The type II -turn

The CD of (3-turns has been characterized1127 by using the peptides c(-L-Ala-L-Ala-Aha-) as a model for a type I turn and c(-L-Ala-D-Ala-Aha-) for a type II turn. The CD spectra for these two peptides are shown in Figure 5. The spectrum for the type I turn is of class C and that for the type II turn is of class B. The latter result is consistent with the calculations of Woody, 125 but the former result is not. Moreover, explicit calculations for the low-energy conformers1127 predicted a class B spectrum for type I and a class C spectrum for type II. However, using a classical dipole interaction model 128129 Sathyanarayanan and Applequist 130 obtained qualitative agreement with experiment for these two model systems. 

Recently, attempts have been made to derive CD spectra of various p turns using deconvolution procedures (see below). Employing an approach termed convex constraint analysis, Perczel, Fasman, and others [58-61] have derived CD spectra for both types I and H turns. Three basis spectra were extracted for a data base of fourteen peptides which displayed either types I or II p turns. One basis spectrum for type I turns resembled a class C spectrum and the other a variation of a class B. The type II turn is said to display a classic class B spectrum [59-61],... 

The type II turns, with fi-, y-clustering at more favorable values of fi = 30°, y = -30°, and the II turns with fi = -30°, y - -25°, appear to display a more normal hydrogen-bond geometry because the out-of-plane angles fi are con- x siderably reduced. There are, however, steric limitations requiring Gly to be in position 3 of the turn which limits their frequencies [591]. 

I—III Table XXII gives similar data for )3 turns of types I —III. In Table XXIII we present the results for the type II turns with Ala in the third position. The effects of variations in dihedral angles on the amide frequencies are complex, and rather than considering them in detail the original paper should be consulted for specifics (Krimm and Bandekar, 1980). 

The physical adsorption of gases by non-porous solids, in the vast majority of cases, gives rise to a Type II isotherm. From the Type II isotherm of a given gas on a particular solid it is possible in principle to derive a value of the monolayer capacity of the solid, which in turn can be used to calculate the specific surface of the solid. The monolayer capacity is defined as the amount of adsorbate which can be accommodated in a completely filled, single molecular layer—a monolayer—on the surface of unit mass (1 g) of the solid. It is related to the specific surface area A, the surface area of 1 g of the solid, by the simple equation... 

Figure 2.8 Adjacent antiparallel P strands are joined by hairpin loops. Such loops are frequently short and do not have regular secondary structure. Nevertheless, many loop regions in different proteins have similar structures, (a) Histogram showing the frequency of hairpin loops of different lengths in 62 different proteins, (b) The two most frequently occurring two-residue hairpin loops Type I turn to the left and Type II turn to the right. Bonds within the hairpin loop are green, [(a) Adapted from B.L. Sibanda and J.M. Thornton, Nature 316 170-174, 1985.]...

Fig. 2.31 Comparison of the turn segment found in hairpin 122 with a naturally-occuring type II / -turn of a-polypeptides together with backbone dihedral angles in degrees. In the case of 122, the angles were extracted from one low energy conformer derived from NMR data and shown in Fig. 2.30. Torsion angles with comparable values are shown in bold [191, 195]...

Tight turns can combine with other types of structure in a number of ways. In addition to their classic role of joining )8 strands, they often occur at the ends of a-helices (see Section II,A). A type II turn forms a rather common combination next to a Cl /3 bulge (see Section II,D). Isogai et al. (1980) have surveyed the occurrence of successive tight turns, which either form approximately helical features or else form more complex chain reversals than single turns. 

The Lys(Nic) and Dap(Nic) residues were incorporated into a simple hexa-peptide structure which contained a constrained type II -turn (Fig. 26). Dithionite reduction of both Lys(Nic) and Dap(Nic) peptides rapidly generated... 

It is interesting that a unique secondary structural element, designated the half-turn, was indentified in preliminary NMR studies of rabbit metallothionein-2 (Wagner etal., 1986). The half-turn element is defined as a type II turn with (f>3 rotated from 90° to -90° its occurrence in the metallothionein-2 structure arises from the constraints placed on the relatively short polypeptide chain by the metal clusters. Although these constraints are not well understood and are certainly difficult to predict, the continued biophysical study of metallothionein-2 will certainly improve our understanding of protein-metal cluster interactions. 

Type 1 intrazeolite photooxygenation of alkenes has been also reported to give mainly allylic hydroperoxides (Scheme 42). In this process, the charge transfer band of the alkene—O2 complex within Na-Y was irradiated to form the alkene radical cation and superoxide ion. The radical ion pair in turn gives the allylic hydroperoxides via an allylic radical intermediate. On the other hand, for the Type II pathway, singlet molecular oxygen ( O2) is produced by energy transfer from the triplet excited state of a photosensitizer to 02. 

Further support for this assignment of CD spectra for the two most common types of (3-tums has been provided by studies of cyclic hexapeptides. 92,131132 The prediction of a class C spectrum for the type IT turn was verified by studies of cyclic peptides with the o-Xaa -L-Pro sequence. 131-133 A peptide with the sequence L-Pro-D-Ala, expected to have a variant of a type II turn, 126 was found 134 to have a class C spectrum (mirror image of a class C spectrum), in accordance with predictions. 125 A type VI turn, with a d.v-Xaa -Pro bond has been studied in c(-L-Phe-L-Pro-Aha-) and found to have a strong negative band at -212 nm, 133 but data below 200 nm were not reported. Of course, there may be significant aromatic contributions in the spectrum of this peptide. 

The types IV and type V isotherms resemble the type II and type III isotherms, respectively, at the bottom or low-pressure end. However, at the high-pressure end they turn toward the P/Pq = 1 line and as indicated... 

Figure 2-24 Tight turns found in polypeptide chains. Two types of 3 turn are shown. A third variant, the type III or 310 turn resembles the type I turn but has the cp, y angles of a 310 helix. Type II P turns containing proline and tighter y turns are thought to be major structural components of elastin. Another P turn, lacking the hydrogen bond has a cz s-proline residue at position 3.

The most stable elements of secondary structure of peptides and proteins are turns, helices, and extended conformations. Within each of these 3D-structures the most commonly found representatives are (3-turns,a-helices, and antiparallel (3-sheet conformations, respectively. y-TurnsJ5 310-helices, poly(Pro) helices, and (3-sheet conformations with a parallel strand arrangement have also been observed, although less frequently. Among the many types of (3-turns classified, type-I, type-II, and type-VI are the most usual, all being stabilized by an intramolecular i <— i+3 (backbone)C=0 -H—N(backbone) H-bond and characterized by either a tram (type-I and type-II) or a cis (type-VI) conformation about the internal peptide bond. In the type-I (3-turn a helical i+1 residue and a quasi-helical 1+2 residue are found, whereas in the type-II (3-turn the i+1 residue is semi-extended and the 1+2 residue is also quasi-helical but left-handed. This latter corner position may be easily occupied by the achiral Gly or a D-amino acid residue. 

Preparation of a mimetic of the cyclic peptide jaspamide was reported in 1988. 87 Compound 41 (Scheme 17) was designed to mimic the type-II (1-turn of the peptide, which contained the proposed pharmacophoric phenol and 2-bromoindole functional groups. This analogue displayed interesting insecticidal activity against the tobacco budworm, Heliothis vireseins. 

At the second position (i+l), Pro is the most common amino acid in type I and type II turns because of the restriction of to about -60°. Ser also exhibits a reasonable preference for this position since its side chain oxygen can form... 

Another change that is commonly made in peptides is the reversal of the chirality of one or more amino acid residues (reviewed in Rose et al., 1985). This is a particularly popular modification, because protected d-amino acids are commercially available, and the resulting analogs, if active, would have enhanced stabilities to enzymatic degradation. The chirality of the amino acids in the central two positions (/ + 1 and i + 2) of a turn have a profound effect on the type of turn that is formed. If the central two residues are both of the l configuration, a type I turn is often formed. If the residue at position + 1 is l and that at position i + 2 is d (an l, d pair) then a type II turn is stabilized, while a d, l pair at the central position will stabilize a type II turn (Rose et al., 1985). For this reason, type II turns are often referred to as l, d turns and type II turns as d, l turns. 

Woody [56] classified representative CD spectra for p turns based upon theoretical determinations. For types I and II, CD spectra similar to p sheets, but with red-shifted extrema, were predicted. These were referred to as class B spectra, with the standard p sheet spectrum termed as class A. Class C spectra resembled the CD pattern of an a helix, and were predicted to arise for type II turns. Since then, numerous p turn models have been examined and most experimental results agree with the theoretical studies [14]. Notable exceptions include type I turns which exhibit class C spectra rather than the class B predicted for such structures. Gierasch et al. [57] have suggested that the discrepancy may arise from the presence of a cis -proline residue (y - -50°), and that it is the cis -proline residue which produces the C-type spectrum regardless of the turn type. 

The lifetimes t of unfavorable conformations are determined by whatever decay reactions — physical and chemical — are available to each conformer. The decay rates r/1 of favorable conformations include rates of hydrogen abstraction. Quantum yields for hydrogen abstraction are determined by the relative rates of hydrogen abstraction and of decay, no matter what conformers they arise from. The type II reaction of acyclic ketones falls into this general class. The unit quantum yield for triplet state y-hydrogen abstraction in many ketones indicates that conformational change is faster than hydrogen abstraction which, in turn, is faster than any other form of decay. 

In view of the fact that Piv-LPro-Gly-NHMe adopts a classical type II / -turn, it is of interest to explore the influence of introducing additional CH2 units within the peptide chain, for example, Piv-LPro-y-Abu-NHMe (Fig. 15). Again, we have determined the structure of this material [71] directly from powder X-ray diffraction data using the GA technique for structure solution. With one molecule in the asymmetric unit, each structure in the GA calculation was defined by 13 variables (seven variable torsion angles). The torsion angle of the peptide bond of the LPro residue was restricted to be either 0° or 180°, and the other... 

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