Hydration Dynamics and Coupled Water–Protein Fluctuations Probed by Intrinsic Tryptophan

Zhong, Dongping

doi:10.1002/9780470508602.ch3

Cited by 32 publications

(72 citation statements)

References 221 publications

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“…1B. Based on the methodology we developed to follow the Stokes shifts of tryptophan with time (11,12), we derived the solvation correlation functions for the 10 mutants. Fig.…”

Section: Resultsmentioning

confidence: 99%

Dynamics and mechanism of ultrafast water–protein interactions

Qin

Wang

Zhong

2016

Proc. Natl. Acad. Sci. U.S.A.

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129

157

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Protein hydration is essential to its structure, dynamics, and function, but water-protein interactions have not been directly observed in real time at physiological temperature to our awareness. By using a tryptophan scan with femtosecond spectroscopy, we simultaneously measured the hydration water dynamics and protein side-chain motions with temperature dependence. We observed the heterogeneous hydration dynamics around the global protein surface with two types of coupled motions, collective water/side-chain reorientation in a few picoseconds and cooperative water/sidechain restructuring in tens of picoseconds. The ultrafast dynamics in hundreds of femtoseconds is from the outer-layer, bulk-type mobile water molecules in the hydration shell. We also found that the hydration water dynamics are always faster than protein sidechain relaxations but with the same energy barriers, indicating hydration shell fluctuations driving protein side-chain motions on the picosecond time scales and thus elucidating their ultimate relationship.hydration shell dynamics | protein side-chain motion | water-driven relaxation | coupled fluctuation | tryptophan scan W ater-protein interactions are critical to protein structural stability and flexibility, functional dynamics, and biological activities (1, 2). Various methods such as neutron scattering (3), NMR (4), laser spectroscopy (5, 6), and molecular dynamics (MD) simulations (7) have been used to reveal protein surface hydration and coupled water-protein dynamics on different time and length scales. Hydration water molecules often participate in various protein functions and their motions even directly "control" protein fluctuations (2, 8). Frauenfelder et al. recently proposed a unified model for protein dynamics (8): large-scale protein motions are slaved to the fluctuations of bulk solvent and controlled by solvent viscosity while internal protein motions are slaved to the fluctuations of the hydration shell and controlled by hydration water. However, direct measurements of such coupled fluctuations at physiological temperature are challenging as a result of the ultrafast nature of water motions, and therefore most studies are indirect or at low temperature (3, 4). Here, we used a tryptophan (W) scan to probe global surface hydration (9) and used femtosecond spectroscopy to follow hydration water motions and local side-chain fluctuations in real time. With temperature dependence, we systematically measured their dynamics and thus finally elucidate their ultimate relationship. Results and DiscussionTryptophan Scan and Femtosecond Fluorescence Spectroscopy. We used DNA polymerase IV (Dpo4) (10), a hyperthermal enzyme without a single tryptophan residue, as a model protein, and designed 10 tryptophan mutants, one at a time, to probe four different domains (Fig. 1A). We performed systematic measurements of tryptophan fluorescence intensity changes with wavelength and time and thereby constructed 3D fluorescence profiles (SI Appendix, SI Note 1). One example of an R176W mutant is ...

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“…1B. Based on the methodology we developed to follow the Stokes shifts of tryptophan with time (11,12), we derived the solvation correlation functions for the 10 mutants. Fig.…”

Section: Resultsmentioning

confidence: 99%

Dynamics and mechanism of ultrafast water–protein interactions

Qin

Wang

Zhong

2016

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

129

157

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“…[25] Water molecules can interact with the protein surface and occupy internal cavities and deep clefts, which optimizes spatial configurations and minimizes energetic pathways. [26] Because of the uncertainty of the effect of this process in organic solvents, the amount of added buffer has to be optimized for any specific catalytic system. For this reason, we evaluated the dependence of the reaction rate versus the buffer concentration.…”

Section: Optimization Of Water Requirement For Oxidation In An Organimentioning

confidence: 99%

A Novel Synthesis of Bioactive Catechols by Layer‐by‐Layer Immobilized Tyrosinase in an Organic Solvent Medium

et al. 2011

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Commercial and extracted mushroom tyrosinases were supported on Eupergit C 250 L and protected by a coating of oppositely charged polyelectrolytes by means of the layer‐by‐layer technique. The kinetic parameters (Km, Vmax, and Vmax/Km) of these novel biocatalysts in both organic and aqueous media were evaluated, showing tyrosinase to be more reactive in organic solvent than in buffer solution. Heterogeneous tyrosinase systems were used for the oxidation of a large group of phenol derivatives to the corresponding catechols. Different enzyme reactivities were found depending on the substrate structure. The catalyst activity was retained for successive runs. Catechols are difficult to synthesize through traditional chemical methods under environmentally friendly conditions; the use of immobilized tyrosinase opens a novel synthetic alternative to this interesting biologically active family of substances.

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“…fluorescence protein | fluorescence probe | unnatural amino acid | imaging O f the amino acids that are inherently responsible for the fluorescence of proteins, tyrosine (Tyr), tryptophan (Trp), and phenylalanine (Phe), Trp is the most widely used fluorescence reporter of protein structure, function, and dynamics, as its fluorescence quantum yield (QY) is comparatively large and is also sensitive to environment (1)(2)(3). However, Trp absorbs/emits in the UV wavelength region and has low photostability.…”

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confidence: 99%

Blue fluorescent amino acid for biological spectroscopy and microscopy

Hilaire

Ahmed

Lin

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

111

119

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Many fluorescent proteins are currently available for biological spectroscopy and imaging measurements, allowing a wide range of biochemical and biophysical processes and interactions to be studied at various length scales. However, in applications where a small fluorescence reporter is required or desirable, the choice of fluorophores is rather limited. As such, continued effort has been devoted to the development of amino acid-based fluorophores that do not require a specific environment and additional time to mature and have a large fluorescence quantum yield, long fluorescence lifetime, good photostability, and an emission spectrum in the visible region. Herein, we show that a tryptophan analog, 4-cyanotryptophan, which differs from tryptophan by only two atoms, is the smallest fluorescent amino acid that meets these requirements and has great potential to enable in vitro and in vivo spectroscopic and microscopic measurements of proteins.fluorescence protein | fluorescence probe | unnatural amino acid | imaging O f the amino acids that are inherently responsible for the fluorescence of proteins, tyrosine (Tyr), tryptophan (Trp), and phenylalanine (Phe), Trp is the most widely used fluorescence reporter of protein structure, function, and dynamics, as its fluorescence quantum yield (QY) is comparatively large and is also sensitive to environment (1-3). However, Trp absorbs/emits in the UV wavelength region and has low photostability. Combined, these factors render this naturally occurring fluorescent amino acid hardly useful as a fluorophore for single-molecule measurements (4) and imaging applications, especially under in vivo conditions. For this reason, significant efforts have been devoted to identifying small unnatural fluorophores (5-11) that could overcome this limitation. So far, only naphthalene-based fluorophores, such as prodan (8, 9) and aladan (11) have been shown to be useful in this regard. However, these fluorophores are not structurally based on any naturally occurring amino acids and are larger in size than Trp, making them less attractive in applications where there are stringent requirements for the fluorophore size and structure. Therefore, the development of a smaller, ideally amino acid-based, fluorophore that does not require additional time to mature, have a large fluorescence QY, long fluorescence lifetime, good photostability, and an emission spectrum in the visible range, would enhance biological research. Herein, we show that a Trp analog, 4-cyanotryptophan (4CN-Trp), meets these requirements and has great potential to expand biological fluorescence spectroscopy and microscopy into additional territory.Many past studies have focused on Trp-based unnatural amino acids, including azatryptophans (5, 6, 12) and various indole-ring substituted analogs (13-16), aiming to identify useful biological fluorophores. Whereas some Trp analogs indeed exhibit improved fluorescent properties over Trp, none of them has found broad applications due to certain photophysical limitations. Recently, Ta...

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Hydration Dynamics and Coupled Water–Protein Fluctuations Probed by Intrinsic Tryptophan

Cited by 32 publications

References 221 publications

Dynamics and mechanism of ultrafast water–protein interactions

Dynamics and mechanism of ultrafast water–protein interactions

A Novel Synthesis of Bioactive Catechols by Layer‐by‐Layer Immobilized Tyrosinase in an Organic Solvent Medium

Blue fluorescent amino acid for biological spectroscopy and microscopy

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