02056nas a2200229   4500008004100000022001400041245012700055210006900182260007300251300001200324490000800336520116700344653001501511653002501526653002001551653002101571653003401592653002901626100001901655700002501674856012701699       2013                        eng d  a0301-462200aSurface induced collapse of A beta(1-42) with the F19A replacement following adsorption on a single walled carbon nanotube0 aSurface induced collapse of A beta142 with the F19A replacement   aPO BOX 211, 1000 AE AMSTERDAM, NETHERLANDSbELSEVIER SCIENCE BVcDEC  a108-1150 v1843 a<p>Spontaneous adsorption of the A beta peptide on the surface of a single-walled carbon nanotube, resulting in the prevention of its intrinsic propensity to form collapsed states, could be a plausible means to hinder the peptide's initial nucleation and self-assembly. We report here the effects of sharply reducing both aromatic and hydrophobic character within the peptide's central hydrophobic core on its free and surface behavior. In such an altered peptide, complete surface adsorption is found to induce, rather than prevent, the adsorbed peptide's collapse. The weakened surface interactions of the central hydrophobic core allow its greater translational mobility on the surface, thereby facilitating interactions that lead to compaction. Both the adsorption and the subsequent collapse are accompanied by a loss of surface hydration in the modified peptide. We further find that such a two-step dewetting leads to hydration levels comparable to that obtained after compaction of the free peptide. These insights may be leveraged for designing molecular surfaces for disrupting intrinsic A beta behavior. (C) 2013 Elsevier B.V. All rights reserved.</p>10aAdsorption10aAmyloid beta peptide10acarbon nanotube10aLateral mobility10amolecular dynamics simulation10aSurface induced collapse1 aJana, Asis, K.1 aSengupta, Neelanjana  uhttps://library.ncl.res.in/content/surface-induced-collapse-beta1-42-f19a-replacement-following-adsorption-single-walled-002203nas a2200157   4500008004100000022001400041245015000055210006900205260011000274300001400384490000700398520146100405100002401866700002501890856013001915       2016                        eng d  a1742-206X00aSignatures of protein thermal denaturation and local hydrophobicity in domain specific hydration behavior: a comparative molecular dynamics study0 aSignatures of protein thermal denaturation and local hydrophobic  aTHOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLANDbROYAL SOC CHEMISTRYcFEB  a1139-11500 v123 a<p>We investigate, using atomistic molecular dynamics simulations, the association of surface hydration accompanying local unfolding in the mesophilic protein Yfh1 under a series of thermal conditions spanning its cold and heat denaturation temperatures. The results are benchmarked against the thermally stable protein, Ubq, and behavior at the maximum stability temperature. Local unfolding in Yfh1, predominantly in the beta sheet regions, is in qualitative agreement with recent solution NMR studies; the corresponding Ubq unfolding is not observed. Interestingly, all domains, except for the beta sheet domains of Yfh1, show increased effective surface hydrophobicity with increase in temperature, as reflected by the density fluctuations of the hydration layer. Velocity autocorrelation functions (VACF) of oxygen atoms of water within the hydration layers and the corresponding vibrational density of states (VDOS) are used to characterize alteration in dynamical behavior accompanying the temperature dependent local unfolding. Enhanced caging effects accompanying transverse oscillations of the water molecules are found to occur with the increase in temperature preferentially for the beta sheet domains of Yfh1. Helical domains of both proteins exhibit similar trends in VDOS with changes in temperature. This work demonstrates the existence of key signatures of the local onset of protein thermal denaturation in solvent dynamical behavior.</p>1 aChatterjee, Prathit1 aSengupta, Neelanjana  uhttps://library.ncl.res.in/content/signatures-protein-thermal-denaturation-and-local-hydrophobicity-domain-specific-hydration02390nas a2200169   4500008004100000245014700041210006900188260000800257300001200265490000800277520172200285100002002007700001902027700002502046700001702071856013202088       2017                        eng d00aStructural and dynamics studies of the TetR family protein, CprB from Streptomyces coelicolor in complex with its biological operator sequence0 aStructural and dynamics studies of the TetR family protein CprB   cMAy  a134-1460 v1983 aIn Streptomycetes, tetracycline repressor family of transcription regulators (TetR-FTRs) controls various biological processes including antibiotic biosynthesis, cellular morphology and innate resistance. Here, we focus on understanding the structural basis of transcription regulation by CprB, a member of TetR-FTRs from S. coelicolor. CprB is implicated as a receptor of gamma-butyrolactones, a class of quorum sensing molecules, responsible for initiating secondary metabolic pathways. In order to understand the molecular mechanism of DNA recognition, the X-ray structure of CprB in complex with its biological relevant operator sequence was solved to a resolution of 3.95 angstrom. Furthermore, to refine and compliment the results, atomistic molecular dynamics simulations were carried out using the X-ray structure as the template. The studies reveal that CprB binds to DNA as dimer of dimers with this mode of interaction results in minimal distortion in the DNA, enabling these proteins to recognize multiple sequences with varying affinity. Another crucial finding from our simulation results was that the positively charged N-terminal arm of CprB brings extra stability to the protein-DNA complex by interacting with the minor-groove of the DNA and anchoring itself to the phosphate backbone. Corroborating electrophoretic mobility shift assay and fluorescence anisotropy experiments showed that the mutant AN6-CprB exhibited about 7-8 fold reduced DNA binding. Comparison with other TetR-FTRs reveals that this strategy is also employed by over 25% of TetR-FTRs, where N-terminal anchoring mechanism is used to enhance selectivity for a particular DNA sequence. (C) 2017 Elsevier Inc. All rights reserved.1 aBhukya, Hussain1 aJana, Asis, K.1 aSengupta, Neelanjana1 aAnand, Ruchi  uhttps://library.ncl.res.in/content/structural-and-dynamics-studies-tetr-family-protein-cprb-streptomyces-coelicolor-complex-its