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582 results on '"Levy, Yaakov"'

17. Cold denaturation induces inversion of dipole and spin transfer in chiral peptide monolayers.

Author

Eckshtain-Levi, Meital, Capua, Eyal, Refaely-Abramson, Sivan, Sarkar, Soumyajit, Gavrilov, Yulian, Mathew, Shinto P, Paltiel, Yossi, Levy, Yaakov, Kronik, Leeor, and Naaman, Ron

Subjects
Aminoisobutyric Acids, Alanine, Oligopeptides, Protein Structure, Secondary, Protein Denaturation, Electron Transport, Electrons, Cold Temperature, Molecular Dynamics Simulation, Protein Structure, Secondary
Abstract

Chirality-induced spin selectivity is a recently-discovered effect, which results in spin selectivity for electrons transmitted through chiral peptide monolayers. Here, we use this spin selectivity to probe the organization of self-assembled α-helix peptide monolayers and examine the relation between structural and spin transfer phenomena. We show that the α-helix structure of oligopeptides based on alanine and aminoisobutyric acid is transformed to a more linear one upon cooling. This process is similar to the known cold denaturation in peptides, but here the self-assembled monolayer plays the role of the solvent. The structural change results in a flip in the direction of the electrical dipole moment of the adsorbed molecules. The dipole flip is accompanied by a concomitant change in the spin that is preferred in electron transfer through the molecules, observed via a new solid-state hybrid organic-inorganic device that is based on the Hall effect, but operates with no external magnetic field or magnetic material.

Published
2016

21. Aromatic Residues in Proteins: Re-Evaluating the Geometry and Energetics of π–π, Cation−π, and CH−π Interactions

Author

Calinsky, Rivka and Levy, Yaakov

Abstract

Aromatic residues can participate in various biomolecular interactions, such as π–π, cation−π, and CH−π interactions, which are essential for protein structure and function. Here, we re-evaluate the geometry and energetics of these interactions using quantum mechanical (QM) calculations, focusing on pairwise interactions involving the aromatic amino acids Phe, Tyr, and Trp and the cationic amino acids Arg and Lys. Our findings reveal that π–π interactions, while energetically favorable, are less abundant in structured proteins than commonly assumed and are often overshadowed by previously underappreciated, yet prevalent, CH−π interactions. Cation−π interactions, particularly those involving Arg, show strong binding energies and a specific geometric preference toward stacked conformations, despite the global QM minimum, suggesting that a rather perpendicular T-shape conformation should be more favorable. Our results support a more nuanced understanding of protein stabilization via interactions involving aromatic residues. On the one hand, our results challenge the traditional emphasis on π–π interactions in structured proteins by showing that CH−π and cation−π interactions contribute significantly to their structure. On the other hand, π–π interactions appear to be key stabilizers in solvated regions and thus may be particularly important to the stabilization of intrinsically disordered proteins.

Published
2024
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23. Sound-mediated nucleation and growth of amyloid fibrils.

Author

Kozell, Anna, Solomonov, Aleksei, Gaidarov, Roman, Benyamin, Doron, Rosenhek-Goldian, Irit, Greenblatt, Harry Mark, Levy, Yaakov, Amir, Ariel, Raviv, Uri, and Shimanovich, Ulyana

Subjects
SMALL-angle X-ray scattering, MOLECULAR self-assembly, SOUND energy, MOLECULAR dynamics, X-ray scattering
Abstract

Mechanical energy, specifically in the form of ultrasound, can induce pressure variations and temperature fluctuations when applied to an aqueous media. These conditions can both positively and negatively affect protein complexes, consequently altering their stability, folding patterns, and self-assembling behavior. Despite much scientific progress, our current understanding of the effects of ultrasound on the self-assembly of amyloidogenic proteins remains limited. In the present study, we demonstrate that when the amplitude of the delivered ultrasonic energy is sufficiently low, it can induce refolding of specific motifs in protein monomers, which is sufficient for primary nucleation; this has been revealed by MD. These ultrasound-induced structural changes are initiated by pressure perturbations and are accelerated by a temperature factor. Furthermore, the prolonged action of low-amplitude ultrasound enables the elongation of amyloid protein nanofibrils directly from natively folded monomeric lysozyme protein, in a controlled manner, until it reaches a critical length. Using solution X-ray scattering, we determined that nanofibrillar assemblies, formed either under the action of sound or from natively fibrillated lysozyme, share identical structural characteristics. Thus, these results provide insights into the effects of ultrasound on fibrillar protein self-assembly and lay the foundation for the potential use of sound energy in protein chemistry. [ABSTRACT FROM AUTHOR]

Published
2024
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31. Histidine in Proteins: pH-Dependent Interplay between π–π, Cation–π, and CH–π Interactions

Author

Calinsky, Rivka and Levy, Yaakov

Abstract

Histidine (His) stands out as the most versatile natural amino acid due to its side chain’s facile propensity to protonate at physiological pH, leading to a transition from aromatic to cationic characteristics and thereby enabling diverse biomolecular interactions. In this study, our objective was to quantify the energetics and geometries of pairwise interactions involving His at varying pH levels. Through quantum chemical calculations, we discovered that His exhibits robust participation in both π–π and cation–π interactions, underscoring its ability to adopt a π or cationic nature, akin to other common residues. Of particular note, we found that the affinity of protonated His for aromatic residues (via cation–π interactions) is greater than the affinity of neutral His for either cationic residues (also via cation–π interactions) or aromatic residues (via π–π interactions). Furthermore, His frequently engages in CH–π interactions, and notably, depending on its protonation state, we found that some instances of hydrogen bonding by His exhibit greater stability than is typical for interamino acid hydrogen bonds. The strength of the pH-dependent pairwise energies of His with aromatic residues is supported by the abundance of pairwise interactions with His of low and high predicted pKavalues. Overall, our findings illustrate the contribution of His interactions to protein stability and its potential involvement in conformational changes despite its relatively low abundance in proteins.

Published
2024
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