Lab's main interests

Our main interest is protein chemistry and we use various experimental and computational tools to analyse and manipulate the structure and biophysical/biochemical properties of proteins.

As a specific field of investigation, we have several projects aiming at better understanding the biophysics of protein and peptide solubility and amorphous aggregation. One practical outcome of our study on solubility is the design of short peptide tags that can dramatically increase protein solubility.

Using mutational anaylsis, we are looking at the formation of small, soluble aggregates or oligomers that will or will not extend to full aggregation and then precipitation. In addition, we characterize the effect of mutations on the solubility and aggregation of proteins, as well as the physiological effect of soluble aggregates.

As a theoretical characterization of protein solubility, we recently started large scale all-atom molecular dyanmics calculations of multi peptide systems. The calculation is carried out using 27 to 54 tetra peptides randomly disposed in a 100 cubic Angstrom box filled with 30,000 water molecules. We use AMBER 8 on a 32 node MD GRAPE 3 in collaboration in collaboration with Dr. Makoto Taiji (RIKEN) and Atsushi Suenaga (Nihon University)

An ongoing field of investigation is the understanding of protein folding, stability, activity and protein protein interaction. To this end, we use biochemical methods, spectroscopic methods, crystallography combined with mutational analysis such as alanine scaning, sequence simplification.

Our last field of investigation is the identification of protein domains that can fold independently from amino acid sequence. We use bioinfomatics tools such as neural networks random forest and SVM to analyze the characteristics of protein domain linker sequences and as a result predict protein domain boundaries. Our main motivation in this project is to develop prediction tools for enabling the indetificaion of novel domains from proteomes.

Lab group members as of April 12, 2018

March 25 2019: Kalpana NAUTIYAL was awarded a PhD in Engineering. Congratualtion for 5 years of hard work. Miss. Shiho MIURA was awarded a Master degree, and Miss Yukari SHIWAKU, Haruki TAKAGI, and Hanako MAEDA graduated.

March 26 2018: Goalm M KABIR M was awarded a PhD in Engineering. Congratualtion for 5 years of hard work. Mr. Naoki KAMURA was awarded a Master degree, and Mr Shin KOHARA, Katsuhiko HIROSE, and Yuhki MATSUZAWA graduated. Congratualtions

March 21: Maxime DORET a M1 student from CBS Montpellier arrived and will stay here until mid of June.

Februay 1- April 7, 2018: Tomoyuki Saotome and Shiho Miura (pics) went to Centre de Biophysique Structural, Monpellier University for, respectively, a 9 and 3 weeks exchange program sponsored by JASSO. We thank Prof Pierre Emanuel Milhiet and Prof Christian Roumestand all CBS members for organizing the exchange and hosting the students .

Novermber 2017-January 2018: Dr. Islam MM. is visiting us as a JASSO scholar. It will be an excellent opportunity to continue our long standing collaborations on the folding of BPTI and the immunogenicity of the dengue's ed3 protein.

September 2017-March 2018: MAmtaz from Dr. Islam's laboratory is visiting us as a JASSO exchange Student. She is working on the purification of DENGUE ED3 protein.

October 2017: Dr. Punitha Vermulungen (Inspire Assistant Professor Madras University, India) started her 2-year contract as a JSPS postdoctoral fellow. She will work on the folding and missfolding of a single SS bonded Bovine PancreaticTrypsin Inhibitor.

July 2017-November 2017: Dr. Wu Nan a graduate from the lab and now an Assistant Professor in is visiting us as a guest scientist. He will work on the NMR of Gaussia Luciferase, which was the enzyme he worked on during his PhD thesis.

May 2017: Dr. Richa Tambi finished her 2-year contract as a JSPS postdoctoral fellow(pic). She went to Dubai where her husband, she married last year, is waiting her. Dr. Tambi published her results on the SVM prediction of protein domain boundaries in a JCAMD paper, and presented her results at the Japanese Biophysical meeting, and the Japanese protein society meeting. She also actively participated to a JSPS programs for interacting with high school students.(Science dialog Program).

March 2017: Soichiro IDE was awarded a Master degre, and Kurumi HAGIWARA, Shiho MIURA, Marine LIMOUZIN were awarded a Bachlor degree. Congratulation.

Selected publications

Nautiyal Kalpanaut, Yutaka Kuroda.A SEP tag enhances the expression, solubility and yield of recombinant TEV protease without altering its activity. New Biotechnology in press (2018)

Kuroda Yutaka. Biophysical Studies of protein solubility and aggregation by systematic mutational analysis and a helical polymerization model, Biophysical Review, in press (2018)

Shigeyoshi Nakamura, Tomonori Saotome, Akiko Nakazawa, Masao Fukuda, Yutaka Kuroda, and Shun-ichi Kidokoro Thermodynamics of the thermal denaturation of acid molten globule state of cytochrome c Indicate a reversible high-temperature oligomerization process, Biochemistry, 56 (18), pp 2372-2378 (2017).

Yutaka Kuroda, Atsushi Suenaga, Yuji Sato, Satoshi Kosuda & Makoto Taiji、All-atom molecular dynamics analysis of multi-peptide systems reproduces peptide solubility in line with experimental observations, Scientific Reports 6, Article number: 19479 (2016 Jan28)

Kulkarni R Manjiri, Numoto Nobutaka, Ito Nobutoshi, Kuroda Yutaka* Modeling and experimental assessment of a buried Leu-Ile mutation in Dengue envelope protein domain III, Biochemical and Biophysical research Communications i471(1):163-8 ( 2016). (Jan 2016)

Elahi M, Islam MM, Noguchi K, Yohda M, Toh H, Kuroda Y. Computational prediction and experimental characterization of a "size switch type repacking" during the evolution of dengue envelope protein domain III (ED3). Biochim Biophys Acta. Proteins and Proteomics , 1844(3):585-92 (2014)

Dellarole M, Kobayashi K, Rouget JB, Caro A, Roche J, Islam MM., Garcia-Moreno EB, Kuroda Y, Royer CA., Probing the Physical Determinants of Thermal Expansion of Folded Proteins, J Phys Chem B, 117(42):12742-12749 (2013)

All publications




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