ABSTRACT
Biomolecular recognition is complex. The balance between the different molecular properties that contribute to molecular recognition, such as shape, electrostatics, dynamics and entropy, varies from case to case. This, along with the extent of experimental characterization, influences the choice of appropriate computational approaches to study biomolecular interactions. Here, we present computational studies of cytochrome P450 enzymes and their interactions with small molecules and with other proteins. These interactions exemplify some of the diversity of molecular determinants of binding affinity and specificity observed for proteins and we discuss some of the challenges that they pose for molecular modelling and simulation.
Subject(s)
Cytochrome P-450 Enzyme System/metabolism , Models, Molecular , Binding Sites , Computational Biology/methods , Cytochrome P-450 Enzyme System/chemistry , Ligands , Models, Chemical , Protein Binding/drug effects , Protein Structure, Tertiary , Proteins/chemistry , Proteins/metabolism , Structure-Activity Relationship , Substrate SpecificityABSTRACT
We describe a new approach to the study of protein-protein interaction using Fourier transform infrared spectroscopy (FTIR). This approach is based on the combination of FTIR technique with both protein titration experiments and the principal component analysis (factor analysis) of the IR absorption spectra in the 1500-1800 cm(-1) region for the protein mixtures. We have applied this approach to the interaction of the heme domain with the FMN domain of bacterial monooxygenase cytochrome P450BM-3 (CYP102A1). The analysis reveals that the first principal component reflects the protein-protein complex formation because the loading factors show a clear systematic dependence on the concentration of the heme domain according to a titration curve with a dissociation constant of approximately 5 microM. The spectrum of the first principal component has been assigned to structural changes in the secondary structure (increase of beta-sheet and alpha-helix and decrease of turn structures), amino acid side chains (protonation of aspartate and C-terminal COO group), and deprotonation of a propionic acid COOD group in the heme.