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Comparative Modeling and Analysis of Extremophilic D-Ala-D-Ala Carboxypeptidases.

ABSTRACT: Understanding the molecular adaptations of organisms to extreme environments requires a comparative analysis of protein structure, function, and dynamics across species found in different environmental conditions. Computational studies can be particularly useful in this pursuit, allowing exploratory studies of large numbers of proteins under different thermal and chemical conditions that would be infeasible to carry out experimentally. Here, we perform such a study of the MEROPS family S11, S12, and S13 proteases from psychophilic, mesophilic, and thermophilic bacteria. Using a combination of protein structure prediction, atomistic molecular dynamics, and trajectory analysis, we examine both conserved features and trends across thermal groups. Our findings suggest a number of hypotheses for experimental investigation.

SUBMITTER: Diessner EM

PROVIDER: S-EPMC9953012 | biostudies-literature | 2023 Feb

REPOSITORIES: biostudies-literature

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Comparative Modeling and Analysis of Extremophilic D-Ala-D-Ala Carboxypeptidases.

Diessner Elizabeth M EM Takahashi Gemma R GR Martin Rachel W RW Butts Carter T CT

Biomolecules 20230209 2

Understanding the molecular adaptations of organisms to extreme environments requires a comparative analysis of protein structure, function, and dynamics across species found in different environmental conditions. Computational studies can be particularly useful in this pursuit, allowing exploratory studies of large numbers of proteins under different thermal and chemical conditions that would be infeasible to carry out experimentally. Here, we perform such a study of the MEROPS family S11, S12, ...[more]

PMID: 36830697

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