Biochemistry, Biophysics, and Structural Biology Commons^™

Pentanary And Hexanary Alkali Lanthanide Germanates Grown From Lanthanide Rich Flux Growth Reactions, Gregory Morrison, K. Pilar Zamorano, Virginia G. Jones, Ethan N. Adams, Hans Conrad Zur Loye

Faculty Publications

Single crystals of five compounds of a new structure type, the K3Nd52Ge12O100F7 type, were grown from lanthanide rich reactions using a KF/KCl flux: K3Ln52Ge12O100F7 (Ln = Nd, Eu), K3Ln52Ge12O100+δF7-δ (Ln = Pr, Tb), and K3Ca0.872Nd51.128Ge12O99.128F7.872. The five compounds crystallize in the cubic space group I-43d with lattice parameter 22.0350(2) Å for K3Nd52Ge12O100F7. The structure consists of a 3D checkerboard of LnX8, LnX7, LnX6, and GeO4 polyhedra, where X = O/F, and can be conceptually derived from the fluorite structure. K3Eu52Ge12O100F7 exhibits the fluorescence typical of Eu³⁺.

Proteomic Approaches To Investigate Pp2a-B55 Substrates And Cellular Function, Brennan C. Mcewan

Dartmouth College Ph.D Dissertations

Cell division is controlled in large part by reversible protein phosphorylation. The phosphorylation state of proteins during mitosis and other phases of the cell cycle represents a careful balance of activity between kinases and opposing phosphatases. The phosphoprotein phosphatase (PPP) family is responsible for the majority of serine and threonine dephosphorylation. Members of the PPP family are composed of a catalytic subunit paired with a regulatory subunit that targets them towards specific substrates.

The most abundant PPP, PPP2A, paired with its regulatory B55 subunit, is thought to be the phosphatase responsible for the dephosphorylation of substrates during mitotic exit. Despite …

Chemistry And Biochemistry Affiliated Publications: Snapshot Of The Research Publications 2019-2024., Jeremy J. Smith, Lutishoor Salisbury

University Libraries Faculty Publications and Presentations

This report highlights the chemistry and biochemistry faculty publications for the period 2019-2024. It includes tables identifying the types of publications, the characteristics of the authors, inter-departmental and external cooperation, summary of the citations of the publications, and the JCR ranking of the journals in which they published.

Detection Method For Escherichia Coli Using Real-Time Polymerase Chain Reaction Targeting The Yhav Gene, Muktiningsih Nurjayadi, Anisa Fitriyanti, Royna Rahma Musie, Gusti Angieta Putri, Puan Aqila Azizah, Helzi Angelina, Grace Grace, Ananda Indah Putri Sihombing, Agus Setiawan, Jefferson Lynford Declan, Gladys Indira Putri, Dandy Akbar Juliansyah, Siti Fatimah, Ayu Berkahingrum, Irma Ratna Kartika, Fera Kurniadewi, Vira Saamia, Shyi-Tien Chen, Bassam Aboemolak, Hesham Ali El Enshasy

Makara Journal of Science

Escherichia coli is a foodborne pathogenic bacterium that can cause diarrhea, while yhaV is a virulence-associated gene linked to the toxin–antitoxin system in E. coli. This study was aimed at evaluating the confirmation, specificity, and sensitivity of a yhaV gene primer using real-time polymerase chain reaction. The yhaV-targeting PCR successfully amplified a DNA fragment with an amplicon length of 207 bp (base pairs) under an annealing temperature optimized to a range of 54 °C to 62 °C via gradient PCR. The PCR using the primer pair produced a consistent Ct (cycle threshold) of 14.14 ± 0.05 and showed …

Fish Oil And Vernonia Amygdalina Leaves-Supplemented Biscuits Increased Insulin Secretion And Suppressed Pro-Inflammatory Cytokines In Type 2 Diabetic Wistar Rats, Omolola Soji-Omoniwa, Uthman Olanrewaju Abdulazeez, Christfavour Oluwaseyi Oloba, Samuel Olajuwon Kolawole, Johnson Opeyemi Olayinka, Emmanuel Olorunleke Oludipe, Anuoluwapo Faith Ajediti, Habib Tajudeen Yusuf

Al-Bahir

This research determined the effect of fish oil and Vernonia amygdalina-enriched biscuits (FVSB) on insulin sensitivity and inflammatory cytokines in type 2 diabetic rats. Forty-nine male rats were grouped into seven, i.e. A-G. Type 2 diabetes (T2DM) was induced in groups B-G by administering 230 mg/kg body weight [BW] NAD (ip) and 65 mg/kg BW streptozotocin (ip). Group A represented the control (Non-diabetic + unsupplemented biscuit), B (untreated diabetic), C (diabetic + 120 mg/kg BW metformin), D-F (diabetic + FVSB at 1g, 2g and 3g leaf inclusion respectively), and G (diabetic + conventional biscuit). The experiment lasted 35 days, …

Interleukin-6 (Il-6) Mediated Pathways In Nonalcoholic Fatty Liver Disease (Nafld) And Its Implications On Magnesium And Zinc Mineral Deficiencies: A Scoping Review, Marianne Koleng, Leann Nguyen

Department of Nutrition Student Projects

The prevalence and incidence of Non-Alcoholic Fatty Liver Disease (NAFLD) is rising. In the United States alone, the prevalence of NAFLD is currently 38% and there has been a 50% increase over the last three decades. The present study investigated the role of ultratrace mineral deficiencies, specifically magnesium (Mg) and zinc (Zn), and if so, what nutritional interventions could be made to ameliorate or protect against the development of NAFLD. The role of trace and ultratrace minerals in pro-inflammatory cytokine pathways contributing to NAFLD, specifically Interleukin-6 (IL-6), were investigated. IL-6 is produced by hepatocytes and plays a crucial role in …

Investigating The Role Of Chaperones And Sequestrases In Misfolded Protein Sequestration, Sarah Rose Rolli

Dissertations (1934 -)

Protein homeostasis, or proteostasis, is responsible for a folded and functional proteome and is essential for cell survival. Proteins can misfold during stress or because of mutation. The accumulation of misfolded proteins is observed in many diseases, including Huntington’s disease. Misfolded proteins will clump together into inclusions, which can be sequestered to membrane-less compartments by proteostasis mechanisms. Several proteins, including chaperones, co-chaperones, and other proteins, have been identified as sequestrases that target inclusions and misfolded proteins to different protein quality control (PQC) compartments. The juxtanuclear quality control (JUNQ) compartment forms in the nucleus-vacuole junction in yeast cells, and several soluble …

From Venom To Medicine: Harnessing Animal Toxins For Drug Discovery, Christine Vega, Ying Jia

Research Colloquium

Background: Drug development research has long focused on synthesizing novel therapeutics while overlooking isolation from naturally available sources such as animal venoms. Recently, the discovery of the therapeutic effects of highly bioavailable animal venom caused the field of venom research to soar in popularity. Animal venom serves as a natural, sophisticated tool optimized over millions of years by evolution with the ability to bind to ion channels such as nAChRs, non-specific ligand-gated ion channels distributed throughout the human nervous system. However, purifying individual venom toxins from crude venom is challenging due to its availability. Therefore, synthesizing large quantities of venom …

Structural Analysis Of Pseudomonas Phage Dev Virion-Associated Rna Polymerase (Gp71), James Scherer

All ETDs from UAB

DEV is a Pseudomonas aeruginosa bacteriophage part of a newly reclassified genus called Schitoviridae. This group of bacteriophages is also referred to as “N4-like” phages, after the prototypical Escherichia coli phage N4, originally isolated from sewage water in 19661. N4, and other phages in the group, contain a large, virion-associated RNA polymerase (vRNAP). This vRNAP is vital to the proliferation of the phage, as it performs the transcription of the early gene products and potentially acts as a motor that helps eject the viral genome into the host bacteria. In DEV, the vRNAP is also known as gene product 71 …

Resolution Of Physics And Deep Learning-Based Protein Engineering Filters: A Case Study With A Lipase For Industrial Substrate Hydrolysis, Spencer Gardiner, Peter Dollinger, Filip Kovacic, Jörge Pietruszka, Daniel Ess, Karl-Erich Jaeger, Gunnar F. Schröder, Dennis Della Corte

Faculty Publications

Computational enzyme design remains a powerful yet imperfect tool for optimizing biocatalysts, especially when targeting non-natural substrates. Using design tools we investigated Pseudomonas aeruginosa LipA, a lipase with a flexible lid domain crucial for substrate binding and turnover, aiming to enhance its hydrolysis of the industrially relevant substrate Roche ester. We generated an initial set of single-point mutations based on structural proximity to the active site and evaluated their effects using a computational pipeline integrating molecular dynamics (MD) simulations, density functional theory (DFT) calculations, and ensemble-based energy scoring. While we identified several active variants, attempts to rank them by activity …

Binding Of A [2fe-2s] Cluster Drives Dimerization Of Ferric Uptake Regulator (Fur) In Escherichia Coli, Fatemeh Najafi, Aidan G. Purcell, Finbar H. Homes, Huangen Ding

Faculty Publications

The ferric uptake regulator (Fur) is a global transcription factor that reversibly binds an iron-sulfur [2Fe-2S] cluster via the cysteine residues (site 3) in response to elevation of intracellular free Fe content in Escherichia coli. Here, we report that when E. coli Fur is expressed in E. coli cells grown in M9 medium supplemented with Fe or zinc (Zn), purified Fur binds a [2Fe-2S] cluster or Zn(II), respectively. While apo-form Fur is a monomer and has no DNA-binding activity, both the [2Fe-2S] cluster-bound Fur and the Zn(II)-bound Fur are homodimers and have a similar binding activity for the DNA sequence …

Analysis Of Telomeric Conformational Dynamics At The Single Molecule Level, Arianna Lacen

All ETDs from UAB

In eukaryotes, the telomere serves as a safeguard against DNA damage and loss during replication and other events. To do so, telomeric DNA folds into a variety of protective secondary and tertiary structures whose formation and conformational dynamics have not been well characterized. We have identified a slow conformational rearrangement in telomeric single stranded DNA that results in a G-Quadruplex (G4) that cannot be unfolded by a complementary strand. We have also determined how the accessibility of G4 forming sequences changes in response to different high K+ environments, which may have implications on how the nascent telomeric overhang interacts with …

Virulence Factors And Their Binding Partners: A Biochemical Study, Morgan E. Blake

All ETDs from UAB

Virulence factors are an important mechanism by which viruses combat the host immune system, therefore a thorough understanding of the workings of these proteins will be of significant value in prevention of disease associated with viral infections. In this dissertation we investigate the main virulence factors of two viruses, the Influenza A Virus (IAV) and SARS-CoV-2, and their interactions with host proteins, providing critical information for structure-based drug design. In chapter one we studied the nonstructural protein 1 (NS1) of IAV and its interaction with the 30-kda subunit of the cleavage and polyadenylation specificity factor (CPSF30) to inhibit host cell …

Structural And Functional Investigation Of The Influenza Nuclear Export Protein, Andrew James Staup

All ETDs from UAB

The influenza A nuclear export protein (NEP) is a multi-functional protein that mediates the export of progeny viral ribonucleoprotein (vRNP) complexes from the host nucleus, regulates the activity of the RNA-dependent RNA polymerase (RdRp), and is implicated in zoonosis. It is therefore critical to understand the mechanisms of NEP’s functions at the molecular level to inform its roles in the viral lifecycle and influenza zoonosis. In this dissertation, we report the structure of NEP in complex with the host nuclear export holo-complex as well as investigate the biophysical effects of the adaptive M16I mutation on NEP. We solved the cryo-electron …

The Effects Of Tfeα And Promoter Sequence On Early Events In Archaeal Transcription Initiation, Madolyn Toli

Dissertations and Theses

Expression of genes is dependent on promoter sequences in DNA, which direct transcription by RNA polymerase. Transcription factors interact with promoters and RNAP and are often conserved and are essential for proper gene expression. In this thesis, a functional region of archaeal TFEα, homologous to eukaryotic TFIIEα, has been identified, and specific amino acids in these regions have been determined to have significant importance in TFEα's ability to promote transcription in early initiation. All three Domains of life encode a 16S rRNA promoter, which is responsible for production of the 16S portion of ribosome. Transcription with this promoter is not …

Stayin' Alive (Even Without Oxygen): Retinal Development In Austrofundulus Limnaeus, Carmen Zecilia Rodriguez

Dissertations and Theses

The vertebrate eye is one of the most metabolically active organs in the body and is particularly sensitive to environmental stressors such as oxygen deprivation. Understanding how eye development proceeds under such conditions can provide critical insights into mechanisms of cellular resilience, tissue organization, and developmental plasticity. The annual killifish Austrofundulus limnaeus represents a unique model for investigating these processes due to its remarkable tolerance to anoxia during embryogenesis. However, the wild-type form is heavily pigmented, limiting the effectiveness of traditional imaging techniques for studying eye development. This thesis characterizes eye development and anoxia resilience in both wild-type and melanin-deficient …

Data From: Nek4 Suppresses Cell Proliferation In Bt20 Triple-Negative Breast Cancer Cells By Diminishing Expression Of Cell Cycle Genes, While Its Depletion Mitigates Proliferation In Other Cell Lines, Amanda Ashley

Chemistry & Biochemistry: Datasets

No abstract provided.

The Next Frontier In The Study Of Noncovalent Bonding: Transition Metals, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

As work continues unabated in the study of noncovalent bonding, particularly σ-hole bonds, new challenges have emerged as the participation of transition metals in interactions of this sort is fast becoming appreciated. While there are certain similarities with the halogen, chalcogen, etc, bonds, in which the main group elements participate, there are certain unique properties of these metal atoms that must be analyzed before a complete understanding can be attained. As one example, these atoms tend to act simultaneously as both electron donors and acceptors, a synergistic action that amplifies the overall bond strength. Ideas are expressed in this paper …

Analysis Of Antibody Affinity Maturation And Thermal Stability Of Proteins Using Photophysical Approaches, Claire Baxter

Dissertations

Engineered antibodies (Abs) have found applications in disparate fields such as enzyme catalysis and medicinal therapeutics because of their exquisite binding affinity and specificity. To engineer antibodies for these purposes, a firm understanding of the underlying mechanisms that control Ab affinity and specificity is needed, so these properties can be tightly controlled and adapted to the application at hand. My research characterized the binding site of the anti-fluorescein Ab 4-4-20 using an array of biophysical techniques and gives insight into the binding site interactions that give rise to both affinity and specificity. We utilized Fab fragments of the anti-fluorescein Ab …

Development Of Single Droplet Interface-Specific Sum Frequency Scattering Spectroscopy, Yi Rao

Funded Research Records

No abstract provided.