Characterization of the protein unfolding processes induced by urea and temperature.

Correct folding is critical for the biological activities of proteins. As a contribution to a better understanding of the protein (un)folding problem, we studied the effect of temperature and of urea on peptostreptococcal Protein L destructuration. We performed standard molecular dynamics simulations at 300 K, 350 K, 400 K, and 480 K, both in 10 M urea and in water. Protein L followed at least two alternative unfolding pathways. Urea caused the loss of secondary structure acting preferentially on the beta-sheets, while leaving the alpha-helices almost intact; on the contrary, high temperature preserved the beta-sheets and led to a complete loss of the alpha-helices. These data suggest that urea and high temperature act through different unfolding mechanisms, and protein secondary motives reveal a differential sensitivity to various denaturant treatments. As further validation of our results, replica-exchange molecular dynamics simulations of the temperature-induced unfolding process in the presence of urea were performed. This set of simulations allowed us to compute the thermodynamical parameters of the process and confirmed that, in the configurational space of Protein L unfolding, both of the above pathways are accessible, although to a different relative extent.

Computational and experimental approaches assess the interactions between bovine beta-lactoglobulin and synthetic compounds of pharmacological interest.

Extending a previous investigation, the ability of binding to the model calycin beta-lactoglobulin (BLG) was evaluated both in silico and in vitro for several fluorine-containing (semi-)synthetic molecules of pharmacological and pharmaceutical interest (antibiotics, vastatins, steroid drugs). Simulation procedures included molecular docking according to a Montecarlo-simulated annealing protocol and molecular dynamics; heteronuclear NMR and denaturant gradient gel electrophoresis were the selected experimental techniques. For the tested drugs, ranking of the binding affinity was consistently assessed by computation and by experiment. The affinity for BLG increased in the sequence: 5-fluorosalycilic acid

Computational and experimental approaches for assessing the interactions between the model calycin beta-lactoglobulin and two antibacterial fluoroquinolones.

Norfloxacin and levofloxacin, two fluoroquinolones of different bulk, rigidity and hydrophobicity taken as model ligands, were docked to one apo and two holo crystallographic structures of bovine beta-lactoglobulin (BLG) using different computational approaches. BLG is a member of the lipocalin superfamily. Lipocalins show a typical b-barrel structure encompassing an internal cavity where small hydrophobic molecules are usually bound. Our studies allowed the identification of two putative binding sites in addition to the calyx. The rigid docking approximation resulted in strong repulsive forces when the ligands were docked into the calyx of the apo form. On the contrary, hindrance was not experienced in flexible docking protocols whether on the apo or on the holo BLG forms, due to allowance for side chain rearrangement. K(i) between 10(-7) and 10(-6) M were estimated for norfloxacin at pH 7.4, smaller than 10(-5) M for levofloxacin. Spectroscopic and electrophoretic techniques experimentally validated the occurrence of an interaction between norfloxacin and BLG. Changes in chemical shift and dynamic parameters were observed between the (19)F NMR spectra of the complex and of the ligand. A K(i) (ca 10(-7) M) comparable with the docking results was estimated through a NMR relaxation titration. Stabilization against unfolding was demonstrated by denaturant gradient gel electrophoresis on the complex versus apo BLG. NMR experimental evidence points to a very loose interaction for ofloxacin, the racemic mixture containing levofloxacin. Furthermore, we were able to calculate in silico K(i)'s comparable to the published experimental values for the complexes of palmitic and retinoic acid with BLG.

Structural and dynamic features of apolipoprotein A-I cysteine mutants, Milano and Paris, in synthetic HDL.

Pursuing an established research interest in our group, we built two models for synthetic HDL containing the natural cysteine mutants of apolipoprotein A-I, apolipoprotein A-I Milano (apoA-IM) and apolipoprotein A-I Paris (apoA-IP), both in their homodimeric form. Data on the structural and dynamic properties of such s-HDL are an essential preliminary step for the understanding of the biological activity of the two mutants. Furthermore, comparison between apoA-IM and apoA-IP allows evaluating the effects of the same mutation in a different position in the primary structure and to directly compare our findings with previously published models. We computed for 50 ns in explicit solvent the molecular dynamics of the two complexes and analyzed different properties as a function of time. The proposed s-HDL structures differ significantly from one another and from wild type apolipoprotein A-I. All features of the apoA-IM model are consistent with experimental data. The higher RMSF of apoA-IM has a counterpart in the finding that trypsin, matrix metalloproteases, and chymase degrade apoA-IM much faster than wild type apoA-I; the primary cutting site is correctly identified by molecular dynamics data on our model of apoA-IM-containing s-HDL. The few experimental data for apoA-IP prevent direct comparison with our findings.

Structural features and dynamics properties of human apolipoprotein A-I in a model of synthetic HDL.

High-density lipoproteins (HDL) play a major role in the reverse transport of cholesterol and have antiatherogenic activities. Their major protein component is apolipoprotein (apo) A-I. While apoA-I amphipathic alpha-helix based secondary structure has been extensively investigated, for its lipid-bound tertiary structure only theoretical models have been proposed. In the past years, experimental approaches aimed at a direct visualization of HDL structure have been exploited, but data obtained through different microscopy techniques are conflicting and do not settle the issue. Here we present a 50 ns molecular dynamics simulation of a synthetic HDL containing two molecules of apoA-I and 101 of l-alpha-palmitoyl-oleoyl-phosphatidylcholine. Essential dynamics and structural property investigations suggest that the stabilization of the system is obtained through specific motions, whose driving forces are protein-phospholipid interactions. The most important are: the relative sliding of the two apoA-I molecules along their major axes, the relative rotation of the protein chains, and the out-of-plane deformation around proline hinges. The sliding and the out-of-plane deformation allow apoA-I to optimize its interactions with phospholipids, while the rotation is useful to maximize protein-protein salt bridges. The correspondence between computed parameters and their experimental counterparts contributes to validate our model and its dynamic behaviors. Our findings help in defining a molecular model for apoA-I contained in HDL and suggest a possible mechanism through which apoA-I can vary its diameter and accommodate different numbers of phospholipids during the metabolism of HDL.

Structural and dynamic roles of permanent water molecules in ligand molecular recognition by chicken liver bile acid binding protein.

Chicken liver bile acid binding protein (cL-BABP) crystallizes with water molecules in its binding site. To obtain insights on the role of internal water, we performed two 100 ns molecular dynamics (MD) simulations in explicit solvent for cL-BABP, as apo form and as a complex with two molecules of cholic acid, and analyzed in detail the dynamics properties of all water molecules. The diffusion coefficients of the more persistent internal water molecules are significantly different from the bulk, but similar between the two protein forms. A different number of molecules and a different organization are observed for apo- and holo-cL-BABP. Most water molecules identified in the binding site of the apo-crystal diffuse to the bulk during the simulation. In contrast, almost all the internal waters of the holo-crystal maintain the same interactions with internal sidechains and ligands, which suggests they have a relevant role in protein-ligand molecular recognition. Only in the presence of these water molecules we were able to reproduce, by a classical molecular docking approach, the structure of the complex cL-BABP::cholic acid with a low ligand root mean square deviation (RMSD) with respect to its reference positioning. Literature data reported a conserved pattern of hydrogen bonds between a single water molecule and three amino acid residues of the binding site in a series of crystallized FABP. In cL-BABP, the interactions between this conserved water molecule and the three residues are present in the crystal of both apo- and holo-cL-BABP but are lost immediately after the start of molecular dynamics.

IPG with electrodic plateaus (and other unusual procedures for 2-DE).

We describe some simple changes to the geometry of the IPG strips that make them suitable to the loading of very large sample volumes and of high-salt solutions. Of special relevance is the possibility of using strips with immobilized plateau(s) to either side of the gradient, or to both, also in connection with in-gel rehydration protocols and focusing in stock trays. The only requirement to achieve this is to leave the all-ready-made attitude and go back to custom polymerization of the IPGs in one's laboratory.

A model structure for the heterodimer apoA-IMilano-apoA-II supports its peculiar susceptibility to proteolysis.

In this study, we propose a structure for the heterodimer between apolipoprotein A-I(Milano) and apolipoprotein A-II (apoA-I(M)-apoA-II) in a synthetic high-density lipoprotein (HDL) containing L-alpha-palmitoyloleoyl phosphatidylcholine. We applied bioinformatics/computational tools and procedures, such as molecular docking, molecular and essential dynamics, starting from published crystal structures for apolipoprotein A-I and apolipoprotein A-II. Structural and energetic analyses onto the simulated system showed that the molecular dynamics produced a stabilized synthetic HDL. The essential dynamic analysis showed a deviation from the starting belt structure. Our structural results were validated by limited proteolysis experiments on HDL from apoA-I(M) carriers in comparison with control HDL. The high sensitivity of apoA-I(M)-apoA-II to proteases was in agreement with the high root mean-square fluctuation values and the reduction in secondary structure content from molecular dynamics data. Circular dichroism on synthetic HDL containing apoA-I(M)-apoA-II was consistent with the alpha-helix content computed on the proposed model.