Conformational transition free energy profiles of an adsorbed, lattice model protein by multicanonical Monte Carlo simulation

The effects of tether placement on antibody stability on surfaces

Despite their potential benefits, antibody microarrays have fallen short of performing reliably and have not found widespread use outside of the research setting. Experimental techniques have been unable to determine what is occurring on the surface of an atomic level, so molecular simulation has emerged as the primary method of investigating protein/surface interactions. Simulations of small proteins have indicated that the stability of the protein is a function of the residue on the protein where a tether is placed. The purpose of this research is to see whether these findings also apply to antibodies, with their greater size and complexity. To determine this, 24 tethering locations were selected on the antibody Protein Data Bank (PDB) ID: 1IGT. Replica exchange simulations were run on two different surfaces, one hydrophobic and one hydrophilic, to determine the degree to which these tethering sites stabilize or destabilize the antibody. Results showed that antibodies tethered to hydrophobic surfaces were in general less stable than antibodies tethered to hydrophilic surfaces. Moreover, the stability of the antibody was a function of the tether location on hydrophobic surfaces but not hydrophilic surfaces.

Rapid detection and differentiation of carp oedema virus and cyprinid herpes virus-3 in koi and common carp

Carp oedema virus (CEV) and koi herpes virus (KHV) are of major concern to common carp breeders and koi enthusiasts worldwide. The viruses cause diseases that exhibit similar external signs; thus, it is difficult to distinguish between them clinically. In this study, we developed and optimized rapid and accurate single- and multiplex isothermal diagnostic tools, based on recombinase polymerase amplification (RPA), for detection and differentiation of CEV and KHV. The assays were combined with a lateral flow dipstick to enable visual detection of amplification products and simplify post-amplification analysis. Both CEV- and KHV-RPA assays were specific for their target virus. The lower detection limits of the assays were similar to those of established diagnostic PCR tests for the viruses. A sample preparation method was optimized to eliminate the need for total DNA extraction from fish tissues. The estimated time to perform these RPA assays, from receiving the sample to having a result, is 50 min, compared to 10 and 7 hr for CEV- and KHV-PCR tests, respectively. The assays can be performed in field situations to improve screening of fish and reduce spread of these viruses and thereby enhance the common carp and koi industries.

Interplay of Coil-Globule Transition and Surface Adsorption of a Lattice HP Protein Model

An end-grafted hydrophobic-polar (HP) model protein chain with alternating H and P monomers is studied to examine interactions between the critical adsorption transition due to surface attraction and the collapse transition due to pairwise attractive H–H interactions. We find that the critical adsorption phenomenon can always be observed; however, the critical adsorption temperature T_CAP is influenced by the attractive H–H interactions in some cases. When the collapse temperature T_c is lower than T_CAP, the critical adsorption of the HP chain is similar to that of a homopolymer without intrachain attractions and T_CAP remains unchanged, whereas the collapse transition is suppressed by the adsorption. In contrast, for cases where T_c is close to or higher than T_CAP, T_CAP of the HP chain is increased, indicating that a collapsed chain is more easily adsorbed on the surface. The strength of the H–H attraction also influences the statistical size and shape of the polymer, with strong H–H attractions resulting in adsorbed and collapsed chains adopting two-dimensional, circular conformations.

Generic folding and transition hierarchies for surface adsorption of hydrophobic-polar lattice model proteins

The thermodynamic behavior and structural properties of hydrophobic-polar (HP) lattice proteins interacting with attractive surfaces are studied by means of Wang-Landau sampling. Three benchmark HP sequences (48mer, 67mer, and 103mer) are considered with different types of surfaces, each of which attract either all monomers, only hydrophobic (H) monomers, or only polar (P) monomers, respectively. The diversity of folding behavior in dependence of surface strength is discussed. Analyzing the combined patterns of various structural observables, such as, e.g., the derivatives of the numbers of surface contacts, together with the specific heat, we are able to identify generic categories of folding and transition hierarchies. We also infer a connection between these transition categories and the relative surface strengths, i.e., the ratio of the surface attractive strength to the interchain attraction among H monomers. The validity of our proposed classification scheme is reinforced by the analysis of additional benchmark sequences. We thus believe that the folding hierarchies and identification scheme are generic for HP proteins interacting with attractive surfaces, regardless of chain length, sequence, or surface attraction.

Surface treatment of polymeric materials controlling the adhesion of biomolecules

This review describes different strategies of surface elaboration for a better control of biomolecule adsorption. After a brief description of the fundamental interactions between surfaces and biomolecules, various routes of surface elaboration are presented dealing with the attachment of functional groups mostly thanks to plasma techniques, with the grafting to and from methods, and with the adsorption of surfactants. The grafting of stimuli-responsive polymers is also pointed out. Then, the discussion is focused on the protein adsorption phenomena showing how their interactions with solid surfaces are complex. The adsorption mechanism is proved to be dependent on the solid surface physicochemical properties as well as on the surface and conformation properties of the proteins. Different behaviors are also reported for complex multiple protein solutions.

Conformational transitions of adsorbed proteins on surfaces of varying polarity

Combining a wide range of protein adsorption experiments (three globular proteins on eight well-defined homogeneous surfaces) with Monte Carlo simulations of lattice proteins at different concentrations and on surfaces of varying "polarity", we explore the extent and rheological behavior of adsorbed proteins as a function of substrate polarity, "on" rate constants (k(a)) and steric parameters (|A(1)|) from the random sequential adsorption model, and demonstrate a folding to unfolding transition upon adsorption. We show that model globular proteins (hen egg lysozyme, ribonuclease A, and insulin dimer) behave similarly with respect to adsorption. Experimentally, above a substrate wettability cos theta > 0.4 (where theta is the sessile contact angle of water on a substrate in air), the adsorbed mass, rigidity, and k(a) of the proteins are diminished, while the steric factor |A(1)| is increased, suggesting a lower packing density. To analyze these results, we have invoked computer simulations. We show that changing surface polarity has two profound effects. First, the amount adsorbed increases as the surfaces become more apolar. Further, the proteins become less stable as their adsorbed amount increased because they gain a large number of interprotein and protein-surface interactions. Finally, apolar surfaces served to reduce the unfolding free energy barriers, further facilitating the reorganizing of proteins on these surfaces. Thus, increasing the nonpolar nature of the surfaces resulted in a more rigid adsorbed layer, in good agreement with the experiments.