First records of Sticta weigelii s.str. from Bolivia confirmed by molecular data

The first records of Sticta weigelii s.str. from Bolivia confirmed by molecular data are presented. The species is characterized by the presence of marginal isidia, which are darker than the thallus, usually cylindrical (not flattened), thin, dark brown to black lower tomentum and often partly yellow cyphellae. Previously, the presence of S. weigelii in Bolivia was based only on a morphological concept, encompassing various unrelated species, whereas the occurrence of S. weigelii s.str. was uncertain

Parmelia barrenoae and P. pinnatifida, two lichen species new to some European countries and Turkey

The first records of Parmelia barrenoae from Hungary, Slovakia and Sweden and P. pinnatifida from Denmark, Estonia and Turkey are presented

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

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

Steering protein adsorption at charged surfaces : electric fields and ionic screening

Protein adsorption at charged surfaces is a common process in the development of functional technological devices. Accurately reproducing the environment above the surface in simulations is essential for understanding how the adsorption process can be influenced and utilised. Here we present a simulation strategy that includes the electric field above the charged surface as well as the screening ions in solution, using standard molecular dynamics tools. With this approach we investigate the adsorption of Hen Egg White Lysozyme (HEWL) onto a model charged silica surface. We find that the screening effects of the ions slow down the adsorption process, giving the protein more time to find its optimal orientation as it adsorbs. Furthermore, we find that the concentrated ionic region directly above the surface helps to stabilise the protein structure in its adsorbed state. Together these effects imply that the adsorbed HEWL might retain its biological activity, with its active site exposed to solution rather than to the surface. Furthermore, this work shows how the steering effects of the electric field, coupled to the ionic screening, might be used to develop general strategies for surface functionalization through protein adsorption for technological applications

Critical role of tyrosine-20 in formation of gold nanoclusters within lysozyme : a molecular dynamics study

Lysozyme is one of the most commonly used proteins for encapsulating gold nanoclusters, yielding Ly-AuNC complexes. While possible applications of Ly-AuNCs in environmental, biological and trace metal sensing in solution have been demonstrated, there is currently a poor understanding of the physical characteristics of the Ly-AuNC complex. In this study we have employed fully atomistic molecular dynamics simulations to gain an understanding of the formation of Au clusters within the protein. It was found that in order to form AuNCs in the simulations, an approach of targeted insertion of Au atoms at a critical surface residue was needed. Tyrosine is known to be crucial for the reduction of Au salts experimentally, and our simulations showed that Tyr20 is the key residue for the formation of an AuNC beneath the protein surface in the α-helical domain. It is hoped these observations will aid future improvements and modification of Ly-AuNCs via alterations of the alpha-helix domain or Tyr20

Antibody-protein binding and conformational changes : identifying allosteric signalling pathways to engineer a better effector response

Numerous monoclonal antibodies have been developed successfully for the treatment of various diseases. Nevertheless, the development of biotherapeutic antibodies is complex, expensive, and time-consuming, and to facilitate this process, careful structural analysis beyond the antibody binding site is required to develop a more efficacious antibody. In this work, we focused on protein antigens, since they induce the largest antibody changes, and provide interesting cases to compare and contrast. The structures of 15 anti-protein antibodies were analysed to compare the antigen-bound/unbound forms. Surprisingly, three different classes of binding-induced changes were identified. In class (B1), the antigen binding fragment distorted significantly, and we found changes in the loop region of the heavy chain’s constant domain; this corresponds well with expected allosteric movements. In class (B2), we found changes in the same loop region without the overall distortion. In class (B3), these changes did not present, and only local changes at the complementarity determining regions were found. Consequently, structural analysis of antibodies is crucial for therapeutic development. Careful evaluation of allosteric movements must be undertaken to develop better effector responses, especially during the transformation of these antibodies from small fragments at the discovery stage to full antibodies at the subsequent development stages

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

Lysozyme adsorption at a silica surface using simulation and experiment : effects of pH on protein layer structure

Hen Egg White Lysozyme (HEWL) is a widely used exemplar to study protein adsorption on surfaces and interfaces. Here we use fully atomistic Molecular Dynamics (MD) simulations, Multi-Parametric Surface Plasmon Resonance (MP-SPR), contact angle and zeta potential measurements to study HEWL adsorption at a silica surface. The simulations provide a detailed description of the adsorption mechanism and indicate that at pH7 the main adsorption driving force is electrostatics, supplemented by weaker hydrophobic forces. Moreover, they reveal the preferred orientation of the adsorbed protein and show that its structure is only slightly altered at the interface with the surface. This provides the basis for interpreting the experimental results, which indicate the surface adsorbs a close-packed monolayer at about pH10 where the surface has a large negative zeta potential and the HEWL is positively charged. At higher pH, the adsorption amount of the protein layer is greatly reduced due to the loss of charge on the protein. At lower pH, the smaller zeta potential of the surface leads to lower HEWL adsorption. These interpretations are complemented by the contact angle measurements that show how the hydrophobicity of the surface is greatest when the surface coverage is highest. The simulations provide details of the hydrophobic residues exposed to solution by the adsorbed HEWL, completing the picture of the protein layer structure

Locating the nucleation sites for protein encapsulated gold nanoclusters : a molecular dynamics and fluorescence study

Fluorescent gold nanoclusters encapsulated by proteins have attracted considerable attention in recent years for their unique properties as new fluorescence probes for biological sensing and imaging. However, fundamental questions, such as the nucleation sites of gold nanoclusters within proteins and the fluorescence mechanism remain unsolved. Here we present a study of the location of gold nanoclusters within bovine serum albumin (BSA) combining both fully atomistic molecular dynamic (MD) simulations and fluorescence spectroscopic studies. The MD simulations show gold clusters growing close to a number of cysteine sites across all three domains of BSA, although just two major sites in domains IIB and IA were found to accommodate large clusters comprising more than 12 atoms. The dependence of the fluorescence on pH is found to be compatible with possible nucleation sites in domains IIB and IA. Furthermore, the energy transfer between tryptophan and gold nanoclusters reveals a separation of 29.7 Å, further indicating that gold nanoclusters were most likely located in the major nucleation site in domain IIB. The disclosure of the precise location of the gold nanoclusters and their surrounding amino acid residues should help better understanding of their fluorescence mechanism and aid their optimization as fluorescent nanoprobes