@article { ISI:000316074305086, title = {Competition between adsorption and intrinsic collapse of full-length a beta 1-42 on the surface of a single-walled carbon nanotube: insights from molecular dynamics simulations}, journal = {Biophysical Journal}, volume = {104}, number = {2, 1}, year = {2013}, note = {57th Annual Meeting of the Biophysical-Society, Philadelphia, PA, FEB 02-06, 2013}, month = {JAN}, pages = {508A}, publisher = {Biophys Soc}, address = {600 TECHNOLOGY SQUARE, 5TH FLOOR, CAMBRIDGE, MA 02139 USA}, issn = {0006-3495}, author = {Sengupta, Neelanjana} } @article { ISI:000312217200015, title = {Critical roles of key domains in complete adsorption of a beta peptide on single-walled carbon nanotubes: insights with point mutations and MD simulations}, journal = {Physical Chemistry Chemical Physics}, volume = {15}, number = {3}, year = {2013}, month = {NOV}, pages = {837-844}, publisher = {ROYAL SOC CHEMISTRY}, address = {THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND}, abstract = {

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{\textquoteright}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{\textquoteright}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{\textquoteright}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.

}, issn = {1463-9076}, doi = {10.1039/c2cp42933k}, author = {Jana, Asis K. and Jose, Jaya C. and Sengupta, Neelanjana} } @article { ISI:000341855900027, title = {Cross dimerization of amyloid-beta and alpha synuclein proteins in aqueous environment: a molecular dynamics simulations study}, journal = {Plos One}, volume = {9}, number = {9}, year = {2014}, month = {SEP}, pages = {Article No. : e106883}, publisher = {PUBLIC LIBRARY SCIENCE}, address = {1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA}, abstract = {

Self-assembly of the intrinsically unstructured proteins, amyloid beta (A beta) and alpha synclein (alpha Syn), are associated with Alzheimer{\textquoteright}s Disease, and Parkinson{\textquoteright}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 {\textquoteleft}KTKEGV{\textquoteright} 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.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0106883}, author = {Jose, Jaya C. and Chatterjee, Prathit and Sengupta, Neelanjana} } @article { ISI:000376417400001, title = {Conformational energy landscape of the ritonavir molecule}, journal = {Journal of Physical Chemistry B}, volume = {120}, number = {19}, year = {2016}, month = {MAY}, pages = {4331-4340}, publisher = {AMER CHEMICAL SOC}, address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, abstract = {

Conformational polymorphism of ritonavir, a well-known pharmaceutical drug, is intricately linked to its efficacy in the treatment of acquired immunodeficiency syndrome (AIDS). Polymorphic transition from the crystalline form I to form II leads to the loss of bioactivity. The constituent ritonavir molecules adopt a trans configuration about the carbamate torsion angle in the form I crystal, and a cis configuration in the form II crystal. Investigating the energetics and mechanistic features of conformational transitions at the single molecule level is a key step toward decoding the complex features of the solid state polymorphism. In this work, we employ the energy landscape framework to investigate the conformational transitions of an isolated ritonavir molecule. The landscape is explored using discrete path sampling (DPS) and visualized in terms of disconnectivity graphs. We identify two distinct funnels corresponding to the two molecular forms that are identified by crystallography. The two regions can be reliably distinguished using the carbamate torsion angle, and the corresponding interconversion rates are predicted to follow Arrhenius behavior. The results provide mechanistic insight into pathways for cis \<-\> trans interconversion at the molecular level and may also help in elucidating the polymorphic transitions in the crystal state.

}, issn = {1520-6106}, doi = {10.1021/acs.jpcb.5b12272}, author = {Chakraborty, Debayan and Sengupta, Neelanjana and Wales, David J.} } @article {42692, title = {Conformational features of the Aβ42 peptide monomer and its interaction with the surrounding solvent}, journal = {Physical Chemistry Chemical Physics}, volume = {18}, year = {2016}, month = {OCT}, pages = {30144-30159}, doi = {10.1039/C6CP04925G}, author = {Khatua, Prabir and Jose, Jaya C. and Sengupta, Neelanjana and Bandyopadhyay, Sanjoy} } @article {46105, title = {Cold thermal response of an amyloid oligomer differs from typical globular protein cold denaturation}, journal = {Journal of Physical Chemistry Letters}, volume = {10}, year = {2019}, month = {MAY }, pages = {2453-2457}, type = {Article}, abstract = {

In contrast with the general behavior of folded proteins, the cold thermal response of amyloid assemblies is difficult to elicit with simple models. We exploit exhaustive simulations to evaluate the thermal response of a barrel-shaped model amyloid oligomer, with a distinct hydrophobic core akin to that of folded proteins. Cumulative thermal data over the range of 210-483 K indicate a sharp inflection and rise in structural stability as the temperature is decreased below the melting temperature of the water model. This is not commensurate with the equilibrium free energy profile obtained with core packing as the order parameter. However, energetic analyses and the size of their fluctuations indicate the crucial role of hydration in mediating structural transitions, beyond the expected temperature-dependent hydrophobic effect. Structural ordering of the hydration layer over bulk water is maximized at the transition and vanishes at high temperatures. This is a first direct demonstration of the microscopic influence of hydration water on the low-temperature response of an amyloid assembly close to the cryo-regime.

}, issn = {1948-7185}, doi = {10.1021/acs.jpclett.9b00709}, author = {Menon, Sneha and Sengupta, Neelanjana} }