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Protein Folding01:25

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Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
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The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
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Microfluidic Mixers for Studying Protein Folding
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Evolution and folding of repeat proteins.

Ezequiel A Galpern1,2, Jacopo Marchi3, Thierry Mora3

  • 1Protein Physiology Lab, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina.

Proceedings of the National Academy of Sciences of the United States of America
|July 29, 2022
PubMed
Summary
This summary is machine-generated.

Researchers developed a new method to predict how repeat proteins fold by analyzing evolutionary data. This approach reveals diverse folding mechanisms in Ankyrin repeat proteins, linking sequence properties to folding behavior and stability.

Keywords:
Isingco-evolutionprotein foldingrepeat proteins

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Area of Science:

  • Structural Biology
  • Computational Biology
  • Evolutionary Biology

Background:

  • Repeat proteins, characterized by tandem amino acid stretches, fold into elongated structures.
  • These proteins serve as valuable models for studying the interplay between evolution, protein structure, folding, and function.
  • Understanding repeat protein folding mechanisms is crucial for deciphering their biological roles.

Purpose of the Study:

  • To develop a computational scheme linking evolutionary sequence information to coarse-grained models of repeat protein folding.
  • To investigate the folding mechanisms of thousands of natural Ankyrin repeat proteins.
  • To establish predictive relationships between sequence characteristics and protein folding stability and cooperativity.

Main Methods:

  • Employed an inverse Potts model combined with a mechanistic model of repeat duplications and deletions to derive evolutionary parameters at the single-residue level.
  • Utilized an Ising-like model, informed by these evolutionary parameters, to simulate protein folding dynamics.
  • Analyzed folding curves, domain emergence, and intermediate state populations for thousands of Ankyrin repeat proteins.

Main Results:

  • Identified a multiplicity of folding mechanisms across different Ankyrin repeat protein sequences.
  • Demonstrated that highly similar sequences and strong interactions lead to cooperative, all-or-none folding transitions.
  • Showed that dissimilar elements and weak interactions result in noncooperative, element-by-element folding.
  • Characterized nucleation-propagation and multidomain folding pathways.
  • Established that simple sequence scores can predict the global stability and cooperativity of repeat arrays.

Conclusions:

  • The developed computational framework accurately models repeat protein folding, yielding results consistent with experimental data.
  • Sequence divergence and interaction strength are key determinants of folding mechanisms in repeat proteins.
  • Predictive models based on sequence analysis can effectively forecast the folding behavior and stability of repeat protein arrays.