Faulkner, Matthew, Szabo, Istvan, Weetman, Samantha L 
ORCID: 0000-0002-1355-3283, Sicard, Francois, Huber, Roland G, Bond, Peter J, Rosta, Edina and Liu, Lu-Ning ORCID: 0000-0002-8884-4819
(2020)
Molecular simulations unravel the molecular principles that mediate selective permeability of carboxysome shell protein.
SCIENTIFIC REPORTS, 10 (1).
17501-.
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2020_12 CcmK MD simulations.pdf - Published version Download (13MB) | Preview |
Abstract
Bacterial microcompartments (BMCs) are nanoscale proteinaceous organelles that encapsulate enzymes from the cytoplasm using an icosahedral protein shell that resembles viral capsids. Of particular interest are the carboxysomes (CBs), which sequester the CO<sub>2</sub>-fixing enzymes ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) to enhance carbon assimilation. The carboxysome shell serves as a semi-permeable barrier for passage of metabolites in and out of the carboxysome to enhance CO<sub>2</sub> fixation. How the protein shell directs influx and efflux of molecules in an effective manner has remained elusive. Here we use molecular dynamics and umbrella sampling calculations to determine the free-energy profiles of the metabolic substrates, bicarbonate, CO<sub>2</sub> and ribulose bisphosphate and the product 3-phosphoglycerate associated with their transition through the major carboxysome shell protein CcmK2. We elucidate the electrostatic charge-based permeability and key amino acid residues of CcmK2 functioning in mediating molecular transit through the central pore. Conformational changes of the loops forming the central pore may also be required for transit of specific metabolites. The importance of these in-silico findings is validated experimentally by site-directed mutagenesis of the key CcmK2 residue Serine 39. This study provides insight into the mechanism that mediates molecular transport through the shells of carboxysomes, applicable to other BMCs. It also offers a predictive approach to investigate and manipulate the shell permeability, with the intent of engineering BMC-based metabolic modules for new functions in synthetic biology.
| Item Type: | Article |
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| Uncontrolled Keywords: | Cytoplasm, Organelles, Synechococcus, Carbon Dioxide, Carbon, Glyceric Acids, Ribulose-Bisphosphate Carboxylase, Bacterial Proteins, Mutagenesis, Site-Directed, Permeability, Computer Simulation, Static Electricity, Molecular Dynamics Simulation, Synthetic Biology, Protein Domains |
| Depositing User: | Symplectic Admin |
| Date Deposited: | 15 Oct 2020 12:58 |
| Last Modified: | 18 Jan 2023 23:28 |
| DOI: | 10.1038/s41598-020-74536-5 |
| Related URLs: | |
| URI: | https://livrepository.liverpool.ac.uk/id/eprint/3104270 |
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