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肖潇

木虫 (小有名气)

[求助] 关于文献中的句子看不明白,求分析

They proposed a mechanism of catalysis that involves nucleophilic attack of the active site cysteine that is aided by stabilization of the tetrahedral intermediate by an oxyanion hole formed from the backbone amides of Cys159 and Ala155 (AbPncA numbering). Asp16 was proposed to deprotonate Cys159 to initiate catalysis and to donate a proton to aid the release of NH3 during the tetrahedral intermediate collapse to form the thioester acyl intermediate. Water is then activated by proton abstraction by Asp16 for nucleophilic attack on the covalent acyl-enzyme intermediate to yield a thiolate and nicotinic acid. Transfer of a proton from Asp16 to the active site cysteine completes the catalytic cycle.
其中两句中有两个by,有些弄不明白,这句子是什么意思,求分析,最好能过写清楚句子结构。谢谢了
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理论计算
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肖潇

木虫 (小有名气)

引用回帖:
2楼: Originally posted by wmjiang at 2012-09-03 13:55:49
(1)They proposed a mechanism of catalysis that involves nucleophilic attack of the active site cysteine 【that is aided by stabilization of the tetrahedral intermediate】 【 formed by an oxyanion h ...

谢谢同学。但还是不太明白,为什么就要在前面有一个formed。没有根据啊。
再就是proton abstraction 应该是“去质子作用”的意思。
另外,for nucleophilic attack on the covalent acyl-enzyme intermediate 这个应该是水分子被激活的目的吧,而不是你说的Asp16对covalent acyl-enzyme intermediate的进攻吧。这是我的理解。
谢谢了!
理论计算
4楼2012-09-03 15:59:17
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wmjiang

银虫 (小有名气)

【答案】应助回帖

(1)They proposed a mechanism of catalysis that involves nucleophilic attack of the active site cysteine 【that is aided by stabilization of the tetrahedral intermediate】 【 formed by an oxyanion hole formed from the backbone amides of Cys159 and Ala155 (AbPncA numbering)】.
有人提出了一个活性位点cys的亲核攻击的催化机理,由四面体中间物的稳定来辅助强化,这个四面体中间物就是Cys159 and Ala155 中间的骨架形成的氧离子穴而来的。
(2)
Water is then activated by proton abstraction 【by Asp16 for nucleophilic attack on the covalent acyl-enzyme intermediate】 to yield a thiolate and nicotinic acid.
在Asp16上对共价酰基酶中间物进行亲核攻击所产生的质子吸收能够激活水,从而产生硫醇盐和烟酸
2楼2012-09-03 13:55:49
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wmjiang

银虫 (小有名气)

【答案】应助回帖

(1)formed by an oxyanion hole 在前面补个formed就好理解了
(2)by proton abstraction 是被动语态的by,意思是水被质子吸收激活;
     by Asp16 for nucleophilic attack中by时介词,通过对16号位的天冬氨酸的亲核攻击
3楼2012-09-03 14:00:59
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wmjiang

银虫 (小有名气)

【答案】应助回帖

加formed是可以去这样理解。
后面意义的理解,你自己看吧,我不是化学专业的,没你熟悉
5楼2012-09-03 17:09:30
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