An assessment of optimal time scale of conformational resampling for parallel cascade selection molecular dynamics

Role of Thylakoid Lipids in Protochlorophyllide Oxidoreductase Activation: Allosteric Mechanism Elucidated by a Computational Study

Light-dependent protochlorophyllide oxidoreductase (LPOR) is a chlorophyll synthetase that catalyzes the reduction of protochlorophyllide (Pchlide) to chlorophyllide (Chlide) with indispensable roles in regulating photosynthesis processes. A recent study confirmed that thylakoid lipids (TL) were able to allosterically enhance modulator-induced LPOR activation. However, the allosteric modulation mechanism of LPOR by these compounds remains unclear. Herein, we integrated multiple computational approaches to explore the potential cavities in the Arabidopsis thaliana LPOR and an allosteric site around the helix-G region where high affinity for phosphatidyl glycerol (PG) was identified. Adopting accelerated molecular dynamics simulation for different LPOR states, we rigorously analyzed binary LPOR/PG and ternary LPOR/NADPH/PG complexes in terms of their dynamics, energetics, and attainable allosteric regulation. Our findings clarify the experimental observation of increased NADPH binding affinity for LPOR with PGs. Moreover, the simulations indicated that allosteric regulators targeting LPOR favor a mechanism involving lid opening upon binding to an allosteric hinge pocket mechanism. This understanding paves the way for designing novel LPOR activators and expanding the applications of LPOR.

Selection rules on initial structures in parallel cascade selection molecular dynamics affect conformational sampling efficiency

Parallel cascade selection molecular dynamics (PaCS-MD) is a conformational sampling method for generating transition pathways from a given reactant to a product. In PaCS-MD, initial structures relevant to conformational transitions of proteins are selected and resampled by short-time MD simulations. As a general reaction coordinate, a root-mean-square deviation measured from the product (RMSD) is employed to rank the resampled configurations. Quantitatively, n initial structures are randomly selected from among the top X % of highly ranked configurations and resampled again. In PaCS-MD, the selection of initial structures and their conformational resampling are repeated as a cycle to promote the essential conformational transitions. Therefore, rules for selecting the initial structures might affect the conformational sampling efficiency. In the present study, to address the conformational sampling efficiency depending on the selection rule, the open-closed transition of di-ubiquitin was reproduced by PaCS-MD based on the resampling from the top X = 0.1, 1.0, 2.0, 5.0, 10.0, 25.0, 30.0, 40.0, and 50.0% of highly ranked configurations. Judging from broadness of sampled conformational area and required cycles, we conclude that the resampling from the top ∼2.0% of highly ranked configurations might be the most efficient for generating a set of transition pathways in PaCS-MD.