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Related Concept Videos

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

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...
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...
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...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...

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Cl-pi interactions in protein-ligand complexes.

Yumi N Imai1, Yoshihisa Inoue, Isao Nakanishi

  • 1Department of Theoretical Drug Design, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan. imai_yumi@takeda.co.jp

Protein Science : a Publication of the Protein Society
|April 25, 2008
PubMed
Summary
This summary is machine-generated.

Chlorine-pi (Cl-pi) interactions are identified in protein-ligand complexes. These interactions, primarily driven by dispersion forces, exhibit distinct geometric preferences and vary with aromatic ring properties.

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Area of Science:

  • Structural Biology
  • Computational Chemistry
  • Biophysics

Background:

  • Nonbonded contacts are crucial for understanding molecular interactions in biological systems.
  • Chlorine-pi (Cl-pi) interactions, involving a chlorine atom and an aromatic pi system, have been observed in various protein structures.

Purpose of the Study:

  • To systematically analyze the occurrence and geometry of Cl-pi interactions in protein-ligand complexes from the Protein Data Bank.
  • To investigate the energetic contributions and geometric preferences of Cl-pi interactions using computational methods.

Main Methods:

  • Systematic analysis of nonbonded contacts in protein-ligand complexes from the Protein Data Bank (PDB).
  • Geometric analysis of identified Cl-pi interactions.
  • High-level ab initio calculations using benzene-chlorohydrocarbon model systems.

Main Results:

  • Cl-pi interactions were found in serine proteases and other protein families.
  • Two distinct geometries were observed: 'edge-on' and 'face-on' approaches.
  • Calculations revealed an average interaction energy of -2.01 kcal/mol, with dispersion forces being the primary attractive component.

Conclusions:

  • Cl-pi interactions are a relevant nonbonded contact in protein-ligand complexes.
  • Dispersion forces significantly contribute to the stability of Cl-pi interactions.
  • The geometry and strength of Cl-pi interactions are influenced by pi system properties and chlorine atom positioning.