Daniel A. Harki

Prof. Daniel A. Harki

University of Minnesota, Minneapolis, Minnesota, USA
orcid

Research Focus & Metrics

Academic Career Length

25Years (2002-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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20 December 2016 in Journal of Medicinal Chemistry
Verified
Journal Article
Closed access
PJPaul A. Jackson
Paul A. Jackson
JWJohn C. Widen
John C. Widen
DHDaniel A. Harki
Daniel A. Harki
KBKay M. Brummond
Kay M. Brummond

8 October 2015 in Nature Communications
Verified
Journal Article
Open access
PDF file
JKJaclyn P. Kerr
Jaclyn P. Kerr
PRPatrick Robison
Patrick Robison
GSGuoli Shi
Guoli Shi
ABAlexey I. Bogush
Alexey I. Bogush
AKAaron M. Kempema
Aaron M. Kempema
CWChristopher W. Ward
Christopher W. Ward
In striated muscle, X-ROS is the mechanotransduction pathway by which mechanical stress transduced by the microtubule network elicits reactive oxygen species. X-ROS tunes Ca2+ signalling in healthy muscle, but in diseases such as Duchenne muscular dystrophy (DMD), microtubule alterations drive elevated X-ROS, disrupting Ca2+ homeostasis and impairing function. Here we show that detyrosination, a post-translational modification of α-tubulin, influences X-ROS signalling, contraction speed and cytoskeletal mechanics. In the mdx mouse model of DMD, the pharmacological reduction of detyrosination in vitro ablates aberrant X-ROS and Ca2+ signalling, and in vivo it protects against hallmarks of DMD, including workload-induced arrhythmias and contraction-induced injury in skeletal muscle. We conclude that detyrosinated microtubules increase cytoskeletal stiffness and mechanotransduction in striated muscle and that targeting this post-translational modification may have broad therapeutic potential in muscular dystrophies.

19 December 2016 in Nature Structural & Molecular Biology
Verified
Journal Article
Open access
PDF file
KSKe Shi
Ke Shi
MCMichael A Carpenter
Michael A Carpenter
SBSurajit Banerjee
Surajit Banerjee
NSNadine M Shaban
Nadine M Shaban
KKKayo Kurahashi
Kayo Kurahashi
HAHideki Aihara
Hideki Aihara
Crystal structures of human APOBEC3A and a chimera of APOBEC3B and APOBEC3A bound to ssDNA reveal an unanticipated ‘U-shaped’ binding mode and provide insight into target selectivity. APOBEC-catalyzed cytosine-to-uracil deamination of single-stranded DNA (ssDNA) has beneficial functions in immunity and detrimental effects in cancer. APOBEC enzymes have intrinsic dinucleotide specificities that impart hallmark mutation signatures. Although numerous structures have been solved, mechanisms for global ssDNA recognition and local target-sequence selection remain unclear. Here we report crystal structures of human APOBEC3A and a chimera of human APOBEC3B and APOBEC3A bound to ssDNA at 3.1-Å and 1.7-Å resolution, respectively. These structures reveal a U-shaped DNA conformation, with the specificity-conferring −1 thymine flipped out and the target cytosine inserted deep into the zinc-coordinating active site pocket. The −1 thymine base fits into a groove between flexible loops and makes direct hydrogen bonds with the protein, accounting for the strong 5′-TC preference. These findings explain both conserved and unique properties among APOBEC family members, and they provide a basis for the rational design of inhibitors to impede the evolvability of viruses and tumors.

1 January 2018 in Cell Chemical Biology
Verified
Journal Article
Closed access
MOMargaret E. Olson
Margaret E. Olson
RHReuben S. Harris
Reuben S. Harris
DHDaniel A. Harki
Daniel A. Harki

1 March 2008 in Journal of Biological Chemistry
Verified
Journal Article
Open access
DZDmitry F. Zamyatkin
Dmitry F. Zamyatkin
FPFrancisco Parra
Francisco Parra
JAJosé M. Martín Alonso
José M. Martín Alonso
DHDaniel A. Harki
Daniel A. Harki
BPBlake Peterson
Blake Peterson
KNKenneth Ng
Kenneth Ng
Crystal structures of Norwalk virus polymerase bound to an RNA primer-template duplex and either the natural substrate CTP or the inhibitor 5-nitrocytidine triphosphate have been determined to 1.8A resolution. These structures reveal a closed conformation of the polymerase that differs significantly from previously determined open structures of calicivirus and picornavirus polymerases. These closed complexes are trapped immediately prior to the nucleotidyl transfer reaction, with the triphosphate group of the nucleotide bound to two manganese ions at the active site, poised for reaction to the 3'-hydroxyl group of the RNA primer. The positioning of the 5-nitrocytidine triphosphate nitro group between the alpha-phosphate and the 3'-hydroxyl group of the primer suggests a novel, general approach for the design of antiviral compounds mimicking natural nucleosides and nucleotides.

19 December 2011 in ACS Chemical Biology
Verified
Journal Article
Closed access
MLMing Li
Ming Li
SSShivender M. D. Shandilya
Shivender M. D. Shandilya
MCMichael A. Carpenter
Michael A. Carpenter
ARAnurag Rathore
Anurag Rathore
WBWilliam L. Brown
William L. Brown
RHReuben Harris
Reuben Harris