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.

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.

Individual contributions of the aromatic chromophores to the near-UV Circular Dichroism in class A beta-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.

Interaction of monotopic membrane enzymes with a lipid bilayer: a coarse-grained MD simulation study.

Monotopic membrane proteins bind tightly to cell membranes but do not generally span the lipid bilayer. Their interactions with lipid bilayers may be studied via coarse-grained molecular dynamics (CG-MD) simulations. Understanding such interactions is important as monotopic enzymes frequently act on hydrophobic substrates, while X-ray structures rarely provide direct information about their interactions with membranes.

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.

Neurotoxic disorders of organophosphorus compounds and their managements.

Organophosphorus compounds have been used as pesticides and as chemical warfare nerve agents. The mechanism of toxicity of organophosphorus compounds is the inhibition of acetylcholinesterase, which results in accumulation of acetylcholine and the continued stimulation of acetylcholine receptors. Therefore, they are also called anticholinesterase agents.

Monotopic enzymes and lipid bilayers: a comparative study.

Monotopic proteins make up a class of membrane proteins that bind tightly to, but do not span, cell membranes. We examine and compare how two monotopic proteins, monoamine oxidase B (MAO-B) and cyclooxygenase-2 (COX-2), interact with a phospholipid bilayer using molecular dynamics simulations. Both enzymes form between three and seven hydrogen bonds with the bilayer in our simulations with basic side chains accounting for the majority of these interactions.

Neutron diffraction reveals sequence-specific membrane insertion of pre-fibrillar islet amyloid polypeptide and inhibition by rifampicin.

Human islet amyloid polypeptide (hIAPP) forms amyloid deposits in non-insulin-dependent diabetes mellitus (NIDDM). Pre-fibrillar hIAPP oligomers (in contrast to monomeric IAPP or mature fibrils) increase membrane permeability, suggesting an important role in the disease. In the first structural study of membrane-associated hIAPP, lamellar neutron diffraction shows that oligomeric hIAPP inserts into phospholipid bilayers, and extends across the membrane.

A structural study of the myristoylated N-terminus of ARF1.

The effect of myristoylation on the 15-amino-acid peptide from the membrane-binding N-terminus of ADP ribosylation factor 1 (ARF1) was studied using neutron diffraction and circular dichroism. A previous study on the non-acylated form indicated that the peptide lies parallel to the membrane, at a shallow depth and in the vicinity of the phosphorylcholine headgroups. It was suggested that the helix does not extend past residue 12, an important consequence for the linking region of the ARF1 protein.

Cannabidiol lacks the vanilloid VR1-mediated vasorespiratory effects of capsaicin and anandamide in anaesthetised rats.

The results of vasorespiratory studies in rats anaesthetised with pentobarbital show that (+/-) cannabidiol, a cannabinoid that lacks psychotropic actions and is inactive at cannabinoid (CB) receptors, does not affect respiration or blood pressure when injected (1-2000 microg; 3.2-6360 nmol i.a.

The fusion peptide of simian immunodeficiency virus and the phase behaviour of N-methylated dioleoylphosphatidylethanolamine.

Temperature-scan X-ray scattering was used to study the effect of the fusion peptide of simian immunodeficiency virus (SIV) on the lipid polymorphism of N-methylated dioleoylphosphatidylethanolamine (DOPE-Me), in the presence and absence of one or both of the fusion inhibitors carbobenzoxy-D-phenylalanine-L-phenylalanine-glycine and 1-lauroyl-2-hydroxy-sn-glycero-3-phosphocholine (LPC). Using X-ray diffraction at stations 2.1 and 8.