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Related Concept Videos

Protein Folding01:25

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.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
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Molecular Chaperones and Protein Folding03:00

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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.
The...
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Bacterial Protein Maturation01:26

Bacterial Protein Maturation

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Bacterial protein maturation is a tightly regulated process that ensures newly synthesized polypeptides achieve correct functional conformations. This maturation involves a series of modifications, folding events, and quality control steps, often assisted by specialized chaperone proteins.N-Terminal ModificationsThe maturation of bacterial polypeptides begins cotranslationally as the polypeptide exits the ribosome. The first amino acid, N-formylmethionine (fMet), is typically modified at the...
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Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

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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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Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
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Amyloid Fibrils03:03

Amyloid Fibrils

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Amyloid fibrils are aggregates of misfolded proteins.  Under most circumstances, misfolded proteins are either refolded by chaperone proteins or degraded by the proteasome. However, in the case of a mutation or a disease, these proteins can accumulate to form large clusters and often further assemble to form elongated fibers, called fibrils. 
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Related Experiment Video

Updated: Oct 14, 2025

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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Rational Design of Protein-Specific Folding Modifiers.

Anirban Das1, Anju Yadav1, Mona Gupta1

  • 1Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India.

Journal of the American Chemical Society
|November 1, 2021
PubMed
Summary

Researchers developed a novel "xenonucleus" peptide to accelerate protein refolding. This engineered peptide mimics a protein's natural folding nucleus, speeding up the process for ubiquitin by over 30%.

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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Area of Science:

  • Biochemistry
  • Structural Biology
  • Biophysics

Background:

  • Protein misfolding has significant implications for both biological systems and the pharmaceutical industry.
  • Developing methods to control protein folding is crucial for understanding and treating diseases and for protein-based therapeutics.

Purpose of the Study:

  • To propose and validate a design principle for small-peptide-based, protein-specific folding modifiers.
  • To introduce the concept of a "xenonucleus" as a tool to enhance protein refolding kinetics.

Main Methods:

  • Utilized stopped-flow kinetics, Nuclear Magnetic Resonance (NMR) spectroscopy, and Förster resonance energy transfer (FRET).
  • Employed single-molecule force measurements and molecular dynamics (MD) simulations to analyze folding.
  • Investigated the effect of a designed xenonucleus peptide on ubiquitin refolding.

Main Results:

  • Demonstrated that a xenonucleus significantly accelerates the refolding of ubiquitin by 33 ± 5%.
  • Showed that variants of the xenonucleus peptide had minimal to no effect on refolding rates.
  • Validated the xenonucleus design principle through a combination of experimental and computational techniques.

Conclusions:

  • The xenonucleus approach offers a novel strategy for creating specific, genetically encodable folding catalysts.
  • This method is applicable to proteins with well-defined, contiguous folding nuclei.
  • Provides a new avenue for modulating protein folding in vitro and potentially in vivo.