ArticleActa crystallographica. Section D, Structural biology2020
Quantum refinement with multiple conformations: application to the P-cluster in nitrogenase.
Article in Acta crystallographica. Section D, Structural biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed, 11 citations in OpenAlex.
- Article
- Accelerating reliable multiscale quantum refinement of protein-drug systems enabled by machine learning.Nature communications · 2024Article
- Quantum Mechanical Calculations of Redox Potentials of the Metal Clusters in Nitrogenase.Molecules (Basel, Switzerland) · 2022Article
- Does the crystal structure of vanadium nitrogenase contain a reaction intermediate? Evidence from quantum refinement.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2020Article
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2 authors at 1 institution in 1 country.
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Abstract
X-ray crystallography is the main source of atomistic information on the structure of proteins. Normal crystal structures are obtained as a compromise between the X-ray scattering data and a set of empirical restraints that ensure chemically reasonable bond lengths and angles. However, such restraints are not always available or accurate for nonstandard parts of the structure, for example substrates, inhibitors and metal sites. The method of quantum refinement, in which these empirical restraints are replaced by quantum-mechanical (QM) calculations, has previously been suggested for small but interesting parts of the protein. Here, this approach is extended to allow for multiple conformations in the QM region by performing separate QM calculations for each conformation. This approach is shown to work properly and leads to improved structures in terms of electron-density maps and real-space difference density Z-scores. It is also shown that the quality of the structures can be gauged using QM strain energies. The approach, called ComQumX-2QM, is applied to the P-cluster in two different crystal structures of the enzyme nitrogenase, i.e. an Fe
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