Identification of materials' binding peptide sequences guided by a MALDI-ToF MS depletion assay

Abstract

We introduce a novel technique for an initial identification of peptide sequences that specifically bind to material surfaces based on the matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-ToF MS) depletion method. The technique relies upon time-resolved, sensitive measurements of the MALDI-ToF MS peak signals acquired from a solution containing several peptides placed in contact with an inorganic surface, in our case amorphous SiO2. Large errors intrinsic in the MALDI-ToF MS spectral analysis and uncertainties arising from the adsorption behaviour of peptide mixtures limit the predictive power of the method. However, when combined with other characterisation and modelling techniques, such as High-Performance Liquid Chromatography (HPLC), Atomic Force Microscopy (AFM), Quartz Crystal Microbalance with Dissipation (QCM-D) and Molecular Dynamics (MD), it can be used as a guide to identify novel material-binding peptide sequences, such as TPGSR for SiO2. The strategy presented in this work may have an impact on the design and synthesis of novel hybrid biomaterials based on the biomolecular recognition of inorganic surfaces

Biochemical analyses of the cement float of the goose barnacleDosima fascicularis– a preliminary study

“…In a follow-up study, it is planned to use peptide sequence tags to identify the fulllength proteins by genome or transcriptome sequencing, or by RT-PCR methods (Hennebert et al 2012;Lin et al 2014). Furthermore, the peptides characterised in this study will be used to identify possible inorganic surface binding sequences in a combined computational and experimental approach as described by Steckbeck et al (2014). The peptides can also be the basis for designing fluorescent-labelled nucleic acids for in situ hybridisation probes to localise RNA sequences (Wang & Stewart 2012).…”

Estimation of the free energy of adsorption of a polypeptide on amorphous SiO2from molecular dynamics simulations and force spectroscopy experiments

“…Notable is that both polar (and charged) and non-polar amino acid side chains contribute to surface adhesion, as we already noticed in other studies. 9,35,36,49,61 Also interesting is the fact that the -SH terminal group of cysteine in both cases remains fully hydrated, far from the surface.…”

“…Anti-ice or anti-fouling coatings are also realized through the immobilization of proteins on solid substrates, [3][4][5] and novel biomimetic materials can be synthesized by mineralization of short polypeptide sequences that selectively recognize and strongly bind to inorganic solid phases. [6][7][8][9] Therefore, experimental and simulation effort has been recently spent for a rationalization of the fundamental physical processes that govern the biomoleculesurface interactions at an atomic scale. In this context, several methods that are able to indirectly quantify the free energy of adsorption DG ads of short polypeptides on solid materials have been proposed.…”

“…Therefore, the famous equality of Jarzynski, that calculates the equilibrium free-energy difference between two states from the complete set of non-equilibrium work values associated with each individual trajectory that connects the same states, has had only limited practical applicability so far. 46 In the present article we concentrate on a model system consisting of a tetrapeptide with sequence GCRL (glycine, cysteine, arginine and leucine) 9 interacting with an amorphous SiO 2 surface model at neutral pH, for which we have developed a realistic atomistic structure and an accurate force field in previous works. [47][48][49][50] The adsorption free energy DG ads is theoretically predicted using both equilibrium (Replica Exchange with Solute Tempering combined with MetaDynamics, or briefly RESTMetaD 44 ) and non-equilibrium (SMD) methods via Jarzynski's equality.…”

Modeling and simulation of protein–surface interactions: achievements and challenges

“…Examples include simulations for structural refinement of docked complexes (Aliaga et al 2011;Alvarez-Paggi et al 2013;Brancolini et al 2012Brancolini et al , 2015Imamura et al 2007), and for the investigation of the binding orientations of proteins on surfaces (Alvarez-Paggi et al 2010;Boughton et al 2010;Coppage et al 2013); the kinetic mechanisms of adsorption (Raffaini & Ganazzoli, 2010); the ET pathways and properties of adsorbed proteins (Bizzarri, 2006;Siwko & Corni, 2013;Utesch et al 2012;Zanetti-Polzi et al 2014;Zhou et al 2004); the effects of pH (Emami et al 2014b;Imamura et al 2003;Tosaka et al 2010;Utesch et al 2013) and ionic strength (Bizzarri, 2006) on adsorption; the role of ions in mediating adsorption ; and structural and energetic aspects of adsorption of proteins on surfaces (Apicella et al 2013;Jose & Sengupta, 2013;Hoefling et al 2011;Hung et al 2011;Kubiak-Ossowska & Mulheran, 2010a, b;O'Mahony et al 2013;Vila Verde et al 2009Wang et al 2010a, b;Yu et al 2012a;Steckbeck et al 2014;Sun et al 2014a;Sun et al 2014b). Further, conventional MD can be used to simulate physical perturbations, such as mechanical or electrical forces exerted on molecules in experiments.…”