ArticleProteins2009
Geometric constraints for porphyrin binding in helical protein binding sites.
Article in Proteins, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 22 citations in OpenAlex.
- Protein dynamics govern the oxyferrous state lifetime of an artificial oxygen transport protein.Biophysical journal · 2023Article
- Designing heterotropically activated allosteric conformational switches using supercharging.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Functionalization of Bacterial Microcompartment Shell Proteins With Covalently Attached Heme.Frontiers in bioengineering and biotechnology · 2019Article
- Designed for life: biocompatible de novo designed proteins and components.Journal of the Royal Society, Interface · 2018Review
- Structural principles for computational and de novo design of 4Fe-4S metalloproteins.Biochimica et biophysica acta · 2016Review
- Fast, cheap and out of control--Insights into thermodynamic and informatic constraints on natural protein sequences from de novo protein design.Biochimica et biophysica acta · 2016Article
- Constructing a man-made c-type cytochrome maquetteChemical science · 2014Article
- Rational design of a zinc phthalocyanine binding protein.Journal of structural biology · 2014Article
- Dynamic factors affecting gaseous ligand binding in an artificial oxygen transport protein.Biochemistry · 2013Article
- Modulation of function in a minimalist heme-binding membrane protein.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2012Article
- Manipulating cofactor binding thermodynamics in an artificial oxygen transport protein.Biochemistry · 2011Article
- Structural properties of 2/2 hemoglobins: the group III protein from Helicobacter hepaticus.IUBMB life · 2011Article
- Article
- p3d--Python module for structural bioinformatics.BMC bioinformatics · 2009Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Helical bundles which bind heme and porphyrin cofactors have been popular targets for cofactor-containing de novo protein design. By analyzing a highly nonredundant subset of the protein databank we have determined a rotamer distribution for helical histidines bound to heme cofactors. Analysis of the entire nonredundant database for helical sequence preferences near the ligand histidine demonstrated little preference for amino acid side chain identity, size, or charge. Analysis of the database subdivided by ligand histidine rotamer, however, reveals strong preferences in each case, and computational modeling illuminates the structural basis for some of these findings. The majority of the rotamer distribution matches that predicted by molecular simulation of a single porphyrin-bound histidine residue placed in the center of an all-alanine helix, and the deviations explain two prominent features of natural heme protein binding sites: heme distortion in the case of the cytochromes C in the m166 histidine rotamer, and a highly prevalent glycine residue in the t73 histidine rotamer. These preferences permit derivation of helical consensus sequence templates which predict optimal side chain-cofactor packing interactions for each rotamer. These findings thus promise to guide future design endeavors not only in the creation of higher affinity heme and porphyrin binding sites, but also in the direction of bound cofactor geometry.
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Registered trials
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