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Systems Analysis for Peptide Systems Chemistry

Living systems employ both covalent chemistry and physical assembly to achieve complex behaviors. The emerging field of systems chemistry, inspired by these biological systems, attempts to construct and analyze systems that are simpler than biology, while still embodying biological design principles...

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Detalles Bibliográficos
Autores principales: Grover, Martha A., Hsieh, Ming-Chien, Lynn, David G.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6789875/
https://www.ncbi.nlm.nih.gov/pubmed/31266164
http://dx.doi.org/10.3390/life9030055
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author Grover, Martha A.
Hsieh, Ming-Chien
Lynn, David G.
author_facet Grover, Martha A.
Hsieh, Ming-Chien
Lynn, David G.
author_sort Grover, Martha A.
collection PubMed
description Living systems employ both covalent chemistry and physical assembly to achieve complex behaviors. The emerging field of systems chemistry, inspired by these biological systems, attempts to construct and analyze systems that are simpler than biology, while still embodying biological design principles. Due to the multiple phenomena at play, it can be difficult to predict which phenomena will dominate and when. Conversely, there may be no single rate-limiting step, but rather a reaction network that is difficult to intuit from a purely experimental approach. Mathematical modeling can help to sort out these issues, although it can be challenging to build such models, especially for assembly kinetics. Numerical and statistical methods can play an important role to facilitate the synergistic and iterative use of modeling and experiment, and should be part of a systems chemistry curriculum. Three case studies are presented here, from our work in peptide-based systems, to illustrate some of the tools available for model construction, model simulation, and experimental design. Examples are provided in which these tools help to evaluate hypotheses, uncover design principles, and design new experiments.
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spelling pubmed-67898752019-10-16 Systems Analysis for Peptide Systems Chemistry Grover, Martha A. Hsieh, Ming-Chien Lynn, David G. Life (Basel) Perspective Living systems employ both covalent chemistry and physical assembly to achieve complex behaviors. The emerging field of systems chemistry, inspired by these biological systems, attempts to construct and analyze systems that are simpler than biology, while still embodying biological design principles. Due to the multiple phenomena at play, it can be difficult to predict which phenomena will dominate and when. Conversely, there may be no single rate-limiting step, but rather a reaction network that is difficult to intuit from a purely experimental approach. Mathematical modeling can help to sort out these issues, although it can be challenging to build such models, especially for assembly kinetics. Numerical and statistical methods can play an important role to facilitate the synergistic and iterative use of modeling and experiment, and should be part of a systems chemistry curriculum. Three case studies are presented here, from our work in peptide-based systems, to illustrate some of the tools available for model construction, model simulation, and experimental design. Examples are provided in which these tools help to evaluate hypotheses, uncover design principles, and design new experiments. MDPI 2019-07-01 /pmc/articles/PMC6789875/ /pubmed/31266164 http://dx.doi.org/10.3390/life9030055 Text en © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Perspective
Grover, Martha A.
Hsieh, Ming-Chien
Lynn, David G.
Systems Analysis for Peptide Systems Chemistry
title Systems Analysis for Peptide Systems Chemistry
title_full Systems Analysis for Peptide Systems Chemistry
title_fullStr Systems Analysis for Peptide Systems Chemistry
title_full_unstemmed Systems Analysis for Peptide Systems Chemistry
title_short Systems Analysis for Peptide Systems Chemistry
title_sort systems analysis for peptide systems chemistry
topic Perspective
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6789875/
https://www.ncbi.nlm.nih.gov/pubmed/31266164
http://dx.doi.org/10.3390/life9030055
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