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Molecular Chaperones and Protein Folding03:00

Molecular Chaperones and Protein Folding

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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Protein packing defects "heat up" interfacial water.

María Belén Sierra1, Sebastián R Accordino, J Ariel Rodriguez-Fris

  • 1Sección Fisicoquímica, INQUISUR-UNS-CONICET-Departamento de Química, Universidad Nacional del Sur, Avda. Alem 1253, 8000, Bahía Blanca, Argentina. mbsierra@uns.edu.ar

The European Physical Journal. E, Soft Matter
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Protein binding sites feature packing defects called dehydrons, which attract ligands by exposing the protein backbone. These defects also mobilize surrounding water molecules, facilitating ligand binding and displacement of water.

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Area of Science:

  • Structural biology
  • Biophysics
  • Computational chemistry

Background:

  • Ligand binding necessitates the displacement of water molecules from protein surfaces.
  • Protein binding sites often contain packing defects known as dehydrons, where the protein backbone is exposed to solvent.
  • Dehydrons require intermolecular interactions for stability, suggesting a role in molecular recognition.

Purpose of the Study:

  • To investigate the relationship between protein structural defects (dehydrons) and the dynamics of associated water molecules.
  • To confirm the hypothesis that dehydrons promote local dehydration and create mobile interfacial water.
  • To establish a link between protein structure, hydration dynamics, and ligand binding mechanisms.

Main Methods:

  • Analysis of protein structures to identify packing defects and quantify dehydron exposure.
  • Molecular dynamics simulations to assess the mobility of water molecules in the vicinity of binding sites.
  • Correlation analysis to link structural features (degree of underwrapping) with water dynamics (mobility).

Main Results:

  • A strong correlation was observed between the degree of protein chain underwrapping and the mobility of hydration water.
  • Protein packing defects (dehydrons) were shown to promote local dehydration of binding sites.
  • This dehydration results in a region of highly mobile interfacial water, termed "hot" water.

Conclusions:

  • Protein binding sites with packing defects (dehydrons) are characterized by mobile interfacial water.
  • These mobile water molecules are easily displaced by ligands during the association process.
  • The presence of dehydrons and associated mobile water is a key feature facilitating protein-ligand interactions.