Template for Communications for the Journal of the American Chemical Society

Supplementary Information

Cyclic RGD peptides interfere with binding of the Helicobacter pylori protein CagL to integrinsV3 and 51.

Jens Conradi, Sylwia Huber (née Urman), Katharina Gaus≠, Felix Mertink, Soledad Royo Gracia‡, UlfStrijowski#, Steffen Backert, Norbert Sewald* ()

J. Conradi, S. Huber (née Urman), K. Gaus≠, F. Mertink, S. Royo Gracia‡, U.Strijowski#, N. Sewald

Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany

E-mail:

S. Backert

School of Biomolecular and Biomedical Sciences, University College Dublin, Ardmore House, Belfield Campus, Dublin-4, Ireland

≠Present address: Syngenta, Schaffhauserstrasse, 4332 Stein, Switzerland

Present address: F. Hoffmann – La Roche, Grenzacherstrasse 124, 4070 Basel, Switzerland

#Present address: German Institute of Food Technologies, Professor-von-Klitzing-Straße 7, 49610Quakenbrück, Germany

‡Present address: Institute for Research in Biomedicine, Baldiri Reixac 10, 08028 Barcelona, Spain

*Corresponding author:

Prof. Dr. Norbert Sewald

Bielefeld University

Department of Chemistry

PO Box 10 01 31

D-33501 Bielefeld

Tel. int.: +49-(0)521-106 2051

Fax int.: +49-(0)521-106 8094

E-mail:

Table S1.NMR experiments, acquisition and processing parameters.

Experiment / Pulse Program / TD / NS / Other Processing Parameters
1H / Zg / 32-64 K / 32-64 / 32K, exp., LB 0.3
1H / zg30 / 32K / 32 / T=295, 300, 305, 310, 315, 325K, 120K, exp., LB 0.3
COSY / cosydfph / 2K X 512 / 16 / 2K X 2K, sin2, +/2
COSY / cosydfph / 2K X 256 / 16 / T=295, 300, 305, 310, 315, 325K, 2K X 2K, sin2, +/2
TOCSY / Dipsi2ph / 2K X 256
2K X 512 / 16 / τm=80ms
2K X 2K, sin2, +/2
ROESY / roesyph / 2K X 256
2K X 512 / 16 / τm=200ms
2K X 2K, sin2, +/2
NOESY / noesyph / 4K X 512 / 16 / τm=200,250, 300, 350, 400, 450ms
2K X 2K, sin2, +/2
1H,13C-HSQC / hsqcetgpsisp2
hsqcedetgpsisp / 2K X 256
2K X 512 / 32-64 / JC,H=145Hz
2K X 2K, sin2, +/2
HMBC / hmbcgpndqf
hmbclpndqf / 4K X 512 / 32-48 / JC,H=145Hz
2-4K X 1K, sin2 or sin
1H,15N-HSQC / hsqcetf3gpsi / 2Kx256
2Kx512 / 64-256 / JN,H=90Hz
2K X 256, sin2, +/2
13C / zgpg30 / 64K / 10-32K / 32K, exp., LB 1.0
DEPT-135 / dept135 / 64K / 10K / 32K, exp., LB 1.0

TD: time domain; NS: number of scans; SW: sweep width; O1P: transmitter frequency

Figure S1.Structural analysis of peptides, workflow overview (MD: molecular dynamics, DG: distance geometry, SA: simulated annealing) (Gaus 2009).

Figure S2. Sigmoidal dose-response plots of the competitive cell adhesion assays for cyclic peptides 1-7 inhibiting the binding of WM-115 cells to the CagLWT, CagLRAD and CagLRGA proteins.

Table S2.Distances derived from NOESY correlations of c-(-Arg-Gly-Asp-d-Leu-Ala-) 2 in DMSO-D6, d: distance, exp: experimental value, rMD: average value adopted over all trajectories in restrained molecular dynamics calculations, fMD: average value obtained by the combined trajectories in unrestrained molecular dynamics calculations.

Atom 1 / Atom 2 / d / pm
Exp / Tolerance / rMD / fMD
Arg-1 Hα / Arg-1 HN / 285 / ±28 / 281 / 284
Arg-1 Qβ / d-Leu-4 HN / 361 / ±36 / 569 / 735
Arg-1 Qβ / Arg-1 Hα / 327 / ±33 / 256 / 253
Arg-1 Qβ / Arg-1 Qδ / 404 / ±40 / 274 / 277
Arg-1 Qβ / Arg-1 HN / 408 / ±41 / 274 / 276
Arg-1 Qβ / Gly-2 HN / 381 / ±38 / 267 / 344
Arg-1 Qδ / Arg-1 Hα / 415 / ±41 / 330 / 304
Arg-1 Qγ / Arg-1 Hα / 349 / ±35 / 263 / 270
Arg-1 Qγ / Arg-1 Qβ / 259 / ±26 / 233 / 231
Gly-2 Qα / Asp-3 HN / 371 / ±37 / 287 / 280
Gly-2 Qα / Asp-3 HN / 316 / ±32 / 287 / 280
Asp-3 Hα / Asp-3 HN / 330 / ±33 / 282 / 284
Asp-3 Hα / d-Leu-4 HN / 264 / ±26 / 251 / 221
Asp-3 Qβ / Asp-3 Hα / 333 / ±33 / 255 / 247
Asp-3 Qβ / Asp-3 HN / 361 / ±36 / 267 / 270
d-Leu-4 Hα / d-Leu-4 HN / 344 / ±34 / 277 / 282
d-Leu-4 Hα / Ala-5 HN / 226 / ±23 / 223 / 220
d-Leu-4 Qβ / d-Leu-4 HN / 375 / ±37 / 301 / 273
d-Leu-4 Qβ / d-Leu-4 Hα / 313 / ±31 / 255 / 255
d-Leu-4 Qβ / Ala-5 HN / 432 / ±43 / 370 / 406
Ala-5 Hα / Ala-5 HN / 327 / ±33 / 266 / 278
Ala-5 Mβ / Ala-5 Hα / 322 / ±32 / 242 / 241
Ala-5 Mβ / Ala-5 HN / 271 / ±27 / 273 / 280

Table S3. Distances derived from NOESY correlations of c-(-Arg-Gly-Asp-Leu-d-Ala-) 3 in DMSO-D6, d: distance, exp: experimental value, rMD: average value adopted over all trajectories in restrained molecular dynamics calculations, fMD: average value obtained by the combined trajectories in unrestrained molecular dynamics calculations.

Atom 1 / Atom 2 / d / pm
Exp / Tolerance / rMD / fMD
Arg-1 Hα / Arg-1 HN / 233 / ±23 / 276 / 280
Arg-1 Hα / Gly-2 HN / 268 / ±27 / 220 / 224
Arg-1 Qβ / Arg-1 Hα / 281 / ±28 / 252 / 252
Arg-1 Qβ / Arg-1 Qδ / 342 / ±34 / 271 / 275
Arg-1 Qβ / Arg-1 Hε / 422 / ±42 / 330 / 333
Arg-1 Qβ / Arg-1 HN / 334 / ±33 / 274 / 270
Arg-1 Qβ / Gly-2 HN / 375 / ±37 / 374 / 366
Arg-1 Qδ / Arg-1 Hα / 352 / ±35 / 382 / 325
Arg-1 Qδ / Arg-1 Hε / 356 / ±36 / 185 / 185
Arg-1 Qδ / Arg-1 HN / 453 / ±45 / 437 / 456
Gly-2 Qα / Leu-4 HN / 365 / ±36 / 491 / 483
Asp-3 Qβ / Gly-2 Qα / 438 / ±44 / 521 / 516
Asp-3 Qβ / Asp-3 HN / 251 / ±25 / 281 / 271
Asp-3 Qβ / Leu-4 HN / 303 / ±30 / 271 / 275
Leu-4 Hα / Leu-4 HN / 281 / ±28 / 284 / 285
Leu-4 Qβ / Asp-3 Qβ / 527 / ±53 / 480 / 468
Leu-4 Qβ / Leu-4 Hα / 240 / ±24 / 253 / 254
Leu-4 Qβ / Leu-4 HN / 304 / ±30 / 277 / 276
Leu-4 Qβ / d-Ala-5 HN / 358 / ±36 / 404 / 407
Leu-4 Qδ / Leu-4 Hα / 423 / ±42 / 331 / 342
Leu-4 Hγ / Leu-4 HN / 356 / ±36 / 310 / 330
Leu-4 Hγ / d-Ala-5 HN / 545 / ±55 / 420 / 389
d-Ala-5 Mβ / Arg-1 HN / 386 / ±39 / 396 / 407
d-Ala-5 Mβ / d-Ala-5 HN / 260 / ±26 / 276 / 277

Table S4.Distances derived from NOESY correlations of c-(-Arg-Gly-Asp-d-Leu-Ala-Leu-) 4 in DMSO-D6, d: distance, exp: experimental value, rMD: average value adopted over all trajectories in restrained molecular dynamics calculations, fMD: average value obtained by the combined trajectories in unrestrained molecular dynamics calculations.

Atom 1 / Atom 2 / d / pm
Exp / Tolerance / rMD / fMD
Arg-1 Hα / Asp-3 HN / 331 / ±33 / 378 / 443
Arg-1 Qβ / Arg-1 Hα / 239 / ±24 / 257 / 253
Arg-1 Qβ / Arg-1 Qδ / 259 / ±26 / 270 / 274
Arg-1 Qβ / Arg-1 Hε / 375 / ±37 / 347 / 344
Arg-1 Qδ / Arg-1 Hα / 374 / ±37 / 335 / 310
Arg-1 Qδ / Arg-1 HN / 449 / ±45 / 407 / 430
Arg-1 Qδ / Gly-2 HN / 444 / ±44 / 437 / 457
Arg-1 Qγ / Arg-1 Qδ / 305 / ±31 / 234 / 234
Arg-1 Qγ / Arg-1 Hε / 431 / ±43 / 261 / 259
Arg-1 Qγ / Arg-1 Hα / 344 / ±34 / 263 / 267
Gly-2 Qα / Asp-3 HN / 297 / ±30 / 305 / 281
Asp-3 Hα / Gly-2 HN / 466 / ±47 / 463 / 477
Asp-3 Hα / Asp-3 HN / 297 / ±30 / 277 / 276
Asp-3 Hα / d-Leu-4 HN / 254 / ±25 / 218 / 218
Asp-3 Hβ2 / Gly-2 HN / 607 / ±61 / 549 / 537
Asp-3 Hβ2 / Asp-3 HN / 298 / ±30 / 291 / 257
Asp-3 Hβ2 / d-Leu-4 HN / 546 / ±55 / 431 / 393
Asp-3 Hβ3 / Asp-3 HN / 343 / ±34 / 306 / 304
Asp-3 Hβ3 / d-Leu-4 HN / 527 / ±53 / 378 / 331
d-Leu-4 Hα / d-Leu-4 HN / 308 / ±31 / 271 / 275
d-Leu-4 Qβ / d-Leu-4 Hα / 289 / ±29 / 255 / 256
d-Leu-4 Qβ / d-Leu-4 HN / 267 / ±27 / 269 / 262
d-Leu-4 Qδ / d-Leu-4 Hα / 421 / ±42 / 346 / 336
d-Leu-4 Hγ / d-Leu-4 HN / 334 / ±33 / 251 / 272
Ala-5 Mβ / Ala-5 HN / 284 / ±28 / 274 / 279
Ala-5 Mβ / Leu-6 HN / 356 / ±36 / 349 / 331
Leu-6 Hα / Leu-6 Qδ / 328 / ±33 / 336 / 347
Leu-6 Hα / Arg-1 HN / 256 / ±26 / 233 / 235
Leu-6 Hα / Leu-6 HN / 302 / ±30 / 243 / 253
Leu-6 Qβ / Asp-3 HN / 449 / ±45 / 432 / 462
Leu-6 Qβ / Leu-6 Hα / 287 / ±29 / 255 / 254
Leu-6 Qβ / Leu-6 HN / 364 / ±36 / 289 / 281
Leu-6 Qδ / Leu-6 Qβ / 377 / ±38 / 260 / 259

Table S5.Distances derived from NOESY correlations of c-(-Arg-Gly-Asp-Leu-d-Ala-Leu-) 5 in DMSO-D6, d: distance, exp: experimental value, rMD: average value adopted over all trajectories in restrained molecular dynamics calculations, fMD: average value obtained by the combined trajectories in unrestrained molecular dynamics calculations.

Atom 1 / Atom 2 / d / pm
Exp / Tolerance / rMD / fMD
Arg-1 Hα / Gly-2 HN / 243 / ±24 / 216 / 219
Arg-1 Hα / Asp-3 HN / 439 / ±44 / 493 / 533
Arg-1 Hα / Leu-6 HN / 508 / ±51 / 489 / 484
Arg-1 Qβ / Arg-1 Hα / 243 / ±24 / 255 / 250
Arg-1 Qβ / Arg-1 Qδ / 339 / ±34 / 272 / 273
Arg-1 Qβ / Arg-1 Hε / 424 / ±42 / 350 / 343
Arg-1 Qβ / Arg-1 HN / 318 / ±32 / 290 / 278
Arg-1 Qβ / Gly-2 HN / 374 / ±37 / 347 / 344
Arg-1 Qδ / Arg-1 Hα / 348 / ±35 / 316 / 321
Arg-1 Qδ / Arg-1 Hε / 312 / ±31 / 185 / 185
Arg-1 Qδ / Arg-1 HN / 490 / ±49 / 467 / 450
Arg-1 Qδ / Gly-2 HN / 548 / ±55 / 424 / 434
Arg-1 Qγ / Arg-1 Hα / 242 / ±24 / 267 / 271
Arg-1 Qγ / Arg-1 Qδ / 278 / ±28 / 234 / 234
Arg-1 Qγ / Arg-1 Hε / 369 / ±37 / 260 / 260
Arg-1 Qγ / Arg-1 HN / 319 / ±32 / 337 / 317
Arg-1 Qγ / Gly-2 HN / 380 / ±38 / 391 / 378
Gly-2 Qα / Gly-2 HN / 248 / ±25 / 236 / 237
Gly-2 Qα / Arg-1 Hα / 425 / ±42 / 420 / 424
Gly-2 Qα / Asp-3 Hα / 442 / ±44 / 435 / 429
Gly-2 Qα / Asp-3 HN / 213 / ±21 / 275 / 268
Asp-3 Hβ3 / Asp-3 HN / 320 / ±32 / 282 / 292
Asp-3 Hβ3 / Leu-4 HN / 406 / ±41 / 276 / 293
Leu-4 Hα / D-Ala-5 HN / 213 / ±21 / 215 / 219
Leu-4 Qδ / Leu-4 Hα / 408 / ±41 / 345 / 345
d-Ala-5 Hα / Arg-1 HN / 329 / ±33 / 371 / 383
d-Ala-5 Hα / d-Ala-5 HN / 310 / ±31 / 276 / 274
d-Ala-5 Hα / Leu-6 HN / 206 / ±21 / 211 / 212
d-Ala-5 Mβ / Leu-4 Hα / 531 / ±53 / 472 / 481
dAla-5 Mβ / dAla-5 Hα / 274 / ±27 / 241 / 241
dAla-5 Mβ / dAla-5 HN / 282 / ±28 / 284 / 272
dAla-5 Mβ / Leu-6 Hα / 564 / ±56 / 491 / 493
dAla-5 Mβ / Leu-6 HN / 349 / ±35 / 376 / 384
Leu-6 Hα / Arg-1 HN / 301 / ±30 / 301 / 305
Leu-6 Hα / Leu-6 HN / 310 / ±31 / 277 / 279
Leu-6 Qδ / Leu-6 Hα / 299 / ±30 / 341 / 348

Table S6.Distances derived from NOESY correlations of c-(-Arg-Gly-Asp-Leu-Ala-d-Leu-) 6 in DMSO-D6, d: distance, exp: experimental value, rMD: average value adopted over all trajectories in restrained molecular dynamics calculations, fMD: average value obtained by the combined trajectories in unrestrained molecular dynamics calculations.

Atom 1 / Atom 2 / d / pm
Exp / Tolerance / rMD / fMD
Arg-1 Hα / Arg-1 HN / 319 / ±32 / 279 / 280
Arg-1 Hα / Gly-2 HN / 304 / ±30 / 253 / 232
Arg-1 Qβ / Arg-1 Hα / 284 / ±28 / 247 / 252
Arg-1 Qβ / Arg-1 Qδ / 382 / ±38 / 271 / 272
Arg-1 Qβ / Arg-1 Hε / 452 / ±45 / 340 / 346
Arg-1 Qβ / Arg-1 HN / 393 / ±39 / 279 / 280
Arg-1 Qδ / Arg-1 Hα / 388 / ±39 / 333 / 318
Arg-1 Qδ / Arg-1 Hε / 283 / ±28 / 185 / 185
Gly-2 Qα / Gly-2 HN / 277 / ±28 / 251 / 247
Gly-2 Qα / Asp-3 HN / 433 / ±43 / 252 / 260
Gly-2 Qα / Leu-4 HN / 423 / ±42 / 440 / 447
Gly-2 Qα / Ala-5 HN / 327 / ±33 / 483 / 526
Asp-3 Hα / Asp-3 HN / 358 / ±36 / 256 / 271
Asp-3 Hα / Leu-4 HN / 189 / ±19 / 342 / 340
Asp-3 Qβ / Asp-3 Hα / 281 / ±28 / 232 / 248
Asp-3 Qβ / Asp-3 HN / 336 / ±34 / 285 / 275
Asp-3 Qβ / Leu-4 HN / 311 / ±31 / 306 / 299
Leu-4 Hα / Leu-4 HN / 398 / ±40 / 280 / 280
Leu-4 Hβ2 / Leu-4 Hα / 315 / ±32 / 272 / 272
Leu-4 Hβ2 / Leu-4 HN / 346 / ±35 / 242 / 242
Leu-4 Hβ2 / Ala-5 HN / 324 / ±32 / 278 / 289
Leu-4 Hβ3 / Leu-4 HN / 394 / ±39 / 300 / 309
Leu-4 Hβ3 / Ala-5 HN / 294 / ±29 / 297 / 272
Leu-4 Qδ / Leu-4 Hα / 326 / ±33 / 349 / 337
Leu-4 Hγ / Leu-4 HN / 307 / ±31 / 285 / 288
Ala-5 Hα / Ala-5 HN / 264 / ±26 / 275 / 263
Ala-5 Mβ / Ala-5 Hα / 240 / ±24 / 242 / 242
Ala-5 Mβ / Ala-5 HN / 308 / ±31 / 303 / 294
Ala-5 Mβ / d-Leu-6 HN / 349 / ±35 / 358 / 369
d-Leu-6 Hα / Arg-1 HN / 234 / ±23 / 213 / 218
d-Leu-6 Hα / Gly-2 HN / 404 / ±40 / 395 / 437
d-Leu-6 Hα / D-Leu-6 HN / 325 / ±33 / 272 / 275
d-Leu-6 Qβ / D-Leu-6 Hα / 290 / ±29 / 256 / 256
d-Leu-6 Qβ / D-Leu-6 HN / 311 / ±31 / 258 / 264
d-Leu-6 Qδ / Arg-1 HN / 461 / ±46 / 467 / 505
d-Leu-6 Qδ / d-Leu-6 Hα / 356 / ±36 / 323 / 345

Table S7.Distances derived from ROESY correlations of c-(-Arg-Ala-Asp-d-Leu-Ala) 7 in DMSO-D6, d: distance, exp: experimental value, rMD: average value adopted over all trajectories in restrained molecular dynamics calculations, fMD: average value obtained by the combined trajectories in unrestrained molecular dynamics calculations.

Atom 1 / Atom 2 / d / pm
Exp / Tolerance / rMD / fMD
Arg-1 Hα / Arg-1 Qβ / 247 / ±25 / 378 / 443
Arg-1 Hα / Arg-1 Qγ / 320 / ±32 / 257 / 253
Arg-1Hα / Arg-1 Qδ / 279 / ±28 / 270 / 274
Arg-1HN / Arg-1 Hα / 224 / ±22 / 347 / 344
Arg-1HN / Arg-1 Qβ / 332 / ±33 / 335 / 310
Arg-1HN / Ala-5 Mβ / 340 / ±34 / 407 / 430
Ala-2 HN / Arg-1 Qβ / 271 / ±27 / 437 / 457
Ala-2 HN / Arg-1 HN / 262 / ±26 / 234 / 234
Ala-2 HN / Ala-2 Hα / 240 / ±24 / 261 / 259
Ala-2 HN / Ala-2 Mβ / 365 / ±36 / 263 / 267
Asp-3 Hα / Asp-3 Qβ / 219 / ±22 / 305 / 281
Asp-3 HN / Ala-2 Hα / 267 / ±27 / 463 / 477
Asp-3 HN / Ala-2Mβ / 377 / ±38 / 277 / 276
Asp-3 HN / Asp-3 Hα / 206 / ±21 / 218 / 218
Asp-3HN / Asp-3 Qβ / 288 / ±29 / 549 / 537
d-Leu-4 Hα / d-Leu-4 Qβ / 225 / ±23 / 291 / 257
d-Leu-4 Hα / d-Leu-4 Qδ / 272 / ±27 / 431 / 393
d-Leu-4 Hα / d-Leu-4 Hγ / 333 / ±33 / 306 / 304
d-Leu-4 Qβ / d-Leu-4 Qδ / 270 / ±27 / 378 / 331
d-Leu-4 HN / d-Leu-4 Hα / 238 / ±24 / 271 / 275
d-Leu-4 HN / d-Leu-4 Qβ / 323 / ±32 / 255 / 256
d-Leu-4 HN / d-Leu-4 Hγ / 384 / ±38 / 269 / 262
Ala-5 HN / Arg-1 HN / 270 / ±27 / 346 / 336
Ala-5 HN / d-Leu-4 Hα / 212 / ±21 / 251 / 272
Ala-5 HN / Ala-5 Hα / 240 / ±24 / 274 / 279
Ala-5 HN / Ala-5 Mβ / 297 / ±30 / 349 / 331

Table S8.Comparison of coupling constants JHNHα calculated by Karplus equation from the torsion angles observed in the structure proposal (calc.) to experimentally obtained torsion angles (exp.), secondary structure elements (and the position of the respective amino acid therein), hydrogen bonding observed during the trajectory (population > 5%) and temperature gradients of the chemical shift of the amide protons Δδ/ΔT in ppb/K for c-(-Arg-Gly-Asp-d-Leu-Ala-) 2.

Amino Acid / JHNHα / Secondary Structure Element / Hydrogen bonding / Δδ/ΔT
[ppb/K]
calc. / exp.
Arg-1 / 9.7 / n.o. / βII’ (i+3)
γ (i) / -1.7
Gly-2 / 5.6/7.9 / 3.9/7.9 / γ (i+1) / -3.9
Asp-3 / 9.5 / 7.9 / γ (i+2)
βII’ (i) / Asp-3 HN -
Arg-1 O (15%) / -3.4
d-Leu-4 / 9.7 / 8.5 / βII’ (i+1) / -3.3
Ala-5 / 8.8 / 6.9 / βII’ (i+2) / -3.7

Table S9.Comparison of coupling constants JHNHα calculated by Karplus equation from the torsion angles observed in the structure proposal (calc.) to experimentally obtained torsion angles (exp.), secondary structure elements (and the position of the respective amino acid therein), hydrogen bonding observed during the trajectory (population) and temperature gradients of the chemical shift of the amide protons Δδ/ΔT in ppb/K for c-(-Arg-Gly-Asp-Leu-d-Ala-) 3.

Amino Acid / JHNHα / Secondary Structure Element / Hydrogen bonding / Δδ/ΔT
[ppb/K]
calc. / exp.
Arg-1 / 9.2 / 8.7 / γ (i+2)
γ (i)
βII’ (i)
γi (i+1) / Arg-1 HN -
Leu-4 O (10%) / -5.3
Gly-2 / 3.4/9.6 / 4.7/6.7 / γ (i+1)
βII’ (i+1)
γi (i) / -2.6
Asp-3 / 9.4 / 7.1 / γ (i+2)
βII’ (i+2) / -5.5
Leu-4 / 9.7 / 8.0 / βII’ (i+3)
γ (i) / 0.1
d-Ala-5 / 8.9 / 7.1 / γ (i+1)
γi (i+2) / -6.5

Table S10.Comparison of coupling constants JHNHα calculated by Karplus equation from the torsion angles observed in the structure proposal (calc.) to experimentally obtained torsion angles (exp.), secondary structure elements (and the position of the respective amino acid therein), hydrogen bonding observed during the trajectory (population) and temperature gradients of the chemical shift of the amide protons Δδ/ΔT in ppb/K for c-(-Arg-Gly-Asp-d-Leu-Ala-Leu-) 4.

Amino Acid / JHNHα / Secondary Structure Element / Hydrogen bonding / Δδ/ΔT
[ppb/K]
calc. / exp.
Arg-1 / 3.2 / 3.7 / βII (i+1) / -5.9
Gly-2 / 2.6/9.7 / 5.0/7.2 / βII (i+2) / -9.8
Asp-3 / 9.1 / 6.9 / βII (i+3)
βII’ (i) / Asp-3 HN -
Leu-6 O (29%) / -2.1
d-Leu-4 / 5.2 / 4.9 / βII’ (i+1) / -8.1
Ala-5 / 7.9 / 7.9 / βII’ (i+2) / -8.5
Leu-6 / 8.3 / 9.2 / βII’ (i+3)
βII (i) / Leu-6 HN -
Asp-3 O (23%) / -1.0

Table S11.Comparison of coupling constants JHNHα calculated by Karplus equation from the torsion angles observed in the structure proposal (calc.) to experimentally obtained torsion angles (exp.), secondary structure elements (and the position of the respective amino acid therein), hydrogen bonding observed during the trajectory (population) and temperature gradients of the chemical shift of the amide protons Δδ/ΔT in ppb/K for c-(-Arg-Gly-Asp-Leu-d-Ala-Leu-) 5.

Amino Acid / JHNHα / Secondary Structure Element / Hydrogen bonding / Δδ/ΔT
[ppb/K]
calc. / exp.
Arg-1 / 9.6 / 7.3 / βII’ (i+3)
βII’ (i) / Arg-1 HN -
Leu-4 O (19%) / -2.7
Gly-2 / 6.5/6.7 / 4.8/5.7 / βII‘ (i+1) / -5.9
Asp-3 / 9.6 / 7.7 / βII’ (i+2) / -4.3
Leu-4 / 9.4 / 8.0 / βII’ (i+3)
βII’ (i) / Leu-4 HN -
Arg-1 O (16%) / -1.1
d-Ala-5 / 6.1 / 6.2 / βII’ (i+1) / -7.6
Leu-6 / 8.9 / 7.6 / βII’ (i+2) / -6.7

Table S12.Comparison of coupling constants JHNHα calculated by Karplus equation from the torsion angles observed in the structure proposal (calc.) to experimentally obtained torsion angles (exp.), secondary structure elements (and the position of the respective amino acid therein), hydrogen bonding observed during the trajectory (population) and temperature gradients of the chemical shift of the amide protons Δδ/ΔT in ppb/K for c-(-Arg-Gly-Asp-Leu-Ala-d-Leu-) 6.

Amino Acid / JHNHα / Secondary Structure Element / Hydrogen bonding / Δδ/ΔT
[ppb/K]
calc. / exp.
Arg-1 / 9.7 / 9.5 / βII’ (i+2) / Arg-1 HN -
Leu-4 O (10%, 2nd Cluster) / -6.8
Gly-2 / 4.1/4.6 / 8.7/3.4 / βII’ (i+3)
βI (i) / Gly-2 HN -
Ala-5 O (13%) / -1.6
Asp-3 / 9.6 / 5.9 / βI (i+1) / -5.4
Leu-4 / 9.5 / 9.4 / βI (i+2) / Leu-4 HN -
Arg-1 O (9%) / -4.2
Ala-5 / 9.3 / 6.5 / βI (i+3)
βII’ (i) / -0.3
d-Leu-6 / 6.2 / 5.2 / βII’ (i+1) / -6.7

Figure S3.Analytical RP-HPLC chromatogram of c-(-Arg-Gly-Asp-d-Phe-Val-) 1.

Figure S4.Analytical RP-HPLC chromatogram of c-(-Arg-Gly-Asp-d-Leu-Ala-) 2.

Figure S5.Analytical RP-HPLC chromatogram of c-(-Arg-Gly-Asp-Leu-d-Ala-) 3.

Figure S6.Analytical RP-HPLC chromatogram of c-(-Arg-Gly-Asp-d-Leu-Ala-Leu-) 4.

Figure S7.Analytical RP-HPLC chromatogram of c-(-Arg-Gly-Asp-Leu-d-Ala-Leu-) 5.

Figure S8.Analytical RP-HPLC chromatogram of c-(-Arg-Gly-Asp-Leu-Ala-d-Leu-) 6.

Figure S9.Analytical RP-HPLC chromatogram of c-(-Arg-Ala-Asp-d-Leu-Ala-) 7.

1