Stability of tubular structures based on beta-helical proteins: self-assembled versus polymerized nanoconstructs and wild-type versus mutated sequences

Effect of sequence variation on the mechanical response of amyloid fibrils probed by steered molecular dynamics simulation

The mechanical failure of mature amyloid fibers produces fragments that act as seeds for the growth of new fibrils. Fragmentation may also be correlated with cytotoxicity. We have used steered atomistic molecular dynamics simulations to study the mechanical failure of fibrils formed by the amyloidogenic fragment of human amylin hIAPP20-29 subjected to force applied in a variety of directions. By introducing systematic variations to this peptide sequence in silico, we have also investigated the role of the amino-acid sequence in determining the mechanical stability of amyloid fibrils. Our calculations show that the force required to induce mechanical failure depends on the direction of the applied stress and upon the degree of structural order present in the β-sheet assemblies, which in turn depends on the peptide sequence. The results have implications for the importance of sequence-dependent mechanical properties on seeding the growth of new fibrils and the role of breakage events in cytotoxicity.

Exploring the energy landscape of a molecular engineered analog of a tumor-homing peptide

Recently a new non-coded amino acid was designed as a replacement for Arg, to protect the tumor-homing pentapeptide CREKA (Cys-Arg-Glu-Lys-Ala) from proteases. This constrained Arg analog, denoted c(5)Arg, was engineered to also promote the stability of the CREKA bioactive conformation. The conformational profile of the CREKA analog obtained by replacing Arg by c(5)Arg has been extensively investigated in this work. Two molecular dynamics simulations-based strategies have been employed: a modified simulated annealing and replica exchange. Results obtained using both techniques show that the conformational features of the new analog fulfill the purpose of its design. The new CREKA analog not only preserves the main structural attributes found for the bioactive conformation of the parent peptide but also shows lower flexibility. Moreover, the conformational profile of the mutated peptide narrows towards the most stable structures previously observed for the parent CREKA peptide.

Modeling an electronic conductor based on natural peptide sequences

In this work we used quantum mechanical calculations, molecular dynamics simulations, and QM/MM methods to examine the formation of a pi-stacking ladder and the existence of charge transfer processes in a tubular nanostructure constructed using protein building blocks. Initially, the conformational properties of beta-3-thienylalanine, a synthetic amino acid with an aromatic side group, were studied using quantum mechanical calculations. Next, this amino acid was used to substitute the natural residues at selected positions of the nanotube. Molecular dynamics simulations showed that a rational design of the targeted replacements enhances the stability of the tubular nanostructure and forms a pi-stacking ladder in the inner core of the tube. Finally, QM/MM calculations on the oxidized nanotube evidenced the delocalization of the pi-electron deficiency between the thienyl side groups of the different synthetic residues. The overall results reflected that the system under study is a potential candidate to be used as a nanowire.

Stimuli-responsive properties of peptide-based copolymers studied via directional growth of self-assembled patterns on solid substrate

We studied the self-assembly of peptide-based ABA and CBC triblock-copolymers (obtained by bacterial expression) containing random coiled hydrophilic central B blocks flanked with helical A or C blocks. The A and C blocks were of different compositions with respect to the fraction of lysine residues which provided a higher pH sensitivity of the copolymer solutions. The interchain interactions of the copolymers driven by external stimuli (pH and temperature) were explored in the process of macromolecular self-assembling in the thin films of the copolymer solutions deposited on the solid substrate. The interactions involved in the macromolecular association affected the morphology of the developed patterns. The polypeptide of the B block was not involved in the formation of the secondary structures, while the A and C blocks demonstrated helical folding responsible for the intermolecular association. The mechanism of the responsive behavior of the copolymers is based on the reversible assembling of the helices into coiled-coil structures upon the change of pH or temperature. It was found that at low pH values, when electrostatic repulsion was strong and the A/C blocks unfolded, assembling yielded fractal dendrites. Increasing the pH resulted in the recovery of the helical conformation of the A/C blocks and caused a transition from the fractal to compact structures. An elevation of temperature resulted in the disruption of the dendritic structures. The reported here approach to the evaluation of the intermolecular interactions, based on the analysis of the dendritic patterns, provides a rapid and simple method for the characterization of complex processes of self-assembling biomacromolecules.

Structural analysis of a beta-helical protein motif stabilized by targeted replacements with conformationally constrained amino acids

Here we study conformational stabilization induced in a beta-helical nanostructure by position-specific mutations. The nanostructure is constructed through the self-assembly of the beta-helical building block excised from E. coli galactoside acetyltransferase (PDB code 1krr , chain A; residues 131-165). The mutations involve substitutions by cyclic, conformationally constrained amino acids. Specifically, a complete structural analysis of the Pro-Xaa-Val sequence [with Xaa being Gly, Ac 3c (1-aminocyclopropane-1-carboxylic acid) and Ac 5c (1-aminocyclopentane-1-carboxylic acid)], corresponding to the 148-150 loop region in the wild-type (Gly) and mutated (Ac 3c and Ac 5c) 1krr , has been performed using Molecular Dynamics simulations and X-ray crystallography. Simulations have been performed for the wild-type and mutants of three different systems, namely the building block, the nanoconstruct and the isolated Pro-Xaa-Val tripeptide. Furthermore, the crystalline structures of five peptides of Pro-Xaa-Val or Xaa-Val sequences have been solved by X-ray diffraction analysis and compared with theoretical predictions. Both the theoretical and crystallographic studies indicate that the Pro-Ac n c-Val sequences exhibit a high propensity to adopt turn-like conformations, and this propensity is little affected by the chemical environment. Overall, the results indicate that replacement of Gly149 by Ac 3c or Ac 5c significantly reduce the conformational flexibility of the target site enhancing the structural specificity of the building block and the nanoconstruct derived from the 1krr beta-helical motif.