Complexation Mechanisms of Aqueous Amylose: Molecular Dynamics Study Using 3-Pentadecylphenol.

Molecular dynamics (MD) simulations of linear amylose fragments containing 10 to 40 glucose units were used to study the complexation of the prototypical compound, 3-pentadecylphenol (PDP)─a natural product with surfactant-like properties─in aqueous solution. The amylose-PDP binding leverages mainly hydrophobic interactions together with excluded volume effects. It was found that while the most stable complexes contained PDP inside the helical structure of the amylose in the expected guest-host (inclusion) complexation manner, at higher temperatures, the commonly observed PDP-amylose complexes often involved more nonspecific interactions than inclusion complexation. In the case where a stoichiometric excess of PDP was added to the simulation box, self-aggregation of the small molecule precluded its ability to enter the internal helical part of the oligosaccharide, and as a result, inclusion complexation became ineffective. MD simulation trajectories were analyzed preliminarily using cluster analysis (CA), followed by more rigorous solvent accessible surface area (SASA) determination over the temperature range spanning from 277 to 433 K. It was found that using the SASA of PDP corrected for its intrinsic conformational changes, together with a generic hidden Markov model (HMM), an adequate quantification of the different types of PDP-amylose aggregates was obtained to allow further analysis. The enthalpy change associated with the guest-host binding equilibrium constant (Kgh) in aqueous solution was estimated to be -75 kJ/mol, which is about twice as high as one might expect based on experimentally measured values of similar complexes in the solid state where the (unsolvated) helical structure of amylose remains rigid. On the other hand, the nonspecific binding (Kns) enthalpy change associated with PDP-amylose interactions in the same solution environment was found to be about half of the inclusion complexation value.

Nanoscale Simulation of Plastic Contaminants Migration in Packaging Materials and Potential Leaching into Model Food Fluids.

Polymers are the most commonly used packaging materials for nutrition and consumer products. The ever-growing concern over pollution and potential environmental contamination generated from single-use packaging materials has raised safety questions. Polymers used in these materials often contain impurities, including unreacted monomers and small oligomers. The characterization of transport properties, including diffusion and leaching of these molecules, is largely hampered by the long timescales involved in shelf life experiments. In this work, we employ atomistic molecular simulation techniques to explore the main mechanisms involved in the bulk and interfacial transport of monomer molecules from three polymers commonly employed as packaging materials: polyamide-6, polycarbonate, and poly(methyl methacrylate). Our simulations showed that both hopping and continuous diffusion play important roles in inbound monomer diffusion and that solvent-polymer compatibility significantly affects monomer leaching. These results provide rationalization for monomer leaching in model food formulations as well as bulky industry-relevant molecules. Through this molecular-scale characterization, we offer insights to aid in the design of polymer/consumer product interfaces with reduced risk of contamination and longer shelf life.

Molecular-Scale Exploration of Mechanical Properties and Interactions of Poly(lactic acid) with Cellulose and Chitin.

Poly(lactic acid) (PLA), one of the pillars of the current overarching displacement trend switching from fossil- to natural-based polymers, is often used in association with polysaccharides to increase its mechanical properties. However, the use of PLA/polysaccharide composites is greatly hampered by their poor miscibility, whose underlying nature is still vastly unexplored. This work aims to shed light on the interactions of PLA and two representative polysaccharide molecules (cellulose and chitin) and reveal structure-property relationships from a fundamental perspective using atomistic molecular dynamics. Our computational strategy was able to reproduce key experimental mechanical properties of pure and/or composite materials, reveal a decrease in immiscibility in PLA/chitin compared to PLA/cellulose associations, assert PLA-oriented polysaccharide reorientations, and explore how less effective PLA-polysaccharide hydrogen bonds are related to the poor PLA/polysaccharide miscibility. The connection between the detailed chemical interactions and the composite behavior found in this work is beneficial to the discovery of new biodegradable and natural polymer composite mixtures that can provide needed performance characteristics.

Exploring the Effects of Wetting and Free Fatty Acid Deposition on an Atomistic Hair Fiber Surface Model Incorporating Keratin-Associated Protein 5-1.

The complex development of cosmetic and medical formulations relies on an ever-growing accuracy of predictive models of hair surfaces. Hitherto, modeling efforts have focused on the description of 18-methyl eicosanoic acid (18-MEA), the primary fatty acid covalently attached to the hair surface, without explicit modeling of the protein layer. Herein, the molecular details of the outermost surface of the human hair fiber surface, also called the F-layer, were studied using molecular dynamics (MD) simulations. The F-layer is composed primarily of keratin-associated proteins KAP5 and KAP10, which are decorated with 18-MEA on the outer surface of a hair fiber. In our molecular model, we incorporated KAP5-1 and evaluated the surface properties of 18-MEA through MD simulations, resulting in 18-MEA surface density, layer thickness, and tilt angles in agreement with previous experimental and computational studies. Subsequent models with reduced 18-MEA surface density were also generated to mimic damaged hair surfaces. Response to wetting of virgin and damaged hair showed rearrangement of 18-MEA on the surface, allowing for water penetration into the protein layer. To demonstrate a potential use case for these atomistic models, we deposited naturally occurring fatty acids and measured 18-MEA's response in both dry and wet conditions. As fatty acids are often incorporated in shampoo formulations, this work demonstrates the ability to model the adsorption of ingredients on hair surfaces. This study illustrates, for the first time, the complex behavior of a realistic F-layer at the molecular level and opens up the possibility of studying the adsorption behavior of larger, more complex molecules and formulations.

Shearing friction behaviour of synthetic polymers compared to a functionalized polysaccharide on biomimetic surfaces: models for the prediction of performance of eco-designed formulations.

The substitution of natural, bio-based and/or biodegradable polymers for those of petrochemical origin in consumer formulations has become an active area of research and development as the sourcing and destiny of material components becomes a more critical factor in product design. These polymers often differ from their petroleum-based counterparts in topology, raw material composition and solution behaviour. Effective and efficient reformulation that maintains comparable cosmetic performance to existing products requires a deep understanding of the differences in frictional behaviour between polymers as a function of their molecular structure. In this work, we simulate the tribological behaviour of three topologically distinct polymers in solution with surfactants and in contact with hair-biomimetic patterned surfaces. We compare a generic functionalized polysaccharide to two performant polymers used in shampoo formulations: a strongly positively charged polyelectrolyte and a zwitterionic copolymer. Topological differences are expected to affect rheological properties, as well as their direct interaction with structured biological substrates. Using a refined Martini-style coarse-grained model we describe the polymer-dependent differences in aggregation behaviour as well as selective interactions with a biomimetic model hair surface. Additionally, we introduce a formalism to characterize the response of the solution to shear as an initial study on lubrication properties, which define the sensorial performance of these systems in cosmetics (i.e., manageability, touch, etc.). The tools and techniques presented in this work illustrate the strength of molecular simulation in eco-design of formulation as a complement to experiment. These efforts help advance our understanding of how we can relate complex atomic-scale solution behaviour to relevant macroscopic properties. We expect these techniques to play an increasingly important role in advancing strategies for green polymer formulation design by providing an understanding for how new polymers could reach and even exceed the level of performance of existing polymers.

Characterizing moisture uptake and plasticization effects of water on amorphous amylose starch models using molecular dynamics methods.

Dynamics and thermophysical properties of amorphous starch were explored using molecular dynamics (MD) simulations. Using the OPLS3e force field, simulations of short amylose chains in water were performed to determine force field accuracy. Using well-tempered metadynamics, a free energy map of the two glycosidic angles of an amylose molecule was constructed and compared with other modern force fields. Good agreement of torsional sampling for both solvated and amorphous amylose starch models was observed. Using combined grand canonical Monte Carlo (GCMC)/MD simulations, a moisture sorption isotherm curve is predicted along with temperature dependence. Concentration-dependent activation energies for water transport agree quantitatively with previous experiments. Finally, the plasticization effect of moisture content on amorphous starch was investigated. Predicted glass transition temperature (Tg) depression as a function of moisture content is in line with experimental trends. Further, our calculations provide a value for the dry Tg for amorphous starch, a value which no experimental value is available.

Effects of hypoxanthine substitution in peptide nucleic acids targeting KRAS2 oncogenic mRNA molecules: theory and experiment.

Genetic disorders can arise from single base substitutions in a single gene. A single base substitution for wild type guanine in the twelfth codon of KRAS2 mRNA occurs frequently to initiate lung, pancreatic, and colon cancer. We have observed single base mismatch specificity in radioimaging of mutant KRAS2 mRNA in tumors in mice by in vivo hybridization with radiolabeled peptide nucleic acid (PNA) dodecamers. We hypothesized that multimutant specificity could be achieved with a PNA dodecamer incorporating hypoxanthine, which can form Watson-Crick base pairs with adenine, cytosine, thymine, and uracil. Using molecular dynamics simulations and free energy calculations, we show that hypoxanthine substitutions in PNAs are tolerated in KRAS2 RNA:PNA duplexes where wild type guanine is replaced by mutant uracil or adenine in RNA. To validate our predictions, we synthesized PNA dodecamers with hypoxanthine, and then measured the thermal stability of RNA:PNA duplexes. Circular dichroism thermal melting results showed that hypoxanthine-containing PNAs are more stable in duplexes where hypoxanthine-adenine and hypoxanthine-uracil base pairs are formed than single mismatch duplexes or duplexes containing hypoxanthine-guanine opposition.

Tertiary and quaternary allostery in tetrameric hemoglobin from Scapharca inaequivalvis.

The clam Scapharca inaequivalvis possesses two cooperative oxygen binding hemoglobins in its red cells: a homodimeric HbI and a heterotetrameric A2B2 HbII. Each AB dimeric half of HbII is assembled in a manner very similar to that of the well-studied HbI. This study presents crystal structures of HbII along with oxygen binding data both in the crystalline state and in wet nanoporous silica gels. Despite very similar ligand-linked structural transitions observed in HbI and HbII crystals, HbII in the crystal or encapsulated in silica gels apparently exhibits minimal cooperativity in oxygen binding, in contrast with the full cooperativity exhibited by HbI crystals. However, oxygen binding curves in the crystal indicate the presence of a significant functional inequivalence of A and B chains. When this inequivalence is taken into account, both crystal and R state gel functional data are consistent with the conservation of a tertiary contribution to cooperative oxygen binding, quantitatively similar to that measured for HbI, and are in keeping with the structural information. Furthermore, our results indicate that to fully express cooperative ligand binding, HbII requires quaternary transitions hampered by crystal lattice and gel encapsulation, revealing greater complexity in cooperative function than the direct communication across a dimeric interface observed in HbI.

Molecular determinants of epidermal growth factor binding: a molecular dynamics study.

The epidermal growth factor receptor (EGFR) is a member of the receptor tyrosine kinase family that plays a role in multiple cellular processes. Activation of EGFR requires binding of a ligand on the extracellular domain to promote conformational changes leading to dimerization and transphosphorylation of intracellular kinase domains. Seven ligands are known to bind EGFR with affinities ranging from sub-nanomolar to near micromolar dissociation constants. In the case of EGFR, distinct conformational states assumed upon binding a ligand is thought to be a determining factor in activation of a downstream signaling network. Previous biochemical studies suggest the existence of both low affinity and high affinity EGFR ligands. While these studies have identified functional effects of ligand binding, high-resolution structural data are lacking. To gain a better understanding of the molecular basis of EGFR binding affinities, we docked each EGFR ligand to the putative active state extracellular domain dimer and 25.0 ns molecular dynamics simulations were performed. MM-PBSA/GBSA are efficient computational approaches to approximate free energies of protein-protein interactions and decompose the free energy at the amino acid level. We applied these methods to the last 6.0 ns of each ligand-receptor simulation. MM-PBSA calculations were able to successfully rank all seven of the EGFR ligands based on the two affinity classes: EGF>HB-EGF>TGF-α>BTC>EPR>EPG>AR. Results from energy decomposition identified several interactions that are common among binding ligands. These findings reveal that while several residues are conserved among the EGFR ligand family, no single set of residues determines the affinity class. Instead we found heterogeneous sets of interactions that were driven primarily by electrostatic and Van der Waals forces. These results not only illustrate the complexity of EGFR dynamics but also pave the way for structure-based design of therapeutics targeting EGF ligands or the receptor itself.

Adaptation to tRNA acceptor stem structure by flexible adjustment in the catalytic domain of class I tRNA synthetases.

Class I aminoacyl-tRNA synthetases (aaRSs) use a Rossmann-fold domain to catalyze the synthesis of aminoacyl-tRNAs required for decoding genetic information. While the Rossmann-fold domain is conserved in evolution, the acceptor stem near the aminoacylation site varies among tRNA substrates, raising the question of how the conserved protein fold adapts to RNA sequence variations. Of interest is the existence of an unpaired C-A mismatch at the 1-72 position unique to bacterial initiator tRNA(fMet) and absent from elongator tRNAs. Here we show that the class I methionyl-tRNA synthetase (MetRS) of Escherichia coli and its close structural homolog cysteinyl-tRNA synthetase (CysRS) display distinct patterns of recognition of the 1-72 base pair. While the structural homology of the two enzymes in the Rossmann-fold domain is manifested in a common burst feature of aminoacylation kinetics, CysRS discriminates against unpaired 1-72, whereas MetRS lacks such discrimination. A structure-based alignment of the Rossmann fold identifies the insertion of an α-helical motif, specific to CysRS but absent from MetRS, which docks on 1-72 and may discriminate against mismatches. Indeed, substitutions of the CysRS helical motif abolish the discrimination against unpaired 1-72. Additional structural alignments reveal that with the exception of MetRS, class I tRNA synthetases contain a structural motif that docks on 1-72. This work demonstrates that by flexible insertion of a structural motif to dock on 1-72, the catalytic domain of class I tRNA synthetases can acquire structural plasticity to adapt to changes at the end of the tRNA acceptor stem.

Three dimensional projection environment for molecular design and surgical simulation.

We are developing agents for positron emission tomography (PET) imaging of cancer gene mRNA expression and software to fuse mRNA PET images with anatomical computerized tomography (CT) images to enable volumetric (3D) haptic (touch-and-feel) simulation of pancreatic cancer and surrounding organs prior to surgery in a particular patient. We have identified a novel ligand specific for epidermal growth factor receptor (EGFR) to direct PET agent uptake specifically into cancer cells, and created a volumetric haptic surgical simulation of human pancreatic cancer reconstructed from patient CT data. Young's modulus and the Poisson ratio for each tissue will be adjusted to fit the experience of participating surgeons.