Microenvironment of tryptophan residues in proteins of four structural classes: applications for fluorescence and circular dichroism spectroscopy

Khrustalev, Vladislav Victorovich; Poboinev, Victor Vitoldovich; Stojarov, Aleksander Nicolaevich; Khrustaleva, Tatyana Aleksandrovna

doi:10.1007/s00249-019-01377-0

Cited by 13 publications

(3 citation statements)

References 23 publications

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“…6 is unclear. Literature reports have detailed how interactions between tryptophan residues and aspartic acid can lead to red-shifted tryptophan fluorescence [ [56] , [57] , [58] ]. It is possible that the 360 nm fluorescence signals arise from specific Trp-Asp interactions, in which the dipeptide would penetrate into the azurin β-barrel, although this is unlikely since the barrel is tightly packed without a water core.…”

Section: Discussionmentioning

confidence: 99%

Sequence-specific destabilization of azurin by tetramethylguanidinium-dipeptide ionic liquids

Patel

Clark

DeStefano

et al. 2022

Biochemistry and Biophysics Reports

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Section: Discussionmentioning

confidence: 99%

Sequence-specific destabilization of azurin by tetramethylguanidinium-dipeptide ionic liquids

Patel

Clark

DeStefano

et al. 2022

Biochemistry and Biophysics Reports

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“…In those pentapeptides, amino acid residues are roughly divided into hydrophilic (Ser, Thr, Asp, Glu, Asn, Gln, His, Arg, Lys) and hydrophobic ones (Gly, Ala, Met, Leu, Ile, Val, Phe, Tyr, Trp, Cys, Pro) (Tina et al 2007 ). The methodology of such comparisons has been described in details previously (Khrustalev et al 2019 ).…”

Section: Methodsmentioning

confidence: 99%

The PentUnFOLD algorithm as a tool to distinguish the dark and the light sides of the structural instability of proteins

et al. 2022

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Intrinsically disordered proteins are frequently involved in important regulatory processes in the cell thanks to their ability to bind several different targets performing sometimes even opposite functions. The PentUnFOLD algorithm is a physicochemical method that is based on new propensity scales for disordered, nonstable and stable elements of secondary structure and on the counting of stabilizing and destabilizing intraprotein contacts. Unlike other methods, it works with a PDB file, and it can determine not only those fragments of alpha helices, beta strands, and random coils that can turn into disordered state (the “dark” side of the disorder), but also nonstable regions of alpha helices and beta strands which are able to turn into random coils (the “light” side), and vice versa (H ↔ C, E ↔ C). The scales have been obtained from structural data on disordered regions from the middle parts of amino acid sequences only, and not on their expectedly disordered N- and C-termini. Among other tendencies we have found that regions of both alpha helices and beta strands that can turn into the disordered state are relatively enriched in residues of Ala, Met, Asp, and Lys, while regions of both alpha helices and beta strands that can turn into random coil are relatively enriched in hydrophilic residues, and Cys, Pro, and Gly. Moreover, PentUnFOLD has the option to determine the effect of secondary structure transitions on the stability of a given region of a protein. The PentUnFOLD algorithm is freely available at http://3.17.12.213/pent-un-fold and http://chemres.bsmu.by/PentUnFOLD.htm . Supplementary Information The online version contains supplementary material available at 10.1007/s00726-022-03153-5.

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“…Therefore, chiral recognition has always been a topic of wide concern in chemical/biological research. In order to resolve this problem, numerous analytical methods, including NMR, , liquid chromatography, − fluorescence spectrometry, , circular dichroism, − colorimetric analysis, , capillary electrophoresis, − were developed to achieve the sensitive detection of enantiomers. However, most proposed approaches still faced great challenges, such as the time-consuming treatment of samples, high-cost reagents and bulky equipment, and complex professional operation by a well-trained technician.…”

Section: Introductionmentioning

confidence: 99%

Urchin-Like Chiral Metal–Organic Framework/Reduced Graphene Oxide Nanocomposite for Enantioselective Discrimination of d/l-Tryptophan

Guo

Wei

Lian

et al. 2020

ACS Appl. Nano Mater.

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An urchin-like chiral metal–organic framework/reduced graphene oxide (urchin-CMOF/rGO) nanocomposite was developed as the electrochemical sensing interface for robust, efficient, and high-selective discrimination of tryptophan (Trp) enantiomers. An urchin-CMOF/rGO nanocomposite was elaborately integrated to combine the amplification of electrical conduction by rGO and the enantioselectivity by asymmetric CMOF. On the basis of this novel nanocomposite-mediated sensor, chiral recognition of d/l-Trp was successfully achieved by the differential potential ratiometric method. Different percentages of Trp racemic mixtures were determined in a good linear relationship with specific peak potentials, which effectively detours the nonspecific signal of concomitant interference from most current-based voltammetries. Even in the complex human cerebrospinal fluid, the simulative ratiometric results of Trp-spiked samples were accurately detected with low false negatives. Additionally, diverse CMOF-regulated hybrid materials have great potential for chiral recognition in pharmaceutical monitoring and biochemical analysis.

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Microenvironment of tryptophan residues in proteins of four structural classes: applications for fluorescence and circular dichroism spectroscopy

Cited by 13 publications

References 23 publications

Sequence-specific destabilization of azurin by tetramethylguanidinium-dipeptide ionic liquids

Sequence-specific destabilization of azurin by tetramethylguanidinium-dipeptide ionic liquids

The PentUnFOLD algorithm as a tool to distinguish the dark and the light sides of the structural instability of proteins

Urchin-Like Chiral Metal–Organic Framework/Reduced Graphene Oxide Nanocomposite for Enantioselective Discrimination of d/l-Tryptophan

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