Biochemistry, Biophysics, and Structural Biology Commons^™

Discovery Of Nitric Oxide And Cyclic Gmp In Cell Signaling And Their Role In Drug Development, Ferid Murad

Biochemistry and Molecular Medicine Faculty Publications

No abstract provided.

Detailed Comparison Of The Pnicogen Bond With Chalcogen, Halogen And Hydrogen Bonds, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The characteristics of the pnicogen bond are explored using a variety of quantum chemical techniques. In particular, this interaction is compared with its halogen and chalcogen bond cousins, as well as with the more common H-bond. In general, these bonds are all of comparable strength. More specifically, they are strengthened by the presence of an electronegative substituent on the electron-acceptor atom, and each gains strength as one moves down the appropriate column of the periodic table, for example, from N to P to As. These noncovalent bonds owe their stability to a mixture in nearly equal parts of electrostatic attraction …

Dubious Role Of Mycobacterium Paratuberculosis In Pathogenesis Of Type I Diabetes, Saisathya Thanigachalam

Electronic Theses and Dissertations

Background: Type 1 Diabetes mellitus (TIDM) is a chronic disorder in which the insulin producing beta cells are selectively self-destroyed. Although the etiology of the disease has not been determined, genetic dispositions such as SLC11A1 polymorphism in suffering patients have been reported. The role of pathogenic microorganisms such as Mycobacterium avium subspecies paratuberculosis (MAP) in TIDM has also been recently debated. MAP is already known to cause paratuberculosis in cattle and now it is a strong suspect of causing autoimmune diseases in humans such as Crohn’s disease, multiple sclerosis, autoimmune Thyroiditis, rheumatoid arthritis and autoimmune diabetes. We hypothesis that molecular …

Escherichia Coli Lacking Rpos Are Rare In Natural Populations Of Non-Pathogens, Emily Snyder '11, David M. Gordon, Daniel M. Stoebel

All HMC Faculty Publications and Research

The alternative sigma factor RpoS controls a large regulon that allows E. coli to respond to a variety of stresses. Mutations in rpoS can increase rates of nutrient acquisition at the cost of a decrease in stress resistance. These kinds of mutations evolve rapidly under certain laboratory conditions where nutrient acquisition is especially challenging. The frequency of strains lacking RpoS in natural populations of E. coli is less clear. Such strains have been found at frequencies over 20% in some collections of wild isolates. However, laboratory handling can select for RpoS-null strains and may have affected some of these strain …

Cooperative Cluster Formation, Dna Bending And Base-Flipping By O6-Alkylguanine-Dna Alkyltransferase, Ingrid Tessmer, Manana Melikishvili, Michael G. Fried

Center for Structural Biology Faculty Publications

O⁶-Alkylguanine-DNA alkyltransferase (AGT) repairs mutagenic O⁶-alkylguanine and O⁴-alkylthymine adducts in DNA, protecting the genome and also contributing to the resistance of tumors to chemotherapeutic alkylating agents. AGT binds DNA cooperatively, and cooperative interactions are likely to be important in lesion search and repair. We examined morphologies of complexes on long, unmodified DNAs, using analytical ultracentrifugation and atomic force microscopy. AGT formed clusters of ≤11 proteins. Longer clusters, predicted by the McGhee–von Hippel model, were not seen even at high [protein]. Interestingly, torsional stress due to DNA unwinding has the potential to limit cluster size …

Transplantation Of Pluripotent Stem Cells Confers Cardiac Protection In Dox-Induced Heart Failure Through Notch-1 Pathway, Hilda Merino-Chavez

Electronic Theses and Dissertations

Doxorubicin (DOX) is the antineoplastic drug of preference used to treat a wide variety of malignancies, with high survival rates among treated patients. However, the benefits of this drug have become less appealing due to the side effects that occur such as DOX-induced cardiomyopathy (DIC) and an increased risk of myocardial infarction (MI). Therefore, there is an urgent need to explore the therapeutic options to treat DIC. In this context, adult stem cells have been used as a source to reduce cardiomyocyte apoptosis in DIC; however, the effects of transplanted embryonic stem (ES) cells and induced pluripotent stem (iPS) cells …

Limk1 Promotes Mt1-Mmp Expression And Localization To The Plasma Membrane, Richard Ottman

Electronic Theses and Dissertations

LIM Kinase 1 (LIMK1), a serine/threonine kinase, modulates actin polymerization and microtubule assembly. The function of LIMK1 is regulated by kinases that are activated by Rho and Rac GTPases. LIMK1 is overexpressed in various cancerous cell types and tissues and its overexpression promotes increased invasion and metastasis of breast and prostate cancer cells. Membrane-Type Matrix Metalloproteinase 1 (MT1-MMP) is a member of the zinc-binding collagenase family, which is involved in extracellular matrix breakdown and activation of secreted MMP-2. The balance between activation and inhibition of MT1- MMP and MMP-2 helps maintaining normal extracellular matrix turnover. However, it has been shown …

Bacterial Host Interactions In Cystic Fibrosis, Máire Callaghan, Siobhan Mcclean

Articles

Chronic infection is a hallmark of cystic fibrosis (CF) and the main contributor to morbidity. Microbial infection in CF is complex, due to the number of different species that colonise the CF lung. Their colonisation is facilitated by a host response that is impaired or compromised by highly viscous mucous, zones of hypoxia and the lack of the cystic fibrosis transmembrane regulator (CFTR). Successful dominant CF pathogens combine an effective arsenal to establish infection and counter-attack the host response, together with an ability to adapt readily to an unfavourable environment. Hypermutability is common among CF pathogens facilitating adaptation and as …

First Steps In Growth Of A Polypeptide Toward Β-Sheet Structure, U. Adhikari, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The full conformational energy surface is examined for a molecule in which a dipeptide is attached to the same spacer group as another peptide chain, so as to model the seminal steps of β-sheet formation. This surface is compared with the geometrical preferences of the isolated dipeptide to extract the perturbations induced by interactions with the second peptide strand. These interpeptide interactions remove any tendency of the dipeptide to form a C5 ring structure, one of its two normally stable geometries. A C7 structure, the preferred conformation of the isolated dipeptide, remains as the global minimum in the full molecule. …

Extrapolation To The Complete Basis Set Limit For Binding Energies Of Noncovalent Interactions, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

A means of extrapolating from double and triple-valence basis sets to a complete basis set is examined in the context of the pnicogen bonds in the BH2P⋯NH3 complexes, with B = CH3, H, NH2, CF3, OH, Cl, F, and NO2. Binding energies converge smoothly, and the trends for the various substituents B are unaffected by the basis set size, extrapolation, or level of inclusion of electron correlation, including MP2 and CCSD(T). The approach appears to be successful also for H-bonded systems, in particular the water dimer. In the event that full extrapolation within the context of CCSD(T) is not feasible, …

Estradiol Modulation Of Calcium Dynamics In Pituitary Mmq Lactotroph Cells, Monika Pauckova

Electronic Theses and Dissertations

Pituitary lactotrophs are excitable cells that exhibit spontaneous, calcium influx triggering prolactin (PRL) secretion to stimulate lactation. Lactotrophs express estrogen receptors (ER) and are a well established estrogen-responsive cell system. 17B-estradiol (E2) is known to directly affect lactotrophs by increasing PRL transcription and biosynthesis, intracellular Ca2+ concentration ([Ca2+]i) and PRL secretion. This study demonstrates that the MMQ clonal cell line, isolated from the 7315a rat pituitary tumor, is a model lactotroph cell line that is E2-responsive. Spontaneous and evoked Ca2+ transients were especially sensitive to L-type channel block, but not affected by block of omega-conotoxin-GVIA-sensitive CaV channels or TTX-sensitive voltage-gated …

Tgd1, -2, And -3 Proteins Involved In Lipid Trafficking Form Atp-Binding Cassette (Abc) Transporter With Multiple Substrate-Binding Proteins, Rebecca Roston, Jinpeng Gao, Monika W. Murcha, James Whelan, Christoph Benning

Department of Biochemistry: Faculty Publications

Background: ATP-binding cassette transporters exist in all life forms and usually require only one substrate-binding domain.

Results: The TRIGALACTOSYLDIACYLGLYCEROL (TGD) complex contains 8–12 substrate-binding proteins.

Conclusion: Multiple substrate-binding proteins may be needed by the TGD complex to enhance its putative lipid transport activity.

Significance: Knowing the subunit stoichiometry of the TGD complex furthers understanding of lipid transfer between chloroplast membranes.

Sensitivity Of Noncovalent Bonds To Intermolecular Separation: Hydrogen, Halogen, Chalcogen, And Pnicogen Bonds, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

It is well known that noncovalent bonds are weakened when stretched from their equilibrium intermolecular separation. Quantum chemical calculations are used to examine and compare the sensitivity to stretches of hydrogen, halogen, chalcogen, and pnicogen bonds. NH3 was taken as the universal electron donor, paired with HOH and FH in H-bonds, as well as with FPH2, FSH, and FCl. Even though the binding energies span a wide range, stretching the intermolecular separation by 1 Å cuts this quantity by the same proportion, roughly in half, for each system. Taking the sum of van der Waals radii as an arbitrary cutoff, …

Silica As A Matrix For Encapsulating Proteins:Surface Effects On Protein Structure Assessed By Circular Dichroism Spectroscopy, Daryl K. Eggers, P. J. Calabretta, M. C. Chancellor, C. Torres, G. R. Abel Jr., C. Neihaus, N. J. Birtwhistle, N. M. Khouderchah, G. H. Zemede

Faculty Publications, Chemistry

The encapsulation of biomolecules in solid materials that retain the native properties of the molecule is a desired feature for the development of biosensors and biocatalysts. In the current study, protein entrapment in silica-based materials is explored using the sol-gel technique. This work surveys the effects of silica confinement on the structure of several model polypeptides, including apomyoglobin, copper-zinc superoxide dismutase, polyglutamine, polylysine, and type I antifreeze protein. Changes in the secondary structure of each protein following encapsulation are monitored by circular dichroism spectroscopy. In many cases, silica confinement reduces the fraction of properly-folded protein relative to solution, but addition …

Dynamic Light Scattering And Microelectrophoresis: Main Prospects And Limitations, Vuk Uskoković

Pharmacy Faculty Articles and Research

Microelectrophoresis based on the dynamic light scattering (DLS) effect has been a major tool for assessing and controlling the conditions for stability of colloidal systems. However, both the DLS methods for characterization of the hydrodynamic size of dispersed submicron particles and the theory behind the electrokinetic phenomena are associated with fundamental and practical approximations that limit their sensitivity and information output. Some of these fundamental limitations, including the spherical approximation of DLS measurements and an inability of microelectrophoretic analyses of colloidal systems to detect discrete charges and differ between differently charged particle surfaces due to rotational diffusion and particle orientation …

Preferred Configurations Of Peptide-Peptide Interactions, U. Adhikari, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The natural and fundamental proclivities of interaction between a pair of peptide units are examined using high-level ab initio calculations. The NH···O H-bonded structure is found to be the most stable configuration of the N-methylacetamide (NMA) model dimer, but only slightly more so than a stacked arrangement. The H-bonded geometry is destabilized by only a small amount if the NH group is lifted out of the plane of the proton-accepting amide. This out-of-plane motion is facilitated by a stabilizing charge transfer from the CO π bond to the NH σ* antibonding orbital. The parallel and antiparallel stacked dimers are nearly …

Evaluation Of Dft Methods To Study Reactions Of Benzene With Oh Radical, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Several density functional theory” (DFT) methods are applied to two different reaction channels involving OH• + C6H6, and the results compared with high-level ab initio calculations. The OH• adds directly to one C atom in the first channel, first forming an encounter complex with the OH• poised above the aromatic plane. B3LYP, BH&HLYP, and MPW1K compute an accurate estimate of the overall exothermicity, whereas M05-2X, PBE0, and PBEPBE overestimate this quantity to some degree. With the exceptions of PBEPBE and PBE0, the other methods produce an acceptable barrier to addition. All approaches except BH&HLYP correctly predict an exothermic H• abstraction, …

Structural Polymorphism In Tau Filaments: An Implication For Neurodegenerative Diseases, Ayisha Siddiqua

Electronic Theses and Dissertations

Tau filaments are the pathological hallmark of >20 neurodegenerative diseases including Alzheimer's disease, Pick's disease, and progressive supranuclear palsy. In the adult human brain, six isoforms of tau are expressed that differ by presence or absence of the second of the four semiconserved repeats. As a consequence, half of the tau isoforms have three repeats (3R tau), whereas the other half has four repeats (4R tau).

Site-directed spin labeling of recombinant tau in conjunction with electron paramagnetic resonance spectroscopy was used to obtain structural insights into tau filaments. The studies showed that the filaments of 4R tau and 3R tau …

Β-Casein–Phospholipid Monolayers As Model Systems To Understand Lipid–Protein Interactions In The Milk Fat Globule Membrane, Sophie Gallier, Derek E. Gragson, Rafael Jiménez-Flores, David W. Everett

Chemistry and Biochemistry

Phospholipid–protein monolayer films were studied as model systems to mimic the structure of the native bovine milk fat globule membrane (MFGM) and to understand lipid–protein interactions at the surface of the globule. Phospholipids extracted from bovine raw milk, raw cream, processed milk and buttermilk powder were spread onto the air–water interface of a Langmuir trough, β-casein was then added to the sub-phase, and Langmuir–Blodgett films were studied by epifluorescence microscopy and atomic force microscopy. In all films, β-casein was responsible for clustering of the sphingomyelin- and cholesterol-rich microdomains into larger platforms. This suggests that the same phenomenon may happen at …

Contributions Of Various Noncovalent Bonds To The Interaction Between An Amide And S-Containing Molecules, U. Adhikari, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

N-Methylacetamide, a model of the peptide unit in proteins, is allowed to interact with CH3SH, CH3SCH3, and CH3SSCH3 as models of S-containing amino acid residues. All of the minima are located on the ab initio potential energy surface of each heterodimer. Analysis of the forces holding each complex together identifies a variety of different attractive forces, including SH⋅⋅⋅O, NH⋅⋅⋅S, CH⋅⋅⋅O, CH⋅⋅⋅S, SH⋅⋅⋅π, and CH⋅⋅⋅π H-bonds. Other contributing noncovalent bonds involve charge transfer into σ* and π* antibonds. Whereas some of the H-bonds are strong enough that they represent the sole attractive force in several dimers, albeit not usually in the …