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A comprehensive conformational analysis of tryptophan, its ionic and dimeric forms.

Uppula Purushotham1, G Narahari Sastry

  • 1Center for Molecular Modeling, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, 500607, Andhra Pradesh, India.

Journal of Computational Chemistry
|November 5, 2013
PubMed
Summary

Tryptophan

Keywords:
Conformational analysisDFTNoncovalent interactionsPDB analysisTryptophan dimer

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Area of Science:

  • Biochemistry
  • Computational Chemistry
  • Molecular Biophysics

Background:

  • Tryptophan is an essential amino acid crucial for biological systems.
  • Understanding tryptophan's conformational states is vital for its biological functions.

Purpose of the Study:

  • To conduct a first-principles investigation of tryptophan monomer and dimer conformations.
  • To analyze the role of noncovalent interactions in stabilizing these structures.

Main Methods:

  • First principles calculations were used to explore potential energy surfaces.
  • Systematic conformational analysis identified distinct minima for tryptophan and its dimers.
  • Protein Data Bank analysis examined naturally occurring tryptophan dimer orientations.

Main Results:

  • Identified 62 distinct minima for tryptophan dimers, revealing diverse stable conformations.
  • Hydrogen bonds and various noncovalent interactions (e.g., OH-π, NH-π, CH-π, CH-O, π-π) stabilize structures.
  • Monomers with NH-O hydrogen bonds are more stable; dimers are stabilized by hydrogen bonding or aromatic side-chain interactions.
  • Protein Data Bank analysis showed T-shaped (CH-π) and stacked (π-π) orientations dominate at different distances.

Conclusions:

  • Tryptophan's conformational landscape is complex, influenced by various noncovalent interactions.
  • Hydrogen bonding is key for monomer stability, while dimers exhibit diverse stabilization mechanisms.
  • Observed dimer orientations in biological systems correlate with interaction types and distances.