Proton magnetic resonance and conformational energy calculations of repeat peptides of tropoelastin: the tetrapeptide

Structures and conformation of a benzo-12-crown-4 containing dipeptide

Crystal structures of the dipeptide Boc-12-Crown-4-L-DOPA-Gly-OMe (chi) and Boc-12-Crown-4-D/L-DOPA-Gly-OMe (rac) were solved by single crystal X-ray diffraction. Analysis of the packing differences in the crystal reveals that the presence of a water molecule in chi enables intermolecular contacts with the solvent that result in a different conformation of the dipeptide backbone itself. An uncommon N-H…N interaction stabilizes the peptide in its solid state.

Structure and dynamics of two elastin-like polypentapeptides studied by NMR spectroscopy

The structure and dynamics of two synthetic elastin-like polypentapeptides, poly(G(1)V(1)G(2)V(2)P) and poly(AV(1)GV(2)P), were studied in D(2)O and H(2)O at various temperatures by using (1)H, (2)H,(13)C, and (15)N NMR spectra, relaxations, and PGSE self-diffusivity measurement. Signal assignments were made using COSY, NOESY, HXCORR, HSQC, HMBC, and SSLR INEPT techniques. Temperature-induced conformation changes were studied using (3)J(NHCH) couplings, NOESY connectivity, chemical shifts, and signal intensities. Hydrodynamic radii were derived from self-diffusion coefficients measured by the pulsed-gradient spin-echo (PGSE) method. Selective hydration (hydrophilic or hydrophobic) was explored using NOESY and ROESY spectral methods and longitudinal and transverse (1)H relaxation of HOD and quadrupolar (2)H relaxation of D(2)O. Four different physical states were discerned in different temperature regions for both polymers: state I of a rather extended, statistically shaped and fully hydrated polymer below the critical temperature (approximately 299-300 K); state II, a relatively coiled and globular but disordered preaggregation state, developing in a rather narrow region, 300-303 K, in the case of poly(AV(1)GV(2)P) and in a broader region, overlapping with the next one, in poly(G(1)V(1)G(2)V(2)P); state III, a tightly coiled, more compact state in the region 303-313 K; and, finally, state IV, an aggregated (and eventually flocculating and sedimenting) state beyond 313 K. States II-IV coexist in varying proportions in the whole temperature range above 299 K. A structure characterized by a beta-turn stabilized by H-bonding between the Ala carbonyl and Val(2) NH groups of poly(AV(1)GV(2)P) was detected by NOESY just above the transition temperature. States II and III are progressively more stripped of their hydration sheath but retain some molecules of water confined and relatively immobilized in their coils.

Quantum molecular modeling of the elastinic tetrapeptide Val-Pro-Gly-Gly

The free Val-Pro-Gly-Gly tetrapeptide belonging to the Proline-rich sequences of elastin has been studied both theoretically and experimentally. The molecular modelisation was carried out using AM1 and ab initio quantum computations while the conformation in solution was ascertained by circular dichroism spectroscopy performed on the synthesized tetrapeptide. Experimental and theoretical investigations lead to the conclusion that the most probable structure is constituted by a type II beta-turn.

Structural studies of a synthetic peptide derived from the carboxyl-terminal domain of RNA polymerase II

The conformation of the repeating heptapeptide unit of the carboxyl-terminal domain of RNA Polymerase II, Y1S2P3T4S5P6S7 has been examined using nuclear magnetic resonance spectroscopy and circular dichroism. Nuclear Overhauser effects and CD spectra for the synthetic 56-residue peptide H2N-(S2P3T4S5P6S7Y1)8-COOH in water indicate that the peptide is largely unordered. A small population of folded molecules is observed to contain beta-turns located at Ser2-Pro3-Thr4-Ser5 (SPTS) and Ser5-Pro6-Ser7-Tyr1 (SPSY). CD and NMR results in 90% TFE also indicate an equilibrium population of structures, but the fraction of turns is higher. Similarities of nuclear Overhauser effects in water and in 90% TFE suggest that the structures in TFE are biologically relevant. Based on these observations, the average structure of a single conformer of the heptapeptide repeat in 90% TFE was obtained by a distance geometry-simulated annealing method, using distance restraints extracted from nuclear Overhauser data. NMR spectra of the 56-mer show signals corresponding to only one repeat indicating that each repeat is in an identical environment. Thus it is possible to obtain an average structure of the heptapeptide repeat from NOE data on the 56-mer. Twenty-seven final structures were calculated and the root mean square deviations between the 27 structures and the mean coordinates was 1.52 A for the backbone and 2.2 A for all nonhydrogen atoms. The heptapeptide repeat consists of two overlapping beta-turns which are potentially stabilized by hydrogen bonds. The hydroxyl side chains of Ser2, Ser5, Thr4, and Ser7 all appear to be equally exposed for potential phosphorylation. The tyrosyl side chain of each repeat is folded inwards to the backbone and can potentially hydrogen bond to the carbonyl oxygen of the tyrosine in the preceding repeat. Interation of the average structure of the heptapeptide repeat results in a model of the carboxyl-terminal domain with a regular but unusual secondary structure consisting of a series of staggered beta-turns.

Solid-state studies on synthetic fragments and analogues of elastin

A series of synthetic fragments and analogues of elastin have been investigated, in the solid state, by means of differential scanning calorimetry and thermally stimulated current. Most of the polypeptides were shown to possess both amorphous regions and segments of long-range order. Water, which interacts preferentially with the amorphous zones, behaves as plasticizer, i.e. facilitates the localized motions of polypeptide chains. The results obtained have been correlated with elastin elasticity, in particular as far as the fundamental destructuring role of water is concerned.

Polypeptide models of elastin: CD and NMR studies on synthetic poly(X-Gly-Gly)

Poly(X-Gly-Gly), simple structural models for the hydrophobic, proline-devoid, regions of elastin, have been synthesized and studied by circular dichroism and NMR spectroscopies. The results gave evidence of type II beta-turns as the only ordered structure present in the polymers. The stability of the turns has been shown to decrease on hydration and to increase in the series Leu less than Ala less than Val less than Ile.

Studies of the secondary structures of amelogenin from bovine tooth enamel

Circular dichroism and Fourier transform infrared spectroscopic studies of the major amelogenin protein of developing bovine tooth enamel in solution and in the solid state suggest a unique secondary structure containing beta-sheet and repetitive beta-turn structures. The repetitive beta-turn structure at the C-terminal end results from the unique primary structure of amelogenin.

Isolation, purification and 13C- and 1H-n.m.r. assignments of peptide [1-24] of human serum albumin

Isolation, purification and 360 MHz 1H- and 13C-n.m.r. spectra of the residue corresponding to the NH2-terminal peptide fragment [1-24] of human serum albumin are reported. The various resonances have been assigned to individual amino acid residues and their spatial microenvironment has been determined in a straightforward manner on the basis of (i) pH dependent chemical shifts; (ii) combined use of multiple and selective proton-decoupled 1H- and 13C-n.m.r. spectra; (iii) the characteristic pK values exhibited by protons adjacent to sites of ionization in the molecule; and (iv) comparison of the spectra with the NH2-terminal tripeptide segment of human albumin. The pK values of different ionizable groups all fall in the normal range expected for each titrating sites and support a model of peptide fragment [1-24] in which there is no special structure-forming strong associations. These results are in agreement with those obtained by CD spectroscopy.

The binding of aluminium to [Leu5]-enkephalin. An investigation using 1H, 13C and 27Al NMR spectroscopy

The binding of aluminium ion to [Leu5]-enkephalin has been investigated by 1H, 13C and 27Al NMR spectroscopy in dimethyl sulphoxide solution at different peptide/metal ratio. Analysis of the spectra suggests that Al3+ binds at two metal-binding sites. The binding of Al3+ at the first site involves the Tyr1CO, and Leu5COO- groups to give a 2:1 species in a tetracoordinated structure; whereas the binding of Al3+ at the second site utilizes the NH2 terminal groups of the tyrosine moiety in a 2:2 species. 27Al chemical shift values strongly suggest that the second type of aluminium atom displays an octahedral environment. On this basis, we discuss our data in terms of the coordination of aluminium with [Leu5]-enkephalin.

Preferred solution conformation of des-Arg9-bradykinin and analysis of structure-conformation-activity relationships in the series [Alan]des-Arg9-bradykinin

This paper describes the solution conformation of the vasoactive peptide hormone des-Arg9-bradykinin (Arg-Pro-Pro-Gly-Phe-Ser-Pro-Phe). 1. By 1H-NMR spectroscopy we studied des-Arg9-bradykinin and its fragments bradykinin-(1-5), bradykinin-(1-6) in aqueous solution as a function of pH (titration) and in dimethylsulfoxide solution at two ionic states (cation and neutral ion species). 2. The preferred solution conformation which is most strongly stabilized in dimethylsulfoxide in the neutral ion species includes a distorted beta-turn II involving the N-terminal sequence of Pro2-Pro3-Gly4-Phe5 and most likely a C7-type bend in the C-terminal part Ser-Pro-Phe. 3. A complete series of analogous ([Alan]des Arg9-bradykinin, with n = 1, 2...8) was then investigated by circular dichroism and 1H-NMR spectroscopy in order to study the conformational role played by each residue and to delineate the local and the long-range effects on conformation brought about by the Xaa leads to Ala substitutions. Chosen spectral parameters (circular dichroic spectra, chemical shift variations and vicinal coupling constants) characteristic of the preferred solution conformation of the native sequence of des-Arg9-bradykinin are followed from analogue to analogue. The important conformational role of the arginine-1 side chain and its positive charge and the spatial proximity of the N-terminal and C-terminal groups, i.e. the folded structure of the peptide can be inferred from these data. 4. A comparison of the biological activities of the analogues with the conformative perturbations caused by the chemical alterations shows des-Arg9-bradykinin conformation and receptor affinity to be equally sensitive to single-residue substitutions. The correct orientation of the arginine-1 side chain, the precise geometry of the turn involving residues 2-5 and of the C-terminal Pro-Phe sequence are of primary importance.

Molecular design of a cyclic heptapeptide to mimic the zinc-binding site of carbonic anhydrase. Synthesis and zinc-binding studies by 13C-and 1H-N.M.R. spectroscopy

A cyclic heptapeptide [cyclo-(Gly-L-His-Gly-L-His-L-Gly-L-Gly)] was designed to mimic the Zn(II)-binding site of carbonic anhydrase. The cyclic heptapeptide was synthesized from the linear heptapeptide, Gly-L-His-Gly-L-His-Gly-L-His-Gly-OH, which in turn was obtained by coupling of the fragments, viz. BOC-Gly-L-His-Gly-N3 and L-His-GLy-L-His-Gly-OBzlNO2 followed by deblocking of amino and carboxyl protecting groups. Conversion of the linear heptapeptide to the azide by treatment with diphenylphosphoryl azide was followed by cyclization in high dilution. A homogeneous material was isolated by counter-current distribution followed by gel filtration. It was found to be ninhydrin negative. The n.m.r. spectrum of the material upon integration indicated the proper ratios of various kinds of protons to be expected of the cyclic heptapeptide. A detailed 13C- and 1H-n.m.r. investigation was undertaken to determine the Zn(II)-binding ligands of the cyclic heptapeptide. The assignments for all the resonances were attempted by spin-decoupling method, pH and solvent effects, and by comparison of resonances of similar protons and carbons of model peptides. The n.m.r. titration results of the Zn(II) bound form of the cyclic peptide showed the presence of a 1:1 complex. Upon Zn(II)-binding, the changes in the chemical shift of the imidazole protons were relatively large, indicating that this ring is involved in the complexation. All the peptide -NH-resonances were observable and unaffected; consequently, none of these nitrogens can serve as a ligand. In the case of 13C resonances, addition of 1 equiv. of Zn(II) to the cyclic heptapeptide, te C(2), C(4), and C(5) carbon resonances of this group were dramatically affected and showed a very large change in chemical shift upon complexation. The results demonstrate that Zn(II) binds to all three imidazole residues of the designed cyclic heptapeptide.

15N-NMR of repeat peptides of tropoelastin. The tetrapeptide

The 15N-NMR data obtained in chloroform and methanol are reported for Boc-L-Val1-L-Pro2-Gly3-Gly4-OMe, a repeat tetrapeptide sequence of tropoelastin. Deuterium substitution for labile peptide protons was carried out to delineate solvent-exposed and solvent-shielded peptide nitrogens. Solvent perturbation of the peptide nitrogen resonances together with the hydrogen-deuterium substitution reaffirms the previously derived conformation of the molecule in chloroform which contains a beta-turn (type II) and a 14-membered hydrogen bond to form a cross-beta structure.

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.

Proton magnetic resonance and conformational energy calculations of repeat peptides of tropoelastin. A permutation of the hexapeptide

The conformation of a hexapeptide sequence occurring in tropoelastin is discussed from the results obtained using a combined approach of theoretical conformational energy calculations on HCO-Val-Ala-Prb-Gly-OMe and 1h nmr studies on t-Boc-Val-Ala-Pro-Gly-Val-Gly-OMe in a dilute solution of methanol. Both studies have reasonable concurrence with respect to the preferred conformation of the hexapeptide and an analysis of the combined results suggests that the hexapeptide is stabilized by a beta-turn involving the Ala1,iC=O and Val4,iNH groups and a gamma-turn involving Gly5,iC=O and Gly3,iNH groups. A weaker interaction between Gly3,iC=O and Gly5,iNH groups is also found to be possible. Conformational features of the first valyl residue in the sequence Val-Ala-Pro-Gly-Val-Gly and the last valyl residue in Ala-Pro-Gly-Val-Gly-Val are compared and found to have similar torsion angles. The implications of such a similarity are discussed with respect to the conformation of the polyhexapeptide.

Conformational studies on [Pro3, Gly4]-oxytocin in dimethyl sulfoxide by 1H nuclear magnetic resonance spectroscopy: evidence for a type II beta turn in the cyclic moiety

A model for oxytocin has been previously proposed in which residues 3 and 4 occupy the corner positions in a beta turn (Urry, D. W., & Walter, R (1971) Proc. Natl. Acad. Sci. U.S.A. 68, 956). The analogue [Pro(3),Gly(4)]-oxytocin (PGO) was used in proton magnetic resonance (1H NMR) studies designed to probe the contribution of these corner positions in forming a beta turn. Comparison of various 1H NMR parameters obtained at 220 MHz for backbone amide protons of PGO with those for the corresponding protons of oxytocin suggests that, to a first approximation, these two peptides may have similar backbone conformations in )CD3)2SO. Theoretically, the L-Pro lead toGly sequence in positions 3 and 4 of PGO would allow the formation of either a type I or type II beta turn. The two coupling constants between vicinal amide and C alpha protons for Gly(4) of PGO in (CD3)2SO are compatible with a type II beta turn in which 04, the dihedral angle about the bond between the backbone C alpha and N' atoms of Gly4, is appromximately +92 degrees, but not with a type I beta turn. A survey of peptides studied in other laboratories by X-ray and/or 1H NMR with reported type II beta turns with L-Pro lead toGly or Gly lead to Gly sequences in the corner positions revealed a close correlation between chemical shifts and vicinal coupling constants for the glycl residue in the second corner position. It is suggested that this criterion can form an additional basis for the characterization of beta turns. More studies are needed to determine the particular type of beta turn manifest in the cyclic moiety of oxytocin per se, although a reasonable working hypothesis is that oxytocin, similar to PGO, has a type II beta turn.

Coacervation properties in sequential polypeptide models of elastin. Synthesis of H-(Ala-Pro-Gly-Gly)n-Val-OMe and H-(Ala-Pro-Gly-Val-Gly)n-Val-OMe

Syntheses of two sequential polypeptides H-(Ala-Pro-Gly-Gly)n-Val-OMe and H-(Ala-Pro-Gly-Val-Gly)n-Val-OMe via the p-nitrophenyl active ester procedure are reported. The two polymers were obtained in good yields and the polymers were shown to be of large molecular weights, n greater than 40. These two polypeptides were synthesized as analogs of the two coacervating sequential polypeptides H-(Val-Pro-Gly-Gly)n-Val-OMe, and H-(Val-Pro-Gly-Val-Gly)n-Val-OMe, in which the Val-l residue is replaced by an Ala-l residue. H-(Ala-Pro-Gly-Gly)n-Val-OMe did not coacervate even at as high a temperature as 100 degrees, and H-(Ala-Pro-Gly-Val-Gly)n-Val-OMe did not coacervate; however, it precipitated irreversibly around 65--70 degrees C. This suggests the critical role of the Val-Pro hydrophobic side chain interaction in coacervation.