Time-resolved ElectroSpray Ionization Hydrogen-deuterium Exchange Mass Spectrometry for Studying Protein Structure and Dynamics

Summary

Conformational flexibility plays a critical role in protein function. Herein, we describe the use of time-resolved electrospray ionization mass spectrometry coupled to hydrogen-deuterium exchange for probing the rapid structural changes that drive function in ordered and disordered proteins.

Abstract

Intrinsically disordered proteins (IDPs) have long been a challenge to structural biologists due to their lack of stable secondary structure elements. Hydrogen-Deuterium Exchange (HDX) measured at rapid time scales is uniquely suited to detect structures and hydrogen bonding networks that are briefly populated, allowing for the characterization of transient conformers in native ensembles. Coupling of HDX to mass spectrometry offers several key advantages, including high sensitivity, low sample consumption and no restriction on protein size. This technique has advanced greatly in the last several decades, including the ability to monitor HDX labeling times on the millisecond time scale. In addition, by incorporating the HDX workflow onto a microfluidic platform housing an acidic protease microreactor, we are able to localize dynamic properties at the peptide level. In this study, Time-Resolved ElectroSpray Ionization Mass Spectrometry (TRESI-MS) coupled to HDX was used to provide a detailed picture of residual structure in the tau protein, as well as the conformational shifts induced upon hyperphosphorylation.

Introduction

Over the past several decades, significant advancements have been made in the development of analytical techniques designed to measure protein structure and dynamics^1,2,3,4. While X-ray crystallography remains the principle tool for determining protein structure, high concentrations of protein are needed and extensive optimization is required to produce diffraction quality crystals. Proteins that are difficult to crystallize, such as membrane-associated and intrinsically disordered proteins have classically been studied by hydrogen-deuterium....

Protocol

NOTE: Please consult all relevant material safety data sheets (MSDS) before use. Fumes produced by laser ablation of poly(methyl methacrylate) (PMMA) can be toxic. Be sure that the laser engraver is connected to a working ventilation system. Use all appropriate safety practices when building the microfluidic device including the use of engineering controls (fume hood, sharps container) and personal protective equipment (safety glasses, face mask, gloves, lab coat, full length pants, closed-toe shoes). It is of utmost importance to use High Performance Liquid Chromatography (HPLC) grade reagents whenever possible, with all being of ACS grade or higher to decrease inter....

Results

Digestion profiles of native and phospho-tau were similar, yielding a sequence coverage of 77.1 and 71.7% respectively. Deuterium uptake values of each peptide was determined by fitting the observed isotopic distributions with the theoretical distributions generated using an in-house developed FORTRAN software. The best fitting distributions are shown (Figure 3a) along with the associated deuterium uptake values. Uptake kinetic profiles are then generated, and were well d.......

Discussion

While structural biology methods such as X-ray crystallography and NMR are advantageous because they provide extremely detailed structures of proteins, these pictures are often static. The characterization of transient species and weakly structured domains continues to be elusive when studied by these conventional methods. Therefore, in order to gain dynamic insights on these types of systems it is important to work at rapid time scales. We have successfully applied TRESI-HDX-MS to obtain detailed insights on the conform.......

Materials

List of materials used in this article

Name	Company	Catalog Number	Comments
Poly(methyl methacrylate) or PMMA	Professional Plastics	SACR.250CCP	8.9 cm x 3.8 cm x 0.6 cm
Fused Silica Glass Capillary	Polymicro Technologies	106815-0018	ID: 75 µm, OD: 150 µm
Metal Capillaries	McMaster-Carr	28 ga – 89875K97 30 ga  - 89875K99
Fluorinated Ethylene Propylene (FEP) Tubing	IDEX	1477 1548	ID: 0.007”, OD: 1/16” ID: 0.020”, OD: 1/16”
Standard Polymer Tubing Cutter	IDEX	A-327	for 1/16” and 1/8” OD tubing
Micro Static Mixing Tee	IDEX	M-540	for 1/16” OD tubing
or
Stainless Steel Tee, 0.25 mm Bore	Valco Instruments Co., Inc. (VICI)	ZT1C	for 1/16” OD tubing
PEEK Tee for 1/16” OD Tubing	IDEX	P-727
10-32 Female to Female Luer	IDEX	P-659
10-32 PEEK Double-Winged Nut	IDEX	F-300
Ferrule for 1/16” OD Tubing	IDEX	F-142
100 Series Rotary Tool	Dremel	F013010001
Cut-Off Discs	Jobmate		1/64” thickness
Stereomaster Digital Zoom Microscope	Fisher Scientific	12-563-411
Soldering Iron	Mastercraft	58-6301-2
VersaLaser	Universal Laser
Syringes	Hamilton	81220	500 µL capacity
Syringe Pumps	Harvard Apparatus	70-4501
Name	Company	Catalog Number	Comments
Reagents
NHS-Activated Agarose	Fisher Scientific	26196
Pepsin from Porcine Gastric Mucosa	Sigma-Aldrich	P6887-250MG
Deuterium Oxide	Sigma-Aldrich	151882-10X0.6ML
Acetic Acid	Sigma-Aldrich	695092-100ML
HPLC Grade Water	Fisher Scientific	W5-4
Ammonium Acetate	Sigma-Aldrich	A7330-500G
Sodium Phosphate	Fisher Scientific	S369-500
Sodium Chloride	Fisher Scientific	S671-3
Name	Company	Catalog Number	Comments
Software/Online Tools
CorelDraw X3	Corel
Molecular Weight Calculator		Version 6.49	Open Source MS Tool
mMass		Version 5.5.0	Open Source MS Tool
ExPASy FindPept	Swiss Institute of Bioinformatics
SigmaPlot	Systat Software	Version 11.0
PyMOL	Schrödinger	Version 1.5.0.4
Name	Company	Catalog Number	Comments
Instruments
QStar Elite Hybrid Q-TOF Mass Spectrometer	AB SCIEX