Conformational Manifold of α-Aminoisobutyric Acid (Aib) Containing Alanine-Based Tripeptides in Aqueous Solution Explored by Vibrational Spectroscopy, Electronic Circular Dichroism Spectroscopy, and Molecular Dynamics Simulations

2007 ◽  
Vol 129 (43) ◽  
pp. 13095-13109 ◽  
Author(s):  
Reinhard Schweitzer-Stenner ◽  
Widalys Gonzales ◽  
Gregory T. Bourne ◽  
Jianwen A. Feng ◽  
Garland R. Marshall
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Circular Dichroism ◽  
Molecular Dynamics Simulations ◽  
Vibrational Spectroscopy ◽  
Circular Dichroism Spectroscopy ◽  
Electronic Circular Dichroism ◽  
Aminoisobutyric Acid ◽  
Dynamics Simulations ◽  
Circular Dichroïsm

scholarly journals Electronic Circular Dichroism Spectra of DNA Quadruple Helices Studied by Molecular Dynamics Simulations and Excitonic Calculations Including Charge Transfer States

Molecules ◽  
2021 ◽  
Vol 26 (16) ◽  
pp. 4789
Author(s):  
Haritha Asha ◽  
James A. Green ◽  
Lara Martinez-Fernandez ◽  
Luciana Esposito ◽  
Roberto Improta
Keyword(s):  
Molecular Dynamics ◽  
Circular Dichroism ◽  
Charge Transfer ◽  
Molecular Dynamics Simulations ◽  
Thermal Fluctuations ◽  
Telomeric Sequence ◽  
Quadruple Helix ◽  
Electronic Circular Dichroism ◽  
Dynamics Simulations ◽  
Circular Dichroïsm

We here investigate the Electronic Circular Dichroism (ECD) Spectra of two representative Guanine-rich sequences folded in a Quadruple helix (GQ), by using a recently developed fragment diabatisation based excitonic model (FrDEx). FrDEx can include charge transfer (CT) excited states and consider the effect of the surrounding monomers on the local excitations (LEs). When applied to different structures generated by molecular dynamics simulations on a fragment of the human telomeric sequence (Tel21/22), FrDEx provides spectra fully consistent with the experimental one and in good agreement with that provided by quantum mechanical (QM) method used for its parametrization, i.e., TD-M05-2X. We show that the ECD spectrum is moderately sensitive to the conformation adopted by the bases of the loops and more significantly to the thermal fluctuations of the Guanine tetrads. In particular, we show how changes in the overlap of the tetrads modulate the intensity of the ECD signal. We illustrate how this correlates with changes in the character of the excitonic states at the bottom of the La and Lb bands, with larger LE and CT involvement of bases that are more closely stacked. As an additional test, we utilised FrDEx to compute the ECD spectrum of the monomeric and dimeric forms of a GQ forming sequence T30695 (5’TGGGTGGGTGGGTGGG3’), i.e., a system containing up to 24 Guanine bases, and demonstrated the satisfactory reproduction of the experimental and QM reference results. This study provides new insights on the effects modulating the ECD spectra of GQs and, more generally, further validates FrDEx as an effective tool to predict and assign the spectra of closely stacked multichromophore systems.

scholarly journals Trimethylamine-N-oxide: its hydration structure, surface activity, and biological function, viewed by vibrational spectroscopy and molecular dynamics simulations

2017 ◽  
Vol 19 (10) ◽  
pp. 6909-6920 ◽  
Author(s):  
Tatsuhiko Ohto ◽  
Johannes Hunger ◽  
Ellen H. G. Backus ◽  
Wataru Mizukami ◽  
Mischa Bonn ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Molecular Dynamics Simulations ◽  
Surface Activity ◽  
Vibrational Spectroscopy ◽  
Biological Function ◽  
Molecular Simulations ◽  
Structure Surface ◽  
Dynamics Simulations ◽  
Hydrophilicity And Hydrophobicity

Vibrational spectroscopy and molecular simulations revealed the hydrophilicity and hydrophobicity of TMAO in aqueous solution.

scholarly journals Physicochemical Characterisation of KEIF—The Intrinsically Disordered N-Terminal Region of Magnesium Transporter A

Biomolecules ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 623
Author(s):  
Stéphanie Jephthah ◽  
Linda K. Månsson ◽  
Domagoj Belić ◽  
Jens Preben Morth ◽  
Marie Skepö
Keyword(s):  
Aqueous Solution ◽  
Circular Dichroism ◽  
Driving Forces ◽  
Circular Dichroism Spectroscopy ◽  
Terminal Region ◽  
Single Chain ◽  
Intrinsically Disordered ◽  
Magnesium Transporter ◽  
Dynamics Simulations ◽  
Circular Dichroïsm

Magnesium transporter A (MgtA) is an active transporter responsible for importing magnesium ions into the cytoplasm of prokaryotic cells. This study focuses on the peptide corresponding to the intrinsically disordered N-terminal region of MgtA, referred to as KEIF. Primary-structure and bioinformatic analyses were performed, followed by studies of the undisturbed single chain using a combination of techniques including small-angle X-ray scattering, circular dichroism spectroscopy, and atomistic molecular-dynamics simulations. Moreover, interactions with large unilamellar vesicles were investigated by using dynamic light scattering, laser Doppler velocimetry, cryogenic transmission electron microscopy, and circular dichroism spectroscopy. KEIF was confirmed to be intrinsically disordered in aqueous solution, although extended and containing little β-structure and possibly PPII structure. An increase of helical content was observed in organic solvent, and a similar effect was also seen in aqueous solution containing anionic vesicles. Interactions of cationic KEIF with anionic vesicles led to the hypothesis that KEIF adsorbs to the vesicle surface through electrostatic and entropic driving forces. Considering this, there is a possibility that the biological role of KEIF is to anchor MgtA in the cell membrane, although further investigation is needed to confirm this hypothesis.

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