西澤和久 

              

Kazuhisa Nishizawa MD. PhD at Teikyo University School of Medical Technology

at Itabashi,  Tokyo,  Japan

 

Research Fields:  

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

Membership: 

                            Founding Editor-in-Chief :     Biomedical Research and Clinical Practice (BRCP)                                     

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

                            Editorial Board member of

Comput and Math Methods in Medicine (CMMM),

BioMed Research International,

ISRN Biophys,

Dataset papers in Biophys

                               

What's New ---   

 

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 !  (in press in BRCP)

 

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

                               

 

 

 

 

 

 

 

 

Sample movies for our paper Biophys J. 2008  95:1729-1744.

                                     Movie1 (wmv format, 4.2MB,  simulation#5  -0.15V/nm inward.  S4helix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)

 

sim10-stereo2 This figure is shown here.

 

 

 

 

Index                                                         

 

BD10267_   Supplementary information

1 Supplementary information for indel-MCMC

--------simulation and MCMC based sequence alignment approach

                             September 2001 onward

    

2        Code in C for indel-MCMC (ver.2.0) 

A sequence alignment method taking into account slippage-type changes          

                                                                              February 2002,

 

                               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

 

 

 

     4   Prion and amyloid structure prediction based on MD simulations

                                                         Jan 2006  onward

 

            

 

 

BD10267_   Publication list