over a temperaturerange of 25-90 degree,to investigatedifference in Gibbs energies of secondary structures fora. -. Chymotrypsinogen A (a-ctg). The curve fitting.
The Biophysical Society TheBiophysical Society
of Japan Japan General General Incorporated IncorporatedAssociation Association
of
Time-series analysis of molecutar change and dynamies of collective
encounteredinthisECTisatignmentaccuracyofti]tedprojectionimages,Here,
ET
three
seftware
packages
(IMOD,Inspect3D and
TEMography)
are
wetl
dynamics: Conformationa] behavior
ln our previous Kana Fujii,Masakazu Sekijima!, apptied to ti]tseries a;ignment in different ways, Mikito Toda4 (iGraduate Hiroshi FLijisaki], have acquired titt series from axonemes by cryo-transmission e]ectron PPlomen[s schooi Humanities and Slriences, iVdra Univ.,2GSIC Tbdy,o qf 3Phys., 4Sei. microscopy (cryo-TEM),and reconstructed the 3D stnicture using IMOD, 7lech, NizaponMedical School, NkeraPPbmenls Uhiv,) Inspect3D and Eos we have developed, main]y. IMOD can automatica]ly OuT study aims to analyze time series dataofmo]ecular dynarnics sirnutation for deterrnineti]t axis by using fiducia] markeT, whi]e Inspect3D needs to manua]ly te extraet collective behavior involving side chains and wateT protcins determineti]taxis butgave us more preeise alignment than that of IMOD, molecules. Our methodology consists of the fotlowing two steps/ (1) judgingfrom obtained 3D, Thus we decided te compare them systematically, i, conformutiona] analysis {dihedral principalconponcnt analysis) (2)dynamica] e., our presentpurpose is to eva]uate the qualityof 3D reconstruction and the analysis {thewavelet transformationand singular value decomposition(SVD)). usability of these software packages, show the pros and cons of them time-varyingfeatuTes of Eos more convenient with higher The wavetet transformationenab]es us to investigate systematica]]y and then make our deve]oped invo]ving mu]tipte oscillatory motions, and SVD extracts collective variables ana]ys{s abitity. We acqu{red tiltseT{es of modet structure (phantomdata)and amino residues[1]. axonemes by cryo-TEM, and computed the 3D structure using IMOD, OuT system ischigno[in. In our previouswork, we analyzed time series data Inspect3D,TEMography ancl Eos fromeach ofthem, respeetively. Comparison using imp[icjt so]venl methed fordynamicssimu]ation. He;e, we study data between them will herebe reported and diseussed. usjng explicit so]vent method and wit] conpare these twe cases. tn particu]ar, we aim to extract cot]ective behavior involvingnot only the main cha{n but a[so the side chain. By analyzing relationship efce]lective behavior 1PT187 Gjbbs energies of secondary structures for a-Chymotrypsinogen between the main chain and the side chains, we can understand to what extent A inyestigatedby FT-IR spectroscopy collective behavior involving the main chain provides us with information Koichi Murayama (Grad.Sch. Med., GifiiU}iiv.)
known
and
work, we
,
concerningcol]ectivebehavjorwiththesidechains.Furthermore.weexpectthat
FT-IR spectra were measured over a temperature range of 25-90 degree, to investigatedifference in Gibbs energies of secondary structures for a Chymotrypsinogen A (a-ctg). The curve fitting method combined with Fouricr selfideconvolution teehnique al]owed us to exp]ore detai]sof the secondary structure. The spectra ofa-ctg jn the amide I'region reveat eight bands forantitunn,u-he]ix, P-sheet, intermotecutar3-sheet and side chain paralte[ P-sheet, vibration below 70 degree. Additienat band for disorderedappears over 70 degree in the spectra. Then, Gibbs energies for secondary stmctures and their transition temperatures {T.)were calculated. The T. for the fourbands due to the a-helix, turn and disorderedstructures are found to be around 60 degree. Cerresponding values for anti-para]]e] and side chain are highcr by P-sheet about 67 degree,and those for inter-molecu]ar structures were B-sheet areund 63-64 degree.The Gibbs energies weTe obtained about 11-16 kJmo]'] for a-helix, was much 3-sheetand turn. The value for intermolecularB-sheets higherthan others, suggesting that intermo]ecutarP-sheets formation need more energy thanother secondary structures, In thisstudy, I wi1t discussGibbs energy and Tm values for secondary structures of a-ctg obtained from FT-IR spectroscopy in details.
B-sheet,
TIP3P ET-JbesdiU GeneralizedBorn E7-JVestMUithN"\st"tts6e;,JcgfiopmMv;,7uyv
IPT188
Improvement of sampling efficiency through combirted use molecular dynamics simulations with implieitancl explicit solyent
of
the
study
models
moleeular
side chain
wM
give
us an
functions forother proteins.
[1]M.Kamada,et,ar,Chern,Phys.Lett.502(2011)241-7. (t;,iEUf(R-fivaH7ith\Y:-=V-YgYeMLIts firetpt!esit6tXFYiltsopMvaneth
IPT190
Charaeterization of histone multimers in the gas phase by ion mobility mass spectrometry and molecular dynamics simuLation i,
Kazumi Saikusa Sotaro Fuchigamii, Kyohei Takahashii, Yuuki Asanoi, i, Aritaka Nagadoi Hiroaki Tachiwana2, Hitoshi Kurumizaka2, Mitsunori Ikeguchi!,Yoshifumi Nishirnurai,Satoko Akashii (ifokohamaCity Univ., !PFlaseda Uhiv.) core partic]e(NCP) isthe basicstructural unit of eukaryotic In order to understand the mechanism of the NCP assembly and disassembly,structural characterization of the histone rnuttimers, H2AtH2B dimer and H31H4 tetramer, shoutd be of great he]p. However, these atomic]evelstructures have not been determined.In the present study, human histone mu]timers were prepared and characterized by electrospray ionizationien mobility mass spectrometry (ESI-IM-MS)and molecular dynamics {MD)
Nuc]eosome chromatins.
simutation.Experimental]yobtainedarrivaltimesofthesehistonemultimerions which showed rather wide distributions, suggested that histenemu]timers various
Hiroko KondoT,2, Noriaki Okimotoi, Mukoto TaljiT'2('Dcpartment qf ?Laboratoo, CbmputationalBiotogy,the Uhiverb'ity offt)ig,o, forComputationai MblecuiarDesign,quantitative BiotogyCenter (eBiO, RLKEN)
behavior involving the
of collective
important clue to understand
cenformations.
To
probe
the
confonners'
of the histone multimers wcre canied out it was identifiedthat the histonemultimers had
simulations
structures,
severa[
inso]ution
and
had MD
in vacuo,
In CCS values had more compact tai]Tegions than those with largerCCS values, On the other Variousexperimentaland computational studies have indicatedthat the protein hand, the CCS values of the fo]ded core structure were almost kept identicalin are close]y linked.Investigating their dynamical the analyzed conformers. This irnplies that the disorderedregions brought about conformation and itsfunction theiT functionalproperties. the structural varjety of hjstone multimers, This paper presents that the propertiesis consequently importantto understand The molecular dynamics (MD} simu]ation is powcrfu] toot for these anatyses combination of IM-MS and MD simulation enables cornprehensive characterbecause we can observe the kineticsof proteinut the atomic revel. Itishowever ization of thc gas-phase structures of biomolecular complexes containing isnot enough for examining the significant disorderedregions, thatthe time scale ofthe simulation event including proteinfolding,domain movcment, and so on. Therefore the enhanced sampling methods to overcome this computationa] ]imitationare so ]mportant.
In thisstudy
we
aim
improve]nentof
at
the
by
combining
sampling
efficiency,
and
structure.
the
IPT191
h-*JbEzarema"utereblvr-v'LtvFgmEmvtes;IJ"o fiu{ewtmmvaxvugeth Time-series analysis forprotein dynamics using discrete -'aveLet transform with kernelcanonieal correlation analysis P, Kamadn MikitoToda?, Tatsuya Akutsui (iinsr. Chem. Res.,K[voto
in
reduction
of
addition,
simu]ation
showed
that the
a variety
conibrmers
with
smaller
from implicitsolvent simulations forredueing the sampling space and the latterfor correcting the conformationat distribution sampled by the former Mayumi simu]ation. The rep]ica exchange method was adopted for rough conformatiena] Universit.y, 2Ph.vs. Dept.,Ndra PPlomensUhiv.) sampling with implicit solvent followed by the exp]icit solvent simulation, Here, of protein we perforrned confomiationa] sampting of a mini pretein.:hignolin to examine Structura] dynamicsof proteinsptay an importantrole in expression motions of proteinsmake a large the ecacieney of our method. The results shew thatour new method covered a functions, ]n particular, stow collective To understand a corre[ation between wideT region of conformational space as eompared with thc conventiona] MD contribution to perfonning itsfunctions. to extract slow simu]ation with the explicit solvation mode]. proteinfunctionsand structural dynamics, we need a method collectiveinfonnation, motions from structural dynamics without losing important and correctly characterize them, FoT thispurpose, we use the IPT189 Ipt"T ยข fi7Mh\tCsuIUeskVllnvut-fiff-itcore5StM discrete wave]ct transformation(DWT) forthe tirne-series data of protein dynamics (MD) simulation. DWT is one of structures obtained from motecu]ar EifftojmascreAUtime-frequency analysis methods used for denoisingand data composition. and actual and
simu]ation
those
of
time
explieit
one; the
the
results
forrnerisused
-
S]Ol
NII-Electronic NII-Electronic
Library Service
