<scp>L</scp>-Seryl-<scp>L</scp>-leucine

Słowikowska, J.; Lipkowski, Janusz

doi:10.1107/s0108270100016164

Cited by 3 publications

(3 citation statements)

References 2 publications

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“…The optimized structural parameters are in good agreement with crystallographic data for Thr-and Sercontaining peptides such as H-Ala-Thr-OH, H-Gly-Thr-OH, or H-Ser-Leu-OH with N(H)-C(¼O) angles of 173.9 , 174.3 , and 177.8 , respectively [202][203][204][205]. The salts showed parameters for COO À of 1.200 Å (C¼O) and 1.277 Å (C-OH).…”

Section: Theoretical Characterizationsupporting

confidence: 65%

Protonation and coordination ability of small peptides – theoretical and experimental approaches for elucidation

Lamshöft

Ivanova

2011

Journal of Coordination Chemistry

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This review deals with modern theoretical and experimental approaches as well as structural elucidation of small peptides (SP), their protonated forms and metal complexes. Free peptide bond rotation in amino acids (AA) and peptides yielded various conformers, which may possess differing biological activities. Inter-and/or intramolecular stacking observed in aromatic SP is another phenomenon typical for both peptide salts and complexes. These phenomenological effects can be successfully studied, both theoretically and experimentally, using a combination of the theoretical approximations and physical methods, such as electronic absorption spectroscopy, vibrational spectroscopy (including IR and Raman), nuclear magnetic resonance, mass spectrometry, as well as single-crystal X-ray diffraction. The physical and chemical properties of these systems can be precisely calculated by ab initio and DFT methods, varying basis sets and the results obtained allow elucidation of their conformations as a function of the reaction conditions (pH, type of the solvent, temperature, metal to ligand molar ratio). Although the 3-D structures of many peptides have been determined over the past decades, peptide crystallization is still a major obstacle to crystallographic work and the presence of chiral center/s adds further difficulties. For this reason, a specific part of the review is focused on the study of the absolute structure of the peptides, their salts and metal complexes, discussing the conformational preferences of the peptides during these processes. The available crystallographic data for metal complexes are successfully used for the correlation between the structures and the spectroscopic properties.

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Section: Theoretical Characterizationsupporting

confidence: 65%

Protonation and coordination ability of small peptides – theoretical and experimental approaches for elucidation

Lamshöft

Ivanova

2011

Journal of Coordination Chemistry

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“…Examination of the relative energy differences obtained for the conformations of Leu allows a comparison between theoretical calculations reported here and previously reported experimental data obtained from X-ray [49][50][51][52][53] studies. It is interesting to note that our theoretical calculations are in good agreement with the experimental data, fundamentally in relation to the SC orientation of the global minimum (ag + ) and the second local minimum (ga).…”

Section: Gas Phasementioning

confidence: 72%

Conformational Preferences of N-Acetyl-l-leucine-N‘-methylamide. Gas-Phase and Solution Calculations on the Model Dipeptide

et al. 2007

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A DFT study of N-acetyl-l-leucine-N'-methylamide conformers in the gas phase and in solution was carried out. The theoretical computational analysis revealed 43 different conformations at the B3LYP/6-31G(d) level of theory in the gas phase. In addition, the effects of three solvents (water, acetonitrile, and chloroform) were included in the calculations using the isodensity polarizable continuum model (IPCM) and the Poisson-Boltzmann self-consistent reaction field (PB-SCRF) method. The stability order of the different conformers in solution has been analyzed. The theoretical results were compared with some experimental data (X-ray, IR, and NMR).

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“…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: 97%

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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L-Seryl-L-leucine

Cited by 3 publications

References 2 publications

Protonation and coordination ability of small peptides – theoretical and experimental approaches for elucidation

Protonation and coordination ability of small peptides – theoretical and experimental approaches for elucidation

Conformational Preferences of N-Acetyl-l-leucine-N‘-methylamide. Gas-Phase and Solution Calculations on the Model Dipeptide

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

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