Nonenveloped organelles govern many cellular functions including aspects of signaling. These cellular bodies are made up of proteins and nucleic acids which have condensed, or phase separated out of the components within the cell. The coupling of structure and miscibility properties of polypeptides and nucleotides underly the formation of non-enveloped organelles or biomolecular condensates. We propose theoretical and computational methods to quantify the contributions of number of protein components, structural/conformational disorder and phosphorylation to biomolecular condensate formation. Each of the polypeptide components interact and form an interface with other molecules in the biomolecular condensate. These interactions drive the formation of these cellular structures. This is not a protein or peptide interface prediction project, but rather we seek to understand the interactions and entropic components of the underlying free energy surface driving the creation of the solubility limit and the consequent phase transition forming the condensates. We propose to calculate the properties of polypeptide biomolecular condensates by simulating and analyzing the liquid-liquid phase separation at the all-atom model level. We will explicitly consider the role of peptide disorder, the number of components and their chemical characteristics that allow condensation out of the cytosolic mixture. Deciphering the thermodynamic manifold, entropic versus enthalpic driving forces as well as compositional dependences is necessary to understand the formation and stability of these cellular physiological assemblies. Once condensed the kinetics of the system is governed in part by the diffusion of the components both within the condensate and in its formation or dissolution. The rate constants for polypeptide transport will be explicitly calculated to consider the effects of sequestration given the properties of the sequence. Differentiation of physiological versus pathological assemblies and, as such, plausible therapeutic solutions targeting these structures will not be possible without these fundamental mechanistic insights.
Nonenveloped organelles control many cellular functions including aspects of signaling and are made up of proteins (and nucleic acids) which have separated out of the components on the interior of the cell. Here, we propose theoretical and computational methods to quantify the contributions of protein components to the formation of these cellular bodies. The fundamental mechanistic insights to be gained from these studies will allow an understanding of the difference between physiological and pathological nonenveloped organelles to guide plausible diagnostic and therapeutic solutions.
| Drake, Justin A; Pettitt, B Montgomery (2018) Thermodynamics of Conformational Transitions in a Disordered Protein Backbone Model. Biophys J 114:2799-2810 |
| Sarma, Rahul; Wong, Ka-Yiu; Lynch, Gillian C et al. (2018) Peptide Solubility Limits: Backbone and Side-Chain Interactions. J Phys Chem B 122:3528-3539 |
| Seckfort, Danielle; Montgomery Pettitt, B (2018) Price of disorder in the lac repressor hinge helix. Biopolymers :e23239 |
| Dai, Wei; Chen, Muyuan; Myers, Christopher et al. (2018) Visualizing Individual RuBisCO and Its Assembly into Carboxysomes in Marine Cyanobacteria by Cryo-Electron Tomography. J Mol Biol 430:4156-4167 |
| Kolawole, Abimbola O; Smith, Hong Q; Svoboda, Sophia A et al. (2017) Norovirus Escape from Broadly Neutralizing Antibodies Is Limited to Allostery-Like Mechanisms. mSphere 2: |
| Zhang, Cheng; Drake, Justin A; Ma, Jianpeng et al. (2017) Optimal updating magnitude in adaptive flat-distribution sampling. J Chem Phys 147:174105 |
| Asthagiri, D; Karandur, Deepti; Tomar, Dheeraj S et al. (2017) Intramolecular Interactions Overcome Hydration to Drive the Collapse Transition of Gly15. J Phys Chem B 121:8078-8084 |
| Ou, Shu-Ching; Drake, Justin A; Pettitt, B Montgomery (2017) Nonpolar Solvation Free Energy from Proximal Distribution Functions. J Phys Chem B 121:3555-3564 |
| Chen, Chuanying; Pettitt, B Montgomery (2016) DNA Shape versus Sequence Variations in the Protein Binding Process. Biophys J 110:534-544 |
| Zhang, Cheng; Lai, Chun-Liang; Pettitt, B Montgomery (2016) Accelerating the weighted histogram analysis method by direct inversion in the iterative subspace. Mol Simul 42:1079-1089 |
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