Protein interactions with negatively charged inorganic surfaces

Protein adsorption on charged inorganic solid materials has recently attracted enormous interest owing to its various possible applications, including drug delivery and biomaterial design. The need to combine experimental and computational approaches to get a detailed picture of the adsorbed protein properties is increasingly recognised and emphasised in this review. We discuss the methods frequently used to study protein adsorption and the information they can provide. We focus on model systems containing a silica surface, which is negatively charged and hydrophilic at physiological pH, and two contrasting proteins: bovine serum albumin (BSA) and lysozyme (LSZ) that are both water soluble. At pH 7, BSA has a net negative charge, whereas LSZ is positive. In addition, BSA is moderately sized and flexible, whereas LSZ is small and relatively rigid. These differences in charge and structural nature capture the role of electrostatics and hydrophobic interactions on the adsorption of these proteins, along with the impact of adsorption on protein orientation and function. Understanding these model systems will undoubtedly enhance the potential to extrapolate our knowledge to other systems of interest

Fibronectin module FNIII9 adsorption at contrasting solid model surfaces studied by atomistic molecular dynamics

The mechanism of human fibronectin adhesion synergy region (known as integrin binding region) in repeat 9 (FNIII9) domain adsorption at pH 7 onto various and contrasting model surfaces has been studied using atomistic molecular dynamics simulations. We use an ionic model to mimic mica surface charge density but without a long-range electric field above the surface, a silica model with a long-range electric field similar to that found experimentally, and an Au {111} model with no partial charges or electric field. A detailed description of the adsorption processes and the contrasts between the various model surfaces is provided. In the case of our model silica surface with a long-range electrostatic field, the adsorption is rapid and primarily driven by electrostatics. Because it is negatively charged (?1e), FN III9 readily adsorbs to a positively charged surface. However, due to its partial charge distribution, FNIII9 can also adsorb to the negatively charged mica model because of the absence of a long-range repulsive electric field. The protein dipole moment dictates its contrasting orientation at these surfaces, and the anchoring residues have opposite charges to the surface. Adsorption on the model Au {111} surface is possible, but less specific, and various protein regions might be involved in the interactions with the surface. Despite strongly influencing the protein mobility, adsorption at these model surfaces does not require wholesale FNIII9 conformational changes, which suggests that the biological activity of the adsorbed protein might be preserved

Solute transport in orthorhombic lysozyme crystals: a molecular simulation study

Long-time equilibrium molecular dynamics simulations were performed to study the passage of a substrate, l-arabinose, through nanopores of orthorhombic hen egg white lysozyme crystals. Cross-linked protein crystals (CLPC), as novel biological nanoporous media, consist of an extensive regular matrix of chiral solvent-filled nanopores via which ions and solutes, e.g. sugars and amino acids, travel in and out. We studied the diffusive motion of arabinose inside protein channels. The computed diffusion coefficients within the crystal were orders of magnitudes lower relative to the diffusion coefficient of the solute in water. This study is valuable for understanding the nature of solute–protein interactions and transport phenomena in CLPCs and provides an understanding of biocatalytic and bioseparation processes using CLPC

How negatively charged proteins adsorb to negatively charged surfaces - a molecular dynamics study of BSA adsorption on silica

How proteins adsorb to inorganic material surfaces is critically important for the development of new biotechnologies, since the orientation and structure of the adsorbed proteins impacts their functionality. Whilst it is known that many negatively charged proteins readily adsorb to negatively charged oxide surfaces, a detailed understanding of how this process occurs is lacking. In this work we study the adsorption of BSA, an important transport protein that is negatively charged at physiological conditions, to a model silica surface that is also negatively charged. We use fully atomistic Molecular Dynamics to provide detailed understanding of the non-covalent interactions that bind the BSA to the silica surface. Our results provide new insight into the competing roles of long-range electrostatics and short-range forces, and the consequences this has for the orientation and structure of the adsorbed proteins

Untersuchung der Wirkung von Anästhetika auf Membranen und der Adsorption von Proteinen an Festkörperoberflächen mittels Moleküldynamik-Simulationen

In this thesis, the mechanisms underlying anesthesia and the adsorption of proteins on solid surfaces have been studied using the method of molecular dynamics simulations. It is generally assumed that biological membranes are the site of anesthetic action. However, there is no consensus whether anesthetics act directly by binding to membrane proteins, thereby inhibiting their function, or indirectly by modulating the physical properties of the lipid part of the membrane. In the simulations presented here, distinct changes of lipid bilayer properties in response to the presence of alkanols, a group of anesthetics, have been observed. An anesthetic-induced shift of the equilibrium between different membrane protein conformations, modeled by simple geometric shapes, has been found. In simulations with the ion channel gramicidin A embedded in a lipid bilayer, alkanols distributed inhomogeneously in the bilayer, with almost no alkanol molecules residing in close vicinity to the gramicidin. These results provide evidence for an indirect mode of anesthetic action. Spontaneous protein adsorption on solid-liquid interfaces is the first step in the formation of biofilms. Here, a coarse-grained molecular dynamics scheme has been applied to study this complex process at high resolution, but still reaching the necessary time and length scales. Changes in protein structure and dynamics after adsorption and preferred orientations of proteins on the surface were observed.In dieser Arbeit wurde die Wirkungsweise von Anästhetika und die Adsorption von Proteinen an Festkörperoberflächen mittels Moleküldynamik-Simulationen untersucht. Es wird allgemein angenommen, dass Anästhetika auf biologische Membranen wirken. Umstritten ist jedoch, ob Anästhetika direkt an Membranproteine binden und damit deren Funktion hemmen, oder ob sie indirekt wirken, indem sie die physikalischen Eigenschaften der Lipiddoppelschicht der Membran verändern. Solche indirekten Effekte wurden in den hier vorgestellten Simulationen bei Anwesenheit von Alkanolen, einer Gruppe von Anästhetika, beobachtet. Gleichzeitig wurde eine durch Anästhetika verursachte Verschiebung des Gleichgewichts zwischen unterschiedlichen, vereinfacht dargestellten Proteinkonformationen gefunden. Simulationen eines in einer Lipiddoppelschicht eingebetteten Ionenkanals zeigten eine sehr geringe Konzentration von Alkanolen in unmittelbarer Nähe des Kanals. Diese Ergebnisse deuten auf eine indirekte Wirkungsweise von Anästhetika hin. Spontane Adsorption von Proteinen an fest-flüssig Grenzflächen ist der erste Schritt bei der Bildung von Biofilmen. Um diesen Prozess der Proteinadsorption mit hoher Auflösung auf ausreichend langen Zeit- und Längenskalen zu untersuchen, wurde ein "coarse-grained" Moleküldynamik-Schema verwendet. Es wurden Veränderungen in der Proteinstruktur und -dynamik und bevorzugte Ausrichtungen der Proteine auf der Oberfläche beobachtet

Poly-Sarcosine and Poly(ethylene-glycol) interactions with proteins investigated using molecular dynamics simulations

Nanoparticles coated with hydrophilic polymers often show a reduction in unspecific interactions with the biological environment, which improves their biocompatibility. The molecular determinants of this reduction are not very well understood yet, and their knowledge may help improving nanoparticle design. Here we address, using molecular dynamics simulations, the interactions of human serum albumin, the most abundant serum protein, with two promising hydrophilic polymers used for the coating of therapeutic nanoparticles, poly(ethylene-glycol) and poly-sarcosine. By simulating the protein immersed in a polymer-water mixture, we show that the two polymers have a very similar affinity for the protein surface, both in terms of the amount of polymer adsorbed and also in terms of the type of amino acids mainly involved in the interactions. We further analyze the kinetics of adsorption and how it affects the polymer conformations. Minor differences between the polymers are observed in the thickness of the adsorption layer, that are related to the different degree of flexibility of the two molecules. In comparison poly-alanine, an isomer of poly-sarcosine known to self-aggregate and induce protein aggregation, shows a significantly larger affinity for the protein surface than PEG and PSar, which we show to be related not to a different patterns of interactions with the protein surface, but to the different way the polymer interacts with water

Bovine serum albumin adsorption at a silica surface explored by simulation and experiment

Molecular details of BSA adsorption on a silica surface are revealed by fully atomistic molecular dynamics (MD) simulations (with a 0.5 μs trajectory), supported by dynamic light scattering (DLS), zeta potential, multiparametric surface plasmon resonance (MP-SPR), and contact angle experiments. The experimental and theoretical methods complement one another and lead to a wider understanding of the mechanism of BSA adsorption across a range of pH 3–9. The MD results show how the negatively charged BSA at pH7 adsorbs to the negatively charged silica surface, and reveal a unique orientation with preserved secondary and tertiary structure. The experiments then show that the protein forms complete monolayers at ∼ pH6, just above the protein’s isoelectric point (pH5.1). The surface contact angle is maximum when it is completely coated with protein, and the hydrophobicity of the surface is understood in terms of the simulated protein conformation. The adsorption behavior at higher pH > 6 is also consistently interpreted using the MD picture; both the contact angle and the adsorbed protein mass density decrease with increasing pH, in line with the increasing magnitude of negative charge on both the protein and the surface. At lower pH < 5 the protein starts to unfold, and the adsorbed mass dramatically decreases. The comprehensive picture that emerges for the formation of oriented protein films with preserved native conformation will help guide efforts to create functional films for new technologies

Molecular simulations of transport and separation in Protein crystals

Ph.DDOCTOR OF PHILOSOPH