Interactions of Aromatic Residues in Amyloids: A Survey of Protein Data Bank Crystallographic Data

Stanković, Ivana; Bozinovski, D.M.; Belić, Milivoj R.; Hall, Michael B.; Zarić, Snežana D.

doi:10.1021/acs.cgd.7b01035

Cited by 15 publications

(19 citation statements)

References 39 publications

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“…[29,57] Recently, the single amino acid tyrosine has been shown to self-assemble into cross-β-like fibers through hydrogen bonding and π-π stacking, and the fibrils were shown to mediate the aggregation of proteins through amyloid crossseeding, illustrating the importance of tyrosine residues in controlling the structure and function of proteins. There have been reports on specific local arrangements of sequences that prefer certain secondary structures, e.g., residues that strongly prefer the N-terminal and N+1 positions at the start of an α-helix, general turn-inducing sequences, and repeat positions of the heptad leucine, which favors a coiled-coil or leucine zipper interaction.…”

Section: Tyrosine As a Structural Motifmentioning

confidence: 99%

“…The PCET process couples longdistance electron transfer from the active centers of enzymes and short-distance proton transfer to the surrounding bases. [57] Copyright 2017, American Chemical Society. As shown in the figure, the pK a value of every tyrosine oxidation pathway is in the range of 10 to −2, meaning that at most pH values, the oxidation of tyrosine is coupled to proton transfer.…”

Section: Proton-coupled Electron Transfer Of Tyrosinementioning

confidence: 99%

“…Of the 20 amino acids found in protein structures, tyrosine, phenylalanine, tryptophan, and histidine contain aromatic functional groups. The interactions between these aromatic residues are integral to the proper structure and function of proteins . Recently, the single amino acid tyrosine has been shown to self‐assemble into cross‐β‐like fibers through hydrogen bonding and π–π stacking, and the fibrils were shown to mediate the aggregation of proteins through amyloid cross‐seeding, illustrating the importance of tyrosine residues in controlling the structure and function of proteins .…”

Section: The Role Of Tyrosine In Natural Systemsmentioning

confidence: 99%

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Tyrosine‐Rich Peptides as a Platform for Assembly and Material Synthesis

et al. 2018

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The self‐assembly of biomolecules can provide a new approach for the design of functional systems with a diverse range of hierarchical nanoarchitectures and atomically defined structures. In this regard, peptides, particularly short peptides, are attractive building blocks because of their ease of establishing structure–property relationships, their productive synthesis, and the possibility of their hybridization with other motifs. Several assembling peptides, such as ionic‐complementary peptides, cyclic peptides, peptide amphiphiles, the Fmoc‐peptide, and aromatic dipeptides, are widely studied. Recently, studies on material synthesis and the application of tyrosine‐rich short peptide‐based systems have demonstrated that tyrosine units serve as not only excellent assembly motifs but also multifunctional templates. Tyrosine has a phenolic functional group that contributes to π–π interactions for conformation control and efficient charge transport by proton‐coupled electron‐transfer reactions in natural systems. Here, the critical roles of the tyrosine motif with respect to its electrochemical, chemical, and structural properties are discussed and recent discoveries and advances made in tyrosine‐rich short peptide systems from self‐assembled structures to peptide/inorganic hybrid materials are highlighted. A brief account of the opportunities in design optimization and the applications of tyrosine peptide‐based biomimetic materials is included.

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Section: Tyrosine As a Structural Motifmentioning

confidence: 99%

Section: Proton-coupled Electron Transfer Of Tyrosinementioning

confidence: 99%

Section: The Role Of Tyrosine In Natural Systemsmentioning

confidence: 99%

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Tyrosine‐Rich Peptides as a Platform for Assembly and Material Synthesis

et al. 2018

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“…Studies have demonstrated that valine, isoleucine and alanine have β sheet propensity due to their hydrophobicity and hydrogen bonding characteristics (Han et al, 2011 ; Cui et al, 2014 ). Whereas formation of direct π-π interactions involving phenylalanine do not seem to be important in promoting amyloid aggregation (Stankovic et al, 2017 ).…”

Section: Introductionmentioning

confidence: 99%

Nanostructures Formed by Custom-Made Peptides Based on Amyloid Peptide Sequences and Their Inhibition by 2-Hydroxynaphthoquinone

2020

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Extensive research on amyloid fibril formations shows that certain core sequences within Aβ peptide play an important role in their formation. It is impossible to track these events in vivo. Many proteins and peptides with such core sequences form amyloid fibrils and such Aβ sheet mimics have become excellent tools to study amyloid fibril formation and develop therapeutic strategies. A group of peptides based on amyloid peptide sequences obtained from PDB searches, where glycine residues are substituted with alanine and isoleucine, are tested for aggregation by SEM and ThT binding assay. SEM of different peptide sequences showed morphologically different structures such as nanorods, crystalline needles and nanofibrils. The peptides were co-incubated with HNQ (a quinone) to study its effect on the process of aggregation and/or fibrillation. In conclusion, this group of peptides seem to be Aβ sheet mimics and can be very useful in understanding the different morphologies of amyloid fibrils arising from different peptide sequences and the effective strategies to inhibit or anneal them.

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“…These systems also attracted a lot of attention due to the pieces of evidence of proton transfer and proton tunneling . On the other hand, benzene and its derivatives undergo stacking interactions, which are particularly relevant in living organisms, but are also significant for crystal packing . We have thus chosen the BA as the smallest representative of aromatic carboxylic acids for theoretical analysis of noncovalent interactions.…”

Section: Introductionmentioning

confidence: 99%

Theoretical scrutinization of nine benzoic acid dimers: Stability and energy decomposition analysis

Petrović

Milovanovic

Etinski

et al. 2019

Int J of Quantum Chemistry

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Aromatic carboxylic acids are able to form diverse dimers and multimers due to their hydrogen bond donor and acceptor cites, as well as the aromatic rings. In this work, we examine nine benzoic acid dimers stabilized by hydrogen bonding and stacking interactions. Interacting quantum atoms methodology revealed that dominant attractive interactions in all of them, including hydrogen bonded systems, are due to exchange-correlation. Coulomb interactions are significant only in the most stable dimer with a double hydrogen bond, although the corresponding energy term is almost two times lower compared to the nonclassical one. Since interacting quantum atoms approach treats monomers binding by considering electronic energy only, in order to examine dissociation kinetics we performed density functional theory-based molecular dynamics simulations of selected stacked dimers: in 40% of the studied systems at 300 K thermal energy was sufficient to overpower barrier for dissociation within 1 ps, which resulted in the separation of the monomers, whereas 20% of them remained in the stacked position even after 5 ps. These results highlight the importance of noncovalent interactions, particularly weak stacking interactions, on the structure and dynamics of carboxylic acids and their derivatives.benzoic acid dimer, density functional theory-based molecular dynamics, interacting quantum fragments, noncovalent interactions

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Interactions of Aromatic Residues in Amyloids: A Survey of Protein Data Bank Crystallographic Data

Cited by 15 publications

References 39 publications

Tyrosine‐Rich Peptides as a Platform for Assembly and Material Synthesis

Tyrosine‐Rich Peptides as a Platform for Assembly and Material Synthesis

Nanostructures Formed by Custom-Made Peptides Based on Amyloid Peptide Sequences and Their Inhibition by 2-Hydroxynaphthoquinone

Theoretical scrutinization of nine benzoic acid dimers: Stability and energy decomposition analysis

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