Characterization of the conformation changes of catechins.

<p>The distances among the rings of catechins in the optimized structure (a, b, c and d) and their average distances calculated from MD trajectories (a′, b′, c′ and d′). (a and a′) EC; (b and b′) EGC; (c and c′) ECG; (d and d′) EGCG.</p

Estimation of MD simulation equilibration and analysis of the stability of protein structure.

<p>Time evolutions of a) the backbone RMSD and b) the radius of gyration (<i>R</i>_<i>g</i>) of trypsin in MD simulations. Black color indicates trypsin in catechin-free form; red, blue, dark-cyan and magenta indicate trypsin in the complex with EC, ECG, EGC and EGCG, respectively.</p

Characterization of residues flexibility.

<p>The Cα B-factor for each residue in trypsin computed from MD simulation trajectories in the form of catechin-free (black) and complex with EC (red), ECG (blue), EGC (dark-cyan) and EGCG (magenta), respectively. The orange line represents the Cα B-factor from PDB file. The wiring diagram shows the secondary structure of trypsin. The bar chart at the bottom of picture shows the distance range of the Cα atom to the nearest heavy atom of catechins. The inset enlarges the sequence motifs in the S1 pocket.</p

Analysis of contributions of each component in binding free energy.

<p>Comparison of the binding free energy components of trypsin binding with EC (red), EGC (blue), ECG (dark cyan) and EGCG (magenta).</p

The binding affinity from semi-flexible docking (kcal/mol) and the possibility (in parenthesis) of four types of catechins and their chemical groups binding to the S1 pocket of trypsin.

<p>^a The possibility of ligand binding to the S1 pocket.</p><p>^b The possibility of different groups in each ligand binding to the S1 pocket.</p><p>The binding affinity from semi-flexible docking (kcal/mol) and the possibility (in parenthesis) of four types of catechins and their chemical groups binding to the S1 pocket of trypsin.</p

Representative trypsin-catechin complex structures.

<p>Representative structure models clustered from MD simulation trajectories for trypsin complex with a) EC, b) EGC, c) ECG and d) EGCG. Catechins are shown as ball-and-stick model, trypsin as cartoon. The catalytic triad (Asp102, His57, Ser195) is shown in stick. Residues interact with catechins by hydrogen bond and hydrophobic interaction highlighted by lines.</p

Assembled Structures of Perfluorosulfonic Acid Ionomers Investigated by Anisotropic Modeling and Simulations

Nafion, a classic of perfluorosulfonic acid ionomers, has broad applications in proton conduction, attributed from the unique structures. However, a satisfactory structure model from theoretical calculation and simulation that can match with the well-known experimental observations is still absent. We performed GPU-accelerated molecular dynamics simulations to investigate the assembled structures of Nafion at different water contents based on an anisotropic coarse-grained model equipped with Gay–Berne potential. Accurate parameters for the coarse-grained model are collected by matching energy profiles based on density functional theory calculations. The results show that the hydrophilic phase in Nafion assemblies undergoes a crossover from isolated spherical clusters to interconnected cluster/channel networks with the increase of water content. We found the crystalline domains in polymer matrix and they are suppressed at elevated water content. These microphase-separated structures achieve quantitative agreement with existing experimental observations, including morphologies from electron microscopy and intensity profiles from scattering experiments. This work suggests that accurate consideration of the anisotropy is a key to reveal the formation of unique assembled structures of perfluorosulfonic acid ionomers at different water contents

Crystalline Regio-/Stereoregular Glycine-Bearing Polymers from ROMP: Effect of Microstructures on Materials Performances

Synthesis of amino acid or peptide-bearing polymers with controlled microstructures is still a long-going challenge in polymer chemistry in contrast to natural biopolymers with exactly controlled microstructures like proteins and DNA. Here, a series of new glycine-substituted cyclooctenes monomers were designed and synthesized. Ring-opening metathesis polymerizations (ROMP) of all 3-substituted monomers with Grubbs second-generation catalyst afford glycine-bearing polymers with high head-to-tail regioregularity and high <i>trans</i>-stereoregularity, whereas ROMP of 5-substituted monomers is neither regio- nor stereoselective. Theoretical study revealed that sterically cumbersome glycine substituent in the 3-position is crucial for the high regio- and stereochemistry in the polymerization. Of importance, differential scanning calorimetry and wide-angle X-ray scattering measurements show that unsaturated 3-substituted polymers are semicrystalline due to their high degrees of structure regularity and the strong hydrogen-bonding interactions between glycine side-chains. Such obvious crystallization behaviors before the saturation of the backbone will facilitate its future applications as biomimetic materials. Moreover, 3-substituted polymers with high <i>trans</i>-HT regularity exhibit much bigger water contact angle and higher cloud point than its random 5-substituted analogues, indicating that structure regularity of these glycine-bearing polymers can decide the surface hydrophilicity and thermoresponsive behaviors. These results demonstrate the dependence of glycine-bearing polymer properties on their microstructures. Finally, the less reactive internal <i>trans</i>-double bonds of the polymers undergo thiol–ene addition effectively, allowing the preparation of regiospecific glycine-bearing polymers with a range of features in a facile way

Spearman correlation coefficients between the discrepancy functions (χ) and RMSD.

<p>The correlations are estimated based on 22,5000 decoys generated in the forward MD simulations. The discrepancy function with ten different forms are for q_max = 0.6 Å^-1.</p

Sampling performance of the MD-MC method in five representative trajectories.

<p>The time evolution of RMSD_T for MD-MC (solid line) and MD (dash line), the time evolution of χ_T, as well as 3D structures and SAXS profiles of the initial (I), the target (T) and closest (C) structures for trajectories of Poly-Asn, Poly-Phe, Poly-Pro, Poly-Ala and Poly-Ser are presented.</p