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Side-chain flexibility in proteins upon ligand binding.

R Najmanovich1, J Kuttner, V Sobolev

  • 1Plant Sciences Department, Weizmann Institute of Science, Rehovot, Israel. rafael.najmanovich@weizmann.ac.il

Proteins
|March 29, 2000
PubMed
Summary
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Ligand binding causes minor side-chain changes in protein pockets, primarily involving a few residues. This flexibility scale, with Lys being most flexible, aids in improving docking algorithms and protein engineering.

Area of Science:

  • Structural biology
  • Computational biology
  • Biochemistry

Background:

  • Ligand binding induces structural changes in proteins, from domain movements to subtle side-chain rearrangements.
  • Understanding side-chain flexibility is crucial for refining molecular docking algorithms and advancing protein engineering.

Purpose of the Study:

  • To analyze side-chain conformational changes in protein binding pockets upon ligand binding.
  • To establish a quantitative scale of amino-acid side-chain flexibility.

Main Methods:

  • Construction of two non-redundant databases of holo- and apo-protein structures from the Protein Data Bank (PDB).
  • Identification and analysis of binding pocket residues exhibiting conformational changes after ligand complexation.

Related Experiment Videos

Main Results:

  • Typically, only a small number of residues (≤3 in ~85% of cases) undergo side-chain conformational changes.
  • A flexibility scale was established: Lys > Arg, Gln, Met > Glu, Ile, Leu > Asn, Thr, Val, Tyr, Ser, His, Asp > Cys, Trp, Phe.
  • Large, polar amino acids are generally more flexible than aromatic ones, independent of backbone movement.

Conclusions:

  • The findings support incorporating limited side-chain flexibility into docking algorithms to reduce computational search space.
  • The derived amino-acid flexibility scale can guide protein engineering efforts to modulate binding pocket dynamics.