Polypeptide Secondary Structure Research Articles

Prediction of polypeptide secondary structures analysing the oscillation of the hydropathy profile

The hydropathy profile of a polypeptide can reflect periodicity tightly linked, in particular, with α-helix and β-strand conformations. We have developed an algorithm to detect such periodicity to predict the secondary structure of proteins. The method uses profiles constructed with the weighted average of hydropathy along the primary structure of the polypeptide and does the analysis of the variation of the profile for looking for periodic oscillations, using a variation detecting algorithm, without the definition of an empirical threshold. The independence of the method from known structures makes it particularly reliable for analysing membrane proteins.

Secondary structure of globular proteins at the early and the final stages in protein folding

The ellipticities for an early transient intermediate in refolding observed by kinetic circular dichroism measurements at 220–225 nm for 14 different proteins are summarized, and the ellipticity values are compared with those for the final native proteins and also with the ellipticities expected from a physical theory of protein and polypeptide secondary structure. The results show that a substantial part of the protein secondary structure is in general formed in the earliest detectable intermediate in refolding and that the ellipticities in both the native and the intermediate states are consistent with the physical theory of protein secondary structure.

The polypeptide 3 10-helix

The 3 10-helix, first predicted as a reasonably stable polypeptide secondary structure fifty years ago, has only recently attracted the attention of structural biochemists and protein crystallographers. It represents the third principal structure occurring in globular proteins and has been described at atomic resolution in model peptides and in peptaibol antibiotics.

Toward automating the process of determining polypeptide secondary structure from 1H NMR data

AbstractA computer program has been constructed to perform a qualitative analysis of nuclear magnetic resonance data on polypeptide sequences to identify α‐helical and β‐strand secondary structure segments. The criteria embodied within the program are some of those which have proven useful in studies where secondary structure was described by visual interpretation of NOESY and COSY spectra. Other rules used in these studies, however, remain implicit in the description of the analysis or are ill‐specified, so that they are not used uniformly across studies. The structure of the program presented allows the rules and assumptions of this qualitative method to be modeled explicitly and used consistently, allowing a flexible and understandable framework for investigating both proteins of interest and the method involved in the analysis. The system has been tested on data sets from twelve proteins and was in agreement with 97% of the ø‐helical regions of the proteins when compared to the reports in the literature, as well as with 95% of the residues included, and in agreement with 96% of the β‐strand regions of the proteins, as well as with 90% of the residues included in them. Over the entire primary sequence, the system was in agreement with the placement of 83% of the residues in the major secondary structures.

Conformation of [Cd 7]-metallothionein-2 from rat liver in aqueous solution determined by nuclear magnetic resonance spectroscopy

The three-dimensional structure of [Cd 7]-metallothionein-2 from rat liver was determined in aqueous solution, using nuclear magnetic resonance spectrometry and distance geometry calculations. The experimental data provided proton-proton distance constraints from measurements of nuclear Overhauser effects, constraints on the geometry of the metal-cysteine clusters determined by heteronuclear correlation spectroscopy, and dihedral angle constraints derived from both coupling constants and nuclear Overhauser effects. The structure calculations were performed with the program DISMAN. As in previous studies with rabbit liver metallothionein-2a, the structure calculations were performed separately for the α and β-domains containing the 4 and 3-metal clusters, respectively, since no interdomain constraints were found. For both domains, the global polypeptide fold, the location of polypeptide secondary structure elements, the architecture of the metal-sulfur cluster and the local chirality of the metal co-ordination are very similar to the solution structure of rabbit metallothionein-2a, but show considerable difference relative to the crystal structure of rat metallothionein-2.

Two-dimensional 1H NMR studies of rat atrial natriuretic factor(1–23)

Using a variety of two-dimensional NMR methods, the 1H NMR resonances of rat ANF(1–23) in dimethyl sulfoxide-d6 solution have been assigned. Two-dimensional phase sensitive correlated spectroscopy was used to identify protons that are scalar coupled and were also used to obtain coupling constants (3JNH-αCH) in complicated regions of the spectra. Relayed coherence transfer experiments proved useful in identifying the connectivities between the NH and β-protons of the same amino acid residue. Finally, phase sensitive 2D NOE experiments allowed the identification of protons close in space between adjacent residues, thus providing the sequential assignments as well as conformational information. These preliminary results (chemical shifts, coupling constants, NOEs) were analyzed in terms of possible polypeptide secondary structures and were found to be consistent with a β-type structure or an averaging of solution conformations (random coil).

Prediction of homology and divergence in the secondary structure of polypeptides.

A quantitative procedure is described for the comparison of secondary structure of homologous proteins. Standard predictive methods are used to generate probability profiles from pairs of homologous amino acid sequences; correlation coefficients (R) are then computed between each pair of amino acids for alpha-helix (R alpha), extended structure (R beta), turn (R(t)), and coil (R(c)). R values are >0.2 for correctly aligned homologous sequences. Unrelated or incorrectly aligned sequences give R values near zero. Lack of correlation for a segment of otherwise well-correlated sequences is used to identify structural divergence, which is then evaluated graphically by using difference profiles. A combination of these techniques correctly predicts secondary structural differences between melittin or beta-endorphin and their respective synthetic analogs. The method is potentially useful to describe evolutionary changes in protein secondary structure as well as in the design of peptide analogs.

Anisotropic thermal motion and polypeptide secondary structure studied by X-ray analysis at 0.98A resolution.

aPP is a 36-amino acid polypeptide which forms a stable globular structure stabilised by hydrophobic interactions between a polyproline-like helix and an alpha-helix. Crystals contain dimers and are crosslinked by coordination through zinc ions leading to a well-ordered lattice which diffracts X-rays to a resolution of 0.98A. This gives a 5:1 ratio of observations-to-parameters even when anisotropic thermal ellipsoids defined by six parameters for each non-hydrogen atom were refined using least-squares techniques. Rigid body refinement of groups within the polypeptide was also undertaken. The relationship of the principal axes of individual thermal ellipsoids and the librations of rigid side groups to features of secondary, tertiary, and quaternary structures of aPP and its interactions with water molecules are described.

Anisotropic thermal motion and polypeptide secondary structure studied by X-ray analysis at 0.98 Å resolution

Anisotropic thermal motion and polypeptide secondary structure studied by X-ray analysis at 0.98 Å resolution

Polypeptide secondary structure determination by nuclear magnetic resonance observation of short proton-proton distances

The use of proton-proton nuclear Overhauser enhancement (NOE) distance information for identification of polypeptide secondary structures in non-crystalline proteins was investigated by stereochemical studies of standard secondary structures and by statistical analyses of the secondary structures in the crystal conformations of a group of globular proteins. Both regular helix and β-sheet secondary structures were found to contain a dense network of short 1H- 1H distances. The results obtained imply that the combined information on all these distances obtained from visual inspection of the two-dimensional NOE (NOESY) spectra is sufficient for determination of the helical and β-sheet secondary structures in small globular proteins. Furthermore, cis peptide bonds can be identified from unique, short sequential proton-proton distances. Limitations of this empirical approach are that the exact start or end of a helix may be difficult to define when the adjoining residues form a tight turn, and that unambiguous identification of tight turns can usually be obtained only in the hairpins of antiparallel β-structures. The short distances between protons in pentapeptide segments of the different secondary structures have been tabulated to provide a generally applicable guide for the analysis of NOESY spectra of proteins.

Vibrational circular dichroism of polypeptides. II. Solution amide II and deuteration results

AbstractVibrational CD (VCD) of amide I and II vibrations of several α‐helical polypeptides have been measured in solution. For the amide II as well as the amide I [previously published: Lal, B.B. & Nafie, L.A. (1982) Biopolymers 21, 2161] we find the VCD to be characteristic of the polypeptide secondary structure. Amide II bands of right‐handed α helices were all found to have negative VCD and to have their maximum rotational strength for the parallel (low‐energy) component. However, left‐handed α helices formed from L‐amino acids gave positive amide II bands at higher frequencies than found for the right‐handed helices, indicating that the VCD was sensitive to the stereochemical difference. The amide‐I VCD spectra of some deuterated right‐handed α‐helical polypeptides have a new negative feature to low frequency that does not reflect theoretical predictions but also appears to be stereochemically sensitive. Amide‐II and amide‐A VCD of a few deuterated polypeptides imply retention of the secondary‐structure‐dependent characteristics seen in the hydrogenated VCD.

Nucleotide sequence of the papA gene encoding the Pap pilus subunit of human uropathogenic Escherichia coli.

The papA gene of the uropathogenic strain Escherichia coli J96, coding for the Pap pili subunit, was subjected to DNA sequencing, and found to code for an 185-amino acid-long polypeptide with a 22-amino acid-long signal peptide. Here we present the primary sequence, the hydrophilicity profile, and the predicted polypeptide secondary structure of the Pap pili subunit.

Assignment of the 1H nuclear magnetic resonance spectrum of the proteinase inhibitor IIA from bull seminal plasma by two-dimensional nuclear magnetic resonance at 500 MHz

The assignment of the 1H nuclear magnetic resonance (n.m.r.) spectrum of the protease inhibitor IIA from bull seminal plasma is described and documented. The assignments are based entirely on the amino acid sequence and on two-dimensional n.m.r. experiments at 500 MHz. Individual assignments were obtained at 18 degrees C and 45 degrees C for the backbone protons of all 57 amino acid residues, with the single exception of the N-terminal pyroglutamate amide proton. The amino acid side-chain resonance assignments are complete, with the exception of 17 long side-chains, i.e. Pro13, Met43 and all the Glu, Gln, Lys and Arg, where only one or two resonances of C beta H2 and in some cases C gamma H2 could be identified. The sequential assignments showed that the order of the two C-terminal residues in the previously established primary structure had to be changed; this was then confirmed by chemical methods. The chemical shifts for the assigned resonances at 18 degrees C and 45 degrees C are listed for an aqueous solution at pH 4.9. A preliminary characterization of the polypeptide secondary structure was obtained from the observed patterns of sequential connectivities.

Systematic application of two-dimensional 1H nuclear-magnetic-resonance techniques for studies of proteins. 2. Combined use of correlated spectroscopy and nuclear Overhauser spectroscopy for sequential assignments of backbone resonances and elucidation of polypeptide secondary structures.

This paper describes a new nuclear magnetic resonance approach for the determination of secondary structure in globular proteins. To illustrate the practical application of the new procedure, two-dimensional correlated spectroscopy and two-dimensional nuclear Overhauser enhancement spectroscopy were used to obtain individual assignments for all the backbone protons of the beta-sheet secondary structures in the basic pancreatic trypsin inhibitor. First, combined connectivity diagrams of these two methods recorded in both 2H2O solution and H2O solution of the inhibitor were employed to obtain sequential, individual resonance assignments for the separate strands in the beta sheet. Second, a 2D nuclear Overhauser enhancement spectrum recorded with a long mixing time was used to determine how the separate, extended polypeptide strands are linked by hydrogen bonds in the sheet structures. By combination of these results with the identifications of the amino acid side-chain resonances described in the preceding paper, the beta-sheet structures can, without reference to data on the spatial structure obtained with other techniques, be localized in the amino acid sequence. This investigation confirms results on limited regions of the beta sheet in the inhibitor obtained previously with one-dimensional nuclear magnetic resonance experiments and demonstrates that the entire beta-sheet structure seen in single crystals of the inhibitor is preserved in aqueous solution.

Polypeptide secondary structure may direct the specificity of prohormone conversion

Hormones and other polypeptides secreted by cells are frequently biosynthesized as larger precursors. The necessary enzymic processing of these occurs prior to the secretion of hormones but after the secretion of blood factors and zymogens. These conversion processes are of particular importance in regulatory mechanisms [l] such as blood clotting. At present, the mechanisms of conversion from precursors to hormones are poorly understood in all but a few instances. Furthermore, hormones themselves are sometimes found as several homologous species, each with some activity, but differing in peptide length [2,3] . A clearer understanding of the intracellular processing events may help to distinguish between primary hormonal products and artefacts produced by non-specific enzyme attack [4] . A general mechanism for the intracellular processing of propolypeptides has been proposed. In this a trypsin-like enzyme cuts precursors specifically at adjacent basic ammo acids. The resulting basic COOHterminal residues are then removed by a carboxypeptidase B-like enzyme [5,6] . An example is the release of the C-peptide from proinsulin by cleavage at the carboxyl ends of -Arg-Argand -Lys-Argsequences. Both trypsin and carboxypeptidase B-like activities have been observed during the conversion of proparathyrin [ 161. It is not known whether these enzymes are the same in all cells producing secretory material, or whether they are specific to particular polypeptides. For example albumin, glucagon and parathyrin all retain paired basic amino acid sequences, although

On the conformation, coacervation and function of polymeric models of elastin.

In a recent review (1) entitled “Conformations of the Repeat Peptides of Elastin in Solution: An Application of Proton and Carbon-13 Magnetic Resonance to the Determination of Polypeptide Secondary Structure”, the secondary structures of the monomers and polymers of the repeat peptides of tropoelastin were described. The repeat peptides, as reported by Foster et al. (2) and Gray et al. (3) but with the permutation given in terms of the conformational unit, are Val1-Pro2-Gly3-Gly4, Val1-Pro2-Gly3-Val4-Gly5, and Ala1-Pro2-Gly3-Val4-Gly5-Val6. Derivatives of these monomers, their permutations, oligomers and high polymers were studied in four different solvents dimethylsulfoxide, methanol, trifluoroethanol and water. More recently each of the three monomers have been studied in chloroform and their possible conformations examined by means of extensive conformational energy calculations (4–6). In each solvent and in the conformational energy calculations, all of the repeat peptides were found to contain the β-turn with Pro2 and Gly3 at the corners as a dominant conformational feature (see Figure 1). This β-turn utilizes a hydrogen bond between the C-O of residue 1 and the N-H of residue 4.

Conformations of the repeat peptides of elastin in solution: an application of proton and carbon-13 magnetic resonance to the determination of polypeptide secondary structure.

Conformations of the repeat peptides of elastin in solution: an application of proton and carbon-13 magnetic resonance to the determination of polypeptide secondary structure.

Carbon-13 magnetic resonance evaluation of polypeptide secondary structure and correlation with proton magnetic resonance studies.

With the use of appropriately chosen solvent pairs it is demonstrated that solvent dependence of peptide carbonyl carbon resonances can be correlated with polypeptide secondary structure. Solvent titrations show the peptide carbonyl which is intramolecularly hydrogen bonded to exhibit less chemical shift on going from a dimethylsulfoxide solution to a solution containing a solvent which is a good proton (or deuteron) donor. Effective solvent systems are dimethylsulfoxide paired with water, trifluoroethanol, or methanol. This approach is demonstrated with the pentapeptide of elastin.

Solvent dependence of peptide carbonyl carbon chemical shifts and polypeptide secondary structure: The repeat tetrapeptide of elastin

It is demonstrated that carbon-13 magnetic resonance may be used to evaluate polypeptide secondary structure by noting the solvent dependence of peptide carbonyl carbon chemical shifts. Solvent pairs are utilized in which one solvent is a poor proton (or deuteron) donor and the second is a good proton (or deuteron) donor. The peptide carbonyl carbon resonance of the carbonyl shielded from the solvent by intramolecular hydrogen bonding exhibits less downfield shift on introduction of CD3OD, D2O or 2,2,2-trifluoroethanol-d3 to dimethylsulfoxide-d6 solutions than do those of peptide carbonyls that are more exposed to the solvent. The approach is illustrated with the elastin repeat tetrapeptide, Val1-Pro2-Gly3-Gly4, wherein the Val1C-O is solvent shielded due to intramolecular hydrogen bonding to the Gly4 NH.

IR spectroscopic study of the secondary structure of polypeptides

IR spectroscopic study of the secondary structure of polypeptides