Giovanni Bellesia

Effect of β-sheet propensity on peptide aggregation

The effect of beta-sheet propensity on the structural features of peptide aggregates was investigated using an off-lattice coarse-grained peptide model. A phase diagram as a function of temperature and beta-sheet propensity reveals a diverse family of supramolecular assemblies. Highly rigid peptides (peptides with high beta-sheet propensity) are seen to assemble predominantly into fibrillar structures. Increasing the flexibility of the peptide (reducing beta-sheet propensity) leads to a variety of structures, including fibrils, beta-barrel structures, and amorphous aggregates. Nonfibrillar entities have been suggested as primary causative agents in amyloid diseases and our simulations indicate that mutations that decrease beta-sheet propensity will decrease fibril formation and favor the formation of such toxic oligomers. Parallels between beta-sheet aggregates and nematic liquid crystals are discussed.

Insights into Hydrogen Bonding and Stacking Interactions in Cellulose

In this quantum chemical study, we explore hydrogen bonding (H-bonding) and stacking interactions in different crystalline cellulose allomorphs; namely, cellulose I(β) and cellulose III(I). We consider a model system representing a cellulose crystalline core made from six cellobiose units arranged in three layers with two chains per layer. We calculate the contributions of intrasheet and intersheet interactions to the structure and stability in both cellulose I(β) and cellulose III(I) crystalline cores. Reference structures for this study were generated from molecular dynamics simulations of water-solvated cellulose I(β) and III(I) fibrils. A systematic analysis of various conformations describing different mutual orientations of cellobiose units is performed using the hybrid density functional theory with the M06-2X with 6-31+G(d,p) basis sets. We dissect the nature of the forces that stabilize the cellulose I(β) and cellulose III(I) crystalline cores and quantify the relative strength of H-bonding and stacking interactions. Our calculations demonstrate that individual H-bonding interactions are stronger in cellulose I(β) than in cellulose III(I); however, the total H-bonding contribution to stabilization is larger in cellulose III(I) because of the highly cooperative nature of the H-bonding network. In addition, we observe a significant contribution from cooperative stacking interactions to the stabilization of cellulose I(β). The theory of atoms-in-molecules (AIM) has been employed to characterize and quantify these intermolecular interactions. AIM analyses highlight the role of nonconventional CH···O H-bonding in the cellulose assemblies. Finally, we calculate molecular electrostatic potential maps for the cellulose allomorphs that capture the differences in chemical reactivity of the systems considered in our study.

What Determines the Structure and Stability of KFFE Monomers, Dimers, and Protofibrils?

The self-assembly of the KFFE peptide was studied using replica exchange molecular dynamics simulations with a fully atomic description of the peptide and explicit solvent. The relative roles of the aromatic residues and oppositely charged end groups in stabilizing the earliest oligomers and the end-products of aggregation were investigated. beta and non-beta-peptide conformations compete in the monomeric state as a result of a balancing between the high beta-sheet propensity of the phenylalanine residues and charge-charge interactions that favor non-beta-conformations. Dimers are present in beta- and non-beta-sheet conformations and are stabilized primarily by direct and water-mediated charge-charge interactions between oppositely charged side chains and between oppositely charged termini, with forces between aromatic residues playing a minor role. Dimerization to a beta-sheet, fibril-competent state, is seen to be a cooperative process, with the association process inducing beta-structure in otherwise non-beta-monomers. We propose a model for the KFFE fibril, with mixed interface and antiparallel sheet and strand arrangements, which is consistent with experimental electron microscopy measurements. Both aromatic and charge-charge interactions contribute to the fibril stability, although the dominant contribution arises from electrostatic interactions.

Sequence periodicity and secondary structure propensity in model proteins

We explore the question of whether local effects (originating from the amino acids intrinsic secondary structure propensities) or nonlocal effects (reflecting the sequence of amino acids as a whole) play a larger role in determining the fold of globular proteins. Earlier circular dichroism studies have shown that the pattern of polar, non polar amino acids (nonlocal effect) dominates over the amino acid intrinsic propensity (local effect) in determining the secondary structure of oligomeric peptides. In this article, we present a coarse grained computational model that allows us to quantitatively estimate the role of local and nonlocal factors in determining both the secondary and tertiary structure of small, globular proteins. The amino acid intrinsic secondary structure propensity is modeled by a dihedral potential term. This dihedral potential is parametrized to match with experimental measurements of secondary structure propensity. Similarly, the magnitude of the attraction between hydrophobic residues is parametrized to match the experimental transfer free energies of hydrophobic amino acids. Under these parametrization conditions, we systematically explore the degree of frustration a given polar, non polar pattern can tolerate when the secondary structure intrinsic propensities are in opposition to it. When the parameters are in the biophysically relevant range, we observe that the fold of small, globular proteins is determined by the pattern of polar, non polar amino acids regardless of their instrinsic secondary structure propensities. Our simulations shed new light on previous observations that tertiary interactions are more influential in determining protein structure than secondary structure propensity. The fact that this can be inferred using a simple polymer model that lacks most of the biochemical details points to the fundamental importance of binary patterning in governing folding.

Probing the Early Events Associated with Liquid Ammonia Pretreatment of Native Crystalline Cellulose

Various chemicals are being explored for catalyzing efficient lignocellulose deconstruction. In particular, when liquid ammonia is used to convert the naturally occurring cellulose crystalline phase I(β), to cellulose III(I), the rearrangement of the hydrogen bond network in cellulose III(I) results in enhanced hydrolysis yields. We use molecular dynamics simulations to analyze the interaction between a cellulose I(β) fibril and ammonia. Our simulations reveal that early structural changes in the fibril are driven by the rapid formation of an extended hydrogen bond network between the solvent-exposed surface chains and ammonia that precedes ammonia penetration into the fibril. The emergence of this hydrogen bond network causes relative shifting of the cellulose layers within the fibril that in turn leads to the formation of channels orthogonal to the (100) and (-100) fibril surfaces. The channels allow ammonia molecules to penetrate into the cellulose fibril. These findings provide avenues for improving existing chemical pretreatments to make them more effective and economical.

Effects of surface interactions on peptide aggregate morphology

The formation of peptide aggregates mediated by an attractive surface is investigated using replica exchange molecular dynamics simulations with a coarse-grained peptide representation. In the absence of a surface, the peptides exhibit a range of aggregate morphologies, including amorphous aggregates, β-barrels and multi-layered fibrils, depending on the chiral stiffness of the chain (a measure of its β-sheet propensity). In contrast, aggregate morphology in the presence of an attractive surface depends more on surface attraction than on peptide chain stiffness, with the surface favoring fibrillar structures. Peptide-peptide interactions couple to peptide-surface interactions cooperatively to affect the assembly process both qualitatively (in terms of aggregate morphology) and quantitatively (in terms of transition temperature and transition sharpness). The frequency of ordered fibrillar aggregates, the surface binding transition temperature, and the sharpness of the binding transition all increase with both surface attraction and chain stiffness.

β-sheet propensity controls the kinetic pathways and morphologies of seeded peptide aggregation

The effect of seeds in templating the morphology of peptide aggregates is examined using molecular dynamics simulations and a coarse-grained peptide representation. Varying the nature of the aggregate seed between β-sheet, amorphous, and β-barrel seeds leads to different aggregation pathways and to morphologically different aggregates. Similar effects are seen by varying the β-sheet propensity of the free peptides. For a fibrillar seed and free peptides of high β-sheet propensity, fibrillar growth occurred by means of direct attachment (without structural rearrangement) of free individual peptides and small ordered oligomers onto the seed. For a fibrillar seed and free peptides of low β-sheet propensity, fibrillar growth occurred through a dock-lock mechanism, in which the free peptides first docked onto the seed, and then locked on, extending and aligning to join the fibril. Amorphous seeds absorbed free peptides into themselves indiscriminately, with any fibrillar rearrangement subsequent to this absorption by means of a condensation-ordering transition. Although the mechanisms observed by varying peptide β-sheet propensity are diverse, the initial pathways can always be broken down into the following steps: (i) the free peptides diffuse in the bulk and attach individually to the seed; (ii) the free peptides diffuse and aggregate among themselves; (iii) the free peptide oligomers collide with the seed; and (iv) the free oligomers merge with the seed and rearrange in a manner dependent on the backbone flexibility of both the free and seed peptides. Our simulations indicate that it is possible to sequester peptides from amorphous aggregates into fibrils, and also that aggregate morphology (and thus cytoxicity) can be controlled by introducing seeds of aggregate-compatible peptides with differing β-sheet propensities into the system.

In silico studies of crystalline cellulose and its degradation by enzymes

In this report, the current state of computational studies on crystalline cellulose is reviewed. The discussion is focused on fully atomistic molecular-dynamics simulations as well as on other computational approaches which are relevant in the context of enzymatic degradation of cellulose. Finally, possible directions and necessary improvements for future computational studies in this challenging research field are summarized.

MARTINI Coarse-Grained Model for Crystalline Cellulose Microfibers

Commercial-scale biofuel production requires a deep understanding of the structure and dynamics of its principal target: cellulose. However, an accurate description and modeling of this carbohydrate structure at the mesoscale remains elusive, particularly because of its overwhelming length scale and configurational complexity. We have derived a set of MARTINI coarse-grained force field parameters for the simulation of crystalline cellulose fibers. The model is adapted to reproduce different physicochemical and mechanical properties of native cellulose Iβ. The model is able not only to handle a transition from cellulose Iβ to another cellulose allomorph, cellulose IIII, but also to capture the physical response to temperature and mechanical bending of longer cellulose nanofibers. By developing the MARTINI model of a solid cellulose crystalline fiber from the building blocks of a soluble cellobiose coarse-grained model, we have provided a systematic way to build MARTINI models for other crystalline biopolymers.

Coarse-Grained Model for the Interconversion between Native and Liquid Ammonia-Treated Crystalline Cellulose

We present the results of Langevin dynamics simulations on a coarse-grained model for a structural transition in crystalline cellulose pertinent to the cellulose degradation problem. We analyze two different cellulose crystalline forms: cellulose Iβ (the natural form of cellulose) and cellulose III(I) (obtained after cellulose Iβ is treated with anhydrous liquid ammonia). Cellulose III(I) has been the focus of wide interest in the field of cellulosic biofuels, as it can be efficiently hydrolyzed to readily fermentable glucose (its enzymatic degradation rates are up to 5-fold higher than those of cellulose Iβ). The coarse-grained model presented in this study is based on a simplified geometry and on an effective potential mimicking the changes in both intracrystalline hydrogen bonds and stacking interactions during the transition from cellulose Iβ to cellulose III(I). The model reproduces both structural and thermomechanical properties of cellulose Iβ and III(I). The work presented herein describes the structural transition from cellulose Iβ to cellulose III(I) as driven by the change in the equilibrium state of two degrees of freedom in the cellulose chains. The structural transition from cellulose Iβ to cellulose III(I) is essentially reduced to a search for optimal spatial arrangement of the cellulose chains.