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Anchored design of protein-protein interfaces.

(2011) PLoS One 6

PubMed: 21698112 | PubMedCentral: PMC3117852 | DOI: 10.1371/journal.pone.0020872

PDB Input loop RMSD (Å) Crystal loop RMSD (Å) Input IRMSD (Å) Crystal IRMSD (Å) Input LRMSD (Å) Crystal LRMSD (Å) 1dle 0.09 0.42 0.04 2.24 0.16 1.69 1fc... 0.40 0.43 0.08 0.57 0.08 0.70 1qni 1.99 1.98 0.53 0.94 0.47 1.00 2qpv 0.63 0.68 0.19 0.78 0.23 0.97 3dxv 0.62 0.65 0.14 0.55 0.13 0.60 1u6e 0.13 0.35 0.06 0.59 0.12 0.62 2bwn 1.30 1.35 0.30 0.75 0.29 0.86 1jtp 0.08 0.29 0.07 0.73 0.30 0.97 2hp2 3.43 3.43 1.37 1.52 1.24 1.45 2wya 0.24 0.28 0.06 0.54 0.06 0.88 2obg 0.34 0.36 0.26 0.61 0.58 0.74 2i25 0.11 0.28 0.28 0.61 2.18 2.28 3cgc 2.23 2.26 4.74 4.90 14.16 14.41 3ean 0.06 0.38 0.03 0.91 0.06 0.91 1fec 0.14 0.39 0.03 0.60 0.04 0.72 1zr0 0.17 0.40 0.14 0.47 0.47 1.63 This table summarizes predictions of the AnchoredDesign benchmark.

Represented structures include homodimers of various functions (1fc4, 1qni, 2qpv, 3dxv, 1u6e, 2bwn, 2hp2, 2wya, 3cgc, 3ean, 1fec), two antibody/antigen complexes (1jtp, 2i25), one enzyme/inhibitor complex (1zr0), one engineered binder/target complex (2obg), and one nonbiological crystal dimer (1dle) chosen as a test of weak interactions.

(Å) Dimer type SASA (Å 2 ) Anchor Chain Loop Loop length 1dle A/B 2.1 crystal dimer** 2,800 38 B 36–40*** 8 1fc4 A/B 2 homodimer 10,000 74 B 69–79 11 1qni A/B 2.4 homodimer 11,800 408 B 397–411 15 2qpv A/B 2.35 homodimer 2,900 55 B 50–57 8 3dxv A/B 2.21 homodimer 7,900 291 B 288–299 12 1u6e A/B 1.85 homodimer 6,700 86 B 80–89 10 2bwn A/B 2.1 homodimer 8,500 85 B 77–90 14 1jtp M/B 1.9 heterodimer 1,600 104 B 99–108 10 2hp2 A/B 2.7 homodimer 9,500 2306 B 2294–2309 16 2wya B/C 1.7 homodimer 5,900 1009 C 1003–1012 10 2obg A* 2.35 heterodimer 1,600 1080 A 1077–1086 10 2i25 M/O 1.8 heterodimer 1,400 91 O 86–93 8 3cgc A/B 2.3 homodimer 5,400 429 B 421–434 14 3ean A/B 2.75 homodimer 7,900 473 B 467–474 8 1fec A/B 1.7 homodimer 6,400 459 B 456–463 8 1zr0 A/B 1.8 heterodimer 1,400 15 B 10–17 8 This table collects structural parameters for the complexes used in this work, along with chosen parameters like anchor placement.

Loop conformation errors Structures 1qni and 2hp2 represent a pair of partial failures.

The total (3cgc) and partial (1qni, 2hp2) failures of AnchoredDesign in this benchmark all share a common thread: these tests have loops longer than other, better-predicted complexes.

Publication Year: 2011