寫好英語科技論文的訣竅33194

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9、F A 6 Lh a sb e e ni d e n t i f i e da st hea n i m a le q u i v a l e n to ft h er e c e nt l yd i s c o v e r e dy e a s tH + - A T P a s esu b u n i t8g e n e .R e c e n t l yd i s c o v e r e dy e a s tH + - A T Pa s es u b u n i t8g e n eh a sac o r r e s po n d i n ga n i m a le q u i v a l e

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14、 e( d C )h a sb e e nd e te r m i n e db yd i r e c tm e a s u r e m e n t .dGa n dd Cw e r ed e r i v a t i z e da tt h e5a n d3h y d r o x y l sw i t ht r i i s o p ro p y l s i l y lg r o u p st oo b t a i ns o l u bi l i t yo ft h en u c l e o s i d e si nn o n -a q u e o u ss o l v e n t sa n d

15、t op r e v e n tt h er i b o s eh y d r o x y l sf r o mf o r m i ngh y d r o g e nb o n d s .F r o mi s o p e r i b ol i ct i t r a t i o nm e a s u r e m e n t s ,t h ee n t h a l p yo fd C : d Gb a s ep a i rf o r ma t i o ni s- 6 . 6 5 0 . 3 2k c a l / m o l .坃緰鍂 S 怽 O(W 購祂虘骮 h 埦徖 NHN 0 蜰購祂剉 w 嵥

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26、篘裇皊 0 俌済 w 剉篘裇皊剉輯1/fg 鸑 UO 篘骮蛻Y bO(uO 剉觺済闟齹魦fO 剉觺済 9h,gNe _N-N 胈T 槝鄀 sQ 剉 pencsSO 購汵 penc/f 坃洀鎮(zhèn)梍 eg 剉 0h槝S_Og 哊-N 胈T 槝 KNT1鍕砆歔噀鄗剉h 槝哊 0h 槝颯錘:NO 剉筫誰O 剉觺済 b 觺済剉悥+TaINZPJT 0h 槝/f(u N 錝輯 eg 俰靊O 剉噀鄗 0 擽鍕奲 g 蛻亯g8T _篘剉酧 oe 蹚h 槝 0 詋俌h槝S t e r i cr e s t r i c t i o n si np r o t e i nfo l d i n g :a na l p

27、h a - h e l i xc a n n o tb ef o l l o w e db yac o n t i g u o u sb e t a - s tr a , N 祂錘g 鶺,g 孴 8翂剉/g 韹 eg 歔 INh 槝虘(u 剉 N 汵/g 韹 0 蜰購*N/g 韹 _eQ xvz 剉啒遅孴僛剉蛻亯 0,孨祂擽鍕鵞購*N xvz 啒遅O N*Nt 挌剉簨饛 0俌済-N 胈T 槝/fsQ 嶯銐砆 N*N 顣槝剉筫誰 0 購 N 祂 1擽鍕c 鶴購*NS_MR xvz-N 皊 X*g 銐砆剉顣槝 0 蟘饛銐砆購*N 顣槝剉緰 b c b 0,N祂 _eQO 衏鶴剉濺誰孴僛Y 魜 O&

28、amp;eg 繬 HNHe 済 0O 颯錘Yeu0W 蟘饛O 剉觺済孴僛剉+TIN 0 購虘g*N 婳 P 0 3 A s s e s s i n gs e c o n d a r ys t r u c t u r ea ss i g n m e n t so fp r o t e i ns t r u c t u r e sb yu s i n gp a i r w i s es e q u e n c e - a l i g nm e n tb e n c h m a r k sT h es e c o n d a r ys t r u c t u r eo fap r ot e i nr

29、 e f e r st ot h el o c a lc o n f o r ma t i o no fi t sp o l y p e p t i d eb a c k b o ne .K n o w i n gs e c o n d a r ys t r u c t u r e so fp r o t e i n si se s s e n t i a lf o rt h ei rs t r u c t u r ec l a s s i f i c a t i o n , u n d er s t a n d i n gf o l d i n gd y n a m i c sa n dme

30、 c h a n i s m s ,a n dd i s c o v e r i n gc o n s er v e ds t r u c t u r a l / f u n c t i o n a lm o t i fs .S e c o n d a r ys t r u c t u r ei n f o r m a t io ni sa l s ou s e f u lf o rs e q u e n c ean dm u l t i p l es e q u e n c ea l i g n m e n t ,s t r u c t u r ea l i g n m e n t ,a n

31、 ds e q u e n cet os t r u c t u r ea l i g n m e n t( o rt h re a d i n g ) .A sar e s u l t ,p r e d i c t i n gs e c o n d a r ys t r u c t u r e sf r o mp r o t ei ns e q u e n c e sc o n t i n u e st ob ea na c t i v ef i e l do fr e s e a r c hf i f t ysi xy e a r sa f t e rP a u l i n ga n dt

32、 h a tt h em o s tc o m m o nr e g u l a rp a t t e r n so f ( C o r e yf i r s tp r e d i c t e d- h e l i xa n dt h eP r e d i c t i o na n da p p l i c a ti o no fp r o t e i n ( p r o t e i nb a c k b o n e sa r et h e- s h e e t .s e c o n d a r ys t r u ct u r e sr e l yo np r i o ra s s i g n

33、 m e n toft h es e c o n d a r y - s t r u c t u r ee l e m e nt sf r o mag i v e np r o t e i ns t r u c t u reb yh u m a no rc o m p u t a t i o n a lm e t ho d s .M a n yc o m p u t a t i o n a lm e t h o d sh a v eb e e nd e v e l o p e dt oa u t o m a t et h eas s i g n m e n to fs e c o n d a

34、r ys t r u c t u r es .E x a m p l e sa r eD S S P , S T R I D E ,D E FI N E ,P - S E A ,K A K S I , P - C U R V E ,X T L S ST R ,S E C S T R ,S E G N O ,a n dV o T A P .T he s em e t h o d sa r eb a s e do ne i t h e rt h eh y d r o g e n - b o n dp a t t e r n ,g e o m et r i cf e a t u r e s ,e x

35、 p e r tk n o w l e d g eo rt h e i rc o m b i n a t i o n s .H o w e v e r ,t h e yo f t e nd i s a g r e eo nt h e i ra s si g n m e n t s .F o re x a m p l e ,d i s a g r e e me n ta m o n gD S S P ,P - C U R V E ,a n dD E FI N Ec a nb ea sl a r g ea s2 5 % .M o r eb e t as h e e ti sa s s i g n

36、e db yX T L S ST Ra n dm o r ep i - h e l i xb yS E C S T Rth a nb yD S S P .T h ed i s c r e p a n c ya m on gd i f f e r e n tm e t h o d si sc a u s e dbyn o n - i d e a lc o n f i g u r a t i o n so fh el i c e sa n ds h e e t s .A sar e s u l t ,de f i n i n gt h eb o u n d a r i e sb e t w e e

37、 nhe l i x ,s h e e t ,a n dc o i li sp r o b l e ma t i c a la n das i g n i f i c a n ts o u r c eo fd i s c r e p a n c i e sb e t w e e nd i f f e r en tm e t h o d s .I n c o n s i s t e n ta s s i g n m e n to fs e c o nd a r ys t r u c t u r e sb yd i f f e r e n tm e th o d sh i g h l i g h

38、t st h en e e df o racr i t e r i o no rab e n c h m a r ko fs t a n d a r d a s s i g n m e n t st h a tc o u l db eu s e dtoa s s e s sa n dc o m p a r ea s s i g n m e n tm e t h o d s .O n ep o s s i b i l i t yi st ous et h es e c o n d a r ys t r u c t u r e sa s s ig n e db yt h ea u t h o r

39、sw h os o l v e dth ep r o t e i ns t r u c t u r e s .S T R I D E ,inf a c t ,h a sb e e no p t i m i z e dt oa ch i e v et h eh i g h e s ta g r e e m e n tw i t ht h ea u t h o r s a n n o t a t i o n s .H o w e v e r ,i ti sn o tc l e a rw h a ti st h ec r i t e r i o nu s e df o rm a n u a lo r

40、a u t o m a t i ca s s i g n me n to fs e c o n d a r ys t r u c t u r e sb ydi f f e r e n ta u t h o r s .A n o t h e rp o s s i bi l i t yi st ot r e a tt h ec o n s e n s u sp r e d i c t i o nb ys e v e r a lm e t h o d sa st h eg o l ds t a n d a r d .H o w e v e r ,t h er ei sn oo b v i o u s

41、r e a s o nw h ye a c hm e t h o ds h o u l dw e i g h te q u a l l yi na s s i g n i n gs e c o n d a r ys t r u c t u r e ,孨祂剉 _薡迯(Ww 峞 g 0,孨祂 RZ&q(W梴筫誰-NX(W 剉顣槝 0 鏴酧 o梴筫誰 ?n 剉豐 0R 哊僛霳剉N N 魜 0,N 祂剉, N 錝奲;N 槝蜰N N 魜鏴酧 ol 徹 S b 哊膵 0O 剉濺誰癳酧 o) 06qT薔蛜哊購*N 啒遅騗 g 剉錧O 0,踁祂 _eQ 癳筫誰 v簨哊癳筫誰剉 O 筽 0,擭祂購虘g

42、賬鶴 O亯 0W簨觺済 0 蟢 N*N _ 姅鍕S 靊 xvz 啒遅剉薔蛜孴aINZP 購錧O 剉 wQSO 烻郪觺済孴悥+T 剉aIN 0 N,? ?麐麐孾 _ ?鵞簨噀剉 eg 櫉籗?擽鍕 nnZiZi 哊 0簨钀 R皊(W0R 哊O 橯簨噀剉 gT N 钀 R 0 坃 Y 篘:N簨钀 Rg 緰橯 0 諲霳 88N 鍂 S 愬嫏 Q 繬 HN 0fu88N 齹奲觺済蜰諲霳剉銐蕬0+Ta 孴觺簨-N R 粂鶴 eg 0dk Y諲霳N 刄嶯 颯齹 X(W 剉 vQ 諲銐蕬 0Y 剉簨 ?錘梍 0R 剉觺済孴銐蕬剉膵簨 _薡 0vQ僛颯(u 嶯簨剉匭筟 g耂 pe9e 豐鵞觺済剉 q_蚑NvQ

43、諲 xvz 鴙詋貜g 卂銐砆剉顣槝 eg bck(W 蹚 L 垊 v 錧O2 朾 k+R 篘蜰婲Of f 翂剉藌;R1齹瀃皊剉T 韣錧O) 0 購虘 g N 祂噀鄗-N 剉簨钀 R 0 4 O n eq u e s t i o na b o u tt h ec o m p l e xho m o p o l y m e rp h a s ed i a g r a mp r e s e n te dh e r ei sw h e t h e ri ti sc a u s e db yt h ed i s c o n t i n u o u sf e a t u r eo ft h es q u

44、a r e - w e l lp o t e n t i a l .W ec an n o tg i v ead i r e c ta n s w e rb e c a u set h eD M Ds i m u l a t i o ni sr e q u i r e dt oo b t a i nw e l l - c o n v e r g e dr e s u l tsf o rt h et h e r m o d y n a m i c s .H o w e v er ,t h ec r i t i c a lp h e n o m e n ap r e d i ct e df o r

45、af l u i dc o m p o s e do fp a r ti c l e si n t e r a c t i n gw i t has q u a r e -w e l lp o t e n t i a la r ea sr e a l i s t i ca st h o s ep r e d i c t e df o raf l u i dco m p o s e do fp a r t i c l e si n t e r a c t i n gw i t haL Jp o t e n t i a l .A l s oa na na l o g o u sc o m p l

46、e xp h a s ed i a g r a mi sf o u n di ns i m u l a t i o n so fL Jc l u st e r s .T h ep r e s e n tr e s u l t sf o rs qu a r e - w e l lh o m o p o l y m e r sm a yw e l lb ef o u n di nm o r er e a l i s t i ch o m o po l y m e rm o d e l sa n de v e ni nr e a lpo l y m e r s .購 N 祂vz 哊颯汷愰 b 剉銐蕬

47、 0Xd 亯钀 Rte 莧噀鄗橯孾哊 0O 梺墮 Q 噀鄗剉 Xd 亯哊 0 xQ 媁剉 Xd 亯 S 靊槝啒遅剉蛻亯轛 0Rh 槝)亯 xvz 剉顣槝O 筫誰剉靣 yr觺済剉aIN 孴 q_蚑 0 購虘 g*N 婳 P 0 3 H o wt om a k ea no b j e c t i v ea s s i g n me n to fs e c o n d a r ys t r u c t u r e sb a s edo nap r o t e i ns t r u c t u r ei sa nun s o l v e dp r o b l e m .D e f i n i n gt

48、 h eb ou n d a r i e sb e t w e e nh e l i x ,s h e e t ,an dc o i ls t r u c t u r e si sa r b i t r a r y ,a n dc o m m o n l ya c c e p t e ds t a n d a r da s s i g n m e n t sd on o te x i s t .H e r e ,w ep r o p o s eac r i t e r i o nt h a ta s s es s e ss e c o n d a r y - s t r u c t u r e

49、a s s i g n me n tb a s e do nt h es i m i l a r i t yo fth es e c o n d a r ys t r u c t u r e sa s s i g n e dt os t r u c t u r a l l ya l i g n e dr e s i d u esi ns e q u e n c e - a l i g n m e n tb e n c h m a rk s .T h i sc r i t e r i o ni su s e dt or an ks i xs e c o n d a r y - s t r u c

50、 t u r ea s s i gn m e n tm e t h o d s :S T R I D E ,D S S P ,S E CS T R ,K A K S I ,P - S E A ,a n dS E G N Ow i tht h r e ee s t a b l i s h e ds e q u e n c e - a l ig n m e n tb e n c h m a r k s( P R E F A B ,S A B m ar ka n dS A L I G N ) .S T R I D Ea n dK A K S Ia c h i e v ec o m p a r a b

51、 l es u c c e s sr a t esi na s s i g n i n gt h es a m es e c o n d a rys t r u c t u r ee l e m e n t st os t r u c t u ra l l ya l i g n e dr e s i d u e si nt h et h re eb e n c h m a r k s .T h e i rs u c c e s sr a te sa r eb e t w e e n1 - 4 %h i g h e rt h a nt h o s eo ft h eo t h e rf o u

52、rm e t h o d s .T h ec o n s e n s u so fS T R I D E ,K A K S I ,S E C S T R ,a n dP - S E A ,c a l l e dS K S P ,i m p r o v e sa s s i g n m e n t so v e rt h ebe s ts i n g l em e t h o di ne a c hb e n c h ma r kb ya na d d i t i o n a l1 % .T h e s ere s u l t ss u p p o r tt h eu s e f u l n e

53、 s so ft h es e q u e n c ea l i g n m e n tb e n c h m a rk sa st h eb e n c h m a r k sf o rs e c o n d ar ys t r u c t u r ea s s i g n m e n t .MR$N 錝 H 栶弳 N 顣槝 0,N 錝衏鶴哊銐砆濺誰 0 購汵錝 PTb 椷岪 w 觺済 0te*NXd 亯錘;觺 6e 0鑜aXd 亯虘剉;NSO 钀 R/f 觺済蔛 vQaIN 孴 q_蚑 0;觺1 .w 鵞卂橯O 0=O gY 猂汻眰鰁魰橯O 0 僛/f 褃 f xvz 剉蛻亯N 痵 0 噀鄗橯Y篘w篘(uI嶯裇 h?02 .d 朸椯?N xvz/fhQb 梴_昢剉 NO 諎哊b g 颯錘/ecO 觺簨剉筫誰&T RN 亯籗裇 h?03 .蛻癳 vT t 銐蕬:N 繬 HNZP 購 y 樺OZP