This is SATOH daisuke, Ph.D.
3rise3set@gmail.com (PC)
new3rise@softbank.ne.jp (mobile)
+81-(0)80-4077-4248
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4. 分かると何が嬉しいのか
かると何
タンパク質立体構造の形成過程の
タンパク質立体構造の形成過程の解明
質立体構造
誤った折りたたみが関与する病気の治療
った折りたたみが関与する病気の
関与する病気 これからの話
これからの話
特定の機能を ったタンパク質
特定の機能を持ったタンパク質の設計
タンパク
新規薬剤の
新規薬剤のデザイン
Scrutinize the relationship between molecular fluctuation
and its biochemical function. Disorder Region of Protein
Elucidate the roles of water molecule at active site
free-
Improve the conventional free-energy calculation method
including decomposition method.
Fluctuation at atomistic level
Introduce crowding effect to molecular simulation Coupled folding
Develop Force Field (focused on partial charges and Molecular Chaperon
dihedral angles) of molecular simulation Ribosome
Reconsider the time series of each ensemble of MD Accumulation of Entropy and Enthalpy
trajectory
Analyze capsid proteins (viral coat proteins)
15
5. Fluctuations and Functions 教科書を りかえる!
教科書を塗りかえる!
天然変性タンパク質 ゆらぎと機能)
天然変性タンパク質 (ゆらぎと機能
タンパク ゆらぎと機能
Key and Lock model
自由エネルギー計算(
自由エネルギー計算 Decomposition, Solvation)
エネルギー計算
Induced fit model
GP/GPUによる低コスト高精度な計算
による低コスト高精度な
による 高精度
Preexisting model 直観を積極的に利用(
直観を積極的に利用(MCMC法)
法
6. 自己紹介
理論量子力学
Ca2+ATPase(ポンプ)のシミュレーション
ATPase(ポンプ
ポンプ)
エンドサイトーシス
Intramolecular interactions to 結合自由エネルギー
結合自由エネルギー予測 (decomposition含む)
エネルギー予測 (decomposition含
Intermolecular interactions 自由エネルギー摂動法、
エネルギー摂動法
自由エネルギー摂動法、熱力学的積分法
タンパク質フォールディング
タンパク質
拡張アンサンブル
アンサンブル法
拡張アンサンブル法
免疫応答系受容体の
免疫応答系受容体の分子認識機構
タンパク質 ダイナミクス-
タンパク質のダイナミクス-機能相関研究
SATOH daisuke, Ph.D. 音楽( music)、武術、ダイビング(
)、武術
音楽(minimal music)、武術、ダイビング(空、海)
1 2
残りの研究人生でやっておきたいこと
りの研究人生でやっておきたいこと
研究人生 本日の発表の
本日の発表の流れ
Scrutinize the relationship between molecular fluctuation
and its biochemical function.
Elucidate the roles of water molecule at active site
Improve the conventional free-energy calculation method
free-
今までの研究を数枚のスライドで紹介
までの研究を数枚のスライドで
研究
including decomposition method.
Introduce crowding effect to molecular simulation
今後の研究について概観
今後の研究について概観
について
Develop Force Field (focused on partial charges and
dihedral angles) of molecular simulation
Reconsider the time series of each ensemble of MD
trajectory
Analyze capsid proteins (viral coat proteins)
3 4
7. Multicanonical molecular dynamics Chignolin
Multicanonical molecular dynamics simulation realizes random chignolin,
10 residue peptide, termed chignolin,
walk in the potential energy space. was newly designed based on B1
The trajectory of multicanonical molecular dynamics can escape domain of protein G[1] .
from local minima in the potential energy surface.
free-
The free-energy landscape at an arbitrary temperature can be Chignolin folds spontaneously into a
obtained using a reweighting operation. stable β‐hairpin in water and shows a
Molecular Dynamics Multicanonical Molecular Dynamics cooperative thermal transition.
Traverse energy Any temperature The structure was determined by NMR.
Low probability barriers effectively
Energy
Energy
Energy
N
Chignolin : GYDPETGTWG C
GPM12 : GYDDATKT F G Chignolin (PDB ID:1uao)
[1] S. Honda, K. Yamasaki, Y. Sawada and H. Morii
10 Residue Folded Peptide Designed by Segment Statistics
Configurational space Configurational space Configurational space Structure 12, 1507–1518. (2004).
5 6
Objectives Method
Folding simulation method Sampling method : Multicanonical molecular dynamics
Confirm validity of our method by reproducing the experimental Simulation time : 180 ns
chignolin.
results of chignolin. Solvation effect : generalized Born/surface area model
Force Field : parm99 (modified)
Sequence dependency on protein folding Temperature : 290 K ‐ 700 K
Elucidate the origin of sequence dependency on protein folding Initial structure : fully extended
by comparing the simulation trajectories of chignolin and
GPM12.
Critical interaction for protein folding
amino-
Predict and verify the critical and minimal amino-acid
replacement to fold a stable and unique structure in water.
GLY TYR ASP PRO GLU THR GLY THR TRP GLY
7 8
8. Time evolution Structure
Potential energy Root‐mean‐
Root‐mean‐square deviation (RMSD)
Potential energy [kcal/mol]
Probability
RMSD [Å]
Time [ns] Time [ns]
CαRMSD [Å]
180‐
180‐ns sampling ranging from the denatured state (>7 Å) to Superposition of MD structure that satisfies all We found structures that satisfy 99 % of
the native state (<1 Å)
experimental restraints (pink) on a representative
NMR structure (ivory), which is closest to
experimental restraints and are a quite close to
average structure of 18 models. the experimentally determined structures.[2]
159 folding events [2] D. Satoh, K. Shimizu, S. Nakamura, T. Terada
Folding free-energy landscape of a 10-residue mini-protein, chignolin
FEBS Letters, 580, 3422-3426 (2006).
9 10
GPM12 Cluster analysis
member:
member: 117518 member:
member: 54582 member:
member: 35602 member:
member: 24155
GPM12 is the structural template of p = 0.28 p = 0.15 p = 0.077 p = 0.045
chignolin.
chignolin.
GPM12
The central segment (8 residues) of G-peptide C
GPM12 corresponds to a fragment of Pr
Protein G B1 domain (PDB ID:1pga) 1 2 3 4
45‐
45‐52 of B1 domain of protein G.
Glu5
Thr6 Ala5
member:
member: 8429 member:
member: 3336 member:
member: 2979 member:
member: 1711
GPM12 did not have a specific Gly7 Lys7 Asp4 Pro4 p = 0.021 p = 0.017 p = 0.0075 p = 0.0023
structure under the experimental
chignolin.
condition as chignolin. Thr8 Asp3
Trp9 Phe9 Tyr2
GPM12 : GYDDATKT F G
Gly10 Gly1
Chignolin : GYDPETGTWG 7 17 18 43
COO- NH3+
GPM12
11 12
9. Diverse structures caused by two different salt bridges Salt bridge
Lys7 Asp4
Replacement of Lys7 to Gly (Lys7Gly) is expected to increase
β‐hairpin propensity of GPM12.
Asp3‐
Asp3‐Lys7 and Asp4‐Lys7
Asp4‐
Gly7 to Lys (Gly7Lys) is predicted to destabilize chignolin‐like
chignolin‐
hairpin structure.
GPM12 Chignolin
Asp3
1st cluster Thr6 Ala5 Thr6 Glu5
(P = 0.28)
probability
Gly7 Asp4 Lys7 Pro4
Thr8 Asp3 Thr8 Asp3
Remove Form
salt bridge salt bridge
Phe9 Tyr2 Trp9 Tyr2
distance [Å] Gly10 Gly1 Gly10 Gly1
2nd cluster Lys7 Asp4
(P = 0.15) COO- Lys7Gly NH3+ COO- Gly7Lys NH3+
13 14
GPM12 Lys7Gly GPM12 Lys7Gly
Chignolin Cluster
1st Cluster
Thr6 Ala5 Thr6 Ala5
(NMR structure) (P = 0.30)
Lys7 Asp4 Gly7 Asp4
Thr8 Asp3
mutation
Thr8 Asp3
4O Asp4O
Phe9 Tyr2 Phe9 Tyr2
Gly7N
Gly10 Gly1 Gly10 Gly1
COO- NH3+ COO- NH3+ Gly7N
Lys7O Asp3O
Stabilized Thr8N
Asp3O
Probability
Probability
Thr8O Asp3N native hydrogen bond
1st cluster
non‐
non‐native hydrogen bond
p = 0.30
Removing the salt bridges between Asp4 and Lys7 and Asp3 and Lys7 of GPM12 leads to
Lys7
CαRMSD [Å] CαRMSD [Å] formation of native hydrogen bond between Asp3O and Gly7N.
15 16
10. Chignolin Gly7Lys Chignolin Gly7Lys
Thr6 Glu5 Thr6 Glu5
Cluster
2nd Cluster
Gly7 Pro4 Lys7 Pro4 (P = 0.11)
Asp3‐
Asp3‐Lys7
Thr8 Asp3 mutation Thr8 Asp3
Trp9 Tyr2 Trp9 Tyr2
probability
Gly10 Gly1 Gly10 Gly1
COO- NH3+ COO- NH3+
Destabilized
Probability
Probability
distance [Å]
2nd cluster Asp3
p = 0.11 Lys7
stabilization
Formation of the salt bridge between Asp3 and Lys7 results in stabilization of
non-
non-native hydrogen bond between Pro4O and Lys7N.
CαRMSD [Å] CαRMSD [Å]
17 18
Hydrophobic core GPM12 Asp4Pro
Replacement of Asp4 to Pro (Asp4Pro) is expected to Thr6 Ala5 Thr6 Ala5
stabilizeβ
stabilizeβ‐hairpin structure of GPM12. Lys7 Asp4 Lys7 Pro4
Pro4 to Asp (Pro4Asp) is predicted to destabilize Thr8 Asp3
mutation
Thr8 Asp3
chignolin‐
chignolin‐like hairpin structure.
Phe9 Tyr2 Phe9 Tyr2
GPM12 Chignolin
Thr6 Ala5 Thr6 Glu5 Gly10 Gly1 Gly10 Gly1
Lys7 Pro4 COO- NH3+ COO- NH3+
Gly7 Asp4
Remove
salt bridge Stabilized
Thr8 Asp3 Thr8 Asp3
Probability
Probability
Phe9 Tyr2 Trp9 Tyr2
Form Remove
1st cluster
hydrophobic hydrophobic p = 0.14
Gly10 core Gly1 Gly10 core Gly1
COO- Pro4Asp NH3+ COO- Asp4Pro NH3+ CαRMSD [Å] CαRMSD [Å]
19 20
11. Chignolin Pro4Asp GPM12(D4P/K7G) structure determined by NMR !
Thr6 Glu5 Thr6 Glu5
Gly7 Pro4 Gly7 Asp4 Unfoldable Foldable!!!!!
Thr8 Asp3 mutation Thr8 Asp3
Trp9 Tyr2 Trp9 Tyr2
Gly10 Gly1 Gly10 Gly1
COO- NH3+ COO- NH3+
Destabilized
Probability
Probability
GPM12 MD structures from top Superposition of NMR structures of
three clusters. GPM12(D4P/K7G) (green) on
1st cluster representative NMR structure of
p = 0.41 chignolin (ivory). (PDB ID: 2E4E)
[3] Tohru Terada, Daisuke Satoh, Kentaro Shimizu
Understanding the roles of amino acid residues in tertiary structure
CαRMSD [Å] CαRMSD [Å] formation of chignolin by using molecular dynamics simulation,
Proteins.,73,621-631 (2008).
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Intramolecular interactions to intermolecular interactions Datasets from ZDOCK benchmark2.0 and benchmark3.0
Now we are applying our method to molecular interactions, Hundreds of PDB structures and sequences were retrieved.
especially protein-protein interactions.
protein-
Our standpoint is that flexibility of protein such as induced fit
fit
plays important role on many types of molecular recognition.
We are going to elucidate the relationship molecular dynamics
of flexible or disordered region and its biochemical function.
For example, now we are validating the obtained results of the
benchmark datasets of ZDOCK at a high atomistic resolution.
The missing coordinates are frequently found in those datasets,
so molecular modeling and physicochemical calculation must be
introduced to obtain complete structures. Hwang H., Pierce B., Mintseris J., Janin J., Weng Z. (2008)
Mintseris J, Wiehe K, Pierce B, Anderson R, Chen R, Janin J, Weng Z (2005)
Protein-protein docking benchmark version 3.0.
Protein-Protein Docking Benchmark 2.0: an update
Proteins, 73(3):705-709
Proteins 60(2), 214-216.
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