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Structural evidence for a functionally relevant second camphor binding site in P450cam: model for substrate entry into a P450 active site.

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P450cam has long served as a prototype for the cytochrome P450 (CYP) gene family. But, little is known about how substrate enters its active site pocket, and how access is achieved in a way that minimizes exposure of the reactive heme. We hypothesize that P450cam may first bind substrate transiently

The dynamics of camphor in the cytochrome P450 CYP101D2.

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The recent crystal structures of CYP101D2, a cytochrome P450 protein from the oligotrophic bacterium Novosphingobium aromaticivorans DSM12444 revealed that both the native (substrate-free) and camphor-soaked forms have open conformations. Furthermore, two other potential camphor-binding sites were

Effect of alcohols on binding of camphor to cytochrome P450cam: spectroscopic and stopped flow transient kinetic studies.

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Addition of alcohols to cytochrome P450cam (CYP101) was shown to release the substrate camphor from the heme pocket of the enzyme. The release of the substrate was found to be caused both due to increased solubility of the substrate in solution in presence of alcohol and due to change in the

Spectrophotometric and calorimetric titration studies on molecular recognition of camphor and borneol by nucleobase-modified beta-cyclodextrins.

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A series of modified beta-cyclodextrins with nucleobase substituents, that is, mono(6-ade-6-deoxy)-beta-cyclodextrin (2) and mono(6-ura-6-deoxy)-beta-cyclodextrin (3) as well as mono(6-thy-6-deoxy)-beta-cyclodextrin (4), were selected as molecular receptors to investigate their conformation and

Study of the inclusion of the (R)- and (S)-camphor enantiomers in alpha-cyclodextrin by X-ray crystallography and molecular dynamics.

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The inclusion of (R)- and (S)-camphor compounds in alpha-cyclodextrin has been studied by X-ray crystallography. The crystal structures of the complexes reveal that one guest molecule is accommodated inside the cavity formed by a head-to-head cyclodextrin dimer. In the crystal lattice, the dimers

Effect of camphor/cyclodextrin complexation on the stability of O/W/O multiple emulsions.

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Camphor (CA) encapsulation in oil/water/oil multiple emulsions prepared with cyclodextrin disturbs the emulsifier potential of alpha- and beta-natural cyclodextrins (CD). It was suggested that the size and geometrical fit between the CD cavity and CA could induce CD/CA complex formation in place of

Mechanistic Interplay between Light Switching and Guest Binding in Photochromic [Pd2Dithienylethene4] Coordination Cages.

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Photochromic [Pd₂L₄] coordination cages based on dithienylethene (DTE) ligands L allow triggering guest uptake and release by irradiation with light of different wavelengths. The process involves four consecutive electrocyclic reactions to convert all chromophores between their

Preparation and in vitro/in vivo characterization of porous sublingual tablets containing ternary kneaded solid system of vinpocetine with î-cyclodextrin and hydroxy Acid.

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The demand for sublingual tablets has been growing during the previous decades especially for drugs with extensive hepatic first-pass metabolism. Vinpocetine, a widely used neurotropic agent, has low oral bioavailability due to its poor aqueous solubility and marked first-pass metabolism.

Vapor emissions resulting from Nd:YAG laser interaction with tooth structure.

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The Neodymium:yttrium aluminum garnet (Nd:YAG) dental laser has been cleared by the United States Food and Drug Administration (FDA) for marketing in intraoral soft tissue treatment. The efficacy and safety of the Nd:YAG laser in the treatment of hard dental tissue as well as the effects of dental

Comparison of the construction of a 3-D model for human thromboxane synthase using P450cam and BM-3 as templates: implications for the substrate binding pocket.

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A 3-D model of human thromboxane A2 synthase (TXAS) was constructed using a homology modeling approach based on information from the 2.0 A crystal structure of the hemoprotein domains of cytochrome P450BM-3 and P450cam. P450BM-3 is a bacterial fatty acid monooxygenase resembling eukaryotic

Deuterium magic angle spinning studies of substrates bound to cytochrome P450.

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We report solid-state deuterium magic angle spinning NMR spectra of perdeuterated adamantane bound to the active site of microcrystalline cytochrome P450cam (CP450cam) in its resting state. CP450cam contains a high-spin ferric (Fe3+) heme in the resting state; the isotropic shift was displaced from

CO migration pathways in cytochrome P450cam studied by molecular dynamics simulations.

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Previous laser flash photolysis investigations between 100 and 300 K have shown that the kinetics of CO rebinding with cytochrome P450(cam)(camphor) consist of up to four different processes revealing a complex internal dynamics after ligand dissociation. In the present work, molecular dynamics

Microhydration of verbenone: how the chain of water molecules adapts its structure to the host molecule.

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The microsolvation of verbenone (C10H14O)·(H2O)n (n = 1, 2, 3) was experimentally investigated in a supersonic expansion using a cavity-based Fourier transform microwave spectrometer, in the 2.8-14 GHz frequency range. Thanks to computationally optimized structures at the B3LYP-D3BJ/def2-TZVP and

Machine Learning Based Dimensionality Reduction Facilitates Ligand Diffusion Paths Assessment: A Case of Cytochrome P450cam.

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In this work we propose an application of a nonlinear dimensionality reduction method to represent the high-dimensional configuration space of the ligand-protein dissociation process in a manner facilitating interpretation. Rugged ligand expulsion paths are mapped into 2-dimensional space. The

Thermodynamics of water mediating protein-ligand interactions in cytochrome P450cam: a molecular dynamics study.

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Ordered water molecules are observed by crystallography and nuclear magnetic resonance to mediate protein-ligand interactions. Here, we examine the energetics of hydrating cavities formed at protein-ligand interfaces using molecular dynamics simulations. The free energies of hydrating two cavities

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