title: Molecular dynamics analysis of a series of 22 potential farnesyltransferase substrates containing a CaaX-motif.
abstract: Protein farnesyltransferase (FTase) is an important target in many research fields, more markedly so in cancer investigation since several proteins known to be involved in human cancer development are thought to serve as substrates for FTase and to require farnesylation for proper biological activity. Several FTase inhibitors (FTIs) have advanced into clinical testing. Nevertheless, despite the progress in the field several functional and mechanistic doubts on the FTase catalytic activity have persisted. This work provides some crucial information on this important enzyme by describing the application of molecular dynamics simulations using specifically designed molecular mechanical parameters for a variety of 22 CaaX peptides known to work as natural substrates or inhibitors for this enzyme. The study involves a comparative analysis of several important molecular aspects, at the mechanistic level, of the behavior of substrates and inhibitors at the dynamic level, including the behavior of the enzyme and peptides, as well as their interaction, together with the effect of the solvent. Properties evaluated include the radial distribution function of the water molecules around the catalytically important zinc metal atom and cysteine sulfur of CaaX, the conformations of the substrate and inhibitor and the corresponding RMSF values, critical hydrogen bonds, and several catalytically relevant distances. These results are discussed in light of recent experimental and computational evidence that provides new insights into the activity of this enzyme.
authors.affiliation: REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal. sergio.sousa@fc.up.pt
authors.forename: Sérgio F
authors.initials: SF
authors.lastname: Sousa
authors.forename: João T S
authors.initials: JT
authors.lastname: Coimbra
authors.forename: Diogo
authors.initials: D
authors.lastname: Paramos
authors.forename: Rita
authors.initials: R
authors.lastname: Pinto
authors.forename: Rodrigo S
authors.initials: RS
authors.lastname: Guimarães
authors.forename: Vitor
authors.initials: V
authors.lastname: Teixeira
authors.forename: Pedro A
authors.initials: PA
authors.lastname: Fernandes
authors.forename: Maria J
authors.initials: MJ
authors.lastname: Ramos
mesh_terms: D020816:Amino Acid Motifs; D020134:Catalytic Domain; D004791:Enzyme Inhibitors / Q000737:chemistry; D051231:Farnesyltranstransferase / Q000737:chemistry*; D006801:Humans; D006860:Hydrogen Bonding; D006863:Hydrogen-Ion Concentration; D056004:Molecular Dynamics Simulation; D009842:Oligopeptides / Q000737:chemistry*; D011522:Protons; D013329:Structure-Activity Relationship; D013379:Substrate Specificity; D013816:Thermodynamics; D015032:Zinc / Q000737:chemistry*
chemical_list: D004791:Enzyme Inhibitors; D009842:Oligopeptides; D011522:Protons; D051231:Farnesyltranstransferase; D015032:Zinc