Current Projects
Protein- Protein Interactions
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Proteins, in their nature, are not locked in a single static structure. Instead, they alter among numerous states, sampling a wide variety of conformations. A binding event between two proteins will occur only if each of the interacting partners is found in a certain conformation, which does not necessarily have the minimum energy in the conformational energy landscape. This initial encounter is then followed by a series of mutual adjustments, until a stable complex is formed. In our study, we will attempt to imitate this process of binding between two proteins using computational methods.
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The biological model systems used for this work are two Corona viruses known to cause fatal respiratory illnesses: the SARS Corona Virus (SARS-CoV) and the MERS Corona Virus (MERS-CoV). For each system, we investigate the interaction of the Receptor Binding Domaine (RBD) of the Spike glycoprotein (S protein) coating the viruses, with their cellular receptors as well as neutralizing monoclonal antibodies (nmAbs). In addition, we will compare the WT systems to information obtained for known RBD mutants- the D480A SARS-CoV RBD mutant and the E513A MERS-CoV RBD mutant. We apply the “Dynamic Ensemble Docking” protocol to characterize the interaction between the RBDs of each virus and their counterpart. Consequently, we compare the interaction “fingerprint” of the RBD/receptor complexes to the dynamic interaction pattern of the natural RBD/nmAbs complexes, as well as comparing the WT interactions to the mutated systems. By understanding the common features of the two systems, and the differences between them, we could optimize the production of engineered peptides, possibly leading to more efficient epitope-based vaccines against the each virus.
Drug Translocation Path of MRP1/ABCC1
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Traditional chemotherapeutic drugs, such as doxorubicin (DOX), frequently fail to destroy malignant cancer tumors due to inherent or acquired phenotype known as Multi Drug Resistance (MDR). In the common mechanism, intracellular levels of cytotoxic drugs are reduced below lethal thresholds by active extrusion from the tumor cell, operated by ATP-dependent pumps such as P-glycoprotein and MDR-associated proteins (MRPs).
The coupling between the ATPase reaction and the conformational transitions that occur with drug binding are still vague, however, they presumably consist of two processes: (1) structural deformation of the Nucleotide Binding Domains (NBDs) driven by ATP binding and hydrolysis and (2) mechanical coupling of the NBDs with the TMD (Trans Membrane Domains) leading to release of the bound drug to the extracellular space.
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Our work is directed at the 190KDa multi drug resistance associated protein 1 (MRP1) from the ABC transporter family. We investigate the mechanism and structure of MRP1 as well as the mode by which different compounds interact with the protein. We focus on the interaction with two chemical: (1) DOX- a chemotherapeutic drug, commonly used in traditional cancer therapy and (2) sertraline (SET) - a common SSRI drug used to treat depression, recently found by collaborator Dan Peer's lab to be a highly effective inhibitor of MRP1. We use homology modeling for ABC transporters (CFTR, MRP1) combined with Molecular Dynamics technique to gain a better understanding of the transporter’s structure and mode of operation, upon interaction with each chemical compound.
Symmetry and Quaternary Structure of Oligo-Proteins
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Many proteins and enzymes are composed of number of identical subunits. The arrangement of the subunits in such protein oligomers is governed by the rules of symmetry. Only a limited number of models are allowed. For a hexamers, four models are allowed: (a), cyclic ring; (b), alternating ring; (c), two-layered eclipsed; (d), two-layered staggered. The symmetry in the cyclic ring is C6, and dihedral D3 in remaining three.
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The resolution of the quaternary structure involves determination of the number of subunits, and the relevant allowed model. A number of physical methods have been used for these purposes: analytical ultracentrifugation, light scattering, small angle X-ray scattering (SAXS) and electron microscopy. It is obvious that for those proteins that had been crystallized and their 3-D structure were resolved by X-ray crystallography, the quaternary structure is resolved. Nevertheless, even today, many proteins remain resistant to crystallization and access to X-ray crystallography data collection remains expensive and limited to many protein biochemists.
Cross linking of oligomeric proteins provide a simple method for "counting" the number of subunits in an assembled oligomer. In a recent collaboration we developed a computer assisted method to analyze the quaternary structure in a hexameric protein. The method was successfully tested on a number of proteins with X-ray proven different hexameric structures. We firmly hope that our work will prove to be a useful addition to the arsenal of methods that help study the quaternary structure of oligomeric proteins.