ProtPOS: a python package for the prediction of protein preferred orientation on a surface

β-Glucosidase on clay minerals: Structure and function in the synthesis of octyl glucoside

β-Glucosidase is a biological macromolecule that catalyzes the hydrolysis of various glycosides and oligosaccharides. It may also be used to catalyze the synthesis of glycosides under suitable conditions. Carrier-bound β-glucosidase can enhance the enzymatic activity in the synthesis of glycosides in organic solvent solutions, although the molecular mechanism regulating activity is yet unknown. This study investigated the impact of utilizing montmorillonite (Mmt), attapulgite (Attp), and kaolinite (Kao) as carriers on the activity of β-glucosidase from Prunus dulcis (PdBg). When Attp was used as carriers, the molecular dynamic (MD) simulations found the distance between pNPG and the active site residues E183 and E387 was minimally impacted by the adsorptions, hence PdBg maintained about 81.3 ± 0.89 % of its native activity. Out of the three clay minerals, the relative activity of PdBg loaded on Mmt was the lowest because of the highest electrostatic energy. The substrate channel of PdBg on Kao is directed towards the surface, limiting the accessibility of substrates. Secondary structure and conformation studies revealed that the conformational stability of PdBg in solvent solutions was enhanced by coupling to Attp. Unlike dimethyl sulfoxide (DMSO), N,N-dimethylformamide (DMF) and 1,2-dimethoxyethane (DME), tert-butanol (t-BA) did not penetrate into the active site of PdBg interfering with its binding to the substrate. The maximum yield of n-octyl-β-glucoside (OGP) synthesis catalyzed by Attp-immobilized PdBg reached 48.3 %.

Insights into graphene oxide interaction with human serum albumin in isolated state and in blood plasma

The interactions of graphene oxide (GO), a 2-dimensional nanomaterial with hydrophilic edges, hydrophobic basal plane and large flat surfaces, with biological macromolecules, are of key importance for the development of novel nanomaterials for biomedical applications. To gain more insight into the interaction of GO flakes with human serum albumin (HSA), we examined GO binding to HSA in its isolated state and in blood plasma. Calorimetric data reveal that GO strongly stabilizes free isolated HSA against a thermal challenge at low ionic strength, indicating strong binding interactions, confirmed by the drop in ζ-potential of the HSA/GO assemblies compared to bare GO flakes. However, calorimetry also revealed that the HSA-GO molecular interaction is hampered in blood plasma, the ionic strength being particularly important for the interactions. Molecular modelling calculations are in full concert with these experimental findings, indicating a considerably higher binding affinity for HSA to GO in its partially unfolded state, characteristic to low-ionic-strength environment, than for the native protein conformation, observed under physiological conditions. Therefore, for the first time we demonstrate an impeded interaction between HSA and GO nanoflakes in blood plasma, and suggest that the protein is protected from the plausible toxic effects of GO under native conditions.

Colloidal graphene oxide enhances the activity of a lipase and protects it from oxidative damage: Insights from physicochemical and molecular dynamics investigations

Physical adsorption of lipase from Thermomyces lanuginosus onto single-layer sheets of graphene oxide (GO) was studied using the response surface methodology to evaluate the physicochemical factors - temperature, pH, ionic strength, and concentration - affecting the enzymatic activity and the immobilization efficiency. The immobilization efficiency and the activity of the enzyme were inversely proportional to each other. Specifically, higher pH values increased the immobilization efficacy, but produced changes in the aggregation state and secondary structure of the enzyme, thus decreasing its activity. Lower pH values, in turn, reduced the immobilization efficacy, but increased the activity of the adsorbed lipase. The adsorbed and the free lipase were followed during 600 ns and 3.5 μs, respectively, in molecular dynamics (MD) simulations. MD trajectories showed that irreversible adsorption freezes the enzyme in a state with a correctly opened catalytic cavity, while the active site remains without a direct interaction with the GO adsorbent. In contrast to the interfacial activation of lipases in a hydrophobic environment, where the catalytic pocket attaches to the hydrophobic surface, the adsorption onto GO made the active site of the lipase accessible by altering the tertiary structure of the enzyme, leading to a higher catalytic efficiency. Experimental investigations confirmed that the physical adsorption onto GO induces tertiary structure changes in the lipase and protects it from H₂O₂ by accepting the oxidative damage upon itself. In summary, the physical adsorption of the lipase onto GO is mainly affected by pH and could possibly provide a spreadable and robust catalytic interface for biotechnological applications.

Refined Empirical Force Field to Model Protein-Self-Assembled Monolayer Interactions Based on AMBER14 and GAFF

Understanding protein interaction with material surfaces is important for the development of nanotechnological devices. The structures and dynamics of proteins can be studied via molecular dynamics (MD) if the protein-surface interactions can be accurately modeled. To answer this question, we computed the adsorption free energies of peptides (representing eleven different amino acids) on a hydrophobic self-assembled monolayer (CH₃-SAM) and compared them to the benchmark experimental data set. Our result revealed that existing biomolecular force fields, GAFF and AMBER ff14sb, cannot reproduce the experimental peptide adsorption free energies by Wei and Latour (Langmuir, 2009, 25, 5637-5646). To obtain the improved force fields, we systematically tuned the Lennard-Jones parameters of selected amino acid sidechains and the functional group of SAM with repeated metadynamics and umbrella sampling simulations. The final parameter set has yielded a significant improvement in the free energy values with R = 0.83 and MSE = 0.65 kcal/mol. We applied the refined force field to predict the initial adsorption orientation of lysozyme on CH₃-SAM. Two major orientations-face-down and face-up-were predicted. Our analysis on the protein structure, solvent accessible surface area, and binding of native ligand NAG₃ suggested that lysozyme in the face-up orientation can remain active after initial adsorption. However, because of its weaker affinity (ΔΔG = 7.86 kcal/mol) for the ligand, the bioactivity of the protein is expected to reduce. Our work facilitates the use of MD for the study of protein-SAM systems. The refined force field compatible with GROMACS is available at https://cbbio.cis.um.edu.mo/software/SAMFF .

Controlling Redox Enzyme Orientation at Planar Electrodes

Redox enzymes, which catalyze reactions involving electron transfers in living organisms, are very promising components of biotechnological devices, and can be envisioned for sensing applications as well as for energy conversion. In this context, one of the most significant challenges is to achieve efficient direct electron transfer by tunneling between enzymes and conductive surfaces. Based on various examples of bioelectrochemical studies described in the recent literature, this review discusses the issue of enzyme immobilization at planar electrode interfaces. The fundamental importance of controlling enzyme orientation, how to obtain such orientation, and how it can be verified experimentally or by modeling are the three main directions explored. Since redox enzymes are sizable proteins with anisotropic properties, achieving their functional immobilization requires a specific and controlled orientation on the electrode surface. All the factors influenced by this orientation are described, ranging from electronic conductivity to efficiency of substrate supply. The specificities of the enzymatic molecule, surface properties, and dipole moment, which in turn influence the orientation, are introduced. Various ways of ensuring functional immobilization through tuning of both the enzyme and the electrode surface are then described. Finally, the review deals with analytical techniques that have enabled characterization and quantification of successful achievement of the desired orientation. The rich contributions of electrochemistry, spectroscopy (especially infrared spectroscopy), modeling, and microscopy are featured, along with their limitations.