sarwar Allah Ditta ◽  
Atif Yaqub ◽  
Fouzia Tanvir
Keyword(s):  
Viral Entry ◽  
Nigella Sativa ◽  
Biological Properties ◽  
Amino Acid Sequences ◽  
Molecular Structures ◽  
Surface Glycoprotein ◽  
Spike Protein ◽  
Type I ◽  
Active Components ◽  
Biological Origin

: COVID-19 outbreak hit the world worse at the start of 2020, as of December 11, 2020, more than 1.5 million people have died and more than 68.8 million people have been infected globally. SARS-CoV-2 induces mild to severe progressive respiratory pneumonia, leading to failure of different body organs and ultimately death. Hitherto, there are no specific and potential therapeutic agents available against the virus. The spike protein is a type I surface glycoprotein facilitating entry of the virus into the host cell via hACE2 receptors. The two subunits of the spike protein have a polybasic link as cleavage site (PRAR) in SARS-CoV-2, with additional attachment of O-linked glycans. SARS-CoV and SARS-CoV-2 have 76.5% similarity in amino acid sequences. The pathogenesis and viral entry of SARS-CoV-2 are different from SARS-CoV, therefore, it is a dire need of the time to develop a target-based treatment. Alternative strategies and multidisciplinary research approaches are crucial for developing new antiviral and improved therapies against COVID-19. Nanotechnology has opened new horizons for evaluating the biological properties and efficacy of different materials having biological origin, such as Nigella sativa. It contains various active components such as thymoquinone, thymol, thymohydroquinone, and dithymoquinone with different biological potentials. Metallic nanomaterials have been reported to exhibit antiviral activities against various strains. Understanding molecular interactions and modifying the surface properties of nanomaterials with optimum activity may result in the development of novel antiviral therapies.

scholarly journals A framework to quantify phenotypic and genotypic parallel evolution

2020 ◽  
Author(s):  
Maddie E. James ◽  
Melanie J. Wilkinson ◽  
Henry L. North ◽  
Jan Engelstädter ◽  
Daniel Ortiz-Barrientos
Keyword(s):  
Natural Selection ◽  
Parallel Evolution ◽  
Model Organisms ◽  
Biological Functions ◽  
Narrow Sense ◽  
Ongoing Debate ◽  
Common Framework ◽  
Repeated Evolution ◽  
The Way

AbstractThe independent and repeated adaptation of populations to similar environments often results in the evolution of similar forms. This phenomenon creates a strong correlation between phenotype and environment and is referred to as parallel evolution. However, there is ongoing debate as to when we should call a system either phenotypically or genotypically ‘parallel.’ Here, we suggest a novel and simple framework to quantify parallel evolution at the genotypic and phenotypic levels. Our framework combines both traditional and new approaches to measure parallel evolution, and categorizes them into broad- and narrow-sense scales. We then apply this framework to coastal ecotypes of an Australian wildflower, Senecio lautus, that have evolved in parallel. Our findings show that S. lautus populations inhabiting similar environments have evolved strikingly similar phenotypes. These phenotypes have arisen via mutational changes occurring in different genes, although many share the same biological functions. Our work paves the way towards a common framework to study the repeated evolution of forms in nature.Author summaryWhen organisms face similar ecological conditions, they often evolve similar phenotypic solutions. When this occurs in closely related taxa, it is referred to as parallel evolution. Systems of parallel evolution provide some of the most compelling evidence for the role of natural selection in evolution, as they can be used as natural replicates of the adaptation process. However, there is debate as to when we should call a system ‘parallel’. This debate stems back to the mid 1900s, and although there have been multiple attempts within the literature to clarify terminology, controversy still remains. In this study, we propose a novel framework to quantify phenotypic and genotypic parallel evolution within empirical systems, partitioning parallelism into broad- and narrow-sense components. Our framework is applicable to non-model organisms and provides a common set of analyses to measure parallel evolution, enabling researchers to compare the extent of parallel evolution across different study systems. In turn, this helps to reduce confusion surrounding the term ‘parallel evolution’ at both the phenotypic and genotypic levels. We then apply our framework to two coastal ecotypes of an Australian plant, Senecio lautus. We show that similar phenotypes within each ecotype have evolved via mutational changes in different genes, though some are involved in similar biological functions. Our research not only helps to consolidate the field of parallel evolution, but paves the way to understanding the role of natural selection in the repeated evolution of similar phenotypes within nature.

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