Local dynamics of the photo-switchable protein PYP in ground and signalling state probed by 2D-IR spectroscopy of –SCN labels

2020 ◽  
Vol 22 (40) ◽  
pp. 22963-22972
Author(s):  
Julian M. Schmidt-Engler ◽  
Larissa Blankenburg ◽  
Rene Zangl ◽  
Jan Hoffmann ◽  
Nina Morgner ◽  
...  
Keyword(s):  
Ir Spectroscopy ◽  
Structural Rearrangements ◽  
Dark State ◽  
Local Dynamics ◽  
2D Ir ◽  
Protein Label

We employ 2D-IR spectroscopy of the protein label –SCN to describe the local dynamics in the photo-switchable protein PYP in its dark state (pG) and after photoactivation, concomitant with vast structural rearrangements, in its signalling state (pB).

Exploring the 2D-IR repertoire of the –SCN label to study site-resolved dynamics and solvation in the calcium sensor protein calmodulin

2020 ◽  
Vol 22 (10) ◽  
pp. 5463-5475 ◽  
Author(s):  
Julian M. Schmidt-Engler ◽  
Rene Zangl ◽  
Patrick Guldan ◽  
Nina Morgner ◽  
Jens Bredenbeck
Keyword(s):  
Ir Spectroscopy ◽  
Calcium Uptake ◽  
Calcium Sensor ◽  
Ligand Interaction ◽  
Local Dynamics ◽  
2D Ir ◽  
Sensor Protein ◽  
Protein Ligand Interaction

2D-IR spectroscopy of site-specifically incorporated –SCN labels in the calcium sensor protein calmodulin reveals local dynamics and solvation as they change upon calcium uptake and protein–ligand interaction.

scholarly journals Needles in a haystack: H-bonding in an optogenetic protein observed with isotope labeling and 2D-IR spectroscopy

2021 ◽  
Author(s):  
Jeannette Ruf ◽  
Peter Hamm ◽  
David Buhrke
Keyword(s):  
Ir Spectroscopy ◽  
Isotope Labeling ◽  
Vibrational Modes ◽  
2D Ir

Two vibrational modes in a cyanobacterial protein were isolated with isotope labeling and studied with 2D-IR spectroscopy.

scholarly journals Transparent window 2D IR spectroscopy of proteins

2021 ◽  
Vol 155 (4) ◽  
pp. 040903
Author(s):  
Megan C. Thielges
Keyword(s):  
Ir Spectroscopy ◽  
2D Ir

scholarly journals Structure Changes of a Membrane Polypeptide under an Applied Voltage Observed with Surface-Enhanced 2D IR Spectroscopy

2021 ◽  
Vol 12 (7) ◽  
pp. 1786-1792
Author(s):  
Erin R. Birdsall ◽  
Megan K. Petti ◽  
Vivek Saraswat ◽  
Joshua S. Ostrander ◽  
Michael S. Arnold ◽  
...  
Keyword(s):  
Ir Spectroscopy ◽  
Applied Voltage ◽  
2D Ir ◽  
Structure Changes ◽  
Surface Enhanced

Determination of storage stability of the crude extracts of Ganoderma lucidum using FTIR and 2D-IR spectroscopy

2011 ◽  
Author(s):  
Yew Keong Choong ◽  
Su-Qin Sun ◽  
Qun Zhou ◽  
Zakiah Ismail ◽  
Badrul Amini Abdul Rashid ◽  
...  
Keyword(s):  
Ir Spectroscopy ◽  
Ganoderma Lucidum ◽  
Storage Stability ◽  
2D Ir ◽  
Crude Extracts

Resolving Conformations of Acetylproline-NH2 by Coherent 2D IR Spectroscopy

2005 ◽  
pp. 545-547 ◽  
Author(s):  
Denis Karaiskaj ◽  
Soohwan Sul ◽  
Ying Jiang ◽  
Nien-Hui Ge
Keyword(s):  
Ir Spectroscopy ◽  
2D Ir

scholarly journals Two-dimensional IR spectroscopy of the anti-HIV agent KP1212 reveals protonated and neutral tautomers that influence pH-dependent mutagenicity

2015 ◽  
Vol 112 (11) ◽  
pp. 3229-3234 ◽  
Author(s):  
Chunte Sam Peng ◽  
Bogdan I. Fedeles ◽  
Vipender Singh ◽  
Deyu Li ◽  
Tiffany Amariuta ◽  
...  
Keyword(s):  
Ir Spectroscopy ◽  
Mutation Rates ◽  
Viral Population ◽  
Lethal Mutagenesis ◽  
2D Ir ◽  
Viral Mutation ◽  
Unique Shape ◽  
Ph Dependent ◽  
Mutagenic Property ◽  
Anti Hiv

Antiviral drugs designed to accelerate viral mutation rates can drive a viral population to extinction in a process called lethal mutagenesis. One such molecule is 5,6-dihydro-5-aza-2′-deoxycytidine (KP1212), a selective mutagen that induces A-to-G and G-to-A mutations in the genome of replicating HIV. The mutagenic property of KP1212 was hypothesized to originate from its amino–imino tautomerism, which would explain its ability to base pair with either G or A. To test the multiple tautomer hypothesis, we used 2D IR spectroscopy, which offers subpicosecond time resolution and structural sensitivity to distinguish among rapidly interconverting tautomers. We identified several KP1212 tautomers and found that >60% of neutral KP1212 is present in the enol–imino form. The abundant proportion of this traditionally rare tautomer offers a compelling structure-based mechanism for pairing with adenine. Additionally, the pKa of KP1212 was measured to be 7.0, meaning a substantial population of KP1212 is protonated at physiological pH. Furthermore, the mutagenicity of KP1212 was found to increase dramatically at pH <7, suggesting a significant biological role for the protonated KP1212 molecules. Overall, our data reveal that the bimodal mutagenic properties of KP1212 result from its unique shape shifting ability that utilizes both tautomerization and protonation.

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