Molecular basis for passive immunotherapy of Alzheimer's disease

Gardberg et al. 10.1073/pnas.0705888104.

Supporting Information

Files in this Data Supplement:

SI Table 5
SI Table 6
SI Figure 4
SI Figure 5
SI Table 7
SI Table 8
SI Figure 6
SI Methods

SI Figure 4

Fig. 4. Induced fit. The CDR of PFA1 exhibits rotamer changes with peptide binding (induced fit) in residues HC His-97, Trp-53, and Asp100C. This stereo view displays the apo structure in green and the PFA1-pep structure in blue. The bound peptide on the left side of the image is shown in gray-blue.

SI Figure 5

Fig. 5. The WWDDD motif. A stereo view shows in more detail how the WWDDD motif interacts with the N terminus of the Ab peptide. The Phe 4/Arg 5 segment of the Ab peptide is drawn in blue, and the WWDDD motif of PFA1 is drawn with Carbon (green), Nitrogen (blue), and Oxygen (red).

SI Figure 6

Fig. 6. The potential for cross-reaction-E3K overlay. Stereo view of PFA1 complexes with Ab(2-7) (blue) and GRIP1(110-115) (brown/orange) overlaid. Aside from a change in the rotamer of LC Ser27E, the structure of the antibody appears unaffected, but the Glu3Lys mutation has caused a small change in the peptide's backbone structure. The site of mutation is marked by an arrow. An alternate rotamer conformation for LC Ser27E has been omitted for clarity.

Table 5. Data collection and refinement statistics

	PFA1-tric	PFA1-pep	PFA1-E3K	PFA2 mono	PFA2 tric	PFA2-pep
Data collection
Space group	P1	P1	P2₁	P2₁	P1	P1
Cell dimensions
a, b, c, Å	41.99, 42.83, 58.38	43.07, 70.34, 74.20	41.47, 112.23, 43.18	77.98, 73.41, 93.51	41.56, 42.78, 58.36	42.79, 43.33, 58.46
?°	95.84, 94.77, 91.91	72.32, 86.08, 86.02	90, 93.45, 90	90, 99.97, 90	95.81, 94,81, 91.11	92.51, 94.96, 90.55
Resolution, Å	50.0-2.0	50-1.65	33.3-2.1	50-2.0	20.7-2.3	42.6-2.5
R_sym	0.05(0.19)	0.055(0.467)	†0.162(0.223)	0.090(0.405)	0.072(0.359)	0.071(0.473)
I / I	16.3(4.5)	21.9(2.4)	9.8(4.1)	22.3 (3.3)	10.8 (2.8)	12.4(1.5)
Completeness, %	93.1(85.1)	90.7(66.3)	87.6(65.6)	99.7(99.4)	93.(92.8)	96.0(89.8)
Redundancy	1.9(1.9)	3.1(2.9)	4.6(2.8)	5.6(3.3)	1.7(1.7)	1.9(1.8)
Refinement
Resolution, Å	2.0	1.65	2.1	2.0	2.3	2.5
No. reflections	24063	85892	18995	66770	15633	13105
R_work/R_free	0.177/0.223	0.182/0.225	0.201/0.261	0.230/0.279	0.211/0.278	0.208/0.277
No. atoms (non-H)	3671	7835	3517	7086	3546	3481
Protein	3399	6863	3348	6768	3381	3317
Ligand/ion	0	36 (glycerol) 122(peptide)	12(glycerol) 56(peptide)	48 (glycerol)	0	55
Water	273	813	113	272	165	63
B-factors (Å²)	21.0	18.9	39.5‡	35.3	33.4	53.3‡
Protein	20.6	17.9	39.5‡	35.0	33.5	53.5‡
Ligand/ion	N/A	35.0(glycerol) 20.8 (peptide)	58.4(glycerol) 38.2 (peptide)	56.5	N/A	50.3
Water	26.3	26.7	37.3	38.6	31.4	41.9
rmsd
Bond lengths, Å	0.011	0.012	0.009	0.011	0.010	0.016
Bond angles, °	1.429	1.436	1.169	1.406	1.332	1.573
PDB code	2IPT	2IPU	2ROZ	2IQA	2IQ9	2ROW

*Highest resolution shell is shown in parentheses.

†Data from two crystals of PFA1-E3K were merged to obtain higher completeness, as well as better maps and refinement statistics. This has resulted in an elevated value for R_sym.

‡TLS + residual.

Table 6. RMSD values calculated with PYMOL "align" command

CDR rmsds	PFA1-pep mon1	PFA1-pep mon2	PFA2-apo-tric	PFA2-apo-mono mon1	PFA2-apo-mono mon2	PFA2-pep
PFA1-apo C	0.277	0.243	0.437	0.318	0.319	0.363
PFA1-apo ALL	0.361	0.339	0.467	0.469	0.503	0.447
PFA1-pep mon1 C		0.174	0.457	0.408	0.444	0.246
PFA1-pep mon1 ALL		0.179	0.519	0.515	0.605	0.299
PFA1-pep mon2 C			0.439	0.438	0.449	0.260
PFA1-pep mon2 ALL			0.517	0.551	0.539	0.309
PFA2-apo-tric C				0.342	0.602	0.483
PFA2-apo-tric ALL				0.551	0.719	0.580
PFA2-apo-mono mon1 C					0.288	0.428
PFA2-apo-mono mon1 ALL					0.331	0.617
PFA2-apo-mono mon2 C						0.494
PFA2-apo-mono mon2 ALL						0.814
Average C differences
PFA1: apo-pep	0.26
PFA1: pep-pep	0.174
PFA2: apo-apo	0.411
PFA2: apo-pep	0.468

Table 7. Summary of the A peptide's interactions with PFA1 and PFA2

Peptide residue	Interaction type	Atom	PFA1 residue	PFA2 residue
Ala2	hb	N	Water
		O	LC Val94 N	LC Val94 N
			Water	LC Val94 O
	vdw	All	LC His93	LC Ser92
			LC Val94	LC His93
			Waters	LC Val94
Glu3	hb	N	Water
		O	Two waters
		OE1	LC His27D NE2	LC His27D NE2
			LC Ser27E OG	LC Ser27E OG
		OE2	LC Ser27E N LC Ser27E OG water	LC Ser27E N
				LC Ser27E OG
	vdw	All	Water	LC His27D
			LC His27D	LC Ser27E
			LC Ser27E	LC Ser92
			LC Ser92	LC His93
			LC His93	LC Val94
			LC Val94
	Ip	OE1, OE2	LC His27D	LC His27D
			LC His93	LC His93
Phe4	hb	N	LC Ser92O	LC Ser92 O
		O	LC His27DNE2	LC His27D NE2
			Water
	vdw	All	LC His27D	LC His27D
			LC Gly91	LC Gly91
			LC Ser92	LC Ser92
			LC His93	LC His93
			LC Val94	LC Val94
			LC Leu96	LC Leu96
			HC Trp47	HC Trp47
			HC His50	HC His50
			HC Trp52	HC Trp52
			HC Ser58	HC Asn60
			HC Arg95	HC Arg95
			Two waters
Arg5	hb	N	Water
		NE	HC His97 NE2 water
		NH1	HC Asp54 OD1	HC Asp54 OD2
			HC Asp54 OD2
		NH2	Water	HC Trp53 NE1
			HC Asp54 OD2	HC Asp54 OD2
			HC His97 NE2	HC Asp56 OD2
				HC His97 NE2
	vdw	all	Three waters	HC Trp52
			HC Trp52	HC Trp53
			HC Trp53	HC Asp54
			HC Asp54	HC Asp56
			HC Asp56	HC His97
			HC His97
	ip	NE NH1 NH2	HC Asp56	HC Asp100C
His6	hb	N	Water
		NE2	LC Gly91 O	LC Gly91 O
		ND1	HC Asp100C OD1	HC Asp100C OD1
			HC Asp100C OD2	HC Asp100C OD2
		O	Water
	vdw	All	LC His27D	LC His27D
			LC Asn28	LC Asn28
			LC Tyr32 (pi overlap)	LC Tyr32 (pi overlap)
			LC Gly91	LC Gly91
			LC Ser92	HC Arg95
			HC Arg95	HC His97
			HC His97	HC Asp100C
			HC Asp100C
			Water
	ip	ND1 NE2	LC Glu34	LC Glu34
Asp7	hb	N	HC His97 O	HC His97 O
		OD1	HC His97 ND1	HC His97 O
				HC His97 ND1
		OD2	HC His97 ND1	Water
		O	LC Asn28 ND2
			Water
	vdw	All	LC Asn28	LC Asn28
			HC His97	HC His97
			HC Thr98	HC Asn98
			Water	Water
	ip	OD1 OD2	HC His97	HC His97
Ser8	hb	OXT	Water
	vdw	all