The Unfolding Journey of Superoxide Dismutase 1 Barrels under Crowding: Atomistic Simulations Shed Light on Intermediate States and Their Interactions with Crowders

Comprehensive picture of β-barrel transformation in the fibrillogenesis of odorant-binding proteins

Protein dysfunction can be caused by its fibrillogenesis, which is often initiated by rather subtle structural changes. In the case of odorant-binding proteins (OBPs), fibrillogenesis triggering is mediated by local melting of the peripheral C-terminal domain while maintaining the integrity of the bulk of the molecule, the β-barrel. This work is focused on establishing the sequence and duration of structural transformations of OBPs' β-barrel during fibrillogenesis. We found that β-barrel transformation requires oligomerization of OBPs monomers with unlocked C-terminus, whose formation precedes the fibrillogenesis initiation. The fibrillogenesis lag phase involves the gradual bond weakening within the β-barrel without its destruction. During this phase, oligomeric molecules first experience partial disruption of contacts near the β1-strand, followed by its disorganization and the opening of the internal protein cavity. In the exponential phase, complete β-barrel reorganization in aggregates lasts as long as the lag phase, accompanied by the sequential appearance of prefibrillar forms with cytotoxicity and mature amyloid fibrils. Our findings suggest similarities in the intermediate states accumulated during fibrillogenesis as well as common mechanisms and sequence of structural transitions for proteins of β-barrel topology. This contributes to the identification of relevant targets and possible ways to inhibit amyloidogenesis of these proteins.

In Silico View of Crowding: Biomolecular Processes to Nanomaterial Design

It is widely accepted that deciphering biomolecular structure and function requires going beyond the single-molecule or single-complex paradigm. The densely packed macromolecules, cosolutes, and metabolites in the living cell impose crowding effects on the biomolecular structure and dynamics that need to be accounted for. Molecular simulations have proven to be a powerful tool to advance the current molecular-level understanding of such a highly concentrated, complex milieu. This Mini-Review focuses on summarizing the understanding achieved so far for the effects of crowding on biomolecular processes using computational methods, along with highlighting a new direction in employing crowding as a tool for tunable nanomaterial design. The two schools of thought that form the pillars of the current understanding of crowding effects are discussed. The investigation of crowded solutions using physics-based models that encompass different time and length scales to mimic the intracellular environment are described. The limitations and challenges faced by the current models and simulation methods are addressed, highlighting the gaps to be filled for better agreement with experiments. Crowding can also act as an effective tool to modulate the structure-property-function relationships of nanomaterials, leading to the development of novel functional materials. A few recent studies, mostly experimental, have been summarized in this direction. The Mini-Review concludes with an outlook for future developments in this field in order to enable accurate mimicking of the intracellular environment using simulations and to bridge the gap between biological processes and nanomaterial design.

Stability and deformation of biomolecular condensates under the action of shear flow

Biomolecular condensates play a key role in cytoplasmic compartmentalization and cell functioning. Despite extensive research on the physico-chemical, thermodynamic, or crowding aspects of the formation and stabilization of the condensates, one less studied feature is the role of external perturbative fluid flow. In fact, in living cells, shear stress may arise from streaming or active transport processes. Here, we investigate how biomolecular condensates are deformed under different types of shear flows. We first model Couette flow perturbations via two-way coupling between the condensate dynamics and fluid flow by deploying Lattice Boltzmann Molecular Dynamics. We then show that a simplified approach where the shear flow acts as a static perturbation (one-way coupling) reproduces the main features of the condensate deformation and dynamics as a function of the shear rate. With this approach, which can be easily implemented in molecular dynamics simulations, we analyze the behavior of biomolecular condensates described through residue-based coarse-grained models, including intrinsically disordered proteins and protein/RNA mixtures. At lower shear rates, the fluid triggers the deformation of the condensate (spherical to oblated object), while at higher shear rates, it becomes extremely deformed (oblated or elongated object). At very high shear rates, the condensates are fragmented. We also compare how condensates of different sizes and composition respond to shear perturbation, and how their internal structure is altered by external flow. Finally, we consider the Poiseuille flow that realistically models the behavior in microfluidic devices in order to suggest potential experimental designs for investigating fluid perturbations in vitro.

Computational Approaches to Predict Protein-Protein Interactions in Crowded Cellular Environments

Investigating protein-protein interactions is crucial for understanding cellular biological processes because proteins often function within molecular complexes rather than in isolation. While experimental and computational methods have provided valuable insights into these interactions, they often overlook a critical factor: the crowded cellular environment. This environment significantly impacts protein behavior, including structural stability, diffusion, and ultimately the nature of binding. In this review, we discuss theoretical and computational approaches that allow the modeling of biological systems to guide and complement experiments and can thus significantly advance the investigation, and possibly the predictions, of protein-protein interactions in the crowded environment of cell cytoplasm. We explore topics such as statistical mechanics for lattice simulations, hydrodynamic interactions, diffusion processes in high-viscosity environments, and several methods based on molecular dynamics simulations. By synergistically leveraging methods from biophysics and computational biology, we review the state of the art of computational methods to study the impact of molecular crowding on protein-protein interactions and discuss its potential revolutionizing effects on the characterization of the human interactome.

Myricetin: A Potent Anti-Amyloidogenic Polyphenol against Superoxide Dismutase 1 Aggregation

Amyotrophic lateral sclerosis (ALS) is believed to be caused by the aggregation of misfolded or mutated superoxide dismutase 1 (SOD1). As there is currently no treatment, research into aggregation inhibitors continues. Based on docking, molecular dynamics (MD) simulations, and experimental observations, we propose that myricetin, a plant flavonoid, can act as a potent anti-amyloidogenic polyphenol against SOD1 aggregation. Our MD simulation results showed that myricetin stabilizes the protein interface, destabilizes the preformed fibril, and decreases the rate of fibril elongation. Myricetin inhibits the aggregation of SOD1 in a dose-dependent manner as shown by the ThT aggregation kinetics curves. Our transmission electron microscopy, dynamic light scattering, and circular dichroism experiments indicate that fewer shorter fibrils have formed. Fluorescence spectroscopy results predict the involvement of a static quenching mechanism characterized by a strong binding between protein and myricetin. Importantly, size exclusion chromatography revealed the potential of myricetin for fibril destabilization and depolymerization. These experimental observations complement the MD results. Thus, myricetin is a potent SOD1 aggregation inhibitor that can reduce the fibril load. Using the structure of myricetin as a reference, it is possible to design more effective therapeutic inhibitors against ALS that prevent the disease and reverse its effects.

Acceleration of generalized replica exchange with solute tempering simulations of large biological systems on massively parallel supercomputer

Generalized replica exchange with solute tempering (gREST) is one of the enhanced sampling algorithms for proteins or other systems with rugged energy landscapes. Unlike the replica-exchange molecular dynamics (REMD) method, solvent temperatures are the same in all replicas, while solute temperatures are different and are exchanged frequently between replicas for exploring various solute structures. Here, we apply the gREST scheme to large biological systems containing over one million atoms using a large number of processors in a supercomputer. First, communication time on a multi-dimensional torus network is reduced by matching each replica to MPI processors optimally. This is applicable not only to gREST but also to other multi-copy algorithms. Second, energy evaluations, which are necessary for the multistate bennet acceptance ratio (MBAR) method for free energy estimations, are performed on-the-fly during the gREST simulations. Using these two advanced schemes, we observed 57.72 ns/day performance in 128-replica gREST calculations with 1.5 million atoms system using 16,384 nodes in Fugaku. These schemes implemented in the latest version of GENESIS software could open new possibilities to answer unresolved questions on large biomolecular complex systems with slow conformational dynamics.

Optimized OPEP Force Field for Simulation of Crowded Protein Solutions

Macromolecular crowding has profound effects on the mobility of proteins, with strong implications on the rates of intracellular processes. To describe the dynamics of crowded environments, detailed molecular models are needed, capturing the structures and interactions arising in the crowded system. In this work, we present OPEPv7, which is a coarse-grained force field at amino-acid resolution, suited for rigid-body simulations of the structure and dynamics of crowded solutions formed by globular proteins. Using the OPEP protein model as a starting point, we have refined the intermolecular interactions to match the experimentally observed dynamical slowdown caused by crowding. The resulting force field successfully reproduces the diffusion slowdown in homogeneous and heterogeneous protein solutions at different crowding conditions. Coupled with the lattice Boltzmann technique, it allows the study of dynamical phenomena in protein assemblies and opens the way for the in silico rheology of protein solutions.

Governing dynamics and preferential binding of the AXH domain influence the aggregation pathway of Ataxin-1

The present state of understanding the mechanism of Spinocerebellar Ataxia-1, a fatal neurodegenerative disease linked to the protein Ataxin-1 (ATXN1), is baffled by a set of self-contradictory, and hence, inconclusive observations. This fallacy poses a bottleneck to the effective designing of curable drugs as the field is currently missing the specific druggable site. To understand the fundamentals of pathogenesis, we tried to decipher the intricacies of the extremely complicated landscape by targeting the relevant species that supposedly dictate the structure-function paradigm. The atomic-level description and characterization of the dynamism of the systems reveal the existence of structural polymorphism in all the leading stakeholders of the overall system. The very existence of conformational heterogeneity in every species creates numerous possible combinations of favorable interactions because of the variability in segmental cross-talks and hence claims its role in the choice of routes between functional activity and dysfunctional disease-causing aggregation. Despite this emergent configurational diversity, there is a common mode of operative intermolecular forces that dictates the extent of stability of all the multimeric complexes due to the localized population of a specific type of residue. The present research proposes a dynamic switch mechanism between aggregability and functional activity, based on the logical interpretation of the estimated variables, which is practically dictated by the effective concentration of the interacting species involved in the cell.

Diffusive Dynamics of Bacterial Proteome as a Proxy of Cell Death

Temperature variations have a big impact on bacterial metabolism and death, yet an exhaustive molecular picture of these processes is still missing. For instance, whether thermal death is determined by the deterioration of the whole or a specific part of the proteome is hotly debated. Here, by monitoring the proteome dynamics of E. coli, we clearly show that only a minor fraction of the proteome unfolds at the cell death. First, we prove that the dynamical state of the E. coli proteome is an excellent proxy for temperature-dependent bacterial metabolism and death. The proteome diffusive dynamics peaks at about the bacterial optimal growth temperature, then a dramatic dynamical slowdown is observed that starts just below the cell's death temperature. Next, we show that this slowdown is caused by the unfolding of just a small fraction of proteins that establish an entangling interprotein network, dominated by hydrophobic interactions, across the cytoplasm. Finally, the deduced progress of the proteome unfolding and its diffusive dynamics are both key to correctly reproduce the E. coli growth rate.

A Zn-dependent structural transition of SOD1 modulates its ability to undergo phase separation

The misfolding and mutation of Cu/Zn superoxide dismutase (SOD1) is commonly associated with amyotrophic lateral sclerosis (ALS). SOD1 can accumulate within stress granules (SGs), a type of membraneless organelle, which is believed to form via liquid-liquid phase separation (LLPS). Using wild-type, metal-deficient, and different ALS disease mutants of SOD1 and computer simulations, we report here that the absence of Zn leads to structural disorder within two loop regions of SOD1, triggering SOD1 LLPS and amyloid formation. The addition of exogenous Zn to either metal-free SOD1 or to the severe ALS mutation I113T leads to the stabilization of the loops and impairs SOD1 LLPS and aggregation. Moreover, partial Zn-mediated inhibition of LLPS was observed for another severe ALS mutant, G85R, which shows perturbed Zn-binding. By contrast, the ALS mutant G37R, which shows reduced Cu-binding, does not undergo LLPS. In addition, SOD1 condensates induced by Zn-depletion exhibit greater cellular toxicity than aggregates formed by prolonged incubation under aggregating conditions. Overall, our work establishes a role for Zn-dependent modulation of SOD1 conformation and LLPS properties that may contribute to amyloid formation.

Self-Assembly of Amyloid-Beta (Aβ) Peptides from Solution to Near In Vivo Conditions

Understanding the atomistic resolution changes during the self-assembly of amyloid peptides or proteins is important to develop compounds or conditions to alter the aggregation pathways and suppress the toxicity and potentially aid in the development of drugs. However, the complexity of protein aggregation and the transient order/disorder of oligomers along the pathways to fibril are very challenging. In this Perspective, we discuss computational studies of amyloid polypeptides carried out under various conditions, including conditions closely mimicking in vivo and point out the challenges in obtaining physiologically relevant results, focusing mainly on the amyloid-beta Aβ peptides.

Effects of Protein Crowders and Charge on the Folding of Superoxide Dismutase 1 Variants: A Computational Study

The neurodegenerative disease amyotrophic lateral sclerosis (ALS) is associated with the misfolding and aggregation of the metalloenzyme protein superoxide dismutase 1 (SOD1) via mutations that destabilize the monomer-dimer interface. In a cellular environment, crowding and electrostatic screening play essential roles in the folding and aggregation of the SOD1 monomers. Despite numerous studies on the effects of mutations on SOD1 folding, a clear understanding of the interplay between crowding, folding, and aggregation in vivo remains lacking. Using a structure-based minimal model for molecular dynamics simulations, we investigate the role of self-crowding and charge on the folding stability of SOD1 and the G41D mutant where experimentalists were intrigued by an alteration of the folding mechanism by a single point mutation from glycine to charged aspartic acid. We show that unfolded SOD1 configurations are significantly affected by charge and crowding, a finding that would be extremely costly to achieve with all-atom simulations, while the native state is not significantly altered. The mutation at residue 41 alters the interactions between proteins in the unfolded states instead of those within a protein. This paper suggests electrostatics may play an important role in the folding pathway of SOD1 and modifying the charge via mutation and ion concentration may change the dominant interactions between proteins, with potential impacts for aggregation of the mutants. This work provides a plausible reason for the alteration of the unfolded states to address why the mutant G41D causes the changes to the folding mechanism of SOD1 that have intrigued experimentalists.

Toxic SOD1 trimers are off-pathway in the formation of amyloid-like fibrils in ALS

Accumulation of insoluble amyloid fibrils is widely studied as a critical factor in the pathology of multiple neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), a fatal neurodegenerative disease. Misfolded Cu, Zn superoxide dismutase (SOD1) was the first protein linked to ALS, and non-native SOD1 trimeric oligomers were recently linked to cytotoxicity, while larger oligomers were protective to cells. The balance between trimers and larger aggregates in the process of SOD1 aggregation is, thus, a critical determinant of potential therapeutic approaches to treat ALS. Yet, it is unknown whether these trimeric oligomers are a necessary intermediate for larger aggregate formation or a distinct off-pathway species competing with fibril formation. Depending on the on- or off-pathway scenario of trimer formation, we expect drastically different therapeutic approaches. Here, we show that the toxic SOD1 trimer is an off-pathway intermediate competing with protective fibril formation. We design mutant SOD1 constructs that remain in a trimeric state (super stable trimers) and show that stabilizing the trimeric SOD1 prevents formation of fibrils in vitro and in a motor neuron like cell model (NSC-34). Using size exclusion chromatography, we track the aggregation kinetics of purified SOD1 and show direct competition of trimeric SOD1 with larger oligomer and fibril formation. Finally, we show the trimer is structurally independent of both larger soluble oligomers and insoluble fibrils using circular dichroism spectroscopy and limited proteolysis.

Protein assembly and crowding simulations

Proteins encounter frequent molecular interactions in biological environments. Computer simulations have become an increasingly important tool in providing mechanistic insights into how such interactions in vivo relate to their biological function. The review here focuses on simulations describing protein assembly and molecular crowding effects as two important aspects that are distinguished mainly by how specific and long-lived protein contacts are. On the topic of crowding, recent simulations have provided new insights into how crowding affects protein folding and stability, modulates enzyme activity, and affects diffusive properties. Recent studies of assembly processes focus on assembly pathways, especially for virus capsids, amyloid aggregation pathways, and the role of multivalent interactions leading to phase separation. Also, discussed are technical challenges in achieving increasingly realistic simulations of interactions in cellular environments.

Computational Insights into the Unfolding of a Destabilized Superoxide Dismutase 1 Mutant

In this work, we investigate the β-barrel of superoxide dismutase 1 (SOD1) in a mutated form, the isoleucine 35 to alanine (I35A) mutant, commonly used as a model system to decipher the role of the full-length apoSOD1 protein in amyotrophic lateral sclerosis (ALS). It is known from experiments that the mutation reduces the stability of the SOD1 barrel and makes it largely unfolded in the cell at 37 degrees Celsius. We deploy state-of-the-art computational machinery to examine the thermal destabilization of the I35A mutant by comparing two widely used force fields, Amber a99SB-disp and CHARMM36m. We find that only the latter force field, when combined with the Replica Exchange with Solute Scaling (REST2) approach, reproduces semi-quantitatively the experimentally observed shift in the melting between the original and the mutated SOD1 barrel. In addition, we analyze the unfolding process and the conformational landscape of the mutant, finding these largely similar to those of the wildtype. Nevertheless, we detect an increased presence of partially misfolded states at ambient temperatures. These states, featuring conformational changes in the region of the β-strands β4-β6, might provide a pathway for nonnative aggregation.

Exposure of Von Willebrand Factor Cleavage Site in A1A2A3-Fragment under Extreme Hydrodynamic Shear

Von Willebrand Factor (vWf) is a giant multimeric extracellular blood plasma involved in hemostasis. In this work we present multi-scale simulations of its three-domains fragment A1A2A3. These three domains are essential for the functional regulation of vWf. Namely the A2 domain hosts the site where the protease ADAMTS13 cleavages the multimeric vWf allowing for its length control that prevents thrombotic conditions. The exposure of the cleavage site follows the elongation/unfolding of the domain that is caused by an increased shear stress in blood. By deploying Lattice Boltzmann molecular dynamics simulations based on the OPEP coarse-grained model for proteins, we investigated at molecular level the unfolding of the A2 domain under the action of a perturbing shear flow. We described the structural steps of this unfolding that mainly concerns the β-strand structures of the domain, and we compared the process occurring under shear with that produced by the action of a directional pulling force, a typical condition of single molecule experiments. We observe, that under the action of shear flow, the competition among the elongational and rotational components of the fluid field leads to a complex behaviour of the domain, where elongated structures can be followed by partially collapsed melted globule structures with a very different degree of exposure of the cleavage site. Our simulations pose the base for the development of a multi-scale in-silico description of vWf dynamics and functionality in physiological conditions, including high resolution details for molecular relevant events, e.g., the binding to platelets and collagen during coagulation or thrombosis.

Specific Interactions and Environment Flexibility Tune Protein Stability under Extreme Crowding

Macromolecular crowding influences protein mobility and stability in vivo. A precise description of the crowding effect on protein thermal stability requires the estimate of the combined effects of excluded volume, specific protein-environment interactions, as well as the thermal response of the crowders. Here, we explore an ideal model system, the lysozyme protein in powder state, to dissect the factors controlling the melting of the protein under extreme crowding. By deploying state-of-the art molecular simulations, supported by calorimetric experiments, we assess the role of the environment flexibility and of intermolecular electrostatic interactions. In particular, we show that the temperature-dependent flexibility of the macromolecular crowders, along with specific interactions, significantly alleviates the stabilizing contributions of the static volume effect.

Polyanions Cause Protein Destabilization Similar to That in Live Cells

The structural stability of proteins is found to markedly change upon their transfer to the crowded interior of live cells. For some proteins, the stability increases, while for others, it decreases, depending on both the sequence composition and the type of host cell. The mechanism seems to be linked to the strength and conformational bias of the diffusive in-cell interactions, where protein charge is found to play a decisive role. Because most proteins, nucleotides, and membranes carry a net-negative charge, the intracellular environment behaves like a polyanionic (Z:1) system with electrostatic interactions different from those of standard 1:1 ion solutes. To determine how such polyanion conditions influence protein stability, we use negatively charged polyacetate ions to mimic the net-negatively charged cellular environment. The results show that, per Na+ equivalent, polyacetate destabilizes the model protein SOD1barrel significantly more than monoacetate or NaCl. At an equivalent of 100 mM Na+, the polyacetate destabilization of SOD1barrel is similar to that observed in live cells. By the combined use of equilibrium thermal denaturation, folding kinetics, and high-resolution nuclear magnetic resonance, this destabilization is primarily assigned to preferential interaction between polyacetate and the globally unfolded protein. This interaction is relatively weak and involves mainly the outermost N-terminal region of unfolded SOD1barrel. Our findings point thus to a generic influence of polyanions on protein stability, which adds to the sequence-specific contributions and needs to be considered in the evaluation of in vivo data.

Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis

Protein misfolding and aggregation is observed in many amyloidogenic diseases affecting either the central nervous system or a variety of peripheral tissues. Structural and dynamic characterization of all species along the pathways from monomers to fibrils is challenging by experimental and computational means because they involve intrinsically disordered proteins in most diseases. Yet understanding how amyloid species become toxic is the challenge in developing a treatment for these diseases. Here we review what computer, in vitro, in vivo, and pharmacological experiments tell us about the accumulation and deposition of the oligomers of the (Aβ, tau), α-synuclein, IAPP, and superoxide dismutase 1 proteins, which have been the mainstream concept underlying Alzheimer's disease (AD), Parkinson's disease (PD), type II diabetes (T2D), and amyotrophic lateral sclerosis (ALS) research, respectively, for many years.

Stabilizing or Destabilizing: Simulations of Chymotrypsin Inhibitor 2 under Crowding Reveal Existence of a Crossover Temperature

The effect of macromolecular crowding on the stability of proteins can change with temperature. This dependence might reveal a delicate balance between two factors: the entropic excluded volume and the stability-modulating quinary interactions. Here we computationally investigate the thermal stability of the native state of chymotrypsin inhibitor 2 (CI2), which was previously shown by experiments to be destabilized by protein crowders at room temperature. Mimicking experimental conditions, our enhanced-sampling atomistic simulations of CI2 surrounded by lysozyme and bovine serum albumin reproduce this destabilization but also provide evidence of a crossover temperature above which lysozyme is found to become stabilizing, as previously predicted by analysis of thermodynamic data. We relate this crossover to the different CI2-crowder interactions and the local packing experienced by CI2. In fact, we clearly show that the pronounced stabilization induced by lysozyme at high temperatures stems from the tight local packing created around CI2 by this smaller crowder.