Soft Vibrational Modes Predict Breaking Events during Force-Induced Protein Unfolding

Exploring the unfolding pathways of protein families using Elastic Network Model

We explore how a protein's native structure determines its unfolding process. We examine how the local structural features, like shear, and the global structural properties, like the number of soft modes, change during unfolding. Simulations are performed using a Gaussian Network Model (GNM) with bond breaking for both thermal and force-induced unfolding scenarios. We find that unfolding starts in areas of high shear in the native structure and progressively spreads to the low shear regions. Interestingly, analysis of single domain protein families (Chymotrypsin inhibitor and Barnase) reveal that proteins with distinct unfolding pathways exhibit divergent behavior of the number of soft modes during unfolding. This suggests that the number of soft modes might be a valuable tool for understanding thermal unfolding pathways. Additionally, we found a strong link between a protein's overall structural similarity (TM-score) and its unfolding pathways, highlighting the importance of the native structure in determining how a protein unfolds.

Modeling ultrasonic metafluids: The significance of discrete oscillators

Significant changes in the acoustic response of a fluid can be induced by the suspension of tiny, subwavelength-size discrete micro-oscillators in the fluid. We investigate how the topological properties of these oscillators, such as the mass distribution and connectivity of the oscillator parts, influence the effective dynamic density and compressibility of the fluid in which they are embedded. We demonstrate a superior, metamaterial-like response of the suspension when using micro-oscillators with a high density of low-frequency modes. Such low-frequency modes occur in loosely connected microstructures and make the system much more experimentally feasible due to the larger ultrasonic attenuation length at these frequencies. In addition, the absence of need for an intricately designed structure brings experimental implementation within reach.

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.

First Principles Calculation of Protein-Protein Dimer Affinities of ALS-Associated SOD1 Mutants

Cu,Zn superoxide dismutase (SOD1) is a 32 kDa homodimer that converts toxic oxygen radicals in neurons to less harmful species. The dimerization of SOD1 is essential to the stability of the protein. Monomerization increases the likelihood of SOD1 misfolding into conformations associated with aggregation, cellular toxicity, and neuronal death in familial amyotrophic lateral sclerosis (fALS). The ubiquity of disease-associated mutations throughout the primary sequence of SOD1 suggests an important role of physicochemical processes, including monomerization of SOD1, in the pathology of the disease. Herein, we use a first-principles statistical mechanics method to systematically calculate the free energy of dimer binding for SOD1 using molecular dynamics, which involves sequentially computing conformational, orientational, and separation distance contributions to the binding free energy. We consider the effects of two ALS-associated mutations in SOD1 protein on dimer stability, A4V and D101N, as well as the role of metal binding and disulfide bond formation. We find that the penalty for dimer formation arising from the conformational entropy of disordered loops in SOD1 is significantly larger than that for other protein-protein interactions previously considered. In the case of the disulfide-reduced protein, this leads to a bound complex whose formation is energetically disfavored. Somewhat surprisingly, the loop free energy penalty upon dimerization is still significant for the holoprotein, despite the increased structural order induced by the bound metal cations. This resulted in a surprisingly modest increase in dimer binding free energy of only about 1.5 kcal/mol upon metalation of the protein, suggesting that the most significant stabilizing effects of metalation are on folding stability rather than dimer binding stability. The mutant A4V has an unstable dimer due to weakened monomer-monomer interactions, which are manifested in the calculation by a separation free energy surface with a lower barrier. The mutant D101N has a stable dimer partially due to an unusually rigid β-barrel in the free monomer. D101N also exhibits anticooperativity in loop folding upon dimerization. These computational calculations are, to our knowledge, the most quantitatively accurate calculations of dimer binding stability in SOD1 to date.

Enhancement of protein mechanical stability: Correlated deformations are handcuffed by ligand binding

As revealed by previous experiments, protein mechanical stability can be effectively regulated by ligand binding with the binding site distant from the force-bearing region. However, the mechanism for such long-range allosteric control of protein mechanics is still largely unknown. In this work, we use protein topology-based elastic network model (ENM) and all-atomic steered molecular dynamics (SMD) simulations to study the impact of ligand binding on protein mechanical stability in two systems, i.e., GB1 and CheY-binding P2-domain of CheA (CBDCheA). Both ENM and SMD results show that the ligand binding has considerable and negligible effects on the mechanical stability of these two proteins, respectively. These results are consistent with the experimental observations. A physical mechanism for the enhancement of protein mechanical stability was then proposed: the correlated deformations of the force-bearing region and the binding site are handcuffed by the binding of ligand. The handcuff effect suppresses the propagation of internal force in the force-bearing region, thus improving the resistance to the loading force. Our study indicates that ENM method can effectively identify the structure motifs allosterically related to the deformation in the force bearing region, as well as the force propagation pathway within the structure of the studied proteins. Hence, it should be helpful to understand the molecular origin of the different mechanical properties in response to ligand binding for GB1 and CBDCheA.

Stability and Local Unfolding of SOD1 in the Presence of Protein Crowders

Using NMR and Monte Carlo (MC) methods, we investigate the stability and dynamics of superoxide dismutase 1 (SOD1) in homogeneous crowding environments, where either bovine pancreatic trypsin inhibitor (BPTI) or the B1 domain of streptococcal protein G (PGB1) serves as a crowding agent. By NMR, we show that both crowders, and especially BPTI, cause a drastic loss in the overall stability of SOD1 in its apo monomeric form. Additionally, we determine chemical shift perturbations indicating that SOD1 interacts with the crowder proteins in a residue-specific manner that further depends on the identity of the crowding protein. Furthermore, the specificity of SOD1-crowder interactions is reciprocal: chemical shift perturbations on BPTI and PGB1 identify regions that interact preferentially with SOD1. By MC simulations, we investigate the local unfolding of SOD1 in the absence and presence of the crowders. We find that the crowders primarily interact with the long flexible loops of the folded SOD1 monomer. The basic mechanisms by which the SOD1 β-barrel core unfolds remain unchanged when adding the crowders. In particular, both with and without the crowders, the second β-sheet of the barrel is more dynamic and unfolding-prone than the first. Notably, the MC simulations (exploring the early stages of SOD1 unfolding) and the NMR experiments (under equilibrium conditions) identify largely the same set of PGB1 and BPTI residues as prone to form SOD1 contacts. Thus, contacts stabilizing the unfolded state of SOD1 in many cases appear to form early in the unfolding reaction.