Protonation of glycine, serine and cysteine. Conformations, proton affinities and intrinsic basicities

Noguera, María; Rodrı́guez-Santiago, Luis; Sodupe, Mariona; Bertrán, Juan

doi:10.1016/s0166-1280(00)00686-2

Cited by 84 publications

(104 citation statements)

References 44 publications

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“…By comparison with protonated amino acids, the single nonequivalent fast exchanging site can be attributed to the carboxylic group. Therefore, three equivalent exchanging sites strongly imply that the amino group is the protonation site, in agreement with theoretical results [28]. Sitespecific kinetic studies [9,13] done on a similar system (glycine) give us an opportunity to compare results.…”

Section: H/d Exchange Of Protonated Aliphatic Amino Acidssupporting

confidence: 86%

The gas-phase H/D exchange mechanism of protonated amino acids

Rožman

2005

J. Am. Soc. Mass Spectrom.

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A mass spectrometry and Density Functional Theory study of gas-phase H/D exchange in protonated Ala, Cys, Ile, Leu, Met, and Val is reported. Site-specific rate constants were determined and results identify the ␣-amino group as the protonation site. Lack of exchange on the Cys thiol group is explained by the absence of strong intramolecular hydrogen bonding within the reaction complex. In aliphatic amino acids the presence of a methyl group at the ␤-C atom was found to lower the site-specific H/D exchange rate for amino hydrogens. Study of the exchange mechanism showed that isotopic exchange occurs in two independent reactions: in one, only the carboxylic hydrogen is exchanged and in the other, both carboxylic and amino group hydrogens exchange. The proposed reaction mechanisms, calculated structures of various species, and a number of structural findings are consistent with experimental data. (J Am Soc Mass Spectrom 2005, 16, 1846 -1852

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Section: H/d Exchange Of Protonated Aliphatic Amino Acidssupporting

confidence: 86%

The gas-phase H/D exchange mechanism of protonated amino acids

Rožman

2005

J. Am. Soc. Mass Spectrom.

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“…Cysteine has been a widely studied amino acid due to the availability of substantial crystallographic data, computationally generated low energy metastable states elucidating the structural details of its numerous possible conformations [27][28][29][30][31][32][33][34], and the relative simplicity of the orientation of the constituent atoms. Disparate studies discussing the vibration spectrum assignment in cysteine have been conducted and reported by several authors [35][36][37][38].…”

Section: Amino Acid (Cysteine)mentioning

confidence: 99%

Precise spring constant assignment in elastic network model for identification of vibration frequency and modeshape

Hu¹,

Raj²,

Kim³

et al. 2010

J Mech Sci Technol

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We presented a feasible framework of studying dynamics of macromolecules by applying elastic network model (ENM) and vibration spectroscopy. We first identified the precise force constants of covalent bonds commonly observed in macromolecules by matching their reported Raman shifts data with predicted wavenumbers determined by normal mode analysis (NMA). Assigning the obtained spring constants to other small chemical compounds such as ethynyl isocyanide (C3HN) and diacetylene (C4H2), we not only predicted their vibration wavenumbers precisely but also identified their individual mode shapes from NMA. We extensively tested this chemical information based ENM with one of amino acids, cysteine. Subsequent comparison of frequencies and modeshapes also yields a strong agreement between computed and experimental data. Consequently, the proposed method enables us to identify low frequency modeshapes that are in general functionally important collective motions of macromolecules but have hardly been revealed experimentally even using terahertz spectroscopy.

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“…Many papers well demonstrate the quality of B3LYP functional for amino acids [16][17][18][19][20][21][22][23][24], however, considering the failure of the B3LYP/6-311G(d,p) approach to predict gao global minimum it is useful to test the basis set sufficiency for the gao system. The ectt, ecct, ettt and zccc conformers are presented in Fig.…”

Section: Gao-neutral Conformersmentioning

confidence: 99%

“…The bidentate metal complexes with gaoanion showed another conformation in aqueous solution [12,13]. The discrepancies observed are surprising since B3LYP functional has proved successful in the structural and energetic characterization of amino acids conformers [16][17][18][19][20][21][22][23][24]. This finding prompted us in a comparative study to investigate the influence of the basis set and the amount of HF exchange on the predicted conformer energies of gao and its ions.…”

Section: Introductionmentioning

confidence: 99%