Structural Stability Of Actin And Amyloid-β Peptides Revealed By Molecular Dynamics Simulations

Background:The structural stability of proteins is of great significance for the normal function of proteins.As one of the most abundant proteins in eukaryotes,actin plays an important role in life activities.Actin is the main component of thin muscle filaments.The nucleation process of actin and its oligomeric structure are very important to the study of the biological basis of skeletal muscle mechanical properties.It has shown that muscle fibers begin to grow rapidly after actin forms trimer or more oligomers,but the size of actin nucleation is still controversial,and the atomic details of nucleation process are not clear.At the same time,actin is also the main component of the cytoskeleton.Recent studies have found that destroying the cytoskeleton formed by actin in cancer cells can effectively delay the migration of cancer cells,but the molecular mechanism behind it is still unclear.The analysis of actin nucleation process and the conformational stability of different oligomers formed in the process is important for the analysis of the structural basis of actin mechanical properties,and also provides references for the research and development of new cancer treatment methods.In addition,the self-assembly of another protein,amyloid-β（Aβ）,is closely related to the pathogenesis of Alzheimer’s disease.At present,the process of Aβself-assembly is not clear,and the mechanism of action of some inhibitors（such as fullerol）with Aβis also not clear.Exploring the structural stability of Aβoligomers and its influencing factors,which is of great significance to elucidate the molecular mechanism of Aβpathological aggregation and the research and development of novel anti-amyloid inhibitors.Methods:In this paper,we carried out three studies,and they are carried out using all atomic molecular dynamics simulation.The first study is the stability of different systems during actin nucleation.The second is that effect of fullerol molecule(C₆₀（OH）₂₀)on the stability of actin trimer.The last one is the effect of fullerene(C₆₀)and fullerol molecules(C₆₀ and C₆₀（OH）₆/C₆₀（OH）₁₂)on the stability of Aβ_40/42 trimer.All studies were simulated and analyzed using Gromacs software and self-written programs.Results:（1）The RMSD of actin trimer is smoother and less fluctuant than that of actin dimer.Calculations of the RMSF of three systems showed that the actin trimer of residue 150-200 and 250-300 were more tough than the dimer.The D-loop sequence in trimer is also more stable than that in dimer.In addition,through DSSP calculation,our calculation results show that the 45-50 residue sequence of actin trimer changes less before and after simulation than that of dimer and monomer,which is enough to indicate that the D-loop region of trimer is more stable than that of dimer and monomer.Then we calculated the SASA of each residue of the three systems,but the results showed that the SASA of the three systems did not change much,which indicated that SASA did not contribute much to the stability of the three systems.（2）C₆₀（OH）₂₀ could bind to the actin trimer quickly,but the RMSD,RMSF,DSSP and SASA calculations showed that the binding of C₆₀（OH）₂₀ had little effect on the stability of the actin trimer.Later,we speculated that the binding site of C60（OH）20 might be located at the binding site of the subunits and subunits of the actin trimer,thus affecting the formation of actin fibers.（3）C₆₀/C₆₀（OH）₆/C₆₀（OH）₁₂ had little effect on the stability of Aβ₄₂ and Aβ₄₀trimer,but they showed different binding kinetics,binding sites and interactions when binding to Aβ₄₂-trimer.The increased number of hydroxyl groups C₆₀ carries leads to slower binding dynamics and weaker binding strength.Binding free energy analysis demonstrates that the C₆₀/C₆₀（OH）₆ molecule primarily binds to the C-terminal residues 31–41,whereas C₆₀（OH）₁₂ favors to bind to N-terminal residues 4–14.The hydrophobic interaction plays a critical role in the interplay between Aβand all the three nanoparticles,and theπ-stacking interaction gets weakened as C₆₀ carries more hydroxyls.In addition,the C₆₀（OH）₆ molecule has high affinity to form hydrogen bonds with protein backbones.The binding behaviors of C₆₀/C₆₀（OH）₆/C₆₀（OH）₁₂ to the Aβ₄₀ protofibril resemble with those to Aβ₄₂.Our work provides a detailed picture of fullerene/fullerenols binding to Aβprotofibril,and is helpful to understand the underlying inhibitory mechanism.Conclusions:（1）The actin trimer has more stable conformation than the actin dimer.（2）The binding of C₆₀（OH）₂₀ had no effect on actin stability.（3）C₆₀ and C₆₀（OH）₆ can damage the stability of Aβ₄₂ and Aβ₄₀ trimer,while C₆₀（OH）₁₂ has little effect on the stability of Aβ₄₂ and Aβ₄₀ trimer.The C₆₀（OH）₆molecule readily forms hydrogen bonds with the Aβbackbone and is a highly effective inhibitor.