Probing the Hydrophobic Region of a Lipid Bilayer at Specific Depths Using Vibrational Spectroscopy

Islam, Md Muhaiminul; Nawagamuwage, Sithara U.; Parshin, Igor V.; Richard, Margaret C.; Burin, Alexander L.; Rubtsov, Igor V.

doi:10.1021/jacs.3c10178

Cited by 2 publications

(1 citation statement)

References 89 publications

(158 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…There have also been studies on the changes in peak width and more prominently, asymmetry, reported for azide probes due to the existence of a Fermi resonance peak blue-shifted by around 30–40 cm –1 from the main peak. − In some instances, the prominence and width changes due to the resonance have been directly connected to the angular range of motion explored by the bond between the azide and the linking carbon atom. , Analysis of the molecular dynamics simulations in this work has shown that all measured species have a matching C–N–N angular distribution with a fwhm of 10.5° centered around about 116°, which is not sufficient to explain the subtle differences in FTIR line width (Figure S16).…”

Section: Resultsmentioning

confidence: 99%

Local Crowd, Local Probe: Strengths and Drawbacks of Azidohomoalanine as a Site-Specific Crowding Probe

Shirley,

Baiz

2024

J. Phys. Chem. B

View full text Add to dashboard Cite

Every residue on a protein can be characterized by its interaction with water, in lack or in excess, as water is the matrix of biological systems. Infrared spectroscopy and the implementation of local azidohomoalanine (AHA) probes allow us to move beyond an ensemble or surface-driven conceptualization of water behavior and toward a granular, site-specific picture. In this paper, we examined the role of crowding in modulating both global and local behavior on the β-hairpin, TrpZip2 using a combination of Fourier-transform infrared spectroscopy (FTIR) spectroscopy, two-dimensional infrared (2D IR) spectroscopy, and molecular dynamics simulations. We found that, at the amino acid level, crowding drove dehydration of both sheet and turn peptide sites as well as free AHA. However, the subpicosecond dynamics showed highly individualized responses based on the local environment. Interestingly, while steady-state FTIR measurements revealed similar responses at the amino-acid level to hard versus soft crowding (dehydration), we found that PEG and glucose had opposite stabilizing and destabilizing effects on the protein secondary structure, emphasizing an important distinction in understanding the impact of crowding on protein structure as well as the role of crowding across length scales.

show abstract