Influence of the surrounding environment in re-naturalized ß-barrel membrane proteins.

Outer-membrane porins are currently being used to prepare bioinspired nanomembranes for selective ion transport by immobilizing them into polymeric matrices. However, the fabrication of these protein-integrated devices has been found to be strongly influenced by the instability of the ß-barrel porin structure, which depends on surrounding environment. In this work, molecular dynamics simulations have been used to investigate the structural stability of a representative porin, OmpF, in three different environments: (i) aqueous solution at pH=7; (ii) a solution of neutral detergent in a concentration similar to the critical micelle concentration; and (iii) the protein embedded into a neutral detergent bilayer. The results indicate that the surrounding environment not only alters the stability of the ß-barrel but affects the internal loop responsible of the ions transport, as well as the tendency of the porin proteins to aggregate into trimers. The detergent bilayer preserves the structure of OmpF protein as is found bacteria membranes, while pure aqueous solution induces a strong destabilization of the protein. An intermediate situation occurs for detergent solution. Our results have been rationalized in terms of protein⋯water and protein⋯detergent interactions, which makes them extremely useful for the future design of new generation of bioinspired protein-integrated devices.

Modeling of a C-end rule peptide adsorbed onto gold nanoparticles.

The RPAR peptide, a prototype C-end Rule (CendR) sequence that binds to neuropilin-1 (NRP-1), has potential therapeutic uses as internalization trigger in anticancer nanodevices. Recently, the functionalization of gold nanoparticles with CendR peptides has been proved to be a successful strategy to target the NRP-1 receptor in prostate cancer cells. In this work, we investigate the influence of two gold surface facets, (100) and (111), on the conformational preferences of RPAR using molecular dynamics simulations. Both clustering and conformational analyses revealed that the peptide backbone becomes very rigid upon adsorption onto gold, which is a very fast and favored process, the only flexibility being attributed to the side chains of the two Arg residues. Thus, the different components of RPAR tend to adopt an elongated shape, which is characterized by the pseudo-extended conformation of both the backbone and the Arg side chains. This conformation is very different from the already known bioactive conformation, indicating that RPAR is drastically affected by the substrate. Interestingly, the preferred conformations of the peptide adsorbed onto gold facets are not stabilized by salt bridges and/or specific intramolecular hydrogen bonds, which represent an important difference with respect to the conformations found in other environments (e.g. the peptide in solution and interacting with NRP-1 receptor). However, the conformational changes induced by the substrate are not detrimental for the use of gold nanoparticles as appropriate vehicles for the transport and targeted delivery of the RPAR. Thus, once their high affinity for the NRP-1 receptor induces the targeted delivery of the elongated peptide molecules from the gold nanoparticles, the lack of intramolecular interactions facilitates their evolution towards the bioactive conformation, increasing the therapeutic efficacy of the peptide.

Conformational analysis of a modified RGD adhesive sequence.

The conformational preferences of the Arg-GlE-Asp sequence, where GlE is an engineered amino acid bearing a 3,4-ethylenedioxythiophene (EDOT) ring as side group, have been determined combining density functional theory calculations with a well-established conformational search strategy. Although the Arg-GlE-Asp sequence was designed to prepare a conducting polymer-peptide conjugate with excellent electrochemical and bioadhesive properties, the behavior of such hybrid material as adhesive biointerface is improvable. Results obtained in this work prove that the bioactive characteristics of the parent Arg-Gly-Asp sequence become unstable in Arg-GlE-Asp because of both the steric hindrance caused by the EDOT side group and the repulsive interactions between the oxygen atoms belonging to the backbone amide groups and the EDOT side group. Detailed analyses of the conformational preferences identified in this work have been used to re-engineer the Arg-GlE-Asp sequence for the future development of a new electroactive conjugate with improved bioadhesive properties. The preparation of this new conjugate is in progress. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.

Electroactive polymer-peptide conjugates for adhesive biointerfaces.

Electroactive polymer-peptide conjugates have been synthesized by combining poly(3,4-ethylenedioxythiophene), a polythiophene derivative with outstanding properties, and an Arg-Gly-Asp (RGD)-based peptide in which Gly has been replaced by an exotic amino acid bearing a 3,4-ethylenedioxythiophene ring in the side chain. The incorporation of the peptide at the ends of preformed PEDOT chains has been corroborated by both FTIR and X-ray photoelectron spectroscopy. Although the morphology and topology are not influenced by the incorporation of the peptide at the ends of PEDOT chains, this process largely affects other surface properties. Thus, the wettability of the conjugates is considerably higher than that of PEDOT, independently of the synthetic strategy, whereas the surface roughness only increases when the conjugate is obtained using a competing strategy (i.e. growth of the polymer chains against termination by end capping). The electrochemical activity of the conjugates has been found to be higher than that of PEDOT, evidencing the success of the polymer-peptide links designed by chemical similarity. Density functional theory calculations have been used not only to ascertain the conformational preferences of the peptide but also to interpret the electronic transitions detected by UV-vis spectroscopy. Electroactive surfaces prepared using the conjugates displayed the higher bioactivities in terms of cell adhesion, with the relative viabilities being dependent on the roughness, wettability and electrochemical activity of the conjugate. In addition to the influence of the peptide fragment in the initial cell attachment and subsequent cell spreading and survival, the results indicate that PEDOT promotes the exchange of ions at the conjugate-cell interface.