•Use of steered molecular dynamics to determine molecular binding trajectory in a protein•Comparison of umbrella sampling and jarzynski equality methods for validation•Systematic test of effect of restraints on calculated binding free energy•Comparison of calculated binding free energy with experiment in dehaloperoxidase•General method applicable to full range of substrates and inhibitors that bind to dehaloperoxidaseThe binding free energy of 4-bromophenol (4-BP), an inhibitor that binds in the internal binding site in dehaloperoxidase-hemoglobin (DHP) was calculated using Molecular Dynamics (MD) methods combined with pulling or umbrella sampling. The effects of systematic changes in the pulling speed, pulling force constant and restraint force constant on the calculated potential of mean force (PMF) are presented in this study. The PMFs calculated using steered molecular dynamics (SMD) were validated by umbrella sampling (US) in the strongly restrained regime. A series of restraint force constants ranging from 1000 down to 5 kJ/(mol nm2) were used in SMD simulations. This range was validated using US, however noting that weaker restraints give rise to a broader sampling of configurations. This comparison was further tested by a pulling simulation conducted without any restraints, which was observed to have a value closest to the experimentally measured free energy for binding of 4-BP to DHP based on ultraviolet–visible (UV–vis) and resonance Raman spectroscopies. The protein-inhibitor system is well suited for fundamental study of free energy calculations because the DHP protein is relatively small and the inhibitor is quite rigid. Simulation configuration structures are compared to the X-ray crystallography structures of the binding site of 4-BP in the distal pocket above the heme.

The interactions between proteins and functional biomaterials under different physical and environmental conditions need to be understood when designing biomedical devices. Herein, we present a molecular dynamics simulation study of the fragment antigen-binding (Fab) of trastuzumab (a monoclonal antibody) and its complex with a peptide-modified polyvinyl alcohol (PVA) hydrogel at different pH values. Consistent with experiments, PVA when modified by charged ligands does shrink as a direct response to a drop in the pH. The protein maintains a stable conformation when adsorbed on the hydrogel matrix with a varied pH, showing no signs of denaturation in all simulated systems, suggesting that peptide-grafted PVA is a good biocompatible material. Under neutral conditions, the hydrogel alone stabilizes the interactions between the protein and the peptide ligands. Strikingly under acidic conditions the protein–ligand interactions are disrupted by a collective protonation of ligands. A sharp decrease in the interaction energies, accompanied by the sudden increase of the protein–ligand distance, indicates a rapid pH response in the protein–hydrogel complex. This will be important in protein delivery and purification. The effect of pH on the interactions and the dynamics of the protein and the sudden pH response of the hydrogel at the atomic level present a new functional perspective in developing new hydrogels with desirable properties.

Defective rutile TiO2 (110) surfaces with one bridging-oxygen vacancy pair (OVP) and two next nearest neighbored bridging-oxygen vacancies belonging to the same row (NNN-OVs, i.e., two bridging-oxygen vacancies separated by a single oxygen atom) were studied using density functional theory (DFT) calculations. The results of a perfect surface and a defective surface with single bridging-oxygen vacancy (OV) were also shown. The reactivity of these surfaces was investigated by studying their interaction with a water molecule. Results show the NNN-OVs site is the most favorable site for water adsorption of two modes, molecular and dissociated adsorption, especially for dissociated adsorption. Upon dissociated adsorption on the NNN-OVs site, the whole system would release energy of 2.07 eV, much more than the energy released in any other site. It indicates the high reactivity of NNN-OVs as the best trap center. The 5-fold Ti sites show similar behaviors despite the existence of different defects. Adsorption on this site is the least stable, and molecular adsorption is favored. A water molecule needs to overcome energy barriers of 0.25–0.27 eV to dissociate on 5-fold Ti atoms. However, the recombination barrier is even lower, and the fragments would recombine and exist stably in the molecular mode. Slightly higher barriers are observed on the defective sites.

•OVP site is the most stable site for CH3OH adsorption.•OVP site is not the most active site for CH3OH dissociation.•CH3OH on OVP vs. single OV is different from O2 on OVP vs. single OV.•Different 5-fold Ti sites show similar behaviors.•5-Fold Ti sites are not suitable sites for CH3OH adsorption.The interaction between methanol and the rutile TiO2 (1 1 0) surface with bridging oxygen-vacancy pairs (OVPs) defects is studied with DFT method. The OVP is the most stable site for adsorption of molecular methanol and dissociated fragments, but not the most active one for dissociation process since OVP exhibits slightly higher energy barrier than single bridging oxygen vacancy. In addition, the defect of OVP does not have significantly different influence on the adsorption structure and dissociation process of adsorbed methanol on 5-fold Ti atoms at diverse positions: close to the vacancy or a little further from the vacancy.

The interaction between protein molecules and the hydroxyapatite (HAP) crystal is an important research topic in many fields. However, the nature of their noncovalent bonding is still not clear at the atomic level. In this work, molecular dynamics simulation, steered molecular dynamics simulation, and quantum chemistry calculations were used to study the adsorption-desorption dynamics of BMP-2 on HAP (001) surface. The results suggest that there are three types of functional groups through which BMP-2 can interact with HAP crystallite, and they are −OH, −NH2, and −COO−. Based on the different orientations of protein, each might interact with HAP crystallite individually, or, two or three of them can work cooperatively. Concerning the mechanisms of interaction, it is found that the water-bridged H-bond plays an important role, which is the main force for groups without net charges. If there were more than one set of adsorption groups for a certain orientation of protein, the adsorption-desorption process would likely be stepwise. On the contrary, if there were only one set, there would be only the key-adsorption period. The results of density functional theory calculations confirm the actual existence of this type of water-bridged H-bond. Furthermore, it is also found that the CHARMM27 force field could provide correct structural information qualitatively, although the data are slightly different from those obtained by UB3LYP/6-31G* method.

The interactions between proteins and functional biomaterials under different physical and environmental conditions need to be understood when designing biomedical devices. Herein, we present a molecular dynamics simulation study of the fragment antigen-binding (Fab) of trastuzumab (a monoclonal antibody) and its complex with a peptide-modified polyvinyl alcohol (PVA) hydrogel at different pH values. Consistent with experiments, PVA when modified by charged ligands does shrink as a direct response to a drop in the pH. The protein maintains a stable conformation when adsorbed on the hydrogel matrix with a varied pH, showing no signs of denaturation in all simulated systems, suggesting that peptide-grafted PVA is a good biocompatible material. Under neutral conditions, the hydrogel alone stabilizes the interactions between the protein and the peptide ligands. Strikingly under acidic conditions the protein–ligand interactions are disrupted by a collective protonation of ligands. A sharp decrease in the interaction energies, accompanied by the sudden increase of the protein–ligand distance, indicates a rapid pH response in the protein–hydrogel complex. This will be important in protein delivery and purification. The effect of pH on the interactions and the dynamics of the protein and the sudden pH response of the hydrogel at the atomic level present a new functional perspective in developing new hydrogels with desirable properties.