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Related Concept Videos

Protein Folding01:22

Protein Folding

Overview
Protein Folding01:25

Protein Folding

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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Newman Projections02:06

Newman Projections

Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as conformers.
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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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¹H NMR Chemical Shift Equivalence: Enantiotopic and Diastereotopic Protons00:58

¹H NMR Chemical Shift Equivalence: Enantiotopic and Diastereotopic Protons

Replacing each alpha-hydrogen in chloroethane by bromine (or a different functional group) yields a pair of enantiomers. Such protons are called prochiral or enantiotopic and are related by a mirror plane. Enantiotopic protons are chemically equivalent in an achiral environment. Because most proton NMR spectra are recorded using achiral solvents, enantiotopic hydrogens yield a single signal.
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Updated: May 10, 2026

Residue-Specific Exchange of Proline by Proline Analogs in Fluorescent Proteins: How "Molecular Surgery" of the Backbone Affects Folding and Stability
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Residue-Specific Exchange of Proline by Proline Analogs in Fluorescent Proteins: How "Molecular Surgery" of the Backbone Affects Folding and Stability

Published on: February 3, 2022

On proline isomerization and 3D-domain-swapping.

Ramu Manjula1, Naren Chockalingam1, Ramaswamy Subramanian2

  • 1National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, 560065, India.

Biochemical and Biophysical Research Communications
|May 8, 2026
PubMed
Summary

Introducing proline into protein hinge-loops can control 3D-domain-swapping. This research clarifies proline

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Residue-Specific Exchange of Proline by Proline Analogs in Fluorescent Proteins: How "Molecular Surgery" of the Backbone Affects Folding and Stability
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Isotopic Effect in Double Proton Transfer Process of Porphycene Investigated by Enhanced QM/MM Method

Published on: July 19, 2019

Area of Science:

  • Protein structure and dynamics
  • Biochemistry
  • Molecular biology

Background:

  • 3D-domain-swapping is a protein dimerization mechanism involving domain exchange.
  • Hinge-loop residues, particularly prolines, are implicated in domain-swapping but their precise role is unclear.
  • Previous work engineered monellin variants with hydrophobic residues at the hinge-loop apex to promote domain-swapping.

Purpose of the Study:

  • To investigate the role of proline in 3D-domain-swapping by replacing hinge-loop apex residues with proline.
  • To explore the potential of proline isomerization in designing protein assemblies.
  • To understand how proline's impact on hinge-loop conformation influences domain-swapping.

Main Methods:

  • Engineering of monellin variants with proline at the hinge-loop apex.
  • Structural characterization using X-ray crystallography.
  • Analysis of cis/trans proline isomerization in monomers and dimers.

Main Results:

  • Replacing apex residues with proline generally reduced domain-swapping.
  • Significant domain-swapping was observed only in the QVPAG construct, which had the most hydrophobic hinge-loop.
  • Monomeric variants exhibited cis-proline, while the domain-swapped dimer contained trans-proline.
  • The trans-proline in the QVPAG dimer provided rigidity, enabling potential design of protein assemblies.

Conclusions:

  • Introducing proline into solvent-exposed, tight β-turns can promote cis-proline formation.
  • Mutating natural cis-prolines to hydrophobic residues may induce domain-swapping.
  • Proline isomerization in hinge-loops is a viable strategy for rational design of domain-swapping-driven protein assemblies.
  • This study clarifies the role of prolines in 3D-domain-swapping.