Kazuhisa Nishizawa

Kazuhisa Nishizawa MD. PhD at NIK-Biomolecular Research Group

Research Fields:

Computational Chemistry, Biophysics, Medical Chemistry, Clinical Chemistry, Immunobiology and Molecular Evolution.　

Membership: Editor-in-Chief: Annals of Biomedical Research (ABR)

Editor-in-Chief : Journal of Biophysical Chemistry (JBPC)

Editorial Board member of

Comput and Math Methods in Medicine (CMMM),

BioMed Research International,

What's New ---

Oct 2021: NIK Biomolecular Research Group was launched. Metadynamics simulation analysis of viral peptides

Oct 2018: Simulations with united-atom force fields (that represent CH2 as a single particle), such as GROMOS and OPLS/Berger, show unrealistically weak dimerization propensity for Leu- and Ala-rich helical peptides in DOPC bilayers ( ABR-1-112). For Ile and Val-rich peptides the UA force fields show better agreement with all-atom models.

June 2018: Our 2018 papers ( ABR-1-105 and ABR-1-106 ) show that raft-like bilayers stabilize helix dimer in a sequence-nonspecific manner via a mechanism mediated by both electrostatic and Lennard-Jones energies in simulations.

Sept 2017: Extended conformations of acyl chains in raft-like bilayer increase those lipid atoms which simultaneously contacts to both helical peptides placed in the dimeric state, thereby stabilizing the dimeric state.

March, 2017: Cholesterol- and saturated fatty acid chain-rich phospholipid membrane stabilizes the dimerized state of transmembrane helical peptide in a sequence non-specific manner in atomistic simulations

Jan, 2016, onward: Computational measurement of dimerization propensity of transmembrane helical peptide with sequence (AALALAA)₃ in a lipid bilayer membrane shows remarkable force field-dependency. Please visit here.

Sept 8, 2015 Our paper on gating-modifier peptide GsMTx4 is here.

Apr -- , 2015. We measured the attraction force between Leu-rich transmembrane helices

under a couple of force fields..

July 6, 2014. Shown here is one of our Gromacs .gro and .top files etc., that we used in our study of the potential of mean force of transmembrane helices self-association (J Chem Phys 141: 075101 (2014)).

We studied pore propensity in hemifusion systems using coarse-grained and atomistic simulations.

Biophys J. (2013). 104:1038

“Nishizawa M and Nishizawa K. 　Coarse-grained simulations

of branched bilayer membranes: Effects of cholesterol-dependent phase separation

on curvature-driven lipid sorting J Biophys Chem vol 2 : 268-284 (2011)”

“Nishizawa M and Nishizawa K. Curvature-driven lipid sorting: coarse-grained dynamics simulations of a membrane mimicking a hemifusion intermediate.

J Biophys Chem vol1 (2):86-95 (2010)” (Recommended by Faculty 1000)

and

“Nishizawa M and Nishizawa K. Molecular dynamics simulation analyses of viral fusion peptides in membranes prone to phase transition : effects on membrane curvature, phase behavior and lipid-water interface destabilization.(2010) J Biophys Chem vol 1 (1):19-32 “

MovieA; MovieA2; MovieB

Simulations of an integral Kv channel (Kv1.2/2.1 chimera) (Biophys J , 2009 97:90-100).

Transmembrane electrostatic potential map sliced at the Ca of R3 of the S4 helix of the voltage sensor of Kv1.2 channel. Focused gradient is created by the water filling the external and internal crevices of the voltage sensor domain. Note that we applied an inward electric field to the system and therefore the outer (upper) side of the membrane has more positive potential than that of the inner side. For calculation PMEpot and our own program was used. We show an example of transmembrane potential over simulation time here.

forFigS4a_N3