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Multipolar electrostatics for proteins: atom-atom electrostatic energies in crambin.

Yongna Yuan1, Matthew J L Mills, Paul L A Popelier

  • 1Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester, M1 7DN, United Kingdom; School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom.

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|January 23, 2014
PubMed
Summary

Accurate protein electrostatics require multipole moments. This study shows atom-atom electrostatic interactions in crambin converge well, even for single amino acids, and this finding applies to amyloid beta.

Keywords:
quantum chemical topology • force field • electrostatics • protein • amino acids • peptides • level of theory • ab initio • Multipole Moments • convergence • crambin • Aβ1-42

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Area of Science:

  • Computational Chemistry
  • Structural Biology
  • Biophysics

Background:

  • Accurate electrostatic calculations in biomolecules are crucial for understanding their function.
  • Traditional methods often rely on point charges or multipole moments.
  • Investigating the convergence of atom-atom electrostatic interactions is key to efficient modeling.

Purpose of the Study:

  • To investigate the convergence behavior of atom-atom electrostatic interactions using nuclear-centered multipole moments.
  • To assess the transferability of these findings to other biologically relevant systems like amyloid beta.
  • To determine the influence of neighboring atoms on multipole moments and their range of effect.

Main Methods:

  • Amino acids were extracted from the Protein Data Bank structure of crambin as single amino acids, di-, or tripeptides.
  • Atoms were defined as finite volume electron density fragments using Quantum Chemical Topology (QCT).
  • Atom-atom electrostatic energies were computed using multipole expansion up to interaction rank L=10.

Main Results:

  • The minimum internuclear distances for convergent atom-atom interactions in crambin were consistent across single amino acids, dipeptides, and tripeptides.
  • Electrostatic interaction values showed minimal differences across various computational levels (HF, B3LYP, MP2) and were transferable to amyloid beta.
  • The influence of neighboring atoms on multipole moments was quantifiable, with a determined distance beyond which this influence becomes negligible.

Conclusions:

  • Nuclear-centered multipole moments provide accurate electrostatics, with convergence achieved even at the single amino acid level.
  • The observed convergence behavior is transferable to other polypeptides, including amyloid beta, validating the QCT approach.
  • The study provides insights into the spatial extent of atomic electronic influences, aiding in the development of more efficient molecular simulations.