Multiple molecular recognition mechanisms. Cytochrome P450--a case study.

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.

Do mammalian cytochrome P450s show multiple ligand access pathways and ligand channelling?

Understanding substrate binding and product release in cytochrome P450 (CYP) enzymes is important for explaining their key role in drug metabolism, toxicity, xenobiotic degradation and biosynthesis. Here, molecular simulations of substrate and product exit from the buried active site of a mammalian P450, the microsomal CYP2C5, identified a dominant exit channel, termed pathway (pw) 2c. Previous simulations with soluble bacterial P450s showed a different dominant egress channel, pw2a.

A survey of active site access channels in cytochromes P450.

In cytochrome P450s, the active site is situated deep inside the protein next to the heme cofactor, and is often completely isolated from the surrounding solvent. To identify routes by which substrates may enter into and products exit from the active site, random expulsion molecular dynamics simulations were performed for three cytochrome P450s: CYP101, CYP102A1 and CYP107A1 [J. Mol.

Ab initio vibration and ro-vibrational spectrum of the 1A1 state of He2Si2+.

The low-lying ro-vibrational states for the ground electronic state (1A1) of HeSi2+ have been calculated using an ab initio variational solution of the nuclear Schrödinger equation. A 96 point CCSD(T)/cc-pCVQZ potential energy surface (PES) has been calculated and a Ogilvie-Padé (3,6) potential energy function has been generated. This force field was embedded in the Eckart-Watson Hamiltonian from which the vibrational and ro-vibrational eigenfunctions and eigenenergies have been variationally calculated.