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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...
Protein Folding01:22

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Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Protein-Protein Interfaces02:04

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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
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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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Self-complementarity within proteins: bridging the gap between binding and folding.

Sankar Basu1, Dhananjay Bhattacharyya, Rahul Banerjee

  • 1Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata, India.

Biophysical Journal
|June 21, 2012
PubMed
Summary
This summary is machine-generated.

Researchers quantified electrostatic complementarity (Em) within protein interiors, finding it significant for all amino acids. Combining Em with shape complementarity (Sm) created scoring functions that accurately identify native protein folds and similar folds from low-sequence-identity proteins.

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Area of Science:

  • Structural biology
  • Computational biophysics
  • Protein science

Background:

  • Protein-protein interactions are often predicted using shape and electrostatic complementarity at interfaces.
  • Folding and binding share underlying principles of molecular recognition.

Purpose of the Study:

  • To develop a unified framework for protein folding and binding based on complementarity.
  • To quantify electrostatic complementarity (Em) for residues within protein interiors.
  • To combine Em with shape complementarity (Sm) for improved protein structure analysis.

Main Methods:

  • Estimated electrostatic complementarity (Em) for buried residues within proteins.
  • Combined Em with previously characterized shape complementarity (Sm) of interior residues.
  • Developed two scoring functions using Sm and Em to identify native protein folds from decoys.
  • Created a complementarity plot (Sm vs. Em) for residue analysis.

Main Results:

  • Electrostatic complementarity (Em) values are significant and uniform across all amino acids, including hydrophobic ones.
  • Scoring functions combining Sm and Em demonstrated performance comparable or superior to existing methods for identifying native folds.
  • The functions successfully identified the same fold for proteins with low sequence identity.
  • The complementarity plot revealed residues with suboptimal packing and electrostatics potentially linked to errors.

Conclusions:

  • Amino acids in the native protein interior adhere to stringent shape (Sm) and electrostatic (Em) complementarity constraints, similar to interfacial residues in protein complexes.
  • The developed scoring functions and complementarity plot offer valuable tools for protein structure assessment and fold identification.