Kenji Murakami
University of Pennsylvania · Rehabilitation Medicine
Active 1950–2024
About
Kenji Murakami, Ph.D., is an Associate Professor of Biochemistry and Biophysics at the University of Pennsylvania's Perelman School of Medicine. He also holds positions at the Penn Center for Genome Integrity and the Institute of Structural Biology. His research focuses on the mechanisms of eukaryotic gene expression by RNA polymerase II, particularly the transitions between initiation, elongation, and re-initiation during transcription. His work aims to elucidate how these processes are regulated within the context of chromatin, employing structural techniques such as cryo-electron microscopy and cross-linking mass spectrometry, alongside biochemical dissection of macromolecular complexes. Dr. Murakami's contributions include detailed structural analyses of transcription pre-initiation complexes, DNA-protein organization, and the molecular basis of transcription regulation, advancing understanding of gene expression regulation and its implications in development and disease.
Research topics
- Biochemistry
- Biophysics
- Biology
- Stereochemistry
- Chemistry
- Photochemistry
- Cell biology
- Crystallography
Selected publications
Nature Communications · 2021 · 25 citations
- Chemistry
- Stereochemistry
- Biophysics
. The successful production of a native-like functional SC and determination of its structure illustrate the characteristics of membrane-confined and membrane-external respiratory electron transport pathways in Gram-negative bacteria.
Cryo-EM structure of NPF-bound human Arp2/3 complex and activation mechanism
Science Advances · 2020 · 85 citations
- Cell biology
- Biophysics
- Biology
Actin-related protein (Arp) 2/3 complex nucleates branched actin networks that drive cell motility. It consists of seven proteins, including two actin-related subunits (Arp2 and Arp3). Two nucleation-promoting factors (NPFs) bind Arp2/3 complex during activation, but the order, specific interactions, and contribution of each NPF to activation are unresolved. Here, we report the cryo-electron microscopy structure of recombinantly expressed human Arp2/3 complex with two WASP family NPFs bound and address the mechanism of activation. A cross-linking assay that captures the transition of the Arps into the activated filament-like conformation shows that actin binding to NPFs favors this transition. Actin-NPF binding to Arp2 precedes binding to Arp3 and is sufficient to promote the filament-like conformation but not activation. Structure-guided mutagenesis of the NPF-binding sites reveals their distinct roles in activation and shows that, contrary to budding yeast Arp2/3 complex, NPF-mediated delivery of actin at the barbed end of both Arps is required for activation of human Arp2/3 complex.
Recent grants
Frequent coauthors
- 17 shared
Hee Jong Kim
- 16 shared
Takaya Shimura
- 16 shared
Takeyuki Wakabayashi
The University of Tokyo
- 13 shared
Kuang‐Lei Tsai
The University of Texas MD Anderson Cancer Center
- 13 shared
F. Misaki
- 13 shared
Trevor van Eeuwen
- 12 shared
Masaharu Masuda
- 12 shared
Takashi Joh
Kumamoto City Hospital
Education
- 2004
Ph.D., Physics
University of Tokyo
- 2001
M.Sc., Physics
University of Tokyo
- 1999
B.Sci., Physics
University of Tokyo
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