Search Results - "Treado, John D."

Analyses of protein cores reveal fundamental differences between solution and crystal structures by Mei, Zhe, Treado, John D., Grigas, Alex T., Levine, Zachary A., Regan, Lynne, O'Hern, Corey S.

“…There have been several studies suggesting that protein structures solved by NMR spectroscopy and X‐ray crystallography show significant differences. To…”
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Using physical features of protein core packing to distinguish real proteins from decoys by Grigas, Alex T., Mei, Zhe, Treado, John D., Levine, Zachary A., Regan, Lynne, O'Hern, Corey S.

“…The ability to consistently distinguish real protein structures from computationally generated model decoys is not yet a solved problem. One route to…”
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Localized growth and remodelling drives spongy mesophyll morphogenesis by Treado, John D, Roddy, Adam B, Théroux-Rancourt, Guillaume, Zhang, Liyong, Ambrose, Chris, Brodersen, Craig R, Shattuck, Mark D, O'Hern, Corey S

“…The spongy mesophyll is a complex, porous tissue found in plant leaves that enables carbon capture and provides mechanical stability. Unlike many other…”
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A threonine zipper that mediates protein–protein interactions: Structure and prediction by Oi, Curran, Treado, John D., Levine, Zachary A., Lim, Christopher S., Knecht, Kirsten M., Xiong, Yong, O'Hern, Corey S., Regan, Lynne

“…We present the structure of an engineered protein–protein interface between two beta barrel proteins, which is mediated by interactions between threonine (Thr)…”
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Void distributions reveal structural link between jammed packings and protein cores by Treado, John D, Mei, Zhe, Regan, Lynne, O'Hern, Corey S

“…Dense packing of hydrophobic residues in the cores of globular proteins determines their stability. Recently, we have shown that protein cores possess packing…”
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Cover Image, Volume 88, Issue 9 by Mei, Zhe, Treado, John D., Grigas, Alex T., Levine, Zachary A., Regan, Lynne, O'Hern, Corey S.

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Computational Studies of Packing and Jamming in Biological Systems by Treado, John D

“…The application of coarse-grained computational models to the study of physical systems has explodedin recent years, in part due to the relative simplicity of…”
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Bridging particle deformability and collective response in soft solids by Treado, John D, Wang, Dong, Boromand, Arman, Murrell, Michael P, Shattuck, Mark D, O'Hern, Corey S

“…Phys. Rev. Materials 5, 055605 (2021) Soft, amorphous solids such as tissues, foams, and emulsions are composed of deformable particles. However, the effect of…”
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Localized growth drives spongy mesophyll morphogenesis by Treado, John D, Roddy, Adam B, Théroux-Rancourt, Guillaume, Zhang, Liyong, Ambrose, Chris, Brodersen, Craig, Shattuck, Mark D, O'Hern, Corey S

“…J. R. Soc. Interface (2022) 19: 20220602 The spongy mesophyll is a complex, porous tissue found in plant leaves that enables carbon capture and provides…”
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The structural, vibrational, and mechanical properties of jammed packings of deformable particles in three dimensions by Wang, Dong, Treado, John D, Boromand, Arman, Norwick, Blake, Murrell, Michael P, Shattuck, Mark D, O'Hern, Corey S

“…Soft Matter 17, 9901 (2021) We investigate the structural, vibrational, and mechanical properties of jammed packings of deformable particles with shape degrees…”
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Void distributions reveal structural link between jammed packings and protein cores by Treado, John D, Mei, Zhe, Regan, Lynne, O'Hern, Corey S

“…Phys. Rev. E 99, 022416 (2019) Dense packing of hydrophobic residues in the cores of globular proteins determines their stability. Recently, we have shown that…”
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Using physical features of protein core packing to distinguish real proteins from decoys by Grigas, Alex T, Mei, Zhe, Treado, John D, Levine, Zachary A, Regan, Lynne, O'Hern, Corey S

“…Protein Science 29 (2020) 1931 The ability to consistently distinguish real protein structures from computationally generated model decoys is not yet a solved…”
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Analyses of protein cores reveal fundamental differences between solution and crystal structures by Mei, Zhe, Treado, John D, Grigas, Alex T, Levine, Zachary A, Regan, Lynne, O'Hern, Corey S

“…Proteins: Structure, Function, and Bioinformatics 88 (2020) 1154 There have been several studies suggesting that protein structures solved by NMR spectroscopy…”
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Current MD forcefields fail to capture key features of protein structure and fluctuations: A case study of cyclophilin A and T4 lysozyme by Mei, Zhe, Grigas, Alex T, Treado, John D, Corres, Gabriel Melendez, Vuorte, Maisa, Sammalkorpi, Maria, Regan, Lynne, Levine, Zachary A, O'Hern, Corey S

“…Globular proteins undergo thermal fluctuations in solution, while maintaining an overall well-defined folded structure. In particular, studies have shown that…”
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