Table I.

Chlamydia pneumoniae synthetic peptides: protein sources and H-2^b binding affinities

ID	Peptide Sequence^a	Protein(s)^b^c	Cpn Genome Annotations^d	H-2^b Motif^e	Ratio MFI^f	Binding (IC₅₀ nM)^g
1	NTVVFDAL	60 kDa Omp (Omp2, OmcB)^b ^h	CPn0557, CP0195	K^b	1.69	155,000
2	QESCYGRL			K^b	2.78	344
3	ISVSNPGDL			D^b	2.54	220
4	VLSFNLGDM			D^b	1.49	62,857
5	AEDTNVSLI			D^b	0.95	440,000
6	SKLQYKII	FKBP-type PPIASE (Mip)	CPn0661, CP0086	K^b	1.13	155,000
7	SSEGNNEPIL			D^b/D^b	1.01	293,333
8	QLPPNSLLI			D^b	1.07	293,333
9	DDEEYVIL	10 kDa chaperonin (GroES)^b ^h	CPn0135, CP0637	K^b	0.99	124,000
10	ANEGYDAL	60 kDa chaperonin (GroEL)^b ^h	CPn0134, CP0638	K^b	0.97	11,923
11	TAGANPMDL			D^b	1.47	22,000
12	ISANNDSEI			D^b	1.80	880
13	STEINQPFITM	DnaK (heat shock protein-70)^b ^h	CPn0503, CP0251	D^b/K^b	2.01/2.07	124,000/13,209
14	VLSTNGDTL			D^b	3.30	427
15	FLLFFEFLLV	76 kDa^b ^h	CPn0728, CP0018	K^b/K^b	1.85	20,667
16	LMSGFRQM			K^b	1.43	6,889
17	YASDNQAIL			D^b	2.89	480
18	GFKSNFNKI			K^b/D^b	1.2/0.95	155,000/440,000
19	LVYNYPGV	43 kDa homologs 1–4:4	CPn0929, CP0937	K^b	3.20	23
20	LIYNYPGV	3	CPn0928, CP0938	K^b	2.99	4.1
21	LLVFNYPGI	2	CPn0927, CP0939	D^b/K^b	1.69/1.48	5,167/62,857
22	LIFNYPGV	1	CPn0562, CP0188	K^b	2.81	40
23	HPYLYRLL	1	CPn0562, CP0188	K^b	2.10	194
24	HPTLFKVL	2	CPn0927, CP0939	K^b	2.87	620
25	SIILFLPL	2	CPn0927, CP0939	K^b	3.61	1.0
26	KICQNFILL	1	CPn0562, CP0188	D^b/K^b	2.80/2.95	2,480/2,200
27	ISNGNSDCL	1	CPn0562, CP0188	D^b	3.62	314
28	YSQGNSGLM	2	CPn0927, CP0939	D^b	2.35	889
29	TGKLNLENL	3	CPn0928, CP0938	D^b	1.79	17,600
30	QAPTNRWML	4	CPn0929, CP0937	D^b	3.07	5.6
31	SLLGNATAL	MOMP (OMP1, OmpA)^b ^h	CPn0695, CP0051	D^b	2.98	160
32	SHYAFSPMFEVL	Omp5^b ^h (Pmp10)	CPn0449, CP0303	K^b/K^b	2.66	689
33	ISFAFCQL			K^b	2.91	1.3
34	QPQNYLRL	Omp4^b.h (Pmp11)	CPn0451, CP0302	K^b	1.54	51,667
35	HDQLFSLL			K^b	1.89	2,296
36	GTYHFTKL	Omp85 homolog (YaeT)	CPn0300, CP0458	K^b	2.79	18
37	FQLCNSYDL	OmpB (PorB)	CPn0854, CP1015	D^b	4.29	13
38	NHPVFSPL	IncA homolog	CPn0585, CP0163	K^b	2.61	56
39	LQQRYSRL			K^b	2.91	0.6
TcTSA	VDYNFTIV	T. cruzi TSA1		K^b	3.37	36
OVA	SIINFEKL	OVA		K^b	3.38	11
FLUnp	ASNENMETM	Influenza A nucleoprotein		D^b	3.47	6.2

a Sequence in single-letter amino acid code.
b Cpn proteins from which H-2^b motif-bearing sequences were selected for peptide synthesis; synonyms shown in parentheses.
c Originally reported in Cpn genome sequencing Refs. 33–35.
d Gene name designations as annotated from the sequenced genomes of Cpn strains CWL029 (prefix CPn; Chlamydia Genome Project; reported in Ref. 33; http://chlamydia-www.berkeley.edu;4231) and AR39 (prefix CP; reported in Ref. 34; http://www.tigr.org/tigr-scripts/CMR2/GenomePage3.spl?database=bcp). Cpn strain J138 gene names are commonly those of CWL029 (http://w3.grt.kyusbu-u.ac.jp/J138/; http://www.tigr.org/tigr-scripts/CMR2/GenomePage3.spl?database=ntcp02).
e H-2^b binding motif present in synthetic peptides; H-2K^b binding motif is FY at position 5, and LMIV at position 8; H-2D^b binding motif is N at position 5, and MIL at position 9 (36).
f Binding affinity as assessed by ability of peptides (10 μM) to up-regulate and stabilize K^b or D^b molecules on RMA-S cells. Ratio MFI is MFI in the presence of test peptide over the fluorescence intensity in the absence of peptide (high, ≥2.5; intermediate, 2.0–2.4; low, 1.5–1.9; negative, ≤1.4).
g Binding affinity as measured by quantitative binding assay. IC₅₀ is the nanomolar concentration of peptide capable of inhibiting by 50% the binding of ¹²⁵I-labeled index peptide to purified soluble H-2^b molecules (high, ≤50 nM; intermediate, 50–500 nM; low, 500–10,000 nM; negative, >10,000).
h Originally reported in Refs. 39–44.