J. Am. Chem. SOC.1993,115, 4849-4858
4849
Peptide Models 6 . New @-TurnConformations from ab Initio Calculations Confirmed by X-ray Data s f ProteinsL Andrhs Perczel,t**Michael A. McAllister,t Phl Cshszhr,t*gand Imre G. Csizmadia'*+ Contribution from the Department of Chemistry, University of Toronto, Ontario, Canada M5S 1A I , Department of Organic Chemistry, Eat& University, Budapest 1 1 2 POB 32 H-1518. Hungary, and Apotex Inc., 150 Signet Drive, Weston, Ontario, Canada M9L 1 T9 Received May 20, 1992
Abstract: In an attempt to determine intrinsically stable hairpin geometries, a number of triamide conformations of For-Ala-Ala-NH2were investigatedusing ab initio calculations(HF/3-21 G). Previous ab initio calculationsof selected diamides of single amino acid residues (e.g., For-Ala-NH2) suggested that the a,-type backbone conformation (6 = -54', =-45') is not a minimal energy structure, although in globular proteins the (aL),, units (referred to as a-helices) are the most frequently found conformations. The lack of the aLconformation made the application of ab initio calculations in peptide geometry analyses questionable. In contrast, for triamides (e.g., For-Ala-Ala-NH2) the appearance of the aLbackbone subconformationis confirmed in the a,6, conformation (usually referred to as type I &turn). This intrinsically stable conformation is the most frequently found hairpin structure in proteins. The existence of the eL conformation (4 = d o o , = 120') in chiral diamides (such as For-Ala-NH2, For-Ser-NH2, or For-Val-NH2) has never been confirmed by ab initio studies, although X-ray analyses of proteins revealed the existence of the polyproline I1 conformation [(eL),,] a long time ago. The herein presented stable Y ~ and E ~bDeLhairpin conformations, calculated by abinitiomethods,legitimizethe"missing" e, backbonegeometry. The fact that somelegitimatebackboneconformations (a,and e,) appear only in triamides and not in diamide systems assigns a specific role to triamide models in understanding protein conformations. The importance of some triamide conformations, especially type I and type I1 &turns, is emphasized. This study summarizes all the possible [18 (30) conformations depending on the d or T "selection rule"] hairpin geometries determined for For-Ala-Ala-NH2 using ab initio computations. We were able to identify all 30 ab initio yielded conformationsas backbone substructures of globular proteins, determined by X-ray crystallography. The 30 optimized triamide structures present a unique opportunity to understand the conformational behavior of @-turns@bends or hairpins). This may have far-reaching consequences in understanding the j3-turn-mediated protein folding.
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Introduction Besides the two major secondary structural elements'-) [the a-helix (& = -60° f 30°, qi = -60° f 30°),, and the 8-pleated sheet (& = -150' f 30°, +i = 150' f 30°),], the third most frequently found4Jstructural unit in globular proteins is the @-turn conformation.G8Smith and Pease*reviewed in detail the reverse turns in peptides and proteins. Reverse turns, hairpins, 8-bends, or &turns are structural elements consisting of four successive amino acid residues (labeled 1,2,3, and 4) at positions i, i + 1, i 2, and i 3 in proteins. The variety of definitions suggested in the past quarter of a century clearly illustrates the evolution of the &turn concept. Adhering to the original definitions of Venkatachalam: &turns are classified into conformationaltypes by their values of cji+,, +i+l, &+ andI+i+2 , torsional angles. On the basis of the four backbone torsional angle values of the second
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* Address correspondence to this author. Current address: Laboratoire de Chime Th€orique, UniversitC Nancy 1 C.N.R.S., 54506 Vandoeuore-lesNancy, France. University of Toronto. Edtvijs University. 5 Apotex Inc. 1 Dedicated to the memory of Professor M. KajtBr, the late virtuoso of stereochemistry. (1) Pauling, L.; Corey, R. Proc. Natl. Acad. Sci. U.S.A. 1951, 37, 729+
740. (2) Pauling, L.; Corey, R.; Branson, H. Proc. Natl. Acad. Sci. U.S.A. 1951, 37, 205-21 1. (3) Levitt, M.; Chothia, C. Nature (London) 1976, 261, 552-558. (4) Crawford, J. L.; Lipscomb, W. N.;Schellman,C. G. Proc. Natl. Acud. Sci. U.S.A. 1973, 70, 538-542. (5) Zimmerman, S . S.; Scheraga, H. A. Proc. Narl. Acad. Sci. U.S.A. 1977, 74, 41264129. (6) Venkatachalam, C. Biopolymers 1968, 6, 1425-1436. (7) Sibanda, B. L.; Thorton, J. M. Nurure. (London) 1985,316,170-174. (8) Smith, J.; Pease, L. Crit. Reu. Biochem. 1980, 8, 315-399.
and third residues, there are three major types of folded conformations: I, 11, and I11 &turns (Chart I). About a decade later, in the analysis of the @turn content of globular proteins, a distance criteria was also i n t r o d ~ c e d . ~Accordingly, ~.~ the Cy - C i distance must be shorter than 7 A. Often an intramolecular H-bond can be found in @-turns,where the NH of the i 3 residue points toward the carbonyl oxygen of the ith residue (1 4-type H-bond) as shown in Figure 1. Although this 1 4 hydrogen bond has never been proved to be a necessary condition for @-turns,it is frequently found in peptides and proteins on the basis of X-ray9aqcand NMR structure determinations,"J and therefore a misconception has developed over the years that such a hydrogen bond is an essential structural featureof 0-turns. This H-bond pattern was also used as a criterion for @-turn assignment in proteins.9a~c The Vankatachalam6-predicted +i+2 = 0' value for several types of &turns was not satisfied in several structure assignments in globular proteins. Consequently,Chou and Fa~man~bsuggested a larger tolerance for the +i+2 torsional angle (-50' I +1+2 I 50'). More recently, Wilmot and Thorton" demonstrated that the 1c;+z = 0' criterion is one of the reasons that numberous turns are identified as "distorted." The experimental value of $i+2 is often around 45' or -45'. This finding is in perfect agreement with our previous analysisl2J3 of ab initio Ramachandran maps,
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(9) (a) Levitt, M.J. Mol. Biol. 1976,104,59-107. (b) Chou, P. Y.;Fasman, G. D. J . Mol. Biol. 1977, 115, 135-175. (c) Kabsch, W.; Sander, C. Biopolymers 1983, 22, 2577-2637. (IO) Dyson, H.J.; Rance, M.; Houghten, R. A.; Lerner, R. A.; Wright, P. A. J. Mol. Biol. 1988, 201, 161-200. (11) Wilmot, C. M.; Thorton, J. M. Protein Eng. 1990, 3, 479493. (12) Perczel, A,; Angyan, J. G.; Kajtar, M.;Viviani, W.;Rivail, J.-L.; Marcoccia, J.-F.; Csizmadia, I. G. J . Am. Chem. SOC.1991,113,62564265.
OOO2-7863/93/1515-4849$04.00/0 0 1993 American Chemical Society
Perczel et al.
4850 J. Am. Chem. Soc., Vol. 115, No. 11, 1993
(Left) Hairpin conformation of a polypeptide chain. A schematic illustration of an untwisted &turn and a backbone twisted by T degrees is shown on the right. Figure 2.
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dMODEL g d C R l l l C A L
