1966 年公认的经典是有道理的。但是他不是“第一个”提出的。 在Jardetzky 之前就有了诸多机理的雏形,他自己似乎也没引用所有的文献。 用综述的话说:The model is based on early description of membrane transport function [1, 4 , 5] and was first formulated in a strict sense by Jardetzky. 并且该综述也没有包括所有的有关该模型的文献。 比如老阎老板喜欢引用的那篇。
我不清楚老阎的老板是不是不知道这个经典,所以一直没引1966。 然而他在综述里引的是另一个人Widdas (1952). 后来又承认, 这个模型不够好,并引用了四篇七八十年代的文章支持the concept of a single-binding site , alternating-access model. 注意这些文章都比大阎的早 (另有一篇97年的综述), 如果这是大阎与他老板的背景知识的话, 大阎说自己发明“一个接一个”的机理也是完全不正确的。
这时小颜有2个很接近的GLUT及3个构象。用Nature2015 里的话讲就是“structural resolution of the two closely related GLUTs in THREE distinct confirmations reveals the molecular basis for the alternating access cycle”。
SwiperTheFox 发表评论于
回复 'Stegy223' 的评论 :
暂时没有时间精力详细介绍。 关于rocker switch 与 gating请看Forrester 等2011的综述:
The structural basis of secondary active transport mechanisms
里面写:
This so-called “rocker-switch” mechanism postulates that the
symmetry-related N- and C-terminal halves of the transporter rock
back and forth against each other along the two-fold axis that runs
along the domain interface (Fig. 3A). Thus, from the observed Ci
conformation in which the periplasmic sides of the two domains
close the pathway, pivoting (or rocking) of the domains around the
approximate substrate binding site would result in the Ce conformation
in which the domains become close together at the cytoplasmic
side instead [54]. The global conformational changes in this rockerswitch
mechanism may be caused by the formation and breaking of
inter- and intra-domain salt bridges [72]. For example, it has been
proposed for LacY that salt bridge interactions that characterize the
Ci state might weaken due to high-affinity substrate binding (e.g.,
between Arg144 and Glu126, Fig. 3C) [69]. Such a role for the substrate,
as well as explaining how the energy of binding may be translated
into the conformational change, is also consistent with the 'induced
transition fit' mechanism. In addition, the swiveling motion of each
domain relative to the other would result in different configurations
of the binding site residues in Ce and Ci.
小颜2014 working model 开始触及机理。作者有自由度在讨论部分提出一个working model (是个谦虚的名称) 。 此Working model本身仍是比较漠糊的。 好象没讲“葡萄糖转运蛋白既有rocker switch也有 extracellular gate".
小颜首次开谈机理是在Nature2015. 文章题目“Molecular Basis of ligand recognition and transport by glucose transporters”. Molecular Basis乃机理也。
这时小颜有2个很接近的GLUT及3个构象。用Nature2015 里的话讲就是“structural resolution of the two closely related GLUTs in THREE distinct confirmations reveals the molecular basis for the alternating access cycle”。
老泉 发表评论于
回复 'SwiperTheFox' 的评论 : 可以看出,老闫他老板在96年还在支持五十年代的模式(gating, osmochemistry),也不引六十年代更被当时接受的AAM. 2008年左右他态度变了,至于真正的模型,未定。不同的体系侧重不同.AAM+gating 、也在提。topological model is not dynamic model. Topological model is in 1993 is just a model at that time for that system. 不是我前无古人 后无来者的东东。
回复 'SwiperTheFox' 的评论 : 再送一边给你:“The best characterized members of the family are UhpT and GlpT, both of E. coli, for which detailed topological models have been presented (29, 90, 91).”, 你还是不承认有大阎模型。
回复 'SwiperTheFox' 的评论 : 你再去学习一下大阎的帖子“颜宁博士无法反驳的第五个事实”,里面有很详细的介绍他的贡献。如果你要视而不见,就象你看不见“The best characterized members of the family are UhpT and GlpT, both of E. coli, for which detailed topological models have been presented (29, 90, 91).”一样,那别人又奈你若何?
这段话翻译过来:阎润涛pointed out, 这个general model (Alternating Access)是几十年前提出的. 我们的(包括阎的)实验给这个模型提供了直接的生化证据.
注意: 这个模型是几十年前提出的,不可能是指是阎润涛提出的.
Nekono_88 发表评论于
回复 'SwiperTheFox' 的评论 : 在贴一边:
As pointed out by Yan and Maloney (17), this general model for membrane transport was proposed decades ago based purely on kinetic analyses, and it is only now that molecular biological approaches are providing more direct experimental support for this fundamental hypothesis.
以上1999文章Transmembrane Segment 5 of the Glut1 Glucose Transporter Is an Amphipathic Helix That Forms Part of the Sugar Permeation Pathway*
Mike Mueckler and Carol Makepeace 讨论的最后一段,供参考。
An alternating access model for glucose transport is supported by a large body of kinetic and biophysical data collected over the course of several decades (discussed in ref (10), (58), and (59). 这三篇论文分别是1989,1988 和1983. 注意这里的用词是discussed, 而不是说就这三篇论文做了有关的实验.
在大阎7月8日帖子“颜宁博士无法反驳的第五个事实”下面,你有反复发言,我相信你是看了帖子再发言的。帖子中大阎清清楚楚写着“在葡萄糖载体领域,Yan/Maloney 模型早被广泛接受。比如,Dr. Milton Saier, Jr. 在他长达34页的综述里给出Yan/Maloney的发现是该家族(颜宁团队与Yan/Maloney 研究的载体家族)“最详尽的动态模型”,英文原话: “The best characterized members of the family are UhpT and GlpT, both of E. coli, for which detailed topological models have been presented (29, 90, 91). 其中第90,91就是我们分别发表的《细胞》与《美国科学院院报》论文”。但是你选择是无视,或装看不见,在7月15日的帖子“转运蛋白模型一日游 (五)总结”的最初版本中,我和你讨论,你说“目前看过的文献来看, Yan_Maloney模型只出现在阎的博客里,没有出现在科学杂志里,就是说在科学界不存在”。我只好问你“‘The best characterized members of the family are UhpT and GlpT, both of E. coli, for which detailed topological models have been presented (29, 90, 91).’ 这是被引用了1281次的综述“Major facilitator superfamily(1998)”文章里的原话。其中文献90, 91分别是大阎1993和1995的文章。队友阁下,在这里"models"是啥意思?”。我再说“这就是你‘看了这么多文献,没有一篇文献用模型一词来提阎的两篇论文’。反证”,到这时你才无奈地承认有大阎的模型。
问题2,你读没读大阎7月8日帖子,看没看到大阎帖子写的“最详尽的动态模型”,英文原话: “The best characterized members of the family are UhpT and GlpT, both of E. coli, for which detailed topological models have been presented (29, 90, 91). 其中第90,91就是我们分别发表的《细胞》与《美国科学院院报》论文”?如果看到了,你还在7月16日说“目前看过的文献来看, Yan_Maloney模型只出现在阎的博客里,没有出现在科学杂志里,就是说在科学界不存在”。又是为啥?看你前前后后,忙上忙下,尽干些自打耳光的事,到底啥目的?给我的感觉就是:热捧当红花旦,痛贬退役老生。期待你更精彩的表演。
The failure to observe any pCMBS-sensitive residues within the cytoplasmic half of TM segment 7 is similar to the results obtained from cysteine-scanning mutagenesis of TM segment 5 (15). The inhibition pattern indicates that either pCMBS is not accessible to the cytoplasmic portion of the α-helix from the external solvent or that chemical modification is not sufficient to inhibit transport activity. The former explanation is consistent with the simple alternating conformational model for the mechanism of glucose transport whereby the cytoplasmic and exofacial glucose-binding sites are not accessible to solvent from the opposing side of the lipid membrane. These results are also consistent with the accessibility of the helix 7 TM amino acids in the glucose-6-P antiporter of E. coli (26). 这里26=Yan R. T., Maloney P. C. (1995) Proc. Natl. Acad. Sci. U. S. A. 92:5973–5976. 1999文章:Cysteine-scanning Mutagenesis of Transmembrane Segment 7 of the GLUT1 Glucose Transporter*
Paul W. Hruz? and Mike M. Mueckler§ 讨论的倒数第二段。
Nekono_88 发表评论于
Yan and Maloney (21), using a cysteine substitution experimental approach, have defined three distinct regions within putative transmembrane helix 7 of the bacterial glucose 6-phosphate antiporter, UhpT. They discovered that amino acid residues were either accessible to pCMBS only in intact cells, accessible only in inverted membrane vesicles, or accessible in both circumstances, depending on their relative location within the transmembrane helix. Residues close to the exoplasmic membrane face fell into the first category, residues close to the cytoplasmic membrane face fell into the second category, and residues near the middle of the helix fell into the third category. They interpreted their observations in terms of the classic single-site membrane carrier model (3, 4), where one would expect amino acid residues involved directly in substrate binding (in the middle of helix 7 in the case of UhpT) that become exposed to both aqueous compartments during the course of the transport cycle. Residues that lie on the exofacial side of this region may only be exposed to the exoplasmic compartment, and residues that lie endofacial to this region may only be exposed to the cytoplasmic compartment. Their data provide compelling physical evidence for a general model of facilitative membrane transport derived solely on the basis of kinetic transport data. 1997文章:Identification of an Amino Acid Residue That Lies between the Exofacial Vestibule and Exofacial Substrate-binding Site of the Glut1 Sugar Permeation Pathway*
Mike Mueckler? and Carol Makepeace 讨论第二段。
Nekono_88 发表评论于
讨论的第二段:Our results with Glut1 are reminiscent of those reported for cysteine-scanning mutagenesis experiments conducted on theEscherichia coli lac permease (reviewed in Ref. 16) and the glucose-6-P antiporter (17), both of which belong to the same 12 transmembrane helix superfamily of membrane transporters as Glut1. Helix 7 of the glucose-6-P antiporter and several helices within the lac permease have been shown to possess solvent-accessible faces that appear to line a portion of their respective substrate permeation pathways. Our results extend these findings to a mammalian facilitative transporter, and the results when taken together imply that a similar structural paradigm may exist for cotransporters, antiporters, and facilitative transporters in organisms ranging from E. colito the human.
Nekono_88 发表评论于
回复 'SwiperTheFox' 的评论 : Yan and Maloney (17) demonstrated that residues within helix 7 of the glucose-6-P antiporter that are accessible to the external solvent are clustered along the water-accessible face proximal to the exoplasmic surface of the plasma membrane, and that the 6 residues along the water-accessible face most proximal to the cytoplasmic surface of the plasma membrane are not accessible from the external solvent. Our results with helix 5 of Glut1 are completely consistent with these findings, in that none of the 5 residues predicted to lie closest to the cytoplasmic surface of the membrane displayed sensitivity to pCMBS in the external solvent. These results are consistent with a simple alternating conformation or carrier model for the mechanism of transport whereby the outer binding site is largely inaccessible to cytoplasmic substrate and the inner binding site is largely inaccessible to substrate in the external medium. At least in the case of the glucose-6-P antiporter, there also appears to exist a central transmembrane region that is alternately accessible from either aqueous domain as the transporter moves between its two basic configurations. As pointed out by Yan and Maloney (17), this general model for membrane transport was proposed decades ago based purely on kinetic analyses, and it is only now that molecular biological approaches are providing more direct experimental support for this fundamental hypothesis.
以上1999文章Transmembrane Segment 5 of the Glut1 Glucose Transporter Is an Amphipathic Helix That Forms Part of the Sugar Permeation Pathway*
Mike Mueckler? and Carol Makepeace讨论的最后一段,供参考。
An alternating access model for glucose transport is supported by a large body of kinetic and biophysical data collected over the course of several decades (discussed in ref (10), (58), and (59). 这三篇论文分别是1989,1988 和1983. 注意这里的用词是discussed, 而不是说就这三篇论文做了有关的实验.
1. 颜2014 "通过" 引文30 (Iancu 2013) 间接引了Mueckler 2009的一篇论文;
Mueckler 2009: Model of the Exofacial Substrate-Binding Site and Helical FOlding of the Human Glut1 Glucose Transporter Based on Scanning Mutagenesis.
"On the one hand, structural insights pro-vided by the study of MFS family members are nicely summarized by the rocker-switch mech-anism (35 Wang Science2003'), a term meant to suggest that sub-strate might be ?xed in space at its binding site. On the other hand, alternating access is provided as protein conformational changes al-ternately generate pathways of access to ei-ther surface (51 Maloney 1994' ). As well, one might imagine a gated pore (60), in which substrate moves as through an ion channel, but with gates that al-ternately open and close at either end. "
SwiperTheFox 发表评论于
回复 '老泉' 的评论 :
Rocker Switch vs Gating 值得好好讲一讲:)
老泉 发表评论于
回复 'SwiperTheFox' 的评论 : 可能他后面感觉到他一直(96文)推崇的理论(Mitchell 的,osmochemistry , Mobile barrier, or his gated pore)不被看好。
Historically, transporters located in the cytoplasmic mem-brane have been viewed as undergoing conformational changes in which a central binding site is exposed alter-nately to either the inside of the cell or to the outside but is never exposed simultaneously to both sides [11–13].”
11 Jardetzky, O. (1966) Simple allosteric model for membrane pumps. Nature 211, 969–970
12 Mitchell, P. (1957) A general theory of membrane transport from studies of bacteria. Nature 180, 134–136
13 Yan, R.T. and Maloney, P.C. (1993) Identi?cation of a residue in the translocation pathway of a membrane carrier. Cell 75, 37–44
Solcan, N, et al 2012 “Alternating access mechanism in the POT family of ologopepetide transporters” EMBO Journal 2012, 31, 3411-3421 很漂亮的图5用了个3象 model。
Davidson & Maloney “ABC transporters: how small machines do a big job” Trends in Microbiology 2007, 15:448-455。图 四用了个3象model.
回复 'SwiperTheFox' 的评论 : topological model is presented 只是指topological 方面,不是动态模型,也不能是任何其它模型。而且是93年的topological 研究水平。而且只是presented. 更详细的分子结构构象要晶体结构分析(包括X光衍射计算机模拟)。小颜的结晶分析是五十年来最突出。但是也不是尽头。她说的分辩率是3 A 左右。因此对滚床单的葡萄糖分子的构象,与周围分子空间排列,他们之间形成的氢键键长键角了解还有限吧。就是说他们滚床单的细节还不太清楚。
UhpT TM11 Lies on the Substrate Transport Pathway—
Because the topology of UhpT shows the Lys391-Asp388 salt
bridge to be deep within the hydrophobic sector (15, 19, 39, 40),
it seemed plausible that a water-filled pathway would extend
回复 'SwiperTheFox' 的评论 : "The bestcharacterized members of the family are UhpT and GlpT, both of E. coli, for which detailed topological models have been presented (29, 90, 91)." 这是被引用了1281次的综述“Major facilitator superfamily(1998)”文章里的原话。其中文献90, 91分别是大阎1993和1995的文章。队友阁下,在这里"models"是啥意思?