Design and structural bioinformatic analysis of polypeptide antigens useful for the SRLV serodiagnosis.

Due to their intrinsic genetic, structural and phenotypic variability the Lentiviruses, and specifically small ruminant lentiviruses (SRLV), are considered viral quasispecies with a population structure that consists of extremely large numbers of variant genomes, termed mutant spectra or mutant cloud. Immunoenzymatic tests for SRLVs are available but the dynamic heterogeneity of the virus makes the development of a diagnostic "golden standard" extremely difficult. The ELISA reported in the literature have been obtained using proteins derived from a single strain or they are multi-strain based assay that may increase the sensitivity of the serological diagnosis. Hundreds of SRLV protein sequences derived from different viral strains are deposited in GenBank. The aim of this study is to verify if the database can be exploited with the help of bioinformatics in order to have a more systematic approach in the design of a set of representative protein antigens useful in the SRLV serodiagnosis. Clustering, molecular modelling, molecular dynamics, epitope predictions and aggregative/solubility predictions were the main bioinformatic tools used. This approach led to the design of SRLV antigenic proteins that were expressed by recombinant DNA technology using synthetic genes, analyzed by CD spectroscopy, tested by ELISA and preliminarily compared to currently commercially available detection kits.

Interaction of cisplatin with a CCHC zinc finger motif.

The interaction between cisplatin and an 18-residue CCHC zinc finger motif derived from a retroviral nucleocapsid protein (PyrZf18) has been studied using UV-visible, CD and (1)H NMR spectroscopies and ESI-MS spectrometry. Cisplatin irreversibly blocks the cysteine zinc binding groups in the free peptide and is able to slowly eject zinc from the zinc-peptide complex. The observed end product of the reaction with cisplatin is a complex in which only one ammonia molecule is coordinated to platinum. After an initial binding with two cysteine residues and the formation of the (PyrZf18)-platinum-(NH3)2 complex, a release of one ammonia molecule occurs because of trans-labilization, and the third cysteine is coordinated, leading to a mixture of isomers and/or conformers of the (PyrZf18)-platinum-NH3 complex. The results are discussed with respect to the potential antiretroviral activity of platinum(II) compounds and to the possible interaction of cisplatin with the cellular nucleic acid binding proteins.

8-hydroxyquinoline monomer, water adducts, and dimer. Environmental influences on structure, spectroscopic properties, and relative stability of cis and trans conformers.

The low fluorescence quantum yield of 8-hydroxyquinoline cannot be correctly interpreted without knowing the form that such a compound assumes in different environments. The commonly accepted emission-quenching excited-state proton transfer can follow different reaction paths if 8-hydroxyquinoline is dimeric or monomeric or if it exists in the form of cis and trans conformers; in this light, the knowledge of the compound form in a particular environment is basic. We have performed a spectroscopic and computational investigation aimed at the determination of the form of 8-hydroxyquinoline in different solvents. UV-vis, fluorescence, and IR spectral features have been assigned by ab initio computations based on the density functional theory and time-dependent density functional theory; the density functional theory and MP2 computations have been applied to the determination of the relative stability of the dimeric and monomeric cis and trans forms of 8-hydroxyquinoline in different solvents. Molecular dynamics computations have been used to determine the compound behavior in water solutions. According to our results, 8-hydroxyquinoline shows a clear preference for the cis conformation (as dimer or monomer), but, in water solutions, a small fraction of the trans conformation is also present.

Atomistic simulation of discotic liquid crystals: transition from isotropic to columnar phase example.

Molecular dynamics simulations at atomistic level have been performed on a metal-porphyrazine complex. Starting from an isotropic state, the system was cooled until transition from isotropic to columnar phase was observed; no nematic phase was encountered. Many tools were utilized to follow the system evolution: order parameter, g(r), g(||)(r(||)), g(c)(r(||)), g(perpendicular)(r(perpendicular)), g(2)(r), also density and energy changes. Very long runs were required to get reliable results, times greater than 40 ns of simulation. The structure of columnar phase was analyzed and the organization of molecules in the columns was investigated, along with the role of conformation of side chains. We found that in columnar phase the molecules are tilted versus the column axis and the conformation of side chains changes during the phase transition to allow this kind of organization; moreover the direction of columns axes is different from that of the director.