Kia Balali-Mood

Structure and Dynamics of the Membrane-Bound Cytochrome P450 2C9

The microsomal, membrane-bound, human cytochrome P450 (CYP) 2C9 is a liver-specific monooxygenase essential for drug metabolism. CYPs require electron transfer from the membrane-bound CYP reductase (CPR) for catalysis. The structural details and functional relevance of the CYP-membrane interaction are not understood. From multiple coarse grained molecular simulations started with arbitrary configurations of protein-membrane complexes, we found two predominant orientations of CYP2C9 in the membrane, both consistent with experiments and conserved in atomic-resolution simulations. The dynamics of membrane-bound and soluble CYP2C9 revealed correlations between opening and closing of different tunnels from the enzymes buried active site. The membrane facilitated the opening of a tunnel leading into it by stabilizing the open state of an internal aromatic gate. Other tunnels opened selectively in the simulations of product-bound CYP2C9. We propose that the membrane promotes binding of liposoluble substrates by stabilizing protein conformations with an open access tunnel and provide evidence for selective substrate access and product release routes in mammalian CYPs. The models derived here are suitable for extension to incorporate other CYPs for oligomerization studies or the CYP reductase for studies of the electron transfer mechanism, whereas the modeling procedure is generally applicable to study proteins anchored in the bilayer by a single transmembrane helix.

The interaction of phospholipase A2 with a phospholipid bilayer: coarse-grained molecular dynamics simulations.

A number of membrane-active enzymes act in a complex environment formed by the interface between a lipid bilayer and bulk water. Although x-ray diffraction studies yield structures of isolated enzyme molecules, a detailed characterization of their interactions with the interface requires a measure of how deeply such a membrane-associated protein penetrates into a lipid bilayer. Here, we apply coarse-grained (CG) molecular dynamics (MD) simulations to probe the interaction of porcine pancreatic phospholipase A2 (PLA2) with a lipid bilayer containing palmitoyl-oleoyl-phosphatidyl choline and palmitoyl-oleoyl-phosphatidyl glycerol molecules. We also used a configuration from a CG-MD trajectory to initiate two atomistic (AT) MD simulations. The results of the CG and AT simulations are evaluated by comparison with available experimental data. The membrane-binding surface of PLA2 consists of a patch of hydrophobic residues surrounded by polar and basic residues. We show this proposed footprint interacts preferentially with the anionic headgroups of the palmitoyl-oleoyl-phosphatidyl glycerol molecules. Thus, both electrostatic and hydrophobic interactions determine the location of PLA2 relative to the bilayer. From a general perspective, this study demonstrates that CG-MD simulations may be used to reveal the orientation and location of a membrane-surface-bound protein relative to a lipid bilayer, which may subsequently be refined by AT-MD simulations to probe more detailed interactions.

Conformational effects on the circular dichroism of Human Carbonic Anhydrase II: a multilevel computational study.

Circular Dichroism (CD) spectroscopy is a powerful method for investigating conformational changes in proteins and therefore has numerous applications in structural and molecular biology. Here a computational investigation of the CD spectrum of the Human Carbonic Anhydrase II (HCAII), with main focus on the near-UV CD spectra of the wild-type enzyme and it seven tryptophan mutant forms, is presented and compared to experimental studies. Multilevel computational methods (Molecular Dynamics, Semiempirical Quantum Mechanics, Time-Dependent Density Functional Theory) were applied in order to gain insight into the mechanisms of interaction between the aromatic chromophores within the protein environment and understand how the conformational flexibility of the protein influences these mechanisms. The analysis suggests that combining CD semi empirical calculations, crystal structures and molecular dynamics (MD) could help in achieving a better agreement between the computed and experimental protein spectra and provide some unique insight into the dynamic nature of the mechanisms of chromophore interactions.

Integrating multi-level molecular simulations across heterogeneous resources

Biomolecular simulations play a key role in the study of complex biological processes at microscopic levels in which macromolecules such as proteins are involved. The simulations are usually computationally demanding and no single method can achieve all levels of details. Thus, the simulations at different levels need to be integrated to jointly manifest atomic insights into these processes. This paper presents a grid-based simulation framework to support the integration of multi-level simulations by means of dynamic coupling, automated workflow management, resource-dependent job distribution, and XML-based data representation. The framework provides an e-science infrastructure to support biomolecular simulations on grids. A biomolecular simulation markup language called BioSimML is developed to provide a formatted data representation to the multi-level simulations. Experimental simulations have shown flexible integration and high performance enhancement achieved in molecular simulations based on our framework.

A Multiscale Model for Efficient Simulation of a Membrane Bound Viral Fusion Peptide

Biomolecular simulations have been particularly useful in providing atomic-level insights into biological processes. The simulations can be conducted at atomistic or coarse grained resolution. An atomistic simulation can model atomic details of a biological process but is computationally expensive. A coarse-grained simulation is time-efficient but cannot fully expose atomic details. In order to support efficient simulations of complex biomolecular processes, we have developed a multiscale simulation model that dynamically integrates both atomistic and coarse-grained simulations. The model has been used to simulate a membrane bound viral fusion peptide associating with a phospholipid bilayer. The simulation provides an important pre-requisite in understanding the viral fusion mechanism that can aid the design of better drugs against infectious viruses. The simulation has achieved a high performance with a minimum 8-fold speedup.

Individual contributions of the aromatic chromophores to the near-UV Circular Dichroism in class A β-lactamases: A comparative computational analysis

Class A beta-lactamases are enzymes which are responsible for the bacterial resistance against antibiotics and therefore are of great importance in rational inhibitor design. In this paper we comparatively analyze all the individual contributions of the aromatic chromophores in three class A beta-lactamases (from Staphylococcus aureus, Streptomyces albus and Bacillus licheniformis) to their near-UV Circular Dichroism. The analysis is performed using recently developed procedure based on established theoretical method. We found that in beta-lactamase from S. albus the most significant contributions to the total near-UV CD intensity exhibit Y251 and Y229. In the tryptophan-containing beta-lactamases from B. licheniformis and S. albus, W229 and W251 express the strongest individual contributions. A comparative analysis of the individual contributions of conservative chromophores in class A enzymes namely W165, W210, W229, W251, Y97 and Y105 is presented.