The structure of o-bromocarbobenzoxy-glycyl-L-prolyl-L-leucyl-glycyl-L-proline ethyl acetate monohydrate: a substrate of the enzyme, collagenase

Crystal structure and conformational analysis of angiotensinogen fragments

The tripeptide acetyl-L-prolyl-L-phenylalanyl-L-histidine crystallizes in the orthorhombic space group P2(1)2(1)2(1) with eight molecules in a unit cell of dimensions a = 9.028(2), b = 140.54(6) and c = 42.41(1)A. The structure has been solved by direct methods and refined to an R value of 0.056 for 2904 observed reflections. The molecule exists as a zwitterion with terminal (His)CO2- and (imidazole)H+ as charged groups. The two peptide molecules in the structure adopt a type I beta-turn with Pro and Phe as the corner residues. The main conformational difference between the two crystallographically independent molecules is seen to be in the histidine side-chain orientations. The molecules arrange themselves in sheets perpendicular to the c axis. All hydrophobic side chains lie on one side of the sheets thus generated, whereas the hydrophilic groups are located on the other side. An interesting feature of the crystal structure is the existence of a water layer between adjacent peptide sheets. The conformational study of the isolated Ac-His-Pro-Phe-His-MA using energy calculations gives a rather limited number of stable conformers. The most stable corresponds to a type I beta-turn stabilized through two hydrogen bonds, followed by a less stable type II beta-turn (delta E = 2.0 kcal) and a partly helical structure (delta E = 2.6 kcal).

Conformation and mobility of tyrosine side chain in tetrapeptides. Specific effects of cis- and trans-proline in Tyr-Pro- and Pro-Tyr-segments

We examined the properties of tyrosine in four free tetrapeptides: Ala-Ala-Tyr-Ala (AATA), Ala-Pro-Tyr-Ala (APTA), Ala-Tyr-Ala-Ala (ATAA) and Ala-Tyr-Pro-Ala (ATPA) by CD, n.m.r. and energy calculations. Experimental data (the aromatic 1Lb signal, rotamer populations around the C alpha-C beta bond (chi 1), rotations around C beta-C gamma(chi 2), chemical shifts of ortho- and meta-protons in the phenolic ring (in aqueous and Me2SO solutions), NH proton temperature coefficients and vicinal coupling constants 3JNH-C alpha H in the backbone (Me2SO solution) were compared with calculated minimum energy conformations. We find qualitative agreement between the results of the different techniques with respect to global tendencies of conformational behaviour: we present experimental evidence showing that the presence of proline in the sequence has a more pronounced effect on the side chain organization of the residues preceding it than on one succeeding it. This steric influence of proline on its immediate neighbor is even stronger in the cis isomer than in the more common trans isomer. The strong preference for Rotamer II (chi 1 = 180 degrees) over Rotamer I (chi 1 = -60 degrees) in ATPA (cis-form) concomitant with a noticeable deviation of chi 2 is a striking example.

Preferred conformation of the benzyloxycarbonyl-amino group in peptides

Structural parameters, derived from X-ray crystallographic data, have been compiled for 35 derivatives of amino acids, peptides, and related compounds, which contain the N-terminal benzyloxycarbonyl (Z) group. The geometry of the urethane moiety of this end group is closely similar to that of the tert-butoxycarbonyl (Boc) group, except for a relaxation of some bond angles because the Z group is sterically less crowded than the Boc group. For the same reason, the Z group has greater conformational flexibility. As a result, packing forces in the crystal may cause greater deformations of bond angles, resulting in larger variations of observed bond lengths and bond angles than in Boc-peptide crystals. The aromatic rings of the Z end groups tend to stack in crystals. Conformational energy calculations indicate that most conformations of Z-amino acid-N'-methylamides and of corresponding Boc derivatives have similar dihedral angles and relative energies, i.e. the nature of the N-terminal end group has little effect on the conformational preferences of the residue next to it. In particular, the computed fraction of molecules with a cis urethane (C-N) bond is similar for the two derivatives: 0.51 and 0.42 in Boc-Pro-NHCH3 and Z-Pro-NHCH3, respectively, and 0.02 in the two Ala derivatives. There exist several computed conformations of Z-Ala-NHCH3 and Z-Pro-NHCH3 in which the phenyl ring and the C-terminal methylamide group are close to each other. Because of favorable nonbonded interactions, such conformations are of low energy.

Spectroscopic study of the conformations of proline-containing oligopeptides in the crystalline state and in solution

A conformational study has been carried out on a series of linear proline-containing oligopeptides (ZGP, ZGPL, ZGPLG and ZGPLGP) in both the crystalline state and in DMSO-d6 solution, using Raman and n.m.r. spectroscopy. The amide I and III bands in the Raman spectra of the crystalline forms indicate the presence of the type I beta-bend conformation in ZGPLG and ZGPLGP, but not in ZGP and ZGPL. This result is in agreement with X-ray data on these molecules. The Raman spectra of these peptides in solution indicate that more than one conformation is present, i.e. that the beta-bend structure of the solid form of ZGPLG and ZGPLGP is destabilized by DMSO-d6. 13C and 1H n.m.r. data also demonstrate the presence of more than one conformation in ZGP, ZGPL, ZGPLG and ZGPLGP in DMSO-d6 solution. These isomers differ in their conformation (cis and trans) about their Gly-Pro peptide bonds and possibly about the c alpha-C' bond of the C-terminal proline in ZGPLGP. For ZGP, ZGPL, ZGPLG and ZGPLGP, the ensemble of conformations in DMSO-d6 includes C5 and C7 hydrogen-bonded rings; in addition, ZGPLGP may contain a small percentage of a beta-bend conformation (at Pro2-Leu3) with trans peptides in both Gly-Pro moieties.

Reverse turns in peptides and proteins

The evidence that reverse turns frequently occur as structural components of proteins, as well as of linear and cyclic peptides, is overwhelming. This review summarizes and examines critically the experimental evidence derived from physical methods such as 1H and 13C nuclear magnetic resonance spectroscopy, spin-lattice relaxation time, circular dichroism, IR spectroscopy, and X-ray crystallography. Secondly, theoretical evidence obtained from energy calculations, which rely on empirical energy functions, and correlative methods, which rely on algorithms based on the frequency of occurrence of amino acids, is evaluated. In particular, those theoretical studies for which complementary physical studies have been completed are emphasized. Finally, examples of structure-function relationships involving reverse turns and their biological recognition are demonstrated.

Intramolecularly hydrogen-bonded peptide conformations

Over the past few years the possible occurrence of intramolecularly hydrogen-bonded structures in linear and cyclic peptides has attracted increasing attention. In this review emphasis is given to solid-state studies, particularly by X-ray diffraction and infrared absorption techniques. Conformational energy calculations are also considered. The discussion is focused both on model peptides and biological activity polypeptide molecules. The tetrapeptide system (Formula: see text), examined allows one to discuss the extended C5 structure and the various folded conformations, namely the C7 (gamma-turn), C8, C10 (beta-turn), C11, and C13 conformations. The four latter forms may include cis peptide configurations. The oxy-analogs to the C7, C10, and C13 conformations and structures containing bifurcated hydrogen bonds are also discussed. The last sections describe intramolecularly hydrogen-bonded peptide structures involving: (1) a side-chain group, (2) the N-protecting group (in synthetic model compounds), and (3) a beta-amino acid.

New paths in the molecular orbital approach to solvation of biological molecules

This review is devoted to the presentation of recent developments in a field of theoretical molecular biophysics which seem to open large possibilities for progress in a hitherto relatively unexplored although very important direction. It is concerned with the establishment of a new methodology in the molecular orbital approach to the problem of the solvation of biological molecules. The methodology is still in an initial stage, susceptible of many refinements and its practical applications may also be considered as being in their beginnings. Nevertheless the successes obtained so far and the interest which they aroused in a number of laboratories incite us to present already now the general principles and the available results so as to offer a possibility of evaluating the advantages, present-day limitations and future potentialities of the procedure, which could then be explored by all those interested. This review may thus be said to be to a large extent oriented towards the future, with the acknowledged aim of producing an acceleration and widening of researches in this field. Possible progress in this respect is interesting from a double point of view.

Insulin, its chemistry and biochemistry

It is fifty years, this year, since insulin was successfully used to treat patients suffering from diabetes. It is thirty years since A. C. Chibnall gave the Bakerian lecture on ‘Amino acid analysis and the structure of proteins’, (1942), including insulin, and ten years since F. G. Young gave the Croonian lecture on ‘Insulin and its action’ (1962). It is difficult not to feel that this is a particularly appropriate moment at which to discuss, once again, insulin, its chemistry and biochemistry, its structure and function. Chibnall did, of course, warn us in 1942 to beware of the ‘hypnotic power of numerology’. The most serious reason for discussing insulin today is not the existence of the recurring anniversaries (other dates are more important in the history of the study of insulin), but the fact that we still do not know how it works in living creatures. Very recently we have acquired a great wealth of new information about the actual arrangement in space of the atoms in insulin molecules in crystals. We can begin to answer many of the questions chemists and biochemists have been asking about the behaviour of insulin for years past. It seems useful to give here some of these answers in the hope that they may guide further experiments towards the complete understanding of the action of insulin that still eludes us.