ArticleProtein science : a publication of the Protein Society2017
On contribution of known atomic partial charges of protein backbone in electrostatic potential density maps.
Article in Protein science : a publication of the Protein Society, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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7 citing papers in PubMed, 21 citations in OpenAlex.
- Exploiting the full potential of cryo-EM maps.BBA advances · 2024Article
- How to correct relative voxel scale factors for calculations of vector-difference Fourier maps in cryo-EM.Journal of structural biology · 2022Article
- Jusanin, a New Flavonoid fromMolecules (Basel, Switzerland) · 2022Article
- Opportunities and challenges for assigning cofactors in cryo-EM density maps of chlorophyll-containing proteins.Communications biology · 2020Review
- CryoEM maps are full of potential.Current opinion in structural biology · 2019Review
- Effects of aligned α-helix peptide dipoles on experimental electrostatic potentials.Protein science : a publication of the Protein Society · 2017Article
- Experimental charge density from electron microscopic maps.Protein science : a publication of the Protein Society · 2017Article
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1 author at 1 institution in 1 country.
Funding
Abstract
Partial charges of atoms in a molecule and electrostatic potential (ESP) density for that molecule are known to bear a strong correlation. In order to generate a set of point-field force field parameters for molecular dynamics, Kollman and coworkers have extracted atomic partial charges for each of all 20 amino acids using restrained partial charge-fitting procedures from theoretical ESP density obtained from condensed-state quantum mechanics. The magnitude of atomic partial charges for neutral peptide backbone they have obtained is similar to that of partial atomic charges for ionized carboxylate side chain atoms. In this study, the effect of these known atomic partial charges on ESP is examined using computer simulations and compared with the experimental ESP density recently obtained for proteins using electron microscopy. It is found that the observed ESP density maps are most consistent with the simulations that include atomic partial charges of protein backbone. Therefore, atomic partial charges are integral part of atomic properties in protein molecules and should be included in model refinement.
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