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Structure, Dynamics, and Function of Photoreceptors and Fluorescent Proteins
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Structure, Dynamics, and Function of Photoreceptors and Fluorescent Proteins

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: closed (31 July 2023) | Viewed by 3380

Special Issue Editor

Prof. Dr. Chong Fang

E-Mail Website
Guest Editor
Department of Chemistry, Oregon State University, Corvallis, OR 97331, USA
Interests: fluorescent proteins; biosensors; chemosensors; photoswitchable and photoconvertible fluorescent proteins; femtosecond-stimulated Raman; transient absorption; excited-state dynamics; fluorogenicity; redder probes; rational protein design; battery electrolytes; materials characterization
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Light-sensitive proteins, ranging from photoreceptors for sensing and responding to light in various organisms to fluorescent proteins for bioimaging, have fascinated scientists, engineers, and the general public for decades. Well-known and diverse examples have included green fluorescent protein (GFP), fluorogen-activating protein, rhodopsin, phytochrome, cyanobacteriochrome, LOV, and BLUF, which can promote various biosensing, optogenetic, and even optoelectronic applications across multiple disciplines. Recent developments in experimental, theoretical, and computational toolsets have enabled exciting advances in the mechanistic understanding, rational design, and targeted engineering of such biological and biomimetic systems, from structural, dynamic, and/or functional perspectives. The desirable properties include photochromicity, photostability, photoredox, photocatalysis, a large Stokes shift, and redder electronic transitions. This Special Issue will collect original research papers and review articles on the mechanism- and application-driven characterizations and utilizations of photoreceptors and fluorescent proteins, highlighting the rich portfolio of techniques and methodologies being implemented and/or innovated.

Prof. Dr. Chong Fang
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • fluorescent proteins (FPs) and FP-based biosensors
  • photoreceptor proteins
  • photoswitchable and photoconvertible proteins
  • proteins with noncanonical amino acids
  • electronic and vibrational spectroscopies
  • steady-state and time-resolved spectra
  • theoretical modeling and computational advances
  • chromophore–protein interactions
  • ultrafast laser spectroscopy and femtochemistry
  • bioimaging and optogenetics

Published Papers (2 papers)

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Research

36 pages, 7111 KiB  
Article
Structural Characterization of Fluorescent Proteins Using Tunable Femtosecond Stimulated Raman Spectroscopy
by Cheng Chen, J. Nathan Henderson, Dmitry A. Ruchkin, Jacob M. Kirsh, Mikhail S. Baranov, Alexey M. Bogdanov, Jeremy H. Mills, Steven G. Boxer and Chong Fang
Int. J. Mol. Sci. 2023, 24(15), 11991; https://doi.org/10.3390/ijms241511991 - 26 Jul 2023
Cited by 3 | Viewed by 1666
Abstract
The versatile functions of fluorescent proteins (FPs) as fluorescence biomarkers depend on their intrinsic chromophores interacting with the protein environment. Besides X-ray crystallography, vibrational spectroscopy represents a highly valuable tool for characterizing the chromophore structure and revealing the roles of chromophore–environment interactions. In [...] Read more.
The versatile functions of fluorescent proteins (FPs) as fluorescence biomarkers depend on their intrinsic chromophores interacting with the protein environment. Besides X-ray crystallography, vibrational spectroscopy represents a highly valuable tool for characterizing the chromophore structure and revealing the roles of chromophore–environment interactions. In this work, we aim to benchmark the ground-state vibrational signatures of a series of FPs with emission colors spanning from green, yellow, orange, to red, as well as the solvated model chromophores for some of these FPs, using wavelength-tunable femtosecond stimulated Raman spectroscopy (FSRS) in conjunction with quantum calculations. We systematically analyzed and discussed four factors underlying the vibrational properties of FP chromophores: sidechain structure, conjugation structure, chromophore conformation, and the protein environment. A prominent bond-stretching mode characteristic of the quinoidal resonance structure is found to be conserved in most FPs and model chromophores investigated, which can be used as a vibrational marker to interpret chromophore–environment interactions and structural effects on the electronic properties of the chromophore. The fundamental insights gained for these light-sensing units (e.g., protein active sites) substantiate the unique and powerful capability of wavelength-tunable FSRS in delineating FP chromophore properties with high sensitivity and resolution in solution and protein matrices. The comprehensive characterization for various FPs across a colorful palette could also serve as a solid foundation for future spectroscopic studies and the rational engineering of FPs with diverse and improved functions. Full article
(This article belongs to the Special Issue Structure, Dynamics, and Function of Photoreceptors and Fluorescent Proteins)
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11 pages, 2858 KiB  
Article
Investigation of Excited-State Intramolecular Proton Transfer and Structural Dynamics in Bis-Benzimidazole Derivative (BBM)
by Junhan Xie, Ziyu Wang, Ruixue Zhu, Jiaming Jiang, Tsu-Chien Weng, Yi Ren, Shuhua Han, Yifan Huang and Weimin Liu
Int. J. Mol. Sci. 2023, 24(11), 9438; https://doi.org/10.3390/ijms24119438 - 29 May 2023
Cited by 1 | Viewed by 1330
Abstract
The bis-benzimidazole derivative (BBM) molecule, consisting of two 2-(2′-hydroxyphenyl) benzimidazole (HBI) halves, has been synthesized and successfully utilized as a ratiometric fluorescence sensor for the sensitive detection of Cu2+ based on enol–keto excited-state intramolecular proton transfer (ESIPT). In this study, we strategically [...] Read more.
The bis-benzimidazole derivative (BBM) molecule, consisting of two 2-(2′-hydroxyphenyl) benzimidazole (HBI) halves, has been synthesized and successfully utilized as a ratiometric fluorescence sensor for the sensitive detection of Cu2+ based on enol–keto excited-state intramolecular proton transfer (ESIPT). In this study, we strategically implement femtosecond stimulated Raman spectroscopy and several time-resolved electronic spectroscopies, aided by quantum chemical calculations to investigate the detailed primary photodynamics of the BBM molecule. The results demonstrate that the ESIPT from BBM-enol* to BBM-keto* was observed in only one of the HBI halves with a time constant of 300 fs; after that, the rotation of the dihedral angle between the two HBI halves generated a planarized BBM-keto* isomer in 3 ps, leading to a dynamic redshift of BBM-keto* emission. Full article
(This article belongs to the Special Issue Structure, Dynamics, and Function of Photoreceptors and Fluorescent Proteins)
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