Electrostatic phenomena are ubiquitous in biological processes such as protein folding, binding, and catalysis. Our current knowledge of electrostatic effects on protein stability is mainly derived from protein engineering experiments and theoretical studies using static-structure based Poisson-Boltzmann calculations. However, while macroscopic measurements often can not isolate electrostatic effects from others, the accuracy of theoretical predictions is limited by the lack of explicit treatment of protein dielectric response, conformational dynamics and effects due to residual structures in the unfolded state. As a result, despite two decades of research, important questions such as how and to what extent electrostatic interactions modulate protein stability have not been adequately answered. The lack of accurate means to predict electrostatic contributions not only hampers fundamental understanding of protein stability but also poses a roadblock for advancing computational protein design.
The specific aims of this application are 1) to advance atomic-level studies of pH-dependent phenomena by further developing continuous constant pH molecular dynamics and related methodologies, and 2) to improve quantitative prediction and detailed understanding of electrostatic modulation of protein stability by studying several model systems including the N-terminal domain of ribosomal L9 protein, villin headpiece subdomain, leucine zipper, and meso-, thermo- and hyperthermophilic variants of peripheral subunit binding domain. The proposed method development will provide the community with powerful tools for studying a wide range of electrostatic phenomena in biology. The insights gained in the application studies are expected to shift the native-centric paradigm of protein stability and function and transform the static-structure based view of protein electrostatics. They will also help establish general principles for computational protein design.
We plan to develop new simulation techniques, theoretical approaches and experimental strategies to significantly advance the state of the art in the study of electrostatic phenomena in biology. By exploiting a novel set of methods, approaches and tools that the PI has developed and will continue to develop in this application, we seek to shift the native-centric paradigm of protein stability and function, and transform the static-structure based view of protein electrostatics.
|Shen, Jana (2018) Zooming in on a small multidrug transporter reveals details of asymmetric protonation. Proc Natl Acad Sci U S A 115:8060-8062|
|Yue, Zhi; Shen, Jana (2018) pH-Dependent cooperativity and existence of a dry molten globule in the folding of a miniprotein BBL. Phys Chem Chem Phys 20:3523-3530|
|Yue, Zhi; Chen, Wei; Zgurskaya, Helen I et al. (2017) Constant pH Molecular Dynamics Reveals How Proton Release Drives the Conformational Transition of a Transmembrane Efflux Pump. J Chem Theory Comput 13:6405-6414|
|Harris, Robert C; Tsai, Cheng-Chieh; Ellis, Christopher R et al. (2017) Proton-Coupled Conformational Allostery Modulates the Inhibitor Selectivity for ?-Secretase. J Phys Chem Lett 8:4832-4837|
|Ellis, Christopher R; Tsai, Cheng-Chieh; Lin, Fang-Yu et al. (2017) Conformational dynamics of cathepsin D and binding to a small-molecule BACE1 inhibitor. J Comput Chem 38:1260-1269|
|Ellis, Christopher R; Tsai, Cheng-Chieh; Hou, Xinjun et al. (2016) Constant pH Molecular Dynamics Reveals pH-Modulated Binding of Two Small-Molecule BACE1 Inhibitors. J Phys Chem Lett 7:944-9|
|Chen, Wei; Huang, Yandong; Shen, Jana (2016) Conformational Activation of a Transmembrane Proton Channel from Constant pH Molecular Dynamics. J Phys Chem Lett 7:3961-3966|
|Huang, Yandong; Chen, Wei; Wallace, Jason A et al. (2016) All-Atom Continuous Constant pH Molecular Dynamics With Particle Mesh Ewald and Titratable Water. J Chem Theory Comput 12:5411-5421|
|Huang, Yandong; Chen, Wei; Dotson, David L et al. (2016) Mechanism of pH-dependent activation of the sodium-proton antiporter NhaA. Nat Commun 7:12940|
|Morrow, Brian H; Payne, Gregory F; Shen, Jana (2015) pH-Responsive Self-Assembly of Polysaccharide through a Rugged Energy Landscape. J Am Chem Soc 137:13024-30|
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