Molecular Mechanism of Protein Unfolding under Shear: A Lattice Boltzmann Molecular Dynamics Study

Proteins are marginally stable soft-matter entities that can be disrupted using a variety of perturbative stresses, including thermal, chemical, or mechanical ones. Fluid under extreme flow conditions is a possible route to probe the weakness of biomolecules and collect information on the molecular cohesive interactions that secure their stability. Moreover, in many cases, physiological flow triggers the functional response of specialized proteins as occurring in blood coagulation or cell adhesion. We deploy the Lattice Boltzmann molecular dynamics technique based on the coarse-grained model for protein OPEP to study the mechanism of protein unfolding under Couette flow. Our simulations provide a clear view of how structural elements of the proteins are affected by shear, and for the simple study case, the β-hairpin, we exploited the analogy to pulling experiments to quantify the mechanical forces acting on the protein under shear

Coarse-Grained Simulations of RNA and DNA Duplexes

Although RNAs play many cellular functions, little is known about the dynamics and thermodynamics of these molecules. In principle, all-atom molecular dynamics simulations can investigate these issues, but with current computer facilities, these simulations have been limited to small RNAs and to short times. HiRe-RNA, a recently proposed high-resolution coarse-grained RNA that captures many geometric details such as base pairing and stacking, is able to fold RNA molecules to near-native structures in a short computational time. So far, it had been applied to simple hairpins, and here we present its application to duplexes of a couple dozen nucleotides and show how with replica exchange molecular dynamics (REMD) we can easily predict the correct double helix from a completely random configuration and study the dissociation curve. To show the versatility of our model, we present an application to a double stranded DNA molecule as well. A reconstruction algorithm allows us to obtain full atom structures from the coarse-grained model. Through atomistic molecular dynamics (MD), we can compare the dynamics starting from a representative structure of a low temperature replica or from the experimental structure, and show how the two are statistically identical, highlighting the validity of a coarse-grained approach for structured RNAs and DNAs

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

High-Resolution Structures of the Amyloid‑β 1–42 Dimers from the Comparison of Four Atomistic Force Fields

The dimer of the amyloid-β peptide Aβ of 42 residues is the smallest toxic species in Alzheimer’s disease, but its equilibrium structures are unknown. Here we determined the equilibrium ensembles generated by the four atomistic OPLS-AA, CHARMM22*, AMBER99sb-ildn, and AMBERsb14 force fields with the TIP3P water model. On the basis of 144 μs replica exchange molecular dynamics simulations (with 750 ns per replica), we find that the four force fields lead to random coil ensembles with calculated cross-collision sections, hydrodynamics properties, and small-angle X-ray scattering profiles independent of the force field. There are, however, marked differences in secondary structure, with the AMBERsb14 and CHARMM22* ensembles overestimating the CD-derived helix content, and the OPLS-AA and AMBER99sb-ildn secondary structure contents in agreement with CD data. Also the intramolecular beta-hairpin content spanning residues 17–21 and 30–36 varies between 1.5% and 13%. Overall, there are significant differences in tertiary and quaternary conformations among all force fields, and the key finding, irrespective of the force field, is that the dimer is stabilized by nonspecific interactions, explaining therefore its possible transient binding to multiple cellular partners and, in part, its toxicity

Distinct Dimerization for Various Alloforms of the Amyloid-Beta Protein: Aβ_1–40, Aβ_1–42, and Aβ_1–40(D23N)

The Amyloid-beta protein is related to Alzheimer’s disease, and various experiments have shown that oligomers as small as the dimer are cytotoxic. Two alloforms are mainly produced: Aβ_1–40 and Aβ_1–42. They have very different oligomer distributions, and it was recently suggested, from experimental studies, that this variation may originate from structural differences in their dimer structures. Little structural information is available on the Aβ dimer, however, and to complement experimental observations, we simulated the folding of the wild-type Aβ_1–40 and Aβ_1–42 dimers as well as the mutated Aβ_1–40(D23N) dimer using an accurate coarse-grained force field coupled to Hamiltonian-temperature replica exchange molecular dynamics. The D23N variant impedes the salt-bridge formation between D23 and K28 seen in the wild-type Aβ, leading to very different fibrillation properties and final amyloid fibrils. Our results show that the Aβ_1–42 dimer has a higher propensity than the Aβ_1–40 dimer to form β-strands at the central hydrophobic core (residues 17–21) and at the C-terminal (residues 30–42), which are two segments crucial to the oligomerization of Aβ. The free energy landscape of the Aβ_1–42 dimer is also broader and more complex than that of the Aβ_1–40 dimer. Interestingly, D23N also impacts the free energy landscape by increasing the population of configurations with higher β-strand propensities when compared against Aβ₄₀. In addition, while Aβ_1–40(D23N) displays a higher β-strand propensity at the C-terminal, its solvent accessibility does not change with respect to the wild-type sequence. Overall, our results show the strong impact of the two amino acids Ile41-Ala42 and the salt-bridge D23–K28 on the folding of the Aβ dimer

Improved PEP-FOLD Approach for Peptide and Miniprotein Structure Prediction

Peptides and mini proteins have many biological and biomedical implications, which motivates the development of accurate methods, suitable for large-scale experiments, to predict their experimental or native conformations solely from sequences. In this study, we report PEP-FOLD2, an improved coarse grained approach for peptide de novo structure prediction and compare it with PEP-FOLD1 and the state-of-the-art Rosetta program. Using a benchmark of 56 structurally diverse peptides with 25–52 amino acids and a total of 600 simulations for each system, PEP-FOLD2 generates higher quality models than PEP-FOLD1, and PEP-FOLD2 and Rosetta generate near-native or native models for 95% and 88% of the targets, respectively. In the situation where we do not have any experimental structures at hand, PEP-FOLD2 and Rosetta return a near-native or native conformation among the top five best scored models for 80% and 75% of the targets, respectively. While the PEP-FOLD2 prediction rate is better than the ROSETTA prediction rate by 5%, this improvement is non-negligible because PEP-FOLD2 explores a larger conformational space than ROSETTA and consists of a single coarse-grained phase. Our results indicate that if the coarse-grained PEP-FOLD2 method is approaching maturity, we are not at the end of the game of mini-protein structure prediction, but this opens new perspectives for large-scale in silico experiments

Atomic and Dynamic Insights into the Beneficial Effect of the 1,4-Naphthoquinon-2-yl‑l‑tryptophan Inhibitor on Alzheimer’s Aβ1–42 Dimer in Terms of Aggregation and Toxicity

Aggregation of the amyloid β protein (Aβ) peptide with 40 or 42 residues is one key feature in Alzheimer’s disease (AD). The 1,4-naphthoquinon-2-yl-l-tryptophan (NQTrp) molecule was reported to alter Aβ self-assembly and reduce toxicity. Though nuclear magnetic resonance experiments and various simulations provided atomic information about the interaction of NQTrp with Aβ peptides spanning the regions of residues 12–28 and 17–42, none of these studies were conducted on the full-length Aβ1–42 peptide. To this end, we performed extensive atomistic replica exchange molecular dynamics simulations of Aβ1–42 dimer with two NQTrp molecules in explicit solvent, by using a force field known to fold diverse proteins correctly. The interactions between NQTrp and Aβ1–42, which change the Aβ interface by reducing most of the intermolecular contacts, are found to be very dynamic and multiple, leading to many transient binding sites. The most favorable binding residues are Arg5, Asp7, Tyr10, His13, Lys16, Lys18, Phe19/Phe20, and Leu34/Met35, providing therefore a completely different picture from <i>in vitro</i> and <i>in silico</i> experiments with NQTrp with shorter Aβ fragments. Importantly, the 10 hot residues that we identified explain the beneficial effect of NQTrp in reducing both the level of Aβ1–42 aggregation and toxicity. Our results also indicate that there is room to design more efficient drugs targeting Aβ1–42 dimer against AD

Molecular Mechanism of the Inhibition of EGCG on the Alzheimer Aβ_1–42 Dimer

Growing evidence supports that amyloid β (Aβ) oligomers are the major causative agents leading to neural cell death in Alzheimer’s disease. The polyphenol (−)-epigallocatechin gallate (EGCG) was recently reported to inhibit Aβ fibrillization and redirect Aβ aggregation into unstructured, off-pathway oligomers. Given the experimental challenge to characterize the structures of Aβ/EGCG complexes, we performed extensive atomistic replica exchange molecular dynamics simulations of Aβ_1–42 dimer in the present and absence of EGCG in explicit solvent. Our equilibrium Aβ dimeric structures free of EGCG are consistent with the collision cross section from ion-mobility mass spectrometry and the secondary structure composition from circular dichroism experiment. In the presence of EGCG, the Aβ structures are characterized by increased inter-center-of-mass distances, reduced interchain and intrachain contacts, reduced β-sheet content, and increased coil and α-helix contents. Analysis of the free energy surfaces reveals that the Aβ dimer with EGCG adopts new conformations, affecting therefore its propensity to adopt fibril-prone states. Overall, this study provides, for the first time, insights on the equilibrium structures of Aβ_1–42 dimer in explicit aqueous solution and an atomic picture of the EGCG-mediated conformational change on Aβ dimer

Importance of the Ion-Pair Interactions in the OPEP Coarse-Grained Force Field: Parametrization and Validation

We have derived new effective interactions that improve the description of ion pairs in the Optimized Potential for Efficient protein structure Prediction (OPEP) coarse-grained force field without introducing explicit electrostatic terms. The iterative Boltzmann inversion method was used to extract these potentials from all-atom simulations by targeting the radial distribution function of the distance between the center of mass of the side chains. The new potentials have been tested on several systems that differ in structural properties, thermodynamic stabilities, and number of ion pairs. Our modeling, by refining the packing of the charged amino acids, impacts the stability of secondary structure motifs and the population of intermediate states during temperature folding/unfolding; it also improves the aggregation propensity of peptides. The new version of the OPEP force field has the potentiality to describe more realistically a large spectrum of situations where salt-bridges are key interactions

Effect of the English Familial Disease Mutation (H6R) on the Monomers and Dimers of Aβ40 and Aβ42

The self-assembly of the amyloid beta (Aβ) peptides into senile plaques is the hallmark of Alzheimer’s disease. Recent experiments have shown that the English familial disease mutation (H6R) speeds up the fibril formation process of alloforms Aβ₄₀ and Aβ₄₂ peptides altering their toxicity to cells. We used all-atom molecular dynamics simulations at microsecond time scales with the OPLS-AA force field and TIP4P explicit water model to study the structural dynamics of the monomer and dimer of H6R sequences of both peptides. The reason behind the self-assembly acceleration is common that upon mutation the net charge is reduced leading to the weaker repulsive interaction between chains that facilitates the peptide association. In addition, our estimation of the solvation free energy shows that the mutation enhances the hydrophobicity of both peptides speeding up their aggregation. However, we can show that the acceleration mechanisms are different for different peptides: the rate of fibril formation of Aβ₄₂ increases due to increased β-structure at the C-terminal in both monomer and dimer and enhanced stability of salt bridge Asp23-Lys28 in monomer, while the enhancement of turn at residues 25–29 and reduction of coil in regions 10–13, 26–19, and 30–34 would play the key role for Aβ₄₀. Overall, our study provides a detailed atomistic picture of the H6R-mediated conformational changes that are consistent with the experimental findings and highlights the important role of the N-terminal in Aβ peptide aggregation