Abstract
Many areas of biochemistry and molecular biology, both fundamental and applications-orientated, require an accurate construction, representation and understanding of the protein molecular surface and its interaction with other, usually small, molecules. There are however many situations when the protein molecular surface gets in physical contact with larger objects, either biological, such as membranes, or artificial, such as nanoparticles. The contribution presents a methodology for describing and quantifying the molecular properties of proteins, by geometrical and physico-chemical mapping of the molecular surfaces, with several analytical relationships being proposed for molecular surface properties. The relevance of the molecular surface-derived properties has been demonstrated through the calculation of the statistical strength of the prediction of protein adsorption. It is expected that the extension of this methodology to other phenomena involving proteins near solid surfaces, in particular the protein interaction with nanoparticles, will result in important benefits in the understanding and design of protein-specific solid surfaces.
Highlights
IntroductionThe applications enumerated above, almost exclusively focused on biomolecular interactions, necessitate the construction of the molecular surface at a resolution scale similar to the size of the molecule that interacts with the protein, e.g., up to 5A , which is approximately the dimension of a large solvent molecule
There are many situations when the protein molecular surface is in physical contact with larger objects, either biological or artificial
The nanoparticle:protein interaction can either amplify the beneficial effects of nanoparticles, e.g., protein aggregation around a nanoparticle can create a ‘protein corona’ [27,28], which could be essential for the nanoparticle uptake in the cell, where its therapeutic action can unfold [29]; or it can induce the change of conformation and the bioactivity of the proteins attached to the nanoparticle [30,31], cascading in nanoparticle-induced nanotoxicity [32,33]
Summary
The applications enumerated above, almost exclusively focused on biomolecular interactions, necessitate the construction of the molecular surface at a resolution scale similar to the size of the molecule that interacts with the protein, e.g., up to 5A , which is approximately the dimension of a large solvent molecule. The long range selfassembly of proteins, e.g., cytoskeleton formation [12], formation of amyloid plaques and tangles [13], occurs through biomolecular recognition of larger areas on the molecular surface. Biomolecules interact with solid surfaces on which they are immobilized, either by design, or unintentionally [14,15], for applications as diverse as biomaterials [14,16], chromatography [17] membrane research [18,19], biomedical micro- and nano-devices [20,21], such as biosensors [22], microarrays [23,24] and lab-on-a-chip devices [25], where the preservation of the bioactivity of the immobilized proteins is paramount. The nanoparticle:protein interaction can either amplify the beneficial effects of nanoparticles, e.g., protein aggregation around a nanoparticle can create a ‘protein corona’ [27,28], which could be essential for the nanoparticle uptake in the cell, where its therapeutic action can unfold [29]; or it can induce the change of conformation and the bioactivity of the proteins attached to the nanoparticle [30,31], cascading in nanoparticle-induced nanotoxicity [32,33]
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