Boriana Marintcheva

eIF1A/eIF5B interaction network and its functions in translation initiation complex assembly and remodeling

Eukaryotic translation initiation is a highly regulated process involving multiple steps, from 43S pre-initiation complex (PIC) assembly, to ribosomal subunit joining. Subunit joining is controlled by the G-protein eukaryotic translation initiation factor 5B (eIF5B). Another protein, eIF1A, is involved in virtually all steps, including subunit joining. The intrinsically disordered eIF1A C-terminal tail (eIF1A-CTT) binds to eIF5B Domain-4 (eIF5B-D4). The ribosomal complex undergoes conformational rearrangements at every step of translation initiation; however, the underlying molecular mechanisms are poorly understood. Here we report three novel interactions involving eIF5B and eIF1A: (i) a second binding interface between eIF5B and eIF1A; (ii) a dynamic intramolecular interaction in eIF1A between the folded domain and eIF1A-CTT; and (iii) an intramolecular interaction between eIF5B-D3 and -D4. The intramolecular interactions within eIF1A and eIF5B interfere with one or both eIF5B/eIF1A contact interfaces, but are disrupted on the ribosome at different stages of translation initiation. Therefore, our results indicate that the interactions between eIF1A and eIF5B are being continuously rearranged during translation initiation. We present a model how the dynamic eIF1A/eIF5B interaction network can promote remodeling of the translation initiation complexes, and the roles in the process played by intrinsically disordered protein segments.

Motivating Students to Learn Biology Vocabulary with Wikipedia

Timely learning of specialized science vocabulary is critical for building a solid knowledge base in any scientific discipline. To motivate students to dedicate time and effort mastering biology vocabulary, I have designed a vocabulary exercise utilizing the popular web encyclopedia Wikipedia. The exercise creates an opportunity for students to connect the challenge of vocabulary learning to a prior positive experience of self-guided learning using a content source they are familiar and comfortable with.

Chapter 5 – Phage Display

Phage display is a powerful technique for studying protein–ligand interactions most frequently applied to protein–protein, protein–peptide, and protein–nucleic acids interactions. The genetic code for the protein/peptide of interest is inserted in the genome of a phage and subsequently “displayed” on the surface of the viral particle as a fusion to natural coat protein. Libraries of protein/peptide variants are tested against ligand(s) of interest. Proteins/peptides binding to the specific target are selected by 3–5 rounds of affinity-driven biopanning and subsequently identified by sequencing the genome of the phages displaying them. Phage display is widely used for a selection of proteins/peptides with desired binding properties for the purpose of a broad array of therapeutic, research, and nanotechnology-related applications.

Modeling Influenza Antigenic Shift and Drift with LEGO Bricks

The concepts of antigenic shift and drift could be found in almost every microbiology and virology syllabus, usually taught in the context of Influenza virus biology. They are central to understanding viral diversity and evolution and have direct application to anti-flu vaccine design and effectiveness. To aid student understanding of the concepts, I have developed an exercise to visualize the mechanistic aspects of antigenic shift and drift using LEGO bricks. This hands-on/minds-on exercise asks students to replicate viruses taking into account the error-prone nature of Influenza RNA polymerase and to package model virions from a host cell infected with two different Influenza strains, while keeping track of the level of diversity of newly propagated viral particles. The exercise can be executed in any type of classroom for about 10 minutes and if desired, extended to emphasize quantitative skills, molecular biology concepts, or to trigger discussion of key issues in vaccine design.

Dynamic Model Visualizing the Process of Viral Plaque Formation

In Microbiology and Virology courses, viral plaques are often presented to students as the way one can visualize viruses/bacteriophages. While students generally grasp the idea that counting plaques is essentially the same as counting viruses in their sample (assuming that one virus entering the cell is sufficient for productive infection), the process of plaque formation itself remains largely obscure. Many students fail to appreciate that viral plaques are actually a “laboratory-made” phenomenon allowing us to observe and study the growth of lytic viruses. The latter often presents a challenge for the interpretation of experimental data related to viral growth and drug discovery using plaque reduction assay. The hands-on model described here creates an opportunity for students to experience the process of viral plaque formation while engaging multiple senses and creating a lasting impression.