Adsorption of genetically engineered proteins studied by time‐of‐flight secondary ion mass spectrometry (TOF‐SIMS). Part A: data acquisition and principal component analysis (PCA)

Abstract

Recent progress in the adaptation of combinatorial biology selection protocols to materials science has created a new class of polypeptides with specific affinity to inorganics. Here, we use one of the genetically engineered proteins, a gold binding protein (GBP-1), to assess quantitatively its binding specificity to Au, Ag and Pd surfaces by using time-of-flight secondary ion mass spectroscopy (TOF-SIMS). The GBP-1, originally selected using cell-surface display techniques, consisting of 14 amino acids with a sequence of MHGKTQATSGTIQS, was used in this study. Three-repeat and single-repeat forms of GBP-1 were prepared. In earlier studies, GBP-1 was shown to bind to Au particles and self-assemble on flat Au surfaces. Through the fingerprint analysis of these specific peptides, their role in binding can be investigated in terms of their contribution to surface interaction possibly forming the right molecular architecture for binding. To achieve this purpose, a large-sized data matrix produced by TOF-SIMS must be properly treated for analysis. In Part A, we use principal component analysis (PCA) to visualize the spectral variations for a variety of adsorption conditions and suggest possible contribution of the specific types of amino acids (binding site) to the interactions.

Molecular biomimetics: nanotechnology and bionanotechnology using genetically engineered peptides

“…Recently, conventional spectroscopy techniques, such as X-ray photoelectron spectroscopy and timeof-flight secondary ion mass spectroscopy techniques, have also been shown to provide the fingerprint of peptide adsorption on to surfaces (Coen et al 2001;Suzuki et al 2007). Although difficult to carry out, the application of solid and liquid state NMR could provide quantitative information of molecular conformations of peptides, essential information towards the understanding of the mechanism of polypeptide binding on to solids (Evans 2003).…”

Surface composition of insulin and albumin adsorbed on polymer substrates as revealed by multivariate analysis of ToF‐SIMS data

“…[10] ToF-SIMS combined with PCA enabled obtaining information about the possible binding mechanisms between the proteins and the surfaces. [5,11] Finally, ToF-SIMS and PCA were used to distinguish changes in protein conformation/orientation under different adsorption conditions [12] or surface properties. [5,13] Partial least squares (PLS) regression has been used successfully in the past for determining the relationships between the surface chemical ToF-SIMS information (X) and a given surface property (Y) (i.e.…”

Hydrophobin can prevent secondary protein adsorption on hydrophobic substrates without exchange

“…PCA facilitates clustering of different spectra according to the major differences between them and has proven a very powerful tool for the identification and quantification of mixed protein adsorbates [19, 20, 33–35]. The peak list used is shown in Table 1 including the loadings of the first three principal components, which together describe 99% of all variance in the dataset.…”

“…[19], summarized in Table 1. The principal component analysis itself was performed using BASF-software developed in LabVIEW (version 7.1, National Instruments).…”