Nature Search

Essential structural elements in tRNA^Pro for EF-P-mediated alleviation of translation stalling

Ribosomes tend to stall during the translation of consecutive proline residues, which can be rescued by the co-translational factor EF-P. Here the authors identify a structural element of tRNA^Proresponsible for specific recognition by EF-P and stimulation of Pro-Pro peptide bond formation.

Takayuki Katoh
Ingo Wohlgemuth
Hiroaki Suga
ResearchOpen Access24 May 2016
Nature Communications

Volume: 7, P: 1-12
A super versatile flexizyme system with phenol esters for genetic code reprogramming

Genetic code reprogramming enables ribosomal incorporation of nonproteinogenic amino acids for peptide development. The authors introduce a flexizyme system using phenol esters, improving aminoacylation efficiency and expanding ribosomal synthesis of diverse nonstandard peptides.

Yun-Kyu Choi
Takayuki Katoh
Hiroaki Suga
ResearchOpen Access20 May 2025
Nature Communications

Volume: 16, P: 1-10
Author Correction: Structural basis for the drug extrusion mechanism by a MATE multidrug transporter

Yoshiki Tanaka
Christopher J. Hipolito
Osamu Nureki
Amendments and Corrections30 Jan 2020
Nature

Volume: 578, P: E19
In vitro selection of macrocyclic peptide inhibitors containing cyclic γ^2,4-amino acids targeting the SARS-CoV-2 main protease

In vitro screening of a ribosomally synthesized macrocyclic peptide library containing cyclic γ^2,4-amino acids (cγAA) afforded the discovery of potent inhibitors of the SARS-CoV-2 main protease (M^pro). A co-crystal structure revealed the contribution of this cγAA to M^pro binding and the proteolytic stability of these macrocycles.

Takashi Miura
Tika R. Malla
Hiroaki Suga
ResearchOpen Access22 May 2023
Nature Chemistry

Volume: 15, P: 998-1005
Ribosomal synthesis and de novo discovery of bioactive foldamer peptides containing cyclic β-amino acids

Cyclic β-amino acids can add useful properties to peptides, such as inducing turn structures or providing resistance to proteases. To harness these properties up to ten consecutive cyclic β-amino acids have now been ribosomally incorporated via genetic code reprogramming into a foldamer peptide library that has been screened for potent binders against a protein target, human factor XIIa.

Takayuki Katoh
Toru Sengoku
Hiroaki Suga
Research24 Aug 2020
Nature Chemistry

Volume: 12, P: 1081-1088
HIF-1α-PDK1 axis-induced active glycolysis plays an essential role in macrophage migratory capacity

Migration to the inflamed tissue demands energy production in an increasingly hypoxic environment. Here the authors show that during migration, HIF1α-induced PDK1 uniquely adapts macrophage metabolism to mild hypoxia by promoting glycolysis while preserving cytochrome c oxidase activity.

Hiroaki Semba
Norihiko Takeda
Issei Komuro
ResearchOpen Access18 May 2016
Nature Communications

Volume: 7, P: 1-10
Highly selective inhibition of histone demethylases by de novo macrocyclic peptides

JmjC histone demethylases (KDMs) are cancer targets due to their links to cell proliferation, but selective inhibition remains a challenge. Here the authors identify potent inhibitors of KDM4A-C—viain vitroselection from a vast library of cyclic peptides—that show selectivity over other KDMs.

Akane Kawamura
Martin Münzel
Christopher J. Schofield
ResearchOpen Access06 Apr 2017
Nature Communications

Volume: 8, P: 1-10
Macrocyclic peptides exhibit antiviral effects against influenza virus HA and prevent pneumonia in animal models

Here, the authors report bi-functional, wide tropic macrocycles that bind the influenza viral envelope protein hemagglutinin and inhibit virus infection by blocking adsorption and fusion and show efficacy in preventing severe pneumonia at later stages of infection in mouse and non-human primate cynomolgus macaque models.

Makoto Saito
Yasushi Itoh
Michinori Kohara
ResearchOpen Access11 May 2021
Nature Communications

Volume: 12, P: 1-11
An aminoacylation ribozyme evolved from a natural tRNA-sensing T-box riboswitch

The authors develop a ribozyme, Tx2.1, that is capable of aminoacylating tRNA with specificity for the anticodon from directed evolution of a T-box riboswitch. Tx2.1 could be used to charge non-natural amino acids in an in vitro translation system.

Satoshi Ishida
Naohiro Terasaka
Hiroaki Suga
Research23 Mar 2020
Nature Chemical Biology

Volume: 16, P: 702-709
Expanding the amino acid repertoire of ribosomal polypeptide synthesis via the artificial division of codon boxes

The repertoire of amino acids available for ribosomal peptide synthesis is limited by the genetic code. Now, a method to reduce the redundancy of codons has been developed based on the artificial division of codon boxes. This method enables non-proteinogenic amino acids to be included in peptides without sacrificing proteinogenic ones.

Yoshihiko Iwane
Azusa Hitomi
Hiroaki Suga
Research01 Feb 2016
Nature Chemistry

Volume: 8, P: 317-325
Macrophage hypoxia signaling regulates cardiac fibrosis via Oncostatin M

Fibrosis is a hallmark of several cardiac pathologies and its underlying mechanisms are still poorly defined. Here the authors show that macrophage hypoxia signaling following transverse aortic constriction in mice suppresses the activation of cardiac fibroblasts by secreting oncostatin M.

Hajime Abe
Norihiko Takeda
Issei Komuro
ResearchOpen Access27 Jun 2019
Nature Communications

Volume: 10, P: 1-10
Updated Japanese multicenter registry study evaluates the efficacy and safety of proton beam therapy for treating extrahepatic cholangiocarcinoma

Hideya Yamazaki
Kei Shibuya
Masayuki Ohtsuka
ResearchOpen Access02 Jul 2025
Scientific Reports

Volume: 15, P: 1-8
Reprogramming the genetic code with flexizymes

Flexizymes can be used to prepare nonproteinogenic aminoacyl-tRNAs (npAA-tRNAs) by activating amino acids with suitable leaving groups, leading to ribosomal incorporation of npAAs by genetic code reprogramming. This enables the ribosomal synthesis of unique peptides and proteins containing various npAAs.

Takayuki Katoh
Hiroaki Suga
Reviews21 Oct 2024
Nature Reviews Chemistry

Volume: 8, P: 879-892
Mutation of ARX causes abnormal development of forebrain and testes in mice and X-linked lissencephaly with abnormal genitalia in humans

Kunio Kitamura
Masako Yanazawa
Ken-ichirou Morohashi
Research15 Oct 2002
Nature Genetics

Volume: 32, P: 359-369
Motor torque measurement of Halobacterium salinarum archaellar suggests a general model for ATP-driven rotary motors

Seiji Iwata et al. report protocols for visualizing and measuring the torque of the rotary propeller (archaellar) used by the Archea Halobacterium salinarum. They find that the estimated work done in a single rotation is more than expected and propose a new model for the mechanism of ATP-driven rotary motors.

Seiji Iwata
Yoshiaki Kinosita
Takayuki Nishizaka
ResearchOpen Access24 May 2019
Communications Biology

Volume: 2, P: 1-6
Few-photon color imaging using energy-dispersive superconducting transition-edge sensor spectrometry

Kazuki Niwa
Takayuki Numata
Daiji Fukuda
ResearchOpen Access04 Apr 2017
Scientific Reports

Volume: 7, P: 1-7
Mathematical mechanistic model representing the cancer immunity cycle under radiation effects

Taisuke Takayanagi
Koichi Miyazaki
Kenji Chamoto
ResearchOpen Access06 Jun 2025
Scientific Reports

Volume: 15, P: 1-14
Three-dimensional tracking of microbeads attached to the tip of single isolated tracheal cilia beating under external load

Takanobu A. Katoh
Koji Ikegami
Takayuki Nishizaka
ResearchOpen Access22 Oct 2018
Scientific Reports

Volume: 8, P: 1-9
Loss of function of the IAA-glucose hydrolase gene TGW6 enhances rice grain weight and increases yield

Ken Ishimaru and colleagues show that loss of function of the rice gene TGW6 enhances rice grain weight and increases yield. TGW6 encodes a protein with IAA-glucose hydrolase activity.

Ken Ishimaru
Naoki Hirotsu
Etsuko Katoh
Research14 Apr 2013
Nature Genetics

Volume: 45, P: 707-711
Structural basis for the drug extrusion mechanism by a MATE multidrug transporter

Several X-ray crystal structures of an H⁺-driven multidrug and toxic compound extrusion (MATE) transporter from Pyrococcus furiosus are presented, whose complex structure with macrocyclic peptides may help facilitate the discovery of efficient inhibitors of MATE transporters.

Yoshiki Tanaka
Christopher J. Hipolito
Osamu Nureki
Research27 Mar 2013
Nature

Volume: 496, P: 247-251
An orthogonal ribosome-tRNA pair via engineering of the peptidyl transferase center

Genetic code reprogramming has generally focused on changing the translation step of protein expression, altering what each codon specifies. Mutations in the peptidyl transferase center, along with compensatory mutations in the C-termini of tRNAs, now provide an alternate method to create fully orthogonal ribosomes.

Naohiro Terasaka
Gosuke Hayashi
Hiroaki Suga
Research08 Jun 2014
Nature Chemical Biology

Volume: 10, P: 555-557
Flexizymes for genetic code reprogramming

Yuki Goto
Takayuki Katoh
Hiroaki Suga
Protocols12 May 2011
Nature Protocols

Volume: 6, P: 779-790
Acetic-acid-induced jasmonate signaling in root enhances drought avoidance in rice

Daisuke Ogawa
Yuya Suzuki
Yoshiki Habu
ResearchOpen Access18 Mar 2021
Scientific Reports

Volume: 11, P: 1-13
Parvovirus B19 infection in adult patients after allogeneic stem cell transplantation: our experience of five cases and literature review

Daisuke Katoh
Yotaro Ochi
Takayuki Ishikawa
Correspondence14 May 2019
Bone Marrow Transplantation

Volume: 55, P: 653-656

Search

Essential structural elements in tRNA^Pro for EF-P-mediated alleviation of translation stalling

A super versatile flexizyme system with phenol esters for genetic code reprogramming

Author Correction: Structural basis for the drug extrusion mechanism by a MATE multidrug transporter

In vitro selection of macrocyclic peptide inhibitors containing cyclic γ^2,4-amino acids targeting the SARS-CoV-2 main protease

Ribosomal synthesis and de novo discovery of bioactive foldamer peptides containing cyclic β-amino acids

HIF-1α-PDK1 axis-induced active glycolysis plays an essential role in macrophage migratory capacity

Highly selective inhibition of histone demethylases by de novo macrocyclic peptides

Macrocyclic peptides exhibit antiviral effects against influenza virus HA and prevent pneumonia in animal models

An aminoacylation ribozyme evolved from a natural tRNA-sensing T-box riboswitch

Expanding the amino acid repertoire of ribosomal polypeptide synthesis via the artificial division of codon boxes

Macrophage hypoxia signaling regulates cardiac fibrosis via Oncostatin M

Updated Japanese multicenter registry study evaluates the efficacy and safety of proton beam therapy for treating extrahepatic cholangiocarcinoma

Reprogramming the genetic code with flexizymes

Mutation of ARX causes abnormal development of forebrain and testes in mice and X-linked lissencephaly with abnormal genitalia in humans

Motor torque measurement of Halobacterium salinarum archaellar suggests a general model for ATP-driven rotary motors

Few-photon color imaging using energy-dispersive superconducting transition-edge sensor spectrometry

Mathematical mechanistic model representing the cancer immunity cycle under radiation effects

Three-dimensional tracking of microbeads attached to the tip of single isolated tracheal cilia beating under external load

Loss of function of the IAA-glucose hydrolase gene TGW6 enhances rice grain weight and increases yield

Structural basis for the drug extrusion mechanism by a MATE multidrug transporter

An orthogonal ribosome-tRNA pair via engineering of the peptidyl transferase center

Flexizymes for genetic code reprogramming

Acetic-acid-induced jasmonate signaling in root enhances drought avoidance in rice

Parvovirus B19 infection in adult patients after allogeneic stem cell transplantation: our experience of five cases and literature review

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