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613 results on '"Kozbial A"'

1. Optimized detection modality for double resonance alignment based optical magnetometer

Author

Akbar, A., Kozbiál, M., Elson, L., Meraki, A., Kolodyński, J., and Jensen, K.

Subjects
Physics - Optics, Physics - Atomic Physics
Abstract

In this work, we present a comprehensive and comparative analysis of two detection modalities, i.e., polarization rotation and absorption measurement of light, for a double resonance alignment based optical magnetometer (DRAM). We derive algebraic expressions for magnetometry signals based on multipole moments description. Experiments are carried out using a room-temperature paraffin-coated Caesium vapour cell and measuring either the polarization rotation or absorption of the transmitted laser light. A detailed experimental analysis of the resonance spectra is performed to validate the theoretical findings for various input parameters. The results signify the use of a single isotropic relaxation rate thus simplifying the data analysis for optimization of the DRAM. The sensitivity measurements are performed and reveal that the polarization rotation detection mode yields larger signals and better sensitivity than absorption measurement of light., Comment: 14 pages, 10 figures

Published
2024

2. Spin noise spectroscopy of an alignment-based atomic magnetometer

Author

Kozbial, Marcin, Elson, Lucy, Rushton, Lucas M., Akbar, Ali, Meraki, Adil, Jensen, Kasper, and Kolodynski, Jan

Subjects
Physics - Atomic Physics, Quantum Physics
Abstract

Optically pumped magnetometers (OPMs) are revolutionising the task of magnetic-field sensing due to their extremely high sensitivity combined with technological improvements in miniaturisation which have led to compact and portable devices. OPMs can be based on spin-oriented or spin-aligned atomic ensembles which are spin-polarized through optical pumping with circular or linear polarized light, respectively. Characterisation of OPMs and the dynamical properties of their noise is important for applications in real-time sensing tasks. In our work, we experimentally perform spin noise spectroscopy of an alignment-based magnetometer. Moreover, we propose a stochastic model that predicts the noise power spectra exhibited by the device when, apart from the strong magnetic field responsible for the Larmor precession of the spin, white noise is applied in the perpendicular direction aligned with the pumping-probing beam. By varying the strength of the noise applied as well as the linear-polarisation angle of incoming light, we verify the model to accurately predict the heights of the Larmor-induced spectral peaks and their corresponding line-widths. Our work paves the way for alignment-based magnetometers to become operational in real-time sensing tasks., Comment: 16 pages, 7 figures, published version

Published
2023
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3. Zero-field optical magnetometer based on spin-alignment

Author

Meraki, Adil, Elson, Lucy, Ho, Nok, Akbar, Ali, Koźbiał, Marcin, Kołodyński, Jan, and Jensen, Kasper

Subjects
Physics - Applied Physics, Physics - Atomic Physics, Quantum Physics
Abstract

Optically-pumped magnetometers are an important instrument for imaging biological magnetic signals without the need for cryogenic cooling. These magnetometers are presently available in the commercial market and utilize the principles of atomic alignment or orientation, enabling remarkable sensitivity and precision in the measurement of magnetic fields. This research focuses on utilizing a spin-aligned atomic ensemble for magnetometry at zero-field. A novel approach is introduced, which involves evaluating how the linear polarization of light rotates as it passes through the atomic vapor to null the magnetic field. Analytical expressions are derived for the resulting spin alignment and photodetection signals. Experimental results are provided, demonstrating good agreement with the theoretical predictions. The sensitivity and bandwidth of the magnetometer are characterized based on the detected polarization rotation signal. Lastly, the practical utility of the magnetometer for medical applications is demonstrated by successfully detecting a synthetic cardiac signal., Comment: Main text is 11 pages and 7 figures, and the supplementary is 6 pages and 2 figures

Published
2023
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5. Assessment of Baseline Ultrawidefield Fluorescein Angiographic Quantitative Leakage Parameters with Ultrawidefield Fundus Features and Clinical Parameters in Diabetic Retinopathy in Protocol AA

Author

Harara, Abla M., Palacios, Angela N., Berger, Brian B., Corak, Boris, Luong, Bianca, Jhaveri, Chirag D., Wilson, Daniela Mariel, Jonna, Gowtham, Gunderson, Ivana, Hosein, Kimberly, Reid, Ryan M., Chexal, Saradha, Moore, Tori, Seidu, Tina A., Gatavaski, Valerie, Ren, Yong, Stern, Bradley A., Benvenutti, Celia E., Oude-Reimerink, Dinah S., Shaheen, Jenny, Grybas, John, Vitale-Kuhn, Julianne, Staffne, Jessica L., Ventimiglia, Katie M., Allis, Megan, Monk, Mary K., Thomas, Marc E., Massu, Nicole M., Edwards, Paul Andrew, Troszak, Tracy A., Irons, Amber N., Rego, Brittany, Han, Dennis P., Dorsey, Eleanor, Nelson, Erika, Sheppard, Hannah, Beringer, Joseph R., Kim, Judy E., Keller, Kristy L., Packard, Krissa L., Altmann, Marriner L., Goldberg, Mara, Chen, Nickolas, Winter, Pat A., Bourgeois, Shay, Jacobo, Samantha, Moebius, Stephanie J., Connor, Thomas B., Barwick, Vicki, Williams, Vesper V., Wirostko, William J., Ghuman, A. Thomas, Leslie, Anita H., Sharma, Ashish G., Kiesel, Cheryl, Dyshanowitz, Danielle, Knips, Eileen, Wing, Glenn, Walker, Joseph P., Raskauskas, Paul A., Kiesel, Raymond K., Schlossman, Deborah K., Weimann, Elizabeth S., Sharuk, George S., Kwak, Hanna, Cavallerano, Jerry D., Rhee, Jae W., Sampani, Konstantina, Tran, Katie V., Bestourous, Leila, Miranda, Linette, Krigman, Michael N., Stockman, Margaret E., Arrigg, Paul G., Cavicchi, Robert W., Kirby, Rita K., Glynn, Shireen, Papaconstantinou, Steve L., Shah, Sabera T., Murtha, Timothy J., Carli, William, Finch, Autumn K., Gentile, Angella K., Price, Angela K., Murphy, Brittany A., Rowland, Beverly O., Fleming, Christina J., Mahr, Courtney, Shore, Carol A., Browning, David, McClain, Donna, Breglio, Erica, Lester, Gina M., Herby, Jenna T., Bratcher, Kayla A., Clark, Loraine M., Jackson, Lisa A., Watson, Lynn, McOwen, Michael D., Punjabi, Omar S., Bojaj, Swann J., Ennis, Sarah A., Fredenberg, Sherry L., Jones, Taylor S., Ragin, Teneisha A., Balasubramaniam, Uma M., Ornelas, Blanca, Rodriquez, Brenda, Edwards, Carla, Carns, Danielle R., Tonner, Eileen E., Woo, Kisung, Richine, Len, MacCumber, Mathew W., Merrill, Pauline Townsend, Kociborski, Sarah, Harless, Ashley M., Harris, Charlotte, White, Lorraine, Maturi, Raj K., Asher, Julie, Walsh, Justin, Wheeler, Jeff, Milstead, Katie, Oliver, Kristina, Lovelady, Lisa, Anderson, Nicholas G., Coppola, Patricia, Lince, Raul E., Shuler, R. Keith, Morris, Steve, Oelrich, Sarah M., Gardner, Brandon S., Moore, Bob, Cain, Dennis, Donohue, Deborah, Emmert, David, Adeyemo, Kemi, Levin, Lisa K., Frey, Mary, Rhoton, Nick, Bressler, Susan, Solomon, Sharon D., Ford, Amy L., Hughes, Ashley, Brewer, Alisha N., Booth, JoAnn T., Lunsford, Keven W., Ukleya, Lauren D., Burris, Russ, Kingsley, Ronald M., Almeida, Shannon R., Icks, Sonny, Shah, Vinay A., Bergman, Vanessa A., Castellarin, Alessandro A., Shook, Aimee H., Walker, Aimee, Pieramici, Dante J., Hong, Gina, Avery, Kelly, McKee, Kate M., Giust, Matthew, Munoz, Marco A., Fishbein, Sarah, Camp, Alecia B., Baker, Carl W., Baker, Jil D., Sedberry, Kylie S., Lambert, Lynnette F., Orr, Margaret J., Alcaraz, Sonya L., Kettler, Samantha, Caldwell, Tracey M., Miller, Abigail, Dorr, Christine M., Hampton, G. Robert, Brown, Jamin S., Barker, Jeffrey P., Rosenberg, Kevin I., Kwasniewski, Lynn M., Sienkiewycz, Laurie J., Spuches, Lisa, Manley, Michelle L., Robarge, Nicole E., DeSantis, Stefanie R., DeForge, Teresa M., Brucker, Alexander J., Kim, Benjamin J., Berger, Jim M., DuPont, Joan C., Drossner, Sheri, Freeman, Sara, Studebaker, Ashley, Payne, John F., Wells, John A., Spivey, Robbin, Ogbuewu, Tiffany N., Swinford, Tiffany R., Guillory, Adrienne, Hutson, Amy, Schefler, Amy C., Shah, Ankoor R., Almanza, Belinda A., Dives, Brenda, Richter, Beau A., Stoever, Cary A., Brown, David M., Foerster, Danee, Garcia, David, Rodriguez, Diana, Park, Daniel, Chen, Eric, Kegley, Eric N., Quellar, Elizabeth, Twining, Garret L., Koger-Grifaldo, Heather, Ortega, Ilsa, Carranza, Jolene, Major, James C., Williamson, Kimberly, Burt, Lindsay, Salinas, Luis R., Wolff, Lisa M., Benz, Matthew S., Estes, Maura A., James, Miranda F., Berry, Meredith, Vela, Melina, Landaverde, Nubia, Webb, Nina A., Fish, Richard H., Kim, Rosa Y., Yee, Rebecca, Karani, Sadia Y., Supapo, Stacy M., Dodel, Tamara L., McCoy, Tyneisha, Wong, Tien P., Sneed, Veronica A., Barnhart, Cassandra J., Cantrell, Debra, DuBose, Elizabeth L., Sharpe, Houston P., Ulrich, Jan Niklas, Bhansali, Kanika A., Esquejo, Rona Lyn, Garg, Seema, Grout, Sean, McKinney, Allen, Bobbitt, Brenda J., Wendel, Ceara L., Fagan, Damanda F., Andrews, Jacqueline, Holmes, Krystal Nikki, Seyez, Karen L., Williamson, Kimberly A., Moinfar, Nader, Walters, Paige N., Carlton, Steve, Rehling, Shannon M., Williams, Shana E., Reed, Tiara L., VandeVelde, Amber R., Yeager, Frank T., Fox, Gregory M., Batlle, Ivan R., Bruce, Kiersten, Pippin, Katherine, Ainley, Lexie R., Singh, Ravi S.J., Adamo, Ashley M., Guardado, Adrian, Patel, Apurva K., Puckett, Brian S., Hoerner, Christine, Ma, Colin, Clark, David J., Flato, Inessa M., Cohen, Joshua, Charpentier, Margaret E., Kopfer, Marcia, Peters, Mark A., Smith, Pualani, Tlucek, Paul S., Hobbs, Stephen, Ho, Stephanie L., Metzger, Ashley M., McCalla, Alesia K., Thompson, Amy, Ringrose, Christine, Sandler, Dallas R., Leder, Henry A., Belz, Jennifer L., Starr, JoAnn, Simmons, Jennifer L., Orr, Peggy R., Sotirakos, Peter, Singletary, Pamela V., Cain, Terri, Coffey, Teresa, Carter, Tiffany M., Robinson, Twyla J., Shah, Chirag P., Cammarata, Dominique, Kruger, Jennifer L., Colegrove, Lindsey, Graham, Margie, Gleason, Shane T., Noel, Bryan, Damron, Catherine, Holcomb, Diana M., Slade, Edward A., Van Arsdall, Jeanne, Bicknell, Lisa, Buck, Michelle, Stone, Thomas W., Farooq, Amina, Parsons, Brook, Singh, Harinderjit, Ivey, Ken, Foster, Lindsay Allison, Woodward, Michele, Ortiz, Siobhan O., Bailey, Thomas, Mynampati A, Bharani Krishna, White, Cheryl L., Hamdani, Ghulam Shabbir, Smith, Jazzmin N., Chalam, Kakarla V., Sambhav, Kumar, Babaria, Romesh, Grover, Sandeep, Carroll, Catherine, Chau, Felix Y., Lim, Jennifer I., Talasnik, Lauren A., Janowicz, Mark, Stankovic, Natasa, Berlatsky, Sarah L., Niec, Marcia, Sun, Jie, Johnson, Tametha, Ovando, Yesenia, Nakoski, Brenda, Mein, Calvin E., Wienecke, Christopher Sean, Castillo, Elaine, Baker, Jaynee, San Roman, Jonathan, Adams, Lydia, Kirschbaum, Lita, Chica, Moises A., Cloudt, Sara L., Moore, Tori R., Sabates, Felix N., Gallimore, Gary S., Chen, Yin C., Swann, Adrienne C., Cadwell, Deborah M., Diddie, Kenneth R., Boisvert, Taryn F., Tessau, Carrie D., Bowers, Jack, Nielsen, Jared S., Rostvold, Jay, Spillman, Jamie, Alliman, Kyle J., Boender, Lisa M., Johnson, Marilyn A., Parker, Marianne, Bix, Paula L., Ridgway, Spencer D., Woehl, Tami Jo, Stonewall, Whitney, Brown, Christopher M., Lema, Gareth M.C., Wiechelt, Luann, Yoganathan, Pradeepa, Boglione, Sandra L., Montesclaros, Chris A., Mangham, Cory, Karsaliya, Gopal, Le, Phillip V., Wong, Robert W., Godfrey, Anne Marie, Kuzmanovic, Aleksandra, Kirker, Andrew William, Harrison, Bryan, Forooghian, Farzin, Elvena, Garnet Louise, Hall, Laura J., Turhal, Bilgin, Brown, Ian, Kotei, Isaac A., Chen, Lina, Brent, Michael Henry, Moon, Michelle, Sutakovic, Olivera, Chang, Angela, Godfrey, Anne-Marie, Albiani, David, Maberley, David A.L., Navajas, Eduardo Vitor, Grant, Kelly, Tran, Khoi A., Jovanovic, Mira, Cao, Sijia, Wiens, Theresa, Kozbial, Andrzej, Orlin, Anton, Lenane, Courtney Nichole, Herder, Susan P., Kiss, Szilard, Reeves, Tom, Cruess, Alan F., Dean, Andrea, Hoskin-Mott, Ann, Morrison, Christine, Caldwell, Meggie D., Hynes, Mitzi, Gupta, R. Rishi, Durling, Stacey, MacDonnell, Trina, Beck, Roy W., Baptista, Alyssa, Beaulieu, Wesley T., Calhoun, Claire T., Constantine, Sharon R., Correia, Isabella, Dale, Brian B., Dupre, Simone S., Franklin, Crystal A., Galusic, Sandra, Huggins, Meagan, Hunter, Brenda L., Johnson, Paula A., Josic, Kristin, Kelly, Brittany, Maguire, Maureen G., Meadows, Britney, Stockdale, Cynthia R., Zokruah, Alice, Bhargava, Sangeeta, Barkmeier, Andrew J., Baskin, Darrell, Blodi, Barbra, Chew, Emily, Ferris, Frederick L., Jaffe, Glenn J., Bressler, Neil M., Lujan, Brandon, Tolls, Dorothy, Sheridan, Daniel, Pitoc, Cloyd M., Anne C Aquino, Lizzie, Salva, Claude Michael G., Lewis, Drew, Stainback, Jeffery, Makkena, Vijaya, Winter, Katrina, Mora, Adiel, Harrington, Chris, Vinh, Doc-Lap, Ehlers, Justis P., Yordi, Sari, Martin, Alison, Srivastava, Sunil K., and Sun, Jenifer K.

Published
2024
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7. Heterologous vector versus homologous mRNA COVID-19 booster vaccination in non-seroconverted immunosuppressed patients: a randomized controlled trial

Author

Daniel Mrak, Daniela Sieghart, Elisabeth Simader, Selma Tobudic, Helga Radner, Peter Mandl, Lisa Göschl, Maximilian Koblischke, Nikolaus Hommer, Angelika Wagner, Margareta Mayer, Lorenz Schubert, Lukas Hartl, Karin Kozbial, Philipp Hofer, Felix Kartnig, Thomas Hummel, Andreas Kerschbaumer, Thomas Deimel, Antonia Puchner, Venugopal Gudipati, Renate Thalhammer, Petra Munda, Keziban Uyanik-Ünal, Andreas Zuckermann, Gottfried Novacek, Thomas Reiberger, Erika Garner-Spitzer, Roman Reindl-Schwaighofer, Renate Kain, Stefan Winkler, Josef S. Smolen, Karin Stiasny, Gottfried F. Fischer, Thomas Perkmann, Helmuth Haslacher, Markus Zeitlinger, Ursula Wiedermann, Judith H. Aberle, Daniel Aletaha, Leonhard X. Heinz, and Michael Bonelli

Subjects
Science
Abstract

Optimizing COVID-19 vaccination strategies for patients under immunosuppressive medication is of high importance. In this clinical trial including non-seroconverted immunosuppressed patients, a homologous mRNA booster vaccination resulted in higher seroconversion rate than a switch to a vector-based vaccine.

Published
2022
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9. Heterologous vector versus homologous mRNA COVID-19 booster vaccination in non-seroconverted immunosuppressed patients: a randomized controlled trial

Author

Mrak, Daniel, Sieghart, Daniela, Simader, Elisabeth, Tobudic, Selma, Radner, Helga, Mandl, Peter, Göschl, Lisa, Koblischke, Maximilian, Hommer, Nikolaus, Wagner, Angelika, Mayer, Margareta, Schubert, Lorenz, Hartl, Lukas, Kozbial, Karin, Hofer, Philipp, Kartnig, Felix, Hummel, Thomas, Kerschbaumer, Andreas, Deimel, Thomas, Puchner, Antonia, Gudipati, Venugopal, Thalhammer, Renate, Munda, Petra, Uyanik-Ünal, Keziban, Zuckermann, Andreas, Novacek, Gottfried, Reiberger, Thomas, Garner-Spitzer, Erika, Reindl-Schwaighofer, Roman, Kain, Renate, Winkler, Stefan, Smolen, Josef S., Stiasny, Karin, Fischer, Gottfried F., Perkmann, Thomas, Haslacher, Helmuth, Zeitlinger, Markus, Wiedermann, Ursula, Aberle, Judith H., Aletaha, Daniel, Heinz, Leonhard X., and Bonelli, Michael

Published
2022
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10. WSTĘP

Author

Koźbiał, Krzysztof and Natanek, Mirosław

Published
2020

11. Collection, Analysis and Summarization of Video Content

Author

Koźbiał, Arian, Leszczuk, Mikołaj, Kacprzyk, Janusz, Series Editor, Pal, Nikhil R., Advisory Editor, Bello Perez, Rafael, Advisory Editor, Corchado, Emilio S., Advisory Editor, Hagras, Hani, Advisory Editor, Kóczy, László T., Advisory Editor, Kreinovich, Vladik, Advisory Editor, Lin, Chin-Teng, Advisory Editor, Lu, Jie, Advisory Editor, Melin, Patricia, Advisory Editor, Nedjah, Nadia, Advisory Editor, Nguyen, Ngoc Thanh, Advisory Editor, Wang, Jun, Advisory Editor, Choroś, Kazimierz, editor, Kopel, Marek, editor, Kukla, Elżbieta, editor, and Siemiński, Andrzej, editor

Published
2019
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12. A First Summarization System of a Video in a Target Language

Author

Smaïli, Kamel, Fohr, Dominique, González-Gallardo, Carlos-Emiliano, Grega, Michał, Janowski, Lucjan, Jouvet, Denis, Komorowski, Artur, Koźbiał, Arian, Langlois, David, Leszczuk, Mikołaj, Mella, Odile, Menacer, Mohamed A., Mendez, Amaia, Linhares Pontes, Elvys, SanJuan, Eric, Świst, Damian, Torres-Moreno, Juan-Manuel, Garcia-Zapirain, Begona, Kacprzyk, Janusz, Series Editor, Pal, Nikhil R., Advisory Editor, Bello Perez, Rafael, Advisory Editor, Corchado, Emilio S., Advisory Editor, Hagras, Hani, Advisory Editor, Kóczy, László T., Advisory Editor, Kreinovich, Vladik, Advisory Editor, Lin, Chin-Teng, Advisory Editor, Lu, Jie, Advisory Editor, Melin, Patricia, Advisory Editor, Nedjah, Nadia, Advisory Editor, Nguyen, Ngoc Thanh, Advisory Editor, Wang, Jun, Advisory Editor, Choroś, Kazimierz, editor, Kopel, Marek, editor, Kukla, Elżbieta, editor, and Siemiński, Andrzej, editor

Published
2019
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15. Ligand-Dependent Enhancer Activation Regulated by Topoisomerase-I Activity

Author

Puc, Janusz, Kozbial, Piotr, Li, Wenbo, Tan, Yuliang, Liu, Zhijie, Suter, Tom, Ohgi, Kenneth A, Zhang, Jie, Aggarwal, Aneel K, and Rosenfeld, Michael G

Subjects
Biochemistry and Cell Biology, Biomedical and Clinical Sciences, Biological Sciences, Genetics, Cancer, Rare Diseases, 1.1 Normal biological development and functioning, Underpinning research, Cell Line, Tumor, DNA Breaks, Single-Stranded, DNA Repair, DNA Topoisomerases, Type I, DNA-Binding Proteins, Enhancer Elements, Genetic, Gene Expression Regulation, Gene Knockdown Techniques, Homeodomain Proteins, Humans, MRE11 Homologue Protein, Receptors, Androgen, Transcription Factors, Transcription, Genetic, Medical and Health Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences
Abstract

The discovery that enhancers are regulated transcription units, encoding eRNAs, has raised new questions about the mechanisms of their activation. Here, we report an unexpected molecular mechanism that underlies ligand-dependent enhancer activation, based on DNA nicking to relieve torsional stress from eRNA synthesis. Using dihydrotestosterone (DHT)-induced binding of androgen receptor (AR) to prostate cancer cell enhancers as a model, we show rapid recruitment, within minutes, of DNA topoisomerase I (TOP1) to a large cohort of AR-regulated enhancers. Furthermore, we show that the DNA nicking activity of TOP1 is a prerequisite for robust eRNA synthesis and enhancer activation and is kinetically accompanied by the recruitment of ATR and the MRN complex, followed by additional components of DNA damage repair machinery to the AR-regulated enhancers. Together, our studies reveal a linkage between eRNA synthesis and ligand-dependent TOP1-mediated nicking-a strategy exerting quantitative effects on eRNA expression in regulating AR-bound enhancer-dependent transcriptional programs.

Published
2015

17. A First Summarization System of a Video in a Target Language.

Author

Kamel Smaïli, Dominique Fohr, Carlos-Emiliano González-Gallardo, Michal Grega, Lucjan Janowski, Denis Jouvet, Artur Komorowski, Arian Kozbial, David Langlois, Mikolaj Leszczuk, Odile Mella, Mohamed Amine Menacer, Amaia Méndez, Elvys Linhares Pontes, Eric SanJuan, Damian Swist, Juan-Manuel Torres-Moreno, and Begoña García Zapirain

Published
2018
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21. Video Summarization Framework for Newscasts and Reports – Work in Progress

Author

Leszczuk, Mikołaj, Grega, Michał, Koźbiał, Arian, Gliwski, Jarosław, Wasieczko, Krzysztof, Smaïli, Kamel, Barbosa, Simone Diniz Junqueira, Series editor, Chen, Phoebe, Series editor, Filipe, Joaquim, Series editor, Kotenko, Igor, Series editor, Sivalingam, Krishna M., Series editor, Washio, Takashi, Series editor, Yuan, Junsong, Series editor, Zhou, Lizhu, Series editor, Dziech, Andrzej, editor, and Czyżewski, Andrzej, editor

Published
2017
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24. The crystal structure of a bacterial Sufu‐like protein defines a novel group of bacterial proteins that are similar to the N‐terminal domain of human Sufu

Author

Das, Debanu, Finn, Robert D, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Bakolitsa, Constantina, Cai, Xiaohui, Carlton, Dennis, Chen, Connie, Chiu, Hsiu‐Ju, Chiu, Michelle, Clayton, Thomas, Deller, Marc C, Duan, Lian, Ellrott, Kyle, Farr, Carol L, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Anna, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Krishna, S Sri, Kumar, Abhinav, Lam, Winnie W, Marciano, David, Miller, Mitchell D, Morse, Andrew T, Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Puckett, Christina, Reyes, Ron, Tien, Henry J, Trame, Christine B, van den Bedem, Henry, Weekes, Dana, Wooten, Tiffany, Xu, Qingping, Yeh, Andrew, Zhou, Jiadong, Hodgson, Keith O, Wooley, John, Elsliger, Marc‐André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A

Subjects
Biochemistry and Cell Biology, Biological Sciences, 1.1 Normal biological development and functioning, Underpinning research, Aetiology, 2.2 Factors relating to the physical environment, Amino Acid Sequence, Bacterial Proteins, Crystallography, Humans, Models, Molecular, Molecular Sequence Annotation, Molecular Sequence Data, Neisseria gonorrhoeae, Protein Structure, Tertiary, Repressor Proteins, Reproducibility of Results, Sequence Alignment, Sequence Analysis, Protein, Sequence Homology, Amino Acid, Static Electricity, Structural Homology, Protein, NGO1391, UniProt Q5F6Z8, Pfam PF05076, suppressor of fused, sufu-like, structural genomics, Computation Theory and Mathematics, Other Information and Computing Sciences, Biophysics, Biochemistry and cell biology, Medicinal and biomolecular chemistry
Abstract

Sufu (Suppressor of Fused), a two-domain protein, plays a critical role in regulating Hedgehog signaling and is conserved from flies to humans. A few bacterial Sufu-like proteins have previously been identified based on sequence similarity to the N-terminal domain of eukaryotic Sufu proteins, but none have been structurally or biochemically characterized and their function in bacteria is unknown. We have determined the crystal structure of a more distantly related Sufu-like homolog, NGO1391 from Neisseria gonorrhoeae, at 1.4 Å resolution, which provides the first biophysical characterization of a bacterial Sufu-like protein. The structure revealed a striking similarity to the N-terminal domain of human Sufu (r.m.s.d. of 2.6 Å over 93% of the NGO1391 protein), despite an extremely low sequence identity of ∼15%. Subsequent sequence analysis revealed that NGO1391 defines a new subset of smaller, Sufu-like proteins that are present in ∼200 bacterial species and has resulted in expansion of the SUFU (PF05076) family in Pfam.

Published
2010

25. The structure of Jann_2411 (DUF1470) from Jannaschia sp. at 1.45 Å resolution reveals a new fold (the ABATE domain) and suggests its possible role as a transcription regulator

Author

Bakolitsa, Constantina, Bateman, Alex, Jin, Kevin K, McMullan, Daniel, Krishna, S Sri, Miller, Mitchell D, Abdubek, Polat, Acosta, Claire, Astakhova, Tamara, Axelrod, Herbert L, Burra, Prasad, Carlton, Dennis, Chiu, Hsiu-Ju, Clayton, Thomas, Das, Debanu, Deller, Marc C, Duan, Lian, Elias, Ylva, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Anna, Grzechnik, Slawomir K, Han, Gye Won, Jaroszewski, Lukasz, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Kumar, Abhinav, Marciano, David, Morse, Andrew T, Murphy, Kevin D, Nigoghossian, Edward, Okach, Linda, Oommachen, Silvya, Paulsen, Jessica, Reyes, Ron, Rife, Christopher L, Sefcovic, Natasha, Tien, Henry, Trame, Christine B, Trout, Christina V, van den Bedem, Henry, Weekes, Dana, White, Aprilfawn, Xu, Qingping, Hodgson, Keith O, Wooley, John, Elsliger, Marc-André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott, and Wilson, Ian A

Subjects
Genetics, Underpinning research, 1.1 Normal biological development and functioning, 2.1 Biological and endogenous factors, Aetiology, Generic health relevance, Amino Acid Sequence, Bacterial Proteins, Crystallography, X-Ray, Models, Molecular, Molecular Sequence Data, Protein Structure, Quaternary, Protein Structure, Tertiary, Rhodobacteraceae, Sequence Alignment, Zinc Fingers, Chemical Sciences, Biological Sciences, Biophysics
Abstract

The crystal structure of Jann_2411 from Jannaschia sp. strain CCS1, a member of the Pfam PF07336 family classified as a domain of unknown function (DUF1470), was solved to a resolution of 1.45 Å by multiple-wavelength anomalous dispersion (MAD). This protein is the first structural representative of the DUF1470 Pfam family. Structural analysis revealed a two-domain organization, with the N-terminal domain presenting a new fold called the ABATE domain that may bind an as yet unknown ligand. The C-terminal domain forms a treble-clef zinc finger that is likely to be involved in DNA binding. Analysis of the Jann_2411 protein and the broader ABATE-domain family suggests a role as stress-induced transcriptional regulators.

Published
2010

26. Structures of the first representatives of Pfam family PF06684 (DUF1185) reveal a novel variant of the Bacillus chorismate mutase fold and suggest a role in amino‐acid metabolism

Author

Bakolitsa, Constantina, Kumar, Abhinav, Jin, Kevin K, McMullan, Daniel, Krishna, S Sri, Miller, Mitchell D, Abdubek, Polat, Acosta, Claire, Astakhova, Tamara, Axelrod, Herbert L, Burra, Prasad, Carlton, Dennis, Chen, Connie, Chiu, Hsiu-Ju, Clayton, Thomas, Das, Debanu, Deller, Marc C, Duan, Lian, Elias, Ylva, Ellrott, Kyle, Ernst, Dustin, Farr, Carol L, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Anna, Grzechnik, Slawomir K, Han, Gye Won, Jaroszewski, Lukasz, Johnson, Hope A, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Marciano, David, Morse, Andrew T, Murphy, Kevin D, Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Paulsen, Jessica, Puckett, Christina, Reyes, Ron, Rife, Christopher L, Sefcovic, Natasha, Tien, Henry J, Trame, Christine B, Trout, Christina V, van den Bedem, Henry, Weekes, Dana, White, Aprilfawn, Xu, Qingping, Hodgson, Keith O, Wooley, John, Elsliger, Marc-Andre, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A

Subjects
Biochemistry and Cell Biology, Bioinformatics and Computational Biology, Biological Sciences, Genetics, 2.1 Biological and endogenous factors, Aetiology, Generic health relevance, Amino Acid Sequence, Amino Acids, Bacillus, Bordetella bronchiseptica, Chorismate Mutase, Crystallography, X-Ray, Models, Molecular, Molecular Sequence Data, Protein Folding, Protein Structure, Quaternary, Protein Structure, Tertiary, Rhodobacteraceae, Structural Homology, Protein, Chemical Sciences, Biophysics, Biological sciences, Chemical sciences
Abstract

The crystal structures of BB2672 and SPO0826 were determined to resolutions of 1.7 and 2.1 Å by single-wavelength anomalous dispersion and multiple-wavelength anomalous dispersion, respectively, using the semi-automated high-throughput pipeline of the Joint Center for Structural Genomics (JCSG) as part of the NIGMS Protein Structure Initiative (PSI). These proteins are the first structural representatives of the PF06684 (DUF1185) Pfam family. Structural analysis revealed that both structures adopt a variant of the Bacillus chorismate mutase fold (BCM). The biological unit of both proteins is a hexamer and analysis of homologs indicates that the oligomer interface residues are highly conserved. The conformation of the critical regions for oligomerization appears to be dependent on pH or salt concentration, suggesting that this protein might be subject to environmental regulation. Structural similarities to BCM and genome-context analysis suggest a function in amino-acid synthesis.

Published
2010

27. Conformational changes associated with the binding of zinc acetate at the putative active site of XcTcmJ, a cupin from Xanthomonas campestris pv. campestris

Author

Axelrod, Herbert L, Kozbial, Piotr, McMullan, Daniel, Krishna, S Sri, Miller, Mitchell D, Abdubek, Polat, Acosta, Claire, Astakhova, Tamara, Carlton, Dennis, Caruthers, Jonathan, Chiu, Hsiu-Ju, Clayton, Thomas, Deller, Marc C, Duan, Lian, Elias, Ylva, Feuerhelm, Julie, Grzechnik, Slawomir K, Grant, Joanna C, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kumar, Abhinav, Marciano, David, Morse, Andrew T, Murphy, Kevin D, Nigoghossian, Edward, Okach, Linda, Oommachen, Silvya, Paulsen, Jessica, Reyes, Ron, Rife, Christopher L, Tien, Henry J, Trout, Christina V, van den Bedem, Henry, Weekes, Dana, White, Aprilfawn, Xu, Qingping, Zubieta, Chloe, Hodgson, Keith O, Wooley, John, Elsliger, Marc-André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A

Subjects
1.1 Normal biological development and functioning, Underpinning research, Amino Acid Sequence, Bacterial Proteins, Catalytic Domain, Conserved Sequence, Crystallography, X-Ray, Models, Molecular, Molecular Sequence Data, Protein Interaction Domains and Motifs, Sequence Alignment, Structural Homology, Protein, Xanthomonas campestris, Zinc Acetate, Chemical Sciences, Biological Sciences, Biophysics
Abstract

In the plant pathogen Xanthomonas campestris pv. campestris, the product of the tcmJ gene, XcTcmJ, encodes a protein belonging to the RmlC family of cupins. XcTcmJ was crystallized in a monoclinic space group (C2) in the presence of zinc acetate and the structure was determined to 1.6 Å resolution. Previously, the apo structure has been reported in the absence of any bound metal ion [Chin et al. (2006), Proteins, 65, 1046-1050]. The most significant difference between the apo structure and the structure of XcTcmJ described here is a reorganization of the binding site for zinc acetate, which was most likely acquired from the crystallization solution. This site is located in the conserved metal ion-binding domain at the putative active site of XcTcmJ. In addition, an acetate was also bound within coordination distance of the zinc. In order to accommodate this binding, rearrangement of a conserved histidine ligand is required as well as several nearby residues within and around the putative active site. These observations indicate that binding of zinc serves a functional role in this cupin protein.

Published
2010

28. The structure of the first representative of Pfam family PF06475 reveals a new fold with possible involvement in glycolipid metabolism

Author

Bakolitsa, Constantina, Kumar, Abhinav, McMullan, Daniel, Krishna, S Sri, Miller, Mitchell D, Carlton, Dennis, Najmanovich, Rafael, Abdubek, Polat, Astakhova, Tamara, Chiu, Hsiu-Ju, Clayton, Thomas, Deller, Marc C, Duan, Lian, Elias, Ylva, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Slawomir K, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Marciano, David, Morse, Andrew T, Nigoghossian, Edward, Okach, Linda, Oommachen, Silvya, Paulsen, Jessica, Reyes, Ron, Rife, Christopher L, Trout, Christina V, van den Bedem, Henry, Weekes, Dana, White, Aprilfawn, Xu, Qingping, Hodgson, Keith O, Wooley, John, Elsliger, Marc-André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A

Subjects
2.2 Factors relating to the physical environment, Aetiology, 2.1 Biological and endogenous factors, Amino Acid Sequence, Bacterial Proteins, Crystallography, X-Ray, Genome, Bacterial, Glycolipids, Models, Molecular, Molecular Sequence Data, Protein Folding, Protein Structure, Quaternary, Protein Structure, Tertiary, Pseudomonas aeruginosa, Chemical Sciences, Biological Sciences, Biophysics
Abstract

The crystal structure of PA1994 from Pseudomonas aeruginosa, a member of the Pfam PF06475 family classified as a domain of unknown function (DUF1089), reveals a novel fold comprising a 15-stranded β-sheet wrapped around a single α-helix that assembles into a tight dimeric arrangement. The remote structural similarity to lipoprotein localization factors, in addition to the presence of an acidic pocket that is conserved in DUF1089 homologs, phospholipid-binding and sugar-binding proteins, indicate a role for PA1994 and the DUF1089 family in glycolipid metabolism. Genome-context analysis lends further support to the involvement of this family of proteins in glycolipid metabolism and indicates possible activation of DUF1089 homologs under conditions of bacterial cell-wall stress or host-pathogen interactions.

Published
2010

29. Structure of a putative NTP pyrophosphohydrolase: YP_001813558.1 from Exiguobacterium sibiricum 255‐15

Author

Han, Gye Won, Elsliger, Marc-André, Yeates, Todd O, Xu, Qingping, Murzin, Alexey G, Krishna, S Sri, Jaroszewski, Lukasz, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Carlton, Dennis, Chen, Connie, Chiu, Hsiu-Ju, Clayton, Thomas, Das, Debanu, Deller, Marc C, Duan, Lian, Ernst, Dustin, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Anna, Jin, Kevin K, Johnson, Hope A, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Kumar, Abhinav, Lam, Winnie W, Marciano, David, McMullan, Daniel, Miller, Mitchell D, Morse, Andrew T, Nigoghossian, Edward, Okach, Linda, Reyes, Ron, Rife, Christopher L, Sefcovic, Natasha, Tien, Henry J, Trame, Christine B, van den Bedem, Henry, Weekes, Dana, Hodgson, Keith O, Wooley, John, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A

Subjects
Prevention, 1.1 Normal biological development and functioning, Underpinning research, Amino Acid Sequence, Bacillales, Crystallography, X-Ray, Models, Molecular, Molecular Sequence Data, Protein Multimerization, Protein Structure, Quaternary, Protein Structure, Tertiary, Pyrophosphatases, Structural Homology, Protein, Chemical Sciences, Biological Sciences, Biophysics
Abstract

The crystal structure of a putative NTPase, YP_001813558.1 from Exiguobacterium sibiricum 255-15 (PF09934, DUF2166) was determined to 1.78 Å resolution. YP_001813558.1 and its homologs (dimeric dUTPases, MazG proteins and HisE-encoded phosphoribosyl ATP pyrophosphohydrolases) form a superfamily of all-α-helical NTP pyrophosphatases. In dimeric dUTPase-like proteins, a central four-helix bundle forms the active site. However, in YP_001813558.1, an unexpected intertwined swapping of two of the helices that compose the conserved helix bundle results in a `linked dimer' that has not previously been observed for this family. Interestingly, despite this novel mode of dimerization, the metal-binding site for divalent cations, such as magnesium, that are essential for NTPase activity is still conserved. Furthermore, the active-site residues that are involved in sugar binding of the NTPs are also conserved when compared with other α-helical NTPases, but those that recognize the nucleotide bases are not conserved, suggesting a different substrate specificity.

Published
2010

30. Structure of a membrane‐attack complex/perforin (MACPF) family protein from the human gut symbiont Bacteroides thetaiotaomicron

Author

Xu, Qingping, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Bakolitsa, Constantina, Cai, Xiaohui, Carlton, Dennis, Chen, Connie, Chiu, Hsiu-Ju, Clayton, Thomas, Das, Debanu, Deller, Marc C, Duan, Lian, Ellrott, Kyle, Farr, Carol L, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Anna, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Krishna, S Sri, Kumar, Abhinav, Lam, Winnie W, Marciano, David, Miller, Mitchell D, Morse, Andrew T, Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Puckett, Christina, Reyes, Ron, Tien, Henry J, Trame, Christine B, van den Bedem, Henry, Weekes, Dana, Wooten, Tiffany, Yeh, Andrew, Zhou, Jiadong, Hodgson, Keith O, Wooley, John, Elsliger, Marc-André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A

Subjects
Genetics, Aetiology, 1.1 Normal biological development and functioning, 2.2 Factors relating to the physical environment, Underpinning research, Infection, Amino Acid Sequence, Bacterial Proteins, Bacteroides, Crystallography, X-Ray, Models, Molecular, Molecular Sequence Data, Perforin, Protein Structure, Tertiary, Sequence Alignment, Structural Homology, Protein, Chemical Sciences, Biological Sciences, Biophysics
Abstract

Membrane-attack complex/perforin (MACPF) proteins are transmembrane pore-forming proteins that are important in both human immunity and the virulence of pathogens. Bacterial MACPFs are found in diverse bacterial species, including most human gut-associated Bacteroides species. The crystal structure of a bacterial MACPF-domain-containing protein BT_3439 (Bth-MACPF) from B. thetaiotaomicron, a predominant member of the mammalian intestinal microbiota, has been determined. Bth-MACPF contains a membrane-attack complex/perforin (MACPF) domain and two novel C-terminal domains that resemble ribonuclease H and interleukin 8, respectively. The entire protein adopts a flat crescent shape, characteristic of other MACPF proteins, that may be important for oligomerization. This Bth-MACPF structure provides new features and insights not observed in two previous MACPF structures. Genomic context analysis infers that Bth-MACPF may be involved in a novel protein-transport or nutrient-uptake system, suggesting an important role for these MACPF proteins, which were likely to have been inherited from eukaryotes via horizontal gene transfer, in the adaptation of commensal bacteria to the host environment.

Published
2010

31. Structures of three members of Pfam PF02663 (FmdE) implicated in microbial methanogenesis reveal a conserved α+β core domain and an auxiliary C‐terminal treble‐clef zinc finger

Author

Axelrod, Herbert L, Das, Debanu, Abdubek, Polat, Astakhova, Tamara, Bakolitsa, Constantina, Carlton, Dennis, Chen, Connie, Chiu, Hsiu-Ju, Clayton, Thomas, Deller, Marc C, Duan, Lian, Ellrott, Kyle, Farr, Carol L, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Anna, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Krishna, S Sri, Kumar, Abhinav, Lam, Winnie W, Marciano, David, McMullan, Daniel, Miller, Mitchell D, Morse, Andrew T, Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Puckett, Christina, Reyes, Ron, Sefcovic, Natasha, Tien, Henry J, Trame, Christine B, van den Bedem, Henry, Weekes, Dana, Wooten, Tiffany, Xu, Qingping, Hodgson, Keith O, Wooley, John, Elsliger, Marc-André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A

Subjects
Biochemistry and Cell Biology, Biological Sciences, Genetics, Rare Diseases, Aldehyde Oxidoreductases, Amino Acid Sequence, Crystallography, X-Ray, Desulfitobacterium, Methane, Models, Molecular, Molecular Sequence Data, Protein Structure, Secondary, Protein Structure, Tertiary, Structural Homology, Protein, Zinc Fingers, Chemical Sciences, Biophysics, Biological sciences, Chemical sciences
Abstract

Examination of the genomic context for members of the FmdE Pfam family (PF02663), such as the protein encoded by the fmdE gene from the methanogenic archaeon Methanobacterium thermoautotrophicum, indicates that 13 of them are co-transcribed with genes encoding subunits of molybdenum formylmethanofuran dehydrogenase (EC 1.2.99.5), an enzyme that is involved in microbial methane production. Here, the first crystal structures from PF02663 are described, representing two bacterial and one archaeal species: B8FYU2_DESHY from the anaerobic dehalogenating bacterium Desulfitobacterium hafniense DCB-2, Q2LQ23_SYNAS from the syntrophic bacterium Syntrophus aciditrophicus SB and Q9HJ63_THEAC from the thermoacidophilic archaeon Thermoplasma acidophilum. Two of these proteins, Q9HJ63_THEAC and Q2LQ23_SYNAS, contain two domains: an N-terminal thioredoxin-like α+β core domain (NTD) consisting of a five-stranded, mixed β-sheet flanked by several α-helices and a C-terminal zinc-finger domain (CTD). B8FYU2_DESHY, on the other hand, is composed solely of the NTD. The CTD of Q9HJ63_THEAC and Q2LQ23_SYNAS is best characterized as a treble-clef zinc finger. Two significant structural differences between Q9HJ63_THEAC and Q2LQ23_SYNAS involve their metal binding. First, zinc is bound to the putative active site on the NTD of Q9HJ63_THEAC, but is absent from the NTD of Q2LQ23_SYNAS. Second, whereas the structure of the CTD of Q2LQ23_SYNAS shows four Cys side chains within coordination distance of the Zn atom, the structure of Q9HJ63_THEAC is atypical for a treble-cleft zinc finger in that three Cys side chains and an Asp side chain are within coordination distance of the zinc.

Published
2010

32. Structure of the γ‐d‐glutamyl‐l‐diamino acid endopeptidase YkfC from Bacillus cereus in complex with l‐Ala‐γ‐d‐Glu: insights into substrate recognition by NlpC/P60 cysteine peptidases

Author

Xu, Qingping, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Bakolitsa, Constantina, Cai, Xiaohui, Carlton, Dennis, Chen, Connie, Chiu, Hsiu-Ju, Chiu, Michelle, Clayton, Thomas, Das, Debanu, Deller, Marc C, Duan, Lian, Ellrott, Kyle, Farr, Carol L, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Anna, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Krishna, S Sri, Kumar, Abhinav, Lam, Winnie W, Marciano, David, Miller, Mitchell D, Morse, Andrew T, Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Puckett, Christina, Reyes, Ron, Tien, Henry J, Trame, Christine B, van den Bedem, Henry, Weekes, Dana, Wooten, Tiffany, Yeh, Andrew, Hodgson, Keith O, Wooley, John, Elsliger, Marc-André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A

Subjects
Biochemistry and Cell Biology, Biological Sciences, Infectious Diseases, Amino Acid Sequence, Bacillus cereus, Crystallography, X-Ray, Cysteine Proteases, Endopeptidases, Genome, Bacterial, Models, Molecular, Molecular Sequence Data, Protein Binding, Protein Structure, Tertiary, Sequence Alignment, Structural Homology, Protein, Substrate Specificity, Chemical Sciences, Biophysics, Biological sciences, Chemical sciences
Abstract

Dipeptidyl-peptidase VI from Bacillus sphaericus and YkfC from Bacillus subtilis have both previously been characterized as highly specific γ-D-glutamyl-L-diamino acid endopeptidases. The crystal structure of a YkfC ortholog from Bacillus cereus (BcYkfC) at 1.8 Å resolution revealed that it contains two N-terminal bacterial SH3 (SH3b) domains in addition to the C-terminal catalytic NlpC/P60 domain that is ubiquitous in the very large family of cell-wall-related cysteine peptidases. A bound reaction product (L-Ala-γ-D-Glu) enabled the identification of conserved sequence and structural signatures for recognition of L-Ala and γ-D-Glu and, therefore, provides a clear framework for understanding the substrate specificity observed in dipeptidyl-peptidase VI, YkfC and other NlpC/P60 domains in general. The first SH3b domain plays an important role in defining substrate specificity by contributing to the formation of the active site, such that only murein peptides with a free N-terminal alanine are allowed. A conserved tyrosine in the SH3b domain of the YkfC subfamily is correlated with the presence of a conserved acidic residue in the NlpC/P60 domain and both residues interact with the free amine group of the alanine. This structural feature allows the definition of a subfamily of NlpC/P60 enzymes with the same N-terminal substrate requirements, including a previously characterized cyanobacterial L-alanine-γ-D-glutamate endopeptidase that contains the two key components (an NlpC/P60 domain attached to an SH3b domain) for assembly of a YkfC-like active site.

Published
2010

33. The structure of Haemophilus influenzae prephenate dehydrogenase suggests unique features of bifunctional TyrA enzymes

Author

Chiu, Hsiu-Ju, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Carlton, Dennis, Clayton, Thomas, Das, Debanu, Deller, Marc C, Duan, Lian, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Anna, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Krishna, S Sri, Kumar, Abhinav, Marciano, David, McMullan, Daniel, Miller, Mitchell D, Morse, Andrew T, Nigoghossian, Edward, Okach, Linda, Reyes, Ron, Tien, Henry J, Trame, Christine B, van den Bedem, Henry, Weekes, Dana, Xu, Qingping, Hodgson, Keith O, Wooley, John, Elsliger, Marc-André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A

Subjects
Underpinning research, 1.1 Normal biological development and functioning, Bacterial Proteins, Crystallography, X-Ray, Haemophilus influenzae, Multienzyme Complexes, Prephenate Dehydrogenase, Chemical Sciences, Biological Sciences, Biophysics
Abstract

Chorismate mutase/prephenate dehydrogenase from Haemophilus influenzae Rd KW20 is a bifunctional enzyme that catalyzes the rearrangement of chorismate to prephenate and the NAD(P)(+)-dependent oxidative decarboxylation of prephenate to 4-hydroxyphenylpyruvate in tyrosine biosynthesis. The crystal structure of the prephenate dehydrogenase component (HinfPDH) of the TyrA protein from H. influenzae Rd KW20 in complex with the inhibitor tyrosine and cofactor NAD(+) has been determined to 2.0 Å resolution. HinfPDH is a dimeric enzyme, with each monomer consisting of an N-terminal α/β dinucleotide-binding domain and a C-terminal α-helical dimerization domain. The structure reveals key active-site residues at the domain interface, including His200, Arg297 and Ser179 that are involved in catalysis and/or ligand binding and are highly conserved in TyrA proteins from all three kingdoms of life. Tyrosine is bound directly at the catalytic site, suggesting that it is a competitive inhibitor of HinfPDH. Comparisons with its structural homologues reveal important differences around the active site, including the absence of an α-β motif in HinfPDH that is present in other TyrA proteins, such as Synechocystis sp. arogenate dehydrogenase. Residues from this motif are involved in discrimination between NADP(+) and NAD(+). The loop between β5 and β6 in the N-terminal domain is much shorter in HinfPDH and an extra helix is present at the C-terminus. Furthermore, HinfPDH adopts a more closed conformation compared with TyrA proteins that do not have tyrosine bound. This conformational change brings the substrate, cofactor and active-site residues into close proximity for catalysis. An ionic network consisting of Arg297 (a key residue for tyrosine binding), a water molecule, Asp206 (from the loop between β5 and β6) and Arg365' (from the additional C-terminal helix of the adjacent monomer) is observed that might be involved in gating the active site.

Published
2010

34. Structure of Bacteroides thetaiotaomicron BT2081 at 2.05 Å resolution: the first structural representative of a new protein family that may play a role in carbohydrate metabolism

Author

Yeh, Andrew P, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Bakolitsa, Constantina, Cai, Xiaohui, Carlton, Dennis, Chen, Connie, Chiu, Hsiu-Ju, Chiu, Michelle, Clayton, Thomas, Das, Debanu, Deller, Marc C, Duan, Lian, Ellrott, Kyle, Farr, Carol L, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Anna, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Krishna, S Sri, Kumar, Abhinav, Lam, Winnie W, Marciano, David, McMullan, Daniel, Miller, Mitchell D, Morse, Andrew T, Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Puckett, Christina, Reyes, Ron, Tien, Henry J, Trame, Christine B, van den Bedem, Henry, Weekes, Dana, Wooten, Tiffany, Xu, Qingping, Hodgson, Keith O, Wooley, John, Elsliger, Marc-André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A

Subjects
Biochemistry and Cell Biology, Biological Sciences, 1.1 Normal biological development and functioning, Underpinning research, Amino Acid Sequence, Bacterial Proteins, Bacteroides, Binding Sites, Carbohydrate Metabolism, Carbohydrates, Crystallography, X-Ray, Models, Molecular, Molecular Sequence Data, Protein Structure, Tertiary, Sequence Alignment, Structural Homology, Protein, Chemical Sciences, Biophysics, Biological sciences, Chemical sciences
Abstract

BT2081 from Bacteroides thetaiotaomicron (GenBank accession code NP_810994.1) is a member of a novel protein family consisting of over 160 members, most of which are found in the different classes of Bacteroidetes. Genome-context analysis lends support to the involvement of this family in carbohydrate metabolism, which plays a key role in B. thetaiotaomicron as a predominant bacterial symbiont in the human distal gut microbiome. The crystal structure of BT2081 at 2.05 Å resolution represents the first structure from this new protein family. BT2081 consists of an N-terminal domain, which adopts a β-sandwich immunoglobulin-like fold, and a larger C-terminal domain with a β-sandwich jelly-roll fold. Structural analyses reveal that both domains are similar to those found in various carbohydrate-active enzymes. The C-terminal β-jelly-roll domain contains a potential carbohydrate-binding site that is highly conserved among BT2081 homologs and is situated in the same location as the carbohydrate-binding sites that are found in structurally similar glycoside hydrolases (GHs). However, in BT2081 this site is partially occluded by surrounding loops, which results in a deep solvent-accessible pocket rather than a shallower solvent-exposed cleft.

Published
2010

35. The structure of BVU2987 from Bacteroides vulgatus reveals a superfamily of bacterial periplasmic proteins with possible inhibitory function

Author

Das, Debanu, Finn, Robert D, Carlton, Dennis, Miller, Mitchell D, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Bakolitsa, Constantina, Chen, Connie, Chiu, Hsiu-Ju, Chiu, Michelle, Clayton, Thomas, Deller, Marc C, Duan, Lian, Ellrott, Kyle, Ernst, Dustin, Farr, Carol L, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Anna, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Krishna, S Sri, Kumar, Abhinav, Marciano, David, McMullan, Daniel, Morse, Andrew T, Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Puckett, Christina, Reyes, Ron, Rife, Christopher L, Sefcovic, Natasha, Tien, Henry J, Trame, Christine B, van den Bedem, Henry, Weekes, Dana, Wooten, Tiffany, Xu, Qingping, Hodgson, Keith O, Wooley, John, Elsliger, Marc-André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A

Subjects
Biochemistry and Cell Biology, Biological Sciences, Emerging Infectious Diseases, Infectious Diseases, Biodefense, Vaccine Related, Prevention, Underpinning research, 1.1 Normal biological development and functioning, Amino Acid Sequence, Bacteroides, Conserved Sequence, Crystallography, X-Ray, Models, Molecular, Molecular Sequence Data, Periplasmic Proteins, Protein Binding, Protein Structure, Tertiary, Sequence Alignment, Structural Homology, Protein, Chemical Sciences, Biophysics, Biological sciences, Chemical sciences
Abstract

Proteins that contain the DUF2874 domain constitute a new Pfam family PF11396. Members of this family have predominantly been identified in microbes found in the human gut and oral cavity. The crystal structure of one member of this family, BVU2987 from Bacteroides vulgatus, has been determined, revealing a β-lactamase inhibitor protein-like structure with a tandem repeat of domains. Sequence analysis and structural comparisons reveal that BVU2987 and other DUF2874 proteins are related to β-lactamase inhibitor protein, PepSY and SmpA_OmlA proteins and hence are likely to function as inhibitory proteins.

Published
2010

36. The structure of KPN03535 (gi|152972051), a novel putative lipoprotein from Klebsiella pneumoniae, reveals an OB‐fold

Author

Das, Debanu, Kozbial, Piotr, Han, Gye Won, Carlton, Dennis, Jaroszewski, Lukasz, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Bakolitsa, Constantina, Chen, Connie, Chiu, Hsiu-Ju, Chiu, Michelle, Clayton, Thomas, Deller, Marc C, Duan, Lian, Ellrott, Kyle, Elsliger, Marc-André, Ernst, Dustin, Farr, Carol L, Feuerhelm, Julie, Grzechnik, Anna, Grant, Joanna C, Jin, Kevin K, Johnson, Hope A, Klock, Heath E, Knuth, Mark W, Krishna, S Sri, Kumar, Abhinav, Marciano, David, McMullan, Daniel, Miller, Mitchell D, Morse, Andrew T, Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Oommachen, Silvya, Paulsen, Jessica, Puckett, Christina, Reyes, Ron, Rife, Christopher L, Sefcovic, Natasha, Tien, Henry J, Trame, Christine B, van den Bedem, Henry, Weekes, Dana, Wooten, Tiffany, Xu, Qingping, Hodgson, Keith O, Wooley, John, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A

Subjects
Biochemistry and Cell Biology, Bioinformatics and Computational Biology, Biological Sciences, Pneumonia, Hematology, Lung, Infectious Diseases, Pneumonia & Influenza, Aetiology, Underpinning research, 2.1 Biological and endogenous factors, 1.1 Normal biological development and functioning, Infection, Amino Acid Sequence, Bacterial Proteins, Crystallography, X-Ray, Klebsiella pneumoniae, Lipoproteins, Models, Molecular, Molecular Sequence Data, Protein Folding, Protein Structure, Tertiary, Chemical Sciences, Biophysics, Biological sciences, Chemical sciences
Abstract

KPN03535 (gi|152972051) is a putative lipoprotein of unknown function that is secreted by Klebsiella pneumoniae MGH 78578. The crystal structure reveals that despite a lack of any detectable sequence similarity to known structures, it is a novel variant of the OB-fold and structurally similar to the bacterial Cpx-pathway protein NlpE, single-stranded DNA-binding (SSB) proteins and toxins. K. pneumoniae MGH 78578 forms part of the normal human skin, mouth and gut flora and is an opportunistic pathogen that is linked to about 8% of all hospital-acquired infections in the USA. This structure provides the foundation for further investigations into this divergent member of the OB-fold family.

Published
2010

37. Open and closed conformations of two SpoIIAA‐like proteins (YP_749275.1 and YP_001095227.1) provide insights into membrane association and ligand binding

Author

Kumar, Abhinav, Lomize, Andrei, Jin, Kevin K, Carlton, Dennis, Miller, Mitchell D, Jaroszewski, Lukasz, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Chiu, Hsiu-Ju, Clayton, Thomas, Das, Debanu, Deller, Marc C, Duan, Lian, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Anna, Han, Gye Won, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Krishna, S Sri, Marciano, David, McMullan, Daniel, Morse, Andrew T, Nigoghossian, Edward, Okach, Linda, Reyes, Ron, Rife, Christopher L, Sefcovic, Natasha, Tien, Henry J, Trame, Christine B, van den Bedem, Henry, Weekes, Dana, Xu, Qingping, Hodgson, Keith O, Wooley, John, Elsliger, Marc-André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A

Subjects
Bioengineering, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Amino Acid Sequence, Bacterial Proteins, Cell Membrane, Crystallography, X-Ray, Ligands, Models, Molecular, Molecular Sequence Data, Protein Binding, Protein Structure, Quaternary, Protein Structure, Tertiary, Sequence Alignment, Sequence Homology, Amino Acid, Shewanella, Structural Homology, Protein, Chemical Sciences, Biological Sciences, Biophysics
Abstract

The crystal structures of the proteins encoded by the YP_749275.1 and YP_001095227.1 genes from Shewanella frigidimarina and S. loihica, respectively, have been determined at 1.8 and 2.25 Å resolution, respectively. These proteins are members of a novel family of bacterial proteins that adopt the α/β SpoIIAA-like fold found in STAS and CRAL-TRIO domains. Despite sharing 54% sequence identity, these two proteins adopt distinct conformations arising from different dispositions of their α2 and α3 helices. In the `open' conformation (YP_001095227.1), these helices are 15 Å apart, leading to the creation of a deep nonpolar cavity. In the `closed' structure (YP_749275.1), the helices partially unfold and rearrange, occluding the cavity and decreasing the solvent-exposed hydrophobic surface. These two complementary structures are reminiscent of the conformational switch in CRAL-TRIO carriers of hydrophobic compounds. It is suggested that both proteins may associate with the lipid bilayer in their `open' monomeric state by inserting their amphiphilic helices, α2 and α3, into the lipid bilayer. These bacterial proteins may function as carriers of nonpolar substances or as interfacially activated enzymes.

Published
2010

38. Structure of LP2179, the first representative of Pfam family PF08866, suggests a new fold with a role in amino‐acid metabolism

Author

Bakolitsa, Constantina, Kumar, Abhinav, Carlton, Dennis, Miller, Mitchell D, Krishna, S Sri, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Chiu, Hsiu-Ju, Clayton, Thomas, Deller, Marc C, Duan, Lian, Elsliger, Marc-André, Feuerhelm, Julie, Grzechnik, Slawomir K, Grant, Joanna C, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Marciano, David, McMullan, Daniel, Morse, Andrew T, Nigoghossian, Edward, Okach, Linda, Oommachen, Silvya, Paulsen, Jessica, Reyes, Ron, Rife, Christopher L, Tien, Henry J, Trout, Christina V, van den Bedem, Henry, Weekes, Dana, Xu, Qingping, Hodgson, Keith O, Wooley, John, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A

Subjects
Genetics, Human Genome, Biotechnology, Amino Acid Sequence, Amino Acids, Bacterial Proteins, Crystallography, X-Ray, Lactobacillus plantarum, Models, Molecular, Molecular Sequence Data, Protein Folding, Protein Structure, Tertiary, Sequence Alignment, Structural Homology, Protein, Chemical Sciences, Biological Sciences, Biophysics
Abstract

The structure of LP2179, a member of the PF08866 (DUF1831) family, suggests a novel α+β fold comprising two β-sheets packed against a single helix. A remote structural similarity to two other uncharacterized protein families specific to the Bacillus genus (PF08868 and PF08968), as well as to prokaryotic S-adenosylmethionine decarboxylases, is consistent with a role in amino-acid metabolism. Genomic neighborhood analysis of LP2179 supports this functional assignment, which might also then be extended to PF08868 and PF08968.

Published
2010

39. Structure of BT_3984, a member of the SusD/RagB family of nutrient‐binding molecules

Author

Bakolitsa, Constantina, Xu, Qingping, Rife, Christopher L, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Carlton, Dennis, Chen, Connie, Chiu, Hsiu-Ju, Clayton, Thomas, Das, Debanu, Deller, Marc C, Duan, Lian, Ellrott, Kyle, Farr, Carol L, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Anna, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Krishna, S Sri, Kumar, Abhinav, Lam, Winnie W, Marciano, David, McMullan, Daniel, Miller, Mitchell D, Morse, Andrew T, Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Puckett, Christina, Reyes, Ron, Tien, Henry J, Trame, Christine B, van den Bedem, Henry, Weekes, Dana, Hodgson, Keith O, Wooley, John, Elsliger, Marc-André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A

Subjects
Biochemistry and Cell Biology, Biological Sciences, Vaccine Related, Genetics, 1.1 Normal biological development and functioning, Underpinning research, Amino Acid Sequence, Bacterial Proteins, Bacteroides, Crystallography, X-Ray, Models, Molecular, Molecular Sequence Data, Protein Structure, Tertiary, Structural Homology, Protein, Chemical Sciences, Biophysics, Biological sciences, Chemical sciences
Abstract

The crystal structure of the Bacteroides thetaiotaomicron protein BT_3984 was determined to a resolution of 1.7 Å and was the first structure to be determined from the extensive SusD family of polysaccharide-binding proteins. SusD is an essential component of the sus operon that defines the paradigm for glycan utilization in dominant members of the human gut microbiota. Structural analysis of BT_3984 revealed an N-terminal region containing several tetratricopeptide repeats (TPRs), while the signature C-terminal region is less structured and contains extensive loop regions. Sequence and structure analysis of BT_3984 suggests the presence of binding interfaces for other proteins from the polysaccharide-utilization complex.

Published
2010

40. Structure of the first representative of Pfam family PF04016 (DUF364) reveals enolase and Rossmann‐like folds that combine to form a unique active site with a possible role in heavy‐metal chelation

Author

Miller, Mitchell D, Aravind, L, Bakolitsa, Constantina, Rife, Christopher L, Carlton, Dennis, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Chiu, Hsiu-Ju, Clayton, Thomas, Deller, Marc C, Duan, Lian, Feuerhelm, Julie, Grant, Joanna C, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Krishna, S Sri, Kumar, Abhinav, Marciano, David, McMullan, Daniel, Morse, Andrew T, Nigoghossian, Edward, Okach, Linda, Reyes, Ron, van den Bedem, Henry, Weekes, Dana, Xu, Qingping, Hodgson, Keith O, Wooley, John, Elsliger, Marc-André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A

Subjects
Human Genome, Biotechnology, Genetics, 1.1 Normal biological development and functioning, Underpinning research, Amino Acid Sequence, Bacterial Proteins, Catalytic Domain, Crystallography, X-Ray, Desulfitobacterium, Metals, Heavy, Models, Molecular, Molecular Sequence Data, Phosphopyruvate Hydratase, Protein Binding, Protein Folding, Protein Structure, Tertiary, Chemical Sciences, Biological Sciences, Biophysics
Abstract

The crystal structure of Dhaf4260 from Desulfitobacterium hafniense DCB-2 was determined by single-wavelength anomalous diffraction (SAD) to a resolution of 2.01 Å using the semi-automated high-throughput pipeline of the Joint Center for Structural Genomics (JCSG) as part of the NIGMS Protein Structure Initiative (PSI). This protein structure is the first representative of the PF04016 (DUF364) Pfam family and reveals a novel combination of two well known domains (an enolase N-terminal-like fold followed by a Rossmann-like domain). Structural and bioinformatic analyses reveal partial similarities to Rossmann-like methyltransferases, with residues from the enolase-like fold combining to form a unique active site that is likely to be involved in the condensation or hydrolysis of molecules implicated in the synthesis of flavins, pterins or other siderophores. The genome context of Dhaf4260 and homologs additionally supports a role in heavy-metal chelation.

Published
2010

41. The structure of the first representative of Pfam family PF09836 reveals a two‐domain organization and suggests involvement in transcriptional regulation

Author

Das, Debanu, Grishin, Nick V, Kumar, Abhinav, Carlton, Dennis, Bakolitsa, Constantina, Miller, Mitchell D, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Burra, Prasad, Chen, Connie, Chiu, Hsiu-Ju, Chiu, Michelle, Clayton, Thomas, Deller, Marc C, Duan, Lian, Ellrott, Kyle, Ernst, Dustin, Farr, Carol L, Feuerhelm, Julie, Grzechnik, Anna, Grzechnik, Slawomir K, Grant, Joanna C, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Johnson, Hope A, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Krishna, S Sri, Marciano, David, McMullan, Daniel, Morse, Andrew T, Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Oommachen, Silvya, Paulsen, Jessica, Puckett, Christina, Reyes, Ron, Rife, Christopher L, Sefcovic, Natasha, Tien, Henry J, Trame, Christine B, van den Bedem, Henry, Weekes, Dana, Wooten, Tiffany, Xu, Qingping, Hodgson, Keith O, Wooley, John, Elsliger, Marc-André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A

Subjects
Biochemistry and Cell Biology, Biological Sciences, Genetics, Underpinning research, 1.1 Normal biological development and functioning, Amino Acid Sequence, Bacterial Proteins, Crystallography, X-Ray, Gene Expression Regulation, Genome, Bacterial, Models, Molecular, Molecular Sequence Data, Neisseria gonorrhoeae, Protein Structure, Quaternary, Protein Structure, Tertiary, Structural Homology, Protein, Transcription, Genetic, Chemical Sciences, Biophysics, Biological sciences, Chemical sciences
Abstract

Proteins with the DUF2063 domain constitute a new Pfam family, PF09836. The crystal structure of a member of this family, NGO1945 from Neisseria gonorrhoeae, has been determined and reveals that the N-terminal DUF2063 domain is likely to be a DNA-binding domain. In conjunction with the rest of the protein, NGO1945 is likely to be involved in transcriptional regulation, which is consistent with genomic neighborhood analysis. Of the 216 currently known proteins that contain a DUF2063 domain, the most significant sequence homologs of NGO1945 (∼40-99% sequence identity) are from various Neisseria and Haemophilus species. As these are important human pathogens, NGO1945 represents an interesting candidate for further exploration via biochemical studies and possible therapeutic intervention.

Published
2010

42. Structure of the first representative of Pfam family PF09410 (DUF2006) reveals a structural signature of the calycin superfamily that suggests a role in lipid metabolism

Author

Chiu, Hsiu-Ju, Bakolitsa, Constantina, Skerra, Arne, Lomize, Andrei, Carlton, Dennis, Miller, Mitchell D, Krishna, S Sri, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Clayton, Thomas, Deller, Marc C, Duan, Lian, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Slawomir K, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Kumar, Abhinav, Marciano, David, McMullan, Daniel, Morse, Andrew T, Nigoghossian, Edward, Okach, Linda, Paulsen, Jessica, Reyes, Ron, Rife, Christopher L, van den Bedem, Henry, Weekes, Dana, Xu, Qingping, Hodgson, Keith O, Wooley, John, Elsliger, Marc-André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A

Subjects
1.1 Normal biological development and functioning, Underpinning research, 2.1 Biological and endogenous factors, Aetiology, Generic health relevance, Amino Acid Sequence, Bacterial Proteins, Crystallography, X-Ray, Databases, Genetic, Lipid Metabolism, Models, Molecular, Molecular Sequence Data, Nitrosomonas europaea, Oxidative Stress, Protein Structure, Tertiary, Sequence Alignment, Sequence Homology, Amino Acid, Chemical Sciences, Biological Sciences, Biophysics
Abstract

The first structural representative of the domain of unknown function DUF2006 family, also known as Pfam family PF09410, comprises a lipocalin-like fold with domain duplication. The finding of the calycin signature in the N-terminal domain, combined with remote sequence similarity to two other protein families (PF07143 and PF08622) implicated in isoprenoid metabolism and the oxidative stress response, support an involvement in lipid metabolism. Clusters of conserved residues that interact with ligand mimetics suggest that the binding and regulation sites map to the N-terminal domain and to the interdomain interface, respectively.

Published
2010

43. Structures of the first representatives of Pfam family PF06938 (DUF1285) reveal a new fold with repeated structural motifs and possible involvement in signal transduction

Author

Han, Gye Won, Bakolitsa, Constantina, Miller, Mitchell D, Kumar, Abhinav, Carlton, Dennis, Najmanovich, Rafael J, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Chen, Connie, Chiu, Hsiu-Ju, Clayton, Thomas, Das, Debanu, Deller, Marc C, Duan, Lian, Ernst, Dustin, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Anna, Jaroszewski, Lukasz, Jin, Kevin K, Johnson, Hope A, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Krishna, S Sri, Marciano, David, McMullan, Daniel, Morse, Andrew T, Nigoghossian, Edward, Okach, Linda, Reyes, Ron, Rife, Christopher L, Sefcovic, Natasha, Tien, Henry J, Trame, Christine B, van den Bedem, Henry, Weekes, Dana, Xu, Qingping, Hodgson, Keith O, Wooley, John, Elsliger, Marc-André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A

Subjects
Biochemistry and Cell Biology, Biological Sciences, Biotechnology, Human Genome, Genetics, 1.1 Normal biological development and functioning, Underpinning research, Aetiology, 2.1 Biological and endogenous factors, Generic health relevance, Amino Acid Sequence, Bacterial Proteins, Crystallography, X-Ray, Genome, Bacterial, Models, Molecular, Molecular Sequence Data, Protein Folding, Protein Structure, Secondary, Protein Structure, Tertiary, Rhodobacteraceae, Shewanella, Signal Transduction, Structural Homology, Protein, Chemical Sciences, Biophysics, Biological sciences, Chemical sciences
Abstract

The crystal structures of SPO0140 and Sbal_2486 were determined using the semiautomated high-throughput pipeline of the Joint Center for Structural Genomics (JCSG) as part of the NIGMS Protein Structure Initiative (PSI). The structures revealed a conserved core with domain duplication and a superficial similarity of the C-terminal domain to pleckstrin homology-like folds. The conservation of the domain interface indicates a potential binding site that is likely to involve a nucleotide-based ligand, with genome-context and gene-fusion analyses additionally supporting a role for this family in signal transduction, possibly during oxidative stress.

Published
2010

44. A conserved fold for fimbrial components revealed by the crystal structure of a putative fimbrial assembly protein (BT1062) from Bacteroides thetaiotaomicron at 2.2 Å resolution

Author

Xu, Qingping, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Bakolitsa, Constantina, Cai, Xiaohui, Carlton, Dennis, Chen, Connie, Chiu, Hsiu-Ju, Chiu, Michelle, Clayton, Thomas, Das, Debanu, Deller, Marc C, Duan, Lian, Ellrott, Kyle, Farr, Carol L, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Anna, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Krishna, S Sri, Kumar, Abhinav, Marciano, David, McMullan, Daniel, Miller, Mitchell D, Morse, Andrew T, Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Puckett, Christina, Reyes, Ron, Sefcovic, Natasha, Tien, Henry J, Trame, Christine B, van den Bedem, Henry, Weekes, Dana, Wooten, Tiffany, Yeh, Andrew, Zhou, Jiadong, Hodgson, Keith O, Wooley, John, Elsliger, Marc-Andre, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A

Subjects
Biochemistry and Cell Biology, Biological Sciences, Genetics, Digestive Diseases, Amino Acid Sequence, Bacteroides, Crystallography, X-Ray, Fimbriae Proteins, Fimbriae, Bacterial, Models, Molecular, Molecular Sequence Data, Protein Folding, Protein Structure, Tertiary, Sequence Alignment, Structural Homology, Protein, Chemical Sciences, Biophysics, Biological sciences, Chemical sciences
Abstract

BT1062 from Bacteroides thetaiotaomicron is a homolog of Mfa2 (PGN0288 or PG0179), which is a component of the minor fimbriae in Porphyromonas gingivalis. The crystal structure of BT1062 revealed a conserved fold that is widely adopted by fimbrial components.

Published
2010

45. Next-Generation Technical Services (NGTS): New Modes for Organizing and Providing Access to Special Collections, Archive, and Digital Formats: Final Report

Author

Dekker, Harrison, Dooley, Jim, Kozbial, Ardys, Lin, Emily, Milenkiewicz, Eric, Mix, Lisa, Perry, Sue, and Turner, Adrian

Subjects
Libraries, Library Technical Services, Library Special Collections, Archives, Digital Formats
Abstract

Imagine a UC library with more than half a million volumes, carefully acquired and protected, many of them singular or not commonly held by others in the world. Imagine the contents lining thirteen and a half miles from end to end—more than one Bancroft Library’s worth of material—but all of it invisible and inaccessible to users. That library represents the self-reported aggregate of the unprocessed backlog of special collections and archives materials owned by UC.The UC Libraries have the opportunity to bring such a library online, and make its contents discoverable and accessible to researchers, within this next decade. The UC Libraries also have the opportunity to prevent the creation of such a backlog of newly created scholarly content, much of it in digital format. Collective commitment is needed to invest the time and initial resources to follow through and to capture these opportunities.

Published
2010

46. Chronopolis: Preserving our Digital Heritage

Author

Minor, David, Sutton, Don, Kozbial, Ardys, Burek, Michael, and Smorul, Michael

Abstract

The Chronopolis Digital Preservation Initiative, one of the Library of Congress' latest efforts to collect and preserve atrisk digital information, has completed its first year of service as a multi-member partnership to meet the archival needs of a wide range of cultural and social domains. In this paper we will explore the major themes within Chronopolis.

Published
2009

49. Further Development of a Shared Cataloging Resource for the Visual Resources Community: UCAI Phase Two:  Final Report

Author

Barnhart, Linda, Schottlaender, Brian E.C., Westbrook, Brad, Cowles, Kevin Esme, Rose-Sandler, Trish, and Kozbial, Ardys

Subjects
Art images, union catalogs, aggregated metadata, work-surrogate relationships, VRA Core, cataloging
Abstract

This report describes efforts  to advance and stabilize the intrastructure for a shared cataloging utility for art images by developing a set of production-quality tools that operate on a large, standardized set of legacy metadata.

Published
2006

50. Developing a University Learning Community of Critical Readers and Writers: The Story of a Liberal Arts and IEP Partnership

Author

Ernst, Beth Kozbial, Wonder, Kelly, and Adler, Julie

Abstract

Integrating English language learners into the academic mainstream is a critically important goal. For students who are learning content in their second or third language as well as negotiating the university's social context, integrating into the mainstream academic environment can be challenging. Instructors at a public university intensive English program (IEP) addressed these problems by developing a common reading project and creating a learning community composed of U.S. native-English-speaking freshman in a critical reading class and intermediate- and advanced-level IEP students in integrated skills courses. Communities of practice, inquiry, and creativity were built through the process of coplanning and coteaching and through methods and activities implemented in the classroom. Through collaboration on a common reading and theme, "Night" by Elie Wiesel, and genocide, the instructors built a supportive learning environment that was mutually beneficial to both groups. In this article, the instructors discuss the nature of the learning community, present theories related to cross-cultural learning communities, and explain how intercultural communities support the distinctive goals of a liberal arts education. Then they describe the process of developing curriculum for the common reading project and share findings from student questionnaires evaluating the project.

Published
2016
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