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Related Concept Videos

The Unfolded Protein Response01:37

The Unfolded Protein Response

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The ER is the hub of protein synthesis in a cell. It has robust systems to quality control protein folding and also for degradation of terminally misfolded proteins. Under normal conditions, a small proportion of misfolded proteins that cannot be salvaged need to be transported to the cytoplasm by the ER-associated degradation or ERAD pathways. However, if the ERAD cannot handle the misfolded proteins, the cell activates the unfolded protein response or UPR to adjust the protein folding...
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Regulation of Nuclear Protein Sorting01:45

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Nuclear protein sorting regulates nucleus composition and gene expression, crucial for determining the fate of a eukaryotic cell. Hence, the entry and exit of molecules across the nuclear envelope is a tightly controlled process. Nuclear protein sorting can be inhibited by one of the following ways: 1) masking cargo signal sequences, 2) modifying the nuclear receptor's affinity for cargo, 3) controlling the nuclear pore size, 4) retaining the cargo during its transit to the cytosol or the...
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Protein Folding Quality Check in the RER01:29

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ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
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Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
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Protein Modifications in the RER01:26

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Modification of secretory and transmembrane proteins entering the rough ER begins in the ER lumen. These modifications aid in protein folding and stabilize the acquired tertiary structure. Protein modifications in the rough ER co-occur at different stages of protein folding.
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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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Related Experiment Video

Updated: Mar 12, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Single-engineered-residue solvation perturbations regulate global protein architecture and function.

Yingya Liu1, Jihang Zhai1, Shanshan Cao2

  • 1School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China.

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|March 11, 2026
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Altering protein surface hydrophobicity with spiropyran reveals how water networks mediate structural changes. Local hydrophobic shifts significantly impact protein hydration, dynamics, and function, offering new insights for drug design.

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Area of Science:

  • Biochemistry and Molecular Biology
  • Physical Chemistry
  • Structural Biology

Background:

  • Protein-water interactions are crucial for protein structure, stability, dynamics, and function.
  • Understanding how local water perturbations affect protein dynamics is challenging due to interface heterogeneity.

Purpose of the Study:

  • To investigate the impact of residue-specific hydrophobic perturbations on protein hydration and dynamics.
  • To explore the role of interfacial water networks in mediating structural and functional changes in proteins.

Main Methods:

  • Introduction of a photochromic molecule, spiropyran, to reversibly modify protein surface hydrophobicity at specific residues.
  • Analysis of global protein hydration patterns and structural dynamics following controlled hydrophobic perturbations.

Main Results:

  • Residue-level changes in hydrophobicity induce significant global alterations in protein hydration patterns.
  • Hydration shifts propagate in an amino acid sequence-dependent manner, influencing protein architecture and catalytic activity.
  • Interfacial water networks mediate the propagation of local perturbations into broader structural and functional fluctuations.

Conclusions:

  • Interfacial water networks are key mediators of protein structural and functional responses to local surface changes.
  • The study shifts the paradigm from 'structure-function' to 'structure-hydration-function' for understanding protein behavior.
  • Findings offer novel perspectives for protein architecture studies and future drug design strategies.