Molecular and thermodynamic mechanisms for protein adaptation

Zhao, Qinyi

doi:10.1007/s00249-022-01618-9

Cited by 5 publications

(3 citation statements)

References 82 publications

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“…More recently, Panja et al explored statistically how microbial proteins undergo selective changes to adapt to environments of different kinds, both in terms of amino acid composition and in their ordering [80], a result in line with the weak selection concept [81]. According to these and other previous results, salinity, pH and temperature would represent the major environmental drivers of how proteins evolve [4, 82–84], modifying the catalytic kinetics, substrate specificity or conditional stability while maintaining the same function [66, 85].…”

Section: Discussionmentioning

confidence: 91%

“…modifying the catalytic kinetics, substrate specificity or conditional stability while maintaining the same function [69,86].…”

Section: How the Environment Constrains Microbial Protein Diversifica...mentioning

confidence: 99%

“…Neutral drift undoubtedly contributes to protein suband neo-functionalization [66]. However, the observed functional plasticity in a population of sequences may be constrained by selection, allowing different kinetics in diverse environments, even modifying the substrate preferences [67][68][69]. We can expect that sequence variants adapted to similar conditions will converge in similarity.…”

Section: Diversification Of Functional Protein Sequencesmentioning

confidence: 99%

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Quantifying Microbial Guilds

Rivas-Santisteban

Yubero

Robaina-Estévez

et al. 2023

Preprint

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The ecological role of microorganisms is of utmost importance due to their multiple interactions with the environment. However, assessing the contribution of individual taxonomic groups has proven difficult despite the availability of high throughput data, hindering our understanding of such complex systems. Here, we propose a quantitative definition of guild that is readily applicable to metagenomic data. Our framework focuses on the functional character of protein sequences, as well as their diversifying nature. First, we discriminate functional sequences from the whole sequence space corresponding to a gene annotation to then quantify their contribution to the guild composition across environments. In addition, we distinguish between sequence spaces that have different ways of carrying out the function. We demonstrate the validity of our approach by quantifying the guild of ammonia oxidation, and further reveal novel ecological dynamics of putrescine uptake guild in marine ecosystems. Thus, guilds help elucidate the functional role of different taxonomic groups with profound implications in the study of microbial communities.

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Section: Discussionmentioning

confidence: 91%

“…modifying the catalytic kinetics, substrate specificity or conditional stability while maintaining the same function [69,86].…”

Section: How the Environment Constrains Microbial Protein Diversifica...mentioning

confidence: 99%

Section: Diversification Of Functional Protein Sequencesmentioning

confidence: 99%

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Quantifying Microbial Guilds

Rivas-Santisteban

Yubero

Robaina-Estévez

et al. 2023

Preprint

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Thermal Inactivation, Denaturation and Aggregation Processes of Papain‐Like Proteases

Koroleva,

Lavlinskaya,

Holyavka

et al. 2024

Chemistry & Biodiversity

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The investigation into the behavior of ficin, bromelain, papain under thermal conditions holds both theoretical and practical significance. The production processes of medicines and cosmetics often involve exposure to high temperatures, particularly during the final product sterilization phase. Hence, it's crucial to identify the "critical" temperatures for each component within the mixture for effective technological regulation. In light of this, the objective of this study was to examine the thermal inactivation, aggregation, and denaturation processes of three papain‐like proteases: ficin, bromelain, papain. To achieve this goal, the following experiments were conducted: (1) determination of the quantity of inactivated proteases using enzyme kinetics with BAPNA as a substrate; (2) differential scanning calorimetry (DSC); (3) assessment of protein aggregation using dynamic light scattering (DLS) and spectrophotometric analysis at 280 nm. Our findings suggest that the inactivation of ficin and papain exhibits single decay step which characterized by a rapid decline, then preservation of the same residual activity by enzyme stabilization. Only bromelain shows two steps with different kinetics. The molecular sizes of the active and inactive forms are similar across ficin, bromelain, and papain. Furthermore, the denaturation of these forms occurs at approximately the same rate and is accompanied by protein aggregation.

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Thermodynamic understanding of flower pigmentation

Zhao¹

2023

Biosystems

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Molecular and thermodynamic mechanisms for protein adaptation

Cited by 5 publications

References 82 publications

Quantifying Microbial Guilds

Quantifying Microbial Guilds

Thermal Inactivation, Denaturation and Aggregation Processes of Papain‐Like Proteases

Thermodynamic understanding of flower pigmentation

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