02204nas a2200169   4500008004100000022001400041245015900055210006900214260011000283300001200393490000700405520142700412100001901839700001901858700002501877856013201902       2013                        eng d  a1463-907600aCritical roles of key domains in complete adsorption of a beta peptide on single-walled carbon nanotubes: insights with point mutations and MD simulations0 aCritical roles of key domains in complete adsorption of a beta p  aTHOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLANDbROYAL SOC CHEMISTRYcNOV  a837-8440 v153 a<p>Owing to the influence of nanomaterials on biomacromolecular behavior, their potential applications are rapidly gaining attention. Based on atomistic molecular dynamics simulation studies we have recently reported that the full-length A beta peptide, whose self-assembly is associated with Alzheimer's disease, adsorbs rapidly on single-walled carbon nanotubes, thereby losing its natural propensity to collapse. Here, we investigate the mechanistic overlap between the peptide's compactification and its adsorption, while decoupling the roles of hydrophobicity and aromaticity via point mutations. The collapse mechanism is correlated with interactions between the central hydrophobic core (HP1) and the peptide's C-terminal domain, which are almost exactly compensated by interactions arising from the nanotube after complete adsorption. Adsorption is initiated by HP1 and consolidated by strong interactions arising from the N-terminal domain. Altering the hydrophobicity, but not the aromatic character, of the central residue in HP1 decreases the collapse probability. On the other hand, the adsorption propensity is dramatically reduced when either the hydrophobicity or the aromatic character in HP1 is compromised. The hydrophobicity of HP1 is responsible for dewetting transitions that facilitate its initial interactions with the nanotube, which then lead to very favorable interactions with the nanotube.</p>1 aJana, Asis, K.1 aJose, Jaya, C.1 aSengupta, Neelanjana  uhttps://library.ncl.res.in/content/critical-roles-key-domains-complete-adsorption-beta-peptide-single-walled-carbon-nanotubes-002706nas a2200169   4500008004100000022001400041245013100055210006900186260009100255300002600346490000600372520195800378100001902336700002402355700002502379856013202404       2014                        eng d  a1932-620300aCross dimerization of amyloid-beta and alpha synuclein proteins in aqueous environment: a molecular dynamics simulations study0 aCross dimerization of amyloidbeta and alpha synuclein proteins i  a1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USAbPUBLIC LIBRARY SCIENCEcSEP  aArticle No. : e1068830 v93 a<p>Self-assembly of the intrinsically unstructured proteins, amyloid beta (A beta) and alpha synclein (alpha Syn), are associated with Alzheimer's Disease, and Parkinson's and Lewy Body Diseases, respectively. Importantly, pathological overlaps between these neurodegenerative diseases, and the possibilities of interactions between A beta and alpha Syn in biological milieu emerge from several recent clinical reports and in vitro studies. Nevertheless, there are very few molecular level studies that have probed the nature of spontaneous interactions between these two sequentially dissimilar proteins and key characteristics of the resulting cross complexes. In this study, we have used atomistic molecular dynamics simulations to probe the possibility of cross dimerization between alpha Syn(1-95) and A beta(1-42), and thereby gain insights into their plausible early assembly pathways in aqueous environment. Our analyses indicate a strong probability of association between the two sequences, with inter-protein attractive electrostatic interactions playing dominant roles. Principal component analysis revealed significant heterogeneity in the strength and nature of the associations in the key interaction modes. In most, the interactions of repeating Lys residues, mainly in the imperfect repeats `KTKEGV' present in alpha Syn(1-95) were found to be essential for cross interactions and formation of inter-protein salt bridges. Additionally, a hydrophobicity driven interaction mode devoid of salt bridges, where the non-amyloid component (NAC) region of alpha Syn(1-95) came in contact with the hydrophobic core of A beta(1-42) was observed. The existence of such hetero complexes, and therefore hetero assembly pathways may lead to polymorphic aggregates with variations in pathological attributes. Our results provide a perspective on development of therapeutic strategies for preventing pathogenic interactions between these proteins.</p>1 aJose, Jaya, C.1 aChatterjee, Prathit1 aSengupta, Neelanjana  uhttps://library.ncl.res.in/content/cross-dimerization-amyloid-beta-and-alpha-synuclein-proteins-aqueous-environment-molecular-000624nas a2200157   4500008004100000245010600041210007000147260000800217300001600225490000700241100001900248700001900267700002500286700002600311856012900337       2016                        eng d00aConformational features of the Aβ42 peptide monomer and its interaction with the surrounding solvent0 aConformational features of the Aβ42 peptide monomer and its inte  cOCT  a30144-301590 v181 aKhatua, Prabir1 aJose, Jaya, C.1 aSengupta, Neelanjana1 aBandyopadhyay, Sanjoy  uhttps://library.ncl.res.in/content/conformational-features-a%CE%B242-peptide-monomer-and-its-interaction-surrounding-solvent