Prediction of structural stability of short beta-hairpin peptides by molecular dynamics and knowledge-based potentials

Table 1 The 40 peptides studied in this work

Peptide Name ^A	*Peptide ID* ^B	Peptide Sequence^C	Template (PDB)^D	Substitutions^E
TrpZip
TrpZip1	T1	S-W TW-EGNK-W TW-K	1LE0	None
TrpZip2	T2	S-W TW-ENGK-W TW-K	1LE1	None
TrpZip3	T3	S-W TW-EpNK-W TW-K	1LE0	G6→D-proline
TrpZip4	T4	GEW TWDDATKTW TW TE	1LE3	None
TrpZip5	T5	GEW TYDDATKT FTW TE	1LE3	W5→ Y
				W12→ F
TrpZip6	T6	GEW TWDDATKTW TVTE	1LE3	W14→V
TrpZip7	T7	GEW VWDDATKTW HW TE	1LE3	T4→ V
				T13→H
TrpZip8	T8	GEW HWDDATKTW VW TE	1LE3	T4→H
				T13→V
TrpZip9	T9	GEW VWDDATKTW VW TE	1LE3	T4→V
				T13→V
BhpW
TT	B1	C TWEGNKL TC	1N09	None
HT	B2	C HWEGNKL TC	1N09	T2→H
TH	B3	C TWEGNKL HC	1N09	T9→H
LT	B4	C LWEGNKL TC	1N09	T2→L
TL	B5	C TWEGNKL LC	1N09	T9→L
VT	B6	C VWEGNKL TC	1N09	T2→V
TV	B7	C TWEGNKL VC	1N09	T9→V
VH	B8	C VWEGNKL HC	1N0D	None
HV	B9	C HWEGNKL VC	1N0C	None
TW	B10	C TWEGNKL WC	1N09	T9→W
FT	B11	C WFEGNKL TC	1N09	T2→ W
				W3→F
TF	B12	C TWEGNKL FC	1N09	T9→F
TI	B13	C TWEGNKL IC	1N09	T9→I
				T13→V
BHKE/MBH
BHKE	M1	RGK ITVNG KTYEGR	1J4M	W4→ I
				Y6→V
				I9→K
MBH6	M2	RGK WTPNG HTDEGR		Y6→ P
				I9→H
MBH8	M3	RGK WTYNG HTDEGR		I9→H
				Y11→D
				I9→H
MBH10	M4	RGK WTDNG ITYEGR		Y6→D
MBH12	M5	RGK WTYNG ITYEGR		None
MBH20	M6	RGK YTPNG ITDEGR		W4→Y
				Y6→ P
				Y11→D
MBH21	M7	RGK YTYNG ITDEGR		W4→Y
				Y11→D
MBH28	M8	RGK YTDNG ITYEGR		W4→Y
				Y6→D
MBH36	M9	RGKYTYNGNTYEGR		Y6→D
				I9→N
EPO
EPO3	E1	SC HFGPLGW VCK	1KVG	None
EPO4	E2	SC RAQPLGW LCK		H3→R
				F4→ A
EPO8	E3	SC HFGPLGW LCK		V10→L
EPO9	E4	SC RAGPLGW LCK		V10→L
				H3→ R
				F4→A
EPO11	E5	SC HAGPLGW LCK		F4→A
				V10→L
EPO12	E6	SC RFGPLGW LCK		H3→ R
				V10→L
EPO14	E7	SC HAGPLGW VCK		F4→A
EPO16	E8	SC RAGPLGW VCK		H3→R
				F4→A
EPO21	E9	SC RFGPLGW VCK		H3→R

Columns are as follows: A – Peptide name in the literature [14-19]. B – Peptide ID in figures 3-5. C – Amino acid sequence. Bold letters indicate invariant residues, p = D-proline. D – Protein Data Bank (PDB) [50] code of the NMR structures used as a template. For each NMR ensemble the first structure was employed. E. The amino acid substitutions applied on the templates in order to prepare the peptide models.

ISSN: 1472-6807