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Articles 61 - 69 of 69
Full-Text Articles in Biophysics
Proton Pumping In Cytochrome C Oxidase, Jianxun Lu
Proton Pumping In Cytochrome C Oxidase, Jianxun Lu
Dissertations, Theses, and Capstone Projects
Cytochrome c oxidase (CcO) is a large trans-membrane protein, which is the final enzyme in the respiratory electron transport chain in mitochondria or aerobic bacteria. It implements proton pumping through the mitochondrial membrane against the electrochemical gradient, by utilizing the chemical energy released by reducing O2 to water. The active site of the chemical reaction is called the Binuclear Center (BNC) that is made up of heme a3, CuB, a Tyrosine residue and their ligands. The protein is reduced four times by electron from cytochromes c to reduce O2 and to generate four different …
De Novo Design And Engineering Of Functional Metal And Porphyrin-Binding Protein Domains, Bernard Howard Everson
De Novo Design And Engineering Of Functional Metal And Porphyrin-Binding Protein Domains, Bernard Howard Everson
Dissertations, Theses, and Capstone Projects
In this work, I describe an approach to the rational, iterative design and characterization of two functional cofactor-binding protein domains. First, a hybrid computational/experimental method was developed with the aim of algorithmically generating a suite of porphyrin-binding protein sequences with minimal mutual sequence information. This method was explored by generating libraries of sequences, which were then expressed and evaluated for function. One successful sequence is shown to bind a variety of porphyrin-like cofactors, and exhibits light- activated electron transfer in mixed hemin:chlorin e6 and hemin:Zn(II)-protoporphyrin IX complexes. These results imply that many sophisticated functions such as cofactor binding and electron …
Using Multiconformation Continuum Electrostatics Model For Pka And Proton Transfer Pathway Calculations In Protein, Xuyu Zhu
Dissertations, Theses, and Capstone Projects
Residue protonation state changes and proton transfer reactions in protein are basic and ubiquitous reactions in biological chemistry. The Multiconformation Continuum Electrostatics (MCCE) program is applied here to calculate the pKa of residues in the specially engineered protein staphylococcal nuclease (SNase) and further modified to investigate the unidirectional proton transfer mechanism in the proton pump protein bacteriorhodopsin. The pKa$_s$ are obtained by Monte Carlo sampling of coupled side chain protonations and positions as a function of pH in MCCE. The pKa$_s$ of 96 acids and bases introduced into buried sites in the SNase protein were calculated and the results compared …
Design And Optimization Of A De Novo Protein Charge Separation Dyad, Andrew C. Mutter
Design And Optimization Of A De Novo Protein Charge Separation Dyad, Andrew C. Mutter
Dissertations, Theses, and Capstone Projects
The ever-increasing demand for cheap, plentiful energy to fuel the needs of a growing population requires research into alternative clean energy. Solar irradiation has the potential to power the planet many times over; the challenge is efficient capture and conversion of this energy source. Nature has already solved this problem with photosynthesis, which harvests solar irradiation converting it to stored chemical energy and is the source of the energy for life. The goal of my dissertation is to use de novo designed protein to mimic the charge separation system in photosynthesis. A stable protein scaffold will be designed and used …
Interactions Of Eukaryotic Translation Initiation Factors And 3' Untranslated Region Of Barley Yellow Dwarf Virus Mrna During Protein Synthesis: A Study Of Equilibrium Binding, Kinetics And Thermodynamics, Bidisha Banerjee
Dissertations, Theses, and Capstone Projects
Eukaryotic initiation factor (eIF) 4F binding to mRNA is the first committed step in cap-dependent protein synthesis. Barley Yellow Dwarf Virus (BYDV) employs a cap-independent mechanism of translation initiation which is mediated by a structural element BTE (BYDV translation element) located in the 3’ UTR of its mRNA. eIF4F bound the BTE and a translational inactive mutant with high affinity; thus questioning the role of eIF4F in translation of BYDV. To examine the effects of eIF4F in BYDV translation initiation, BTE mutants with widely different in vitro translation efficiencies ranging from 5-164% compared to WT were studied. Using fluorescence anisotropy …
Recruitment Of The Ribosomal 40s Subunit To The 3'Untranslated Region Of A Viral Mrna, Via The Eif4 Complex, Facilitates Cap-Independent Translation, Sohani Das Sharma
Recruitment Of The Ribosomal 40s Subunit To The 3'Untranslated Region Of A Viral Mrna, Via The Eif4 Complex, Facilitates Cap-Independent Translation, Sohani Das Sharma
Dissertations, Theses, and Capstone Projects
Translation of uncapped plant viral RNAs can be facilitated by either an internal ribosomal entry site (IRES) in the 5' untranslated region (UTR) or a cap-independent translation element (CITE) in the 3' UTR. Barley yellow dwarf virus (BYDV) mRNA, which lacks both cap and poly(A) tail, has a translation element (3'BTE) in its 3' UTR that is essential for efficient translation initiation at the 5'-proximal AUG. This mechanism requires binding of the eukaryotic initiation factor 4G (eIF4G) subunit of the heterodimer eIF4F to the 3'BTE and base pairing between the 3'BTE and the 5' UTR. Here we investigate how this …
Computational Insights Into The Oxygen Evolving Complex Of Photosystem Ιι, Muhamed Amin
Computational Insights Into The Oxygen Evolving Complex Of Photosystem Ιι, Muhamed Amin
Dissertations, Theses, and Capstone Projects
The Oxygen Evolving Complex (OEC) of Photosystem II (PSII) is a unique Mn4O5Ca2+ cluster that catalyzes the photoactivated water splitting reaction. The OEC is a model system for bio-inspired artificial systems to use solar energy to pull electrons from water to produce fuel. The OEC goes through a cycle of 5 S states storing 4 holes, via electron transfer to P680+, the primary electron donor in PSII to generate a high valence S4 state that oxidizes water. The key questions are what controls the order of oxidation and deprotonation of the OEC complex and how does the PSII protein modulate …
Conformational Features Of The Human U2-U6 Snrna Complex, Ravichandra Bachu
Conformational Features Of The Human U2-U6 Snrna Complex, Ravichandra Bachu
Dissertations, Theses, and Capstone Projects
The splicing of precursor messenger (pre-m) RNA, during which noncoding intervening sequences are excised and flanking coding regions ligated, is an integral reaction of gene expression. In eukaryotes, it is carried out by a dynamic RNA-protein complex called the spliceosome, in which five small nuclear (sn) RNA components are actively involved in recognition and chemical aspects of the process. A complex formed between U2 and U6 snRNAs is implicated in the chemistry of pre-mRNA splicing. The catalytic activity of the U2-U6 snRNA complex is dependent on the presence of Mg2+ ions, and the complex has been shown to have several …
An Experimental Investigation Into The Mechanisms Of Bacterial Evolution, Zhenmao Wan
An Experimental Investigation Into The Mechanisms Of Bacterial Evolution, Zhenmao Wan
Dissertations, Theses, and Capstone Projects
This thesis studies the two fundamental mechanisms of bacterial evolution — horizontal gene transfer and spontaneous mutation, in the bacterium Escherichia coli through novel experimental assays and mathematical simulations. First, I will develop a growth assay utilizing the quantitative polymerase chain reaction (qPCR) to provide real-time enumeration of genetic marker abundance within bacterial populations. Second, I will focus on horizontal gene transfer in E. coli occurring through a process called conjugation. By fitting the qPCR data to a resource limited, logistic growth model, I will obtain estimated values of several key parameters governing the dynamics of DNA transfer through conjugation …