w******e
发帖数: 1187 | 1 对ligand-receptor interaction的polyvalency一直很困惑：理论上targeting
ligand要通过polyvalency来提高apparent kd，就要ligand和receptor的
positioning和density恰好match，像齿轮一样嵌合，才能有效。可是ms
在NP上做polyvalency的人很少会去根据receptor的具体情况做一堆计算然后
决定如何incorporate ligand，polyvalency带来的好处也是从几倍到几万倍
不等。我的问题是，到底有没有组做rational polyvalency design？理想
状态下（比如3个ligand跟3个receptor同时完美结合），polyvalency对
apparent kd的贡献有没有个公式？最后如果可以很容易的通过polyvalency
提高kd和specificity，为什么还要强调antibody/aptamer的kd？搞几十个
phage display选出的peptide行不行？
请牛人指点（给个link什么的也成）。//bow |
w******e
发帖数: 1187 | 2 顶
【在 w******e 的大作中提到】
: 对ligand-receptor interaction的polyvalency一直很困惑：理论上targeting
: ligand要通过polyvalency来提高apparent kd，就要ligand和receptor的
: positioning和density恰好match，像齿轮一样嵌合，才能有效。可是ms
: 在NP上做polyvalency的人很少会去根据receptor的具体情况做一堆计算然后
: 决定如何incorporate ligand，polyvalency带来的好处也是从几倍到几万倍
: 不等。我的问题是，到底有没有组做rational polyvalency design？理想
: 状态下（比如3个ligand跟3个receptor同时完美结合），polyvalency对
: apparent kd的贡献有没有个公式？最后如果可以很容易的通过polyvalency
: 提高kd和specificity，为什么还要强调antibody/aptamer的kd？搞几十个
: phage display选出的peptide行不行？
|
s******y
发帖数: 28562 | 3
这个必须通过一些假设才能比较容易的列出公式。
首先，你得知道（或者假说）不同的ligand 之间是否必须有先后的关系，
还有是否有协同关系（就是结合了一个之后是否会促进或者妨碍另外一个的
结合）
如果在最简单情况下，可以假设有３个 ligand， 它们是完全独立的，
没有先后关系，但是有完全协同关系，就是只要有一个结合上去，立刻就
让三个都结合上去了（这个假设一般是不对的），那么结合的公式就成了：
Ligand A [OR] Ligand B [OR] ligand C
最后如果可以很容易的通过polyvalency
因为巧妇难为无米之炊。如果单个aptamer的结合能力不够强的话，光靠
polyvalency 是不够的。而且，也不是每一种情况都可以设计polyvalency的
【在 w******e 的大作中提到】
: 对ligand-receptor interaction的polyvalency一直很困惑：理论上targeting
: ligand要通过polyvalency来提高apparent kd，就要ligand和receptor的
: positioning和density恰好match，像齿轮一样嵌合，才能有效。可是ms
: 在NP上做polyvalency的人很少会去根据receptor的具体情况做一堆计算然后
: 决定如何incorporate ligand，polyvalency带来的好处也是从几倍到几万倍
: 不等。我的问题是，到底有没有组做rational polyvalency design？理想
: 状态下（比如3个ligand跟3个receptor同时完美结合），polyvalency对
: apparent kd的贡献有没有个公式？最后如果可以很容易的通过polyvalency
: 提高kd和specificity，为什么还要强调antibody/aptamer的kd？搞几十个
: phage display选出的peptide行不行？
|
w******e
发帖数: 1187 | 4 thx for the input. It seems to me that a reasonable process of polyvalent
interaction is: (assuming that the multiple ligands and multiple receptors
are each immobolised in such position that allow every of them bind to each
other) 1. the ligand patch and receptor patch bump into each other by
diffusion
; 2. one or a few ligand - receptor pair start the interaction process,
which
is determined by their individual kon/koff; 3. once the initial interaction
happened, the ligand and receptor patch c |
w******e
发帖数: 1187 | 5 bm is so kind... However, I'm just pulling this stuff off my @$$, so pls
take it w/ a pitcher of salt hehe
receptors
each
interaction
【在 w******e 的大作中提到】
: thx for the input. It seems to me that a reasonable process of polyvalent
: interaction is: (assuming that the multiple ligands and multiple receptors
: are each immobolised in such position that allow every of them bind to each
: other) 1. the ligand patch and receptor patch bump into each other by
: diffusion
: ; 2. one or a few ligand - receptor pair start the interaction process,
: which
: is determined by their individual kon/koff; 3. once the initial interaction
: happened, the ligand and receptor patch c
|
s******y
发帖数: 28562 | 6 那么目前用多肽做出来的aptamer, 最高结合力有多少？
能不能给我推荐几个peptide aptamer and protein target pair? 最好是结合力比较
高一点的，而且靶蛋白本身是可溶的（最好不要是膜蛋白）。
我对这个一直有兴趣，很想知道有什么已知的 peptide aptamer kd <10E-8 的？
先谢谢了！
receptors
each
interaction
【在 w******e 的大作中提到】
: thx for the input. It seems to me that a reasonable process of polyvalent
: interaction is: (assuming that the multiple ligands and multiple receptors
: are each immobolised in such position that allow every of them bind to each
: other) 1. the ligand patch and receptor patch bump into each other by
: diffusion
: ; 2. one or a few ligand - receptor pair start the interaction process,
: which
: is determined by their individual kon/koff; 3. once the initial interaction
: happened, the ligand and receptor patch c
|
w******e
发帖数: 1187 | 7 1st of all, I actually don't do peptide aptamer myself, so don't trust
me too much:) following is the impression I got from reading.
afaik, the peptide w/ best kd is some RGD variant--there are a loooot
of variants, such as dimer/multimer of RGD, cyclic RGD, peptidomimetic
RGD, etc. It seems to me that no linear peptides has very good kd (again
from very small sample size), since peptide chain is too flexible.
circulirization/stapling is believed to increase kd by confining the
possible conforma
【在 s******y 的大作中提到】
: 那么目前用多肽做出来的aptamer, 最高结合力有多少？
: 能不能给我推荐几个peptide aptamer and protein target pair? 最好是结合力比较
: 高一点的，而且靶蛋白本身是可溶的（最好不要是膜蛋白）。
: 我对这个一直有兴趣，很想知道有什么已知的 peptide aptamer kd <10E-8 的？
: 先谢谢了！
:
: receptors
: each
: interaction
|
w******e
发帖数: 1187 | 8 I tried to look up some kd info on RGD variant, but so far only
came up w/ this:
Modification of the amino acids
flanking the RGD sequence led to the synthesis
of EMD121974 (Cilengitide) inhibiting
aVb3 integrin binding to vitronectin with
an IC50 of 0.6 nM versus 900 nM for the
aIIbb3 integrin (Smith 2003).
I'm sure I read somewhere w/ more detailed description on peptide kd
(they are few and are b/w thou). I'll let u know when I come across
such info again.
one more thing, based on my even mor
【在 w******e 的大作中提到】
: 1st of all, I actually don't do peptide aptamer myself, so don't trust
: me too much:) following is the impression I got from reading.
: afaik, the peptide w/ best kd is some RGD variant--there are a loooot
: of variants, such as dimer/multimer of RGD, cyclic RGD, peptidomimetic
: RGD, etc. It seems to me that no linear peptides has very good kd (again
: from very small sample size), since peptide chain is too flexible.
: circulirization/stapling is believed to increase kd by confining the
: possible conforma
|
s******y
发帖数: 28562 | 9 Thanks!
The reason people are interested in RGD peptide is because it mimics the
extracellular matrix and binds to the integrins, I believe.
I actually don't really care what kind of peptide it is. However I am kind
of planning to do some pilot experiments by myself and I prefer to use
something that can be handled easily. Therefore, I would like to have
something that is sovlable and cytoplasmic (which will be easy for
expression and require minimal posttranslational modification). While the
ex
【在 w******e 的大作中提到】
: 1st of all, I actually don't do peptide aptamer myself, so don't trust
: me too much:) following is the impression I got from reading.
: afaik, the peptide w/ best kd is some RGD variant--there are a loooot
: of variants, such as dimer/multimer of RGD, cyclic RGD, peptidomimetic
: RGD, etc. It seems to me that no linear peptides has very good kd (again
: from very small sample size), since peptide chain is too flexible.
: circulirization/stapling is believed to increase kd by confining the
: possible conforma
|
T**********t
发帖数: 1604 | 10 进来学习。。。
我都不知道有peptide aptamer，我都三年没学习了，别说刘少奇，就是刘亦菲我都赶
不上了。 |
|
|
w******e
发帖数: 1187 | 11 check this out:
Direct inhibition of the NOTCH
transcription factor complex
Vol 462| 12 November 2009| doi:10.1038/nature08543
I know very little about how mature stapling & rational peptide design is,
but this paper surely scares me. it fits your requirement somewhat but I
believe the kd is bad. you may be able to find sth similar to this if
you search keywords like "fragment-based blabla". I never delve in
very deep but always feel curious about it. pls let me know if you find
something cool:)
【在 s******y 的大作中提到】
: Thanks!
: The reason people are interested in RGD peptide is because it mimics the
: extracellular matrix and binds to the integrins, I believe.
: I actually don't really care what kind of peptide it is. However I am kind
: of planning to do some pilot experiments by myself and I prefer to use
: something that can be handled easily. Therefore, I would like to have
: something that is sovlable and cytoplasmic (which will be easy for
: expression and require minimal posttranslational modification). While the
: ex
|
w******e
发帖数: 1187 | 12 you seem to be quite knowledgable:) r u working on library screening/
targeted delivery stuff too?
【在 T**********t 的大作中提到】
: 进来学习。。。
: 我都不知道有peptide aptamer，我都三年没学习了，别说刘少奇，就是刘亦菲我都赶
: 不上了。
|
s******y
发帖数: 28562 | 13 Thanks! That will be very helpful for sure.
I will aslo be looking on the sametime. If I found something cool I will
share it here with you
【在 w******e 的大作中提到】
: check this out:
: Direct inhibition of the NOTCH
: transcription factor complex
: Vol 462| 12 November 2009| doi:10.1038/nature08543
: I know very little about how mature stapling & rational peptide design is,
: but this paper surely scares me. it fits your requirement somewhat but I
: believe the kd is bad. you may be able to find sth similar to this if
: you search keywords like "fragment-based blabla". I never delve in
: very deep but always feel curious about it. pls let me know if you find
: something cool:)
|
T**********t
发帖数: 1604 | 14 汗死，看你问的好多问题都是我想问还问不出的，你比我渊博多了。。。我也做
aptamer啊，算是同行。
【在 w******e 的大作中提到】
: you seem to be quite knowledgable:) r u working on library screening/
: targeted delivery stuff too?
|
w******e
发帖数: 1187 | 15 赞啊！握个手先：）做aptamer的人太少了呵呵（我很多同学都没听说过这个
东东，每次都要从头解释。。。）我也是刚入道。这个版上amedio和biotechen
是专家。以后多交流！
【在 T**********t 的大作中提到】
: 汗死，看你问的好多问题都是我想问还问不出的，你比我渊博多了。。。我也做
: aptamer啊，算是同行。
|
