Simulating Water-Protein Interactions
Milton T. W. Hearn, Ph.D., professor at Monash University and director of the Centre for Sustainable Chemical Manufacturing, delivered a keynote address entitled “Water—Why the Sudden Interest in its Use in RP, HIC and MM Bioseparations?” With the growing popularity of these novel separation techniques, there appears to be greater interest in understanding the potential effects, whether favorable or unfavorable, of water on the biomolecules being purified and their interactions with various chromatography resins, bead-based media, and solvents.
These interactions and effects can become particularly important when these processes are scaled up to industrial-scale bioseparations and bulk water is present in columns, resins, and buffers.
Dr. Hearn stated that water is fundamental in protein folding, mainly due to its role in defining hydrogen bonding and hydrophobic interactions: “water is indispensable for biomolecular recognition.” Water molecules “have an invaluable role in governing structure, stability, dynamics, and function,” he added.
Available data on water/protein-ligand molecular interactions have largely been extracted from protein crystallography and related spectroscopic databases. Previous studies have indicated that “water contributes to the exquisite specificity” of some highly complex protein-ligand surface complexes. In some cases water can also drive promiscuous (unfavorable) binding events.
Dr. Hearn explained why it is important to understand whether bulk water makes biomolecules, and proteins in particular, shrink, expand, or remain the same size as they would appear in their crystal structures.
He discussed the effects of interactions of ionic, ionizable, and non-ionic compounds with water, how these might change their bulk or atomistic structures, and how that could impact the separation of these molecules when they become solvated or dissolvated. Other parameters to consider are how the thermodynamics and mobilities of ligands and ligand-complexes are influenced by changes in water structure.
The information gained from these types of analyses is being used to carry out knowledge-based design of more advanced purification strategies and “smart” separation materials. The goal is to develop downstream processes with improved sustainability and mass intensification that allow industry to use water more efficiently, either alone or in combination with other solvents, or to eliminate the need for water in some methods, replacing it with nonaqueous media such as ionic liquids.
Dr. Hearn presented studies carried out by his research group that included a new computational method for rapidly determining the “wettability” of the atoms within a biomolecule, allowing the researchers to characterize its hydrophobicity at the atomic level. He also described the use of nanostructured chemical surfaces that change their hydrophobicity/hydrophilicity in a graded manner on application of an external stimulus.
In addition, Dr. Hearn’s team is identifying new classes of ligands from chemical library screens that tend to interact with biomolecules in a way that minimizes entropic disruption of tertiary or higher-order structure and yields favorable enthalpic changes.
Understanding water-protein interactions and the effects of water hydration forces is critical. Dr. Hearn’s group employs molecular dynamics simulations to understand dehydration events and determine energy potentials. Using a knowledge-based interactive approach, these simulations and the derived energy potentials can be used to generate models, which are used to determine whether the water molecules lead to structural reorganization, bulk structural rearrangement, or surface structural rearrangements and novel interactions.
The models can be generated based on pairwise interactions, in which each pair of residues is allowed to interact directly with a molecule. These interactions can derive from short-range contacts or from long-range contacts, in which water may become part of a folded protein structure, or may be excluded from a protein structure but still play a role in stabilizing the folded protein state.
Dr. Hearn noted that in addition to having short- vs. long-range interactions with biomolecules, it may also have short- vs. long-lived interactions, and it is important to understand the basis and impact of these multiple states of interaction.
In silico simulation of peptide or protein interactions in a chromatographic environment is useful for predicting what a downstream separation process might look like and how it might change by modifying various parameters. But it is still a simulation and the actual experiments need to follow. Experimental strategies may include synchroton-based analysis, utilizing x-ray, neutron diffraction, NOE-NMR, or femtosecond fluorescence measurements to reveal binding sites, structure, and dynamics of water at interfaces.
Dr. Hearn also spoke about the use of innovative 2D and 3D nanotechnology in which various surface configurations are designed and fabricated to produce confined systems in which water and proteins can interact and these interactions can be measured and analyzed.