Basic Information

Faculty

• 医学部
• 国際高等教育院

Email Address

• Email Address

  walinda.erik.6ekyoto-u.ac.jp

Academic Degree

• 修士（生化学）(ベルリン自由大学)
• 博士（工学）(京都大学)

Academic Resume (Graduate Schools)

• ベルリン自由大学, 化学部生化学科, 修了
• 京都大学, 大学院工学研究科博士後期課程分子工学専攻, 修了

Language of Instruction

• English
• German

ID,URL

• J-Global ID

  201601012690712220

researchmap URL

• https://researchmap.jp/7000014118

Research

Research Topics, Overview of the research

• Research Topics

  Structural Dynamics of Proteins

Research Areas

• Life sciences, Medical biochemistry
• Life sciences, Structural biochemistry

Papers

• A fast and simple automated multi-step protein purification method for ÄKTA go systems

  Daichi Morimoto; Erik Walinda

  Protein Expression and Purification, Nov. 2024

  
• Cyclization of ubiquitin chains reinforces their recognition by ZNF216

  Tomoki Sorada; Erik Walinda; Daichi Morimoto

  FEBS Letters, 09 Jun. 2024

  
• A de novo dominant-negative variant is associated with OTULIN-related autoinflammatory syndrome.

  Yukiko Takeda; Masahiro Ueki; Junpei Matsuhiro; Erik Walinda; Takayuki Tanaka; Masafumi Yamada; Hiroaki Fujita; Shunichiro Takezaki; Ichiro Kobayashi; Sakura Tamaki; Sanae Nagata; Noriko Miyake; Naomichi Matsumoto; Mitsujiro Osawa; Takahiro Yasumi; Toshio Heike; Fumiaki Ohtake; Megumu K Saito; Junya Toguchida; Junko Takita; Tadashi Ariga; Kazuhiro Iwai

  The Journal of experimental medicine, 03 Jun. 2024

  Access this paper :

  
• An integrated approach of NMR experiments and MD simulations visualizes structural dynamics of a cyclic multi‐domain protein

  Tomoki Sorada; Erik Walinda; Masahiro Shirakawa; Kenji Sugase; Daichi Morimoto

  Protein Science, 25 Aug. 2023

  
• Solution structure of the HOIL-1L NZF domain reveals a conformational switch regulating linear ubiquitin affinity

  Erik Walinda; Kenji Sugase; Naoki Ishii; Masahiro Shirakawa; Kazuhiro Iwai; Daichi Morimoto

  Journal of Biological Chemistry, Aug. 2023

  
• Conformational Fluctuations and Induced Orientation of a Protein, Its Solvation Shell, and Bulk Water in Weak Non-Unfolding External Electric Fields

  Yusuke Shuto; Erik Walinda; Daichi Morimoto; Kenji Sugase

  The Journal of Physical Chemistry B, 16 Aug. 2023

  Access this paper :

  
• Rheo‐NMR Spectroscopy for Cryogenic‐Probe‐Equipped NMR Instruments to Monitor Protein Aggregation

  Daichi Morimoto; Erik Walinda; Akihiko Yamamoto; Ulrich Scheler; Kenji Sugase

  Current Protocols, Dec. 2022

  
• Counter-flow phenomena studied by nuclear magnetic resonance (NMR) velocimetry and flow simulations

  Benjamin Kohn; Erik Walinda; Kenji Sugase; Daichi Morimoto; Ulrich Scheler

  Physics of Fluids, Jul. 2022

  
• Structural Insights into Methylated DNA Recognition by the Methyl-CpG Binding Domain of MBD6 from Arabidopsis thaliana

  Yutaka Mahana; Izuru Ohki; Erik Walinda; Daichi Morimoto; Kenji Sugase; Masahiro Shirakawa

  ACS Omega, 01 Feb. 2022

  Access this paper :

  
• Expression, solubility monitoring, and purification of the co-folded LUBAC LTM domain by structure-guided tandem folding in autoinducing cultures.

  Erik Walinda; Daichi Morimoto; Tomoki Sorada; Kazuhiro Iwai; Kenji Sugase

  Protein expression and purification, Nov. 2021, Peer-reviewed, Lead author, Corresponding author

  
• Effects of Weak Nonspecific Interactions with ATP on Proteins.

  Mayu Nishizawa; Erik Walinda; Daichi Morimoto; Benjamin Kohn; Ulrich Scheler; Masahiro Shirakawa; Kenji Sugase

  Journal of the American Chemical Society, 11 Aug. 2021, Peer-reviewed, Lead author

  
• Multiple-State Monitoring of SOD1 Amyloid Formation at Single-Residue Resolution by Rheo-NMR Spectroscopy.

  Naoto Iwakawa; Daichi Morimoto; Erik Walinda; Masahiro Shirakawa; Kenji Sugase

  Journal of the American Chemical Society, 21 Jul. 2021, Peer-reviewed

  
• Backbone resonance assignments of the A2 domain of mouse von Willebrand factor.

  Daichi Morimoto; Masanori Osugi; Yutaka Mahana; Erik Walinda; Masahiro Shirakawa; Kenji Sugase

  Biomolecular NMR assignments, 20 Jul. 2021, Peer-reviewed

  
• Molecular recognition and deubiquitination of cyclic K48-linked ubiquitin chains by OTUB1.

  Tomoki Sorada; Daichi Morimoto; Erik Walinda; Kenji Sugase

  Biochemical and biophysical research communications, 12 Jul. 2021, Peer-reviewed

  
• Transient Diffusive Interactions with a Protein Crowder Affect Aggregation Processes of Superoxide Dismutase 1 β-Barrel.

  Naoto Iwakawa; Daichi Morimoto; Erik Walinda; Sarah Leeb; Masahiro Shirakawa; Jens Danielsson; Kenji Sugase

  The journal of physical chemistry. B, 18 Mar. 2021, Peer-reviewed

  
• Structural Dynamic Heterogeneity of Polyubiquitin Subunits Affects Phosphorylation Susceptibility.

  Daichi Morimoto; Erik Walinda; Shingo Takashima; Mayu Nishizawa; Kazuhiro Iwai; Masahiro Shirakawa; Kenji Sugase

  Biochemistry, 02 Mar. 2021, Peer-reviewed, Lead author

  
• Structural dynamics of double-stranded DNA with epigenome modification.

  Ayako Furukawa; Erik Walinda; Kyohei Arita; Kenji Sugase

  Nucleic acids research, 25 Jan. 2021, Peer-reviewed

  
• Rigorous analysis of the interaction between proteins and low water-solubility drugs by qNMR-aided NMR titration experiments

  Takuya Hirakawa; Erik Walinda; Daichi Morimoto; Kenji Sugase

  Physical Chemistry Chemical Physics, 2021

  
• Quantitative monitoring of ubiquitination/deubiquitination reaction cycles by 18O-incorporation.

  Yuka Tanaka; Daichi Morimoto; Erik Walinda; Kenji Sugase; Masahiro Shirakawa

  Biochemical and biophysical research communications, 20 Aug. 2020, Peer-reviewed

  
• Pinpoint analysis of a protein in slow exchange using F1F2-selective ZZ-exchange spectroscopy: assignment and kinetic analysis

  Mayu Nishizawa; Erik Walinda; Daichi Morimoto; Kenji Sugase

  Journal of Biomolecular NMR, May 2020, Peer-reviewed

  
• Tracking the 3D Rotational Dynamics in Nanoscopic Biological Systems.

  Ryuji Igarashi; Takuma Sugi; Shingo Sotoma; Takuya Genjo; Yuta Kumiya; Erik Walinda; Hiroshi Ueno; Kazuhiro Ikeda; Hitoshi Sumiya; Hidehito Tochio; Yohsuke Yoshinari; Yoshie Harada; Masahiro Shirakawa

  Journal of the American Chemical Society, 14 Apr. 2020, Peer-reviewed

  
• Visualizing protein motion in Couette flow by all-atom molecular dynamics

  Erik Walinda; Daichi Morimoto; Masahiro Shirakawa; Ulrich Scheler; Kenji Sugase

  Biochim Biophys Acta Gen Subj, Jun. 2019, Peer-reviewed, Invited

  
• NMR resonance assignments of the NZF domain of mouse HOIL-1L free and bound to linear di-ubiquitin

  Naoki Ishii; Erik Walinda; Naoto Iwakawa; Daichi Morimoto; Kazuhiro Iwai; Kenji Sugase; Masahiro Shirakawa

  Biomol NMR Assign, Apr. 2019, Peer-reviewed

  
• Backbone and side-chain resonance assignments of the methyl-CpG-binding domain of MBD6 from Arabidopsis thaliana

  Naoto Iwakawa; Yutaka Mahana; Arina Ono; Izuru Ohki; Erik Walinda; Daichi Morimoto; Kenji Sugase; Masahiro Shirakawa

  Biomol NMR Assign, Sep. 2018, Peer-reviewed

  
• Resolving biomolecular motion and interactions by R2 and R1ρ relaxation dispersion NMR

  Erik Walinda; Daichi Morimoto; Kenji Sugase

  Methods, 2018, Peer-reviewed, Invited

  Access this paper :

  
• Cooperative Domain Formation by Homologous Motifs in HOIL-1L and SHARPIN Plays A Crucial Role in LUBAC Stabilization

  Hiroaki Fujita; Akira Tokunaga; Satoshi Shimizu; Amanda L. Whiting; Francisco Aguilar-Alonso; Kenji Takagi; Erik Walinda; Yoshiteru Sasaki; Taketo Shimokawa; Tsunehiro Mizushima; Izuru Ohki; Mariko Ariyoshi; Hidehito Tochio; Federico Bernal; Masahiro Shirakawa; Kazuhiro Iwai

  Cell Reports, 24 Apr. 2018, Peer-reviewed

  Access this paper :

  
• Overview of Relaxation Dispersion NMR Spectroscopy to Study Protein Dynamics and Protein‐Ligand Interactions

  Erik Walinda; Daichi Morimoto; Kenji Sugase

  Curr. Protoc. Protein Sci., Apr. 2018, Peer-reviewed, Invited

  
• Hydrogen-Deuterium Exchange Profiles of Polyubiquitin Fibrils

  Daichi Morimoto; Ryo Nishizawa; Erik Walinda; Shingo Takashima; Kenji Sugase; Masahiro Shirakawa

  Polymers, Jan. 2018, Peer-reviewed, Invited

  Access this paper :

  
• Isolation and characterization of a minimal building block of polyubiquitin fibrils

  Daichi Morimoto; Erik Walinda; Mayo Shinke; Kenji Sugase; Masahiro Shirakawa

  Sci Rep, Jan. 2018, Peer-reviewed

  
• Elucidating functional dynamics by R1ρ and R2 relaxation dispersion NMR spectroscopy

  Erik Walinda; Kenji Sugase

  Experimental Approaches of NMR Spectroscopy: Methodology and Application to Life Science and Materials Science, 23 Nov. 2017, Peer-reviewed

  
• Real-Time Observation of the Interaction between Thioflavin T and an Amyloid Protein by Using High-Sensitivity Rheo-NMR

  Naoto Iwakawa; Daichi Morimoto; Erik Walinda; Yasushi Kanata; Masahiro Shirakawa; Kenji Sugase

  Int J Mol Sci, Oct. 2017, Peer-reviewed

  Access this paper :

  
• High-Sensitivity Rheo-NMR Spectroscopy for Protein Studies

  Daichi Morimoto; Erik Walinda; Naoto Iwakawa; Mayu Nishizawa; Yasushi Kawata; Akihiko Yamamoto; Masahiro Shirakawa; Ulrich Scheler; Kenji Sugase

  ANALYTICAL CHEMISTRY, Jul. 2017, Peer-reviewed

  
• 

  Biological and Physicochemical Functions of Ubiquitylation Revealed by Synthetic Chemistry Approaches

  Daichi Morimoto; Erik Walinda; Kenji Sugase; Masahiro Shirakawa

  Int J Mol Sci, May 2017, Peer-reviewed, Invited

  Access this paper :

  
• 

  F (1) F (2)-selective NMR spectroscopy

  Erik Walinda; Daichi Morimoto; Masahiro Shirakawa; Kenji Sugase

  JOURNAL OF BIOMOLECULAR NMR, May 2017, Peer-reviewed

  
• Backbone resonance assignments of monomeric SOD1 in dilute and crowded environments

  Naoto Iwakawa; Daichi Morimoto; Erik Walinda; Kenji Sugase; Masahiro Shirakawa

  BIOMOLECULAR NMR ASSIGNMENTS, Apr. 2017, Peer-reviewed

  
• 

  Practical considerations for investigation of protein conformational dynamics by 15N R1ρ relaxation dispersion

  Erik Walinda; Daichi Morimoto; Masahiro Shirakawa; Kenji Sugase

  J Biomol NMR, Feb. 2017, Peer-reviewed

  
• Ubiquitylation Directly Induces Fold Destabilization of Proteins

  Daichi Morimoto; Erik Walinda; Harumi Fukada; Kenji Sugase; Masahiro Shirakawa

  SCIENTIFIC REPORTS, Dec. 2016, Peer-reviewed

  Access this paper :

  
• Dual Function of Phosphoubiquitin in E3 Activation of Parkin

  Erik Walinda; Daichi Morimoto; Kenji Sugase; Masahiro Shirakawa

  JOURNAL OF BIOLOGICAL CHEMISTRY, Aug. 2016, Peer-reviewed

  
• Efficient identification and analysis of chemical exchange in biomolecules by R-1 rho relaxation dispersion with Amaterasu

  Erik Walinda; Daichi Morimoto; Mayu Nishizawa; Masahiro Shirakawa; Kenji Sugase

  BIOINFORMATICS, Aug. 2016, Peer-reviewed

  
• The unexpected role of polyubiquitin chains in the formation of fibrillar aggregates

  Daichi Morimoto; Erik Walinda; Harumi Fukada; Yu-Shin Sou; Shun Kageyama; Masaru Hoshino; Takashi Fujii; Hikaru Tsuchiya; Yasushi Saeki; Kyohei Arita; Mariko Ariyoshi; Hidehito Tochio; Kazuhiro Iwai; Keiichi Namba; Masaaki Komatsu; Keiji Tanaka; Masahiro Shirakawa

  Nature Communications, Jan. 2015, Peer-reviewed

  Access this paper :

  
• Solution Structure of the Ubiquitin-associated ( UBA) Domain of Human Autophagy Receptor NBR1 and Its Interaction with Ubiquitin and Polyubiquitin

  Erik Walinda; Daichi Morimoto; Kenji Sugase; Tsuyoshi Konuma; Hidehito Tochio; Masahiro Shirakawa

  JOURNAL OF BIOLOGICAL CHEMISTRY, May 2014, Peer-reviewed, Lead author

  

Misc.

• シロイヌナズナのDNA結合タンパク質MBD6の構造解析

  真鼻裕; 岩川直都; 尾野有菜; 大木出; WALINDA Erik; 森本大智; 菅瀬謙治; 白川昌宏

  日本分子生物学会年会プログラム・要旨集(Web), 2018

  
• ユビキチン化に伴うタンパク質構造不安定化

  森本大智; WALINDA Erik; 菅瀬謙治; 深田はるみ; 曽友深; 蔭山俊; 蔭山俊; 星野大; 藤井高志; 土屋光; 佐伯泰; 有田恭平; 有吉眞理子; 杤尾豪人; 岩井一宏; 難波啓一; 難波啓一; 小松雅明; 小松雅明; 田中啓二; 白川昌宏

  Abstracts. Annual Meeting of the NMR Society of Japan, 2014

  
• LUBACリガーゼ形成における相同性の高いHOIL-1L、SHARPINのUBLの機能的差異

  藤田 宏明; 清水 覚司; 徳永 暉; Walinda Erik; 高木 賢治; 水島 恒裕; 栃尾 豪人; 岩井 一宏

  日本生化学会大会・日本分子生物学会年会合同大会講演要旨集, Dec. 2015

  

Books and Other Publications

• Experimental Approaches of NMR Spectroscopy

  Erik Walinda; Kenji Sugase, Joint work, 195-225

  Springer, Jan. 2018, Not refereed

  

Awards

• 23 Aug. 2024

  ＩＣＭＲＢＳ２０２４　ポスター賞

External funds: Kakenhi

• Competitive linear ubiquitin binding in NFkB-signaling

  Grant-in-Aid for Early-Career Scientists

  Basic Section 43040:Biophysics-related

  Kyoto University

  Erik WALINDA

  From 01 Apr. 2020, To 31 Mar. 2023, Project Closed

  ubiquitin;ubiquitin binding;NZF domain;M1 ubiquitin chains;linear ubiquitin chains;NMR spectroscopy;ITC;MD simulations;M1-linked chains;polyubiquitin;binding domains;Protein binding;Molecular competition;Linear polyubiquitin;NF-kappa B;Ubiquitin

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-20K15756/
• Velocity imaging of turbulence flow using Rheo-NMR

  Fund for the Promotion of Joint International Research (Fostering Joint International Research (B))

  Medium-sized Section 13:Condensed matter physics and related fields

  Kyoto University

  Kenji Sugase

  From 09 Oct. 2018, To 31 Mar. 2022, Project Closed

  Rheo-NMR;速度イメージング;off-center Couette cell;乱流;タンパク質凝集;線維化

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-18KK0075/
• Dynamic Character of the Ubiquitin System

  Grant-in-Aid for Early-Career Scientists

  Basic Section 43040:Biophysics-related

  Kyoto University

  ERIK WALINDA

  From 01 Apr. 2018, To 31 Mar. 2021, Project Closed

  ubiquitin;ubiquitin binding;UBA domain;K48-linked chains;K63-linked chains;M1-linked chains;solution NMR;molecular dynamics;millisecond dynamics;polyubiquitin;binding domains;protein dynamics;protein binding;nanosecond dynamics;Protein binding;Ubiquitin;Molecular recognition;Protein dynamics;ユビキチン;NMR;蛋白質;生物物理

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-18K14665/
• Regulation of NF-kB signaling through competitive interactions against linear polyubiquitin

  Grant-in-Aid for Scientific Research (C)

  Basic Section 43040:Biophysics-related

  Kyoto University

  Walinda Erik

  From 01 Apr. 2022, To 31 Mar. 2025, Granted

  ubiquitin;linear ubiquitin;ubiquitin binding;M1-linked chains;HOIL-1L;NZF domain;zinc finger;Ubiquitin;NF-kB signaling;Binding proteins;Chemical physics;Competitive binding

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-22K06161/
• Development of analytical platform for proteins in electric field and its application

  Fund for the Promotion of Joint International Research (Fostering Joint International Research (B))

  Medium-sized Section 43:Biology at molecular to cellular levels, and related fields

  Kyoto University

  菅瀬 謙治

  From 07 Oct. 2022, To 31 Mar. 2026, Granted

  電場;NMR;タンパク質;電気泳動;凝集;分子動力学計算

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-22KK0098/

Education

Teaching subject(s)

• From 01 Apr. 2024, To 31 Mar. 2025

  ILAS Seminar-E2

  Z002, Spring, Institute for Liberal Arts and Sciences, 2
• From 01 Apr. 2024, To 31 Mar. 2025

  ILAS Seminar-E2

  Z002, Fall, Institute for Liberal Arts and Sciences, 2
• From 01 Apr. 2024, To 31 Mar. 2025

  Introduction to Molecular Biotechnology-E2

  N491, Spring, Institute for Liberal Arts and Sciences, 2
• From 01 Apr. 2024, To 31 Mar. 2025

  Medical English

  E001, Fall, Graduate School of Medicine, 2
• From 01 Apr. 2023, To 31 Mar. 2024

  ILAS Seminar-E2

  Z002, Spring, Institute for Liberal Arts and Sciences, 2
• From 01 Apr. 2023, To 31 Mar. 2024

  ILAS Seminar-E2

  Z002, Fall, Institute for Liberal Arts and Sciences, 2
• From 01 Apr. 2023, To 31 Mar. 2024

  Medical English

  E001, Fall, Graduate School of Medicine, 2
• From 01 Apr. 2022, To 31 Mar. 2023

  Medical English

  E001, Fall, Graduate School of Medicine, 2
• From 01 Apr. 2022, To 31 Mar. 2023

  ILAS Seminar-E2

  Z002, Spring, Institute for Liberal Arts and Sciences, 2
• From 01 Apr. 2022, To 31 Mar. 2023

  ILAS Seminar-E2

  Z002, Fall, Institute for Liberal Arts and Sciences, 2
• From Apr. 2016, To Mar. 2017

  ILAS Seminar-E2

  Spring, 全学共通科目
• From Apr. 2016, To Mar. 2017

  ILAS Seminar-E2

  Fall, 全学共通科目
• From Apr. 2016, To Mar. 2017

  Medical English

  Fall, 医学研究科
• From Apr. 2017, To Mar. 2018

  ILAS Seminar-E2

  Spring, 全学共通科目
• From Apr. 2017, To Mar. 2018

  ILAS Seminar-E2

  Fall, 全学共通科目
• From Apr. 2017, To Mar. 2018

  Medical English

  Fall, 医学研究科
• From Apr. 2018, To Mar. 2019

  ILAS Seminar-E2

  Spring, 全学共通科目
• From Apr. 2018, To Mar. 2019

  ILAS Seminar-E2

  Fall, 全学共通科目
• From Apr. 2018, To Mar. 2019

  Medical English

  Fall, 医学研究科
• From Apr. 2019, To Mar. 2020

  ILAS Seminar-E2

  Spring, 全学共通科目
• From Apr. 2019, To Mar. 2020

  ILAS Seminar-E2

  Fall, 全学共通科目
• From Apr. 2019, To Mar. 2020

  Medical English

  Fall, 医学研究科
• From Apr. 2020, To Mar. 2021

  ILAS Seminar-E2 :Biochemistry Principles

  Fall, 全学共通科目
• From Apr. 2020, To Mar. 2021

  ILAS Seminar-E2 :Introduction to Biomedical Presentation and Debate

  Spring, 全学共通科目
• From Apr. 2020, To Mar. 2021

  ILAS Seminar-E2 :Introduction to life science and scientific conversation

  Spring, 全学共通科目
• From Apr. 2020, To Mar. 2021

  Medical English

  Fall, 医学研究科
• From Apr. 2021, To Mar. 2022

  ILAS Seminar-E2 :Biochemistry Principles

  Fall, 全学共通科目
• From Apr. 2021, To Mar. 2022

  ILAS Seminar-E2 :Introduction to Biomedical Presentation and Debate

  Spring, 全学共通科目
• From Apr. 2021, To Mar. 2022

  ILAS Seminar-E2 :Introduction to life science and scientific conversation

  Spring, 全学共通科目
• From Apr. 2021, To Mar. 2022

  Medical English

  Fall, 医学研究科

Part-time lecturer

• From 01 Apr. 2017, To 31 Mar. 2018

  Pharmaceutical English 2

  前期・後期, 京都薬科大学, 薬学部
• From 01 Apr. 2018, To 13 Sep. 2018

  Pharmaceutical English 2

  前期, 京都薬科大学, 薬学部