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Related Concept Videos

Noncovalent Attractions in Biomolecules02:35

Noncovalent Attractions in Biomolecules

Noncovalent attractions are associations within and between molecules that influence the shape and structural stability of complexes. These interactions differ from covalent bonding in that they do not involve sharing of electrons.
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
Coupled Reactions01:17

Coupled Reactions

Cellular processes such as building and breaking down complex molecules occur through stepwise chemical reactions. Some of these chemical reactions are spontaneous and release energy, whereas others require energy to proceed. Cells often couple the energy-releasing reaction with the energy-requiring one to carry out important cell functions. 
Energy in adenosine triphosphate or ATP molecules is easily accessible to do work. ATP powers the majority of energy-requiring cellular reactions. Cells...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Noncovalent Attractions in Biomolecules02:35

Noncovalent Attractions in Biomolecules

Noncovalent attractions are associations within and between molecules that influence the shape and structural stability of complexes. These interactions differ from covalent bonding in that they do not involve sharing of electrons.
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...

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Updated: Jun 6, 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

Functionally important residues from graph analysis of coevolved dynamic couplings.

Manming Xu1, Sarath Chandra Dantu2, James A Garnett3

  • 1UCL School of Pharmacy, London, United Kingdom.

Elife
|March 28, 2025
PubMed
Summary
This summary is machine-generated.

DyNoPy integrates coevolution and molecular dynamics to predict protein function. This method reveals evolutionary influences on protein dynamics, aiding in drug design for challenges like antibiotic resistance.

Keywords:
DyNoPycoevolutionmolecular biophysicsmolecular dynamicsstructural biology

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Last Updated: Jun 6, 2026

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

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Published on: July 14, 2015

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Area of Science:

  • Computational Biology
  • Protein Dynamics
  • Evolutionary Biology

Background:

  • Protein dynamics are crucial for biological functions and drug development.
  • Current methods for predicting functional residues overlook evolutionary impacts on dynamics.
  • Evolutionary processes fine-tune protein dynamics via compensatory mutations.

Purpose of the Study:

  • To introduce DyNoPy, a novel computational method.
  • To model the influence of evolution on protein dynamics.
  • To reveal hidden correlations between functional sites.

Main Methods:

  • DyNoPy combines residue coevolution analysis with molecular dynamics simulations.
  • A graph model of residue-residue interactions is constructed.
  • Coevolved dynamical couplings are leveraged to identify critical sites.

Main Results:

  • DyNoPy successfully predicts and analyzes protein evolution and dynamics.
  • Hidden correlations between functional sites were revealed.
  • Effectiveness demonstrated on SHV-1 and PDC-3 β-lactamases.

Conclusions:

  • DyNoPy offers a powerful approach to understanding protein dynamics and evolution.
  • The method has potential for informing drug design.
  • DyNoPy can help address healthcare challenges such as antibiotic resistance.