Cholesterol Corrects Altered Conformation of MHC-II Protein in Leishmania donovani Infected Macrophages: Implication in Therapy

Previously we reported that Kala-azar patients show progressive decrease in serum cholesterol as a function of splenic parasite burden. Splenic macrophages (MΦ) of Leishmania donovani (LD) infected mice show decrease in membrane cholesterol, while LD infected macrophages (I-MΦ) show defective T cell stimulating ability that could be corrected by liposomal delivery of cholesterol. T helper cells recognize peptide antigen in the context of class II MHC molecule. It is known that the conformation of a large number of membrane proteins is dependent on membrane cholesterol. In this investigation we tried to understand the influence of decreased membrane cholesterol in I-MΦ on the conformation of MHC-II protein and peptide-MHC-II stability, and its bearing on the antigen specific T-cell activatio

Open Babel: An open chemical toolbox

Background: A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de facto standards have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chemistry data, differences in the data stored by different formats (0D versus 3D, for example), and competition between software along with a lack of vendorneutral formats. Results: We discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion. Conclusions: Open Babel presents a solution to the proliferation of multiple chemical file formats. In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chemical data in areas such as organic chemistry, drug design, materials science, and computational chemistry. It is freely available under an open-source license fro

Membrane cholesterol access into a G-protein-coupled receptor

Cholesterol is a key component of cell membranes with a proven modulatory role on the function and ligand-binding properties of G-protein-coupled receptors (GPCRs). Crystal structures of prototypical GPCRs such as the adenosine A2A receptor (A2AR) have confirmed that cholesterol finds stable binding sites at the receptor surface suggesting an allosteric role of this lipid. Here we combine experimental and computational approaches to show that cholesterol can spontaneously enter the A2AR-binding pocket from the membrane milieu using the same portal gate previously suggested for opsin ligands. We confirm the presence of cholesterol inside the receptor by chemical modification of the A2AR interior in a biotinylation assay. Overall, we show that cholesterol’s impact on A2AR-binding affinity goes beyond pure allosteric modulation and unveils a new interaction mode between cholesterol and the A2AR that could potentially apply to other GPCRs

Fractal dimension as a measure of surface roughness of G protein-coupled receptors: implications for structure and function

Protein surface roughness is a structural property associated with ligand-protein and protein-protein binding interfaces. In this work we apply for the first time the concept of surface roughness, expressed as the fractal dimension, to address structure and function of G protein-coupled receptors (GPCRs) which are an important group of drug targets. We calculate the exposure ratio and the fractal dimension for helix-forming residues of the β(2) adrenergic receptor (β(2)AR), a model system in GPCR studies, in different conformational states: in complex with agonist, antagonist and partial inverse agonists. We show that both exposure ratio and roughness exhibit periodicity which results from the helical structure of GPCRs. The pattern of roughness and exposure ratio of a protein patch depends on its environment: the residues most exposed to membrane are in general most rough whereas parts of receptors mediating interhelical contacts in a monomer or protein complex are much smoother. We also find that intracellular ends (TM3, TM5, TM6 and TM7) which are relevant for G protein binding and thus receptor signaling, are exposed but smooth. Mapping the values of residual fractal dimension onto receptor 3D structures makes it possible to conclude that the binding sites of orthosteric ligands as well as of cholesterol are characterized with significantly higher roughness than the average for the whole protein. In summary, our study suggests that identification of specific patterns of roughness could be a novel approach to spot possible binding sites which could serve as original drug targets for GPCRs modulation