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Conserved Binding Sites01:49

Conserved Binding Sites

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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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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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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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Ligand Binding and Linkage00:49

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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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Protein Organization01:24

Protein Organization

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Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
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Fast Local Alignment of Protein Pockets (FLAPP): A System-Compiled Program for Large-Scale Binding Site Alignment.

Santhosh Sankar1, Naren Chandran Sakthivel1, Nagasuma Chandra1,2

  • 1Department of Biochemistry, Indian Institute of Science, Bangalore 560012, Karnataka, India.

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FLAPP rapidly aligns protein binding sites at the atomic level, enabling faster protein function and drug discovery. This computational tool significantly reduces analysis time for large-scale structural comparisons.

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Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Drug Discovery

Background:

  • Protein function is determined by sequence, structure, and binding site arrangement.
  • Sequence analysis offers initial insights, while structural data provides higher resolution for function inference.
  • Large-scale structural comparison of binding sites is computationally expensive and underutilized.

Purpose of the Study:

  • To develop a rapid algorithm for atomic-level alignment of protein binding sites.
  • To enable efficient large-scale structural comparisons for inferring protein function and aiding drug discovery.
  • To validate the accuracy and speed of the developed algorithm.

Main Methods:

  • Developed FLAPP algorithm combining graph clique matching and modern CPU architectures.
  • Achieved rapid atomic-level binding site alignments.
  • Validated FLAPP through rigorous multi-level complexity assessments and a case study.

Main Results:

  • FLAPP aligns binding sites in milliseconds on standard desktop machines.
  • PDB-wide scans are completed within 1-2 minutes.
  • Demonstrated accurate alignments and validated through a vitamin B12 binding site case study.

Conclusions:

  • FLAPP offers a computationally efficient solution for large-scale binding site analysis.
  • The tool facilitates insights into protein function and accelerates drug discovery, including target identification and polypharmacology.
  • FLAPP is expected to be invaluable for the scientific community in analyzing millions of site pairs.