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Ligand Binding Sites02:40

Ligand Binding Sites

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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.
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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...
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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.
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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...
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PL-PatchSurfer: a novel molecular local surface-based method for exploring protein-ligand interactions.

Bingjie Hu1, Xiaolei Zhu2, Lyman Monroe3

  • 1Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA. hub@purdue.edu.

International Journal of Molecular Sciences
|August 29, 2014
PubMed
Summary
This summary is machine-generated.

We developed PL-PatchSurfer, a novel computational method using surface patches to predict protein-ligand interactions. This approach enhances drug discovery by improving the accuracy of identifying potential drug candidates based on structural complementarity.

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Area of Science:

  • Computational chemistry
  • Structural biology
  • Drug discovery

Background:

  • Structure-based computational methods are crucial for understanding protein-ligand interactions.
  • Surface representations offer advantages in speed and robustness compared to other molecular representations.

Purpose of the Study:

  • To introduce PL-PatchSurfer, a novel surface patch-based method for protein-ligand binding prediction.
  • To evaluate the performance of PL-PatchSurfer against existing methods and on diverse datasets.

Main Methods:

  • Representing protein binding pockets and ligand surfaces as segmented surface patches.
  • Characterizing patches using geometrical shape and electrostatic potential via 3D Zernike descriptors (3DZD).
  • Optimizing the search algorithm using the PDBbind dataset.

Main Results:

  • PL-PatchSurfer outperformed a pocket-similarity based ligand prediction program.
  • The method demonstrated high early enrichment on larger, diverse datasets.
  • PL-PatchSurfer is the first surface patch-based method for ligand complementarity at protein binding sites.

Conclusions:

  • PL-PatchSurfer offers a robust and efficient approach for predicting protein-ligand interactions.
  • The surface patch methodology holds significant potential for advancing drug design and target identification.