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Biochemistry, Biophysics, and Structural Biology Commons

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Retrospective Theses and Dissertations

2006

Biophysics

Articles 1 - 5 of 5

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

Structural And Functional Studies On Snares-Mediated Membrane Fusion , Yong Chen Jan 2006

Structural And Functional Studies On Snares-Mediated Membrane Fusion , Yong Chen

Retrospective Theses and Dissertations

Membrane fusion is an essential biological process for vesicle trafficking in eukaryotic cells. Soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) are a family of proteins that have been recognized as key components of protein complexes that drive membrane fusion. The SNARE proteins localized in opposite membranes form a SNARE complex, which bridges the two membranes into close proximity and promotes fusion. Despite considerable sequence divergence among SNARE proteins, this fusion machinery is conserved structurally, mechanistically and evolutionally from yeast to human;Site-directed spin labeling (SDSL) and electron paramagnetic resonance (EPR) are well established techniques to study the structures of membrane ...


An Examination Of Hexacoordinate Hemoglobins Using The Techniques Of Biochemistry, Biophysics And Molecular Biology , James Thomas Trent Iii Jan 2006

An Examination Of Hexacoordinate Hemoglobins Using The Techniques Of Biochemistry, Biophysics And Molecular Biology , James Thomas Trent Iii

Retrospective Theses and Dissertations

Hexacoordinate hemoglobins are found in a truly diverse array of organisms, ranging from cyanobacteria to humans. The prevalence of these proteins in nature coupled with very high sequence identity between species homologues suggests they have a role vital to life. The high sequence identity also implies that hxHb structural features, including the hexacoordination phenomenon, are critical aspects of the physiological function. A detailed understanding of the ligand binding behavior of these proteins will not only facilitate efforts towards discovering their physiological role(s), but will also help explain how hxHbs perform their function. This dissertation consists of four published papers ...


A Penalty Function Method For Constrained Molecular Dynamics , Ajith Gunaratne Jan 2006

A Penalty Function Method For Constrained Molecular Dynamics , Ajith Gunaratne

Retrospective Theses and Dissertations

We propose a penalty-function method for constrained molecular dynamic simulation by defining a quadratic penalty function for the constraints. The simulation with such a method can be done by using a conventional, unconstrained solver only with the penalty parameter increased in an appropriate manner as the simulation proceeds. More specifically, we scale the constraints with their force constants when forming the penalty terms. The resulting force function can then be viewed as a smooth continuation of the original force field as the penalty parameter increases. The penalty function method is easy to implement and costs less than a Lagrange multiplier ...


Structural Characterization Of Ligand Binding In Hexacoordinate Hemoglobins , Julie Anne Hoy Jan 2006

Structural Characterization Of Ligand Binding In Hexacoordinate Hemoglobins , Julie Anne Hoy

Retrospective Theses and Dissertations

Hemoglobins are ancient proteins that predate the divergence of prokaryotes and eukaryotes. Although the most thoroughly studied hemoglobins are mammalian oxygen transporters, it has become clear that this function is a recent evolutionary advancement coinciding with the "oxygen revolution" and the development of multicellular organisms. Hemoglobins capable of oxygen transport are highly specialized structurally to maintain pentacoordination of the heme and appropriate ligand rate and equilibrium constants, while preventing autooxidation due to bound oxygen. Their predecessors however, adopt a more energetically favorable hexacoordinate conformation that precludes oxygen transport;Despite the fact that hexacoordinate hemoglobins are ubiquitous in biological organisms, little ...


Studies Of Intermediates In Snare-Induced Membrane Fusion , Fan Zhang Jan 2006

Studies Of Intermediates In Snare-Induced Membrane Fusion , Fan Zhang

Retrospective Theses and Dissertations

The purpose of this course of study is to understand the intermediates during SNAREs assembly and the membrane fusion mediated by SNAREs. SNAREs have been proposed to be the minimal machinery for the membrane fusion. According to the location distribution, SNAREs can be classified as either v-(vesicles) or t-(target) SNAREs. The assembly of three SNARE components from the opposing membranes into the ternary complex is believed to provide the ultimate driving force for merging the separate bilayers into a continuous entity. Before this step the t-SNAREs associate as the binary complex on the target membrane to serve as ...