Quantum refinement - a combination of quantum chemistry and protein crystallography.

Ulf Ryde, Kristina Nilsson

Research output: Contribution to journalReview articlepeer-review

45 Citations (SciVal)

Abstract

The combination of quantum mechanics and molecular mechanics (QM/MM) is one of the most promising approaches to study the structure, function, and properties of proteins. We here review our applications of QM/MM methods to alcohol dehydrogenase, blue copper proteins, iron–sulphur clusters, ferrochelatase, and myoglobin. We also describe our new quantum refinement method, which is a combination of quantum chemistry and protein crystallography. It has been shown to work properly and it can be used to improve the structure of protein metal centres in terms of the crystallographic Rfree factor and electron-density maps. It can be used to determine the protonation status of metal-bound solvent molecules in proteins by refining the various possible states and see which fits the crystallographic raw data best. Applications to ferrochelatase, cytochrome c553, alcohol dehydrogenase, myoglobin, and methylmalonyl coenzyme A mutase are described.
Original languageEnglish
Pages (from-to)259-275
JournalJournal of molecular structure. Theochem
Volume632
Issue number1-3
DOIs
Publication statusPublished - 2003

Bibliographical note

The information about affiliations in this record was updated in December 2015.
The record was previously connected to the following departments: Theoretical Chemistry (S) (011001039)

Subject classification (UKÄ)

  • Theoretical Chemistry

Keywords

  • Combined quantum mechanics and molecular mechanics
  • Crystallographic refinement
  • Metalloproteins
  • Density functional theory
  • Protonation status

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