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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...
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.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.

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Related Experiment Video

Updated: Jul 10, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

High-resolution design of a protein loop.

Xiaozhen Hu1, Huanchen Wang, Hengming Ke

  • 1Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA.

Proceedings of the National Academy of Sciences of the United States of America
|November 1, 2007
PubMed
Summary

Designing specific protein loop conformations is now possible using computational methods. This study demonstrates successful de novo design of 10-residue loops, with one achieving high structural accuracy.

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Area of Science:

  • Computational Biology
  • Protein Engineering
  • Structural Biology

Background:

  • Protein loops, despite irregular structures, are crucial for protein function.
  • Traditional de novo protein design often focuses on regular secondary structures, neglecting longer loops.

Purpose of the Study:

  • To develop and test a computational protocol for designing longer protein loops with specific conformations.
  • To investigate the feasibility of high-resolution de novo protein loop design.

Main Methods:

  • Utilized the Rosetta molecular modeling program to optimize loop sequence and conformation.
  • Employed flexible backbone trajectories to search for low-energy sequence-structure pairs.
  • Experimentally characterized three designed 10-residue loops for the beta-sandwich protein tenascin.

Main Results:

  • All three designed loops (LoopA, LoopB, LoopC) adopted stable folded structures.
  • LoopB closely matched the designed model with high structural accuracy (0.46 Å RMSD).
  • LoopA exhibited an unexpected strand-swapped dimeric structure at low pH, highlighting sensitivity to energetics.

Conclusions:

  • High-resolution de novo design of protein loops is achievable.
  • Protein loop design is sensitive to subtle energetic changes, potentially altering low free energy structures.
  • The developed protocol offers a promising approach for engineering functional protein loops.