An In Silico Methodology That Facilitates Decision Making in the Engineering of Nanoscale Protein Materials.

Under the need for new functional and biocompatible materials for biomedical applications, protein engineering allows the design of assemblable polypeptides, which, as convenient building blocks of supramolecular complexes, can be produced in recombinant cells by simple and scalable methodologies. However, the stability of such materials is often overlooked or disregarded, becoming a potential bottleneck in the development and viability of novel products. In this context, we propose a design strategy based on in silico tools to detect instability areas in protein materials and to facilitate the decision making in the rational mutagenesis aimed to increase their stability and solubility. As a case study, we demonstrate the potential of this methodology to improve the stability of a humanized scaffold protein (a domain of the human nidogen), with the ability to oligomerize into regular nanoparticles usable to deliver payload drugs to tumor cells. Several nidogen mutants suggested by the method showed important and measurable improvements in their structural stability while retaining the functionalities and production yields of the original protein. Then, we propose the procedure developed here as a cost-effective routine tool in the design and optimization of multimeric protein materials prior to any experimental testing.

StarD7 behaves as a fusogenic protein in model and cell membrane bilayers.

StarD7 is a surface active protein, structurally related with the START lipid transport family. So, the present work was aimed at elucidating a potential mechanism of action for StarD7 that could be related to its interaction with a lipid-membrane interface. We applied an assay based on the fluorescence de-quenching of BD-HPC-labeled DMPC-DMPS 4:1 mol/mol SUVs (donor liposomes) induced by the dilution with non-labeled DMPC-DMPS 4:1 mol/mol LUVs (acceptor liposomes). Recombinant StarD7 accelerated the dilution of BD-HPC in a concentration-dependent manner. This result could have been explained by either a bilayer fusion or monomeric transport of the labeled lipid between donor and acceptor liposomes. Further experiments (fluorescence energy transfer between DPH-HPC/BD-HPC, liposome size distribution analysis by dynamic light scattering, and the multinuclear giant cell formation induced by recombinant StarD7) strongly indicated that bilayer fusion was the mechanism responsible for the StarD7-induced lipid dilution. The efficiency of lipid dilution was dependent on StarD7 electrostatic interactions with the lipid-water interface, as shown by the pH- and salt-induced modulation. Moreover, this process was favored by phosphatidylethanolamine which is known to stabilize non-lamellar phases considered as intermediary in the fusion process. Altogether these findings allow postulate StarD7 as a fusogenic protein.

Surface behavior and peptide-lipid interactions of the cyclic neuropeptide melanin concentrating hormone.

The kinetics and the thermodynamics of melanin concentrating hormone (MCH) adsorption, penetration, and mixing with membrane components are reported. MCH behaved as a surface active peptide, forming stable monolayers at a lipid-free air-water interface, with an equilibrium spreading pressure, a collapse pressure, and a minimal molecular area of 11 mN/m, 13 mN/m, and 140 A (2), respectively. Additional peptide interfacial stabilization was achieved in the presence of lipids, as evidenced by the expansion observed at pi > pi sp in monolayers containing premixtures of MCH with zwitterionic or charged lipids. The MCH-monolayer association and dissociation rate constants were 9.52 x 10 (-4) microM (-1) min (-1) and 8.83 x 10 (-4) min (-1), respectively. The binding of MCH to the dpPC-water interface had a K d = 930 nM at 10 mN/m. MCH penetration in lipid monolayers occurred even up to pi cutoff = 29-32 mN/m. The interaction stability, binding orientation, and miscibility of MCH in monolayers depended on the lipid type, the MCH molar fraction in the mixture, and the molecular packing of the monolayer. This predicted its heterogeneous distribution between different self-separated membrane domains. Our results demonstrated the ability of MCH to incorporate itself into biomembranes and supports the possibility that MCH affects the activity of mechanosensitive membrane proteins through mechanisms unrelated with binding to specific receptors.

Determination of liposome permeability of ionizable carbamates of zidovudine by steady state fluorescence spectroscopy.

In the present paper the relative permeabilities of AZT-Pyp and AZT-Ethy across a phospholipid bilayer were estimated by the means of fluorescence spectroscopy. The center of spectral mass of both non-encapsulated AZT-derivatives (AZT-der) emission spectra increased as a function of the illumination time inside the spectrofluorimeter cell. This phenomenon was even more evident when drugs were incubated under an UV mercury lamp, suggesting its photolytic origin. AZT-der were protected from photolysis inside liposomes and decomposed upon irradiation when they were free in the aqueous phase. The time-dependent decrease in the fluorescence intensity at a constant wavelength was fitted to a two-exponential equation and the values of rate constants for permeability and photolysis were calculated. It was concluded that AZT-Pyp but not AZT-Ethy diffused across the bilayer. This behavior correlated with the molecular volumes of AZT-Pyp (379.6A(3)) and AZT-Ethy (450.5A(3)), determined from the minimum energy conformations but not with previously reported logP values. These results reinforce the concept that not only lipophilicity but also membrane structure and AZT-der molecular size had a critical influence in passive diffusion across bilayers and may help in future refinements of other AZT-der molecular design.

Effect of partitioning equilibria on the activity of beta-galactosidase in heterogeneous media.

We had demonstrated that membrane adsorption or penetration differentially modulated beta-Galactosidase (beta-Gal) activity against soluble substrates (Coll. and Surf., 24, 21, 2002). In a heterogeneous media, not only the enzyme but also the rest of the chemical species taking part in a chemical reaction would eventually interact with the available surfaces. The aim of the present work was to investigate if, in addition to changes in the intrinsic mechanism of the reaction at the lipid-water interface, the kinetics of enzyme-catalyzed reactions could be significantly affected by the partitioning of the substrate (ortho-nitro-phenyl galactopyranoside (ONPG)), the product (ortho-nitro-phenol (ONP)) and the enzyme (E. coli beta-Gal) towards the membrane. Multilamellar vesicles of sPC were used as model membranes. Membrane-water partition coefficients (Pm/w) were determined according to the theory and methodology developed previously (J. Neurosci. Meth. 36, 203, 1991). The values of Pm/w obtained (PONPG =0, PONP =50 and P beta-Gal = 118) were applied to a two-compartment model, which assumed a free access of the substrate to the enzyme and a nucleophile-like activatory effect exerted, within the membrane compartment, by the lipid-water interface. This model: (i) reproduced the lipid concentration-dependence we had observed previously in Vmax, (ii) predicted the values of k4 = 3.54 x 10(7) s-1 and the extinction coefficient of the aglycone in the membrane phase, 4012 M(-1) cm-1, with p < 0.0001 and p < 0.02, respectively, as well as for P beta-Gal =117 (which was poor (p=0.6716) but gave a numerical value within the same order of magnitude that the experimental value) and (iii) emphasized the importance of the more efficient reaction mechanism in the membrane phase compared with that in the aqueous phase (k4>>k3).

PEG-induced molecular crowding leads to a relaxed conformation, higher thermal stability and lower catalytic efficiency of Escherichia coli ß-galactosidase.

Enzymatic activities were historically assayed in dilute solutions where molecular crowding, molecular confinement and their consequences were not taken into account. Here we report how macromolecular crowding tunes catalytic parameters for the tetrameric ß-Galactosidase from Escherichia coli, ß-Gal. We detected increases in KM (weaker substrate binding) and a nonlinear variation in Vmax, with a minimum at 25% W/P of the crowding agent (polyethyleneglycol molecular mass 6000, PEG(6000)) resulting in a linear decrease in the catalytic efficiency (kcat/KM) within the whole [PEG(6000)] range tested). Presence of crowding agent affected ß-Gal structural content and increased its thermal resistance. Steady state fluorescence and Fourier transformed infrared spectroscopic observations are compatible with crowding-induced disordering and restricted internal dynamics as a result of excluded volume and solvent structuring effects. This leads to a non-optimal substrate-binding site and a less conformationally strained protein.

Membrane topology modulates beta-galactosidase activity against soluble substrates.

The effect of bio-surfaces of contrasting curvature, on the kinetic parameters of ortho-nitrophenyl-beta-D-galactopiranoside hydrolysis catalyzed by E. coli beta-galactosidase, was investigated. The self-aggregating state and structure of the amphiphiles (Phosphatidylcholine, Lubrol-PX, Triton X-100, DocNa, SDS and CTAB) were inferred from their c.m.c. values and light-scattering measurements. Low curvature phosphatidylcholine or mixed phosphatidylcholine-detergent vesicles increased V(max) without affecting K(M). High curvature micellar structures containing ionic detergents modulated negatively the enzyme activity (decreased or abolished V(max) and increased K(M)). Neither micelles containing non-ionic detergents nor the amphiphiles in a monomeric form, affected enzyme activity. CTAB at a concentration below its c.m.c but incorporated into a bilayer, became an activator (K(M) decreased respect to the control). Non-enzymatic interfacial hydrolysis of the substrate was discarded. Enzyme-membrane interaction and membrane elasticity, were evaluated using monomolecular layers at the air-water interface. Beyond particular molecular structures, topology affected the direction of the modulatory effects exerted by these amphiphiles on beta-galactosidase activity.

ß-galactosidase at the membrane-water interface: a case of an active enzyme with non-native conformation.

Previously we demonstrated that Escherichia coli beta-galactosidase (ß-Gal) binds to zwitterionic lipid membranes improving its catalytic activity. To understand the activation mechanism from the protein perspective, here the thermal dependence of the catalytic activity was evaluated in conjunction with parameters derived from spectroscopy and calorimetry, in the presence and absence of egg-yolk phosphatidylcholine vesicles. In solution, the native state of ß-Gal exhibits a loose conformation according to the λmax of fluorescence emission, which is in the upper end of the emission range for most proteins. A non-two state thermal unfolding mechanism was derived from DSC experiments and supported by the sequential unfolding temperatures exhibited by fluorescence (55°C) and CD (60°C) spectroscopies. Quenching of ß-Gal's intrinsic fluorescence, provided evidence for a novel and even looser folding for the lipid-bound protein. However, DSC data showed that the thermal unfolding in the presence of lipids occurred with a significant decrease in ΔH compared to what happened in solution, suggesting that only the population of non-bound protein molecules were involved in this process. Concluding, upon binding to a lipid-water interface ß-Gal becomes trapped in a partially unfolded state, more active than that of the native protein in solution.