In the past several years, our work has concentrated in several distinct areas. Crystallographic studies of proteases and their inhibitors Crystallographic studies of proteases and their inhibitors have been an important area of research of this Section since its establishment. We have been particularly active in the investigation of structure-function relationship in aspartic proteases, including clinically important retroviral enzymes. Our studies of HIV protease, although no longer a major target of active research, are still ongoing and concentrate on the investigation of drug-resistant variants and their complexes with inhibitors. We have investigated retroviral proteases from several other sources such as FIV, RSV, HTLV-1, and XMRV. A number of inhibitor complexes of HTLV-1 PR have been analyzed, with the aim of assisting in the development of drugs against HTLV-caused leukemia. XMRV protease was found to share properties of both dimeric retroviral aspartic protease, as well as monomeric pepsin-like enzymes. Complexes of XMRV PR with several inhibitors, including an AIDS drug, have been solved and analyzed. The structures of two plasmepsins, PL-1 and HAP, including their complexes with inhibitors, provided information useful for design of anti-malarial drugs. We have studied the structures of two inhibitors of serine proteases with anticancer properties, EcTI and CrataBL. Lectins and antibodies for the prevention of AIDS We have been involved in studies of several lectins with antiviral activities, some of them currently being developed in pre-clinical trials as potential drugs preventing HIV infection. We have solved the structure of griffithsin, as free protein and complexed with a number of mono- and disaccharides, explaining the structural basis for its tight binding to branched mannose-rich carbohydrates. We have reengineered griffithsin into a monomeric form and solved its structure with a complex oligosaccharide, elucidating the basis of its antiviral properties. A number of constructs of griffithsin containing tandem repeats of multiple monomers were prepared and shown to increase their antiviral activity. We have also solved atomic-resolution structure of another lectin, scytovirin. We have solved structures of Fab constructs of antibodies directed against HIV-1 gp41 complexed with different gp41 mimics. These structures allowed us to postulate why some closely related antibodies are neutralizing, while others are not. Cytokines and cytokine receptors Our Section has been investigating the crystal structures of several cytokines and has made progress in preparing their receptor complexes. We have purified and crystallized complexes of IL-10 with its specific receptor and are studying complexes of several other cytokines related to IL-10, such as IL-19, IL-20, and IL-22. We have solved the structure of interferon lambda-1 complexed with its receptor, finding considerable differences in the receptor-ligand interactions between different family members. Crystallographic studies of the Taz2 domain of p300 and its interactions with C/EBP transcriptional activators Transcriptional activation by C/EBP proteins relies on recruitment of the histone acetyl transferases (HATs) CBP/p300 to the promoter/enhancer region. Members of the C/EBP family bind to the Taz2 domain of p300/CBP and trigger p300/CBP phosphorylation. Two short helical sequence motifs, homology boxes A and B, which are conserved between C/EBP activators and comprise their minimal TADs, are necessary for p300/CBP binding. In order to gain insights into C/EBP:p300/CBP interactions we initiated x-ray crystallographic studies of the p300 Taz2 complexed to various peptide ligands. We determined the crystal structure of a segment of the human p300 protein (residues 1723-1836) corresponding to the extended zinc-binding Taz2 domain. Residues 1813-1834 from this construct form a helical extension of the C-terminal helix and make extensive crystal contactinteractions with the peptide binding site on Taz2. We utilized this observation to investigate Taz2 binding to C/EBP proteins. We engineered a chimeric protein in which the entire helical extension of the extended Taz2 domain was substituted by residues comprising the minimal TAD of C/EBPepsilon. As expected, the crystal structure of this peptide (PDB ID:3T92), revealed that the segment corresponding to the C/EBPepsilon TAD forms two helices connected by a short linker and interacts with the core structure of Taz2 from the symmetry-related molecule. The C/EBPepsilon binding site on Taz2 overlaps with the known binding site of STAT1. We postulate that other members of the C/EBP family interact with the Taz2 domain in the same manner. We also propose a possible structural framework for C/EBPbeta-dependent phosphorylation of the p300 C-terminus by protein kinase HIPK2.

National Institute of Health (NIH)
National Cancer Institute (NCI)
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National Cancer Institute Division of Basic Sciences
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Aranko, A Sesilja; Oeemig, Jesper S; Zhou, Dongwen et al. (2014) Structure-based engineering and comparison of novel split inteins for protein ligation. Mol Biosyst 10:1023-34
Zheng, Heping; Hou, Jing; Zimmerman, Matthew D et al. (2014) The future of crystallography in drug discovery. Expert Opin Drug Discov 9:125-37
Pletneva, Nadya V; Pletnev, Vladimir Z; Souslova, Ekaterina et al. (2013) Yellow fluorescent protein phiYFPv (Phialidium): structure and structure-based mutagenesis. Acta Crystallogr D Biol Crystallogr 69:1005-12
Zhou, Dongwen; Lobo, Yara A; Batista, Isabel F C et al. (2013) Crystal structures of a plant trypsin inhibitor from Enterolobium contortisiliquum (EcTI) and of its complex with bovine trypsin. PLoS One 8:e62252
Yao, Jianzhuang; Wlodawer, Alexander; Guo, Hong (2013) Understanding the autocatalytic process of pro-kumamolisin activation from molecular dynamics and quantum mechanical/molecular mechanical (QM/MM) free-energy simulations. Chemistry 19:10849-52
Ferreira, Rodrigo da Silva; Zhou, Dongwen; Ferreira, Joana Gasperazzo et al. (2013) Crystal Structure of Crataeva tapia Bark Protein (CrataBL) and Its Effect in Human Prostate Cancer Cell Lines. PLoS One 8:e64426
Li, Mi; Gustchina, Alla; Glesner, Jill et al. (2011) Carbohydrates contribute to the interactions between cockroach allergen Bla g 2 and a monoclonal antibody. J Immunol 186:333-40
Li, Mi; Dimaio, Frank; Zhou, Dongwen et al. (2011) Crystal structure of XMRV protease differs from the structures of other retropepsins. Nat Struct Mol Biol 18:227-9
Bhaumik, Prasenjit; Xiao, Huogen; Parr, Charity L et al. (2009) Crystal structures of the histo-aspartic protease (HAP) from Plasmodium falciparum. J Mol Biol 388:520-40
Feng, Hanqiao; Jenkins, Lisa M Miller; Durell, Stewart R et al. (2009) Structural basis for p300 Taz2-p53 TAD1 binding and modulation by phosphorylation. Structure 17:202-10

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