Structure of the α-helix

Structure of the α-helix

Structure of the β Sheet

Protein Dynamics

Basics of Quenching HDX Hydrogen exchange of amide protons is catalyzed by H 2 O, OH -, and H 3 O +, but it s most dominated by base catalyzed reactions. Ka Kb Kw 6.95E-01 1.87E+08 5.27E-04 In addition to lowering the ph, chemical kinetics are considerable slowed with decreasing temperature. Place of Quenched Reaction My hand In a Theoretical Lab In a UAB Lab On Ice (0C) In the -20C Fridge In the -80C Fridge In Liquid Nitrogen Half Life of Back Exchange 1 minute 4 minutes 7 minutes 1 hour 14 hours 7 Years When Hell Freezes Over

For exchange to occur: Kinetics of HDX 1. The site needs to be at least transiently exposed to the bulk solvent. 2. The site must be available to form new hydrogen bonds. If it is either exposed with an unavailable site for hydrogen bonding or buried (most always hydrogen bonded in this case), it is described as protected. In HDX experiments, the degree of protection (P f ) is empirically determined by the extent the rate of exchange (k ex ) is slowed from the predicted chemical rate (k ch ). Deuterium Uptake 1.2 1 0.8 0.6 0.4 0.2 Kch Kex 0 0 0.2 0.4 0.6 Time (s)

Kinetic Range of Protection A wide span of different kinetics can be observed for the range of protection that can occur within a single protein. Deuterium Uptake 1.2 1 0.8 0.6 0.4 0.2 0 1.2 1 0.8 0.6 0.4 0.2 0 1.2 1 0.8 0.6 0.4 0.2 0 0 0.25 0.5 0.75 1 0 20 40 60 0 200 400 600 Time (s) Unprotecte d log Pf 0.5 log Pf 1 log Pf 2 log Pf 3 log Pf 4 Unprotecte d log Pf 0.5 log Pf 1 log Pf 2 log Pf 3 log Pf 4 Unprotecte d log Pf 0.5 log Pf 1 log Pf 2 log Pf 3 log Pf 4

Kinetic Range of Protection A wide span of different kinetics can be observed for the range of protection that can occur within a single protein. Deuterium Uptake 1.2 1 0.8 0.6 0.4 0.2 0 0.001 0.1 10 1000 Time (s) Unprotecte d log Pf 0.5 log Pf 1 log Pf 2 log Pf 3 log Pf 4 Log Pf 6 Because of this, the data is more reasonably visualized on the log scale.

Aspergillus Protease Complements Pepsin FRACTION BURIED 0-0.2 0.2-0.4 0.4-0.6

Data Analysis using HDExaminer Calculate isotope distribution using known chemical composition Calculate theoretical spectra for peptide +1, +2, +3. Deutrons Fit experimental spectra with Gaussian distributed sum of calculated spectra Assess quality of fit, calculate percent exchange

Heat Map Showing Exchange Kinetics 121 125 130 135 140 145 150 155 160 165 170 175 180 Q S L R E L I S D L E H R L Q G S V M E L L Q G V D G V I K R T E N V T L K K P E T F P K N Q R R V F R A P D L K G M L 0.50s 1s 3s 10s 12s 30s 90s 5m 15m 45m 2h 8h 181 185 190 195 200 205 210 215 220 225 230 235 240 E V F R E L T D V R R Y W V D V T V A P N N I S C A V I S E D K R Q V S S P K P Q I I Y G A R G T R Y Q T F V N F N Y C 0.50s 1s 3s 10s 12s 30s 90s 5m 15m 45m 2h 8h 241 245 250 255 260 265 270 275 280 285 290 295 300 T G I L G S Q S I T S G K H Y W E V D V S K K T A W I L G V C A G F Q P D A M C N I E K N E N Y Q P K Y G Y W V I G L E 0.50s 1s 3s 10s 12s 30s 90s 5m 15m 45m 2h 8h

Phi29 Scaffold Has a Helix-Loop-Helix Motif and a Disordered Tail Marc C Morais et al., Nature Structural Biology 2003

Both Free and Bound Scaffold Exchange Bimodally 10 min 3 min 100 % 0 100 % 0 Free scaffold 13+ Prohead scaffold 100 % 0 100 % 0 1 min 100 % 0 Partially exchanged species 100 % 0 40 sec 100 % 100 % 0 0 10 sec 100 % 0 Fully exchanged species 100 % 0 0 sec 100 % 100 % 0 857 858 859 860 861 862 863 864 m/z m/z 0 857 858 859 860 861 862 863 864 m/z m/z

What does Bimodality Indicate? A group of residues open cooperatively & completely exchange before close again. surface residues exchanged 1 3 4 2 slower components opened cooperatively 3 exchanged 2 4 closed 4 1 857 858 859 860 861 862 863 864 m/z

The Bimodality Maps to N-terminal Helix-Loop-Helix R 20-31 45 min 691.41 690.92 690.40 691.92 692.42 692.92 45 min 3.2min 689.91 690.90 690.41 691.91 691.41 692.42 692.92 693.43 3.2min 1.2min 6.40 688.42 688.90 689.90 689.41 690.41 691.41 691.92 692.42 692.92 693.39 1.2min 689.41 689.91 40 sec 688.40 688.90 690.41 691.42 691.91 692.42 692.93 693.45 40 sec 20 sec 0 sec 687.39 688.39 687.90 687.89 689.40 688.90 689.92 690.41 690.91 691.41 20 sec 687 688 689 690 691 692 693 694 m/z 687 688 689 690 691 692 693 694 m/z

Peptides Derived from H-L-H Region Have Similar Opening Kinetics R 20-31 100 R 1-19 R 32-38 % completely exchanged species 80 60 40 20 0 R 1-19 R 20-31 R 32-38 Whole protein 0 20 40 60 80 100 120 140 160 180 580 600 exchange time ( sec )

The Cooperative Motions can Be Frozen by Lowering the Temperature 30 hr 20 C 30 hr 10 C 7 min 5 min 9 hr 4.5 hr 1.5 hr 3 min 20 sec 3 min 20 sec 686 687 688 689 690 691 692 693 686 687 688 689 690 691 692 693 m/z m/z

Does Bimodality Originate from Opening of the Interface between Helices 1 & 2? 2.58 Å L3C & N35C Tethered Form

The Tethered Form Cannot Open Cooperatively Oxidized Form ( Tethered ) 10 min Reduced form 10 min 5 min 1 min 2 min 20 sec 1 min 10 sec 10 sec 686 687 688 689 690 691 692 693 694 686 687 688 689 690 691 692 693 694

Non-covalent or Native Mass Spectrometry We can ionize intact protein complexes using ESI!!

What Can We Learn? Stoichiometry of complex Relative affinity and topology Rates of subunit exchange Assembly pathways

Parameters for Non-covalent Mass Spectrometry Generally done with ToF instruments Direct (nanospray) infusion out of volatile buffers (typically ammonium acetate)

Displacement of Contaminating Buffer by Competion

Effect of Pressure on Spectral Quality Increasing vacuum

+ K d = k off / k on

Subunit Exchange in NAD Synthetase A B C 1.0 Heterodimer/ homodimer (RU) 0.9 0.8 0.7 0.6 0.5 0.4 0 10 20 30 40 50 60 Time (min)

Portal Motor Packages DNA Into Phage Head

Native Mass Spectrometry Can Determine the Stoichiometry of Macromolecular Complexes Phi-29 Portal Complex m/z = 8938 m/(z+1) = 8756 m/(z+2) = 8581 m = 429,052 m/12 = 35,754 Monomer = 35,747

Detection of Intermediates and Sub-populations

Complexes Formed in Vitro Larger Diameters Connector Dodecamers Complexes Number of Particles 60 40 20 0 60 40 20 Connector Connector/Scaffold Complexes 0 10 12 14 16 18 20 22 24 26 Diameter (nm) Negative-stained EM

Native Mass Spectrometry Demonstrates Scaffold Binds as a Dimer Scaffolding :Connector at 2:1 Input Ratio 12mer connector + 2 scaffold + 4 scaffold + 6 scaffold

Increasing the Scaffolding to Connector Ratio Increases the Scaffolding Saturation 2:1 25:1

Scaffolding Binds Non-cooperatively with a K d of ~20 µm 0.30 0.25 0.20 Experimental 15uM connector dimer/ 30uM scaffold dimer 15uM connector dimer/145um scaffold dimer 5uM connector dimer/125um scaffold dimer 0.40 0.35 0.30 0.25 K d = 50 µm 0.15 0.20 0.10 0.15 0.10 0.05 0.05 0.00 0 1 2 3 4 5 6 0 2 4 # of bound 6 scaffold 8 dimer 10 12 2:1 0.00 0 1 2 3 4 5 6 0 2 4 6 8 10 12 0.40 0.35 0.30 0.25 0.20 K d = 20 µm 10:1 25:1 0.7 0.6 0.5 0.4 K d = 100 µm 0.15 0.3 0.10 0.2 0.05 0.1 0.00 0 1 2 3 4 5 6 0 2 4 6 8 10 12 0.0 0 1 2 3 4 5 6 0 2 4 6 8 10 12

Obtaining Shape Information Put a device that separates ions by shape in front of MS (Imagine a size exclusion column) One such device is a drift tube This is a tube filled with gas. The progress of the molecules is retarded as they are buffeted by gas.

Ion Mobility Mass Spec (IMS) Provides information about the Size and shape of a molecule In the gas phase

How do we derive collision cross section from drift time? What good is it? another dimension of separation provide shape information

Direct Measurement of Charge on Complexes (CDMS)

Basis of CDMS Ion Trap Analyze individual ions for 95 ms Frequency mass/charge Induced current - charge What is the dynamic range of a single molecule

420 molecules of 46,500 Da = 19.58082 Mda Unknown number of scaffolding protein of mol wt = 35,000 Da

Bacteriophage Capsids 23.60 MDa 112 scaffolding +/- 19.84 MDa

Schematic of Crosslinking Experiments.

Lysine Reactive DST Cross-Linker DST: Spacer Arm 6.4 Å Lys + Lys Trypsin Digestion Lys Lys Lys Lys Mass: A+B+114 D

Isotopically Coded Crosslinkers BS3-11.4 Å Lys - 6-6.5 Å Average Cα Distance of BS3 Crosslinked Lysines Rappsilber J Struct Biol 2011; 173:530

Isotopically Coded Crosslinkers BS3-11.4 Å Lys - 6-6.5 Å Average Cα Distance of BS3 Crosslinked Lysines Rappsilber J Struct Biol 2011; 173:530

DST Cross-Linking Profiles Conn Complex Conn Complex Conn/D Complex Conn/M Scaf/D Scaf/M 200K 123K 80K 36K Conn/D CS2 CS1 Conn/M 15 % SDS-PAGE 7.5 % SDS-PAGE

Identification of Scaffolding/Connector Interfaces by Chemical Crosslinking Scaffolding 83-98 Cross-Linked to Connector 4-5/19-20 731.3822 100 731.7161 80 60 40 20 0 * * 732.0504 * 732.3409 NL: 4.59E2 ComplexHigh_FT#968-1052 RT: 18.33-19.90 Scaffolding 53-68 Cross-Linked to Connector 94-105 * [M+3H] 3+ theo = 731.3813 [M+3H] 3+ exp = 731.3822 Error (ppm) = 1.2 ppm AV: 85 T: FTMS + p ESI Full ms [ 300.00-2000.00] NL: 100 80 60 40 660.7504 660.9508 661.1513 661.3516 [M+5H] 5+ theo = 660.7490 [M+5H] 5+ exp = 660.7504 Error (ppm) = 2 ppm 661.5517 20 661.7528 0 Peptides were sequenced by MS/MS.

Docking Model of Connector/Scaffolding Complexes 1 st step: ZDOCK ( optimize shape complementarity, deslovation, electrostatics) Use entire scaffolding dimer Use connector dimer Block interior surface of connector Generate #2000 models 2 nd step: filter with SF66-Conn102 cross-link distance constraint Use 8 Å constraint, 26 models Scaffolding orientation Defined by SF83 Conn4/19 cross-link Select model #25 6.38 Å 3 rd step: model verification by mutagenesis