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Full-Text Articles in Biochemistry, Biophysics, and Structural Biology

Structure-Function Relationships In Hexacoordinate Heme Proteins: Mechanism Of Cytoglobin Interactions With Exogenous Ligands, Antonija Tangar Jun 2018

Structure-Function Relationships In Hexacoordinate Heme Proteins: Mechanism Of Cytoglobin Interactions With Exogenous Ligands, Antonija Tangar

FIU Electronic Theses and Dissertations

Cytoglobin (Cygb) and neuroglobin (Ngb) are among the newest members of vertebrate globin family characterized by a classical 3-over-3 α-helical fold and a heme prosthetic group capable of reversibly binding small ligands such as O2, CO and NO. The physiological functions of Cygb and Ngb remain to be determined; however, current data suggest that both proteins have a significant role in cytoprotection in hypoxic and genotoxic conditions. Cytoglobin and Ngb are distinct from their better-known counterparts, hemoglobin (Hb) and myoglobin (Mb), in several structural features. First, in the absence of an external ligand, the sixth coordination site of the ...


Thermally-Assisted Acoustofluidic Separation For Bioanalytical Applications, Ata Dolatmoradi Jun 2017

Thermally-Assisted Acoustofluidic Separation For Bioanalytical Applications, Ata Dolatmoradi

FIU Electronic Theses and Dissertations

Changes in the biomechanical properties of cells accompanying the development of various pathological conditions have been increasingly reported as biomarkers for various diseases and as a predictor of disease progression stages. For instance, cancer cells have been found to be less stiff compared to their healthy counterparts due to the proteomic and lipidomic dysregulations conferred by the underlying pathology. The separation and selective recovery of cells or extracellular vesicles secreted from such cells that have undergone these changes have been suggested to be of diagnostic and prognostic value.

This dissertation first describes the implementation of a stiffness-based separation of phosphatidylcholine-based ...


Thermodynamics And Kinetics Of Ligand Photodissociation In Heme Proteins And Formation Of Dna I-Motif, David S. Butcher Mar 2017

Thermodynamics And Kinetics Of Ligand Photodissociation In Heme Proteins And Formation Of Dna I-Motif, David S. Butcher

FIU Electronic Theses and Dissertations

Heme proteins carry out a diverse array of functions in vivo while maintaining a well-conserved 3-over-3 α-helical structure. Human hemoglobin (Hb) is well-known for its oxygen transport function. Type 1 non-symbiotic hemoglobins (nsHb1) in plants and bacterial flavohemoglobins (fHb) from a variety of bacterial species have been predicted to carry out a nitric oxide dioxygenase function. In nsHb1 and fHb this function has been linked to protection from nitrosative stress. Herein, I combine photoacoustic calorimetry (PAC), transient absorption spectroscopy (TA), and classical molecular dynamics (cMD) simulations to characterize molecular mechanism of diatomic ligand interactions with a hexa-coordinate globin from plant ...


Conformational Dynamics And Stability Associated With Magnesium Or Calcium Binding To Dream In The Regulation Of Interactions Between Dream And Dna Or Presenilins, Khoa Ngoc Pham Jun 2016

Conformational Dynamics And Stability Associated With Magnesium Or Calcium Binding To Dream In The Regulation Of Interactions Between Dream And Dna Or Presenilins, Khoa Ngoc Pham

FIU Electronic Theses and Dissertations

Downstream regulatory element antagonist modulator (DREAM) is involved in various interactions with targets both inside and outside of the nucleus. In the cytoplasm, DREAM interacts with the C-terminal fragments of presenilins to facilitate the production of β-amyloid plaques in Alzheimer’s disease. In the nucleus, Ca2+ free DREAM directly binds to specific downstream regulatory elements of prodynorphin/c-fos gene to repress the gene transcription in pain modulation. These interactions are regulated by Ca2+ and/or Mg2+ association at the EF-hands in DREAM. Therefore, understanding the conformational dynamics and stability associated with Ca2+ and/or Mg ...


Protein-Ligand Interactions And Allosteric Regulation Of Activity In Dream Protein, Walter G. Gonzalez Mar 2016

Protein-Ligand Interactions And Allosteric Regulation Of Activity In Dream Protein, Walter G. Gonzalez

FIU Electronic Theses and Dissertations

Downstream regulatory antagonist modulator (DREAM) is a calcium sensing protein that co-assembles with KV4 potassium channels to regulate ion currents as well as with DNA in the nucleus, where it regulates gene expression. The interaction of DREAM with A-type KV4 channels and DNA has been shown to regulate neuronal signaling, pain sensing, and memory retention. The role of DREAM in modulation of pain, onset of Alzheimer’s disease, and cardiac pacemaking has set this protein as a novel therapeutic target. Moreover, previous results have shown a Ca2+ dependent interaction between DREAM and KV4 ...


Multimode Analysis Of Nanoscale Biomolecular Interactions, Purushottam Babu Tiwari Feb 2015

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 ...


Theoretical Investigation Of Intra- And Inter-Cellular Spatiotemporal Calcium Patterns In Microcirculation, Jaimit B. Parikh Jan 2015

Theoretical Investigation Of Intra- And Inter-Cellular Spatiotemporal Calcium Patterns In Microcirculation, Jaimit B. Parikh

FIU Electronic Theses and Dissertations

Microcirculatory vessels are lined by endothelial cells (ECs) which are surrounded by a single or multiple layer of smooth muscle cells (SMCs). Spontaneous and agonist induced spatiotemporal calcium (Ca2+) events are generated in ECs and SMCs, and regulated by complex bi-directional signaling between the two layers which ultimately determines the vessel tone. The contractile state of microcirculatory vessels is an important factor in the determination of vascular resistance, blood flow and blood pressure. This dissertation presents theoretical insights into some of the important and currently unresolved phenomena in microvascular tone regulation. Compartmental and continuum models of isolated EC and ...


Conformational Dynamics Associated With Ligand Binding To Vertebrate Hexa-Coordinate Hemoglobins, Luisana Astudillo Mar 2014

Conformational Dynamics Associated With Ligand Binding To Vertebrate Hexa-Coordinate Hemoglobins, Luisana Astudillo

FIU Electronic Theses and Dissertations

Neuroglobin (Ngb) and cytoglobin (Cygb) are two new additions to the globin family, exhibiting heme iron hexa-coordination, a disulfide bond and large internal cavities. These proteins are implicated in cytoprotection under hypoxic-ischemic conditions, but the molecular basis of their cytoprotective function is unclear.

Herein, a photothermal and spectroscopic study of the interactions of diatomic ligands with Ngb, Cygb, myoglobin and hemoglobin is presented. The impact of the disulfide bond in Ngb and Cygb and role of conserved residues in Ngb His64, Val68, Cys55, Cys120 and Tyr44 on conformational dynamics associated with ligand binding/dissociation were investigated. Transient absorption and photoacoustic ...