zhang, t., he, y., wang, j.w., wu, l.j., zheng, c.d., hao, q., gu, y.x. and fan, h.f. (2012)...
TRANSCRIPT
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Zhang, T., He, Y., Wang, J.W., Wu, L.J., Zheng, C.D., Hao, Q., Gu, Y.X. and Fan, H.F. (2012)
Institute of Physics, Chinese Academy of SciencesBeijing, P. R. China
OASIS & IPCAS
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OASIS (One-wavelength Anomalous scattering or Single Isomorphous Substitution)
A direct-method phase extension/refinement program based on a partial structure, which can be just the heavy-atom sub-structure or it can be from fragments to a nearly complete model
SAD/SIR information will be beneficial but not compulsory
IPCAS (Iterative Protein Crystal-structure Automatic Solution )
A pipeline from reflection files (*.sca or *.mtz) to a structure model (*.pdb and *.mtz)
Phasing: OASIS, ShelxC/D/E, PHASERDensity modification: DM, RESOLVE
Model building/refinement: ARP/wARP, PHENIX.AutoBuild, Buccaneer
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为什么要搞方法研究并发展自动化计算技术?
这是综合竞争能力的
基础之一
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结构测定周期
过去 现在青霉素 ~ 3 年 1 ~ 2 天维生素 B12 ~ 8 年 1 ~ 2 天胰岛素 ~ 14 年 ~ 1 周肌红 / 血红蛋白
> 20 年 ~ 1 周
回顾历史
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OASIS 的特色直接法相位推演
1. 基于 SAD/SIR 信息 2. 基于部分结构模型或碎片 3. 基于部分已知相位
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1947 D. Harker & J. Kasper1952 D. Sayre1950’s J. Karle & H. Hauptman1964 I. L. Karle & J. Karle1970’s M. M. Woolfson1985 Nobel Prize awarded to J. Karle & H. Hauptman
晶体学中的直接法
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直接法应用于蛋白质晶体学Ab initio direct methods: SAYTAN (M.M. Woolfson’s team, 1988 ~) SnB (H.A. Hauptman’s team, 1993 ~) SHELXD (G.M. Sheldrick’s team, 1994 ~) ACORN (M.M. Woolfson’s team, 2000 ~)
Direct-method phase extension/refinement:(Combining direct methods with other protein phasing methods) Fan, H.F. Acta Phys. Sin. 21, 1114-1118 (1965) Sayre, D. Acta Cryst. A28, 210-212 (1972) Hauptman, H.A. Acta Cryst. A38, 632-641; 289-294 (1982) Giacovazzo, C. Acta Cryst. A39, 585-592 (1983) Fan, H.F. & Gu, Y.X. Acta Cryst. A41, 280-284 (1985)
OASIS Hao, Q., Gu, Y.X., Zheng, C.D. & Fan, H.F. J. Appl. Cryst. 33, 980-981 (2000)
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• SAD/SIR iterationIterative phasing/model building based on the heavy-atom substructure bearing SAD/SIR information
• MR iterationIterative phasing/model building based on a structure model, which can be from fragments to a nearly complete model without SAD/SIR information
• Phase extensionIterative phasing/model building based on a subset of known phases
• SAD/SIR iterationIterative phasing/model building based on the heavy-atom substructure bearing SAD/SIR information
• MR iterationIterative phasing/model building based on a structure model, which can be from fragments to a nearly complete model without SAD/SIR information
• Phase extensionIterative phasing/model building based on a subset of known phases
IPCAS 的特色
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‘SAD iteration’ in IPCAS
Acta Cryst. D60, 1991-1996 (2004)Acta Cryst. D62, 883-890 (2006)
OASIS
DMRESOLVE
AutoBuild (Phenix)ARP/wARP/RefMacBuccaneer/RefMac
Direct-method SAD phasing
SAD data
Ok?
End
Partial structure
Density modification
Model buildingand refinement
Yes
No
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Bimodal distributionfrom SAD
" " "
The phase ofF”
P
Phase information available in SAD given the known heavy-atom substructure
Phase information available in SAD given the known heavy-atom substructure
Peaked at
"2
jjj
N
jj lzkyhxifiF
ano
2exp"1
"
1
Sim distribution
2 Cochrandistribution
Peaked atany where
from 0 to 2p
3
Direct-method SAD phasing
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Acta Cryst. A41, 280-284 (1985)
, 3
1 1tanh sin
2 2
sin sin
best best
P
m m
h h
h' h h' h h' h' h h' hh'
Cochran distribution combined with
bimodal SAD distribution
Sim distribution
Bimodal SAD distribution
" h h h
Direct-method SAD phasing
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X-rays l=0.92Å 2.9Å Ba-SAD dataRedundancy=3.9
SCIENCE 306, 104 (2004)
X-rays l=0.9789Å 3.3Å Se-SAD dataRedundancy=3.3
Nat. Struct. Mol. Biol. 13, 589 (2006)
X-rays Cu-Ka2.1Å S-SAD dataActa Cryst. D61, 1533 (2005) Chinese Phys. B 17, 1 (2008)
SAD phasing by OASIS
SAD phasing by OASIS
l=0.9796Å; 2.3ÅSe-SAD dataAuto-Rickshaw builta 57% model beforeand a 89% modelafter using OASIS
J. Mol. Biol. 383, 49–61 (2008)
X-rays Cr-Ka 2.3Å S-SAD data
213 residues
with 2 S atoms in
the ASU 。
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Direct method phase
refinement
Ok?
End
Partial structure
Density modification
Model buildingand refinement
‘MR iteration’ in IPCAS
OASIS
DMRESOLVE
AutoBuild (Phenix)ARP/wARP/RefMacBuccaneer/RefMac
Yes
No
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, 3
1 1tanh sin
2 2
sin sin best best
P
m m
h h
h' h h' h h' h' h h' hh'
Partial structure
" h h h
Phasing part of ‘MR iteration’
j”h is a set of ‘reference phases’ calculated each cycle from randomly selected 5% of the current structure model;|Djh| is defined as the absolute difference
between the current phase and j”h
Acta Cryst. D63, 793-799 (2007)
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46 residues13 with side chains
MRmodelMRmodel
Cycle 2
ARP/wARP-DMiterationCycle 1
FinalmodelFinalmodel215 residues
Cycle 1 Cycle 3
OASIS-DM-ARP/wARP iteration
Cycle 7Cycle 5201 residuesall with side chains
E7_C–Im7_C E7_C–Im7_C
MR-model completion with E7_C–Im7_C data (1ujz)
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Model resulting fromSAD phasing
MR iterationOasis - DM -
Buccaneer - Refmac
Final1086 residues
in the AU
MR iteration based on a Phenix SAD model Tom70p (2gw1) 3.3Å Se-SAD data, redundancy = 3.3
Residues build 1074 906
Residues assigned 1017 207
R / R free0.285 / 0.403 0.48 / 0.59
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Model resulting from MRSAD phasing
MR iterationOasis - DM -
Buccaneer - Refmac
Final1356 residues
in the AU
MR iteration based on an Auto-Rickshaw MRSAD model TM1782 (1vkn) 1.8Å Se-SAD data, redundancy = 6.1
Residues build 1369 1234
Residues assigned 1353 1068
R / R free0.230 / 0.300 0.261/0.342
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A latest application of MR model completion
MBP-NDM1 Data (2.25Å resolution) was used (Zhang and Hao, The FASEB Journal, 2011)
Target structure Without OASIS With OASIS
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, 3
1 1tanh sin
2 2
sin sin
best best
P
m m
h h
h' h h' h h' h' h h' hh'
As defined in MR iteration
Direct-method phase extension
" h h h
Input known phases to be kept fixed until the resultant model becomes big enough
Initial model
Phenix.Autobuildrunning with ‘quick’
and ‘helixes & strands only’
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AutoBuild quick +20 cycles of
Oasis-DM-Buccaneeriteration
Starting with 4.5Å knownphases and2.8Å Fobs
Finalmodel
AutoBuild quick +20 cycles of
DM-Buccaneeriteration
1h3i Phase extension from 4.5 to 2.8Å
An example of direct-method phase extension
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SIRAS data
DM, AutoBuild
Partial model
MR completion
Native data
SIRAS phasing SAD phasing
End
Derivative 21
Treatment of SIRAS data
1
DM, AutoBuild
Partial model
MR completion
SIRAS phasing
End
SIRAS data
SAD phasing
DM, AutoBuild
Partial model
MR completion
Native data
End
Derivative 2
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SIRAS resultant model improved by the ‘MR iteration’ of OASIS-IPCAS
SIRAS model from2.13Å native &2.65Å Hg-derivative data
Model after ‘MR iteration’based on the SIRAS model and 2.13Å native data
Final model
1
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Better results from SAD phasing of the derivative followed by direct-method aided model completion of the native
2
Direct-method SAD phasing of 2.65Å derivative data
Direct-method aided model completion applied to 2.13Å native data
Final model
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4.0Å model from direct-method SAD phasing
2.13Å model after direct-method phase extension
2.13Å model after direct-method aided model completion
SIRAS data with derivative at 4Å resolution– a simulation: Hg-derivative data truncated to 4.0Å
Final Model
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谢谢!谢谢!