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Publication
Featured researches published by Pai-Chi Li.
Journal of Computational Chemistry | 2014
Pai-Chi Li; Naoyuki Miyashita; Wonpil Im; Satoshi Ishido; Yuji Sugita
Structural information of a transmembrane (TM) helix dimer is useful in understanding molecular mechanisms of important biological phenomena such as signal transduction across the cell membrane. Here, we describe an umbrella sampling (US) scheme for predicting the structure of a TM helix dimer in implicit membrane using the interhelical crossing angle and the TM–TM relative rotation angles as the reaction coordinates. This scheme conducts an efficient conformational search on TM–TM contact interfaces, and its robustness is tested by predicting the structures of glycophorin A (GpA) and receptor tyrosine kinase EphA1 (EphA1) TM dimers. The nuclear magnetic resonance (NMR) structures of both proteins correspond to the global free‐energy minimum states in their free‐energy landscapes. In addition, using the landscape of GpA as a reference, we also examine the protocols of temperature replica‐exchange molecular dynamics (REMD) simulations for structure prediction of TM helix dimers in implicit membrane. A wide temperature range in REMD simulations, for example, 250–1000 K, is required to efficiently obtain a free‐energy landscape consistent with the US simulations. The interhelical crossing angle and the TM–TM relative rotation angles can be used as reaction coordinates in multidimensional US and be good measures for conformational sampling of REMD simulations.
Journal of Virology | 2012
Mizuho Kajikawa; Pai-Chi Li; Eiji Goto; Naoyuki Miyashita; Masami Aoki-Kawasumi; Mari Mito-Yoshida; Mika Ikegaya; Yuji Sugita; Satoshi Ishido
ABSTRACT Kaposis sarcoma-associated herpesvirus (KSHV), a human tumor virus, encodes two homologous membrane-associated E3 ubiquitin ligases, modulator of immune recognition 1 (MIR1) and MIR2, to evade host immunity. Both MIR1 and MIR2 downregulate the surface expression of major histocompatibility complex class I (MHC I) molecules through ubiquitin-mediated endocytosis followed by lysosomal degradation. Since MIR2 additionally downregulates a costimulatory molecule (B7-2) and an integrin ligand (intercellular adhesion molecule 1 [ICAM-1]), MIR2 is thought to be a more important molecule for immune evasion than MIR1; however, the molecular basis of the MIR2 substrate specificity remains unclear. To address this issue, we determined which regions of B7-2 and MIR2 are required for MIR2-mediated B7-2 downregulation. Experiments with chimeras made by swapping domains between human B7-2 and CD8α, a non-MIR2 substrate, and between MIR1 and MIR2 demonstrated a significant contribution of the juxtamembrane (JM) region of B7-2 and the intertransmembrane (ITM) region of MIR2 to MIR2-mediated downregulation. Structure prediction and mutagenesis analyses indicate that Phe119 and Ser120 in the MIR2 ITM region and Asp244 in the B7-2 JM region contribute to the recognition of B7-2 by MIR2. This finding provides new insight into the molecular basis of substrate recognition by MIR family members.
Biophysical Journal | 2016
Koichiro Shirota; Kiyoshi Yagi; Takehiko Inaba; Pai-Chi Li; Michio Murata; Yuji Sugita; Toshihide Kobayashi
Physical Chemistry Chemical Physics | 2015
Kiyoshi Yagi; Pai-Chi Li; Koichiro Shirota; Toshihide Kobayashi; Yuji Sugita
Combinatorics, Probability & Computing | 2012
Yuji Sugita; Naoyuki Miyashita; Pai-Chi Li; Takao Yoda; Yuko Okamoto
生物物理 | 2014
Koichiro Shirota; Takehiko Inaba; Pai-Chi Li; Kiyoshi Yagi; Yuji Sugita; Toshihide Kobayashi
生物物理 | 2014
Yumi Kashihara; Naoyuki Miyashita; Pai-Chi Li; Yuji Sugita
Seibutsu Butsuri | 2014
Koichiro Shirota; Takehiko Inaba; Pai-Chi Li; Kiyoshi Yagi; Yuji Sugita; Toshihide Kobayashi
Seibutsu Butsuri | 2014
Yumi Kashihara; Naoyuki Miyashita; Pai-Chi Li; Yuji Sugita
Seibutsu Butsuri | 2014
Pai-Chi Li; Kiyoshi Yagi; Koichiro Shirota; Toshihide Kobayashi; Yuji Sugita