CO Photodissociation Dynamics in Cytochrome P450BM3 Studied by Subpicosecond Visible and Mid-Infrared Spectroscopy

Ligand diffusion in proteins via enhanced sampling in molecular dynamics

Computational simulations in biophysics describe the dynamics and functions of biological macromolecules at the atomic level. Among motions particularly important for life are the transport processes in heterogeneous media. The process of ligand diffusion inside proteins is an example of a complex rare event that can be modeled using molecular dynamics simulations. The study of physical interactions between a ligand and its biological target is of paramount importance for the design of novel drugs and enzymes. Unfortunately, the process of ligand diffusion is difficult to study experimentally. The need for identifying the ligand egress pathways and understanding how ligands migrate through protein tunnels has spurred the development of several methodological approaches to this problem. The complex topology of protein channels and the transient nature of the ligand passage pose difficulties in the modeling of the ligand entry/escape pathways by canonical molecular dynamics simulations. In this review, we report a methodology involving a reconstruction of the ligand diffusion reaction coordinates and the free-energy profiles along these reaction coordinates using enhanced sampling of conformational space. We illustrate the above methods on several ligand-protein systems, including cytochromes and G-protein-coupled receptors. The methods are general and may be adopted to other transport processes in living matter.

P450(BM3) (CYP102A1): connecting the dots

P450(BM3) (CYP102A1), a fatty acid hydroxylase from Bacillus megaterium, has been extensively studied over a period of almost forty years. The enzyme has been redesigned to catalyse the oxidation of non-natural substrates as diverse as pharmaceuticals, terpenes and gaseous alkanes using a variety of engineering strategies. Crystal structures have provided a basis for several of the catalytic effects brought about by mutagenesis, while changes to reduction potentials, inter-domain electron transfer rates and catalytic parameters have yielded functional insights. Areas of active research interest include drug metabolite production, the development of process-scale techniques, unravelling general mechanistic aspects of P450 chemistry, methane oxidation, and improving selectivity control to allow the synthesis of fine chemicals. This review draws together the disparate research themes and places them in a historical context with the aim of creating a resource that can be used as a gateway to the field.

Triggered infrared spectroscopy for investigating metalloprotein chemistry

Recent developments in infrared (IR) spectroscopic time resolution, sensitivity and sample manipulation make this technique a powerful addition to the suite of complementary approaches for the study of time-resolved chemistry at metal centres within proteins. Application of IR spectroscopy to proteins has often targeted the amide bands as probes for gross structural change. This article focuses on the possibilities arising from recent IR technical developments for studies that monitor localized vibrational oscillators in proteins--native or exogenous ligands such as NO, CO, SCN(-) or CN(-), or genetically or chemically introduced probes with IR-active vibrations. These report on the electronic and coordination state of metals, the kinetics, intermediates and reaction pathways of ligand release, hydrogen-bonding interactions between the protein and IR probe, and the electrostatic character of sites in a protein. Metalloprotein reactions can be triggered by light/dark transitions, an electrochemical step, a change in solute composition or equilibration with a new gas atmosphere, and spectra can be obtained over a range of time domains as far as the sub-picosecond level. We can expect to see IR spectroscopy exploited, alongside other spectroscopies, and crystallography, to elucidate reactions of a wide range of metalloprotein chemistry with relevance to cell metabolism, health and energy catalysis.