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Special Issue "Vibrational Probes of Biomolecular Structure and Dynamics"

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Physical Chemistry".

Deadline for manuscript submissions: 15 February 2019

Special Issue Editor

Guest Editor
Prof. Dr. Chong Fang

Department of Chemistry, 153 Gilbert Hall, Oregon State University, Corvallis, OR 97331, USA
Website | E-Mail
Phone: 5417376704
Interests: femtosecond Raman; vibrational probes; structural dynamics; fluorescent proteins; photoacids; photophysics and photochemistry; excited state processes; energy relaxation; proton transfer; hydrogen bonding interactions; nonlinear optics; ultrafast spectroscopy

Special Issue Information

Dear Colleagues,

The past few decades have seen tremendous progress in understanding the structure–function relationships of biomolecular systems from microscopic motions to macroscopic properties. Among all the molecular characterization methods, vibrational probes stand out as a versatile and fruitful endeavor because they are highly sensitive to local environment and can be designed, modified, positioned, and controlled to reveal previously unavailable, unknown, or unattainable information about the system under investigation.

The vibrational probes used for steady-state biomolecular structural determination include functional groups and chemical compounds such as carbonyl, nitrile, azide, and cyanamide, while the time-resolved studies can use those characteristic probes to track equilibrium processes (e.g., anharmonic coupling, H-bonding interactions, spectral diffusion, chemical exchange, energy transport) and non-equilibrium processes (e.g., protein folding and unfolding, cooling, electron and proton transfer, transient absorption, fluorescence). Such a wealth of information has been obtained by active researchers across the modern disciplines of physical chemistry and chemical physics, biophysics and biochemistry, ultrafast spectroscopy and nonlinear optics, chemical biology, imaging and microscopy. Individual or pairs of isotopically labeled, engineered or non-natural probes, in conjunction with various advanced spectroscopic and microscopic techniques based on light-matter interactions, have further expanded the repertoire of vibrational toolset.

The aim of this Special Issue is to bring together leading experts across disciplines and highlight recent advances utilizing vibrational probes to study biomolecular structure and dynamics. Both original research articles and reviews are welcome, and articles that report or propose new ideas and new directions to stimulate future development and applications are particularly welcome.

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 papers will be 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. Molecules is an international peer-reviewed open access bimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). 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

  • structure-function relationships
  • molecular spectroscopy
  • imaging and microscopy
  • protein engineering
  • bioprobe development
  • potential energy surface
  • vibrational dynamics
  • functional motions and interactions
  • equilibrium and non-equilibrium processes

Published Papers (4 papers)

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Research

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Open AccessArticle Do Osmolytes Impact the Structure and Dynamics of Myoglobin?
Molecules 2018, 23(12), 3189; https://doi.org/10.3390/molecules23123189
Received: 22 October 2018 / Revised: 30 November 2018 / Accepted: 2 December 2018 / Published: 3 December 2018
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Abstract
Osmolytes are small organic compounds that can affect the stability of proteins in living cells. The mechanism of osmolytes’ protective effects on protein structure and dynamics has not been fully explained, but in general, two possibilities have been suggested and examined: a direct
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Osmolytes are small organic compounds that can affect the stability of proteins in living cells. The mechanism of osmolytes’ protective effects on protein structure and dynamics has not been fully explained, but in general, two possibilities have been suggested and examined: a direct interaction of osmolytes with proteins (water replacement hypothesis), and an indirect interaction (vitrification hypothesis). Here, to investigate these two possible mechanisms, we studied myoglobin-osmolyte systems using FTIR, UV-vis, CD, and femtosecond IR pump-probe spectroscopy. Interestingly, noticeable changes are observed in both the lifetime of the CO stretch of CO-bound myoglobin and the spectra of UV-vis, CD, and FTIR upon addition of the osmolytes. In addition, the temperature-dependent CD studies reveal that the protein’s thermal stability depends on molecular structure, hydrogen-bonding ability, and size of osmolytes. We anticipate that the present experimental results provide important clues about the complicated and intricate mechanism of osmolyte effects on protein structure and dynamics in a crowded cellular environment. Full article
(This article belongs to the Special Issue Vibrational Probes of Biomolecular Structure and Dynamics)
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Open AccessArticle Time-Resolved Spectroscopic Study of N,N-Di(4-bromo)nitrenium Ions in Selected Solutions
Molecules 2018, 23(12), 3182; https://doi.org/10.3390/molecules23123182
Received: 8 November 2018 / Revised: 26 November 2018 / Accepted: 30 November 2018 / Published: 3 December 2018
PDF Full-text (1650 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Nitrenium ions are important reactive intermediates in chemistry and biology. In this work, femtosecond and nanosecond transient absorption (fs-TA and ns-TA) along with nanosecond time-resolved resonance Raman (ns-TR3) experiments were employed to examine the photochemical pathways of N-(4,4′-dibromodiphenylamino)-2,4,6-trimethylpyridinium BF4
[...] Read more.
Nitrenium ions are important reactive intermediates in chemistry and biology. In this work, femtosecond and nanosecond transient absorption (fs-TA and ns-TA) along with nanosecond time-resolved resonance Raman (ns-TR3) experiments were employed to examine the photochemical pathways of N-(4,4′-dibromodiphenylamino)-2,4,6-trimethylpyridinium BF4 (salt (DN) from just absorption of a photon of light to the production of the important N,N-di(4-bromophenyl)nitrenium ion 2. In acetonitrile (MeCN), the formation of halogenated diarylnitrenium ion 2 was observed within 4 ps, showing the vibrational spectra with strong intensity. The nucleophilic adduct reaction of ion 2 with H2O was also examined in aqueous solutions. The direct detection of the unique ortho adduct intermediate 3 shows that there is an efficient and exclusive reaction pathway for 2 with H2O. The results shown in this paper give new characterization of 2, which can be used to design time-resolved spectroscopy investigations of covalent addition reactions of nitrenium ions with other molecules in future studies. Full article
(This article belongs to the Special Issue Vibrational Probes of Biomolecular Structure and Dynamics)
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Open AccessFeature PaperArticle Excited State Structural Evolution of a GFP Single-Site Mutant Tracked by Tunable Femtosecond-Stimulated Raman Spectroscopy
Molecules 2018, 23(9), 2226; https://doi.org/10.3390/molecules23092226
Received: 26 July 2018 / Revised: 29 August 2018 / Accepted: 31 August 2018 / Published: 1 September 2018
Cited by 1 | PDF Full-text (4139 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Tracking vibrational motions during a photochemical or photophysical process has gained momentum, due to its sensitivity to the progression of reaction and change of environment. In this work, we implemented an advanced ultrafast vibrational technique, femtosecond-stimulated Raman spectroscopy (FSRS), to monitor the excited
[...] Read more.
Tracking vibrational motions during a photochemical or photophysical process has gained momentum, due to its sensitivity to the progression of reaction and change of environment. In this work, we implemented an advanced ultrafast vibrational technique, femtosecond-stimulated Raman spectroscopy (FSRS), to monitor the excited state structural evolution of an engineered green fluorescent protein (GFP) single-site mutant S205V. This mutation alters the original excited state proton transfer (ESPT) chain. By strategically tuning the Raman pump to different wavelengths (i.e., 801, 539, and 504 nm) to achieve pre-resonance with transient excited state electronic bands, the characteristic Raman modes of the excited protonated (A*) chromophore species and intermediate deprotonated (I*) species can be selectively monitored. The inhomogeneous distribution/population of A* species go through ESPT with a similar ~300 ps time constant, confirming that bridging a water molecule to protein residue T203 in the ESPT chain is the rate-limiting step. Some A* species undergo vibrational cooling through high-frequency motions on the ~190 ps time scale. At early times, a portion of the largely protonated A* species could also undergo vibrational cooling or return to the ground state with a ~80 ps time constant. On the photoproduct side, a ~1330 cm−1 delocalized motion is observed, with dispersive line shapes in both the Stokes and anti-Stokes FSRS with a pre-resonance Raman pump, which indicates strong vibronic coupling, as the mode could facilitate the I* species to reach a relatively stable state (e.g., the main fluorescent state) after conversion from A*. Our findings disentangle the contributions of various vibrational motions active during the ESPT reaction, and offer new structural dynamics insights into the fluorescence mechanisms of engineered GFPs and other analogous autofluorescent proteins. Full article
(This article belongs to the Special Issue Vibrational Probes of Biomolecular Structure and Dynamics)
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Review

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Open AccessReview Vibrational Approach to the Dynamics and Structure of Protein Amyloids
Molecules 2019, 24(1), 186; https://doi.org/10.3390/molecules24010186
Received: 13 December 2018 / Revised: 31 December 2018 / Accepted: 2 January 2019 / Published: 6 January 2019
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Abstract
Amyloid diseases, including neurodegenerative diseases such as Alzheimer’s and Parkinson’s, are linked to a poorly understood progression of protein misfolding and aggregation events that culminate in tissue-selective deposition and human pathology. Elucidation of the mechanistic details of protein aggregation and the structural features
[...] Read more.
Amyloid diseases, including neurodegenerative diseases such as Alzheimer’s and Parkinson’s, are linked to a poorly understood progression of protein misfolding and aggregation events that culminate in tissue-selective deposition and human pathology. Elucidation of the mechanistic details of protein aggregation and the structural features of the aggregates is critical for a comprehensive understanding of the mechanisms of protein oligomerization and fibrillization. Vibrational spectroscopies, such as Fourier transform infrared (FTIR) and Raman, are powerful tools that are sensitive to the secondary structure of proteins and have been widely used to investigate protein misfolding and aggregation. We address the application of the vibrational approaches in recent studies of conformational dynamics and structural characteristics of protein oligomers and amyloid fibrils. In particular, introduction of isotope labelled carbonyl into a peptide backbone, and incorporation of the extrinsic unnatural amino acids with vibrational moieties on the side chain, have greatly expanded the ability of vibrational spectroscopy to obtain site-specific structural and dynamic information. The applications of these methods in recent studies of protein aggregation are also reviewed. Full article
(This article belongs to the Special Issue Vibrational Probes of Biomolecular Structure and Dynamics)
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