User profiles for Hafumi Nishi

Hafumi Nishi

Graduate school of information sciences, Tohoku University
Verified email at ecei.tohoku.ac.jp
Cited by 1535

Molecular mechanisms of disease-causing missense mutations

S Stefl, H Nishi, M Petukh, AR Panchenko… - Journal of molecular …, 2013 - Elsevier
Genetic variations resulting in a change of amino acid sequence can have a dramatic effect
on stability, hydrogen bond network, conformational dynamics, activity and many other …

[HTML][HTML] Physicochemical mechanisms of protein regulation by phosphorylation

H Nishi, A Shaytan, AR Panchenko - Frontiers in genetics, 2014 - frontiersin.org
Phosphorylation offers a dynamic way to regulate protein activity and subcellular localization,
which is achieved through its reversibility and fast kinetics. Adding or removing a dianionic …

Caught in self-interaction: evolutionary and functional mechanisms of protein homooligomerization

K Hashimoto, H Nishi, S Bryant… - Physical biology, 2011 - iopscience.iop.org
Many soluble and membrane proteins form homooligomeric complexes in a cell which are
responsible for the diversity and specificity of many pathways, may mediate and regulate …

[PDF][PDF] Phosphorylation in protein-protein binding: effect on stability and function

H Nishi, K Hashimoto, AR Panchenko - Structure, 2011 - cell.com
Posttranslational modifications offer a dynamic way to regulate protein activity, subcellular
localization, and stability. Here we estimate the effect of phosphorylation on protein binding …

[HTML][HTML] Cancer missense mutations alter binding properties of proteins and their interaction networks

H Nishi, M Tyagi, S Teng, BA Shoemaker… - PloS one, 2013 - journals.plos.org
Many studies have shown that missense mutations might play an important role in carcinogenesis.
However, the extent to which cancer mutations might affect biomolecular interactions …

New tools and functions in data‐out activities at Protein Data Bank Japan (PDBj)

…, H Wako, S Endo, Y Tsuchiya, H Sato, H Nishi… - Protein …, 2018 - Wiley Online Library
The Protein Data Bank Japan (PDBj), a member of the worldwide Protein Data Bank (wwPDB),
accepts and processes the deposited data of experimentally determined biological …

Regulation of protein–protein binding by coupling between phosphorylation and intrinsic disorder: analysis of human protein complexes

H Nishi, JH Fong, C Chang, SA Teichmann… - Molecular …, 2013 - pubs.rsc.org
Phosphorylation offers a dynamic way to regulate protein activity, subcellular localization,
and stability. The majority of signaling pathways involve an extensive set of protein–protein …

[HTML][HTML] Crosstalk between signaling pathways provided by single and multiple protein phosphorylation sites

H Nishi, E Demir, AR Panchenko - Journal of molecular biology, 2015 - Elsevier
Cellular fate depends on the spatiotemporal separation and integration of signaling processes
that can be provided by phosphorylation events. In this study, we identify the crucial …

Evolutionary, physicochemical, and functional mechanisms of protein homooligomerization

H Nishi, K Hashimoto, T Madej… - Progress in molecular …, 2013 - Elsevier
Protein homooligomers afford several important benefits for the cell; they mediate and
regulate gene expression, activity of many enzymes, ion channels, receptors, and cell–cell …

Selection of target-binding proteins from the information of weakly enriched phage display libraries by deep sequencing and machine learning

…, Y Saito, Y Kurumida, H Nakazawa, S Kawada, H Nishi… - MAbs, 2023 - Taylor & Francis
Despite the advances in surface-display systems for directed evolution, variants with high
affinity are not always enriched due to undesirable biases that increase target-unrelated …