Computational Life Science Group(Division of Materials and Life Sciences)<Group Member>RNA(alphabetical order)

1) Stuffs
Boero, Mauro (Assoc. Prof): First principles molecular dynamics (CPMD) simulation
Tateno, Masaru (Assoc. Prof): Quantum structural biology and structural bioinformatics
2) Students
Hagiwara, Yohsuke (D1):
Computational biophysics on protein structure and reactions
Miura, Kazutaka (D1):
Computational molecular design of biological materials
Nishimura, Tatsunori (D1): Bioinformatics on cellular reaction network systems
Kitta, Kazushi (M2):
Structural bioinformatics on protein‐protein recognitionKang Ji Young (M1):
Computational biophysics on protein structure and reactions
Kuroyanagi, Shigehide (M1): Computational biophysics on molecular transport and reactions
3) Post‐doc
from January of the next year (Kamiya, Katsumasa: moved)

Research themes in our group
Mechanisms of Formation and Reactions of Biological Molecularsystems Æ Fundamental Principles
1) Dynamical mechanisms in the formation of protein 3D structures
For the van der Waals energy, conventional MM andQM calculations cannot accurately evaluate in some cases !
Æ Serious problems: misleading of formation processesof protein 3D structures
Æ Both of accuracy and efficiency are required in MD
calculations.
2) Reaction mechanisms of biological macromolecules such as protein, DNA, and RNA
Enzymatic reaction:
Riboyzme, ATP synthase (ATPase), Aminoacyl‐tRNA synthetase (ARS),
Cytochrome c oxydase (CcO), Transamidase, etc.
Electron / proton transport:
Cytochrome c oxydase (CcO), double‐stranded DNA
Binding reaction:
Specific recognition of protein‐protein, protein‐DNA, etc.
3) Dynamical behavior of cellular reaction network systems in a cell
Signal transduction of external signals into a cellHigh S/N ratio, Amplification of weak signals in a cell4) Engineering and design of functions of biologocal macromolecules
Pharmaceutical drugs against serious deceases, such as cancer, diabetes, etc.

Development of algorithms and calculation systems
1) Dynamical mechanisms in the formation of protein 3D structures
Development of calculation algorithm of van der Waals
energy/force with the high level accuracy and efficiency
Æ 100 ns scale molecular dynamics simulations(coupled with Replica Exchange method)2) Reaction mechanisms of biological macromoleculesEnzymatic reaction, Electron / proton transportÆ QM/MM hybrid calculation program using the all QM region
electron based DFT
Binding reaction:
Æ Docking algorithm and system of protein and DNA molecules
Æ Fully‐solvated dynamical docking (FSDD) algorithm for protein‐ligand molecules
MM region
3) Dynamical behavior of cellular reaction network systems in a cell
Systems have been developed in order to solve a large
set of ordinary differential equations (ODE) and tooptimize parameters in reaction network systems.
4) Engineering and design of functions of biologocal macromolecules
Molecular docking schemes for protei‐lligand have been developed and sophisticated.

Research phase of several projects in our groupThemes

Phase I

Protein Folding

Development & implementationof fast & accurate calculation
method of the vdW interaction

Phase II

Phase III

Replica exchange moleculardynamics (REMD) simulations
are being performed now.

Extension of the analyses toseveral large proteinsCalculations using PACS-CS

Reaction
Mechanisms

Development of a QM/MMhybrid calculation program basedon the all-electron calculation

Applications of the QM/MM hybrid calculation program:aminoacyl-tRNA synthetase, cytochrome c oxydase,transamidase, Ah receptor, etc.
Calculations using PACS-CS

Applications of the QM/MM hybrid calculation program based on Car-Parrinello MD (CPMD):
riboyzme, ATP synthase, cytochrome c oxydase, charge transfer of double-stranded DNA, etc.
Collaborations with the Condensed
Collaborations with theComputer Science Group Matter Physics Group Calculations using PACS-CS

Cellularsignaling
network

Mathematical modeling anddevelopment of calculation &optimization program, of cellularsignaling reaction network

Applications of the calculation / optimization program: FGF
signaling network cascade, multicellular network systems,etc.
Parallelization of the program
Collaborations with theComputer Science GroupCalculations using PACS-CSYear2005

2007
Start from Sep. 2005

Dec. 20072009Car‐Parrinello Molecular Dynamics• Euler‐Lagrange equations of motion for electrons, ions
thermostats & Co.

温度（temperature）

Metadynamics: filling the minima of the FES•Free MD with an additional penalty potential•Always move in the direction that minimizes the total energy,
i.e. following the minimum energy path (Car-Parrinello)•Continuous and smooth dynamics
cf.:M. Iannuzzi, A. Laio and M. Parrinello, Phys. Rev. Lett. 2003, 90, 238302
A. Laio and M. Parrinello, Proc. Nat. Ac. Sci. 2002, 99, 12562

V(s)sReconstruction of the FES:
what the V(s,t) potential does
The (meta)dynamical gaussian potential V(s,t) has the shaper rt'⎛s −s ⎞r⎟V ( s , t ) = ∑ W ⋅ exp⎜ −2 ⎟⎜2δσt '< t⎝⎠and when it has completed its job (large t) and filled all the local
minima, then its shape is similar to the FES:

rrlim V ( s , t ) = − F ( s ) + const.
t →∞In practice: the number of gaussians required to fill a minimum
is proportional to (1/δσ)n (n = dimensionality of the problem) andW / δσ e

−1 / 2

2 1/ 2= γ fαγ ≈ 0.5

Computational analysis of reaction mechanismsof biomacromolecules: Ribozyme (RNA enzyme)
3D structure of riboyzme:
An example of hammerhead ribozyme

Extracted models
usedO(R)
O(S)

Activation barriers in solution
for the different cases consideredOne
Mg2+OneMg2+(close toO2’)(close toO5’)

60.1

57.3

58.5

55.5

NometalionsΔE

Two
Mg2+OneMg2++OH-

Two
Mg2++OH-55.2

46.5

51.6

43.8

54.0

44.7

49.2

41.9

(kcal/mol)

ΔF(kcal/mol)Error bar ~ 2.0 kcal/molSingle‐metal‐ion reaction:
only one Mg close to O2’
1. RNA structure is distorted. Æ High energy barrier !
2. Reaction path is inconsistent to the known experimental
result Æ Incorrect reaction path !
cf. Sawata, S., et al, J. Am. Chem. Soc., 117 (1995),
2357-2358.
Therefore, absence of kinetic isotope effects on thecleavage of the phosphodiester bonds by ribozymes
can be interpreted only by a mechanism in whichtransfer of a proton does not take place in thetransition state.

Conclusions
1. The double-metal-ion mechanism in the presence of OHis definitely identified to be favored in the ribozyme catalytic
reaction.
2. In the single-metal-ion mechanism, the intermediate structure
was distorted, and thus, the activation barrier was increased.
3. Furthermore, the reaction path simulated was inconsistent to
the previous experimental results, thus being incorrect.
4. Thus, the two Mg2+ cations avoid the structural distortion
in a concerted way !
5. In this way, the double metal ions exclusively select thereaction path.

QM/MM hybrid calculations
for full ribozyme structure(work in progress)

The interacting QM/MM
part of the system

D‐RESPr 1 < r < r2
QM
r < r1Crystal structure of
Cytochrome c Oxidase(CcO)

Cytochrome c‐4e

4H+
Subunit Ⅱ

Subunit Ⅲ
Membrane

Function of CcO:
active proton transfer acrossthe inner membrane of
mitochondria
Æ generation of gradient ofchemical potential: ΔμÆ ATP synthesis by F1 motor(ATP syntase)
Translocation
4H+O24e‐

Subunit Ⅰ

2H2O

Chemical
4H+4e‐

Proton transfer across a peptide bond in theH‐pathway of Cytochrome c Oxidase (CcO)•Contrary to the K‐ and D‐ paths, involving only a proton wire mechanism
along a regular hydrogen bond network, this peculiar path implies thetransit of protons across a peptide group..

Reaction pathway as sampled by metadynamics
Tautomerization
reaction scheme

Simulated
Reactionsteps

Free energy landscape and main configurations

Main Steps of the Process~ kBT

S205
D51
S441-D442Y440-S441~ 13 kcal/mol

Conclusions on CcO• Protons can be transferred across a peptide bond between
Tyr‐440 and Ser‐441of CcO via a tautomerization• A proton is initially provided to the Y440‐S441 peptidegroup by a H‐bound water molecule (becoming OH3+).
• Then the amide proton of the imidic acid is transferred in abarrierless way to the deprotonated carboxyl D51 groupresulting in the formation of enol Y440‐S441 without
inducing substantial conformational changes• An enol‐to‐keto tautomerization completes the reaction via
a two step H+ transfer in the two adjacent Y440‐S441 andS441‐D442 peptide groups with a barrier ΔF = 13 kcal/mol.
• A direct proton transfer would require at least 60 kcal/mol
and would induce a lot of bond stress, thus becoming
unfeasible.

Tyr440‐Ser441

CuA

Heme aHeme a3

CuB

Proton (H+) Transfer by Cytochrome c Oxydase (CcO)
O2 + 4H+ + 4e-

Free Energy

Active Proton Transfer

2H2OCytochrome
c4H+4e‐Subunit
Subunit O2Ⅱ 4e‐
Ⅲ
2H2O 4e‐ Subunit
ⅠTranslocation
4H+ Chemical
4H+Electron (e-) Transfer by Cytochrome c (Cc)Cc Æ CcO(e-)

Bioinformatics Æ classical MDÆ QM/MM hybrid calculations

Æ The crystal of the complex has
not been obtained, in spite of much
efforts by experimentalists!
Æ Theoretical molecular docking
method has been developed by ourgroup, based on informatical graphtheory coupled to molecularcalculations.

Cc

Structural prediction of the Cc‐
CcO complex by using
bioinformatical moleculardocking schemes developed byKitta and Tateno.

CcO

Science 112 (1998), 923-930.

e-Schematic representation of a novel docking calculation
Protein 1
Protein 2
algorithm for protein‐protein
All complexes (~4×108)

Determination of the atoms locatedaround the molecular surface
Selection of the atoms involvinghydrogen bonds

Screened complexes (~ 8×105)

Construction of the graphClique detection
Docking
Steric‐clash screening
Top score candidates (~150)

Protein‐Protein Complex

Evaluation of the candidates(implemented by using C/C++ and Perl)Research phase of several projects in our group
ThemesPhase I

Protein Folding

Development & implementationof fast & accurate calculation
method of the vdW interaction

Phase II

Phase III

Replica exchange molecular
dynamics (REMD) simulations
are being performed now.

Extension of the analyses toseveral large proteinsCalculations using PACS-CS

Reaction
Mechanisms

Development of a QM/MMhybrid calculation program basedon the all-electron calculation

Applications of the QM/MM hybrid calculation program:aminoacyl-tRNA synthetase, cytochrome c oxydase,transamidase, Ah receptor, etc.
Calculations using PACS-CS

Applications of the QM/MM hybrid calculation program based on Car-Parrinello MD (CPMD):
riboyzme, ATP synthase, cytochrome c oxydase, charge transfer of double-stranded DNA, etc.
Collaborations with the Condensed
Collaborations with theComputer Science Group Matter Physics Group Calculations using PACS-CS

Cellularsignaling
network

Mathematical modeling anddevelopment of calculation &optimization program, of cellularsignaling reaction network

Applications of the calculation / optimization program: FGF
signaling network cascade, multicellular network systems,
etc.
Parallelization of the program
Collaborations with theComputer Science GroupCalculations using PACS-CSYear2005

2007
Start from Sep. 2005

Dec. 20072009