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Research Output 1996 2019

2019

Cyanuric acid hydrolase reveal conformational flexibility and asymmetry important for catalysis

Shi, K., Cho, S., Aukema, K. G., Lee, T., Bera, A. K., Seffernick, J. L., Wackett, L. P. & Aihara, H., Jun 1 2019, In : PloS one. 14, 6, e0216979.

Research output: Contribution to journalArticle

Open Access
Hydrolases
hydrolases
Catalysis
catalytic activity
acids
4 Citations (Scopus)

Determinants of Oligonucleotide Selectivity of APOBEC3B

Wagner, J. R., Demir, Ö., Carpenter, M. A., Aihara, H., Harki, D. A., Harris, R. & Amaro, R. E., May 28 2019, In : Journal of Chemical Information and Modeling. 59, 5, p. 2264-2273 10 p.

Research output: Contribution to journalArticle

Oligonucleotides
Binding sites
DNA
Binding Sites
determinants
Magic angle spinning
Distance measurement
Membrane Proteins
Nuclear magnetic resonance
Biopolymers

Inhibiting APOBEC3 Activity with Single-Stranded DNA Containing 2′-Deoxyzebularine Analogues

Kvach, M. V., Barzak, F. M., Harjes, S., Schares, H. A. M., Jameson, G. B., Ayoub, A. M., Moorthy, R., Aihara, H., Harris, R., Filichev, V. V., Harki, D. A. & Harjes, E., Feb 5 2019, In : Biochemistry. 58, 5, p. 391-400 10 p.

Research output: Contribution to journalArticle

Open Access
Single-Stranded DNA
Cytidine
Mutagenesis
Calorimetry
Fluorescence Polarization

Insight into subtilisin E-S7 cleavage pattern based on crystal structure and hydrolysates peptide analysis

Tang, H., Zhang, J., Shi, K., Aihara, H. & Du, G., May 7 2019, In : Biochemical and Biophysical Research Communications. 512, 3, p. 623-628 6 p.

Research output: Contribution to journalArticle

ethyl-2-methylthio-4-methyl-5-pyrimidine carboxylate
Subtilisins
Crystal structure
Peptides
Protein Engineering

Novel Deazaflavin Analogues Potently Inhibited Tyrosyl DNA Phosphodiesterase 2 (TDP2) and Strongly Sensitized Cancer Cells toward Treatment with Topoisomerase II (TOP2) Poison Etoposide

Kankanala, J., Ribeiro, C. J. A., Kiselev, E., Ravji, A., Williams, J., Xie, J., Aihara, H., Pommier, Y. & Wang, Z., May 9 2019, In : Journal of Medicinal Chemistry. 62, 9, p. 4669-4682 14 p.

Research output: Contribution to journalArticle

Type II DNA Topoisomerase
Poisons
Etoposide
Phosphodiesterase Inhibitors
Permeability

Selectivity, ligand deconstruction, and cellular activity analysis of a BPTF bromodomain inhibitor

Kirberger, S. E., Ycas, P. D., Johnson, J. A., Chen, C., Ciccone, M. F., Woo, R. W. L., Urick, A. K., Zahid, H., Shi, K., Aihara, H., McAllister, S. D., Kashani-Sabet, M., Shi, J., Dickson, A., Dos Santos, C. O. & Pomerantz, W. C., Jan 1 2019, In : Organic and Biomolecular Chemistry. 17, 7, p. 2020-2027 8 p.

Research output: Contribution to journalArticle

inhibitors
selectivity
Ligands
ligands
proteins

The anti-parasitic agent suramin and several of its analogues are inhibitors of the DNA binding protein Mcm10

Paulson, C. N., John, K., Baxley, R. M., Kurniawan, F., Orellana, K., Francis, R., Sobeck, A., Eichman, B. F., Chazin, W. J., Aihara, H., Georg, G., Hawkinson, J. E. & Bielinsky, A. K., Aug 1 2019, In : Open biology. 9, 8, 190117.

Research output: Contribution to journalArticle

Open Access
Minichromosome Maintenance Proteins
Suramin
DNA-Binding Proteins
Fluorescence Polarization
Surface Plasmon Resonance
2 Citations (Scopus)

Triazolopyrimidine and triazolopyridine scaffolds as TDP2 inhibitors

Ribeiro, C. J. A., Kankanala, J., Xie, J., Williams, J., Aihara, H. & Wang, Z., Jan 15 2019, In : Bioorganic and Medicinal Chemistry Letters. 29, 2, p. 257-261 5 p.

Research output: Contribution to journalArticle

Phosphodiesterase Inhibitors
Scaffolds
Poisons
Type II DNA Topoisomerase
Cytotoxicity
2018
1 Citation (Scopus)

Comment on structural basis of DUX4/IGH-driven transactivation

Aihara, H., Shi, K., Lee, J. K., Bosnakovski, D. & Kyba, M., Sep 1 2018, In : Leukemia. 32, 9, p. 2090-2092 3 p.

Research output: Contribution to journalLetter

Open Access
Transcriptional Activation
1 Citation (Scopus)

Crystal Structure of Entamoeba histolytica Cdc45 Suggests a Conformational Switch that May Regulate DNA Replication

Kurniawan, F., Shi, K., Kurahashi, K., Bielinsky, A. K. & Aihara, H., May 25 2018, In : iScience. 3, p. 102-109 8 p.

Research output: Contribution to journalArticle

Open Access
Entamoeba histolytica
DNA replication
crystal structure
DNA Replication
biophysics

Crystal Structure of Entamoeba histolytica Cdc45 Suggests a Conformational Switch that May Regulate DNA Replication.

Kurniawan, F., Shi, K., Kurahashi, K., Bielinsky, A. K. & Aihara, H., May 25 2018, In : iScience. 3, p. 102-109 8 p.

Research output: Contribution to journalArticle

Crystal structure
Switches
Conformations
DNA
Proteins
3 Citations (Scopus)

Crystal structure of lipid A disaccharide synthase LpxB from Escherichia coli

Bohl, T. E., Shi, K., Lee, J. K. & Aihara, H., Dec 1 2018, In : Nature Communications. 9, 1, 377.

Research output: Contribution to journalArticle

Escherichia
Escherichia coli
Lipopolysaccharides
lipids
biosynthesis
1 Citation (Scopus)

Crystal Structure of the Double Homeodomain of DUX4 in Complex with DNA

Lee, J. K., Bosnakovski, D., Toso, E. A., Dinh, T., Banerjee, S., Bohl, T. E., Shi, K., Orellana, K., Kyba, M. & Aihara, H., Dec 11 2018, In : Cell Reports. 25, 11, p. 2955-2962.e3

Research output: Contribution to journalArticle

Facioscapulohumeral Muscular Dystrophy
Primates
Crystal structure
DNA
arginine glutamate
1 Citation (Scopus)
Lipopolysaccharides
Lipid A
Proteins
Membranes
Anti-Bacterial Agents

Differential assembly of Rous sarcoma virus tetrameric and octameric intasomes is regulated by the C-terminal domain and tail region of integrase

Bera, S., Pandey, K. K., Aihara, H. & Grandgenett, D. P., Jan 1 2018, In : Journal of Biological Chemistry. 293, 42, p. 16440-16452 13 p.

Research output: Contribution to journalArticle

Rous sarcoma virus
Integrases
Viruses
Viral DNA
Terminal Repeat Sequences
1 Citation (Scopus)

Importance of homo-dimerization of Fanconi-associated nuclease 1 in DNA flap cleavage

Rao, T., Longerich, S., Zhao, W., Aihara, H., Sung, P. & Xiong, Y., Apr 1 2018, In : DNA Repair. 64, p. 53-58 6 p.

Research output: Contribution to journalArticle

DNA Cleavage
Dimerization
DNA
Flap Endonucleases
Flaps
5 Citations (Scopus)

New fluorescence-based high-throughput screening assay for small molecule inhibitors of tyrosyl-DNA phosphodiesterase 2 (TDP2)

Ribeiro, C. J. A., Kankanala, J., Shi, K., Kurahashi, K., Kiselev, E., Ravji, A., Pommier, Y., Aihara, H. & Wang, Z., Jun 15 2018, In : European Journal of Pharmaceutical Sciences. 118, p. 67-79 13 p.

Research output: Contribution to journalArticle

High-Throughput Screening Assays
Fluorescence
Phosphodiesterase Inhibitors
Libraries
Gels

Oligomerization of retrovirus integrases

Grandgenett, D. P. & Aihara, H., Jan 1 2018, Subcellular Biochemistry. Springer New York, p. 211-243 33 p. (Subcellular Biochemistry; vol. 88).

Research output: Chapter in Book/Report/Conference proceedingChapter

Integrases
Oligomerization
Retroviridae
Viruses
Alpharetrovirus
5 Citations (Scopus)

T4 DNA ligase structure reveals a prototypical ATP-dependent ligase with a unique mode of sliding clamp interaction

Shi, K., Bohl, T. E., Park, J., Zasada, A., Malik, S., Banerjee, S., Tran, V., Li, N., Yin, Z., Kurniawan, F., Orellana, K. & Aihara, H., Jan 1 2018, In : Nucleic acids research. 46, 19, p. 10474-10488 15 p.

Research output: Contribution to journalArticle

DNA Ligases
Ligases
Adenosine Triphosphate
Archaeal DNA
DNA
13 Citations (Scopus)

The Antiviral and Cancer Genomic DNA Deaminase APOBEC3H Is Regulated by an RNA-Mediated Dimerization Mechanism

Shaban, N. M., Shi, K., Lauer, K. V., Carpenter, M. A., Richards, C. M., Salamango, D., Wang, J., Lopresti, M. W., Banerjee, S., Levin-Klein, R., Brown, W. L., Aihara, H. & Harris, R., Jan 4 2018, In : Molecular Cell. 69, 1, p. 75-86.e9

Research output: Contribution to journalArticle

Dimerization
Antiviral Agents
RNA
DNA
Neoplasms
2 Citations (Scopus)

The substrate-binding cap of the UDP-diacylglucosamine pyrophosphatase LpxH is highly flexible, enabling facile substrate binding and product release

Bohl, T. E., Ieong, P., Lee, J. K., Lee, T., Kankanala, J., Shi, K., Demir, Ö., Kurahashi, K., Amaro, R. E., Wang, Z. & Aihara, H., Jan 1 2018, In : Journal of Biological Chemistry. 293, 21, p. 7969-7981 13 p.

Research output: Contribution to journalArticle

Open Access
Pyrophosphatases
Uridine Diphosphate
Lipopolysaccharides
Substrates
Anti-Bacterial Agents
2017
2 Citations (Scopus)

A C-terminal "tail" region in the rous sarcoma virus integrase provides high plasticity of functional integrase oligomerization during intasome assembly

Pandey, K. K., Bera, S., Shi, K., Aihara, H. & Grandgenett, D. P., Mar 24 2017, In : Journal of Biological Chemistry. 292, 12, p. 5018-5030 13 p.

Research output: Contribution to journalArticle

Rous sarcoma virus
Integrases
Oligomerization
Viruses
Plasticity
6 Citations (Scopus)

Conformational switch regulates the DNA cytosine deaminase activity of human APOBEC3B

Shi, K., Demir, Ö., Carpenter, M. A., Wagner, J., Kurahashi, K., Harris, R., Amaro, R. E. & Aihara, H., Dec 1 2017, In : Scientific reports. 7, 1, 17415.

Research output: Contribution to journalArticle

Cytosine Deaminase
Human Activities
Catalytic Domain
Single-Stranded DNA
DNA
1 Citation (Scopus)

Five fatty aldehyde dehydrogenase enzymes from Marinobacter and Acinetobacter spp. and structural insights into the aldehyde binding pocket

Bertram, J. H., Mulliner, K. M., Shi, K., Plunkett, M. H., Nixon, P., Serratore, N. A., Douglas, C. J., Aihara, H. & Barney, B. M., Jun 1 2017, In : Applied and environmental microbiology. 83, 12, e00018-17.

Research output: Contribution to journalArticle

long-chain-aldehyde dehydrogenase
Marinobacter
aldehyde dehydrogenase
Acinetobacter
aldehyde
65 Citations (Scopus)

Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B

Shi, K., Carpenter, M. A., Banerjee, S., Shaban, N. M., Kurahashi, K., Salamango, D. J., McCann, J. L., Starrett, G. J., Duffy, J. V., Demir, Ö., Amaro, R. E., Harki, D. A., Harris, R. S. & Aihara, H., Feb 1 2017, In : Nature Structural and Molecular Biology. 24, 2, p. 131-139 9 p.

Research output: Contribution to journalArticle

Deamination
Single-Stranded DNA
Cytosine
Mutagenesis
Thymine
2016
18 Citations (Scopus)

1.92 Angstrom Zinc-Free APOBEC3F Catalytic Domain Crystal Structure

Shaban, N. M., Shi, K., Li, M., Aihara, H. & Harris, R., Jun 5 2016, In : Journal of Molecular Biology. 428, 11, p. 2307-2316 10 p.

Research output: Contribution to journalArticle

Zinc
Catalytic Domain
Disulfides
Cytosine Deaminase
Metals
31 Citations (Scopus)

Crystal structure of the Rous sarcoma virus intasome

Yin, Z., Shi, K., Banerjee, S., Pandey, K. K., Bera, S., Grandgenett, D. P. & Aihara, H., Feb 17 2016, In : Nature. 530, 7590, p. 362-366 5 p.

Research output: Contribution to journalArticle

Rous sarcoma virus
Integrases
Viral DNA
Retroviridae
Spumavirus
13 Citations (Scopus)

Deazaflavin Inhibitors of Tyrosyl-DNA Phosphodiesterase 2 (TDP2) Specific for the Human Enzyme and Active against Cellular TDP2

Marchand, C., Abdelmalak, M., Kankanala, J., Huang, S. Y., Kiselev, E., Fesen, K., Kurahashi, K., Sasanuma, H., Takeda, S., Aihara, H., Wang, Z. & Pommier, Y., Jul 15 2016, In : ACS Chemical Biology. 11, 7, p. 1925-1933 9 p.

Research output: Contribution to journalArticle

Enzymes
Phosphodiesterase Inhibitors
Derivatives
Drug Residues
Topoisomerase II Inhibitors
20 Citations (Scopus)

DNA-binding sequence specificity of DUX4

Zhang, Y., Lee, J. K., Toso, E. A., Lee, J. S., Choi, S. H., Slattery, M., Aihara, H. & Kyba, M., Jan 28 2016, In : Skeletal Muscle. 6, 1, 8.

Research output: Contribution to journalArticle

Consensus Sequence
Transcriptional Activation
DNA
Facioscapulohumeral Muscular Dystrophy
Chromatin
8 Citations (Scopus)

Importance for the repair of topoisomerase II-mediated DNA damage

Rao, T., Gao, R., Takada, S., Abo, M. A., Chen, X., Walters, K. J., Pommier, Y. & Aihara, H., Dec 1 2016, In : Nucleic acids research. 44, 21, p. 10201-10215 15 p.

Research output: Contribution to journalArticle

Type II DNA Topoisomerase
DNA Damage
Ubiquitin
DNA Repair
tyrosyl-DNA phosphodiesterase
20 Citations (Scopus)

Isoquinoline-1,3-diones as Selective Inhibitors of Tyrosyl DNA Phosphodiesterase II (TDP2)

Kankanala, J., Marchand, C., Abdelmalak, M., Aihara, H., Pommier, Y. & Wang, Z., Mar 24 2016, In : Journal of Medicinal Chemistry. 59, 6, p. 2734-2746 13 p.

Research output: Contribution to journalArticle

spleen exonuclease
Type II DNA Topoisomerase
Poisons
Drug Delivery Systems
Structure-Activity Relationship
19 Citations (Scopus)

Structures of Rpn1 T1:Rad23 and hRpn13:hPLIC2 Reveal Distinct Binding Mechanisms between Substrate Receptors and Shuttle Factors of the Proteasome

Chen, X., Randles, L., Shi, K., Tarasov, S. G., Aihara, H. & Walters, K. J., Aug 2 2016, In : Structure. 24, 8, p. 1257-1270 14 p.

Research output: Contribution to journalArticle

Proteasome Endopeptidase Complex
Ubiquitin
Ubiquitins
Amino Acid Substitution
2015
38 Citations (Scopus)

An ancient protein-DNA interaction underlying metazoan sex determination

Murphy, M. W., Lee, J. K., Rojo, S., Gearhart, M. D., Kurahashi, K., Banerjee, S., Loeuille, G. A., Bashamboo, A., McElreavey, K., Zarkower, D., Aihara, H. & Bardwell, V. J., Jun 3 2015, In : Nature Structural and Molecular Biology. 22, 6, p. 442-451 10 p.

Research output: Contribution to journalArticle

DNA
Sexual Development
Proteins
Exonucleases
Chromatin Immunoprecipitation
43 Citations (Scopus)

Crystal structure of the DNA deaminase APOBEC3B catalytic domain

Shi, K., Carpenter, M. A., Kurahashi, K., Harris, R. S. & Aihara, H., Nov 20 2015, In : Journal of Biological Chemistry. 290, 47, p. 28120-28130 11 p.

Research output: Contribution to journalArticle

Single-Stranded DNA
Catalytic Domain
Mutagenesis
Crystal structure
Tumors
2014
6 Citations (Scopus)
Azorhizobium caulinodans
Hydrolases
crystal structure
hydrolases
Crystal structure
4 Citations (Scopus)

Rous sarcoma virus synaptic complex capable of concerted integration is kinetically trapped by human immunodeficiency virus integrase strand transfer inhibitors

Pandey, K. K., Bera, S., Korolev, S., Campbell, M., Yin, Z., Aihara, H. & Grandgenett, D. P., Jul 11 2014, In : Journal of Biological Chemistry. 289, 28, p. 19648-19658 11 p.

Research output: Contribution to journalArticle

Rous sarcoma virus
Integrases
Viruses
HIV
Size exclusion chromatography
2013
8 Citations (Scopus)

An Enzyme-Catalyzed Multistep DNA Refolding Mechanism in Hairpin Telomere Formation

Shi, K., Huang, W. M. & Aihara, H., Jan 1 2013, In : PLoS Biology. 11, 1, e1001472.

Research output: Contribution to journalArticle

telomeres
Telomere
Chromosomes
DNA
chromosomes
7 Citations (Scopus)

A Possible Role for the Asymmetric C-Terminal Domain Dimer of Rous Sarcoma Virus Integrase in Viral DNA Binding

Shi, K., Pandey, K. K., Bera, S., Vora, A. C., Grandgenett, D. P. & Aihara, H., Feb 22 2013, In : PloS one. 8, 2, e56892.

Research output: Contribution to journalArticle

Rous sarcoma virus
Integrases
Viral DNA
Viruses
Dimers
2 Citations (Scopus)
Azorhizobium caulinodans
cyanuric acid
Hydrolases
Crystallization
X-Ray Diffraction
11 Citations (Scopus)
Cruciform DNA
Thermus thermophilus
Holliday Junction Resolvases
Recombinational DNA Repair
Single-Stranded DNA Breaks
2012
10 Citations (Scopus)

Linear chromosome-generating system of agrobacterium tumefaciens C58: Protelomerase generates and protects hairpin ends

Huang, W. M., DaGloria, J., Fox, H., Ruan, Q., Tillou, J., Shi, K., Aihara, H., Aron, J. & Casjens, S., Jul 20 2012, In : Journal of Biological Chemistry. 287, 30, p. 25551-25563 13 p.

Research output: Contribution to journalArticle

Agrobacterium tumefaciens
Chromosomes
Telomere
Agrobacterium
Plasmids
38 Citations (Scopus)

Structural basis for recognition of 5′-phosphotyrosine adducts by Tdp2

Shi, K., Kurahashi, K., Gao, R., Tsutakawa, S. E., Tainer, J. A., Pommier, Y. & Aihara, H., Dec 1 2012, In : Nature Structural and Molecular Biology. 19, 12, p. 1372-1377 6 p.

Research output: Contribution to journalArticle

Phosphotyrosine
DNA Repair Enzymes
Molecular Mimicry
Picornaviridae
Type I DNA Topoisomerase
2007
29 Citations (Scopus)

An Interlocked Dimer of the Protelomerase TelK Distorts DNA Structure for the Formation of Hairpin Telomeres

Aihara, H., Huang, W. M. & Ellenberger, T., Sep 21 2007, In : Molecular Cell. 27, 6, p. 901-913 13 p.

Research output: Contribution to journalArticle

Telomere
DNA
Chromosomes
Klebsiella oxytoca
DNA Cleavage
2006
46 Citations (Scopus)

DNA arms do the legwork to ensure the directionality of λ site-specific recombination

Radman-Livaja, M., Biswas, T., Ellenberger, T., Landy, A. & Aihara, H., Feb 1 2006, In : Current Opinion in Structural Biology. 16, 1, p. 42-50 9 p.

Research output: Contribution to journalReview article

Genetic Recombination
DNA
Cruciform DNA
Coliphages
Integrases
2005
121 Citations (Scopus)

A structural basis for allosteric control of DNA recombination by λ integrase

Biswas, T., Aihara, H., Radman-Livaja, M., Filman, D., Landy, A. & Ellenberger, T., Jun 23 2005, In : Nature. 435, 7045, p. 1059-1066 8 p.

Research output: Contribution to journalArticle

Integrases
Genetic Recombination
DNA
Bacteriophages
Chromosomes
10 Citations (Scopus)

Non-equivalent interactions between amino-terminal domains of neighboring λ integrase protomers direct holliday junction resolution

Lee, S. Y., Radman-Livaja, M., Warren, D., Aihara, H., Ellenberger, T. & Landy, A., Jan 21 2005, In : Journal of Molecular Biology. 345, 3, p. 475-485 11 p.

Research output: Contribution to journalArticle

Cruciform DNA
Integrases
Protein Subunits
Genetic Recombination
Recombinases
2004
12 Citations (Scopus)

Two structural features of λ integrase that are critical DNA cleavege by multimers but not by monomers

Lee, S. Y., Aihara, H., Ellenberger, T. & Landy, A., Mar 2 2004, In : Proceedings of the National Academy of Sciences of the United States of America. 101, 9, p. 2770-2775 6 p.

Research output: Contribution to journalArticle

Integrases
DNA
Cruciform DNA
DNA Cleavage
Salts
2003
37 Citations (Scopus)

A conformational switch controls the DNA cleavage activity of λ integrase

Aihara, H., Kwon, H. J., Nunes-Düby, S. E., Landy, A. & Ellenberger, T., Jul 1 2003, In : Molecular Cell. 12, 1, p. 187-198 12 p.

Research output: Contribution to journalArticle

Integrases
DNA Cleavage
DNA
Catalytic Domain
Recombinases
21 Citations (Scopus)

An NMR study on the interaction of Escherichia coli Dinl with RecA-ssDNA complexes

Yoshimasu, M., Aihara, H., Ito, Y., Rajesh, S., Ishibe, S., Mikawa, T., Yokoyama, S. & Shibata, T., Mar 15 2003, In : Nucleic acids research. 31, 6, p. 1735-1743 9 p.

Research output: Contribution to journalReview article

Peptide Hydrolases
Magnetic Resonance Spectroscopy
Escherichia coli
Single-Stranded DNA
Protein Subunits