Molecular Mechanism Of Catecholamines Affecting The Aggregation Of Amyloid-? And ?-synuclein

Purpose:Alzheimer's disease?AD?and Parkinson's disease?PD?are the two most common neurodegenerative diseases,affecting tens of millions of people worldwide.The aggregation of amyloid-??A??and?-synuclein??S?is closely associated with AD and PD.Search of potential inhibitors has become one of the most active research directions,and finding the effective inhibitors is crucial for the development of AD and PD drug design.Recently,numerous experimental studies?in vivo and in vitro?demonstrated that catecholamines can slow down the kinetics of A?and?S fibrillization and inhibit the aggregation of A?and?S,and also reduce the neurotoxic of aggregates.However,the underlying inhibitory and disruptive mechanisms remain elusive.In this study,we examined the influence of catecholamines on the structure of toxic aggregates and kinetics of aggregation,and revealed the molecular mechanism by which catecholamines with different concentration inhibit A?and?S aggregation,providing valuable information for developing new drug candidates against AD and PD.Meanwhile,exercise can be considered as a stressor that is able to stimulate the release of catecholamines.As a health-promoting way in modern society,exercise has been shown to prevent AD and PD by reducing the production of A?and?S aggregates,promoting aggregate clearance,and inhibiting the neurotoxicity of aggregates.Our study may be help to reveal the biological mechanisms by which exercise prevents and alleviates AD and PD.Methods:Using the methods of all-atom molecular dynamics?MD?simulation and extensive replica-exchange molecular dynamic?REMD?simulations,this study investigated the influences of catecholamines?consisting of dopamine?DA?,norepinephrine?NE?and epinephrine?EP?molecules?on the aggregation of full-length/core fragment of A?and?S.MD trajectories were analyzed using the GROMACS toolkits and in-house-developed codes.The AMBER99SB-ILDN force field was chosen to describe the atomic interaction of the proteins,and the GAFF force field was used to model molecules.Results:?1?NE molecules greatly reduce the content of inter-peptide?-sheet and long?-strand,and suppress the formation of?-hairpin.Binding of NE molecules to A?peptides decreases the average inter-chain contact surface area?CSA?value and inter-chain main chain H-bond number.Five dominant binding sites are identified,and the central hydrophobic core 16KLVFFA21 site and C-terminal 31IIGLMV36hydrophobic site are the two most favorable ones.NE molecules have the lowest binding energy with hydrophobic residues I41,I31 and L17,and aromatic residues Y10,F4 and F20,and form H-bonds most with the negatively charged residues E11,E22,D7,E3,D23 and D1.The cation-?interaction between R5 and NE molecules are observed in our REMD simulations.NE molecules decrease the?-sheet content of A?protofibril and reduce the number of H-bonds in the A?protofibril.Besides,NE molecules form H-bonds most with residues D1,A2,D23,and A42.?2?With the increment of oligomer size?from dimer to pentamer?,the C?-RMSD of?S_44-96?Greek-key-like core?oligomers gradually decreases,and the?-sheet probability of?S_44-964-96 oligomers gradually increases.DA/NE molecules can both reduce the?-sheet probability of?S trimer and tetramer,and NE displays a higher disruptive effect than DA.In addition,NE molecules form more backbone H-bonds with?S than DA.Half/most of E46-K80 salt bridges in trimer/tetramer are preserved.Upon addition of DA/NE molecules,E46-K80 distance becomes larger and its distribution becomes much broader.Three dominant binding sites are identified for both DA and NE molecules on?S trimer and tetramer,among which two binding sites are quite similar:residues 57-70 and 81-83.The different binding site is located at the terminal region of?S Greek-key-like core.DA is more prone to bind to the N-terminal region?residues 45-52?,while NE is not.Two disruptive modes are found,and the mode of binding to turn region but disrupting the adjacent?-sheet is the dominant one.?3?DA/NE markedly decrease the?-sheet probability of A?_1-40-40 trimer.The?-sheet probability of A?trimer is continuously reduced with the increment of the concentration of molecules.EP molecules have less effect on the?-sheet structure of A?trimer under the simulated concentration.The?-sheet probabilities for N-terminal region residues 2-10,C-terminal residues 32-37 and N-terminal region 1-10,C-terminal regin 34-38 are significantly reduced upon the addition of DA and NE molecules,respectively.DA/NE molecules can reduce the number of H-bonds in the A?trimer,while EP molecules can not.DA molecules have a high binding probability with residues D7,F20 and H14.Residues H13,G9,K28 and residues F4,H14,M35 display a high binding probability with NE and EP molecules,respectively.?4?DA,NE and EP molecules can reduce the?-sheet probability of?S_68-78?NACore?hexamer.The?-sheet probability of NACore hexamer gradually decreases with the increment of the concentration of molecules,and NE displays a higher disruptive effect than DA and EP.Specific to amino acid residues,the?-sheet probabilities of residues A76 and V77?critical residues responsible for the?S aggregation?are decreased in all systems.The peptides display a larger solvent accessible surface area?SASA?peak value in the presence of molecules with different concentration,and the inter-chain contact number decreases upon the addition of molecules.The calculation of the binding probability reveals that DA and NE molecules separately have a high contact probability with residues G73,V77,A78 and residues T72,A76,V77,A78.EP displays a dispersed binding site with NACore hexamer.Besides,hydrophobic residues V77 and A78 have a high contact probability with all of three molecules.Conclusions:?1?This is the first simulation study to investigate the molecular mechanism of NE molecules in inhibiting the aggregation of full length A?_1-42-42 peptide.We found that NE molecules can significantly inhibit the?-sheet formation of A?peptides and suppress the formation of?-hairpin structures,leading to a more disordered coil-rich A?dimer.The binding of NE molecules to two regions?CHC and C-terminal hydrophobic regions?that playing key roles in the A?aggregation can effectively prevent A?fibrillization.Hydrophobic,aromatic stacking,hydrogen-bonding and cation-?interactions synergistically contribute to the binding of NE molecules to A?peptides.Meanwhile,NE molecules can destabilize A?protofibril by forming H-bonds with residues of A?peptides.?2?The trimer is the critical nucleus for the?S_44-964-96 fibril formation,and the tetramer is the minimal stable nucleus.When DA/NE molecules bind to the fibril-like trimer and tetramer,they strongly destabilize the?S protofibrils by disrupting the?-sheet structure and inter-chain E46-K80 salt bridges,and NE displays a higher disruptive effect than DA.Two common binding sites are identified for both DA and NE molecules on?S oligomers:residues 57-70 and 81-83.A different binding site is also observed,which is located at the N-terminal region?residues 45-52?.The binding of DA/NE molecules to?S oligomers is mostly driven by hydrophobic and electrostatic interactions.We found two disruptive modes,and binding to turn region of?S oligomers but disrupting the adjacent?-sheet structure is the dominant one.?3?DA/NE molecules can disrupt the?-sheet structure of A?_1-40-40 trimer by reducing the?-sheet probability of N-terminal and C-terminal residues.The?-sheet probability of A?trimer continuously reduces with the increment of the concentration of DA and NE.EP molecules have less effect on the?-sheet structure of A?trimer.DA molecules displays the highest disruptive effects among three molecules.DA/NE molecules can impede the formation of main chain H-bond and induce the formation of loosely packed coil-rich conformations,thus destabilizing A?trimer.DA molecules mostly bind to N-terminal region spanning residues 6-14,CHC region19-20 and C-terminal residues 38-40,and electrostatic and aromatic stacking interactions play key role in the DA-A?interaction.NE molecules have a preference to bind to the A?trimer at three sites:residues 4-11 in the N-terminal region,residues20-25 in the CHC region and residues 38-40 in the C-terminal region.Four binding sites are identified for EP molecules on A?trimer:residues 3-11,14-16,17-20 and32-40.The binding of EP molecules to A?trimer is mostly driven by aromatic stacking and hydrophobic interactions.?4?DA,NE and EP molecules can disrupt the?-sheet structure of?S_68-78?NACore?hexamer by decreasing the?-sheet probability of hexamer.NE molecules displays a higher disruptive effect than DA and EP molecules.The interaction of DA,NE and EP with NACore hexamer prevents the formation of main chain H-bond and decreases the inter-chain contact number,thus destabilizing preformed NACore hexamer.The binding of DA,NE and EP molecules to NACore hexamer is mostly driven by hydrophobic interactions.Hydrophobic residues V77 and A78 play an important role in the binding of molecules to NACore hexamer.