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Related Concept Videos

Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
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...
Crystal Field Theory - Octahedral Complexes02:58

Crystal Field Theory - Octahedral Complexes

Crystal Field Theory
To explain the observed behavior of transition metal complexes (such as colors), a model involving electrostatic interactions between the electrons from the ligands and the electrons in the unhybridized d orbitals of the central metal atom has been developed. This electrostatic model is crystal field theory (CFT). It helps to understand, interpret, and predict the colors, magnetic behavior, and some structures of coordination compounds of transition metals.
CFT focuses on...
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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Exploring Protein-Glycan Interactions: Advances in Nuclear Magnetic Resonance
10:07

Exploring Protein-Glycan Interactions: Advances in Nuclear Magnetic Resonance

Published on: August 26, 2025

Quantum mechanical effect in protein-ligand interaction.

Ying-Qi Jing1, Ke-Li Han

  • 1Dalian Institute of Chemical Physics, Chinese Academy of Sciences, State Key Laboratory of Molecular Reaction Dynamics, Dalian 116023, China +86 411 843 79293 ; +86 411 846 75584 ; klhan@dicp.ac.cn.

Expert Opinion on Drug Discovery
|July 25, 2012
PubMed
Summary
This summary is machine-generated.

Quantum mechanics (QM) methods offer molecular insights into protein-ligand interactions. These QM-based approaches are crucial for understanding biomolecular systems and advancing structure-based drug design.

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Related Experiment Videos

Last Updated: May 20, 2026

Exploring Protein-Glycan Interactions: Advances in Nuclear Magnetic Resonance
10:07

Exploring Protein-Glycan Interactions: Advances in Nuclear Magnetic Resonance

Published on: August 26, 2025

Single-Molecule Measurement of Protein Interaction Dynamics Within Biomolecular Condensates
06:48

Single-Molecule Measurement of Protein Interaction Dynamics Within Biomolecular Condensates

Published on: January 5, 2024

Determination of Protein-ligand Interactions Using Differential Scanning Fluorimetry
13:26

Determination of Protein-ligand Interactions Using Differential Scanning Fluorimetry

Published on: September 13, 2014

Area of Science:

  • Computational chemistry
  • Biophysics
  • Molecular modeling

Background:

  • Quantum mechanics (QM) represents a significant scientific achievement.
  • QM-based methods are increasingly vital for studying protein-ligand interactions.
  • These methods provide molecular-level insights into biomolecular systems.

Purpose of the Study:

  • To review applications of QM-based methods in protein-ligand interactions.
  • To illustrate diverse QM approaches for analyzing biomolecular systems.
  • To highlight the role of QM in understanding biochemical mechanisms.

Main Methods:

  • Density functional theory (DFT) for simplified active site models (e.g., CYP450-ethanol).
  • Generalized hybrid orbital (GHO) approach for metalloprotein ligand identification.
  • Molecular fractionation with conjugate caps (MFCC) for interaction energy calculations (e.g., thrombin-inhibitor complexes).

Main Results:

  • QM calculations provide detailed descriptions of biochemical mechanisms.
  • Analysis of protein-ligand interactions reveals structural and energetic properties.
  • Different QM methods yield specific insights into distinct biological systems.

Conclusions:

  • QM-based methods are essential for structure-based drug design.
  • These methods continue to be indispensable tools in biological research.
  • Further development of accurate and efficient QM methods is ongoing.