From phage display to structure: an interplay of enthalpy and entropy in the binding of the LDHSLHS polypeptide to silica

Abstract

ARTICLE This journal isPolypeptide based biosilica composites show promise as next generation multi-functional nano-platforms for diagnostics and bio-catalytic applications. Following identification of a strong silica binder (LDHSLHS) by phage display, we conduct structural analysis of the polypeptide at the interface with amorphous silica nanoparticles in an aqueous environment. Our approach relies on modelling of Infrared and Raman spectral responses using predictions of molecular dynamics simulations and quantum studies of the normal modes for several potential structures. By simultaneously fitting both Infrared and Raman responses in the Amide spectral region, we show that the main structural conformer has a beta-like central region and helix-twisted terminals. Classical simulations, as conducted previously (Chem. Mater., 2014, 26, 5725), predict that association of the main structure with the interface is stimulated by electrostatic interactions though surface binding also requires spatially distributed sodium ions to compensate negatively charged acidic silanol groups. Accordingly, diffusion of sodium ions would contribute to a stochastic character of the peptides association with the surface. Consistent with the described dynamics at the interface, results from isothermal titration calorimetry (ITC) confirm significant enhancement of polypeptide binding to silica under higher concentrations of Na + . The results of this study suggest that the tertiary structure of a phage capsid protein plays a significant role in regulating the conformation of peptide LDHSLHS, increasing its binding to silica during the phage display process. The results presented here support design-led engineering of polypeptide-silica nanocomposites for bio-technological applications. . †Electronic supplementary information (ESI) available. It provides details on: a) details on MD simulations and extracted structural properties along trajectories b) details of DFT studies on the normal modes of imidazole ring of methyl terminated histidine under different protonation conditions; c) the details on the normal modes of the structural cases including relative contributions of carbonyls and carboxyl groups into the described normal modes; d) results of isothermal titration calorimetry.

Anchoring of a hydrophobic heptapeptide (AFILPTG) on silica facilitates peptide unfolding at the abiotic–biotic interface

“…Replica exchange and molecular dynamics in water. Compared to our previous report on structural behaviour of the LD polypeptide [17], here, we make additional efforts to try sampling full configurational space of the polypeptide when in water. For this purpose, we conduct replica exchange molecular dynamics (REMD) with the CHARMM force field in NAMD environment [21,31] using the generalized Born implicit solvent model with a "soft" cut-off (12 Å ) to speed up computation [22].…”

“…However, it is clear that phage identification of mineralspecific primary sequences is just the first step towards the development of predictable bio-mineral structural organization. Mastering bio-silica engineering requires building systematic knowledge to In a recent publication [17] we adopted predictions of classical simulations and quantum chemistry to address structural properties of an hydrophilic LDHSLHS (LD) polypeptide -one of several sequences we determined to be silica specific [12]. In particular, we took advantage of the noncoincidence of infrared and Raman responses [18] to extract the major (beta-like central region with helix-twisted terminals) and the minor secondary structural conformations of the LDHSLHS polypeptide at its interface with amorphous silica nanoparticles in an aqueous environment, and alone in water.…”

“…To address structure and mechanisms of interactions of the AF polypeptide when next to silica, here, we elaborate further the approach we introduced previously [17]. Specifically, in the present study (a) we use replica exchange molecular dynamics (REMD) [21,22] to sample configurational space for initial structural guesses; (b) we combine optical responses sensitive to skeletal motions (infrared and Raman) with circular dichroism (CD) which is sensitive to electronic and magnetic components; and (c) we combine experimental data with quantum chemical (DFT) studies of relevant structural cases of the peptide in water and in the presence of silica to extract plausible structural conformations and discuss the thermodynamics of binding.…”

Confining a Protein-Containing Water Nanodroplet inside Silica Nanochannels

“…In this rapidly advancing field, modeling is crucial for understanding at molecular-level the interactions of biomolecules with silica [2,40] in the presence of water. Indeed, theoretical studies on proteins at silica interfaces have experienced an impressive growth in the last few years [2,41,42,43,44], uncovering important microscopic features of the interaction with flat surfaces. The simulation of lysozyme [45,46], papain [47], and fragments of various proteins [48,49,50] on silica surfaces, for instance, revealed conformational changes, and in some cases even a certain degree of unfolding of the biomolecule upon surface adhesion.…”

Combinatorial Discovery and Validation of Heptapeptides with UTP Binding Induced Structure

“…The latter has been used effectively to find peptides that bind to antibodies, cell surface proteins, carbohydrate antigens, [10] metal surfaces, [11] nanoparticles, [12] polymers [13] and macrocycles, [14] as well as for sequences that form dynamically interchanging complexes with ATP [15] and peptide catalysts. [16] In addition, molecular dynamics simulations have been used to predict the interaction of thereby identified sequences with gold [17] and silica [18] surfaces. Combining experimental screening with computation has been applied successfully to protein design and evolution [19] as well as directed discovery of peptides.…”