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Proton Pumping Mechanism In Cytochrome C Oxidase, Xiuhong Cai 2020 The Graduate Center, City University of New York

Proton Pumping Mechanism In Cytochrome C Oxidase, Xiuhong Cai

All Dissertations, Theses, and Capstone Projects

Cytochrome c Oxidase (CcO), is the terminal electron acceptor in the membrane bound aerobic respiratory chain. It reduces O2 to water. The energy released by this reaction is stored by pumping protons from the high pH, N-side of the membrane to the low pH, P-side. The generated proton gradient provides the motive force for synthesis of ATP by the ATP synthase.

Building a proton gradient across the membrane requires that proton transport must occur along controllable proton pathways to prevent proton leakage to the N-side. It has been suggested that CcO function requires proton transfer channels in both the ...


Biological Physics Student Edition 2020: Chapter 1, Philip C. Nelson 2020 University of Pennsylvania

Biological Physics Student Edition 2020: Chapter 1, Philip C. Nelson

Department of Physics Papers

Chapter 1: What the Ancients Knew


Characterizing The Long-Range And Short-Range Interactions Stabilizing A Model Sh3 Recognition Complex, Colin McClure 2020 Skidmore College

Characterizing The Long-Range And Short-Range Interactions Stabilizing A Model Sh3 Recognition Complex, Colin Mcclure

Senior Theses

SH3 domains are common recognition domains found in many protein complexes of all eukaryotes. Their regulatory functions are involved in cell proliferation, differentiation, cytoskeleton modification and are vital for cellular communication. We have used Molecular Dynamics (MD) simulations to computationally model a common interaction between the AbpSH3 domain and the intrinsically disordered peptide, ArkA. This work is in collaboration with and in support of previous experimental studies of the complex aimed to characterize the binding pathway including NMR, ITC, and chemical denaturation. Specifically, my work focuses on the long-range electrostatic interactions involved in stabilizing the bound AbpSH3- ArkA complex. Previous ...


Functional Analysis Of A Critical Glycine (Glycine 12) In Beta-Type Connexins Of Human Skin, Rasheed Bailey 2020 State University of New York College at Buffalo - Buffalo State College

Functional Analysis Of A Critical Glycine (Glycine 12) In Beta-Type Connexins Of Human Skin, Rasheed Bailey

Biology Theses

At least five beta-type connexins are expressed in various layers of the skin (Cx26, Cx30, Cx30.3, Cx31, and Cx32) and all include a glycine residue at position 12. Glycine12 (G12) is located about halfway through the cytoplasmic amino terminus and has been the focus of several studies related to connexin diseases and gap junction channel structure. The importance of this residue is evident in the severity and diversity of diseases associated with amino acid substitutions at G12 including hereditary forms of skin disease, deafness and neuropathy. This study uses bioinformatic analysis in combination with mutational analysis and electrophysiology to ...


Investigating The Interactions Between Individual Calmodulin And Hiv-1 Protein Domains, Riley K. Kendall, Jerry LaRue 2020 Chapman University

Investigating The Interactions Between Individual Calmodulin And Hiv-1 Protein Domains, Riley K. Kendall, Jerry Larue

Student Scholar Symposium Abstracts and Posters

The World Health Organization found that 37.9 million people were living with HIV by the end of 2018. HIV is a virus that weakens the immune system through viral replication and the destruction of CD4+ T-cells, which are white blood cells that detect infection and make antibodies. A cure for HIV has not yet been discovered. HIV-1 contains a Gag polyprotein which regulates the stages of viral replication. Previous studies suggest that the myristoyl group of a matrix protein peptide found on the Gag polyprotein, MA, forms a complex with a calcium-binding, multifunctional regulatory protein called Calmodulin (CaM). CaM ...


Effect Of Charged Lipids On The Ionization Behavior Of Glutamic Acid Containing Transmembrane Helices, Brooke Nunn 2020 University of Arkansas, Fayetteville

Effect Of Charged Lipids On The Ionization Behavior Of Glutamic Acid Containing Transmembrane Helices, Brooke Nunn

Chemistry & Biochemistry Undergraduate Honors Theses

Transmembrane proteins make up critical components of living cells. Protein function can be greatly impacted by the charged state of its respective components, the side chains of amino acid residues. Thus far, in the lipid membrane, little is known about the properties of residues such as glutamic acid. To explore these properties, I have included glutamic acid in a suitable model peptide-lipid system for fundamental biophysical experiments. Within the system, I have placed a glutamic acid residue instead of leucine in the L14 position of the helical hydrophobic peptide GWALP23 (acetyl-GGALWLALALALAL14ALALWLAGA-amide). Substitutions of glutamine and aspartic acid serve ...


Effect Of Ph And Lipid Composition On Membrane-Spanning Helices With Glutamic Acid Examined By Solid-State Nmr, Kelsey Marr 2020 University of Arkansas, Fayetteville

Effect Of Ph And Lipid Composition On Membrane-Spanning Helices With Glutamic Acid Examined By Solid-State Nmr, Kelsey Marr

Chemistry & Biochemistry Undergraduate Honors Theses

Transmembrane proteins constitute about 30% of the proteins in a mammalian cell and are involved in major biological processes. The dynamic properties of membrane proteins and the ionization states of particular side chains are important for biological function. The biophysical properties of membrane proteins nevertheless can be difficult to decode, particularly for glutamic acid in the lipid environment of cell membranes. To study the ionization of glutamic acid in transmembrane peptides, guest glutamic acid residues were substituted into the well-defined model helix of GWALP23 (acetyl-GGAL4WLALALALALAL16ALWLAGA-amide). These guest residues were placed at position L16 or L4 and specific 2H-labeled alanine residues ...


The Role Of Conformational Dynamics In Isocyanide Hydratase Catalysis, Medhanjali Dasgupta 2020 University of Nebraska - Lincoln

The Role Of Conformational Dynamics In Isocyanide Hydratase Catalysis, Medhanjali Dasgupta

Theses and Dissertations in Biochemistry

Post-translational modification of cysteine residues can regulate protein function and is essential for catalysis by cysteine-dependent enzymes. Covalent modifications neutralize charge on the reactive cysteine thiolate anion and thus alter the active site electrostatic environment. Although a vast number of enzymes rely on cysteine modification for function, precisely how altered structural and electrostatic states of cysteine affect protein dynamics, which in turn, affects catalysis, remains poorly understood.

Here we use X-ray crystallography, computer simulations, site directed mutagenesis and enzyme kinetics to characterize how covalent modification of the active site cysteine residue in the enzyme, isocyanide hydratase (ICH), affects the protein ...


Stride-A Fluorescence Method For Direct, Specific In Situ Detection Of Individual Single- Or Double-Strand Dna Breaks In Fixed Cells, Magdalena M. Kordon, Miroslaw Zarebski, Kamil Solarczyk, Hanhui Ma, Thoru Pederson, Jurek W. Dobrucki 2020 Jagiellonian University

Stride-A Fluorescence Method For Direct, Specific In Situ Detection Of Individual Single- Or Double-Strand Dna Breaks In Fixed Cells, Magdalena M. Kordon, Miroslaw Zarebski, Kamil Solarczyk, Hanhui Ma, Thoru Pederson, Jurek W. Dobrucki

Open Access Articles

We here describe a technique termed STRIDE (SensiTive Recognition of Individual DNA Ends), which enables highly sensitive, specific, direct in situ detection of single- or double-strand DNA breaks (sSTRIDE or dSTRIDE), in nuclei of single cells, using fluorescence microscopy. The sensitivity of STRIDE was tested using a specially developed CRISPR/Cas9 DNA damage induction system, capable of inducing small clusters or individual single- or double-strand breaks. STRIDE exhibits significantly higher sensitivity and specificity of detection of DNA breaks than the commonly used terminal deoxynucleotidyl transferase dUTP nick-end labeling assay or methods based on monitoring of recruitment of repair proteins or ...


Bubble Lab Exercise, Peter Beltramo 2020 University of Massachusetts Amherst

Bubble Lab Exercise, Peter Beltramo

Science and Engineering Saturday Seminars

The cell membrane is a ubiquitous component in mammalian cells which control many vital biological functions. It consists of a phospholipid bilayer with embedded protein molecules which serve to transport molecules between the interior and exterior of the cell. Understanding what makes cell membranes so important and how they function requires concepts from physics, chemistry, and of course biology, but it is difficult to learn and conceptualize the structure and function of membranes due to their nanoscopic size and dynamic nature which can’t be properly appreciated in a static textbook. This activity draws analogies between the chemistry and structure ...


Probing The Secondary Structure Of Intrinsically Disordered Squid Reflectin Protein Through Ssnmr, Harriet Austin 2020 University of Central Florida

Probing The Secondary Structure Of Intrinsically Disordered Squid Reflectin Protein Through Ssnmr, Harriet Austin

Digital Repository: Showcase of Undergraduate Research Excellence

No abstract provided.


Nitroxide Human Serum Albumin Incorporated Nanoflowers With Dual Enzyme-Like Activities, Can Cai 2020 Georgia Southern University

Nitroxide Human Serum Albumin Incorporated Nanoflowers With Dual Enzyme-Like Activities, Can Cai

Electronic Theses and Dissertations

In this work, nitroxide 2,2,6,6-tetramethylpiperdine 1-oxyl (Tempo), human serum albumin (HSA), CuSO4 and phosphate buffered saline (PBS) were used to synthesis the hybrid nanoflowers. Scanning electron microscopy (SEM), electron paramagnetic resonance (EPR), and Fourier-transform infrared spectroscopy (FTIR) were used for characterization of the nanoflowers.The SEM spectra illustrated the morphologies of the hybrid nanoflowers. The FTIR spectra corroborated the presence of PNA in the hybrid nanoflowers, while the EPR spectra confirmed the intermolecular interaction of nitroxides bound to the human serum albumin incorporated into the nanoflowers. The catalase mimetic activity and corresponding kinetic parameters of nanoflowers ...


The Structure Of The Endogenous Esx-3 Secretion System, Nicole Poweleit, Nadine Czudnochowski, Rachel Nakagawa, Donovan Trinidad, Kenan C. Murphy, Christopher M. Sassetti, Oren S. Rosenberg 2019 University of California, San Francisco

The Structure Of The Endogenous Esx-3 Secretion System, Nicole Poweleit, Nadine Czudnochowski, Rachel Nakagawa, Donovan Trinidad, Kenan C. Murphy, Christopher M. Sassetti, Oren S. Rosenberg

Open Access Articles

The ESX (or Type VII) secretion systems are protein export systems in mycobacteria and many Gram-positive bacteria that mediate a broad range of functions including virulence, conjugation, and metabolic regulation. These systems translocate folded dimers of WXG100-superfamily protein substrates across the cytoplasmic membrane. We report the cryo-electron microscopy structure of an ESX-3 system, purified using an epitope tag inserted with recombineering into the chromosome of the model organism Mycobacterium smegmatis. The structure reveals a stacked architecture that extends above and below the inner membrane of the bacterium. The ESX-3 protomer complex is assembled from a single copy of the EccB3 ...


Development And Application Of Mass Spectrometry-Based Protein Footprinting In Structural Proteomics, Ming Cheng 2019 Washington University in St. Louis

Development And Application Of Mass Spectrometry-Based Protein Footprinting In Structural Proteomics, Ming Cheng

Arts & Sciences Electronic Theses and Dissertations

Integral mass spectrometry (MS) has emerged as an important tool for protein structural characterization. It readouts are a broad range of structural information, including stoichiometry, interactions, conformations and conformation change, and dynamics. Protein footprinting is a pivotal component in the intergral MS toolkit.My dissertation centers around the development and application of protein footprinting to characterize protein structure. It is divided into seven chapters.Chapter 1 serves as the introduction for integral mass spectrometry in structural proteomic.In Chapter 2, we extended the fast-photochemical oxidation of proteins (FPOP) platform by adding the trifluoromethyl radical (•CF3) as a new reagent. We ...


Structural Organization And Dynamics Of Homodimeric Cytohesin Family Arf Gtpase Exchange Factors In Solution And On Membranes, Sanchaita Das, Andrew W. Malaby, Agata Nawrotek, Wenhua Zhang, Mahel Zeghouf, Sarah Maslen, Mark Skehel, Srinivas Chakravarthy, Thomas C. Irving, Osman Bilsel, Jacqueline Cherfils, David G. Lambright 2019 University of Massachusetts Medical School

Structural Organization And Dynamics Of Homodimeric Cytohesin Family Arf Gtpase Exchange Factors In Solution And On Membranes, Sanchaita Das, Andrew W. Malaby, Agata Nawrotek, Wenhua Zhang, Mahel Zeghouf, Sarah Maslen, Mark Skehel, Srinivas Chakravarthy, Thomas C. Irving, Osman Bilsel, Jacqueline Cherfils, David G. Lambright

Open Access Articles

Membrane dynamic processes require Arf GTPase activation by guanine nucleotide exchange factors (GEFs) with a Sec7 domain. Cytohesin family Arf GEFs function in signaling and cell migration through Arf GTPase activation on the plasma membrane and endosomes. In this study, the structural organization of two cytohesins (Grp1 and ARNO) was investigated in solution by size exclusion-small angle X-ray scattering and negative stain-electron microscopy and on membranes by dynamic light scattering, hydrogen-deuterium exchange-mass spectrometry and guanosine diphosphate (GDP)/guanosine triphosphate (GTP) exchange assays. The results suggest that cytohesins form elongated dimers with a central coiled coil and membrane-binding pleckstrin-homology (PH) domains ...


Lattice Arrangement Of Myosin Filaments Correlates With Fiber Type In Rat Skeletal Muscle, Weikang Ma, Kyounghwan Lee, Shixin Yang, Thomas C. Irving, Roger Craig 2019 Illinois Institute of Technology

Lattice Arrangement Of Myosin Filaments Correlates With Fiber Type In Rat Skeletal Muscle, Weikang Ma, Kyounghwan Lee, Shixin Yang, Thomas C. Irving, Roger Craig

Radiology Publications

The thick (myosin-containing) filaments of vertebrate skeletal muscle are arranged in a hexagonal lattice, interleaved with an array of thin (actin-containing) filaments with which they interact to produce contraction. X-ray diffraction and EM have shown that there are two types of thick filament lattice. In the simple lattice, all filaments have the same orientation about their long axis, while in the superlattice, nearest neighbors have rotations differing by 0 degrees or 60 degrees . Tetrapods (amphibians, reptiles, birds, and mammals) typically have only a superlattice, while the simple lattice is confined to fish. We have performed x-ray diffraction and electron microscopy ...


Rotational Tuning Of Transmembrane Helix Properties Based On The Precise Placements Of Aromatic And Charged Residues, Matthew J. McKay 2019 University of Arkansas, Fayetteville

Rotational Tuning Of Transmembrane Helix Properties Based On The Precise Placements Of Aromatic And Charged Residues, Matthew J. Mckay

Theses and Dissertations

Designed model transmembrane peptides and oriented 2H and 15N solid-state nuclear magnetic resonance (NMR) spectroscopy were used to analyze how simple sequence modifications can influence peptide structure, behavior and dynamics as well as for determining the pKa of glutamic acid at the membrane interface. The GW5,19ALP23 (acetyl-GGALW(LA)6LWLAGA-amide) peptide framework adopts a well-defined tilted orientation in lipid bilayers (DLPC, DMPC and DOPC) and undergoes low amounts of dynamic motion. The sequence was initially modified by moving the Trp residues outwards to positions 4 and 20. This new sequence GW4,20ALP23 (acetyl-GGAW(AL)7AWAGA-amide) displays high amounts of signal ...


Influence Of Single And Multiple Histidine Residues And Their Ionization Properties On Transmembrane Helix Dynamics, Orientations And Fraying, Fahmida Afrose 2019 University of Arkansas, Fayetteville

Influence Of Single And Multiple Histidine Residues And Their Ionization Properties On Transmembrane Helix Dynamics, Orientations And Fraying, Fahmida Afrose

Theses and Dissertations

Since aromatic and charged residues are often present in various locations of transmembrane helices of integral membrane proteins, their impacts on the molecular properties of transmembrane proteins and their interactions with lipids are of particular interest in many studies. In this work, I used solid-state deuterium NMR spectroscopy in designed model peptide GWALP23 [GGALW(LA)6LWLAGA] with selective deuterium labels to addresses the pH dependence and influence of single and multiple “guest” histidine residues in the orientation and dynamic behaviors of transmembrane proteins. The mutations include Gly to His (G2/22 to H2/22), Trp to His (W5/19 to ...


Electropermeabilization Does Not Correlate With Plasma Membrane Lipid Oxidation, Olga Michel, Andrei G. Pakhomov, Maura Casciola, Jolanta Saczko, Julita Kulbacka, Olga N. Pakhomova 2019 Old Dominion University

Electropermeabilization Does Not Correlate With Plasma Membrane Lipid Oxidation, Olga Michel, Andrei G. Pakhomov, Maura Casciola, Jolanta Saczko, Julita Kulbacka, Olga N. Pakhomova

Bioelectrics Publications

The permeabilized condition of the cell membrane after electroporation can last minutes but the underlying mechanisms remain elusive. Previous studies suggest that lipid peroxidation could be responsible for the lasting leaky state of the membrane. The present study aims to link oxidation within the plasma membrane of live cells to permeabilization by electric pulses. We have introduced a method for the detection of oxidation by ratiometric fluorescence measurements of BODIPY-C11 dye using total internal reflection fluorescence (TIRF) microscopy, limiting the signal to the cell membrane. CHO-K1 cells were cultured on glass coverslips coated with an electroconductive indium tin oxide (ITO ...


Structure And Assembly Of Calcium Homeostasis Modulator Proteins, Johanna L. Syrjanen, Kevin Michalski, Tsung-Han Chou, Timothy Grant, Shanlin Rao, Noriko Simorowski, Stephen J. Tucker, Nikolaus Grigorieff, Hiro Furukawa 2019 WM Keck Structural Biology Laboratory

Structure And Assembly Of Calcium Homeostasis Modulator Proteins, Johanna L. Syrjanen, Kevin Michalski, Tsung-Han Chou, Timothy Grant, Shanlin Rao, Noriko Simorowski, Stephen J. Tucker, Nikolaus Grigorieff, Hiro Furukawa

University of Massachusetts Medical School Faculty Publications

Biological membranes of many tissues and organs contain large-pore channels designed to permeate a wide variety of ions and metabolites. Examples include connexin, innexin, and pannexin, which form gap junctions and/or bona fide cell surface channels. The most recently identified large-pore channels are the calcium homeostasis modulators (CALHMs), which permeate ions and ATP in a voltage-dependent manner to control neuronal excitability, taste signaling, and pathologies of depression and Alzheimer’s disease. Despite such critical biological roles, the structures and patterns of oligomeric assembly remain unclear. Here, we reveal the first structures of two CALHMs, CALHM1 and CALHM2, by single ...


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