Alignment Media Preparation: Difference between revisions

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=== Brief Description ===
=== Brief Description ===


NH RDC are easily acquired and for the purpose of protein structure validation and refinement and the data can be collected on samples labeled only with <sup>15</sup>N. Obtaining RDC in two different alignment media greatly improve the quality of refinement and can aid in dimer structure determination; 500ul of a 0.5-0.6mM sample is usually sufficient for this purpose.  
NH RDC are easily acquired and for the purpose of protein structure validation and refinement and the data can be collected on samples labeled only with <sup>15</sup>N. Obtaining RDC in two different alignment media greatly improve the quality of refinement and can aid in dimer structure determination; 500ul of a 0.5-0.6mM sample is usually sufficient for this purpose.  
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*Record the <sup>2</sup>H splitting by running the s2pul expt with tn=lk (for Varian instrument). The range of the splitting should be around ~+/-8~10 Hz.
*Record the <sup>2</sup>H splitting by running the s2pul expt with tn=lk (for Varian instrument). The range of the splitting should be around ~+/-8~10 Hz.


==== Polyacrylamide Gel (Compress and Stretch)  ====
==== Polyacrylamide Gel (Compressed and Stretched)  ====


Chemicals used in preparing this alignment medium can are:  
Chemicals used in preparing this alignment medium can are:  
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:'''Sigma Aldrich 282731''', 2-Acrylamido-2-methyl-1-propanesulfonic acid
:'''Sigma Aldrich 282731''', 2-Acrylamido-2-methyl-1-propanesulfonic acid


===== Compressed Gels can be made Positive, Negative and Neutral  =====
===== Compressed Gels - Positive, Negative and Neutral  =====


*Mix stock solutions of 40% acrylamide and N,N'-methylenebisacrylamide in a 19:1 ratio with 40% charged acrylate derivatives containing N,N'-methylenebisacrylamide as desired in a 19:1 ratio.
*Mix stock solutions of 40% acrylamide and N,N'-methylenebisacrylamide in a 19:1 ratio with 40% charged acrylate derivatives containing N,N'-methylenebisacrylamide as desired in a 19:1 ratio.

Revision as of 17:54, 23 April 2012

Brief Description

NH RDC are easily acquired and for the purpose of protein structure validation and refinement and the data can be collected on samples labeled only with 15N. Obtaining RDC in two different alignment media greatly improve the quality of refinement and can aid in dimer structure determination; 500ul of a 0.5-0.6mM sample is usually sufficient for this purpose.

Data Acquisition to RDC Calculation

Detail description on data acquisition

Alignment Media Preparation

Isotropic Sample Measurement

The first sample to be observed is an isotropic sample. Dilute one half of the sample by a factor of two as this will give a reference at the concentration of most aligned samples. This can be important in cases of weak dimers. Measure the pH as this will be useful in selecting media later.

PEG Biclle

Alignment of the protein sample in PEG(C12E5/hexanol). This is used as a first alignement media because it produced primarily steric alignment (useful in dimer geometry predictions), the success rate is high, and it can be doped with other charged detergents to give a second alignment media .

Chemical used for this preparation:

Sigma Aldrich 76437, Pentaethylene glycol monododecyl ether (C12E5 PEG)
Sigma Aldrich H13303, Hexanol
Sigma Aldrich 855820, Cetyltrimethylammonium bromide (CTAB)
Sigma Aldrich O4003, Sodium octyl sulfate (SOS)
Sigma Aldrich 436143, Sodium dodecyl sulfate (SDS)

The preparation procedure is as follow:

  • Mix 50ul of C12E5 (pentaethylene glycol monododecyl ether) with 200ul of buffer and 50ul of D2O by vortexing (REF [1]).
  • Add approx 16ul of hexanol, in aliquots of 2ul with vortexing after each addition. The solution will go from clear to milky, then to translucent and viscous with lots of bubbles. Continue to add hexanol until the solution goes clear again. If it becomes milky/turbid again, you have gone past the nematic phase.
  • Sample Content:
155 uL of Protein
55 uL of 16% PEG stock solution
20 uL of D2O
Final PEG concentration is 4.2%.
  • Record the 2H splitting by running the s2pul expt with tn=lk (for Varian instrument). The range of the splitting should be around ~+/-20Hz.
  • PEG can be doped with either cetyltrimethyl ammonium bromide (CTAB) for positively charged proteins or sodium octyl sulphate (SOS) for negatively charged proteins. Charging the medium to be like the protein prevents association and gives higher resolution spectra. A suitable ratio of PEG:CTAB/SOS is ~30:1.

Pf1 Phage

Preparation of a Pf1 phage alignment sample is fairly straightforward (REF[2]). The protein sample is diluted by the alignment medium.

Chemical used for this preparation:

ASLA Biotech P-50-P, Pf1 phage 50 mg/mL

The preparation procedure is as follows:

  • Start with a protein stock 1-2 mM and a pf1 phage stock of 50 mg/mL. Prepare a sample of 12.5 mg/mL of phage.
  • Sample Content:
155 uL of Protein
55 uL of Pf1 phage
20 uL of D2O
Final phage concentration is 12.5 mg/mL
  • Record the 2H splitting by running the s2pul expt with tn=lk (for Varian instrument). The range of the splitting should be around ~+/-8~10 Hz.

Polyacrylamide Gel (Compressed and Stretched)

Chemicals used in preparing this alignment medium can are:

Bio-Rad 161-0144, 40%Acrylamide/Bis solution 19:1
Bio-Rad 161-0733, 10X TBE
Bio-Rad 161-0700, APS
Bio-Rad 161-0800, TEMED
Sigma Aldrich M7279-25G, N,N'-methylenebisacrylamide (BIS)
Sigma Aldrich 448281, (3-Acrylamidopropyl)trimethylammonium chloride solution
Sigma Aldrich 282731, 2-Acrylamido-2-methyl-1-propanesulfonic acid
Compressed Gels - Positive, Negative and Neutral
  • Mix stock solutions of 40% acrylamide and N,N'-methylenebisacrylamide in a 19:1 ratio with 40% charged acrylate derivatives containing N,N'-methylenebisacrylamide as desired in a 19:1 ratio.
  • Dilute the mixtures 10x with TBE buffer (0.9 M TRIS, 0.9 M borate, 0.02 M EDTA, pH 8.2) to a final 7% concentration.
  • Polymerization is initiated by the addition of 0.15% ammoniumperoxide sulfate and 1% tetramethylethylenediamine (TEMED).
  • To introduce negative charges, use acrylic acid or 2-acrylamido-2-methyl-1-propanesulfonic acid. Positive charge can be introduced by addition of (3-acrylamidopropyl)-trimethylammonium chloride (APTMAC) or N-(2-acryloamidoethyl) triethylammonium iodide. For neutral gels omit the charged species; for zwitterionic gels use equivalent amounts of acrylic acid and APTMAC. For 50% charged gels use 50% content of the charged specie and 50% acrylamide.
  • Add 130ul of the mixture to plastic tubes with a 3.2 mm inner diameter and keep them overnight allowing polymerization to occur.
  • Wash the polymerized gels extensively in deionized water (three cycles over a period of 2 days). The gels will increase in size due to electro osmotic swelling.
  • Dry the gels over a 2 day period at room temperature on a teflon pan.

References

  1. Ruckert M and Otting G (2000), JACS, 122, 7793-7797
  2. Hansen MR, Mueller L, Pardi A (1998), Nat Struct Biol, 5, 1065-1074




Updated by Hsiau-Wei Lee, 2011