Simulating Protein Adsorption for Experimental Comparison


Book Description

Many biological processes and technological applications involve proteins coming into contact with a solid surface. Generally, we know that proteins experience some degree of conformational change at the solid/liquid interface, and can measure these changes in the lab. However, while many experimental techniques exist for characterizing surface-bound proteins, none have been able to resolve high-precision structures. Computer simulation offers a unique route to determining how proteins adsorb. Herein, we apply a popular statistical sampling technique - Parallel Tempering Metadynamics - to all-atom molecular dynamics simulations of ex- plicitly solvated proteins interacting with solid surfaces. We show that by biasing specific degrees of freedom - or collective variables - a protein can be influenced to exhaustively explore conformational space both on and off a surface. The results from these simulations can be post-processed to reveal details such as: surface- bound conformations, orientations, and finer structural details like interatomic distances and Ramachandran angles - which, in turn, can be compared to, and validated by, experimental measurements. Ultimately, this work should convey the descriptive power that can arise from a mutually beneficial partnership between surface science and computer simulation in the context of biomolecular adsorption.







Proteins at Solid-Liquid Interfaces


Book Description

This book opens with a description of fundamental aspects of protein adsorption to surfaces, a phenomenon that plays a key role in biotechnological applications, especially at solid-liquid interfaces. Presented here are methods for studying adsorption kinetics and conformational changes such as optical waveguide lightmode spectroscopy (OWLS). Also described are sensitive bench techniques for measuring the orientation and structure of proteins at solid-liquid interfaces, including total internal reflection ellipsometry (TIRE), dual polarisation interferometry (DPI) and time of flight - secondary ion mass spectrometry (TOF–SIMS). A model study of fibronectin at polymer surfaces is included, as are studies using microporous membranes and textiles with immobilized enzymes for large-scale applications. Biocompatibility, anti-fouling properties and surface modification to modulate the adsorption and activity of biomolecules are among the other topics addressed in this invaluable book.













Adsorption, Aggregation and Structure Formation in Systems of Charged Particles


Book Description

This thesis presents studies on the interaction of soft materials like surfactants and proteins with hard silica nanomaterials. Due to its interdisciplinary nature it combines concepts from the fields of physical chemistry, nanoscience and materials science, yielding to fundamental insights into the structure-directing forces operating at the nano-scale. It is shown that the morphology of surfactant micellar aggregates adsorbed at the surface of nanoparticles and inside tubular nanopores can be tuned on demand by the co-adsorption of a surface modifier. The interaction of globular proteins with silica nanoparticles is dominated by electrostatic interactions and can be controlled by pH and ionic strength, while the bridging of nanoparticles by adsorbed protein molecules leads to large-scale hybrid aggregates of protein with the nanoparticles. Concepts emerging from the role of electrostatic interactions in the hetero-aggregation of nanoparticles with protein molecules are used for the co-assembly of charged microbeads into linear clusters and chains of controllable length.







Surface and Interface Chemistry of Clay Minerals


Book Description

Surface and Interface Chemistry of Clay Minerals, Volume 9, delivers a fundamental understanding of the surface and interface chemistry of clay minerals, thus serving as a valuable resource for researchers active in the fields of materials chemistry and sustainable chemistry. Clay minerals, with surfaces ranging from hydrophilic, to hydrophobic, are widely studied and used as adsorbents. Adsorption can occur at the edges and surfaces of clay mineral layers and particles, and in the interlayer region. This diversity in properties and the possibility to tune the surface properties of clay minerals to match the properties of adsorbed molecules is the basis for study. This book requires a fundamental understanding of the surface and interface chemistry of clay minerals, and of the interaction between adsorbate and adsorbent. It is an essential resource for clay scientists, geologists, chemists, physicists, material scientists, researchers, and students. - Presents scientists and engineers with a resource they can rely on for their own research and work involving clay minerals - Includes an in-depth look at ion exchange, adsorption of inorganic and organic molecules, including polymers and proteins, and catalysis occurring at the surfaces of clay minerals - Includes materials chemistry of clay minerals with chiral clay minerals, optical materials and functional films