Low-Energy Tautomers and Conformers of Neutral and Protonated Arginine

Rak, Janusz; Skurski, Piotr; Simons, Jack; Gutowski, Maciej

doi:10.1021/ja011357l

Cited by 143 publications

(225 citation statements)

References 42 publications

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“…If the peptide ions were present as zwitterions, then we would expect some variation in the collision cross-sections for the peptide and methyl ester ions owing to a reduction in the interaction between charge sites [47,48]. Our molecular dynamics simulation and molecular orbital calculations also suggest that charge-solvated species represent the most stable conformations of the [M ϩ H] ϩ ions, which is consistent with Simon's studies [31]. Theoretical collision cross-sections for [M ϩ H] ϩ ions for arginine-containing di-and tripeptide and C-terminal methylated derivatives (see Table 2) were calculated by using Mobcal [49].…”

Section: Resultssupporting

confidence: 89%

“…We assumed that protonation occurred on the guanidine group owing to the high proton affinity (PA ϭ 251.2 kcal/mol) for arginine [23], but we also considered whether the most stable structure of the [M ϩ H] ϩ ion is a charge-solvated species, as suggested by Simon et al [31], or zwitterionic species, as suggested by Strittmatter and Williams [28]. To address this question, we used a combination of collision cross-sections obtained by using ion mobility spectrometry (IMS) [45] [46].…”

Section: Resultsmentioning

confidence: 99%

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A mechanistic study of the H/D exchange reactions of protonated arginine and arginine-containing Di- and tripeptides

Huang

Marini

McLean

et al. 2009

J. Am. Soc. Mass Spectrom.

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The gas-phase H/D exchange reactions of arginine (R) and arginine-containing di-and tri-peptide (gly-arg (GR), arg-gly (RG), gly-gly-arg (GGR), gly-arg-gly (GRG) and arg-gly-gly (RGG)) [M ϩ H] ϩ ions with deuterated ammonia (ND 3 ) were investigated by using Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR), ion mobility-mass spectrometry (IM-MS), ab initio and density functional theory-based molecular orbital calculations and molecular modeling. Three exchanges are observed for arginine and argininecontaining tri-peptide [M ϩ H] [15]. Valentine and Clemmer used ion mobility-mass spectrometry to examine the conformation dependence of H/D exchange reactions, and suggested that ion conformation has a significant effect on H/D exchange [16,17].Compared with the intensive investigations carried out on the conformational characterization of peptides and proteins using solution-phase H/D exchange reaction chemistry, the corresponding gas-phase studies are much less comprehensive. The key question regarding gas-phase H/D exchange is: does the "solvent molecule," i.e., H/D exchange reagent, sample the entire "available surface area" of the peptide/protein ion, or is H/D exchange limited by other factors? For example, are all solution phase labile hydrogen atoms exchangeable in the gas phase and are the reactivities of all exchangeable hydrogen atoms similar? Dookeran and Harrison studied the H/D exchange reactions of 18 naturally occurring amino acids and selected di-and tripeptides with ND 3 , and reported that amino acid [M ϩ H] ϩ ions containing hydroxyl, carboxyl, and amine side chains exchange all labile hydrogen atoms, whereas the side-chain hydrogen atoms of glutamine, asparagine, and histidine [M ϩ H] ϩ ions exchange less readily, and tyrosine and arginine [M ϩ H] ϩ ions do not undergo significant exchange [18]. In a separate study, Lebrilla et al. found that the carboxylic acid group of glycine and aliphatic amino acid [M ϩ H] ϩ ions (alanine, valine, leucine, isoleucine, and proline) undergo H/D exchange three to 10 times faster than the NAddress reprint requests to Dr.

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Section: Resultssupporting

confidence: 89%

Section: Resultsmentioning

confidence: 99%

A mechanistic study of the H/D exchange reactions of protonated arginine and arginine-containing Di- and tripeptides

Huang

Marini

McLean

et al. 2009

J. Am. Soc. Mass Spectrom.

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“…Because of the coarse grid in its first step, the SUMM approach turned out to be inefficient for such a situation. The success of the remaining algorithms is compared in Figure 4, which gives the relative RI-MP2/TZVPP//B3LYP/ TZVPP energies of the generated conformers with respect to structure (C5) given by Rak et al 5 For a better comparison only the MMFF94 conformers are given. As one can see in Figure 4 the stochastic MCMM algorithm produces only one conformer that is lower in energy than C5.…”

Section: Conformational Search Strategiesmentioning

confidence: 99%

“…As noted before, the structures C5 and Z3 were already described in the literature. 5 Furthermore, the multiple hydrogen binding patterns within the stacked structures comprehend hydrogen bonds of the type NÀ ÀHÁÁÁO from the guanidine to the protonated hydroxyl oxygen (N1, N3, N4). Such hydrogen bond types have not been mentioned for the arginine monomer yet.…”

Section: Electronic Structure Optimizationsmentioning

confidence: 99%

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Conformational analysis of arginine in gas phase—A strategy for scanning the potential energy surface effectively

et al. 2007

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Abstract:The determination of all possible low-lying energy conformers of flexible molecules is of fundamental interest for various applications. It necessitates a reliable conformational search that is able to detect all important minimum structures and calculates the energies on an adequate level of theory. This work presents a strategy to identify low-energy conformers using arginine as an example by means of a force-field based conformational search in combination with high-level geometry optimizations (RI-MP2/TZVPP1). The methods used for various stages in the conformational search strategy are shown and various pitfalls are discussed. We can show that electronic energies calculated on a DFT level of theory with standard exchange-correlation functionals strongly underestimate the intramolecular stabilization resulting from stacked orientations of the guanidine and carbonyl moiety of arginine due to the deficiency of DFT to describe dispersion effects. In this case by usage of electron correlation methods, low energy conformers comprising stacked arrangements that are counterintuitive become favorable.

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How Important Is Molecular Rigidity for the Complex Stability of Artificial Host–Guest Systems? A Theoretical Study on Self‐Assembly of Gas‐Phase Arginine

Schlund

Schmuck

Engels

2007

Chemistry A European J

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Arginine forms much less stable dimers than 2-(guanidiniocarbonyl)-1H-pyrrole-5-carboxylate although the principal binding interactions are very similar. The reasons for this difference are addressed in this work by state-of-the-art ab initio computations. The investigation shows that the extraordinary high stability of the 2-(guanidiniocarbonyl)-1H-pyrrole-5-carboxylate dimer results to about 50 % from the rigidity of its monomer. Within this study monomer and dimer conformers of arginine were calculated leading to new low lying structures which have not been reported before as well as new global minima are predicted. In these structures stacking interactions with the guanidinium moiety are especially important. For the monomer we predict the energy minimum to be the canonical form with the lowest lying zwitterionic structure being only 9 kJ mol(-1) less stable. During the course of these calculations we found that DFT did not predict the structures and their relative energy correctly in comparison to perturbation theory (MP2) and some potential reasons for the failure of DFT in these cases are discussed. Vibrational frequencies of the various structures are presented and a suitable wavenumber region for an experimental determination of the global minimum of the arginine monomer is identified. The effect of molecular rigidity on the self-assembly is probed using a local minimum of the arginine monomer which does not possess any intramolecular stabilizing effects. Our results suggest that the deliberate control of the conformational flexibility is a powerful instrument to steer the complex affinity of artificial hosts.

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Low-Energy Tautomers and Conformers of Neutral and Protonated Arginine

Cited by 143 publications

References 42 publications

A mechanistic study of the H/D exchange reactions of protonated arginine and arginine-containing Di- and tripeptides

A mechanistic study of the H/D exchange reactions of protonated arginine and arginine-containing Di- and tripeptides

Conformational analysis of arginine in gas phase—A strategy for scanning the potential energy surface effectively

How Important Is Molecular Rigidity for the Complex Stability of Artificial Host–Guest Systems? A Theoretical Study on Self‐Assembly of Gas‐Phase Arginine

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