Biological and Chemical Physics Commons^™

The Role Of Conformational Changes In Viral And Bacterial Protein Functions, Md Lokman Hossen

FIU Electronic Theses and Dissertations

Proteins do versatile work in cells. They require a cascade of structural changes to perform different tasks like binding to the other neighboring biomolecules, transporting small chemicals, activating a chemical reaction, etc. The structural conformations of proteins can be critical in changing their working ability. In this dissertation, I investigated the role of conformational changes of viral protein, e.g., spike and envelope protein of SARS-CoV-2, and bacterial protein, e.g., multidrug transporter and toxic extrusion protein- PfMATE from Pyrococcus furiosus. Also, I performed molecular docking-based drug screening targeting the E protein to suggest a set of drugs that can be repurposed …

In Silico Identification Of Vaccine Candidates Against Viral Infections, Prabin Baral

FIU Electronic Theses and Dissertations

There are many viral diseases without effective treatments or vaccines. These viruses can cause catastrophic epidemics such as the Lassa, Ebola, and Marburg viruses. Similarly, the recent coronavirus pandemic is of great concern as new variants are continuously emerging with decreased susceptibility to antibodies and vaccines that were developed for earlier strains. A critical step in the immune system’s fight against viruses involves an immunological protein molecule binding to a viral protein molecule. I investigate the atomic and molecular details of binding site recognition and binding interactions and dynamics for three important viruses.

Antigens are molecules, such as viral proteins, …

Structural Dynamics Of Membrane Interacting Viral Proteins, Nisha Bhattarai

FIU Electronic Theses and Dissertations

Viruses do not possess complete cellular machinery but have the ability to reproduce by utilizing cellular machinery inside host cells. They are nanoscale machines that rapidly modify (evolve) their molecular components to cause disease and death. Therefore, emergence of deadly infectious viruses is a monumental health concern and understanding how viruses are able to enter, replicate, assemble and egress from the host cell is important to mitigate the threat.

A fully active, infectious viral structure is known as a virion. A virion contains genetic material and is enclosed by a capsid. The capsid is a protein shell and some viruses …

Investigations Of Cell-Penetrating And Membrane-Pore Forming Peptides, Rudramani Pokhrel

FIU Electronic Theses and Dissertations

Cell-penetrating and membrane-pore forming peptides are a class of membrane-active peptides. They are short sequence peptides having both hydrophilic and lipophilic combinations of amino acids. These peptides can have contrast functional diversity. Peptides encoded by viruses function as viroporins and play a critical role in viral replication, propagation, and pathogenesis. One such peptide is the Ebola virus delta peptide, which forms a pore in the host cell membrane. Another set of pore-forming peptides are antimicrobial Lantibiotic peptides that may be useful for killing antibiotic resistant bacteria by disrupting the bacterial membrane through two different possible mechanisms. Not only can they …

Multifunctional Nanopipette For Single Nanoparticles And Proteins Analysis, Popular Pandey

FIU Electronic Theses and Dissertations

Complex biological processes occur in the nanoscale (1-100 nm) regime. ‘DNA’ which is just 2 nm in dimension is a fundamental building block of all life. ‘Hemoglobin’, a blood protein that transports oxygen throughout our body is only 5 nm in diameter. Importantly, the structure, composition, and dynamics of these nanoscale entities determine their biological function. A slight alteration in the structure and composition can lead to the malfunction of the protein which is key to various diseases including cancer. Therefore, the single-molecule measurement approach is essential to characterize both the average properties and the rare …

Folding Of Bovine Pancreatic Trypsin Inhibitor (Bpti) Is Faster Using Aromatic Thiols And Their Corresponding Disulfides, Ram Prasad Marahatta

FIU Electronic Theses and Dissertations

Improvement in the in vitro oxidative folding of disulfide-containing proteins, such as extracellular and pharmaceutically important proteins, is required. Traditional folding methods using small molecule aliphatic thiol and disulfide, such as glutathione (GSH) and glutathione disulfide (GSSG) are slow and low yielding. Small molecule aromatic thiols and disulfides show great potentiality because aromatic thiols have low pKa values, close to the thiol pKa of protein disulfide isomerase (PDI), higher nucleophilicity and good leaving group ability. Our studies showed that thiols with a positively charged group, quaternary ammonium salts (QAS), are better than thiols with negatively charged groups such as phosphonic …

Scanning Ion Conductance Microscopy For Single Cell Imaging And Analysis, Namuna Panday

FIU Electronic Theses and Dissertations

Most biological experiments are performed on an ensemble of cells under the assumption that all cells are identical. However, recent evidence from single cells studies reveals that this assumption is incorrect. Individual cells within the same generation may differ dramatically, and these differences have important consequences for the health and function of the entire living body. I have used Scanning Ion Conductance Microscopy (SICM) for imaging and analysis of topographical change of single cell membrane, which is difficult to be revealed by optical microscopes. Morphological change in the fixed and live HeLa cell membrane during endocytosis of conjugated polymer nanoparticles …

Molecular Dynamics Investigations Of Structural Conversions In Transformer Proteins, Jeevan Gc

FIU Electronic Theses and Dissertations

Multifunctional proteins that undergo major structural changes to perform different functions are known as “Transformer Proteins”, which is a recently identified class of proteins. One such protein that shows a remarkable structural plasticity and has two distinct functions is the transcription antiterminator, RfaH. Depending on the interactions between its N-terminal domain and its C-terminal domain, the RfaH CTD exists as either an all-α-helix bundle or all-β-barrel structure. Another example of a transformer protein is the Ebola virus protein VP40 (eVP40), which exists in different conformations and oligomeric states (dimer, hexamer, and octamer), depending on the required function.I performed Molecular Dynamics …

Rate Kinetics And Molecular Dynamics Of The Structural Transitions In Amyloidogenic Proteins, Timothy Michael Steckmann

FIU Electronic Theses and Dissertations

Amyloid fibril aggregation is associated with several horrific diseases such as Alzheimer’s, Creutzfeld-Jacob, diabetes, Parkinson’s and others. The process of amyloid aggregation involves forming myriad different metastable intermediate aggregates. Amyloid fibrils are composed of proteins that originate in an innocuous α-helix or random-coil structure. The α-helices convert their structure to β-strands that aggregate into β-sheets, and then into protofibrils, and ultimately into fully formed amyloid fibrils. On the basis of experimental data, I have developed a mathematical model for the kinetics of the reaction pathways and determined rate parameters for peptide secondary structural conversion and aggregation during the entire fibrillogenesis …

Multimode Analysis Of Nanoscale Biomolecular Interactions, Purushottam Babu Tiwari

FIU Electronic Theses and Dissertations

Biomolecular interactions, including protein-protein, protein-DNA, and protein-ligand interactions, are of special importance in all biological systems. These interactions may occer during the loading of biomolecules to interfaces, the translocation of biomolecules through transmembrane protein pores, and the movement of biomolecules in a crowded intracellular environment. The molecular interaction of a protein with its binding partners is crucial in fundamental biological processes such as electron transfer, intracellular signal transmission and regulation, neuroprotective mechanisms, and regulation of DNA topology. In this dissertation, a customized surface plasmon resonance (SPR) has been optimized and new theoretical and label free experimental methods with related analytical …

Structural Flexibility And Oxygen Diffusion Pathways In Monomeric Fluorescent Proteins, Chola K. Regmi

FIU Electronic Theses and Dissertations

Fluorescent proteins are valuable tools as biochemical markers for studying cellular processes. Red fluorescent proteins (RFPs) are highly desirable for in vivo applications because they absorb and emit light in the red region of the spectrum where cellular autofluorescence is low. The naturally occurring fluorescent proteins with emission peaks in this region of the spectrum occur in dimeric or tetrameric forms. The development of mutant monomeric variants of RFPs has resulted in several novel FPs known as mFruits. Though oxygen is required for maturation of the chromophore, it is known that photobleaching of FPs is oxygen sensitive, and oxygen-free conditions …

An Ethnographic Study: Becoming A Physics Expert In A Biophysics Research Group, Idaykis Rodriguez

FIU Electronic Theses and Dissertations

Expertise in physics has been traditionally studied in cognitive science, where physics expertise is understood through the difference between novice and expert problem solving skills. The cognitive perspective of physics experts only create a partial model of physics expertise and does not take into account the development of physics experts in the natural context of research. This dissertation takes a social and cultural perspective of learning through apprenticeship to model the development of physics expertise of physics graduate students in a research group. I use a qualitative methodological approach of an ethnographic case study to observe and video record the …