Theoretical Conformational Analysis on Silk Fibroin Model Polypeptide with Ala-Gly Repeated Sequence

Polymer Journal, Vol. 22, No.5, pp. 416----425 (1990) Theoretical Conformational Analysis on Silk Fibroin Model Polypeptide with Ala-Gly Repeated Sequence Masahito OKA t, Y oshihiro BABA, Akihiro KAGEMOTO, and Akio NAKAJIMA* Departments of General Education and * Applied Chemistry, Osaka Institute of Technology, Omiya, Asahi-ku, Osaka 535, Japan (Received September 8, 1989) ABSTRACT: Theoretical conformational analysis was carried out for Ac--{Ala-GlY)12-NHMe, which was a model polypeptide of Bombyx mori silk fibroin, using ECEPP and the conformational energy minimization procedure. The hypothesis on the interaction in polypeptide molecules was also used for the analysis. Calculated results showed that right-handed IX-helix and left-handed p4 . 6 _helix were the lowest-energy and 2nd low-energy conformations, respectively. Several stable conformations, which were related to the already proposed model structures of silk fibroin, were also found in the theoretically obtained conformational ensemble of Ac--{Ala-GlY)12-NHMe. KEY WORDS Conformational Analysis / ECEPP / Poly(Ala-Gly) / Silk Fibroin / Helical Structure / p-Helix / The native conformation of pep tides and proteins is uniquely decided by their aminoacid sequences. By change of temperature, pH and ionic strength, the native conformation is transformed to the other stable conformation. This means that the ensemble of stable conformations of peptide and proteins is decided by their amino-acid sequences and that their relative stabilities are changed by the given environment. So, it is very important to know the relation between the relative stabilities of conformations and the amino-acid sequences of pep tides and proteins as a primary step for recognizing the biological functions in molecular level. Helical conformations of poly(Val-ProGly-Gly) were theoretically analyzed by the molecular force field method as an elastinmodel polypeptide. 1 The y-helix, which is essentially different from the well-known rj,- and fJ-helices and fJ-sheet structure, was proposed t 416 as a model conformation of elastin. Helical conformations of polY(L-Ala-D-Ala) were also theoretically analyzed, and the relative stabilities of rj,- and fJ-helices were shown as a function of conformational energy.2 It is shown that a right-handed fJ4.6-helix is the most stable helical conformation and that several fJ6-helices are also stable helical conformations. These results indicate that conformational stabilities of polypeptides essentially depend on the amino-acid sequences for two cases of the model polypeptides composed of repeated Val-Pro-Gly-Gly and L-Ala-D-Ala sequences. Bombyx mori silk fibroin has repeated sequences composed of an alternation of Gly residue with two thirds Ala and one third Ser, i.e., Ala-Gly-Ala-Gly-Ser-Gly, and takes two structures known as silk I and silk II forms depending on the given environments such as solvent, temperature and existence of stress. 3,4 It is known that silk II structure corresponds To whom all correspondence should be addressed. Polym. J., Vol. 22, No.5, 1990 Conformation of Poly(Ala-Gly) to the f3-sheet structure, however, silk I structure has not been clearly decided yet because of the difficulty to obtain an oriented sample for X-ray crystallography. In this paper, the repeated sequence Ala-Gly-Ala-Gly-Ser-Gly of Bombyx mori silk fibroin is simplified as a model sequence Ala-Gly. This treatment is based on the following experimental and theoretical results. (I) Silk fibroin with silk I structure and poly(Ala-Gly) with form II present the same X-ray diffraction pattern,5,6 and the same 13C chemical shifts of ca, cP and C = 0 of Ala and C = 0 of Gly residues. 7 (2) residue and The precise conformational preferences of amino-acid residues depend on the character of side-chain groups, but overall stabilities of backbone conformations of Ser residue are almost similar to Ala residue 8 -11 (M. Oka and A. Nakajima, unpublished data). Helical conformations of poly(Ala-Gly) are theoretically analyzed by the conformational energy minimization procedure and the three-steps method which have already been used in the previous theoretical works for poly(ValPro-Gly-Gly)l and polY(L-Ala-o-Ala).2 as single-residue minima. 69 minimum-energy conformations were obtained for dipeptide with AE < 10 kcal mol-I. All 69 minimumenergy conformations of Ac-Ala-Gly-NHMe were used as the starting conformations of the peptide having two repeating units of Ala-Gly, i.e., Ac-(Ala-GlY)2-NHMe. During minimization, the conditions of helical conformation 1,2 was used. Then, all minimum-energy conformations of Ac-(Ala-Glyh-NHMe (AE < 10 kcal mol- 1) were used as the starting conformations for the minimization of conformational energy of Ac-(Ala-GlY)12-NHMe. Selection of the starting conformations in the first set is based on the hierarchy of interactions in peptide, polypeptide and protein systems. 1,2 The second set was selected by the following method. Conformational energy of Ac-(Ala-GlY)12-NHMe was calculated by changing ¢ Ala and t/J Ala at 15° intervals and fixing (¢Gly, t/JGly) to the energy minima of Ac-Gly-NHMe (i.e., (83°, -76°), (-83°,76°), (180°,180°), (173°, -62°), (-173°,62°), (72°, 53°), and ( - 72°, - 53°)), and fixing x ila = 60° and all other dihedral angles to 180°. 37 local minima in (¢ Ala' t/J Ala) space were selected as starting conformations. Energy minimizations were carried out for all conformations in the THEORETICAL above two starting-conformation sets with the All conformational energy calculations were condition of helical conformation. 1,2 A bend (occuring at i + 1 and i + 2th residues) carried out with the energy functions of ECEPP,12 and minimization was continued is defined as a conformation in which R 7 A until conformational energy did not change by (R is the distance between ith ca and i + 3th more than 0.001 kcal mol- 1 between successive ca atoms.) and also classified into eleven types iterations. During minimizations, all ¢, 1/1, and given in Table I of ref 14. A polar hydrogen Xl for Ala and Gly residues were allowed to atom and an oxygen or nitrogen atom with an vary. All other backbone dihedral angles were interatomic distance of less than 2.3 A are regarded to be hydrogen-bonded. Conformafixed at 180°. Two sets of starting conformations were tional space is divided into 16 regions with the used. The first set was obtained by the following conformational letter codes as shown in Figure method. Conformational energies of Ac- I of ref 13. The conformational energy per Ala-Gly-NHMe were minimized using all whole molecule, AE, is defined by AE = E - Eo, combinations of single-residue minima of Ala where Eo is the value of E at the global and Gly13 as starting conformations. (¢, 1/1)= minimum on the potential energy surface of (-75°, 140°) for Ala, and (¢,t/J)=(-75°, the particular molecules, and AEres is defined 140°) and (75°, -140°) for Gly were also used by AEres = AE/m, where m (...truncated)