Solution properties of Tim21ims

Figure 20: Intramolecular long range interactions in Tim23ims. PRE profile of Tim23ims T11C obtained with paramagnetic tag (MTSL) conjugated at position 11 (T11C) of Tim23ims. The intensity ratios are derived from signal intensity ¹H-¹⁵N HSQC spectra of Tim23ims T11C with MTSL paramagnetic (oxidized) and DTT added (reduced). The error bars are obtained based on the S/N values.

Deviations from intensity ratio of 1 beyond residue 25 are indicative of presence long range interactions.

Some resonances such as N40, D54, L58 and L71 that shows more severe broadening in comparison to its neighboring resonances are labeled.

3.1.4 Solution properties of Tim21ims

3.1.4.1 Association state of Tim21ims in solution

Size exclusion chromatography (SEC) was used to characterize the solution state of Tim21ims in terms of its shape and molecular weight. Notably, Tim21ims^103-225 contains one cysteine residue and in order to prevent intermolecular disulphide interactions size exclusion chromatography was performed under reducing conditions (5mM DTT). The SEC chromatogram of purified Tim21ims shows two peaks at elution volume maximum of 75ml (peak 1) and 85ml (peak2) respectively, which roughly correspond to the retention time of globular folded protein of 30kDa and 15kDa respectively (in comparison to S-75 standards) (Figure21, A). The SEC chromatogram of the reinjection (of pooled elution fractions) of peak 1 again showed a similar two

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peak pattern with identical retention time as seen before (Figure21, B). The identity of each eluted peak was further confirmed using ESI-MS (and 15% SDS-PAGE), which showed identical mass corresponding to monomeric Tim21ims. These results implied that Tim21ims exists in equilibrium as monomer and dimer in solution.

Furthermore, in order to characterize the structural differences between the monomeric and dimeric fractions of Tim21ims, the fingerprint spectrum of proteins i.e.¹H-¹⁵N HSQC spectrum for each fraction was acquired .The overlay of ¹H-¹⁵N HSQC of Tim21ims for both the peaks (i.e. with elution volume 75ml, dimeric-Tim21ims and 85ml, monomeric-dimeric-Tim21ims) at two different concentrations of 10µM and 1mM respectively, were nearly identical in chemical shift position for most of resonances expect for the small chemical shift changes in resonances belonging to β-strand 2 and 3. The three histidine residues in β-β-strand 3 and a histidine residue (H221) at C-terminal end was also perturbed (Figure 21, C). The pH was kept constant for 10µM and 1mM samples, additional control pH titration of Tim21ims was also performed to clarify the reason for the changes in CSP at two different concentrations of Tim21ims. Upon pH titration of Tim21ims, the β-strand 2, 3 and 4 were perturbed (Appendix Figure 5). However, the magnitude and direction of the chemical shift changes in Tim21ims as a function of pH are different. These results suggest that the concentration dependent changes in the chemical shift position of resonances of Tim21ims could be a characteristic of chemical exchange between different states of Tim21ims.

Additionally, correlation time of Tim21ims at concentration 1mM was found to be ~8.6ns that roughly corresponds to the size of the monomeric Tim21ims (15kDa).

The two results for expected dimeric fraction from SEC, (a) the similar chemical shift position of resonances in ¹H-¹⁵N HSQC spectra and (b) molecular weight similar to monomeric Tim21ims indicate that the SEC eluted dimeric fraction of Tim21ims is not stable and rapidly dissociates to monomeric Tim21ims. Thus, effectively low populations of dimeric-Tim21ims are present in both the samples (10µM and 1mM) and could not be observed by NMR. The NMR observable (chemical shift and the intensity of each residue) of Tim21ims in ¹H-¹⁵N HSQC spectra for both the SEC eluted fractions is an average weighted population of two states of Tim21ims with major contribution from a monomeric state up to the concentration of 1mM in Tim21ims.

3.1 Intermembrane space domains (ims) of mitochondrial translocases 77

Figure 21:Tim21ims exhibits monomer-dimer equilibrium in solution. (A) SEC chromatogram of purified Tim21ims showing two peaks at elution volume of 75 and 85 ml. (B) SEC chromatogram of elution peak at 75ml obtained upon its reinjection. (C) Left: Overlay of a section of ¹H-¹⁵N HSQC of Tim21ims at different concentration 10µM (red) from the peak eluted at 75ml and 1mM (black) from the peak eluted maximum at 85ml in SEC, acquired with 128 and 16 transients respectively at 298K.

The resonances that showed chemical shift perturbations are highlighted by black boxes. Right:

Average chemical shift perturbation (CSP) plot for these two ¹H-¹⁵N HSQC’s as a function of the sequence and secondary structural elements of Tim21ims. Two short β-strands represented by asterisk (٭) are absent in NMR structure, details in Figure 24. (D) The cartoon representation of Tim21ims (NMR model 1) is mapped with the residues showing a magnitude of CSP greater than 0.004 ppm. All perturbed histidine residues are colored as blue while other residues are colored in red. The secondary structural elements and N and C terminus of Tim21im are labeled as N and C respectively.

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3.1.4.2 Solution structure of monomeric Tim21ims

Despite the observance of significant amide-proton chemical shift dispersion (Figure 21C), the normalized intensities (w.r.t last residue) of the peaks in the ¹H-¹⁵N HSQC spectrum of Tim21ims were not uniform (Figure 22). Some of the residues (such as 130, 131, 135) show higher intensity ratio than average intensity ratio, whereas others show low intensity ratio (such as 141, 142, 144, 149, 151) indicating the presence of variable motion at different time scale in NMR. Loops and the highly flexible parts of proteins show higher intensity (dynamics at ps-ns time scale) whereas the regions undergoing chemical exchange are less intense (dynamics at µs-ms time scale). The residues in the two short β* strands are less intense. This interesting observation of non-uniform intensity in Tim21ims led us to probe the chemical exchange and local dynamics at the various sites in Tim21ims.

Figure 22: Signal intensity variation in ¹H-¹⁵N HSQC of Tim21ims as a function its residue number.

The residues belonging to region 130-133 and 144-155 shows the significant variation along with isolated residues in loops connecting strands in β-sheet. Last residue was used to normalize the intensity for all resonances, the error bars are based on the S/N ratio as described in materials and methods. The secondary structural elements of Tim21ims are shown at the bottom. The two β*-strands in grey are present in X-ray structure and are absent in NMR structure of Tim21ims (described in section 3.1.4.2).

3.1 Intermembrane space domains (ims) of mitochondrial translocases 79

Hence, ¹⁵N-R2 values and ¹H-¹⁵N Het NOE were measured for Tim21ims in solution.

The ¹H-¹⁵N HetNOE intensity ratio of residue is inversely proportional to the degree of fluctuations of (NH) amide bond vector at picosecond to nanosecond time scale. In Tim21ims, most of the residues have an intensity ratio above 0.65, which is expected for an ordered part of protein i.e. secondary structures and rigid loops. Some of residues corresponding to loop1 in Tim21 (residues 126-138) have ¹H-¹⁵N-HetNOE values lower than 0.4 indicating it to be flexible at this time scale. Additionally, residues (145-155) belonging to β1*and β2*-strands are mostly missing in the analysis due to resonance overlap and extremely weak resonance in reference spectrum. However, this region has two well isolated residues 148 and 153 that have low ¹H-¹⁵N-HetNOE value, suggesting β1*and β2*-strands are flexible (Figure 23, A).

Thereafter, ¹⁵N R₂ values of Tim21ims were measured to probe the microsecond to millisecond chemical exchange. The measured ¹⁵N R₂ values are cumulative sum of the intrinsic ¹⁵N R₂ and the R_ex (contribution due to chemical exchange). The residues possibly the exchange between the monomeric and dimeric Tim21ims (Figure 23, B).

Taken together, these results suggested that in solution, the conformation of Tim21ims could adopt different structure under solution conditions with the major changes localized to aforementioned regions. To this end, the monomer structure of Tim21ims was determined using NMR spectroscopy by Lukasz Jaremko and Mariusz Jaremko in our group.

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Figure 23: ¹⁵N relaxation of apo Tim21ims in solution recorded in 700MHz at 298K. The values of ¹⁵

N-1H Het NOE (A) and ¹⁵N R₂ (B) are plotted as a function of residue number. The non-proline residues with either overlapping peaks or peaks with low S/N were omitted from the analysis and they appear as blank in plot. The lower panel shows the schematic representation of secondary structural elements in Tim21ims. (C) Two views of the cartoon representation Tim21ims (NMR model 1) mapped with the residues exhibiting ¹⁵N R₂ value higher than 19 sec ^-1 in red and lower than 12 sec^-1in blue color.

3.1 Intermembrane space domains (ims) of mitochondrial translocases 81

The backbone RMSD for the structured regions of 20 low energy conformers of Tim21ims determined by NMR with respect to mean structure was found to be 0.47 ± 0.09 Å indicating the NMR structures converges well. The comparison between NMR structure and X-ray structure of Tim21ims revealed that two α-helices are conserved in both the structures. However, two small β-strands (out of 8 observed in X-ray structure i.e. β1*and β2*) involving residues 144-146 and 151-153 are not well defined in NMR structure (Figure 24). This region has a higher RMSD of value of 2.40±0.88 Å (marked with label 2 in Figure 25, B and C) in 20 low energy conformers in comparison to mean NMR structure. In addition, 20 low energy conformers have higher backbone RMSD as expected for the N-terminal (additional residues due to cloning exigencies) and C-terminal residues (marked with label 4 in Figure 25, B and C) as 2.01±0.66 Å. Indeed, residues 144-146 and 151-153 (β1*and β2* strand) exhibits low signal intensity in ¹

H-15N-HSQC spectra as well as low ¹H-¹⁵N HetNOE values in comparison to other parts of protein. Additionally, residues in region 146-156 (β1*and β2*) show higher B-factors and possess crystal contacts with the C- terminal residues that lead to multiple conformations of this region in crystal and thus the uncertainty in their position i.e.

static disorder in B factor.

Figure 24: Comparison of secondary structure elements present in X-ray structure (A) and NMR structure (B) of Tim21ims by the schematic representation of Tim21_IMS fold. The secondary structure elements for X-ray and NMR structure of Tim21ims were defined using DSSP program (http://www.cmbi.ru.nl/dssp.html). Two β-strands (β1* and β2*) highlighted in red are not well defined in ensemble of NMR structure.

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Figure 25: Structure of Tim21ims differs in solution:(A) Two views of cartoon representation of Tim21ims generated from crystal structure (PDB id:2CIU ) and is color coded accorded to the B-factors using PYMOL with blue,green and red exhibiting gradient of B-factor from 0-95.Cartoon (B) and Ribbon (C) representation of superposition of 20 lowest energy NMR conformers (white) with X-ray structure of Tim21ims(red) .The differences in NMR conformers and X-ray structure involve regions (1) Loop involving residues C128-L138, (2) residues 145-154 involving β1*and β2*strand , (3) Loop connecting β-strand 2 and 3, (4) C-terminal residues 221-225.

3.1 Intermembrane space domains (ims) of mitochondrial translocases 83 content in proteins. The lack of prominent CD signal at 195nm and 215nm indicates that disordered parts are dominantly absent. However, it is often difficult to predict accurately the secondary structure content by CD spectrum, which is mainly dominated by α-helices.

The ¹H-¹⁵N TROSY-HSQC spectra of Tim50 ^164-361 ims displayed approximately 127 well dispersed resonances in contrast to the expected 178 from this 198 residue construct with 19 prolines (Figure 26, B). As expected for well folded protein, ¹H-¹⁵N TROSY-HSQC display broad amide dispersion encompassing characteristic regions of beta strands and alpha helices. The lack of 40 peaks in, ¹H-¹⁵N TROSY-HSQC spectrum could be attributed to chemical exchange occurring at intermediate NMR timescale for these peaks. This chemical exchange could be conformational or exchange with water for solvent accessible regions corresponding to loops or other flexible parts of Tim50ims.

The detailed inspection of X-Ray structure (PDB id: 3QLE) of Tim50^176-361 ims corresponding to Tim50^164-361 ims construct (that lacks an N-terminal 12 residues).

highlights nearly thirty residues with higher B factors indicating that these resonances might be missing ¹H-¹⁵N TROSY-HSQC spectra of Tim50^164-361 if they exhibits chemical exchange at the slower NMR timescale (µs-millisecond) (Qian et al. 2011).

Interestingly, an alpha helix (residues 241-251) and beta hairpin loop (residues 205-215) showed higher B factors in addition to expected loop region (Figure 26C). The absence of concentration dependent changes in the ¹H-¹⁵N TROSY-HSQC spectrum ofTim50 ^164-361 ims (concentration ranging from 50µM to 350µM), indicate the absence of oligomerisation of Tim50^164-361ims.