Alignment Media Preparation

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 of 16% PEG stock solution is as follows:

• Mix 50ul of C₁₂E₅ (pentaethylene glycol monododecyl ether) with 200ul of buffer and 50ul of D₂O by vortexing (REF ).
• 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.
• 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. If the protein sample is less than the pI it will be positively charged and if it is more than the pI it will be negatively charged.

Pf1 Phage

Preparation of a Pf1 phage alignment sample is fairly straightforward (REF). 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 of 16% PEG stock solution 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 (Compress and Stretch)

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 can be made 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

Updated by Hsiau-Wei Lee, 2011