Effects of Tir and Map binding on CesT

In order to explore the effector binding region on the surface of CesT, ²H¹⁵N-labeled CesT was titrated with Tir108 and His₇-Map84 (see 6.2.4). This approach allows for the identification of the binding surface of CesT specific for Tir and Map based on chemical shift perturbation. Start and end ¹⁵N-TROSY-HSQC spectra for the CesT/Tir108 and the CesT/His₇-Map84 titration are shown in Figure 6.17.For both complexes, slow exchange is observed between free and bound CesT and almost all peak positions are changed. In order to reassign the backbone resonances of CesT in

10 9 8

Figure6.16: Overlay of¹⁵N-HSQC spectra of TirN and TirN bound to CesT at 303 K.

Spectra were measured at 800 MHz. Peaks of Tir108 superimpose well with TirN and are labeled with the residue number. Signals which do not belong to Tir108 and are affected upon addition of CesT are indicated by circles: Violet circles mark peaks which show significantly decreased intensity or which vanished and blue circles mark shifted peaks.

complex with Tir108 as well as in complex with Map84, 3D triple resonance spectra were acquired for the two different ²H,¹⁵N,¹³C-CesT/effector complex samples (Ap-pendix Table B.5 and B.4). 93 % of the backbone amide resonances, 96 % of the C_α and C’ resonances and 95 % of the C_β resonances could be reassigned for CesT in complex with Map84. To analyse the structural changes of CesT upon Map84 binding, the secondary chemical shifts were calculated and subtracted from the sec-ondary chemical shift of free CesT (Figure 6.18). No secondary structure changes were observed for CesT upon Map binding. Furthermore, averaged amide chemical shift perturbations were determined (see 3.5.5) in order to map the binding surface

130

Figure 6.17: Overlay of¹⁵N-TROSY-HSQC spectra of free CesT (black) and effector-bound CesT: (A) Red peaks correspond to CesT in complex with Tir108 and (B) green peaks correspond to CesT in complex with Map84. Assigned peaks are indicated by the sequence number.

for Map84 on CesT (Figure 6.19). Strongly shifted residues in the chemical shift perturbation plot (Figure 6.19), in the structure-based sequence alignment of TTSS chaperone (Figure 6.20) and on the surface of CesT (Figure 6.21) are colored

identi-Δδ(CαCβC’) (ppm)

0 20 40 60 80 100 120 140

residue

-10 -10

-5 -5

0 0

5 5

10 10

ΔΔδ(CαCβC’) (ppm)

Figure6.18: Secondary structure of CesT bound to Map84. Secondary chemical shifts

∆Cα - ∆C_β + ∆C’ of CesT bound to Map84 (black) and secondary chemical shift difference for ∆C_α - ∆C_β + ∆C’ between free and bound CesT (red) plotted against the residue number. Secondary structure regions of the X-ray structure are indicated.

Residues proposed to form hydrophobic patches are labeled by blue squares [162].

ΔδHN (ppm) 0.6

0 20 40 60 80 100 120 140

residue 0

0.1 0.2 0.3 0.4 0.5

Figure 6.19: Chemical shift changes of CesT upon formation of the CesT/Map84 complex. Residues shifted>0.4 ppm,>0.3 ppm and>0.2 ppm are colored red, orange, yellow and green, respectively, and residues shifted >0.1 ppm are colored green if an adjacent residue is also shifted >0.1 ppm. Secondary structure regions of the X-ray structure are indicated.

cally with red for shifts >0.4 ppm, orange for shifts >0.3 ppm and yellow for shifts

>0.2 ppm. Green indicates residues with shifts >0.1 ppm that have at least one adjacent residue shifted by >0.1 ppm. All strongly shifted peaks (>0.3 ppm) are

CesT MSSRSELLLDRFAEKIGVGSIS FNENRLCSFAIDEIYYISLSDANDEYMM InvB MQHLDIAELVRSALEVSGCDPSLIGGIDSHSTIVLDL FALPSICISVKDDDVW Spa15 MSNINLVQLVRDSLFTIGCPPSIITDLDSHSAITISLD SMPAINIALVNEQVM AvrPphFORF1 MKNSFDRLIDGLAKDYGMPGFPEKKHEHEVYCFEFKEV S IRIYQDKFKWV

CesT IYGVCGKF PTDNPNFALEILNANLWFAENG GPYLCYESGAQSLLLALRFP SigE MCCPFMPL PDDILTLQHFLRLNYT SAVTIGADADNTALVALYRLP SicP LNGMIIPLSPVCGDSIWRQIMVINGELAANNEG TLAYIDAAETLLLIHAIT SycE MFTLPSLD NNDEKETLLSHNI FSQDILKPILSWDEVGGHPVLWNRQP SycH AFMR AG ILTGQSQLYDILRKNLFSPLSG VIRCALDKDDHWLLWSQLN SycT QLFSELGA DLPTNDNLFGEHWPAH VQGR LDGKSILWSQQS InvB IWAQLGA DSMVVLQQRAYEILMTIMEGCHFARGQLLLGEQ NGELTLKALVH Spa15 LWANFDA PSDVKLQSSAYNILNLMLMNFSYSINELVELHRS DEYLQLRVVIK AvrPphFORF1 YFLSDIGV IDNLDSNACQSLLRLNEFNLRT PFFTVGLNEKKDGVVHTRIP

CesT LDDAT PEKLENEIEVVVKSMENLYLVLHNQGITLENEHMKIEEISSSDNKHYYAGR SigE QT ST EEEALTGFELFISNVKQLKEHYA

SicP D LTN TYHIISQLESFVNQQEALKNILQEYAKV SycE LNSLD NNSLYTQLEMLVQGAERLQTSSLISPPRSFS

SycH INDTS GTQLASVLTSLVDKAVTLSCEPTMKKEEDDHRPSSSH SycT SLVGLD IDEMQAWLERFIDDIEQRKEPQNTKFQPNSTSPILFI InvB HPDFLSDGEKFSTALNGSFYNYLEVFSRSLMR

Spa15 DDYVHDGIVF AEILHEFYQRMEILNGVL

AvrPphFORF1 LLNLD NVEMRRVFEALLNLSGEV KKTFGFV

10 20 30 40 50

60 70 80 90 100

110 120 130 140 150

Figure 6.20: Structure-based sequence alignment of nine TTSS chaperones. Con-served residues are highlighted: green for hydrophobic and orange for polar residues.

Differently colored squares above the sequence indicate residues as in Figure6.19. The magenta boxes point at the two regions which are assumed to interact with theβ-motif of the TTSS effector [161]. Secondary structure elements of CesT in the X-ray structure are displayed above the sequence.

hydrophobic, thereby indicating the hydrophobic character of the CesT/ Map84 in-teraction. The only exceptions are the strongly shifted residues Asn136 and Glu137.

These shifts suggest a contribution of electrostatic interactions between Map84 and Glu137 of CesT to the complex formation. The ∼0.2 ppm shifted residues 151-153 were not colored in Figures 6.19, 6.20 and 6.21 because they are not present in the X-ray structure. Altogether, residues exhibiting strong shifts correspond well to the

A B

C D

180 °

180 °

Figure 6.21: Side views of the surface representation of CesT. (A,B) Chemical shift changes upon Map84 binding mapped to the surface of CesT. Residues colored green, yellow, orange and red are identical to Figure 6.19. (C,D) Residue properties mapped to the surface of CesT with charged, polar and hydrophobic residues colored magenta, lightblue and blue. (A,C) are rotated by 180^◦ around the x-axis to generate (B,D).

hydrophobic patches proposed by Birtalanet al.[162]. The binding mode seems to be mainly identical to the homologous chaperone/effector complexes with known struc-ture. Large hydrophobic surfaces are buried in these homologous chaperone/effector complexes and CesT achieves the effector recognition in a similar way through nu-merous hydrophobic interactions. The mapping of the shifted residues onto the 3D surface reveals a narrow band of contact around the circumference of the chaperone.

This path involves almost exclusively hydrophobic residues, revealing that the inter-action is largely hydrophobic in nature. A few additional auxiliary points are also provided by polar or charged interactions and are shifted <0.3 ppm (Figure 6.21).

For residues 29-33 and 113-117, which are indicated by magenta boxes in Figure6.20, the formation of an intermolecular β-sheet with the effector has been proposed [161].

This could be experimentally verified by the chemical shift analysis for residues 29-33, which are most affected upon Map binding. However, the chemical shift perturbation for residues 113-117 is not more significant than for other regions of CesT.

For CesT in complex with Tir108, ∼67 % of the backbone amide resonances were re-assigned (Appendix TableB.9). A reason for the missing reassignments is the quality of the 3D spectra which is inferior to the 3D spectra recorded for CesT in com-plex with Map84. An almost complete reassignment may be achieved with a better CesT/Tir108 sample and with additional 3D spectra. Among the ∼67 % assigned backbone amide resonances, residues with the largest shifts also presented large shifts for CesT in complex with Map84 (Figure 6.22). Therefore, it is likely that the

ΔδHN (ppm)

0 20 40 60 80 100 120 140

residue 0

0.1 0.2 0.3 0.4 0.5 0.6

Figure 6.22: Chemical shift changes of CesT upon formation of the CesT/Tir108 complex (red circles). The black bars show the chemical shift changes of CesT upon formation of the CesT/Map84 complex for comparison. Secondary structure regions of the X-ray structure are indicated.

CesT/Map and the CesT/Tir interaction involve the same surface regions of CesT.

This agrees with previous ELISA and yeast three hybrid results which demonstrate a competition between Map and Tir for CesT binding [30].