Publication:
Tuning the chain length of new pyrene derivatives for site-selective photocleavage of avidin

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Issued Date

2018

Resource Type

Article

File Type

application/pdf

ISSN

10111344

DOI

10.1016/j.jphotobiol.2018.07.001

Other identifier(s)

2-s2.0-85049478108

Rights Holder(s)

Scopus

Bibliographic Citation

Journal of Photochemistry and Photobiology B: Biology. Vol 186, (2018), p.23-30

Suggested Citation

Yenjai S., Kumar C.V., Kuno M., Liwporncharoenvong T., Samosorn S., Buranaprapuk A. Tuning the chain length of new pyrene derivatives for site-selective photocleavage of avidin. Journal of Photochemistry and Photobiology B: Biology. Vol 186, (2018), p.23-30. doi:10.1016/j.jphotobiol.2018.07.001 Retrieved from: https://hdl.handle.net/20.500.14740/5871

Title

Tuning the chain length of new pyrene derivatives for site-selective photocleavage of avidin

Author(s)

Yenjai S.
 Kumar C.V.
 Kuno M.
 Liwporncharoenvong T.
 Samosorn S.
 Buranaprapuk A.

Abstract

Rational design of photoreagents with systematic modifications of their structures can provide valuable information for a better understanding of the protein photocleavage mechanism by these reagents. Variation of the length of the linker connecting the photoactive moiety with the protein anchoring-group allowed us to investigate the control of the protein photocleavage site. A series of new photochemical reagents (PMA-1A, PMA-2A and PMA-3A) with increasing chain lengths is examined in the current study. Using avidin as a model system, we examined the interaction of these probes by UV–Vis, fluorescence spectroscopic methods, photocleavage and computational docking studies. Hypochromism of the absorption spectrum was observed for the binding of these new photochemical reagents with estimated binding constants (Kb) of 6.2 × 105, 6.7 × 105 and 4.6 × 105 M−1, respectively. No significant changes of Stern-Volmer quenching constant (Ksv) with Co(NH3)6Cl3 has been noted and the data indicated that the probes bind near the surface of the protein with sufficient exposure to the solvent. Photoexcitation of the probe-avidin complex, in the presence of Co(NH3)6Cl3, resulted in protein fragmentation, and the cleavage yield decreased with the increase in the linker length, and paralleled with the observed Ksv values. Amino acid sequencing of the photofragments indicated that avidin is cleaved between Thr77 and Val78, as a major cleavage site for all the three photoreagents. This site is proximate to the biotin binding site on avidin, and molecular docking studies indicated that the H-bonding interactions between the polar end-group of the photoreagents and hydrophilic amino acids of avidin were important in positioning the reagent on the protein. The major cleavage site, at residues 77–78, was within 5 Å of the pyrenyl moiety of the probe, and hence, molecular tuning of the linker provided a simple approach to position the photoreagent along the potential photocleavage site. © 2018

Subject(s)

Avidin
 Biotin
 Pyrene derivative
 Avidin
 Cobalt
 Cobalt ammonium complex
 Protein binding
 Pyrene derivative
 Absorption spectroscopy
 Article
 Binding affinity
 Binding site
 Chemical structure
 Controlled study
 Enzyme denaturation
 Hydrogen bond
 Hydrophilicity
 Molecular docking
 Photochemistry
 Priority journal
 Protein cleavage
 Sequence analysis
 Spectrofluorometry
 Amino acid sequence
 Chemistry
 Kinetics
 Light
 Metabolism
 Photolysis
 Protein tertiary structure
 Radiation response
 Synthesis
 Amino Acid Sequence
 Avidin
 Binding Sites
 Cobalt
 Hydrogen Bonding
 Kinetics
 Light
 Molecular Docking Simulation
 Photolysis
 Protein Binding
 Protein Structure, Tertiary
 Pyrenes
 Spectrometry, Fluorescence

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URI

https://hdl.handle.net/20.500.14740/5871

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Scopus: Year 1983-2021

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