Effect of C-terminal truncations on the aggregation propensity of A53E, a familial mutant of α-Synuclein: An Insilico Study

α-Synuclein, an intrinsically disordered protein, is well known for its role on the onset of Parkinson’s Disease (PD), a neurodegenerative disorder. In α-synuclein, several mutations have been known to cause genetic forms of PD. Recently a new familial mutant, A53E of α-synuclein was discovered in a family and found to accelerate the α-synuclein gene, SNCA. But the molecular details about the A53E α-synuclein aggregation were not well studied. It has been recently suggested that two C-terminally truncated α-synuclein (αS C-X): 120 and 123, along with the A53E mutation would cause a more aggressive pathology and an increase in aggregation. So here we demonstrate the effect of C-terminal truncations along with A53E mutation on the aggregation propensity of α-synuclein by comparing the conformational dynamics of A53E full length protein and its C-terminal truncations using molecular dynamics simulation methods. In A53E full length protein we observed stability to be more and also hydrophobic surface (NAC (non-amyloid β component) region), number of molecular interactions and interface area between monomeric units to be relatively less than αS C-X. Our findings in this study suggest that more the residues removed from the C-terminal along with A53E mutation have significant effect on the aggregation propensity of α-synuclein

Structure of DNA-Functionalized Dendrimer Nanoparticles

Atomistic molecular dynamics simulations have been carried out to reveal the characteristic features of ethylenediamine (EDA) cored protonated poly amido amine (PAMAM) dendrimers of generation 3 (G3) and 4 (G4) that are functionalized with single stranded DNAs (ssDNAs). The four ssDNA strands that are attached via alkythiolate [-S (CH2)6-] linker molecule to the free amine groups on the surface of the PAMAM dendrimers observed to undergo a rapid conformational change during the 25 ns long simulation period. From the RMSD values of ssDNAs, we find relative stability in the case of purine rich ssDNA strands than pyrimidine rich ssDNA strands. The degree of wrapping of ssDNA strands on the dendrimer molecule was found to be influenced by the charge ratio of DNA and the dendrimer. As G4 dendrimer contains relatively more positive charge than G3 dendrimer, we observe extensive wrapping of ssDNAs on the G4 dendrimer. The ssDNA strands along with the linkers are seen to penetrate the surface of the dendrimer molecule and approach closer to the center of the dendrimer indicating the soft sphere nature of the dendrimer molecule. The effective radius of DNA-functionalized dendrimer nanoparticle was found to be independent of base composition of ssDNAs and was observed to be around 19.5 {\AA} and 22.4 {\AA} when we used G3 and G4 PAMAM dendrimer as the core of the nanoparticle respectively. The observed effective radius of DNA-functionalized dendrimer molecule apparently indicates the significant shrinkage in the structure that has taken place in dendrimer, linker and DNA strands. As a whole our results describe the characteristic features of DNA-functionalized dendrimer nanoparticle and can be used as strong inputs to design effectively the DNA-dendrimer nanoparticle self-assembly for their active biological applications.Comment: 13 pages, 10 figures, 3 Table

Potential of Mean Force study on the dimerization of non-amyloid-β component of Human α-Synuclein

Self-association of α-Synuclein monomers into oligomeric species and highly ordered amyloid fibrils is linked to Parkinson’s disease (PD). The peptide fragment corresponding to region 61-95 of α-synuclein protein originally termed as non-amyloid β component (NAC) has been suggested to play a critical role in the fibrillation process. To better understand the early events of aggregation process, inter-molecular interactions between the two NAC regions during the formation of dimer is critical. Here we demonstrate the molecular dynamics and potential of mean force (PMF) techniques to study the parallel and anti-parallel dimers of the peptide corresponding to the 71-82 (71VTGVTAVAQKTV82) region of α-synuclein. From the PMF study, we noticed two basins of attraction, one at 10 Ǻ and 14 Ǻ for the parallel and only one basin near 12 Ǻ for the anti-parallel conformation of the dimer of the peptide. From docking study using SymmDock, we noticed higher side chain interactions and interface surface area for the anti-parallel conformation of the dimer of the peptide. Our results thus provide atomistic insights into the structural features of the core fibril forming NAC region during dimerization which may open the way to explore the molecular basis of this disease

Computational investigation on the conformational dynamics of C-terminal truncated α-synuclein bound to membrane

Accelerated progression rates in Parkinson’s disease (PD) have been linked to C-terminal domain (CTD) truncations of monomeric α-Synuclein (α-Syn), which have been suggested to increase amyloid aggregation in vivo and in vitro. In the brain of PD patients, CTD truncated α-Syn was found to have lower cell viability and tends to increase in the formation of fibrils. The CTD of α-Syn acts as a guard for regulating the normal functioning of α-Syn. The absence of the CTD may allow the N-terminal of α-Syn to interact with the membrane thereby affecting the normal functioning of α-Syn, and all of which will affect the etiology of PD. In this study, the conformational dynamics of CTD truncated α-Syn (1–99 and 1–108) monomers and their effect on the protein–membrane interactions were demonstrated using the all-atom molecular dynamics (MD) simulation method. From the MD analyses, it was noticed that among the two truncated monomers, α-Syn (1–108) was found to be more stable, shows rigidness at the N-terminal region and contains a significant number of intermolecular hydrogen bonds between the non-amyloid β-component (NAC) region and membrane, and lesser number of extended strands. Further, the bending angle in the N-terminal domain was found to be lesser in the α-Syn (1–108) in comparison with the α-Syn (1–99). Our findings suggest that the truncation on the CTD of α-Syn affects its interaction with the membrane and subsequently has an impact on the aggregation. Communicated by Ramaswamy H. Sarma</p

Inhibition of Aβ_1–42 peptide aggregation using short ss-oligonucleotide as polyions: an <i>in silico</i> approach

Inhibition of Aβ_1–42 peptide aggregation using short ss-oligonucleotide as polyions: an <i>in silico</i> approac

PAMAM Dendrimer-Drug Interactions: Effect of pH on the Binding and Release Pattern

Understanding the dendrimer-drug interaction is of great importance to design and optimize the dendrimer-based drug delivery system. Using atomistic molecular dynamics (MD) simulations, we have analyzed the release pattern of four ligands (two soluble drugs, namely, salicylic acid (Sal), L-alanine (Ala), and two insoluble drugs, namely, phenylbutazone (Pbz) and primidone (Prim)), which were initially encapsulated inside the ethylenediamine (EDA) cored polyamidoamine (PAMAM) dendrimer using the docking method. We have computed the potential of mean force (PMF) variation with generation 5 (G5)-PAMAM dendrimer complexed with drug molecules using umbrella sampling. From our calculated PMF values, we observe that soluble drugs (Sal and Ala) have lower energy barriers than insoluble drugs (Pbz and Prim). The order of ease of release pattern for these drugs from G5 protonated PAMAM dendrimer was found to be Ala > Sal > Prim > Pbz. In the case of insoluble drugs (Prim and Pbz), because of larger size, we observe much nonpolar contribution, and thus, their larger energy barriers can be reasoned to van der Waals contribution. From the hydrogen bonding analysis of the four PAMAM drug complexes under study, we found intermolecular hydrogen bonding to show less significant contribution to the free energy barrier. Another interesting feature appears while calculating the PMF profile of G5NP (nonprotonated)-PAMAM Pbz and G5NP (nonprotonated)-PAMAM-Sal complex. The PMF was found to be less when the drug is bound to nonprotonated dendrimer compared to the protonated dendrimer. Our results suggest that encapsulation of the drug molecule into the host PAMAM dendrimer should be carried out at higher pH values (near pH 10). When such complex enters the human body, the pH is around 7.4 and at that physiological pH, the dendrimer holds the drug tightly. Hence the release of drug can occur at a controlled rate into the bloodstream. Thus, our findings provide a microscopic picture of the encapsulation and controlled release of drugs in the case of dendrimer-based host-guest systems

Structural dynamics and interactions of Xeroderma pigmentosum complementation group A (XPA_98–210) with damaged DNA

<p>Nucleotide excision repair (NER) in higher organisms repair massive DNA abrasions caused by ultraviolet rays, and various mutagens, where Xeroderma pigmentosum group A (XPA) protein is known to be involved in damage recognition step. Any mutations in XPA cause classical Xeroderma pigmentosum disease. The extent to which XPA is required in the NER is still unclear. Here, we present the comparative study on the structural and conformational changes in globular DNA binding domain of XPA_98–210 in DNA bound and DNA free state. Atomistic molecular dynamics simulation was carried out for both XPA_98–210 systems using AMBER force fields. We observed that XPA_98–210 in presence of damaged DNA exhibited more structural changes compared to XPA_98–210 in its free form. When XPA is in contact with DNA, we found marked stability of the complex due to the formation of characteristic longer antiparallel β-sheets consisting mainly lysine residues.</p

Potential of mean force and molecular dynamics study on the transient interactions between α and β synuclein that drive inhibition of α-synuclein aggregation

<p>Self-association of α-synuclein (αS) into pathogenic oligomeric species and subsequent formation of highly ordered amyloid fibrils is linked to the Parkinson’s disease. So most of the recent studies are now focused on the development of potential therapeutic strategies against this debilitating disease. β-synuclein (βS), a presynaptic protein that co-localizes with αS has been recently reported to act as an inhibitor of αS self-assembly. But the specificity of molecular interaction, nature and location between αS/βS is not known despite the potential importance of βS as an inhibitor of αS. We used molecular dynamics and potential of mean force (PMF) to study association of αS/βS and αS/αS. The calculated PMF indicates that contact wells are significantly deeper and presence of a minimum at αS/βS separation of 13.5 Å with a free energy barrier of 40 kcal/mol. We observed the dissociation energy barrier to be two times higher for the hetero-dimer (αS/βS) than the homo-dimer (αS/αS). We also carried out umbrella samplings involving two degrees of freedom (one being the distance between the monomeric units and the other angle between the long axes of the two monomeric chains) and observed similar PMF profile. We noticed relatively stronger range of transient interactions between the monomeric units in hetero-dimer (αS/βS) than homo-dimer (αS/αS). So our findings suggest that αS readily combines with βS to form hetero-dimer than combining with itself in forming homo-dimer. Hence we see predominant transient interactions between αS and βS can be used to drive inhibition of αS aggregation.</p

DNA assisted self-assembly of PAMAM dendrimers

We report DNA assisted self-assembly of polyamidoamine (PAMAM) dendrimers using all atom Molecular Dynamics (MD) simulations and present a molecular level picture of a DNA-linked PAMAM dendrimer nanocluster, which was first experimentally reported by Choi et al. (Nano Lett., 2004, 4, 391–397). We have used single stranded DNA (ssDNA) to direct the self-assembly process. To explore the effect of pH on this mechanism, we have used both the protonated (low pH) and nonprotonated (high pH) dendrimers. In all cases studied here, we observe that the DNA strand on one dendrimer unit drives self-assembly as it binds to the complementary DNA strand present on the other dendrimer unit, leading to the formation of a DNA-linked dendrimer dimeric complex. However, this binding process strongly depends on the charge of the dendrimer and length of the ssDNA. We observe that the complex with a nonprotonated dendrimer can maintain a DNA length dependent inter-dendrimer distance. In contrast, for complexes with a protonated dendrimer, the inter-dendrimer distance is independent of the DNA length. We attribute this observation to the electrostatic complexation of a negatively charged DNA strand with the positively charged protonated dendrimer