Tyrosine as a Non-perturbing Site-Specific Vibrational Reporter for Protein Dynamics

2017 ◽  
Vol 121 (26) ◽  
pp. 6380-6389 ◽  
Author(s):  
Farzaneh Chalyavi ◽  
David G. Hogle ◽  
Matthew J. Tucker
Keyword(s):  
Protein Dynamics ◽  
Site Specific

scholarly journals Site-specific Protein Dynamics in Communication Pathway from Sensor to Signaling Domain of Oxygen Sensor Protein, HemAT-Bs

2012 ◽  
Vol 287 (24) ◽  
pp. 19973-19984 ◽  
Author(s):  
Samir F. El-Mashtoly ◽  
Minoru Kubo ◽  
Yuzong Gu ◽  
Hitomi Sawai ◽  
Satoru Nakashima ◽  
...  
Keyword(s):  
Protein Dynamics ◽  
Oxygen Sensor ◽  
Specific Protein ◽  
Site Specific ◽  
Sensor Protein ◽  
Signaling Domain ◽  
Communication Pathway

scholarly journals Site-Specific Protein Dynamics Probed by Ultrafast Infrared Spectroscopy of a Noncanonical Amino Acid

2019 ◽  
Vol 123 (45) ◽  
pp. 9592-9597 ◽  
Author(s):  
Christopher R. Hall ◽  
Jinnette Tolentino Collado ◽  
James N. Iuliano ◽  
Agnieszka A. Gil ◽  
Katrin Adamczyk ◽  
...  
Keyword(s):  
Infrared Spectroscopy ◽  
Amino Acid ◽  
Protein Dynamics ◽  
Specific Protein ◽  
Site Specific ◽  
Noncanonical Amino Acid ◽  
Ultrafast Infrared

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 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.

scholarly journals Protein Dynamics from Accurate Low-Field Site-Specific Longitudinal and Transverse Nuclear Spin Relaxation

2019 ◽  
Vol 10 (19) ◽  
pp. 5917-5922 ◽  
Author(s):  
Pavel Kadeřávek ◽  
Nicolas Bolik-Coulon ◽  
Samuel F. Cousin ◽  
Thorsten Marquardsen ◽  
Jean-Max Tyburn ◽  
...  
Keyword(s):  
Protein Dynamics ◽  
Spin Relaxation ◽  
Nuclear Spin ◽  
Nuclear Spin Relaxation ◽  
Field Site ◽  
Site Specific ◽  
Low Field

Carbon−Deuterium Bonds as Site-Specific and Nonperturbative Probes for Time-Resolved Studies of Protein Dynamics and Folding

2011 ◽  
Vol 2 (5) ◽  
pp. 412-416 ◽  
Author(s):  
Jörg Zimmermann ◽  
Megan C. Thielges ◽  
Wayne Yu ◽  
Philip E. Dawson ◽  
Floyd E. Romesberg
Keyword(s):  
Protein Dynamics ◽  
Time Resolved ◽  
Site Specific

Large-cluster and combined fluorescent and gold immunoprobes

1996 ◽  
Vol 54 ◽  
pp. 892-893
Author(s):  
Richard D. Powell ◽  
James F. Hainfeld ◽  
Carol M. R. Halsey ◽  
David L. Spector ◽  
Shelley Kaurin ◽  
...  
Keyword(s):  
Metal Cluster ◽  
Sulfonyl Chloride ◽  
Gel Filtration ◽  
Cross Linking ◽  
Site Specific ◽  
Fab Fragments ◽  
Cluster Label ◽  
Covalently Linked ◽  
Texas Red ◽  
Fold Excess

Two new types of covalently linked, site-specific immunoprobes have been prepared using metal cluster labels, and used to stain components of cells. Combined fluorescein and 1.4 nm “Nanogold” labels were prepared by using the fluorescein-conjugated tris (aryl) phosphine ligand and the amino-substituted ligand in the synthesis of the Nanogold cluster. This cluster label was activated by reaction with a 60-fold excess of (sulfo-Succinimidyl-4-N-maleiniido-cyclohexane-l-carboxylate (sulfo-SMCC) at pH 7.5, separated from excess cross-linking reagent by gel filtration, and mixed in ten-fold excess with Goat Fab’ fragments against mouse IgG (obtained by reduction of F(ab’)2 fragments with 50 mM mercaptoethylamine hydrochloride). Labeled Fab’ fragments were isolated by gel filtration HPLC (Superose-12, Pharmacia). A combined Nanogold and Texas Red label was also prepared, using a Nanogold cluster derivatized with both and its protected analog: the cluster was reacted with an eight-fold excess of Texas Red sulfonyl chloride at pH 9.0, separated from excess Texas Red by gel filtration, then deprotected with HC1 in methanol to yield the amino-substituted label.

The challenge of detecting modifications on proteins

2020 ◽  
Vol 64 (1) ◽  
pp. 135-153 ◽  
Author(s):  
Lauren Elizabeth Smith ◽  
Adelina Rogowska-Wrzesinska
Keyword(s):  
Mass Spectrometry ◽  
Protein Function ◽  
Chemical Properties ◽  
Lysine Acetylation ◽  
Mass Determination ◽  
Post Translational Modifications ◽  
Site Specific ◽  
The Common

Abstract Post-translational modifications (PTMs) are integral to the regulation of protein function, characterising their role in this process is vital to understanding how cells work in both healthy and diseased states. Mass spectrometry (MS) facilitates the mass determination and sequencing of peptides, and thereby also the detection of site-specific PTMs. However, numerous challenges in this field continue to persist. The diverse chemical properties, low abundance, labile nature and instability of many PTMs, in combination with the more practical issues of compatibility with MS and bioinformatics challenges, contribute to the arduous nature of their analysis. In this review, we present an overview of the established MS-based approaches for analysing PTMs and the common complications associated with their investigation, including examples of specific challenges focusing on phosphorylation, lysine acetylation and redox modifications.

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