@article{lindeboom_zhao_jackson_hall_galindo_2021, title={On the liquid demixing of water plus elastin-like polypeptide mixtures: bimodal re-entrant phase behaviour}, volume={23}, ISSN={["1463-9084"]}, DOI={10.1039/d0cp05013j}, abstractNote={Prediction of a new type of global phase diagram for water + ELP mixtures, featuring bimodal re-entrant liquid–liquid equilibrium.}, number={10}, journal={PHYSICAL CHEMISTRY CHEMICAL PHYSICS}, author={Lindeboom, Tom and Zhao, Binwu and Jackson, George and Hall, Carol K. and Galindo, Amparo}, year={2021}, month={Mar}, pages={5936–5944} }
 @article{zhao_stuart_hall_2017, title={Navigating in foldonia: Using accelerated molecular dynamics to explore stability, unfolding and self-healing of the beta-solenoid structure formed by a silk-like polypeptide}, volume={13}, ISSN={["1553-7358"]}, DOI={10.1371/journal.pcbi.1005446}, abstractNote={The β roll molecules with sequence (GAGAGAGQ)10 stack via hydrogen bonding to form fibrils which have been themselves been used to make viral capsids of DNA strands, supramolecular nanotapes and pH-responsive gels. Accelerated molecular dynamics (aMD) simulations are used to investigate the unfolding of a stack of two β roll molecules, (GAGAGAGQ)10, to shed light on the folding mechanism by which silk-inspired polypeptides form fibrils and to identify the dominant forces that keep the silk-inspired polypeptide in a β roll configuration. Our study shows that a molecule in a stack of two β roll molecules unfolds in a step-wise fashion mainly from the C terminal. The bottom template is found to play an important role in stabilizing the β roll structure of the molecule on top by strengthening the hydrogen bonds in the layer that it contacts. Vertical hydrogen bonds within the β roll structure are considerably weaker than lateral hydrogen bonds, signifying the importance of lateral hydrogen bonds in stabilizing the β roll structure. Finally, an intermediate structure was found containing a β hairpin and an anti-parallel β sheet consisting of strands from the top and bottom molecules, revealing the self-healing ability of the β roll stack.}, number={3}, journal={PLOS COMPUTATIONAL BIOLOGY}, author={Zhao, Binwu and Stuart, Martien A. Cohen and Hall, Carol K.}, year={2017}, month={Mar} }
 @article{zhao_stuart_hall_2016, title={Dock 'n roll: folding of a silk-inspired polypeptide into an amyloid-like beta solenoid}, volume={12}, ISSN={["1744-6848"]}, DOI={10.1039/c6sm00169f}, abstractNote={Polypeptides containing the motif ((GA)mGX)n occur in silk and have a strong tendency to self-assemble. For example, polypeptides containing (GAGAGAGX)n, where X = G or H have been observed to form filaments; similar sequences but with X = Q have been used in the design of coat proteins (capsids) for artificial viruses. The structure of the (GAGAGAGX)m filaments has been proposed to be a stack of peptides in a β roll structure with the hydrophobic side chains pointing outwards (hydrophobic shell). Another possible configuration, a β roll or β solenoid structure which has its hydrophobic side chains buried inside (hydrophobic core) was, however, overlooked. We perform ground state analysis as well as atomic-level molecular dynamics simulations, both on single molecules and on two-molecule stacks of the silk-inspired sequence (GAGAGAGQ)10, to decide whether the hydrophobic core or the hydrophobic shell configuration is the most stable one. We find that a stack of two hydrophobic core molecules is energetically more favorable than a stack of two hydrophobic shell molecules. A shell molecule initially placed in a perfect β roll structure tends to rotate its strands, breaking in-plane hydrogen bonds and forming out-of-plane hydrogen bonds, while a core molecule stays in the β roll structure. The hydrophobic shell structure has type II' β turns whereas the core configuration has type II β turns; only the latter secondary structure agrees well with solid-state NMR experiments on a similar sequence (GA)15. We also observe that the core stack has a higher number of intra-molecular hydrogen bonds and a higher number of hydrogen bonds between stack and water than the shell stack. Hence, we conclude that the hydrophobic core configuration is the most likely structure. In the stacked state, each peptide has more intra-molecular hydrogen bonds than a single folded molecule, which suggests that stacking provides the extra stability needed for molecules to reach the folded state.}, number={16}, journal={SOFT MATTER}, author={Zhao, Binwu and Stuart, Martien A. Cohen and Hall, Carol K.}, year={2016}, pages={3721–3729} }
 @article{zhao_li_yingling_hall_2016, title={LCST Behavior is Manifested in a Single Molecule: Elastin-Like polypeptide (VPGVG)n}, volume={17}, ISSN={["1526-4602"]}, url={https://publons.com/publon/9429675/}, DOI={10.1021/acs.biomac.5b01235}, abstractNote={The physical origin of the lower critical solution temperature (LCST) behavior of a variety of fluids, including elastin-like polypeptides (ELPs), has been studied for the past few decades. As is the case for polymer solutions, LCST behavior of ELPs is invariably reported for large systems of molecules and is considered evidence for collective behavior. In contrast, we find evidence for properties changes associated with LCST behavior in a single molecule by performing long atomic-level molecular dynamics simulation on the ELP sequences (Val-Pro-Gly-Val-Gly)n for four different length peptides over a wide range of temperatures. We observe a sharp transition in the number of hydrogen bonds between peptide and water and in the number of water molecules within the first hydration shell as temperature rises; this is used to locate the transition temperature. The dependence of the transition temperatures of ELPs on their lengths agrees well with experiments in that both have the same power law exponents. Our simulations reveal that the tendency for pentamers (VPGVG) in ELPs of all lengths to lose H-bonds with water or to gain H-bonds with themselves as temperature rises is independent of the length of the chain in which they are embedded. Thus, the transition temperature of ELPs in pure water is determined by two factors: the hydrogen bonding tendency of the pentamers and the number of pentamers per ELP. Moreover, the hydrogen bonding tendency of pentamers depends only on their sequences, not on the ELP chain length.}, number={1}, journal={BIOMACROMOLECULES}, publisher={American Chemical Society (ACS)}, author={Zhao, Binwu and Li, Nan K. and Yingling, Yaroslava G. and Hall, Carol K.}, year={2016}, month={Jan}, pages={111–118} }
 @article{xiao_zhao_yang_liang_ren_2016, title={Probe the Binding Mode of Aristololactam-beta-D-glucoside to Phenylalanine Transfer RNA in Silico}, volume={1}, ISSN={["2365-6549"]}, DOI={10.1002/slct.201600603}, abstractNote={Abstract}, number={17}, journal={CHEMISTRYSELECT}, author={Xiao, Xingqing and Zhao, Binwu and Yang, Li and Liang, Xiaodong and Ren, Yingqian}, year={2016}, month={Oct}, pages={5430–5439} }
 @article{xiao_zhao_agris_hall_2016, title={Simulation study of the ability of a computationally-designed peptide to recognize target tRNA(Lys3) and other decoy tRNAs}, volume={25}, ISSN={["1469-896X"]}, DOI={10.1002/pro.3056}, abstractNote={Abstract}, number={12}, journal={PROTEIN SCIENCE}, author={Xiao, Xingqing and Zhao, Binwu and Agris, Paul F. and Hall, Carol K.}, year={2016}, month={Dec}, pages={2243–2255} }
 @article{xiao_zhao_ren_2015, title={Effect of curvature on properties of diblock copolymers confined between two coaxial cylinders: 1. Layer thickness of a curved monolayer}, volume={633}, ISSN={["1873-4448"]}, DOI={10.1016/j.cplett.2015.05.016}, abstractNote={Strong segregation limited theory was employed to deduce the expression for free energy of a curved (A–B) monolayer that is a basic repeating unit in multi-layered concentric structure. The free energy of the monolayer in different curved conditions can be evaluated. Using such cylindrical confinement model, we examined the influences of asymmetry of diblock copolymers on the layer thickness of a curved monolayer. For the diblock copolymers of f = 0.4, the optimal thickness has a slight increase and then decrease as the curvature increases; while for f = 0.6, the optimal thickness has a continuous decrease as the curvature increases.}, journal={CHEMICAL PHYSICS LETTERS}, author={Xiao, Xingqing and Zhao, Binwu and Ren, Yingqian}, year={2015}, month={Jul}, pages={58–64} }
 @article{xiao_zhao_yang_ren_2015, title={Effect of curvature on properties of diblock copolymers confined between two coaxial cylinders: 2. Domain adjustment in a curved bilayer}, volume={639}, ISSN={["1873-4448"]}, DOI={10.1016/j.cplett.2015.10.032}, abstractNote={We study the phase behavior of diblock copolymers in a curved bilayer. Three aspects are discussed in detail: domain size distributions of the two adjacent monolayers within the film, optimal film thickness for a bilayer, and structural transition from a monolayer to a bilayer. One major finding is the determination of transition point in film thickness where the layer-type structure goes from monolayer to bilayer. At high confinement, the transition point increases as the curvature increases regardless of the symmetry of diblock copolymers. At low confinement, the transition point might increase or decrease, depending on the symmetry of diblock copolymers.}, journal={CHEMICAL PHYSICS LETTERS}, author={Xiao, Xingqing and Zhao, Binwu and Yang, Li and Ren, Yingqian}, year={2015}, month={Oct}, pages={326–334} }