Kazuhisa Nishizawa MD. PhD at Teikyo University School of Medical Technology
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),
What's New ---
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
g 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)
“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 “
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.
Sample movies for our paper Biophys J. 2008 95:1729-1744.
Movie1 (wmv format, 4.2MB, simulation#5 -0.15V/nm inward. S4helixの6Å以上の移動あり)
Movie1m (MPEG2 format, 10.5MB, simulation#5 )
Movie2 (wmv format, 4.2MB, simulation#10 0.1V/nm outward.)
Movie2m (MPEG2 format, 8.5MB, simulation#10)
Movie3 (wmv format, 5.1MB, simulation#11 0.2V/nm outward.)
Movie3m (MPEG2 format, 10.2MB, simulation#11)
movie6w (wmv format;5.8MB inward -0.15V/nm electric filed applied, 10ns. 350K)
movie6 (MPEG2 format;13.4MB same simulation as above 日本語解説、参考文献など含む)
movie7w (wmv format ;4.7MB inward -0.2V/nm electric filed applied, 10ns. 350K)
movie7 (MPEG2 format;13.4MB same simulation as above 日本語の簡単な説明含む)
This figure is shown here.
1 Supplementary information for indel-MCMC
--------simulation and MCMC based sequence alignment approach
September 2001 onward
A sequence alignment method taking into account slippage-type changes
Our papers on this project: J Mol Evol. 2002 ;55:706 J Mol Evol. 2005 Feb;60,274.
3 MD simulation of HaTx1 and GsMTx4 in lipid membranes
June 2005 onward
Our papers: Eur Biophys J (2006) 35: 373-381.
Biophys J (2007) 92: 4233-4243
Jan 2006 onward