This collection showcases the books, journal articles, book reviews, and other publications and presentations written by faculty and researchers of the Department of Biochemistry and Molecular Pharmacology.

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Publications from 2010

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RNA polymerase mapping during stress responses reveals widespread nonproductive transcription in yeast, Tae Soo Kim, Chih Long Liu, Moran Yassour, John Holik, Nir Friedman, Stephen Buratowski, and Oliver J. Rando

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Sequence features that drive human promoter function and tissue specificity, Jane M. Landolin, David S. Johnson, Nathan D. Trinklein, Shelley Force Aldred, Catherine Medina, Hennady P. Shulha, Zhiping Weng, and Richard M. Myers

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Myogenic microRNA expression requires ATP-dependent chromatin remodeling enzyme function, Chandrashekara Mallappa, Brian T. Nasipak, Letitiah Etheridge, Elliot J. Androphy, Stephen N. Jones, Charles G. Sagerstrom, Yasuyuki Ohkawa, and Anthony N. Imbalzano

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Optical recognition of converted DNA nucleotides for single-molecule DNA sequencing using nanopore arrays, Ben McNally, Alon Singer, Zhiliang Yu, Yingjie Sun, Zhiping Weng, and Amit Meller

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Clinically relevant doses of chemotherapy agents reversibly block formation of glioblastoma neurospheres, Alicia M. Mihaliak, Candace A. Gilbert, Li Li, Marie-Claire Daou, Richard P. Moser, Andrew Reeves, Brent H. Cochran, and Alonzo H. Ross

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Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells, Zarmik Moqtaderi, Jie Wang, Debasish Raha, Robert J. White, Michael Snyder, Zhiping Weng, and Kevin Struhl

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Evaluating the substrate-envelope hypothesis: structural analysis of novel HIV-1 protease inhibitors designed to be robust against drug resistance, Madhavi N. L. Nalam, Akbar Ali, Michael D. Altman, G. S. Kiran Kumar Reddy, Sripriya Chellappan, Visvaldas Kairys, Aysegul Ozen, Hong Cao, Michael K. Gilson, Bruce Tidor, Tariq M. Rana, and Celia A. Schiffer

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Rationale for more diverse inhibitors in competition with substrates in HIV-1 protease, Nevra Ozer, Celia A. Schiffer, and Turkan Haliloglu

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Combinations of affinity-enhancing mutations in a T cell receptor reveal highly nonadditive effects within and between complementarity determining regions and chains, Brian G. Pierce, Jaafar N. Haidar, Yong Yu, and Zhiping Weng

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Drug resistance against HCV NS3/4A inhibitors is defined by the balance of substrate recognition versus inhibitor binding, Keith P. Romano, Akbar Ali, William E. Royer, and Celia A. Schiffer

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Discovery of a novel function for human Rad51: maintenance of the mitochondrial genome, Jay M. Sage, Otto S. Gildemeister, and Kendall L. Knight

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Crystal structure of the APOBEC3G catalytic domain reveals potential oligomerization interfaces., Shivender Shandilya, Madhavi N. L. Nalam, Ellen A. Nalivaika, Phillip J. Gross, Johnathan C. Valesano, Keisuke Shindo, Ming Li, Mary Munson, William E. Royer, Elena Harjes, Takahide Kono, Hiroshi Matsuo, Reuben S. Harris, Mohan Somasundaran, and Celia A. Schiffer

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Bi-specific MHC heterodimers for characterization of cross-reactive T cells, Zu T. Shen, Michael A. Brehm, Keith A. Daniels, Alexander B. Sigalov, Liisa K. Selin, Raymond M. Welsh, and Lawrence J. Stern

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Therapeutic targeting of C-terminal binding protein in human cancer, Michael W. Straza, Seema Paliwal, Ramesh C. Kovi, Barur R. Rajeshkumar, Peter Trenh, Daniel Parker, Giles F. Whalen, Stephen Lyle, Celia A. Schiffer, and Steven R. Grossman

Publications from 2009

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Maternal and zygotic aldh1a2 activity is required for pancreas development in zebrafish, Kristen Alexa, Seong-Kyu Choe, Nicolas Hirsch, Letitiah Etheridge, Elizabeth Laver, and Charles G. Sagerstrom

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Viral protease inhibitors, Jeffrey Anderson, Celia A. Schiffer, Sook-Kyung Lee, and Ronald I. Swanstrom

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MicroRNAs: regulating a change of heart, Kurt G. Barringhaus and Phillip D. Zamore

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Immunofluorescence imaging of DNA damage response proteins: optimizing protocols for super-resolution microscopy., Brian Thomas Bennett, Jorg Bewersdorf, and Kendall L. Knight

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Alpha- and Beta-Monosaccharide Transport in Human Erythrocytes, Anthony Carruthers and Jeffry M. Leitch

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A convergence of rRNA and mRNA quality control pathways revealed by mechanistic analysis of nonfunctional rRNA decay, Sarah E. Cole, Frederick J. laRiviere, Christopher N. Merrikh, and Melissa J. Moore

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The role of specific checkpoint-induced S-phase transcripts in resistance to replicative stress, Chaitali Dutta and Nicholas R. Rhind

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Long-term statin therapy and CSF cholesterol levels: implications for Alzheimer's disease, Barbara A. Evans, James E. Evans, Stephen P. Baker, Kevin J. Kane, Joan M. Swearer, Douglas A. Hinerfeld, Richard J. Caselli, Ekaterina Rogaeva, Peter St. George-Hyslop, Majaz Moonis, and Daniel A. Pollen

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Small silencing RNAs: an expanding universe, Megha Ghildiyal and Phillip D. Zamore

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Cancer stem cells: cell culture, markers, and targets for new therapies, Candace A. Gilbert and Alonzo H. Ross

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Cellular redistribution of Rad51 in response to DNA damage: novel role for Rad51C., Otto S. Gildemeister, Jay M. Sage, and Kendall L. Knight

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Mutations and Cell Defenses, Otto S. Gildemeister, Jay M. Sage, and Kendall L. Knight

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Structure-based design of a T-cell receptor leads to nearly 100-fold improvement in binding affinity for pepMHC, Jaafar N. Haidar, Brian G. Pierce, Yong Yu, Weiwei Tong, Michael Li, and Zhiping Weng

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Additivity in the analysis and design of HIV protease inhibitors, Robert N. Jorissen, G. S. Kiran Kumar Reddy, Akbar Ali, Michael D. Altman, Sripriya Chellappan, Saima G. Anjum, Bruce Tidor, Celia A. Schiffer, Tariq M. Rana, and Michael K. Gilson

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Toward the design of mutation-resistant enzyme inhibitors: further evaluation of the substrate envelope hypothesis, Visvaldas Kairys, Michael K. Gilson, Viney Lather, Celia A. Schiffer, and Miguel X. Fernandes

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Human immunodeficiency virus type 1 protease-correlated cleavage site mutations enhance inhibitor resistance, Madhavi Kolli, Eric Stawiski, Colombe Chappey, and Celia A. Schiffer

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Collapse of germline piRNAs in the absence of Argonaute3 reveals somatic piRNAs in flies, Chengjian Li, Vasily V. Vagin, Soohyun Lee, Jia Xu, Shengmei Ma, Hualin Xi, Herve Seitz, Michael D. Horwich, Monika Syrzycka, Barry M. Honda, Ellen L. W. Kittler, Maria L. Zapp, Carla Andrea Klattenhoff, Nadine Schultz, William E. Theurkauf, Zhiping Weng, and Phillip D. Zamore

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A host type I interferon response is induced by cytosolic sensing of the bacterial second messenger cyclic-di-GMP, Sarah M. McWhirter, Roman Barbalat, Kathryn M. Monroe, Mary F. Fontana, Mamoru Hyodo, Nathalie T. Joncker, Ken J. Ishii, Shizuo Akira, Marco Colonna, Zhiliang Cheng, Katherine A. Fitzgerald, Yoshihiro Hayakawa, and Russell E. Vance

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Discovery of a novel activator of KCNQ1-KCNE1 K channel complexes., Karen Mruk and William R. Kobertz

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New approaches to HIV protease inhibitor drug design II: testing the substrate envelope hypothesis to avoid drug resistance and discover robust inhibitors, Madhavi N. L. Nalam and Celia A. Schiffer

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Five siRNAs targeting three SNPs may provide therapy for three-quarters of Huntington's disease patients, Edith L. Pfister, Lori A. Kennington, Juerg R. Straubhaar, Sujata Wagh, Wanzhou Liu, Marian DiFiglia, Bernhard Landwehrmeyer, Jean-Paul Vonsattel, Phillip D. Zamore, and Neil Aronin

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Cotranslational and posttranslational N-glycosylation of polypeptides by distinct mammalian OST isoforms, Catalina Ruiz-Canada, Daniel J. Kelleher, and Reid Gilmore

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Regulation of DNA replication by the S-phase DNA damage checkpoint., Nicholas Adrian Willis and Nicholas R. Rhind

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Betaalpha-hairpin clamps brace betaalphabeta modules and can make substantive contributions to the stability of TIM barrel proteins, Xiaoyan Yang, Sagar V. Kathuria, Ramakrishna Vadrevu, and C. Robert Matthews

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Uncovering multiple molecular targets for caffeine using a drug target validation strategy combining A 2A receptor knockout mice with microarray profiling, Liqun Yu, Joana E. Coelho, Xiaoling Zhang, Yutao Fu, Abigail Tillman, Ulas Karaoz, Bertil B. Fredholm, Zhiping Weng, and Jiang-Fan Chen

Publications from 2008

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HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants, Michael D. Altman, Akbar Ali, G. S. Kiran Kumar Reddy, Madhavi N. L. Nalam, Saima G. Anjum, Hong Cao, Sripriya Chellappan, Visvaldas Kairys, Miguel X. Fernandes, Michael K. Gilson, Celia A. Schiffer, Tariq M. Rana, and Bruce Tidor

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Structural analysis of human immunodeficiency virus type 1 CRF01_AE protease in complex with the substrate p1-p6., Rajintha M. Bandaranayake, Moses Prabu-Jeyabalan, Junko Kakizawa, Wataru Sugiura, and Celia A. Schiffer

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Modulation of N-type Calcium Channel Activity by G-proteins and Protein Kinase C, Curtis F. Barrett and Ann R. Rittenhouse

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Analysis of Glucose Transporter Topology and Structural Dynamics., David M. Blodgett, Christopher A. Graybill, and Anthony Carruthers

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Amphetamine-induced decreases in dopamine transporter surface expression are protein kinase C-independent, Ekaterina Boudanova, Deanna M. Navaroli, and Haley E. Melikian

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Insights into interferon regulatory factor activation from the crystal structure of dimeric IRF5, Weijun Chen, Suvana S. Lam, Hema Srinath, Zhaozhao Jiang, John J. Correia, Celia A. Schiffer, Katherine A. Fitzgerald, Kai Lin, and William E. Royer

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Contribution of Ser386 and Ser396 to activation of interferon regulatory factor 3, Weijun Chen, Hema Srinath, Suvana S. Lam, Celia A. Schiffer, William E. Royer, and Kai Lin

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Potent RNAi by short RNA triggers, Chia-ying Chu and Tariq M. Rana

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Autonomy and robustness of translocation through the nuclear pore complex: a single-molecule study, Thomas Dange, David Grunwald, Antje Grunwald, Reiner Peters, and Ulrich Kubitscheck

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RNA target specificity of the embryonic cell fate determinant POS-1, Brian M. Farley, John M. Pagano, and Sean P. Ryder

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The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome, Yutao Fu, Manisha Sinha, Craig L. Peterson, and Zhiping Weng

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Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic cells, Megha Ghildiyal, Herve Seitz, Michael D. Horwich, Chengjian Li, Tingting Du, Soohyun Lee, Jia Xu, Ellen L. W. Kittler, Maria L. Zapp, Zhiping Weng, and Phillip D. Zamore

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Sir2 mediates apoptosis through JNK-dependent pathways in Drosophila, Anthony J. Griswold, Karen T. Chang, Alexander Peter Runko, Melanie A. Knight, and Kyung-Tai Min

Probing intranuclear environments at the single-molecule level, David Grunwald, Robert M Martin, Volker Buschmann, David P Bazett-Jones, Heinrich Leonhardt, Ulrich Kubitscheck, and M Cristina Cardoso

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Calibrating excitation light fluxes for quantitative light microscopy in cell biology, David Grunwald, Shailesh M. Shenoy, Sean Burke, and Robert H. Singer

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Cell biology of mRNA decay, David Grunwald, Robert H. Singer, and Kevin Czaplinski

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Design and delivery of antisense oligonucleotides to block microRNA function in cultured Drosophila and human cells, Michael D. Horwich and Phillip D. Zamore

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Protein-protein docking benchmark version 3.0, Howook Hwang, Brian G. Pierce, Julian Mintseris, Joel Janin, and Zhiping Weng

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An interaction between the SRP receptor and the translocon is critical during cotranslational protein translocation, Ying Jiang, Zhiliang Cheng, Elisabet C. Mandon, and Reid Gilmore

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Kinetic traps in the folding of beta alpha-repeat proteins: CheY initially misfolds before accessing the native conformation., Sagar V. Kathuria, Iain J. Day, Louise A. Wallace, and C. Robert Matthews

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Zinc binding modulates the entire folding free energy surface of human Cu,Zn superoxide dismutase., Can Kayatekin, Jill A. Zitzewitz, and C. Robert Matthews

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Evidence for Interindividual Heterogeneity in the Glucose Gradient across the Human Red Blood Cell Membrane and its Relationship to Hemoglobin Glycation, Paramjit K. Khera, Clinton H. Joiner, Anthony Carruthers, Christopher J. Lindsell, Eric P. Smith, Robert S. Franco, Yancey R. Holmes, and Robert M. Cohen

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Quantitative analysis of single nucleotide polymorphisms within copy number variation, Soohyun Lee, Simon Kasif, Zhiping Weng, and Charles R. Cantor

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Resilience to resistance of HIV-1 protease inhibitors: profile of darunavir, Eric Lefebvre and Celia A. Schiffer

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Linking SNPs to CAG repeat length in Huntington's disease patients, Wanzhao Liu, Lori A. Kennington, H. Diana Rosas, Steven M. Hersch, Jang-Ho Cha, Phillip D. Zamore, and Neil Aronin

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DnaC inactivation in Escherichia coli K-12 induces the SOS response and expression of nucleotide biosynthesis genes, Anders Lobner-Olesen, Monika Slominska-Wojewodzka, Flemming G. Hansen, and Martin G. Marinus

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Unique Asn-linked oligosaccharides of the human pathogen Entamoeba histolytica, Paula Magnelli, John F. Cipollo, Daniel M. Ratner, Jike Cui, Daniel J. Kelleher, Reid Gilmore, Catherine E. Costello, Phillips W. Robbins, and John Samuelson

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Loss of miRNA biogenesis induces p19Arf-p53 signaling and senescence in primary cells, Rajini R. Mudhasani, Zhiqing Zhu, Gyorgy Hutvagner, Christine M. Eischen, Stephen Lyle, Lisa L. Hall, Jeanne B. Lawrence, Anthony N. Imbalzano, and Stephen N. Jones

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Small-molecule inhibition of HIV-1 Vif, Robin S. Nathans, Hong Cao, Natalia Sharova, Akbar Ali, Mark E. Sharkey, Ruzena Stranska, Mario Stevenson, and Tariq M. Rana

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Model for the peptide-free conformation of class II MHC proteins, Corrie A. Painter, Anthony Cruz, Gustavo E. Lopez, Lawrence J. Stern, and Zarixia Zavala-Ruiz

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The Hsk1(Cdc7) replication kinase regulates origin efficiency, Prasanta K. Patel, Naveen Kommajosyula, Adam Rosebrock, Aaron Bensimon, Janet K. Leatherwood, John Bechhoefer, and Nicholas R. Rhind

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Non-obese diabetic-recombination activating gene-1 (NOD-Rag1 null) interleukin (IL)-2 receptor common gamma chain (IL2r gamma null) null mice: a radioresistant model for human lymphohaematopoietic engraftment, Todd Pearson, Leonard D. Shultz, David M. Miller, Marie A. King, Joseph Laning, William Fodor, Amy Cuthbert, Lisa M. Burzenski, Bruce Gott, Bonnie L. Lyons, Oded Foreman, Aldo A. Rossini, and Dale L. Greiner

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As functional nuclear actin comes into view, is it globular, filamentous, or both, Thoru Pederson

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Turning a PAGE: the overnight sensation of SDS-polyacrylamide gel electrophoresis, Thoru Pederson

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A construct with fluorescent indicators for conditional expression of miRNA, Linghua Qiu, Hongyan Wang, Xugang Xia, Hongxia Zhou, and Zuoshang Xu

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KCNE peptides differently affect voltage sensor equilibrium and equilibration rates in KCNQ1 K+ channels, Jessica M. Rocheleau and William R. Kobertz

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Combating Drug Resistance – Identifying Resilient Molecular Targets and Robust Drugs, Celia A. Schiffer

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Argonaute loading improves the 5' precision of both MicroRNAs and their miRNA strands in flies, Herve Seitz, Megha Ghildiyal, and Phillip D. Zamore

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Sec6p anchors the assembled exocyst complex at sites of secretion, Jennifer A. Songer and Mary Munson

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Conversion of red fluorescent protein into a bright blue probe, Oksana M. Subach, Illia S. Gundorov, Masami Yoshimura, Fedor V. Subach, Jinghang Zhang, David Grunwald, Ekaterina A. Souslova, Dmitriy M. Chudakov, and Vladislav V. Verkhusha

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NMR analysis of partially folded states and persistent structure in the alpha subunit of tryptophan synthase: implications for the equilibrium folding mechanism of a 29-kDa TIM barrel protein, Ramakrishna Vadrevu, Ying Wu, and C. Robert Matthews

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Class II major histocompatibility complex tetramer staining: progress, problems, and prospects, Sabrina S. Vollers and Lawrence J. Stern

Publications from 2007

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Coordinated regulation of Toll-like receptor and NOD2 signaling by K63-linked polyubiquitin chains, Derek W. Abbott, Yibin Yang, Jessica E. Hutti, Swetha Madhavarapu, Michelle A. Kelliher, and Lewis C. Cantley

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Computational design and experimental study of tighter binding peptides to an inactivated mutant of HIV-1 protease, Michael D. Altman, Ellen A. Nalivaika, Moses Prabu-Jeyabalan, Celia A. Schiffer, and Bruce Tidor

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Microsecond hydrophobic collapse in the folding of Escherichia coli dihydrofolate reductase, an alpha/beta-type protein, Munehito Arai, Elena Kondrashkina, Can Kayatekin, C. Robert Matthews, Masahiro Iwakura, and Osman Bilsel

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Phosphorylation at serine 208 of the 1alpha,25-dihydroxy Vitamin D3 receptor modulates the interaction with transcriptional coactivators, Gloria Arriagada, Roberto Paredes, Juan Olate, Andre J. Van Wijnen, Jane B. Lian, Gary S. Stein, Janet L. Stein, Sergio Onate, and Martin A. Montecino

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Mass spectrometry analysis of HIV-1 Vif reveals an increase in ordered structure upon oligomerization in regions necessary for viral infectivity, Jared R. Auclair, Karin M. Green, Shivender Shandilya, James E. Evans, Mohan Somasundaran, and Celia A. Schiffer

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The evolution of N-glycan-dependent endoplasmic reticulum quality control factors for glycoprotein folding and degradation, Sulagna Banerjee, Prashanth Vishwanath, Jike Cui, Daniel J. Kelleher, Reid Gilmore, Phillips W. Robbins, and John Samuelson

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Structural basis of GLUT1 inhibition by cytoplasmic ATP, David M. Blodgett, Julie Kelley De Zutter, Kara B. Levine, Pusha Karim, and Anthony Carruthers

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Enterohaemorrhagic and enteropathogenic Escherichia coli Tir proteins trigger a common Nck-independent actin assembly pathway, Michael John Brady, Kenneth Geno Campellone, Megha Ghildiyal, and John M. Leong

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Crystallization and preliminary X-ray analysis of a domain in the Runx2 transcription factor that interacts with the 1alpha,25 dihydroxy vitamin D3 receptor, Carola Bruna, Gloria Arriagada, Jane B. Lian, Gary S. Stein, Marta Bunster, Jose Martinez-Oyanedel, and Martin A. Montecino

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Increased adherence and actin pedestal formation by dam-deficient enterohaemorrhagic Escherichia coli O157:H7, Kenneth Geno Campellone, Andrew J. Roe, Anders Lobner-Olesen, Kenan C. Murphy, Loranne Magoun, Michael John Brady, Arthur Donohue-Rolfe, Saul Tzipori, David L. Gally, John M. Leong, and Martin G. Marinus

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The 1alpha,25-dihydroxy Vitamin D3 receptor preferentially recruits the coactivator SRC-1 during up-regulation of the osteocalcin gene, Loreto Carvallo, Berta Henriquez, Juan Olate, Andre J. Van Wijnen, Jane B. Lian, Gary S. Stein, Sergio Onate, Janet L. Stein, and Martin A. Montecino

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Evaluation of the substrate envelope hypothesis for inhibitors of HIV-1 protease, Sripriya Chellappan, Visvaldas Kairys, Miguel X. Fernandes, Celia A. Schiffer, and Michael K. Gilson

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Design of mutation-resistant HIV protease inhibitors with the substrate envelope hypothesis, Sripriya Chellappan, G. S. Kiran Kumar Reddy, Akbar Ali, Madhavi N. L. Nalam, Saima G. Anjum, Hong Cao, Visvaldas Kairys, Miguel X. Fernandes, Michael D. Altman, Bruce Tidor, Tariq M. Rana, Celia A. Schiffer, and Michael K. Gilson

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Competition between Ski and CREB-binding protein for binding to Smad proteins in transforming growth factor-beta signaling, Weijun Chen, Suvana S. Lam, Hema Srinath, Celia A. Schiffer, William E. Royer, and Kai Lin

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Quantitative analysis of RNA-mediated protein-protein interactions in living cells by FRET, Ya-Lin Chiu, Hong Cao, and Tariq M. Rana

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Mutations in the stalk of the measles virus hemagglutinin protein decrease fusion but do not interfere with virus-specific interaction with the homologous fusion protein, Elizabeth Ann Corey and Ronald M. Iorio

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Altered selectivity of parathyroid hormone (PTH) and PTH-related protein (PTHrP) for distinct conformations of the PTH/PTHrP receptor, Thomas Dean, Jean-Pierre Vilardaga, John T. Potts, and Thomas James Gardella

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Therapeutic silencing of mutant huntingtin with siRNA attenuates striatal and cortical neuropathology and behavioral deficits, Marian DiFiglia, Miguel Sena-Esteves, Kathryn O. Chase, Ellen Sapp, Edith L. Pfister, Meghan B. Sass, Jennifer Yoder, P. Reeves, Rajendra K. Pandey, Kallanthottathil G. Rajeev, Muthiah Manoharan, Dinah W. Y. Sah, Phillip D. Zamore, and Neil Aronin

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TALE-family homeodomain proteins regulate endodermal sonic hedgehog expression and pattern the anterior endoderm, Philip J. Diiorio, Kristen Alexa, Seong-Kyu Choe, Letitiah Etheridge, and Charles G. Sagerstrom