Coarse-Grain Model for Natural Cellulose Fibrils in Explicit Water

Understanding biomass structure and dynamics on multiple time and length scales is important for the development of cellulosic biofuels. To this aim, we have developed a coarse-grain (CG) model for molecular dynamics (MD) simulations of cellulose fibrils in explicit water based on target observables from fully atomistic simulations. This model examines the significance of the presence of explicit solvent and compares results with the previous, implicit solvent CG cellulose models. The present, constraint-free CG model is used to generate a series of noncrystalline fibril structures using a coupling parameter, λ, between fully crystalline and fully amorphous potentials. By exploring various structural parameters, including the root-mean-square deviation, root-mean-square fluctuations, radius of gyration, and persistence length, we find the crystalline-to-amorphous state transition takes place at λ ≈ 0.386. The persistence length of cellulose fibril in the transition region corresponds to that of native cellulose fibrils. The transition between crystalline and amorphous fibrils occurs at larger values of λ in explicit water than in the implicit case. Detailed analysis of individual energetic contribution to the transition reveals that the nonbonded interactions, in particular, that of cellulose–water interaction, plays a significant role in the observed crystalline to amorphous transition of cellulose fibril. The present study thus highlights the importance of solvent presence that cannot be adequately described with the previous implicit solvent model. The present method provides an accurate and constraint-free approach for deriving a variety of structures of cellulose in water, with a wide range of crystallinity, suitable for incorporation into large-scale models of lignocellulosic biomass

All-Atom Molecular Dynamics Simulation of a Photosystem I/Detergent Complex

All-atom molecular dynamics (MD) simulation was used to investigate the solution structure and dynamics of the photosynthetic pigment–protein complex photosystem I (PSI) from <i>Thermosynechococcus elongatus</i> embedded in a toroidal belt of <i>n</i>-dodecyl-β-d-maltoside (DDM) detergent. Evaluation of root-mean-square deviations (RMSDs) relative to the known crystal structure show that the protein complex surrounded by DDM molecules is stable during the 200 ns simulation time, and root-mean-square fluctuation (RMSF) analysis indicates that regions of high local mobility correspond to solvent-exposed regions such as turns in the transmembrane α-helices and flexible loops on the stromal and lumenal faces. Comparing the protein–detergent complex to a pure detergent micelle, the detergent surrounding the PSI trimer is found to be less densely packed but with more ordered detergent tails, contrary to what is seen in most lipid bilayer models. We also investigated any functional implications for the observed conformational dynamics and protein–detergent interactions, discovering interesting structural changes in the psaL subunits associated with maintaining the trimeric structure of the protein. Importantly, we find that the docking of soluble electron mediators such as cytochrome <i>c</i>₆ and ferredoxin to PSI is not significantly impacted by the solubilization of PSI in detergent

Structure and Function of Photosystem I–[FeFe] Hydrogenase Protein Fusions: An All-Atom Molecular Dynamics Study

All-atom molecular dynamics (MD) simulation was used to study the solution dynamics and protein–protein interactions of protein fusions of photosystem I (PSI) from <i>Thermosynechococcus elongatus</i> and an [FeFe]-hydrogenase (FeFe H₂ase) from <i>Clostridium pasteurianum</i>, a unique complex capable of photocatalytic hydrogen production. This study involved fusions of these two proteins via dithiol linkers of different length including decanedithiol, octanedithiol, and hexanedithiol, for which experimental data had previously been obtained. Evaluation of root-mean-squared deviations (RMSDs) relative to the respective crystal structures of PSI and the FeFe H₂ase shows that these fusion complexes approach stable equilibrium conformations during the MD simulations. Investigating protein mobility via root-mean-squared fluctuations (RMSFs) reveals that tethering via the shortest hexanedithiol linker results in increased atomic fluctuations of both PSI and the hydrogenase in these fusion complexes. Evaluation of the inter- and intraprotein electron transfer distances in these fusion complexes indicates that the structural changes in the FeFe H₂ase arising from ligation to PSI via the shortest hexanedithiol linker may hinder electron transport in the hydrogenase, thus providing a molecular level explanation for the observation that the medium-length octanedithiol linker gives the highest hydrogen production rate

Replica-Exchange Molecular Dynamics Simulations of Cellulose Solvated in Water and in the Ionic Liquid 1‑Butyl-3-Methylimidazolium Chloride

Ionic liquids have become a popular solvent for cellulose pretreatment in biorefineries due to their efficiency in dissolution and their reusability. Understanding the interactions between cations, anions, and cellulose is key to the development of better solvents and the improvement of pretreatment conditions. While previous studies described the interactions between ionic liquids and cellulose fibers, shedding light on the initial stages of the cellulose dissolution process, we study the end state of that process by exploring the structure and dynamics of a single cellulose decamer solvated in 1-butyl-3-methyl-imidazolium chloride (BmimCl) and in water using replica-exchange molecular dynamics. In both solvents, global structural features of the cellulose chain are similar. However, analyses of local structural properties show that cellulose explores greater conformational variability in the ionic liquid than in water. For instance, in BmimCl the cellulose intramolecular hydrogen bond O3H′···O5 is disrupted more often resulting in greater flexibility of the solute. Our results indicate that the cellulose chain is more dynamic in BmimCl than in water, which may play a role in the favorable dissolution of cellulose in the ionic liquid. Calculation of the configurational entropy of the cellulose decamer confirms its higher conformational flexibility in BmimCl than in water at elevated temperatures

Relative Binding Affinities of Monolignols to Horseradish Peroxidase

Monolignol binding to the peroxidase active site is the first step in lignin polymerization in plant cell walls. Using molecular dynamics, docking, and free energy perturbation calculations, we investigate the binding of monolignols to horseradish peroxidase C. Our results suggest that <i>p</i>-coumaryl alcohol has the strongest binding affinity followed by sinapyl and coniferyl alcohol. Stacking interactions between the monolignol aromatic rings and nearby phenylalanine residues play an important role in determining the calculated relative binding affinities. <i>p</i>-Coumaryl and coniferyl alcohols bind in a pose productive for reaction in which a direct H-bond is formed between the phenolic −OH group and a water molecule (W2) that may facilitate proton transfer during oxidation. In contrast, in the case of sinapyl alcohol there is no such direct interaction, the phenolic −OH group instead interacting with Pro139. Since proton and electron transfer is the rate-limiting step in monolignol oxidation by peroxidase, the binding pose (and thus the formation of near attack conformation) appears to play a more important role than the overall binding affinity in determining the oxidation rate

Behavior of Bilayer Leaflets in Asymmetric Model Membranes: Atomistic Simulation Studies

Spatial organization within lipid bilayers is an important feature for a range of biological processes. Leaflet compositional asymmetry and lateral lipid organization are just two of the ways in which membrane structure appears to be more complex than initially postulated by the fluid mosaic model. This raises the question of how the phase behavior in one bilayer leaflet may affect the apposing leaflet and how one begins to construct asymmetric model systems to investigate these interleaflet interactions. Here we report on all-atom molecular dynamics simulations (a total of 4.1 μs) of symmetric and asymmetric bilayer systems composed of liquid-ordered (Lo) or liquid-disordered (Ld) leaflets, based on the nanodomain-forming POPC/DSPC/cholesterol system. We begin by analyzing an asymmetric bilayer with leaflets derived from simulations of symmetric Lo and Ld bilayers. In this system, we observe that the properties of the Lo and Ld leaflets are similar to those of the Lo and Ld leaflets in corresponding symmetric systems. However, it is not obvious that mixing the equilibrium structures of their symmetric counterparts is the most appropriate way to construct asymmetric bilayers nor that these structures will manifest interleaflet couplings that lead to domain registry/antiregistry. We therefore constructed and simulated four additional asymmetric bilayer systems by systematically adding or removing lipids in the Ld leaflet to mimic potential density fluctuations. We find that the number of lipids in the Ld leaflet affects its own properties, as well as those of the apposing Lo leaflet. Collectively, the simulations reveal the presence of weak acyl chain interdigitation across bilayer leaflets, suggesting that interdigitation alone does not contribute significantly to the interleaflet coupling in nonphase-separated bilayers of this chemical composition. However, the properties of both leaflets appear to be sensitive to changes in in-plane lipid packing, possibly providing a mechanism for interleaflet coupling by modulating local density and/or curvature fluctuations

Molecular Dynamics Investigation of the Substrate Binding Mechanism in Carboxylesterase

A recombinant carboxylesterase, cloned from <i>Pseudomonas putida</i> and designated as rPPE, is capable of catalyzing the bioresolution of racemic 2-acetoxy-2-(2′-chlorophenyl)­acetate (<i>rac</i>-AcO-CPA) with excellent (<i>S</i>)-enantioselectivity. Semirational design of the enzyme showed that the W187H variant could increase the activity by ∼100-fold compared to the wild type (WT) enzyme. In this study, we performed all-atom molecular dynamics (MD) simulations of both apo-rPPE and rPPE in complex with (<i>S</i>)-AcO-CPA to gain insights into the origin of the increased catalysis in the W187H mutant. Our results show differential binding of (<i>S</i>)-AcO-CPA in the WT and W187H enzymes, especially the interactions of the substrate with the two active site residues Ser159 and His286. The replacement of Trp187 by His leads to considerable structural rearrangement in the active site of W187H. Unlike in the WT rPPE, the cap domain in the W187 mutant shows an open conformation in the simulations of both apo and substrate-bound enzymes. This open conformation exposes the catalytic triad to the solvent through a water accessible channel, which may facilitate the entry of the substrate and/or the exit of the product. Binding free energy calculations confirmed that the substrate binds more strongly in W187H than in WT. On the basis of these computational results, we further predicted that the mutations W187Y and D287G might also be able to increase the substrate binding and thus improve the enzyme’s catalytic efficiency. Experimental binding and kinetic assays on W187Y and D287G show improved catalytic efficiency over WT, but not W187H. Contrary to our prediction, W187Y shows slightly decreased substrate binding coupled with a 100-fold increase in turnover rate, while in D287G the substrate binding is 8 times stronger but with a slightly reduced turnover rate. Our work provides important molecular-level insights into the binding of the (<i>S</i>)-AcO-CPA substrate to carboxylesterase rPPEs, which will help guide future development of more efficient rPPE variants

Theoretical Study of the Initial Stages of Self-Assembly of a Carboxysome’s Facet

Bacterial microcompartments, BMCs, are organelles that exist within wide variety of bacteria and act as nanofactories. Among the different types of known BMCs, the carboxysome has been studied the most. The carboxysome plays an important role in the light-independent part of the photosynthesis process, where its icosahedral-like proteinaceous shell acts as a membrane that controls the transport of metabolites. Although a structural model exists for the carboxysome shell, it remains largely unknown how the shell proteins self-assemble. Understanding the self-assembly process can provide insights into how the shell affects the carboxysome’s function and how it can be modified to create new functionalities, such as artificial nanoreactors and artificial protein membranes. Here, we describe a theoretical framework that employs Monte Carlo simulations with a coarse-grain potential that reproduces well the atomistic potential of mean force; employing this framework, we are able to capture the initial stages of the 2D self-assembly of CcmK2 hexamers, a major protein-shell component of the carboxysome’s facet. The simulations reveal that CcmK2 hexamers self-assemble into clusters that resemble what was seen experimentally in 2D layers. Further analysis of the simulation results suggests that the 2D self-assembly of carboxysome’s facets is driven by a nucleation–growth process, which in turn could play an important role in the hierarchical self-assembly of BMC shells in general

The PMFs for the Interaction between Glu45 and Arg206

<div><p>(A) In the starting structure.</p><p>(B) In the final conformer from the TMD simulation.</p><p>PMF energy is shown on a continuous color scale from 0 (blue) to ≥ 10 kcal/mol (red).</p></div

Structural Changes of β10, Cys loop, and β1–β2 loop during the TMD Simulation

<p>Comparison of the initial structure (silver) and a snapshot from the last 50 ps of the TMD simulation (green), (A) front view; (B) side view rotated 120° with respect to view (A).</p