User:Nathan H. Kipniss/Notebook/20.109 Final Project

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(Papers and Summaries)
(Papers and Summaries)
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-skMLCK demands that CaM is completely folded when binding.
-skMLCK demands that CaM is completely folded when binding.
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Waltersson, Y et al. Mutational effects on the cooperativity of Ca2+ binding in calmodulin.” Biochemistry 32.31 (1993): 7866-71.
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* this paper is a bit dated *
 +
 +
-Asp24 is seemingly understudied (in +Z position, either Asp or Asn).
 +
 +
-Paper addresses Asp22, since Asp in +Y position is conserved across all four binding loops.
 +
 +
-May not be a simple explanation to AA sequence and calcium binding.
 +
 +
- Only one Oxygen in the anionic amino acids coordinate calcium. The other may serve to "recruit" calcium ions
==Papers Currently being read==
==Papers Currently being read==

Revision as of 12:48, 1 May 2012

Contents

Elucidating the function of D24H Inverse Pericam mutant

Background

In module 2 of 20.109, we created the D24H mutant of inverse pericam. The experimental results from the calcium binding assay was surprising as calcium affinity decreased (Kd increase), yet cooperativtiy increased. For a final research idea, I would like to propose the set of experiments that would elucidate how the addition of a histidine into the first binding loop of inverse pericam can make these changes.

[Media:S12_M2D7_TR-Orange.txt]

Fitted Matlab binding curves
Fitted Matlab binding curves

Ideas

-working under the assumption that the SDM did indeed work (sequencing with BLAST, discontinuous mega-blast suggests it did indeed work)

- consider looking at calmodulin only.

- Pharmaceutical companies often need to know how a drug is interacting with a target. These same techniques could be applied to calmodulin and its target, M13. I currently have a request with MIT libraries to purchase a critical paper (see below).


Papers and Summaries

Junker, JP et al. €œSingle-molecule force spectroscopy distinguishes target binding modes of calmodulin. Proceedings of the National Academy of Sciences of the United States of America 106.34 (2009): 14361-6.

-Cooperativtiy in CaM and target proteins is target protein dependent.

- Multiple transitions rates exist in CaM and target protein binding (again, protein dependent).

- for skMLCK, one cooperative transition; no intermediates could be found with this approach.

-potential issues: this paper uses worm like chain models to interpret data. How valid is that approximation/assumption?

- this method slows kinetics to actually observe structural transitions

-skMLCK demands that CaM is completely folded when binding.

Waltersson, Y et al. Mutational effects on the cooperativity of Ca2+ binding in calmodulin.” Biochemistry 32.31 (1993): 7866-71.

  • this paper is a bit dated *

-Asp24 is seemingly understudied (in +Z position, either Asp or Asn).

-Paper addresses Asp22, since Asp in +Y position is conserved across all four binding loops.

-May not be a simple explanation to AA sequence and calcium binding.

- Only one Oxygen in the anionic amino acids coordinate calcium. The other may serve to "recruit" calcium ions

Papers Currently being read

Grossman,M et al. œAchieving broad molecular insights into dynamic protein interactions by integrated structural-kinetic approaches. Current opinion in structural biology 21.5 (2011): 678-85. Web. 1 Mar. 2012.

Scapin, G. Structural Biology and Drug Discovery. Current Pharmaceutical Design. 2006

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