Introduction to Protein Modeling Projects

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  How can we design an inhibitor with an enhanced binding affinity that is selective for MMP12 ?

  Aisha Y. Abdool, Lyla Abbas, Tassnime Sebaei, Emily Schmitt, and Arthur Sikora

  Matrix metalloproteinase 12 (MMP 12) is one of the twenty-three members of the peptidase M10 family which are primarily responsible for the breakdown of the extracellular matrix. MMP12 plays a key factor in the degradation of elastin and is commonly studied in the lungs of smokers, where MMP12 digests the elastin and serves as a chemokine to recruit a pro-inflammatory immune response. Thus, MMP12 is a major therapeutic target in wound healing and scar formation following a myocardial infarction. Students from the Honors Protein Modeling class at Nova Southeastern University modeled the interactions between MMP12 and various inhibitors. Using the protein data bank, an MMP12 protein complexed with the inhibitor called EEG under the code 3LIK was discovered. The structure was imported into JMOL: a protein visualization software. EEG intercalates into the S1 loop of the MMP12 protein without causing any disturbance to the loop's conformation. Murine trials were found with corresponding data for another MMP12 inhibitor known as AS111793 which was shown to reduce inflammation associated with cigarette smoke. A series of inhibitors were created using key components of EEG and AS111793. The binding was modeled on Py-Rx: a screening software used to dock the inhibitors. It was found that the hybrid compound created had a higher binding affinity than AS111793, but less affinity than EEG. This may be because a majority of the solvents and elements were removed from the inhibitor which did not allow the docking to occur.

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  Limiting Iron Acquisition of E. Coli With Anti-TonB1 and AntiTonB2​

  Jose Diaz, Ryan Luib, and Seethal Doki

  The bacteria E Coli infect approximately 200,000 individuals in the United States and can lead to critical illnesses. The transfer of iron from the bloodstream to bacteria is one of the main requirements for the survival. One of the mechanisms to obtain iron by use of siderophores and the protein FhuA was investigated. Undergraduate students grouped into teams to each explain a unique molecular story- modeled in Jmol/Pymol and demonstrated through a poster and PowerPoint. Using the PDB file, 2GRX, a drug to inhibit the TonB-Ton Box interaction which provides the FhuA iron mechanism energy to operate was researched. A protein model was designed to bind to the Ton Box region of FhuA with higher affinity by altering polar and charged residues to nonpolar or aliphatic residues that were present in the original TonB protein through programs Pymol and Jmol. The presence of many nonpolar amino acids in residues 8-16 and 588-592 of FhuA and the charged amino acids in residues 166-170 and 225-235 of TonB suggest that mutations of R166F, N227L, K231A on the tonB will lead to a protein with a stronger interaction with the Ton Box. The change from Arginine 166 to Phenlyalanine facilitates a nonpolar-nonpolar interaction between the TonB and Alanine of FhuA. Similarly, mutating polar asparagine to nonpolar leucine and the change of positively charged Lysine to uncharged Alanine will allow a stronger interaction. These hypothesized interactions of the mutated Anti-TonB1 with the FhuA are based on predicted outcomes because of the limitations of programmed docking of large proteins. Through the research and design of the course, students were able to develop skills with protein interface programs such as Pymol, Jmol, and Pyrx. This project was made possible by Nova Southeastern University and the guidance from Dr. Arthur Sikora and Dr. Emily Schmitt Lavin.

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  Highlighting How the Structure of Marine Bacterial Laminarinase Can Improve Biogeochemical Cycling During Global Climate Change

  Heidi Hellenbrand, Rachel Harris, and Chino Villanueva

  Marine bacterial laminarinase cuts polysaccharides in the process of remineralization, a key process in the ocean biogeochemical cycling of nutrients. We reviewed the protein model of 6JH5 in Jmol to highlight the important areas of the model that relate to thermostability and function and the effects of global climate change on the protein. The catalytic cleft of Glu135 and Glu140 was vital to the depolymerization mechanism. Substrate chain positions 130-143, specifically Trp130 being used for recognition, were important to the proficiency of the structure. The calcium ion on the opposite side of the β-sheet from catalytic cleft increased its degrading activity and thermostability. The residue interactions with Glc(−1) and Glc(−2) were unveiled to be crucial for β-1,3-glycosidic bond selectivity by the enzyme. Previous studies also showed the residue interactions were also important to the protein’s thermostability and thermophilicity. Our research found that the protein’s function will be negatively impacted by global climate changes as temperature beyond the protein’s optimal temperature (6JH5: 20°C) caused by climate change will also decline activity as hydrogen bonds between proteins weaken and being to denature. The function of our protein is important in the biogeochemical cycling of nutrients in the ocean and without its high activity, the cycling of nutrients and DOM like carbon and nitrogen won’t be as proficient.

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  Investigating the Structure of Potential New Drug to Treat Sickle Cell Anemia through Inhibition of the Polymerization of Hemoglobin S​

  Brianna M. Lacasse, Isadora R. De Abreu, and Rathika Manikandan

  Sickle cell anemia is a hematologic disorder impacting over 15 million people worldwide. It is caused by a single point mutation in the gene hemoglobin-Betha, where a glu group is replaced by val (GAG --- GTG) in the seventh codon (glu7val) of chromosome 1. In this study, we are comparing the anti-sickling properties of drugs in varied conditions in order to create a drug that is effective in an O2-independent manner and with a 1:1 stoichiometry for lower dosage purposes. We used Pymol and Jmol to compare the structures of the aldehydes GBT-440 and VZHE-039, which interact on the same binding site to treat sickle cell disease. GBT-440’s bulkiness allows it to have a 1:1 stoichiometry, while VZHE-039’s solubility is due to its interaction with the hemoglobin’s alpha cleft, allowing it to be O2-independent. We identified the pyridine and pyrazole structure from GBT-440 and the methyl hydroxy moite from VZHE-039 as key structures, and created a hypothetical new drug, a hybrid of VZHE-039 and GBT-440. The pose predicted would allow the drug to interact with the sickled hemoglobin in a 1 to 1 ratio and in an O2-independent manner.