title: A comparison of X-ray and calculated structures of the enzyme MTH1.
abstract: Modern computational chemistry methods provide a powerful tool for use in refining the geometry of proteins determined by X-ray crystallography. Specifically, computational methods can be used to correctly place hydrogen atoms unresolved by this experimental method and improve bond geometry accuracy. Using the semiempirical method PM7, the structure of the nucleotide-sanitizing enzyme MTH1, complete with hydrolyzed substrate 8-oxo-dGMP, was optimized and the resulting geometry compared with the original X-ray structure of MTH1. After determining hydrogen atom placement and the identification of ionized sites, the charge distribution in the binding site was explored. Where comparison was possible, all the theoretical predictions were in good agreement with experimental observations. However, when these were combined with additional predictions for which experimental observations were not available, the result was a new and alternative description of the substrate-binding site interaction. An estimate was made of the strengths and weaknesses of the PM7 method for modeling proteins on varying scales, ranging from overall structure to individual interatomic distances. An attempt to correct a known fault in PM7, the under-estimation of steric repulsion, is also described. This work sheds light on the specificity of the enzyme MTH1 toward the substrate 8-oxo-dGTP; information that would facilitate drug development involving MTH1. Graphical Abstract Overlay of the backbone traces of the two MTH1 protein chains (green and orange respectively) in PDB 3ZR0 and the equivalent PM7 structures (magenta and cyan respectively) each optimized separately.
authors.affiliation: Department of Chemistry and Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA.
authors.forename: Hannah
authors.initials: H
authors.lastname: Ryan
authors.affiliation: Department of Chemistry and Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA.|Department of Biochemistry and Biophysics, Stockholm University, S-106 91, Stockholm, Sweden.
authors.forename: Megan
authors.initials: M
authors.lastname: Carter
authors.affiliation: Department of Biochemistry and Biophysics, Stockholm University, S-106 91, Stockholm, Sweden.
authors.forename: Pål
authors.initials: P
authors.lastname: Stenmark
authors.affiliation: Stewart Computational Chemistry, 15210 Paddington Circle, Colorado Springs, CO, 80921, USA.
authors.forename: James J P
authors.initials: JJ
authors.lastname: Stewart
authors.affiliation: In Silico Chemical Consulting, 128 Longwood Ave, Lakeway, TX, 78734, USA. Sonja@insilicochem.us.
authors.forename: Sonja B
authors.initials: SB
authors.lastname: Braun-Sand
mesh_terms: D001665:Binding Sites; D020134:Catalytic Domain; D019295:Computational Biology / Q000379:methods*; D018360:Crystallography, X-Ray; D045643:DNA Repair Enzymes / Q000737:chemistry* / Q000378:metabolism; D006157:Guanosine Monophosphate / Q000031:analogs & derivatives* / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D006860:Hydrogen Bonding; D006868:Hydrolysis; D008958:Models, Molecular; D015394:Molecular Structure; D010744:Phosphoric Monoester Hydrolases / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D000072417:Protein Domains; D013379:Substrate Specificity; D013816:Thermodynamics
chemical_list: C515742:8-oxo-7,8-dihydro-2'-deoxyguanosine-5'-monophosphate; D006157:Guanosine Monophosphate; D010744:Phosphoric Monoester Hydrolases; C078207:8-oxodGTPase; D045643:DNA Repair Enzymes
keywords: 8-oxo-dGMP; Binding site; Enzyme; MTH1; Nudix box; PM7; Salt bridges