Elucidating Polymorph-Selective Bioadsorption on Chitin Surfaces.

Chitin is a naturally abundant biopolymer with low cytotoxicity offering substantial promise in biomedical applications. An enhanced understanding of the polymorph-selective interactions between proteins and chitin surfaces would enable targeted advances in tissue engineering, antimicrobial surfaces, sensing, and drug delivery. This fundamental understanding is scarce and is challenging to obtain via experimental approaches alone. Molecular simulation approaches can offer complementary insights. Here, we use umbrella sampling molecular dynamics simulations to predict the adsorption free energies of nine representative amino acids at four aqueous chitin interfaces, comprising two chitin polymorphs and two different crystal surfaces. Our results demonstrate a clear selectivity for one polymorph over the other at the amino acid level. From these findings we provide a fundamental basis for explaining the polymorph selectivity exhibited by some chitin binding proteins. Our outcomes offer a platform for the future rational design of polymorph-selective chitin binding motifs.

Elucidating the influence of polymorph-dependent interfacial solvent structuring at chitin surfaces.

Interfacial solvent structuring is thought to be influential in mediating the adsorption of biomolecules at aqueous materials interfaces. However, despite the enormous potential for exploitation of aqueous chitin interfaces in industrial, medical and drug-delivery applications, little is known at the molecular-level about such interfacial solvent structuring for chitin. Here we use molecular simulation to predict the structure of the [100] and [010] interfaces of α-chitin and ß-chitin dihydrate in contact with liquid water and saline solution. We find the α-chitin [100] interface supports lateral high-density regions in the first water layer at the interface, which are also present, but not as pronounced, for ß-chitin. The lateral structuring of interfacial ions at the saline/chitin interface is also more pronounced for α-chitin compared with ß-chitin. Our findings provide a foundation for the systematic design of biomolecules with selective binding affinity for different chitin polymorphs.

Testing the transferability of a coarse-grained model to intrinsically disordered proteins.

The intermediate-resolution coarse-grained protein model PLUM [T. Bereau and M. Deserno, J. Chem. Phys., 2009, 130, 235106] is used to simulate small systems of intrinsically disordered proteins involved in biomineralisation. With minor adjustments to reduce bias toward stable secondary structure, the model generates conformational ensembles conforming to structural predictions from atomistic simulation. Without additional structural information as input, the model distinguishes regions of the chain by predicted degree of disorder, manifestation of structure, and involvement in chain dimerisation. The model is also able to distinguish dimerisation behaviour between one intrinsically disordered peptide and a closely related mutant. We contrast this against the poor ability of PLUM to model the S1 quartz-binding peptide.

Equilibrium conformational ensemble of the intrinsically disordered peptide n16N: linking subdomain structures and function in nacre.

n16 is a framework protein family associated with biogenic mineral stabilization, thought to operate at three key interfaces in nacre: protein/ß-chitin, protein/protein, and protein/CaCO3. The N-terminal half of this protein, n16N, is known to be active in conferring this mineral stabilization and organization. While some details relating to the stabilization and organization of the mineral are known, the molecular mechanisms that underpin these processes are not yet established. To provide these molecular-scale details, here we explore current hypotheses regarding the possible subdomain organization of n16N, as related to these three interfaces in nacre, by combining outcomes of Replica Exchange with Solute Tempering molecular dynamics simulations with NMR experiments, to investigate the conformational ensemble of n16N in solution. We verify that n16N lacks a well-defined secondary structure, both with and without the presence of Ca(2+) ions, as identified from previous experiments. Our data support the presence of three different, functional subdomains within n16N. Our results reveal that tyrosine, chiefly located in the center of the peptide, plays a multifunctional role in stabilizing conformations of n16N, for intrapeptide and possibly interpeptide interactions. Complementary NMR spectroscopy data confirm the participation of tyrosine in this stabilization. The C-terminal half of n16N, lacking in tyrosine and highly charged, shows substantive conformational diversity and is proposed as a likely site for nucleation of calcium carbonate. Finally, dominant structures from our predicted conformational ensemble suggest the presentation of key residues thought to be critical to the selective binding to ß-chitin surfaces.