Synthetic buckwheat pollen peptide BPP 1(A P V L Q I K K T G S N) and its analogues BPP 2[( D )A P V L Q I K K T G S N NH 2], BPP 3(A P A L Q L K K N G S Q G NH 2) showed different binding behavior to rape pollen calmodulin(pCaM). Fluorescence titration experiments demonstrated that BPP 1 had no affinity for pCaM while its C terminal amide, BPP 2, had fair affinity for pCaM(dissociation constant of pCaM peptide complex, K d=2.9× 10 -1 μmol/L) due to the decrease in {C terminal polarity.} But compared with BPP 3( K d=8.1× 10 -2 μmol/L), which was also a peptide amide, BPP 2 had a much lower binding ability. In order to investigate other factors influencing peptide affinity for pCaM besides polarity(or hydrophobicity), CD and 2D NMR spectroscopes were used to study the conformations of BPP 1 and BPP 3. It revealed that molecular flexibility could affect peptides ability to bind pCaM. BPP 1 displayed rigid extended peptide bonds in the middle region where the basic amino acid pair Lys 7 Lys 8 is located, flanked by flexible peptide segments on both terminals; while the middle five residue region of BPP 3 exhibited as very flexible segment. Such a structural character might facilitate BPP 3 to adopt a conformation contributive to the interaction of two Lys residues with the acidic residues of pCaM in its peptide binding site and resulted in higher affinity. As this study revealed, both of the two peptides showed the lack of ordered structure in the aqueous solution. It seemed that there was no relationship between peptide affinity for CaM and the propensity of peptide chain to form α helix. This contradicted what most previous researches approved that α helix was an important character of peptide with high affinity for CaM. Fluorescence analysis of BPP 2 (APVLQIKKTGSN) and its analogues BPP 2 [(D) APVLQIKKTGSN NH 2 ], BPP 3 (APALQLKKNGSQG NH 2) showed different binding behavior to rape pollen calmodulin (pCaM). that BPP 1 had no affinity for pCaM while its C terminal amide, BPP 2, had fair affinity for pCaM (dissociation constant of pCaM peptide complex, K d = 2.9 × 10 -1 μmol / L) due to the decrease in { BPP 2 had a much lower binding ability. In order to investigate other factors influencing peptide (K d = 8.1 × 10 -2 μmol / L), which was also a peptide amide, BPP 2 had a much lower binding ability affinity for pCaM besides polarity (or hydrophobicity), CD and 2D NMR spectroscopes were used to study the conformations of BPP 1 and BPP 3. It shows that molecular flexibility could affect peptide  ability to bind pCaM. BP P 1 displayed rigid extended peptide bonds in the middle region where the basic amino acid pair Lys 7 Lys 8 is located, flanked by flexible peptide segments on both terminals; while the middle five residue region of BPP 3 exhibits as very flexible segment. Such a structural character might BPP 3 to adopt a conformation contributive to the interaction of two Lys residues with the acidic residues of pCaM in its peptide binding site and resulted in higher affinity. As this study revealed, both of the two peptides showed the lack of ordered Structure of the aqueous solution. It seemed that there was no relationship between peptide affinity for CaM and the propensity of peptide chain to form α helix. This contradicted what most previous researches approved that α helix was an important character of peptide with high affinity for CaM .