scholarly journals Site-specific 2D IR spectroscopy: a general approach for the characterization of protein dynamics with high spatial and temporal resolution

2019 ◽  
Vol 21 (2) ◽  
pp. 780-788 ◽  
Author(s):  
Sashary Ramos ◽  
Rachel E. Horness ◽  
Jessica A. Collins ◽  
David Haak ◽  
Megan C. Thielges
Keyword(s):  
Ir Spectroscopy ◽  
Spatial Heterogeneity ◽  
Protein Dynamics ◽  
Temporal Resolution ◽  
Protein Structures ◽  
Side Chains ◽  
Conformational Heterogeneity ◽  
Site Specific ◽  
2D Ir

The conformational heterogeneity and dynamics of protein side chains contribute to function, but investigating exactly how is hindered by experimental challenges arising from the fast timescales involved and the spatial heterogeneity of protein structures.

Protein Dynamics by Two-Dimensional Infrared Spectroscopy

2021 ◽  
Vol 14 (1) ◽  
pp. 299-321
Author(s):  
Goran W. Tumbic ◽  
Md Yeathad Hossan ◽  
Megan C. Thielges
Keyword(s):  
Infrared Spectroscopy ◽  
Ir Spectroscopy ◽  
Protein Dynamics ◽  
Two Dimensional ◽  
Spatial And Temporal Scales ◽  
2D Ir ◽  
Functional Dynamics ◽  
Powerful Approach ◽  
Two Dimensional Infrared Spectroscopy

Proteins function as ensembles of interconverting structures. The motions span from picosecond bond rotations to millisecond and longer subunit displacements. Characterization of functional dynamics on all spatial and temporal scales remains challenging experimentally. Two-dimensional infrared spectroscopy (2D IR) is maturing as a powerful approach for investigating proteins and their dynamics. We outline the advantages of IR spectroscopy, describe 2D IR and the information it provides, and introduce vibrational groups for protein analysis. We highlight example studies that illustrate the power and versatility of 2D IR for characterizing protein dynamics and conclude with a brief discussion of the outlook for biomolecular 2D IR.

scholarly journals Direct Observation of Peptide Hydrogel Self-Assembly

2021 ◽  
Author(s):  
Zoë Adams ◽  
Erika Olson ◽  
Zhengwen Lian ◽  
Audrey Kim ◽  
Matthew Holcomb ◽  
...  
Keyword(s):  
Ir Spectroscopy ◽  
Rapid Change ◽  
Stopped Flow ◽  
Side Chains ◽  
Ir Absorption ◽  
Hydrophobic Region ◽  
Site Specific ◽  
Self Assembling ◽  
Wide Range ◽  
Peptide Hydrogel

The characterization of self-assembling molecules presents significant experimental challenges, especially when associated with phase separation or precipitation. Transparent window infrared (IR) spectroscopy leverages site-specific probes that absorb in the “transparent window” region of the biomolecular IR spectrum. Carbon-deuterium (C-D) bonds are especially compelling transparent window probes since they are non-perturbative, can be readily introduced site selectively into peptides and proteins, and their stretch frequencies are sensitive to changes in the local molecular environment. Importantly, IR spectroscopy can be applied to a wide range of molecular samples regardless of solubility or physical state, making it an ideal technique for addressing the solubility challenges presented by self-assembling molecules. Here, we present the first continuous observation of transparent window probes following stopped-flow initiation. To demonstrate utility in a self-assembling system, we selected the MAX1 peptide hydrogel, a biocompatible material that has significant promise for use in tissue regeneration and drug delivery. C-D labeled valine was synthetically introduced into five distinct positions of the twenty-residue MAX1 β-hairpin peptide. Consistent with current structural models, steady-state IR absorption frequencies and linewidths of C-D bonds at all labeled positions indicate that these side chains occupy a hydrophobic region of the hydrogel and that the motion of side chains located in the middle of the hairpin is more restricted than those located on the hairpin ends. Following a rapid change in ionic strength to initiate gelation, the peptide absorption spectra were monitored as function of time, allowing determination of site-specific time constants. We find that within the experimental resolution, MAX1 gelation occurs as a cooperative process. These studies suggest that stopped-flow transparent window FTIR can be extended to other time-resolved applications, such as protein folding and enzyme kinetics.

Ultrafast Protein Dynamics Probed by Site Specific Transient IR Spectroscopy

2020 ◽  
Author(s):  
Christopher R. Hall ◽  
Jinnette Tolentino Collado ◽  
James N. Iuliano ◽  
Katrin Adamczyk ◽  
Andras Lukacs ◽  
...  
Keyword(s):  
Ir Spectroscopy ◽  
Protein Dynamics ◽  
Site Specific

scholarly journals Heterogeneous and Highly Dynamic Interface in Plastocyanin–Cytochrome f Complex Revealed by Site-Specific 2D-IR Spectroscopy

2019 ◽  
Vol 123 (9) ◽  
pp. 2114-2122 ◽  
Author(s):  
Sashary Ramos ◽  
Amanda L. Le Sueur ◽  
Rachel E. Horness ◽  
Jonathan T. Specker ◽  
Jessica A. Collins ◽  
...  
Keyword(s):  
Ir Spectroscopy ◽  
Cytochrome F ◽  
Site Specific ◽  
2D Ir ◽  
Dynamic Interface

Site-Specific Difference 2D-IR Spectroscopy of Bacteriorhodopsin

2009 ◽  
Vol 113 (18) ◽  
pp. 6520-6527 ◽  
Author(s):  
Esben Ravn Andresen ◽  
Peter Hamm
Keyword(s):  
Ir Spectroscopy ◽  
Specific Difference ◽  
Site Specific ◽  
2D Ir
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