Levy Research Group

Research

The main goal of our group is to decipher the first principles of cellular self-organization processes such as protein folding, protein-protein assembly, and protein-DNA recognition. We are focused on advancing our understanding of biomolecules (the sequence-structure-function problem) using a battery of computational and theoretical methods that capture their chemical and physical nature as well as the billions of years of evolutional design.

We are focused on advancing our understanding of biomolecules (the sequence-structure-function problem) using a battery of computational and theoretical methods that capture their chemical and physical nature as well as the billions of years of evolutional design. Our main aim is to decipher the complexity of proteins and nucleic acids that results in self-recognition and cellular communication and therefore a biological function. Unraveling mysteries on the structure, assembly, and interactions at the molecular level have long-term implications for combating medical conditions such as Creuzfeld-Jacob (Mad Cow disease), Alzheimer, and cancer.

We are interested in studying fundamental questions of the mechanisms of protein folding and to formulate the forces that bias an efficient folding. In addition we focus on understanding mechanisms of protein association and the degree of protein plasticity involved in these reactions. We are also investing our efforts in deciphering the mechanisms and kinetics of DNA recognition by monomeric and multimeric proteins with the ultimate goal of understanding cellular communication from physical and molecular viewpoints using theoretical and computational tools, using structure based modeling.

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News

December 8, 2024

Congratulations for Rivka for receiving the 2024 Clifford Felder prize

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Selected Publications

Partial wrapping of single-stranded DNA by replication protein A and modulation through phosphorylation

Chadda R., Kaushik V., Ahmad I. M., Deveryshetty J., Holehouse A. S., Sigurdsson S. T., Biswas G., Levy Y., Bothner B., Cooley R. B., Mehl R. A., Dastvan R., Origanti S. & Antony E. (2024) Nucleic Acids Research. 52, 19, p. 11626-11640

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Single-stranded DNA (ssDNA) intermediates which emerge during DNA metabolic processes are shielded by replication protein A (RPA). RPA binds to ssDNA and acts as a gatekeeper to direct the ssDNA towards downstream DNA metabolic pathways with exceptional specificity. Understanding the mechanistic basis for such RPA-dependent functional specificity requires knowledge of the structural conformation of ssDNA when RPA-bound. Previous studies suggested a stretching of ssDNA by RPA. However, structural investigations uncovered a partial wrapping of ssDNA around RPA. Therefore, to reconcile the models, in this study, we measured the end-to-end distances of free ssDNA and RPAssDNA complexes using single-molecule FRET and double electronelectron resonance (DEER) spectroscopy and found only a small systematic increase in the end-to-end distance of ssDNA upon RPA binding. This change does not align with a linear stretching model but rather supports partial wrapping of ssDNA around the contour of DNA binding domains of RPA. Furthermore, we reveal how phosphorylation at the key Ser-384 site in the RPA70 subunit provides access to the wrapped ssDNA by remodeling the DNA-binding domains. These findings establish a precise structural model for RPA-bound ssDNA, providing valuable insights into how RPA facilitates the remodeling of ssDNA for subsequent downstream processes.

A pH-Dependent Coarse-Grained Model for Disordered Proteins: Histidine Interactions Modulate Conformational Ensembles

Calinsky R. & Levy Y. (2024) Journal of Physical Chemistry Letters. 15, 37, p. 9419-9430

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Histidine (His) presents a unique challenge for modeling disordered protein conformations, as it is versatile and occurs in both the neutral (His⁰) and positively charged (His⁺) states. These His charge states, which are enabled by its imidazole side chain, influence the electrostatic and short-range interactions of His residues, which potentially engage in cation−π, π-π, and charge-charge interactions. Existing coarse-grained (CG) models often simplify His representation by assigning it an average charge, thereby neglecting these potential short-range interactions. To address this gap, we developed a model for intrinsically disordered proteins (IDPs) that accounts for the properties of histidine (H). The resulting IDPH model is a 21-amino acid CG model incorporating both His charge states. We show that interactions involving previously neglected His⁰ are critical for accurate modeling at high pH, where they significantly influence the compaction of His-rich IDPs such as Histatin-5 and CPEB4. These interactions contribute to structural stabilizations primarily via His⁰-His⁰ and His⁰-Arg interactions, which are overlooked in models focusing solely on the charged His⁺ state.

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

Calinsky R. & Levy Y. (2024) Journal Of Physical Chemistry B. 128, 36, p. 8687-8700

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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.

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