Active Binding Modes of Caffeine with Cytochrome P450 1A2 Determine Its Metabolite Profiles.

Caffeine is a very common kind of nervous stimulant, and it is primarily metabolized by Cytochrome P450 1A2 (CYP1A2) in the human body. Over the years, determining the interactions between caffeine and CYP1A2 has been a tough issue. The active binding modes and the catalytic regioselectivity of the metabolism between CYP1A2 and caffeine remain unclear. Here, to investigate the interactions between CYP1A2 and caffeine, we constructed the all-sequence CYP1A2-caffeine-membrane system using a multiple template approach. According to our simulation results, four active binding modes between CYP1A2 and caffeine that correspond to the four metabolic sites of caffeine are determined. What is more, a pre-reaction state for the CYP1A2-catalyzed reaction at caffeine's N3 site is identified. A more preponderant active binding mode might be the reason why the N3 site of caffeine becomes the primary metabolic site. Our findings could enhance our knowledge of the interactions between CYP1A2 and caffeine and help us better understand the regioselectivity of the metabolism between CYP1A2 and caffeine.

How does multiple substrate binding lead to substrate inhibition of CYP2D6 metabolizing dextromethorphan? A theoretical study.

CYP2D6 is one of the most important metalloenzymes involved in the biodegradation of many drug molecules in the human body. It has been found that multiple substrate binding can lead to substrate inhibition of CYP2D6 metabolizing dextromethorphan (DM), but the corresponding theoretical mechanism is rarely reported. Therefore, we chose DM as the probe and performed molecular dynamics simulations and quantum mechanical calculations on CYP2D6-DM systems to investigate the mechanism of how the multiple substrate binding leads to the substrate inhibition of CYP2D6 metabolizing substrates. According to our results, three gate residues (Arg221, Val374, and Phe483) for the catalytic pocket are determined. We also found that the multiple substrate binding can lead to substrate inhibition by reducing the stability of CYP2D6 binding DM and increasing the reactive activation energy of the rate-determining step. Our findings would help to understand the substrate inhibition of CYP2D6 metabolizing the DM and enrich the knowledge of the drug-drug interactions for the cytochrome P450 superfamily.

The regioselectivity of the interaction between dextromethorphan and CYP2D6.

CYP2D6 is an important enzyme of the cytochrome P450 superfamily, and catalyzes nearly 25% of the drugs sold in the market. For decades, the interactions and metabolism between CYP2D6 and substrates have been a hot topic. However, the key factors of the catalytic regioselectivity for CYP2D6 still remain controversial. Here, we construct four systems to explore the interaction between dextromethorphan (DM) and CYP2D6. A new binding mode of CYP2D6 is defined, and two key residues (residue Asp301 and residue Glu216) are discovered working simultaneously to stabilize the DM at the reactive site by forming water bridge hydrogen bonds when CYP2D6 binds DM. Our results also indicate that the substrate concentration could mediate the binding mode between the substrate and CYP2D6 by decreasing the volume of the catalytic pocket, which is not conducive to the O-demethylation of DM but benefits the N-demethylation of DM. These results could shed light on the process of CYP2D6 binding to the substrate, and help to better understand the regioselectivity of CYP2D6 catalyzing the substrates.

A theoretical study on the signal transduction process of bacterial photoreceptor PpSB1 based on the Markov state model.

Light-oxygen-voltage (LOV) domains are blue light sensors and play an important role in signal transduction in many organisms. Generally, LOV domains use chromophores to absorb photons, and then photochemical reactions will occur to convert light energy into chemical energy and transduce it to the main chain of proteins. These reactions can cause conformational rearrangement of proteins, and thus leading to signal transduction. Therefore, it is important to study the signal transduction process of LOV domains for understanding the control mechanism of cellular functions. However, how small photochemical changes in the active sites of the LOV domains lead to large conformational rearrangements of proteins, which in turn lead to signal transduction, has been puzzling us for a long time. Currently, the LOV domains are mainly studied in plants. The signal transduction mechanism of LOV domains in bacteria is still unclear. In this work, the Markov state model (MSM) combined with molecular dynamics (MD) simulations was applied to investigate the signal transduction process of the LOV protein from pseudomonas putida (PpSB1-LOV). The present work will play an important role in understanding the signal transduction mechanism of PpSB1-LOV domains, which may provide theoretical basis for the design and improvement of LOV-based optogenetic tools.

Key Factors in Conformation Transformation of an Important Neuronic Protein Glucose Transport 3 Revealed by Molecular Dynamics Simulation.

Glucose transporters (GLUTs) are an essential kind of protein that exists in the neuron and are responsible for glucose transport. In the present study, we performed molecular dynamic simulations to deeply understand the glucose uptake mechanism. According to our results, we reconstruct the glucose uptake model of the GLUT3, which is similar to the working model of GLUTs raised by Yan et al., and find a new intermediate state ( Yan, N., et al. ( 2015 ) Molecular basis of ligand recognition and transport by glucose transporters , Nature 526 , 391 - 396 ). In addition, we discover the bottleneck residues for the protein conformational switch. Water molecules are also important for the conformational switch by influencing the hydrogen bond networks of the glucose-protein complex, which can cause the obvious rearrangement of corresponding transmembrane segments. Our findings may shed light on the glucose uptake process of this key neuronic transmembrane protein and the functional relationships between the multiple intermediate states.