Daipayan Sarkar

Date: April 2, 2024

Time: 12:00 pm

In-person location: 168 PLB

Zoom: https://bit.ly/prltuesnoon
Meeting ID: 957 9659 6975
Passcode: 420205

Speaker: Daipayan Sarkar

Lab: Vermaas lab

Title: Comparing photosynthetic metabolite free energy and permeability across bacterial microcompartment shell proteins 

Abstract: Bacterial microcompartments (BMC), such as carboxysomes, are organelles found in cyanobacteria that locally concentrate carbon dioxide (CO₂) to improve the efficiency of the enzyme RuBisCO, a key step of photosynthetic carbon fixation in the Calvin-Benson-Bassham cycle. The carboxysome shell is comprised of shell proteins and encapsulates RuBisCO and carbonic anhydrase. Carbonic anhydrase converts soluble bicarbonate to CO₂, increasing the local concentration of CO₂ for RuBisCO. In addition to CO₂, another metabolite ribulose-1,5-bisphosphate (RuBP) also need to permeate through the carboxysome shell to efficiently perform the CO₂ fixation step. Quantifying the free energy and permeability for such metabolites currently remains a challenge and a critical design feature related to the design of synthetic bacterial microcompartments for bioenergy and sustainability applications. Based on all-atom molecular simulations of a synthetic beta-carboxysome shell, we found the permeability of RuBP to be at least two orders of magnitude lower than that of CO₂. However, for carbon fixation within BMCs, equal stoichiometry of RuBP and CO₂ is necessary. This led us to compare the transport across the hexamer and trimer shell proteins based on their energetic cost. To do so we perform replica exchange molecular simulations to predict metabolite permeability across a hexamer-trimer assembly, obtained from a 3Å cryo-EM structure of Haliangium ochraceum (HO) BMC that contains a trimer that is structurally similar to the carboxysome protein CcmP. Indeed, the free-energy profile indicates transport of larger metabolites such as RuBP across the central pore of the stacked trimer is energetically favorable when compared against their hexamer counterpart. These results from molecular simulations presented here provide a detailed mechanistic picture, addressing a fundamental question related to photosynthetic dark reactions and using the shell permeabilities to engineer smart synthetic BMCs for carbon fixation strategies.