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Structural And Functional Characterization Of Hyper-Phosphorylated Grk5 Protein Expressed From E. Coli, Joseph M. Krampen, John Tesmer, Qiuyan Chen 2018 Purdue University

Structural And Functional Characterization Of Hyper-Phosphorylated Grk5 Protein Expressed From E. Coli, Joseph M. Krampen, John Tesmer, Qiuyan Chen

The Summer Undergraduate Research Fellowship (SURF) Symposium

G protein-coupled receptor (GPCR) kinases (GRKs) are proteins in the cell responsible for regulating GPCRs located on the cell membrane. GRKs regulate active GPCRs by phosphorylating them at certain sites which causes them to stop normal signaling on the membrane. This ultimately affects how the cell responds to its environment. GRK5 is a kinase of particular interest due to its involvement in the pathology of diseases such as cardiac failure, cancers, and diabetes. Understanding the structure and function of GRK5 is essential for discovering ways to manipulate its behavior with these diseases, but not much is known about how GRK5 ...


Structural Characterization Of The Dep Domains Of P-Rex1, Samantha R. Allgood, John J.G. Tesmer, Sandeep K. Ravala 2018 Purdue University

Structural Characterization Of The Dep Domains Of P-Rex1, Samantha R. Allgood, John J.G. Tesmer, Sandeep K. Ravala

The Summer Undergraduate Research Fellowship (SURF) Symposium

P-Rex1 is a guanine nucleotide exchange factor for Rho-GTPases, which is indirectly involved in the regulation of cell migration and proliferation. It contains a tandem DH/PH domain archetypal of the Dbl family of GEFs, two DEP and two PDZ domains, and a C-terminal end with weak homology to inositol polyphosphate 4-phosphatase. P-Rex1 is regulated by both intra-domain interactions and interactions with other proteins such as G-protein beta gamma, PKA and phosphatidylinositol (3,4,5)-trisphosphate. Upregulation of P-Rex1 has been found in multiple human cancers, making it a potential target for anti-cancer drug therapies. Therefore, structural characterization of P-Rex1 ...


Crystal Structure Of The Catalytic Domain Of Hiv-1 Restriction Factor Apobec3g In Complex With Ssdna, Atanu Maiti, Wazo Myint, Tapan Kanai, Krista Delviks-Frankenberry, Christina Sierra Rodriguez, Vinay K. Pathak, Celia A. Schiffer, Hiroshi Matsuo 2018 Frederick National Laboratory for Cancer Research

Crystal Structure Of The Catalytic Domain Of Hiv-1 Restriction Factor Apobec3g In Complex With Ssdna, Atanu Maiti, Wazo Myint, Tapan Kanai, Krista Delviks-Frankenberry, Christina Sierra Rodriguez, Vinay K. Pathak, Celia A. Schiffer, Hiroshi Matsuo

Open Access Articles

The human APOBEC3G protein is a cytidine deaminase that generates cytidine to deoxy-uridine mutations in single-stranded DNA (ssDNA), and capable of restricting replication of HIV-1 by generating mutations in viral genome. The mechanism by which APOBEC3G specifically deaminates 5'-CC motifs has remained elusive since structural studies have been hampered due to apparently weak ssDNA binding of the catalytic domain of APOBEC3G. We overcame the problem by generating a highly active variant with higher ssDNA affinity. Here, we present the crystal structure of this variant complexed with a ssDNA substrate at 1.86 A resolution. This structure reveals atomic-level interactions ...


Identification And Folding Of Mirna Through Machine Learning, Xavier Pellow 2018 John Monash Science School

Identification And Folding Of Mirna Through Machine Learning, Xavier Pellow

The International Student Science Fair 2018

As of writing, there is currently no efficient way to accurately identify miRNA or predict the structure of miRNA without the usage of a lab. The purpose of this work is to provide a framework which allows for efficient identification of mature miRNA and folding of pre-miRNA using a feedforward neural network (FFNN) and probabilistic context-free grammar (PCFG) parsing, respectively. After training, the FFNN developed an accuracy of 98%. Out of all control cases using high confidence miRNA, the PCFG used returned folded structures that matched the canonical structures to an accuracy of 81%. The results of this work indicates ...


Synergistic Assembly Of Human Pre-Spliceosomes Across Introns And Exons, Joerg E. Braun, Larry J. Friedman, Jeff Gelles, Melissa J. Moore 2018 University of Massachusetts Medical School

Synergistic Assembly Of Human Pre-Spliceosomes Across Introns And Exons, Joerg E. Braun, Larry J. Friedman, Jeff Gelles, Melissa J. Moore

RNA Therapeutics Institute Publications

Most human genes contain multiple introns, necessitating mechanisms to effectively define exons and ensure their proper connection by spliceosomes. Human spliceosome assembly involves both cross-intron and cross-exon interactions, but how these work together is unclear. We examined in human nuclear extracts dynamic interactions of single pre-mRNA molecules with individual fluorescently tagged spliceosomal subcomplexes to investigate how cross-intron and cross-exon processes jointly promote pre-spliceosome assembly. U1 subcomplex bound to the 5' splice site of an intron acts jointly with U1 bound to the 5' splice site of the next intron to dramatically increase the rate and efficiency by which U2 subcomplex ...


Dynamics Of Human Protein Kinase Aurora A Linked To Drug Selectivity, Warintra Pitsawong, Vanessa Buosi, Renee Otten, Roman V. Agafonov, Adelajda Zorba, Nadja Kern, Steffen Kutter, Gunther Kern, Ricardo Ap Padua, Xavier Meniche, Dorothee Kern 2018 Brandeis University

Dynamics Of Human Protein Kinase Aurora A Linked To Drug Selectivity, Warintra Pitsawong, Vanessa Buosi, Renee Otten, Roman V. Agafonov, Adelajda Zorba, Nadja Kern, Steffen Kutter, Gunther Kern, Ricardo Ap Padua, Xavier Meniche, Dorothee Kern

Open Access Articles

Protein kinases are major drug targets, but the development of highly-selective inhibitors has been challenging due to the similarity of their active sites. The observation of distinct structural states of the fully-conserved Asp-Phe-Gly (DFG) loop has put the concept of conformational selection for the DFG-state at the center of kinase drug discovery. Recently, it was shown that Gleevec selectivity for the Tyr-kinase Abl was instead rooted in conformational changes after drug binding. Here, we investigate whether protein dynamics after binding is a more general paradigm for drug selectivity by characterizing the binding of several approved drugs to the Ser/Thr-kinase ...


Disruption Of Tblpn Expression In T. Brucei By Rna Interference, Matthew Serbonich 2018 The College at Brockport

Disruption Of Tblpn Expression In T. Brucei By Rna Interference, Matthew Serbonich

Senior Honors Theses

Trypanosoma brucei, the causative agent of human African trypanosomiasis, also known as African sleeping sickness, expresses a protein known as TbLpn which plays a critical role in arginine methylation and phospholipid synthesis within T. brucei. In order to determine the effect and potential medical benefits of downregulated TbLpn expression in T. brucei, RNA interference was used by transfecting T. brucei with plasmid DNA through electroporation. After conducting this experimental protocol, T. brucei was unable to be grown successfully in media following transfection and the effect of downregulated TbLpn in T. brucei requires further investigation in order to determine its potential ...


Substrate Sequence Selectivity Of Apobec3a Implicates Intra-Dna Interactions, Tania V. Silvas, Shurong Hou, Wazo Myint, Ellen A. Nalivaika, Mohan Somasundaran, Brian A. Kelch, Hiroshi Matsuo, Nese Kurt Yilmaz, Celia A. Schiffer 2018 University of Massachusetts Medical School

Substrate Sequence Selectivity Of Apobec3a Implicates Intra-Dna Interactions, Tania V. Silvas, Shurong Hou, Wazo Myint, Ellen A. Nalivaika, Mohan Somasundaran, Brian A. Kelch, Hiroshi Matsuo, Nese Kurt Yilmaz, Celia A. Schiffer

Open Access Articles

The APOBEC3 (A3) family of human cytidine deaminases is renowned for providing a first line of defense against many exogenous and endogenous retroviruses. However, the ability of these proteins to deaminate deoxycytidines in ssDNA makes A3s a double-edged sword. When overexpressed, A3s can mutate endogenous genomic DNA resulting in a variety of cancers. Although the sequence context for mutating DNA varies among A3s, the mechanism for substrate sequence specificity is not well understood. To characterize substrate specificity of A3A, a systematic approach was used to quantify the affinity for substrate as a function of sequence context, length, secondary structure, and ...


Investigation Into The Amino Acid Characteristic Of Intrinsically Disordered Proteins, Samantha Patterson 2018 University of Wyoming

Investigation Into The Amino Acid Characteristic Of Intrinsically Disordered Proteins, Samantha Patterson

Honors Theses AY 17/18

Caulobacter crescentus, which belongs to the class of Alphaproteobacteria, has a highly organized cytoplasm that includes complex macromolecular structures at the cell poles. These polar complexes are assembled through the activity of a scaffolding protein, known as the Polar Organizing Protein Z (PopZ). PopZ interacts with other proteins via an N-terminal domain that is mostly intrinsically disordered, and contains, an abundance of proline, glutamte, and aspartate (P,E, and D) residues. Surprisingly, scrambling the order of amino acids in the PED region does not affect PopZ function, suggesting that binding affinity and specificity are not dependent on interactions with individual ...


Structure Determination Of A Bioengineered Human/Porcine Factor Viii For Hemophilia A Treatment, And Improvements To The Human Factor Viii Model, Ian Smith 2018 Western Washington University

Structure Determination Of A Bioengineered Human/Porcine Factor Viii For Hemophilia A Treatment, And Improvements To The Human Factor Viii Model, Ian Smith

Graduate Student Symposium

Blood coagulation factor VIII (FVIII), is a non-enzymatic cofactor which plays a crucial role in the formation of a stable blood clot. Absence or deficiency of FVIII results in the blood disorder hemophilia A; with symptoms including internal hemorrhaging and the inability to stop bleeding from open wounds. Treatment of hemophilia A relies on infusions of blood, plasma, or protein concentrates to replace FVIII. Unfortunately, approximately 30% of patients receiving replacement FVIII generate pathologic anti-FVIII inhibitory antibodies, which both reduce the effectiveness of the FVIII therapeutic and increase the severity of hemophilia A symptoms. We have determined the molecular structure ...


Ph Sensitivity Of Connexin 50 Hemichannels: H95 And Beyond, Leah Volk 2018 State University of New York College at Buffalo - Buffalo State College

Ph Sensitivity Of Connexin 50 Hemichannels: H95 And Beyond, Leah Volk

Biology Theses

Gap junction channels formed by connexin proteins are critical for the health and function of the vertebrate lens. It is important to understand how these channels are affected by pH because a pH gradient exists in lens tissue. Intracellular pH (pHi) is a regulator of gap junction coupling, and different connexins show different sensitivities to pHi. A “Particle-Receptor” model for pH-dependent channel closure involves the intramolecular interaction between the cytoplasmic tail of the connexin and a region near the mouth of the channel dependent on a highly conserved histidine residue at position 95. While this model explains the ...


Diversity, Structure And Sources Of Bacterial Communities In Earthworm Cocoons., Manuel Aira, Marcos Pérez-Losada, Jorge Domínguez 2018 George Washington University

Diversity, Structure And Sources Of Bacterial Communities In Earthworm Cocoons., Manuel Aira, Marcos Pérez-Losada, Jorge Domínguez

Computational Biology Institute

Animals start interactions with the bacteria that will constitute their microbiomes at embryonic stage. After mating, earthworms produce cocoons externally which will be colonized with bacteria from their parents and the environment. Due to the key role bacterial symbionts play on earthworm fitness, it is important to study bacterial colonization during cocoon formation. Here we describe the cocoon microbiome of the earthworms Eisenia andrei and E. fetida, which included 275 and 176 bacterial species, respectively. They were dominated by three vertically-transmitted symbionts, Microbacteriaceae, Verminephrobacter and Ca. Nephrothrix, which accounted for 88% and 66% of the sequences respectively. Verminephrobacter and Ca ...


Glucocorticoids Modulate Gastrointestinal Microbiome In A Wild Bird., José C Noguera, Manuel Aira, Marcos Pérez-Losada, Jorge Domínguez, Alberto Velando 2018 George Washington University

Glucocorticoids Modulate Gastrointestinal Microbiome In A Wild Bird., José C Noguera, Manuel Aira, Marcos Pérez-Losada, Jorge Domínguez, Alberto Velando

Computational Biology Institute

It has recently been hypothesized that stress exposure (e.g. via glucocorticoid secretion) may dysregulate the bacterial gut microbiome, a crucial 'organ' in animal health. However, whether stress exposure (e.g. via glucocorticoid secretion) affects the bacterial gut microbiome of natural populations is unknown. We have experimentally altered the basal glucocorticoid level (corticosterone implants) in a wild avian species, the yellow-legged gull


Ras Hyperactivation Versus Overexpression: Lessons From Ras Dynamics In Candida Albicans, Vavilala A. Pratyusha, Guiliana Soraya Victoria, Mohammad Firoz Khan, Dominic T. Haokip, Bhawna Yadav, Nibedita Pal, Subhash Chandra Sethi, Priyanka Jain, Sneh Lata Singh, Sobhan Sen, Sneha Sudha Komath 2018 Jawaharlal Nehru University

Ras Hyperactivation Versus Overexpression: Lessons From Ras Dynamics In Candida Albicans, Vavilala A. Pratyusha, Guiliana Soraya Victoria, Mohammad Firoz Khan, Dominic T. Haokip, Bhawna Yadav, Nibedita Pal, Subhash Chandra Sethi, Priyanka Jain, Sneh Lata Singh, Sobhan Sen, Sneha Sudha Komath

Open Access Articles

Ras signaling in response to environmental cues is critical for cellular morphogenesis in eukaryotes. This signaling is tightly regulated and its activation involves multiple players. Sometimes Ras signaling may be hyperactivated. In C. albicans, a human pathogenic fungus, we demonstrate that dynamics of hyperactivated Ras1 (Ras1G13V or Ras1 in Hsp90 deficient strains) can be reliably differentiated from that of normal Ras1 at (near) single molecule level using fluorescence correlation spectroscopy (FCS). Ras1 hyperactivation results in significantly slower dynamics due to actin polymerization. Activating actin polymerization by jasplakinolide can produce hyperactivated Ras1 dynamics. In a sterol-deficient hyperfilamentous GPI mutant of C ...


Dynamics Of Human Protein Kinases Linked To Drug Selectivity, Dorothee Kern, Warintra Pitsawong, Brandeis University, Renee Otten, Roman V. Agafonov, Adelajda Zorba, Nadja Kern, Steffen Kutter, Gunther Kern, Ricardo A.P. Pádua, Xavier Meniche 2018 Brandeis University

Dynamics Of Human Protein Kinases Linked To Drug Selectivity, Dorothee Kern, Warintra Pitsawong, Brandeis University, Renee Otten, Roman V. Agafonov, Adelajda Zorba, Nadja Kern, Steffen Kutter, Gunther Kern, Ricardo A.P. Pádua, Xavier Meniche

University of Massachusetts Medical School Faculty Publications

Protein kinases are major drug targets, but the development of highly-selective inhibitors has been challenging due to the similarity of their active sites. The observation of distinct structural states of the fully-conserved Asp-Phe-Gly (DFG) loop has put the concept of conformational selection for the DFG-state at the center of kinase drug discovery. Recently, it was shown that Gleevec selectivity for the Tyr-kinases Abl was instead rooted in conformational changes after drug binding. Here, we investigate whether protein dynamics after binding is a more general paradigm for drug selectivity by characterizing the binding of several approved drugs to the Ser/Thr-kinase ...


Killi-Data News (Winter), Tyrone Genade 2018 Northwestern College, Iowa

Killi-Data News (Winter), Tyrone Genade

Killifish Research Review

Valued readers, it is with a heavy heart that I inform you that this is the last issue of Killi-Data News. The good news is that we will be back as Killifish Research Review. The dissolution of Killi-Data International created a prob- lem: how can the newsletter of a defunct organization live on without that organization? But other additional problems were building in the background. The first issue numbered 15 pages. The previous issue was 28 pages. The number of killifish related papers is increasing while time on our end (the editorial team) is running out. It takes a lot ...


Killi-Data News (Fall), Tyrone Genade 2018 Northwestern College, Iowa

Killi-Data News (Fall), Tyrone Genade

Killifish Research Review

Many interesting papers have been published over the last three months. The large volume of papers coupled with the start of the new college semester (and the workload it brings) delayed this issue of Killi-Data News. But better late than never—or so I hope! In this issue Richard van der Laan provides an insightful review of the recent Aphanius papers as to their taxonomic implications and questions. The systematic issues he raises show the importance of the Molecular project: we need to get more samples of the various cyprinodontiforme families to resolve unsettled systematic and taxonomic issues. In the ...


Killi-Data News (Summer), Tyrone Genade 2018 Northwestern College, Iowa

Killi-Data News (Summer), Tyrone Genade

Killifish Research Review

Over the last three months several interesting and exciting pa- pers have been published. By now most of you have heard the Nothobranchius fish poo news emanating from the Valenzano lab. That paper is reviewed and certainly has repercussions for the health of our captive fish. Polaçik et al have published interesting data with ramifications as to how we breed and incubate annual killifish. The big news in this issue is the paper from the Reznick lab which Jean Huber reviews. The contents of that paper goes to the heart of the question of just what a killifish is. The ...


Killi-Data News (Spring), Tyrone Genade 2018 Northwestern College, Iowa

Killi-Data News (Spring), Tyrone Genade

Killifish Research Review

This is the start of Killi-Data News’ second year. In this first issue of the year we have the usual review of research pub- lications as well as input from Martin Reichard on his lab’s Nothobranchius research. Martin is responding to my reviews of his lab’s work in the previous edition. I am serious about making sure the content in this newsletter is reliable but I erred in the previous edition and Martin has written extensively to correct my mistake in the section “Erratum”. This reply is welcomed and owed to readers. I must confess that I don ...


Killi-Data News (Winter), Tyrone Genade 2018 Northwestern College, Iowa

Killi-Data News (Winter), Tyrone Genade

Killifish Research Review

This is the fourth edition, and concluding issue of the first volume, of Killi-Data News and I am happy that it has been well received by readers. At 25 pages this issue is a bit thin- ner than the last but this is because we agreed to make the cut-off for submissions the 1 st of December so we could get this edition out by the New Year. This is an exciting edition full of new species descrip- tions and analyses that will keep taxonomists busy for years to come. Costa has given us two molecular phylogenies on Melanorivulus as ...


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