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1. Properties of protein unfolded states suggest broad selection for expanded conformational ensembles

   https://doi.org/10.1073/pnas.2003773117  

   Bowman, Micayla A. ; Riback, Joshua A. ; Rodriguez, Anabel ; Guo, Hongyu ; Li, Jun ; Sosnick, Tobin R. ; Clark, Patricia L. ( September 2020 , Proceedings of the National Academy of Sciences)

   Much attention is being paid to conformational biases in the ensembles of intrinsically disordered proteins. However, it is currently unknown whether or how conformational biases within the disordered ensembles of foldable proteins affect function in vivo. Recently, we demonstrated that water can be a good solvent for unfolded polypeptide chains, even those with a hydrophobic and charged sequence composition typical of folded proteins. These results run counter to the generally accepted model that protein folding begins with hydrophobicity-driven chain collapse. Here we investigate what other features, beyond amino acid composition, govern chain collapse. We found that local clustering of hydrophobic and/or charged residues leads to significant collapse of the unfolded ensemble of pertactin, a secreted autotransporter virulence protein fromBordetella pertussis, as measured by small angle X-ray scattering (SAXS). Sequence patterns that lead to collapse also correlate with increased intermolecular polypeptide chain association and aggregation. Crucially, sequence patterns that support an expanded conformational ensemble enhance pertactin secretion to the bacterial cell surface. Similar sequence pattern features are enriched across the large and diverse family of autotransporter virulence proteins, suggesting sequence patterns that favor an expanded conformational ensemble are under selection for efficient autotransporter protein secretion, a necessary prerequisite for virulence. Moremore »broadly, we found that sequence patterns that lead to more expanded conformational ensembles are enriched across water-soluble proteins in general, suggesting protein sequences are under selection to regulate collapse and minimize protein aggregation, in addition to their roles in stabilizing folded protein structures.

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2. The function of peptide-mimetic anionic groups and salt bridges in the antimicrobial activity and conformation of cationic amphiphilic copolymers

   https://doi.org/10.1039/D1RA02730A  

   Bhat, Rajani ; Foster, Leanna L. ; Rani, Garima ; Vemparala, Satyavani ; Kuroda, Kenichi ( June 2021 , RSC Advances)

   Herein we report the synthesis of ternary statistical methacrylate copolymers comprising cationic ammonium (amino-ethyl methacrylate: AEMA), carboxylic acid (propanoic acid methacrylate: PAMA) and hydrophobic (ethyl methacrylate: EMA) side chain monomers, to study the functional role of anionic groups on their antimicrobial and hemolytic activities as well as the conformation of polymer chains. The hydrophobic monomer EMA was maintained at 40 mol% in all the polymers, with different percentages of cationic ammonium (AEMA) and anionic carboxylate (PAMA) side chains, resulting in different total net charge for the polymers. The antimicrobial and hemolytic activities of the copolymer were determined by the net charge of +3 or larger, suggesting that there was no distinct effect of the anionic carboxylate groups on the antimicrobial and hemolytic activities of the copolymers. However, the pH titration and atomic molecular dynamics simulations suggest that anionic groups may play a strong role in controlling the polymer conformation. This was achieved via formation of salt bridges between cationic and anionic groups, transiently crosslinking the polymer chain allowing dynamic switching between compact and extended conformations. These results suggest that inclusion of functional groups in general, other than the canonical hydrophobic and cationic groups in antimicrobial agents, may have broader implicationsmore »in acquiring functional structures required for adequate antimicrobial activity. In order to explain the implications, we propose a molecular model in which formation of intra-chain, transient salt bridges, due to the presence of both anionic and cationic groups along the polymer, may function as “adhesives” which facilitate compact packing of the polymer chain to enable functional group interaction but without rigidly locking down the overall polymer structure, which may adversely affect their functional roles.« less
3. Understanding interfacial segregation in polymer blend films with random and mixed side chain bottlebrush copolymer additives

   https://doi.org/10.1039/D1SM01146D  

   Mei, Hao ; Mahalik, Jyoti P. ; Lee, Dongjoo ; Laws, Travis S. ; Terlier, Tanguy ; Stein, Gila E. ; Kumar, Rajeev ; Verduzco, Rafael ( October 2021 , Soft Matter)

   Bottlebrush polymers are complex macromolecules with tunable physical properties dependent on the chemistry and architecture of both the side chains and the backbone. Prior work has demonstrated that bottlebrush polymer additives can be used to control the interfacial properties of blends with linear polymers but has not specifically addressed the effects of bottlebrush side chain microstructures. Here, using a combination of experiments and self-consistent field theory (SCFT) simulations, we investigated the effects of side chain microstructures by comparing the segregation of bottlebrush additives having random copolymer side chains with bottlebrush additives having a mixture of two different homopolymer side chain chemistries. Specifically, we synthesized bottlebrush polymers with either poly(styrene- ran -methyl methacrylate) side chains or with a mixture of polystyrene (PS) and poly(methyl methacrylate) (PMMA) side chains. The bottlebrush additives were matched in terms of PS and PMMA compositions, and they were blended with linear PS or PMMA chains that ranged in length from shorter to longer than the bottlebrush side chains. Experiments revealed similar behaviors of the two types of bottlebrushes, with a slight preference for mixed side-chain bottlebrushes at the film surface. SCFT simulations were qualitatively consistent with experimental observations, predicting only slight differences in the segregation ofmore »bottlebrush additives driven by side chain microstructures. Specifically, these slight differences were driven by the chemistries of the bottlebrush polymer joints and side chain end-groups, which were entropically repelled and attracted to interfaces, respectively. Using SCFT, we also demonstrated that the interfacial behaviors were dominated by entropic effects with high molecular weight linear polymers, leading to enrichment of bottlebrush near interfaces. Surprisingly, the SCFT simulations showed that the chemistry of the joints connecting the bottlebrush backbones and side chains played a more significant role compared with the side chain end groups in affecting differences in surface excess of bottlebrushes with random and mixed side chains. This work provides new insights into the effects of side chain microstructure on segregation of bottlebrush polymer additives.« less
4. Packing of apolar side chains enables accurate design of highly stable membrane proteins

   https://doi.org/10.1126/science.aav7541  

   Mravic, Marco ; Thomaston, Jessica L. ; Tucker, Maxwell ; Solomon, Paige E. ; Liu, Lijun ; DeGrado, William F. ( March 2019 , Science)

   The features that stabilize the structures of membrane proteins remain poorly understood. Polar interactions contribute modestly, and the hydrophobic effect contributes little to the energetics of apolar side-chain packing in membranes. Disruption of steric packing can destabilize the native folds of membrane proteins, but is packing alone sufficient to drive folding in lipids? If so, then membrane proteins stabilized by this feature should be readily designed and structurally characterized—yet this has not been achieved. Through simulation of the natural protein phospholamban and redesign of variants, we define a steric packing code underlying its assembly. Synthetic membrane proteins designed using this code and stabilized entirely by apolar side chains conform to the intended fold. Although highly stable, the steric complementarity required for their folding is surprisingly stringent. Structural informatics shows that the designed packing motif recurs across the proteome, emphasizing a prominent role for precise apolar packing in membrane protein folding, stabilization, and evolution.
5. pH- and chaotropic anion-induced conformational changes of tertiary amine-containing binary heterografted star molecular bottlebrushes in aqueous solution

   https://doi.org/10.1039/D0PY01466D  

   Kent, Ethan W. ; Lewoczko, Evan M. ; Zhao, Bin ( January 2021 , Polymer Chemistry)

   This article reports on the conformational behavior of binary heterografted three-arm star molecular bottlebrushes composed of poly(ethylene oxide) (PEO) and either poly(2-( N , N -dimethylamino)ethyl methacrylate) (PDMAEMA, the brushes denoted as SMB-1) or poly(2-( N , N -diethylamino)ethyl methacrylate) (PDEAEMA, the brushes denoted as SMB-2) side chains in aqueous solutions in response to pH changes and addition of salts containing chaotropic anions (CAs). PEO was introduced into the brushes as a stabilizer when the tertiary amine-containing side chains collapsed. While a small size decrease of SMB-1 was observed with increasing pH from acidic to basic, SMB-2 exhibited a large and abrupt size transition caused by the pH-induced solubility change of PDEAEMA. Atomic force microscopy imaging revealed a star-to-globule shape transition of SMB-2 upon increasing pH across the p K a ; in contrast, SMB-1 stayed in the starlike state at both low and high pH values. Intriguingly, both SMB-1 and -2 displayed star-to-globule shape transitions in acidic solutions upon addition of salts containing sufficiently strong CAs such as ClO 4 − , with SMB-2 showing a greater sensitivity to moderate CAs than SMB-1. Moreover, superchaotropic anions ( e.g. , Fe(CN) 6 3− and S 2 O 8 2− )more »were significantly more efficient in inducing shape changing than common CAs. The CA-induced shape transitions resulted from the ion pairing of CAs and protonated tertiary amine groups and the high propensity of CAs to associate with hydrophobic moieties in the brushes, which decreased the solubility of the tertiary amine-containing side chains and caused the brushes to collapse. The findings reported here may enable potential applications of molecular bottlebrushes in, e.g. , encapsulation and release of ionic substances.« less