Conformational structures and vibrational spectroscopic investigation of isolated dityrosine and tryptophan-tyrosine dipeptides: A theoretical study

Mayes, Maricris L.; Perreault, Lisa

doi:10.1016/j.comptc.2018.03.031

Cited by 6 publications

(5 citation statements)

References 27 publications

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“…We use the structures of the lowest energy monomers (YY1 and WY1) as determined in ref . Three commonly reported dimer orientations were employed: (i) side by side, where the monomers are adjacent to one another, (ii) parallel displaced (PD), and (iii) T-shaped, where monomers are oriented perpendicularly. ,,, The monomers were also flipped around within these orientations to capture all possible functional group interactions.…”

Section: Methodsmentioning

confidence: 99%

Probing the Nature of Noncovalent Interactions in Dimers of Linear Tyrosine-Based Dipeptides

Mayes

Perreault

2019

ACS Omega

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Tyrosine-based dipeptides self-assemble to form higher order structures. To gain insights into the nature of intermolecular interactions contributing to the early stages of the self-assembly of aromatic dipeptides, we study the dimers of linear dityrosine (YY) and tryptophan–tyrosine (WY) using quantum-chemical methods with dispersion corrections and universal solvation model based on density in combination with energy decomposition and natural bond orbital (NBO) analyses. We find that hydrogen bonding is a dominant stabilizing force. The lowest energy structure for the linear YY dimer is characterized by O carboxyl ···H(O) tyr . In contrast, the lowest energy dimer of linear WY is stabilized by O carboxyl ···H(N) trp and π tyr ···π tyr . The solvent plays a critical role as it can change the strength and nature of interactions. The lowest energy for linear WY dimer in acetone is stabilized by O carboxyl ···H(O) tyr , π trp ···H(C), and π trp ···H(N). The Δ G of dimerization and stabilization energies of solvated dipeptides reveal that the dipeptide systems are more stable in the solvent phase than in gas phase. NBO confirms increased magnitudes for donor–acceptor interaction for the solvated dipeptides.

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Section: Methodsmentioning

confidence: 99%

Probing the Nature of Noncovalent Interactions in Dimers of Linear Tyrosine-Based Dipeptides

Mayes

Perreault

2019

ACS Omega

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“…[11][12][13] Building on these advancements, current studies are looking at other possible protein-like NTs that can be formed from modified FF, [14] l/d amino acids, [15][16][17] and dipeptides from the combination of other aromatic amino acids tryptophan (W) and tyrosine (Y). [18][19][20][21][22] The crystal structure of FFNTs has been well elucidated, [23][24][25][26][27] involving stacks of hexameric rings of FF in a head-to-tail conformation for intramolecular hydrogen bonding. [24,25,28] A single FFNT has an inner diameter of about 10 Å, while the bundles result in tubes with outer diameters ranging from 100-150 nm.…”

Section: Introductionmentioning

confidence: 99%

“…Previously, we studied the noncovalent interactions of tryptophan-and tyrosine-based dipeptide monomers and dimers. [18,19] In this paper, we present the results of extending the bottom-up approach beyond the dimeric size to investigate the stabilities and the underlying interaction energies of the dipeptide systems phenylalanine-tyrosine (FY), tryptophantyrosine (WY), and dityrosine (YY), in both their cyclic and linear forms. We provide insights into the thermodynamics of their formation into oligomeric ring structures of quadmeric, pentameric, hexameric, and heptameric sizes, both in the gas phase and in solution, by quantifying their formation energies.…”

Section: Introductionmentioning

confidence: 99%

“…FFNTs have also been explored for use in the biomedical field as biomimetic scaffolds, sensors, and drug delivery agents due to their relatively nontoxic properties [11–13] . Building on these advancements, current studies are looking at other possible protein‐like NTs that can be formed from modified FF, [14] l/d amino acids, [15–17] and dipeptides from the combination of other aromatic amino acids tryptophan (W) and tyrosine (Y) [18–22] …”

Section: Introductionmentioning

confidence: 99%

“…Previously, we studied the noncovalent interactions of tryptophan‐ and tyrosine‐based dipeptide monomers and dimers [18,19] . In this paper, we present the results of extending the bottom‐up approach beyond the dimeric size to investigate the stabilities and the underlying interaction energies of the dipeptide systems phenylalanine‐tyrosine (FY), tryptophan‐tyrosine (WY), and dityrosine (YY), in both their cyclic and linear forms.…”

Section: Introductionmentioning

confidence: 99%

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Stackable Aromatic Dipeptide Ring Structures toward Nanotube Formation: Thermodynamics and Interactions in Gas‐Phase and Solution

Visayas

Mayes

2021

ChemistrySelect

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Increasing attention has been drawn towards self‐assembling dipeptide nanotube materials (NT) for their tunable properties. Despite recent advances, a fundamental understanding of the conditions that drive the self‐assembly process is still lacking. Here, we report the structures, thermodynamics, and underlying interactions of the nanotube forming potential of cyclic and linear aromatic dipeptides phenylalanine‐tyrosine, tryptophan‐tyrosine, and dityrosine via the piecewise self‐assembly mechanism. The cyclic dipeptides have better favorability of oligomerization in the gas phase than the linear dipeptides, largely due to the enthalpic gain of forming more hydrogen bonds, suggesting that the piecewise mechanism is plausible for vapor deposition methods. Oligomerization in solution, which would require desolvation of free monomers, was shown to be thermodynamically unfavorable, especially in polar solvents, demonstrating the need for an external stimulus for the crystallization of NTs. The generated oligomeric rings show structural robustness and symmetry, allowing excellent stacking potential in both lateral and axial directions. The nature of the sidechains significantly affects the stabilizations within the oligomeric structure. The insights generated can be used as a basis for dipeptide modifications that could enhance targeted NT properties for different applications.

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Luminescence and morphological behaviour of the aromatic dipeptide pair having singular structural variability

et al. 2022

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In the present manuscript, the luminescence and the self‐assembly behaviour of two aromatic dipeptides with a singular structure variable are investigated. The terminally protected dipeptides tryptophan–tyrosine (WYp) and tryptophan–phenylalanine (WFp) were synthesized using a standard solution phase procedure. Significant solvatochromic effect was observed for both the dipeptidyl entities; whilst the influence was more pronounced for the WYp entity when compared with WFp. Interesting morphological variation was observed for WFp and WYp, in which discrete and interconnected nanospheres were observed for the respective dipeptides. The results obtained signify the influence of the singular structural variation on modulating the overall functional behaviour of the short peptides motifs.

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Conformational structures and vibrational spectroscopic investigation of isolated dityrosine and tryptophan-tyrosine dipeptides: A theoretical study

Cited by 6 publications

References 27 publications

Probing the Nature of Noncovalent Interactions in Dimers of Linear Tyrosine-Based Dipeptides

Probing the Nature of Noncovalent Interactions in Dimers of Linear Tyrosine-Based Dipeptides

Stackable Aromatic Dipeptide Ring Structures toward Nanotube Formation: Thermodynamics and Interactions in Gas‐Phase and Solution

Luminescence and morphological behaviour of the aromatic dipeptide pair having singular structural variability

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