The Shape of Leucine in the Gas Phase

Cocinero, Emilio J.; Lesarri, Alberto; Grabow, Jens‐Uwe; López, Juan C.; Alonso, José L.

doi:10.1002/cphc.200600730

Cited by 77 publications

(95 citation statements)

References 43 publications

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“…Therefore, the observed agreement in relative populations of the side-chain conformers would support efficiency of the approximation method employed in the SAAP force field. Preferences of conformers I and IV for the side chain of Leu have also been reported in the gas phase 50 and in the solid state. 51 Similarly, the orders of the populations of v 1 conformers observed for His, Phe, Trp, Tyr in D 2 O 52 were reasonably reproduced by the SAAP force field with the side-chain separation approximation: the relative populations of the conformers with 52 whereas those obtained by the SAAP simulation in water at 300 K were 36, 34, and 30% for His, 37, 33, and 30% for Phe, 38, 35, and 27% for Trp, and 37, 34, and 29% for Tyr.…”

Section: Efficiency Of Side-chain Separation Approximationmentioning

confidence: 91%

The SAAP force field: Development of the single amino acid potentials for 20 proteinogenic amino acids and Monte Carlo molecular simulation for short peptides

et al. 2009

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Molecular simulation by using force field parameters has been widely applied in the fields of peptide and protein research for various purposes. We recently proposed a new all-atom protein force field, called the SAAP force field, which utilizes single amino acid potentials (SAAPs) as the fundamental elements. In this article, whole sets of the SAAP force field parameters in vacuo, in ether, and in water have been developed by ab initio calculation for all 20 proteinogenic amino acids and applied to Monte Carlo molecular simulation for two short peptides. The side-chain separation approximation method was employed to obtain the SAAP parameters for the amino acids with a long side chain. Monte Carlo simulation for Met-enkephalin (CHO-Tyr-Gly-Gly-Phe-Met-NH2) by using the SAAP force field revealed that the conformation in vacuo is mainly controlled by strong electrostatic interactions between the amino acid residues, while the SAAPs and the interamino acid Lennard-Jones potentials are predominant in water. In ether, the conformation would be determined by the combination of the three components. On the other hand, the SAAP simulation for chignolin (H-Gly-Tyr-Asp-Pro-Glu-Thr-Gly-Thr-Trp-Gly-OH) reasonably reproduced a native-like beta-hairpin structure in water although the C-terminal and side-chain conformations were different from the native ones. It was suggested that the SAAP force field is a useful tool for analyzing conformations of polypeptides in terms of intrinsic conformational propensities of the single amino acid units.

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Section: Efficiency Of Side-chain Separation Approximationmentioning

confidence: 91%

The SAAP force field: Development of the single amino acid potentials for 20 proteinogenic amino acids and Monte Carlo molecular simulation for short peptides

et al. 2009

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“…¼ 295-300 C) [115], isoleucine (R¼sec-butyl, m. p. ¼ 288 C) [116], and leucine (R¼iso-butyl, m.p. > 300 C) [117] complete the study of aminoacids with aliphatic non-polar side chains.…”

Section: Valine Isoleucine and Leucinementioning

confidence: 99%

Microwave Spectroscopy of Biomolecular Building Blocks

Alonso

López

2014

Topics in Current Chemistry

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Microwave spectroscopy, considered as the most definitive gas phase structural probe, is able to distinguish between different conformational structures of a molecule, because they have unique spectroscopic constants and give rise to distinct individual rotational spectra.Previously, application of this technique was limited to molecular specimens possessing appreciable vapor pressures, thus discarding the possibility of studying many other molecules of biological importance, in particular those with high melting points, which had a tendency to undergo thermal reactions, and ultimately degradation, upon heating.Nowadays, the combination of laser ablation with Fourier transform microwave spectroscopy techniques, in supersonic jets, has enabled the gas-phase study of such systems. In this chapter, these techniques, including broadband spectroscopy, as well as results of their application into the study of the conformational panorama and structure of biomolecular building blocks, such as amino acids, nucleic bases, and monosaccharides, are briefly discussed, and with them, the tools for conformational assignation - rotational constants, nuclear quadrupole coupling interaction, and dipole moment.

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“…First, the G3MP2 global minima for neutral amino acids match structures inferred from microwave and other gas-phase spectrometric methods. The examples include glycine [3,5], alanine [11][12][13][14][15], isoleucine [16], leucine [17], serine [15,18], tryptophan [19], and valine [20,21]. However, there are some examples in the literature of global minima identified with the B3LYP functional that do not match experimental structures (although many do match).…”

Section: Assessment Of Theoretical Approachmentioning

confidence: 99%

A reevaluation of computed proton affinities for the common α-amino acids

Gronert

Simpson

Conner

2009

J. Am. Soc. Mass Spectrom.

109

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The proton affinities of the 20 common amino acids have been computed at the G3MP2 level using structures derived from broad conformational searches at a variety of levels including G3MP2. In some cases, the conformational surveys identified more stable species than had been used in previous studies of proton affinities, though the differences in energy are sometimes rather small. The present values are likely the most reliable measure of amino acid proton affinities in the gas phase. An analysis of differences between these values and those obtained experimentally via the kinetic method indicates that the extraction of proton affinities from kinetic method data can potentially lead to large errors linked to the estimation of relative protonation entropies. . As noted by these authors, there is substantial variation in the experimental values reported for these species. The origin of this variability is most likely related to the difficulties of completing thermodynamic measurements in the gas phase on materials with low volatility. As a result, many of the experimental values are from kinetic method measurements and are subject to errors associated with the kinetic method approximation (as well as cumulative errors associated with the development of ladder-type scales). Therefore, in these systems, high-level computational work offers an attractive means of resolving differences in the various experimental measurements.While working on a computational study of the conformational preferences of neutral, gaseous amino acids, we realized that it would be possible to improve on the accuracy of the proton affinities reported by Paizs and coworkers. First, their computational strategy relied on the B3LYP approach to identify global minima and, often, they identified conformations for the neutral amino acids that did not match with those reported in previous computational and experimental studies (apparently in some cases this was the result of the search strategy and in others the computational method). For example, Paizs and coworkers concluded that glycine prefers a structure with an internal hydrogen bond between the carboxylic acid and amine groups. Highlevel ab initio, other B3LYP data [2], and experimental data suggest a structure with a syn carboxyl group and a weak interaction between the amine hydrogens and the carbonyl [3][4][5]. While the energetic impact of this problem is generally minor, we feel it is important to report values based on the most appropriate conformations that can be obtained within a computational method. For the protonated amino acids, this problem is less pronounced because the hydrogen bonding interactions are much stronger; most computational methods identify similar structures as the global minimum. Second, values reported by Paizs and coworkers are at 0 K. We have added a correction for the thermal energy of a proton, which amounts to about 1.5 kcal/mol at 298 K, as well as for the neutral and protonated amino acid. Although these corrections cancel to some extent and while the ge...

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The Shape of Leucine in the Gas Phase

Cited by 77 publications

References 43 publications

The SAAP force field: Development of the single amino acid potentials for 20 proteinogenic amino acids and Monte Carlo molecular simulation for short peptides

The SAAP force field: Development of the single amino acid potentials for 20 proteinogenic amino acids and Monte Carlo molecular simulation for short peptides

Microwave Spectroscopy of Biomolecular Building Blocks

A reevaluation of computed proton affinities for the common α-amino acids

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