免费文献传递   相关文献

Directed evolution of R-2-CPA dehalogenase

R-2-氯丙酸脱卤酶的定向进化



全 文 :!11
"!

#
2013
$

%
&
 

 
(
 
)
 
*
 
+
ChineseJournalofBioprocessEngineering
Vol.11No.1
Jan.2013
doi:10.3969/j.issn.1672-3678.2013.01.012
!"#$
:2012-11-07
%&(

,-./01234567
(973
67

89
(2011CB710800);
,-:;<234567
(863
67

89
(2011AA02A209);
,-=
>?@0A‡tBC89
(21076187)
)*+,

¥¦¤
(1986—),
F

“®LJK

PQ23&

23OP

­0â,Ԅ°±

NUû

TÁK
),
LMN
,Email:wjp@zju.edu.cn
R 2
Ž‚T45i}op
žŸs

:
 
 

*+,

!
 
"

()

-./0 10234562307

89
310027)
B
 
C

@AÝÞ
PCR
1ßØ
R 2
¥9:!àQEDŽX

×á"Ç·
Cl-
¬“4š­o<_@b+,-.l
ùâãæ¬

€\âãæ
DehDIV G2
ü
DehDIV E7
252%
ü
387%。
@A
SYBYL
SQd
«?„…®æS”45
,DehDIV G2
09614kJ/mol,DehDIV E7
25498kJ/mol。
™·Qü«?
R 2
¥9:
™ü0Ĝ_

fӜ_Q<\pÄ

DEF
:2
¥9:

!àQ

EDŽX

®æS”
?G>HI
:Q814    
JKLMN
:A    
JOPI
:1672-3678(2013)01-0065-05
DirectedevolutionofR2CPAdehalogenase
QINYingchun,LIUPeng,YANGLirong,XUGang,WUJianping
(DepartmentofChemicalEngineeringandBiologicalEngineering,ZhejiangUniversity,Hangzhou310027,China)
Abstract:BytheerorpronePCRandhighthroughputscreeningbasedonthecolorreactionofchloride
ionconcentration,amutantlibraryofR2CPAdehalogenasewascreatedandscreened.Thespecific
activityofthemutants,caledtheDehDIVG2andDehDIVE7,increasedby248% and396%,
respectively.MoleculardockingoftheenzymeswithsubstrateswascariedoutwithSYBYL.Docking
scoringdisplayedthatDehDIVG2decreasedtheactivationenergyof09614kJ/mol,andDehDIVE7
decreasedtheactivationenergyof25498kJ/mol.Themutantenzymesdecreasedtheactivationenergy,
andincreasedtheafinitywithR2CPA,thustheenzymespecificactivitiesincreased.
Keywords:2chloropropionicacid;dehalogenase;directedevolution;moleculardocking
  
É@²`
S 2
V+,
(S 2 CPA)
”„ô+
,×pÀ‹Œ–—˜.«it

¹×pÀ–


"QR3ÃÄ

—˜

{É@¿ß

•–
æ
S 2 CPA
‹Œ`
D ()
¿ßÖ:žß


¾
L(+)
¿ß:
6~12
†
[1]。
²j
S 2 CPA
.«`)thiÓª

Ð4:žÁŒÂԄ°±:
É@²³
S 2 CPA
`O„p÷˜vÒ
。R 2
CPA
¥§ÔòpàáR¥p
R 2 CPA
–`
Cl,
í
z•ijˆý
2 CPA
`ª2@®¯¿

”hß
Á–Ùڊh`ÜÆÖ
S 2 CPA。

,R
2 CPA
¥§Ô`l{B

1RØÙRâRxWÚ¨
¡Kv
,¨
©¡‰«©ªŽ`
R 2 CPA
¥§Ô

o
ø*÷Ø`
R 2 CPA
¥§Ô

p4h)t
‰«

÷ø*”ìÓ\”_n>?@`}V¸’–
¯–̧


R 2 CPA
¥§Ô1R`%
$[2],
a¤«â
[3]
!¹%$–·¸§
R 2 CPA
¥§Ô
DehDIV R
`0¨


,DehDIV R
š
&E0¨µ*ˆß
pET30a(+)
”‚R‘%
BL21
¿À`)+%

ÅFC56}T

4/Ô`¾Ô1
òì
1043U/mg,
STº2é

˜÷ß`)th
id2

µZ¡˜ê£µ*Ô`¯Ä*÷G#Ô
1È:

äØÙRÈé`¥+ß

p4h)thi
«Š

÷ø:iÙP­T
[4-7]
`Q¼ÀÞ:µ^ïà
¥+3,

›Å*:µ^ïà#ÌÔ1á:`¥+
Ä

p#23¥+Ė¥+Ñ/`*+ånÔS
T12€`â°

1 
QRSTU
1.1 
QR
1.1.1 
%$UxS
‚R‘%
BL21(DE3),DehDIV R
%$æ÷ø
*”ìÓ\””

þVT£yoº)
BL21(DE3)[8]
æ÷ø*”ìÓ\=s°±

.ìxS
pET30a(+)
TjU,
Novagen(WI)
VW

1.1.2 
)—ÔUJÀ
ë°R0xÔ
EcoRI
Ç
HindIII
pq
T4DNA
ÔòÔ
、PfuDNA
_‹Ô
、TaqDNA
_‹Ô
、PCR
h*‰JÀ]TÛj
TaKaRa
VW

•–ƒñ
T=
Sigma
VW
,PCR
¶æt­&)+˜ëV
W‹Œ
,DNA
JÀY³WT=t­&)+˜ë
VW

1.2 
TU
1.2.1 
:µ^ïàO¬
Ôê3­
[9]` Cl
å™O„

ÀÞ§d{0j
Cl+
œ³`망h`:µ^ïàO„

ij"ƒ

˜ž}å™x|
R 2
V+,`ƒ°

!uºð
¥§Ô`1R­syõïà

j¿Àß`
DehI S
¥+3,

:i
96
ºü­s.ì

~ÕÐ
+

z
40μL`4ht™¤l96ԗü–,ûõœ
(
60μL`ÐÇ Hg(SCN)2NY{~,150μL60
g/L` FeNH4(SO4)2·12H2O(}1%K,)x{~Ç
50μLJ9,\DÝØ10minn,”Ô—ä–å™
450nm
D`Æɪ
OD450。
1.2.2 
ef²T
jzÉ)G#`t™šÔ~i
022μm`o
™*o

Õ±t9

A(binding
bufer)
ÎpЃ
10ml/min
ûÖ
Ni2+
jDž¨
Ï

z*on`šÔ~t9

iÍÎ~

Å
10
"
Ïߞ

›iÅ¥ÍÎ~
B(20mmol/LNa3PO4Í
Î~
(pH74),500mmol/LNaCl,250mmol/L
,
-

Å¥

³;Ô~

AKTA
efx²TÁÂ
i¥ÌÏ
(HiTrapDesalting,GEHealthcare)
²T
n`Ô~­s¥Ì

Ö§˜ß`¥Ì³°Çž
â

ÓÉt9^­skž

×ÙÓÉt9^Ö
15mL。
¥Ì~i
SDS PAGE[10]
¯¨²³

“i
jnŒ™Ù

1.2.3 
ef}^™Ù
ef}^:i
Bradford[11]
„™Ù

1.2.4 
Ô¾12™Ù
Ô1ÙÒÖÓ¯ÔST@|
1μmol2 V+,

1μmolCl-*‰`Ô^Ö 1U。p(S) 2
CPA
Õ֝hÜ

:i
Gly NaOH
ÍÎ~
(pH
95)
ÕÖÍÎßÁ

hßÁÖ
1mL,
ܛœ³
Z
30mmol/L,
”
37℃
Dh
0、3、6
Ç
10min。
œ
(
1%
K,›Åh

–—˜pÔ

Ô1µ*˜â
,Ï~¦§Ýå™Üˆ»^O„Î6®

:i:ž~¦§Ý
Agilent1100
ÁÂǘâ,
Ï
Bio RadHPX 87H(30cm×78mm)

R 2
V+,Ç¥§wm,pqÜݖ`

V+,

m,­s¯¨™Ù

™Ù56

\D

Ъ¦Ö

mmol/LH2SO4,ЃÖ06mL/min,Ìîå™ÇÈ
Ö
210nm,
­9^Ö
5μL。2 V+,Çm,`”
Ñ¿Õ¯qÖ
20.86
Ç
12.289min,
#Ì`
—ս˯qÖ

Y=4008x,R2=09991(x
Ö

V+,œ³
(mmol/L),
»°Ö
4008);
Y=2971x,R2 =09997(x
Öm,œ³
(mmol/L),
»°Ö
2971);
²Ô`¾Ô1¬’
(1)


EA1 =ΔA×V1/(k×p×t×V2) (1)
’–

¾Ô1
EA1`(ÑÖU/mg,ΔA֝h¿Õ0
ÌîƳ·ž`+Tª
,V1֝hßÁ`ߞ
(1mL),k
֗սË`»°
,p
ÖÔx^œ³
(mg/mL),t
֝h¿Õ
(min),V2ÖÔ`ߞ(mL)。
4h~ߞÔ1¬’
(2)

EA2 =ΔA×V1/(k×t) (2)
’–

¾Ô1
EA2`(ÑÖ U/mL,ΔA֝h¿Õ
0ÌîƳ·ž`+Tª
,V1hßÁ`ߞ
(1mL),k
֗սË`»°
,t
֝h¿Õ
(min)。
66
&
 

 
(
 
)
 
*
 
+
  
!
11
"
 
2 
XYSZ[
2.1 
8ÀJ‘5ÊýSœ’™6/
p
DehDIV R
ÖDü

”
Mg2+
œ³Ö
7mmol/L、
Mn2+
œ³Ö
04mmol/L
`56D­s…­
PCR
À
,

<â‹C
10~20
"%Š®˜t­&)™½

™#
¥+°Ö
015%。
4/…†…­
PCR
À,«Š

”
‚à¯`¥+}
1~2
"¥+Ñ/

µ*þVT#
Ì
2000
Ï"¥+Ä

¿Œ…­
PCR
¥+3,

Å*

Éïà#Ì`¥+Ä,¡.

*-

§
1 dehDIVR
58À‘
Table1 MutantlibraryofdehDIVR
%{ ¦12
/%
¥+Ñ/
WT 100
E7 138.7 Asp235Gly
G2 125.2 Asp272Glu
E8 86.5 Ala71Glu;Asp248Ala
D2 68.8 Gln242Arg
H3 61.5 Gln188His;Ala299Ser
G9 20.4 Gln103Leu
2.2 
8À5Gp
œ°ò{^UFC56
,¨
^<¥+Ä.ì’
“¾õ

áâ¡ð

*-

æj
DehDIV R
`.ì
ˆß¡Ö
pET30,
*p.ùefq˜ùø,—˜

:
i²T®ú

²T"¥+Ä

²T’“¡ð

*-

G
1 DehDIV R
®¯8À5
SDS PAGE
PQ¥¦
Fig.1 SDSPAGEgelelectrophoresisof
diferentDehDIVRmutants
2.3 
¯¬ý“S>t”
Ö§­dõ23*#¥+ß`á¿Uº+T

“)ӝÇ45cå
Asn203
Ñ/UQRàáRÐ
1—
šÔ~
;2—
²Tnef

3—
¥Ìnef
;4—
—Õef
G
2 DehDIV R
8À
E7
5stGp
Fig.2 Proteinpurificationgelof
DehDIVRmutantE7
Á`c™

ÕjSybyl
–`
advancedprotein
modeling(APM)
Dç
DehDIV R
­s¾ïÀD¯
¨

àCU
DehDIV R
¦2R_:

½Œ¦2R
2371%)`
Î=
PseudomonasputidaPP3
`
DehI
(PDB:3BJX)
ÔÕÖDü

D‰#
DehDIV R
`R^
á¿¡ð

*-

æð

òó

•
Z score
Ö
2157,
ò`³Öò`
(certain)。
Î=
P.putidaPP3` DehI
(PDB:3BJX)`
ϙSTâ°Z,Rø0,1Tx¯
Ä

!
Cl-
`¦OP­¯Ü¯Ä`α 3ÃÄ,!
uST¥§

04Ô
DehDIVR、
¥+ß
DehDIV
G2、DehDIV E7
U
R 2
V+,`òáâ¯q(
ð
4。
æð

òó

ò¯U1Tº`hÐÁ

6
®#Ì
DehDIV G2`
1Tº¾
DehDIV R
¦h`
D@
0964kJ/mol,
!u<#
DehDIV G2`
¾Ô1
á:§
252%;DehDIV E7`
1Tº¾
DehDIV R
¦h`D@
25498kJ/mol,
!u<#
DehDIV E7
¾Ô1á:§
387%。
G
3 DehDIV R
5•–XÊu1—˜S}~
X癚Õ>Aߏ›œ“L9
Fig.3 ThreedimensionalstructureofDehDIVR
activesitescombinedwithsubstratepocket
partmarkedbyatomicaccumulationmodel
76 
!

# ¥¦¤â
:R 2
V+,¥§Ô`ÙP­T
G4 
T4S
R 2
Ž‚5>t”“
Fig.4 Moleculardockingmodelofdehalogenation
enzymeandR2CPA
2.4 
\˜8À54—uvžš
Ôꍥ+Ä,–Ô¾12á:`¥+Ñ/­
s`&‹¯¨

4/(/¥+ŠºG#Ô¾12‚°
á:`­TÔ

¨©

­dõ¥+úÑ/Ô¾
12`€

Ôê¥+Ä
DehDIV E7
Ç
DehDIV
G2
U
R 2
V+,`òáâòó

8>¥+Ñ/
1UST$0Ñ/b

µZÔST
R 2
CPA
˜­Õi

<#ÔUÜ`ዺ@Á

¨©

ϙ

"¥+Ñ/`&‹Õi

h¹òpȂ°³`
@Áዺ

á:ÔST12

µ*
SYBYL
Dˤ

{­TÔ
,¯

Asp272Ser,Asp235Ser;Asp272Val,
Asp235Ser;Asp272Ser,Asp235Val
Ç
Asp272Val,
Asp235Val,¯
q*ÚÖ
DehDIV SS,DehDIV VS,
DehDIV SV
Ç
DehDIV VV。
”¾9`s¢ª
(Threshold)
DZ²ª
(Bloat)
D

àá_*`h¢
_

“p©U
R 2
V+,ò

àá_*`ò¿
ã

¯áâ¡.

*-

tu

"­TÔU
R 2
CPA
`¯Äò

ð
4)。
æð

òÇ.

òó

1T
º¾Ã±Ô@Á§
62282、57266、56848
Ç
50578kJ/mol。
¨©

ϙtu

"­TÔ`Ô¾1
2WG#‚°á:

…­
PCR
Z”:i
DNA
_‹Ô­sC`0¨
‹e¿

µ*kžh56Î*+‹e*+–`¥
+\°

!updÙ`\°PC`0¨–<â¶s
¥+

G#<â¥+ß
[12]。
©O„”ùÏÔ`*÷
tC#§ÚB`Œâ
[13-14]。
uŽ_Ðô”jž
¿¥+\°`àá

¥+\°³ÁgCô3,–
š&E´ß*Ï

¥+\°³:gCô¯‚Ïr¥
+֘L¥+

ƒ„ï̘æ¥+

§
2 
®¯8À5>t”Ÿ>
Table2 Moleculardockingmarkingofdiferentmutants
Total_score Crash Polar D_score PMF_score G_score Chemscore
DehDIV E7 G2 3.02 -0.21 1.25 -46.2625 16.0582 -82.5506 -6.2124
DehDIV SS 2.96 -0.21 1.12 -42.2048 16.5560 -84.4687 -6.2326
DehDIV VS 2.87 -0.23 1.13 -42.2541 16.4343 -84.6918 -6.2309
DehDIV SV 2.86 -0.26 1.24 -46.4942 16.6169 -81.0351 -6.2310
DehDIV VV 2.75 -0.10 2.83 -33.3567 9.0979 -104.4384 -4.4440
 
3 
X
 
[
µ*k2…­
PCR
ßÁ–
Mn2+
œ³

kž¥


<ø0,¥++,”
1~3
"`_*./0

0j{~
Cl-
e(

“µ*U
Hg(SCN)2Ç
Fe(NH4)SO4h4&x§+T`:µ^ïàO
„



˜ž}ijx|
R 2 CPA
—˜þë
12á:`Ô¥+ß`yï

̘Ծ1+T`¥+Ä,

“˜¥+Ä
DehDIV
G2
Ç
DehDIV E7
`¾Ô1¯qá:
252%
Ç
387%,
¥+n
E7
¾Ô1Ö
1447U/mg。
“µ*
SYBYL
ÔUÜ­s¯Äò

ò¯ë-

DehDIV G2
`1TºD@
09614kJ/mol,
DehDIV E7`
1TºD@
25498kJ/mol。
æjÔ
ÇÜ
R 2
V+,`1TºD@

jǺ2á:

!uá:Ô¾12

nŒ23µ*ìÓ#Ìtu
D‰`­TÔ

™Ù•—ß12

“á‹6®âÛ
9D‰M6G#Ô@RxÈ}`¥+Ä

ƒ„JK

[1] AgerDJ.Handbookofchiralchemicals[M].NewYork:Marcel
DekkerInc,1999.
[2] 
Bµ¼

NUû

=ºé

â
.2
V+,¥§ÔwÔ%{`ï
àqÔ@Rx23
[J].
–,&@3¶
,2005,21(6):
537541.
[3] 
a¤«
.C2/C3
§õ,¥§Ô`ïàq·¸.ì
[D].

’“‚@
,2011.
86
&
 

 
(
 
)
 
*
 
+
  
!
11
"
 
[4] ChenK,ArnoldFH.Tuningtheactivityofanenzymeforunusual
environments:sequentialrandommutagenesisofsubtilisinEfor
catalysisindimethylformamide[J].PNAS,1993,90:56185622.
[5] TracewelCA,ArnoldFH.Directedenzymeevolution:climbing
fitnesspeaksoneaminoacidatatime[J].CurOpinChemBiol,
2009,13:39.
[6] HirokiK,KentaroM,AkiraA.DirectedevolutionoftheActinomycete
cytochromeP450MoxA(CYP105)forenhancedactivity[J].Biosci
BiotechnolBiochem,2009,73(9):19221927.
[7] ReetzM T,Tore C,EipperA,etal.Enhancing the
enantioselectivityofanepoxidehydrolasebydirectedevolution
[J].OrgLet,2004,6(2):177180.
[8] 
·¸‰¨·
·J,´
ĵ
·DW.¯
Ä·¸ìÓ`¹
[M].3
:

æ`f

¹

«T

?@0:g
,2005.
[9] KouristR,HohneM,BornscheuerUT.Directedevolutionand
rationalesdesign[J].ChemUnsererZeit,2009,43:132142.
[10] 
º»¼

efxþ×ìÓ;<
[M].
«T

?@0:g
,1999.
[11] YangAG,MaoJF,YaoLB.Biochemistryandmolecularbiology
protocol[M].Beijing:HighEducationPress,2011.
[12] CaldwelR C,JoyeeG F.RandomizationofgenesbyPCR
mutagenesis[J].PCRMethodsAppl,1992,2(1):2833.
[13] YouL,ArnoldFH.DirectedevolutionofsubtilisinEinBacilus
subtilistoenhancetotalactivityinaqueousdimethylformamide
[J].ProteinEng,1996,9(1):7783.
[14] GiverL,GershensonA,FreskgardPO,etal.Directedevolutionof
athermostableesterase[J].PNAS,1998,95(22):
櫒櫒櫒櫒櫒櫒櫒櫒櫒櫒櫒櫒櫒櫒櫒櫒櫒櫒櫒櫒櫒櫒櫒櫒櫒櫒櫒櫒櫒櫒櫒櫒櫒櫒櫒櫒櫒櫒櫒櫒櫒櫒櫒櫒櫒櫒
1280912813.
(Òî
《973
(

˜~‹21pÓ354Ó%5
”———“
stXÊú¢

 ¡7Óó½Zô


Ö§(éU­

&°÷QRT@l`?@01
”973
BCùŒücÕ`@<0Ð
,973
BCùj
2012
$

%
18~19
딓¹‚@¸.óÐ

efá¿|¨

½¾q@<2/

ò擹‚@LËÈDøMN´,

()§!Úö-U,é[G‚@‡BMN

–,?@"v•)
t&;<23*º§\23ü

–,?@"t­˜âT@23*¸*­23ü”t.§´½è&

.
/23Ur/§efbßá¿|¨O„

efbßá¿_Ž,í23­5

efxá¿Uº23

efx
¯Ä*÷âå¿0Î

ʐKüTŸ
973
BCÀÁK

Cnjüpq23&

ÕKr
100
ÚK

ʐ(ÑT
Ÿ“¹‚@

¼Hœ)‚@

’“‚@

’“)t‚@

–,?@"v•)t&;<23*

¹T)t‚
@

–,?@"t­˜âT@23*â

n
973
ÕÂ?@-DÞBMN.§Õá4|
,`
0@<½¾U2/Z?2Kü­s@<0Ð

¦l
23r/

é­U¥¾á:`d".«ˆß

“
973
BC~n`45OP­s§5£


å
 
æ

96 
!

# ¥¦¤â
:R 2
V+,¥§Ô`ÙP­T