Peptide Protein Res Research Articles

Small-scale manual multiple peptide synthesis system. Application to phosphopeptide synthesis.

A system for small-scale (ca. 10-50 mumol) manual multiple peptide synthesis assembled from commercially available solid-phase extraction apparatus is described. This system was used to prepare (on a 15 mumol scale) the five monophosphorylated isomers of the peptide ASTTVSKTE, a proteolytic fragment of the C-terminal region of rhodopsin. The peptides were assembled using serine or threonine active esters without hydroxyl protection at the positions of phosphorylation. Phosphate groups were introduced using postassembly phosphitylation/oxidation according to a published procedure [Andrews, D.M., Kitchin, J. & Seale, P.W. (1991) Int. J. Peptide Protein Res. 38, 469-475; Staerkaer, G., Jakobsen, M.H., Olsen, C.E. & Holm, A., Tetrahedron Lett. 32, 5389-5392; Perich, J.W. (1992) Int. J. Peptide Protein Res. 40 134-140]. The reported system provides a relatively inexpensive approach to multiple peptide synthesis, including synthesis of phosphopeptides, for laboratories whose synthesis requirements do not justify investment in an automated multiple peptide synthesis instrument.

Conformation and hydrogen bonding of N-formylmethionyl peptides

Crystals of N-formyl-L-methionyl-L-phenylalanine (C15H20N2O4S), grown from aqueous methanol solution are orthorhombic, space group, P2(1)2(1)2(1), with cell parameters at 294K of a = 4.900(2), b = 17.947(4), c = 18.726(4)A, V = 1646.8A3, M.W. = 324.4, Z = 4 and Dm = 1.308 g/cc, and as expected, all nearly identical to that of N-f-D-Met-D-Phe studied by Jeffs, Heald, Chodosh & Eggleston (Int. J. Peptide Protein Res. 24, 442-446, 1984). The crystal structure was solved and refined using CAD-4 data (1095 reflections greater than or equal to 3 sigma) to a final R value of 0.042. Molecules related by the alpha-translation form a parallel beta-sheet rather than anti-parallel sheet as stated in the earlier study of Jeffs et al. The formation of the parallel rather than the anti-parallel beta-sheet structure, the use of the C-H ...O hydrogen bonds to stabilize the beta-sheet and the very short O-H ...O hydrogen bond between the carboxyl OH and the N-acyl oxygen atom emerge as the main structural features of the chemotactic N-formyl methionyl peptides.

Phospholemman Transmembrane Structure Reveals Potential Interactions with Na+/K+-ATPase

Phospholemman (PLM) is a 72-residue bitopic cardiac transmembrane protein, which acts as a modulator of the Na(+)/K(+)-ATPase and the Na(+)/Ca(2+) exchanger and possibly forms taurine channels in nonheart tissue. This work presents a high resolution structural model obtained from a combination of site-specific infrared spectroscopy and experimentally constrained high throughput molecular dynamics (MD) simulations. Altogether, 37 experimental constraints, including nine long range orientational constraints, have been used during MD simulations in an explicit lipid bilayer/water system. The resulting tetrameric alpha-helical bundle has an average helix tilt of 7.3 degrees and a crossing angle close to 0 degrees . It does not reveal a hydrophilic pore, but instead strong interactions between various residues occlude any pore. The helix-helix packing is unusual, with Gly(19) and Gly(20) pointing to the outside of the helical bundle, facilitating potential interaction with other transmembrane proteins, thus providing a structural basis for the modulatory effect of PLM on the Na(+)/K(+)-ATPase. A two-stage model of interaction between PLM and the Na(+)/K(+)-ATPase is discussed involving PLM-ATPase interaction and subsequent formation of an unstable PLM trimer, which readily interacts with surrounding ATPase molecules. Further unconstrained MD simulations identified other packing models of PLM, one of which could potentially undergo a conformational transition to an open pore.

Engineered Sarafotoxins as Tissue Inhibitor of Metalloproteinases-like Matrix Metalloproteinase Inhibitors

The sarafotoxins and endothelins are approximately 25-residue peptides that spontaneously fold into a defined tertiary structure with specific pairing of four cysteines into two disulfide bonds. Their structures show an interesting topological similarity to the core of the metalloproteinase interaction sites of the tissue inhibitors of metalloproteinases. Previous work indicates that sarafotoxins and endothelins can be engineered to eliminate or greatly reduce their vasopressive action and that their structural framework can withstand multiple sequence changes. When sarafotoxin 6b, which possesses modest matrix metalloproteinase inhibitory activity, was C-terminally truncated to remove its toxic vasopressive activity, the metalloproteinase inhibitory activity was essentially abolished. However, further changes, based on the sequences of peptides selected from libraries of sarafotoxin variants or suggested by analogy with tissue inhibitors of metalloproteinases, progressively enhanced the matrix metalloproteinase inhibitory activity. Peptide variants with multiple substitutions folded correctly and formed native disulfide bonds. Improvements in matrix metalloproteinase affinity have generated a peptide with micromolar K(i) values for matrix metalloproteinase-1 and -9 that are selective inhibitors of different metalloproteinases. Characterization of its solution structure indicates a close similarity to sarafotoxin but with a more extended C-terminal helix. The effects of N-acetylation and other changes, as well as docking studies, support the hypothesis that the engineered sarafotoxins bind to matrix metalloproteinases in a manner analogous to the tissue inhibitors of metalloproteinases.

Evidence for Domain-specific Recognition of SK and Kv Channels by MTX and HsTx1 Scorpion Toxins

Maurotoxin (MTX) and HsTx1 are two scorpion toxins belonging to the alpha-KTx6 structural family. These 34-residue toxins, cross-linked by four disulfide bridges, share 59% sequence identity and fold along the classical alpha/beta scaffold. Despite these structural similarities, they fully differ in their pharmacological profiles. MTX is highly active on small (SK) and intermediate (IK) conductance Ca(2+)-activated (K(+)) channels and on voltage-gated Kv1.2 channel, whereas HsTx1 potently blocks voltage-gated Kv1.1 and Kv1.3 channels only. Here, we designed and chemically produced MTX-HsTx1, a chimera of both toxins that contains the N-terminal helical region of MTX (sequence 1-16) and the C-terminal beta-sheet region of HsTx1 (sequence 17-34). The three-dimensional structure of the peptide in solution was solved by (1)H NMR. MTX-HsTx1 displays the activity of MTX on SK channel, whereas it exhibits the pharmacological profile of HsTx1 on Kv1.1, Kv1.2, Kv1.3, and IK channels. These data demonstrate that the helical region of MTX exerts a key role in SK channel recognition, whereas the beta-sheet region of HsTx1 is crucial for activity on all other channel types tested.

A new B-chain mutant of insulin: comparison with the insulin crystal structure and role of sulfonate groups in the B-chain structure.

The solution structure of a new B-chain mutant of bovine insulin, in which the cysteines B7 and B19 are replaced by two serines, has been determined by circular dichroism, 2D-NMR and molecular modeling. This structure is compared with that of the oxidized B-chain of bovine insulin [Hawkins et al. (1995) Int. J. Peptide Protein Res.46, 424-433]. Circular dichroism spectroscopy showed in particular that a higher percentage of helical secondary structure for the B-chain mutant is estimated in trifluoroethanol solution in comparison with the oxidized B-chain. 2D-NMR experiments confirmed, among multiple conformations, that the B-chain mutant presents defined secondary structures such as a alpha-helix between residues B9 and B19, and a beta-turn between amino acids B20 and B23 in aqueous trifluoroethanol. The 3D structures, which are consistent with NMR data and were obtained using a simulated annealing protocol, showed that the tertiary structure of the B-chain mutant is better resolved and is more in agreement with the insulin crystal structure than the oxidized B-chain structure described by Hawkins et al. An explanation could be the presence of two sulfonate groups in the oxidized insulin B-chain. Either by their charges and/or their size, such chemical groups could play a destructuring effect and thus could favor peptide flexibility and conformational averaging. Thus, this study provides new insights on the folding of isolated B-chains.

Improving the performance of an acid-labile 4-hydroxymethyl phenoxyacetic acid (HMP) linker on resin and SynPhase? grafted solid-supports

A replacement of the acetic acid moiety by valeric acid within the 4-hydroxymethylphenoxyacetic acid (HMP) linker (Sheppard RC, Williams BJ. Acid-labile resin linkage agents for use in solid phase peptide synthesis. Int. J. Peptide Protein Res. 1982; 20: 451-454) significantly improved its performance in terms of loading capacity, yield and purity of the final products. The results indicated the spacer-linker combination and type of solid supports are important factors for solid-phase synthesis.

Synthetic Rat V1a Vasopressin Receptor Fragments Interfere with Vasopressin Binding via Specific Interaction with the Receptor

To study the vasopressin receptor domains involved in the hormonal binding, we synthesized natural and modified fragments of V1a vasopressin receptor and tested their abilities to affect hormone-receptor interactions. Natural fragments mimicking the external loops one, two, and three were able to inhibit specific vasopressin binding to V1a receptor. In contrast, the natural N-terminal part of the V1a vasopressin receptor was found inactive. One fragment, derived from the external second loop and containing an additional C-terminal cysteine amide, was able to fully inhibit the specific binding of both labeled vasopressin agonist and antagonist to rat liver V1a vasopressin receptor and the vasopressin-sensitive phospholipase C of WRK1 cells. The peptide-mediated inhibition involved specific interactions between the V1a receptor and synthetic V1a vasopressin receptor fragment since 1) it was dependent upon the vasopressin receptor subtype tested (Ki(app) for the peptide: 3.7, 14.6, and 64.5 microM for displacing [3H]vasopressin from rat V1a, V1b, and V2 receptors, respectively; 2) it was specific and did not affect sarcosin 1-angiotensin II binding to rat liver membranes; 3) it was not mimicked by vasopressin receptor unrelated peptides exhibiting putative detergent properties; and 4) no direct interaction between [3H]vasopressin and synthetic peptide linked to an affinity chromatography column could be observed. Such an inhibition affected both the maximal binding capacity of the V1a vasopressin receptor and its affinity for the labeled hormone, depending upon the dose of synthetic peptide used and was partially irreversible. Structure-activity studies using a serie of synthetic fragments revealed the importance of their size and cysteinyl composition. These data indicate that some peptides mimicking extracellular loops of the V1a vasopressin receptor may interact with the vasopressin receptor itself and modify its coupling with phospholipase C.

N-Acetyl-L-phenylalanyl-L-alaninamide

The conformation of the peptide chain in N-acetyl-l-phenylalanyl-l-alaninamide (NAFAA), C14H19N3O3, is rather extended and falls in the E region of the ϕ, ψ map, according to the classification of Zimmerman, Pottle, Nemethy & Scheraga [Macromolecules (1977), 10, 1–9]. The values of ϕ, ψ torsion angles are like those of an anti­parallel β pleated sheet. Side-chain conformation of Phe residue is defined by χ1 = −174.5 (4)° and χ2 = 105.5 (6)° and comes within the B2 class of the observed statistical distribution for the aromatic residues in peptides [Cody, Duax & Hauptman, (1973). Int. J. Peptide Protein Res. 5, 297–308]. Crystal packing is ruled by four intermolecular hydrogen bonds that involve all the donor groups, the acetyl O atom acting as a double acceptor. In the crystal there are ribbons of molecules translated along the a axis of the P21 space group and joined through three hydrogen bonds. The fourth hydrogen bond interconnects screw-related ribbons. The phenylalanyl rings stack parallel to the a direction with interplanar distances of 3.334 (7) A.

Engineering of five 88-residue receptor-adhesive modular proteins containing a parallel alpha-helical coiled coil and two RGD ligand sites.

Several 88-residue proteins were designed, synthesized and examined as receptor-adhesive modular proteins (RAMPs). Three covalent and two noncovalent dimers were made from two 44-residue peptide chains containing three structural modules: RGD-A23a (ligand-spacer-coil) and A9a-RGD (coil-spacer-ligand). The ligand module contained the tripeptide Arg-Gly-Asp (RGD). The coil modules A9a and A23a were five-heptad alpha-helices engineered by Hodges and co-workers [Int. J. Peptide Protein Res. (1992) 40, 171-179]. By circular dichroic spectroscopy, each of these five RAMPs contained an alpha-helical coiled coil. The disulfide-bridged dimer RGD-A23a/RGD-A23a and its reduced form (RGD-A23a)2 had two N-terminal RGD sites. The disulfide-bridged dimer A9a-RGD/A9a-RGD and its reduced form (A9a-RGD)2 had two C-terminal RGD sites. However, the disulfide-bridged heterodimer RGD-A23a/A9a-RGD had one RGD site at each terminus with a 50 Angstrum coiled coil between them. The temperature at the midpoint of unfolding for each of the covalent homodimers RGD-A23a/RGD-A23a (67 degrees C) and A9a-RGD/A9a-RGD (69 degrees C) was slightly higher than that of the corresponding noncovalent homodimer (RGD-A23a)2 (62 degrees C) or (A9a-RGD)2 (68 degrees C) but much lower than that of the covalent heterodimer RGD-A23a/A9a-RGD (79 degrees C). The enthalpy and entropy of thermal unfolding were also significantly greater for the heterodimer than for the four homodimers, consistent with the heterodimer having the most stable coiled coil. Although the distance between its RGD sites was at least 50 Angstrum greater than that for the homodimers, this heterodimeric RAMP was only as active as the homodimers A9a-RGD/A9a-RGD and (A9a-RGD)2 in inhibiting the adhesion of A2058 melanoma cells to extracellular matrix proteins.(ABSTRACT TRUNCATED AT 250 WORDS)

Cloning and sequence analysis of the cDNA for arginine kinase of lobster muscle.

Arginine kinase belongs to an evolutionary conserved family of ATP:guanidino phosphotransferases, whose members play an important role in energy metabolism. In this work, a lambda gt11 lobster muscle library was constructed and screened by using both polyclonal antibodies and two synthetic oligonucleotides. The complete amino acid sequence of arginine kinase (ATP:L-arginine N-phosphotransferase, EC 2.7.3.3) from lobster muscle was determined by cloning and sequencing the DNA complementary to its mRNA. The identity of the clone was confirmed by comparing the amino acid sequence deduced by nucleotide sequence analysis with previously published partial sequences of amino- and carboxyl-terminal regions of the enzyme and some of its fragments (Regnouf, F., Kassab, R., Debuire, B., Richard, C., and Han K. K. (1981) Int. J. Peptide Protein Res. 17, 143-155). The nucleotide sequence of the cDNA was found to contain an open reading frame encoding 355 amino acid residues with a calculated molecular mass of 39,830 daltons. This enzyme exhibits a significant sequence identity to those of representative members of the guanidino kinase family, including creatine kinase. This report represents the first molecular cloning and sequencing of an ATP-guanidino phosphotransferase which is not a creatine kinase isoform.

Affinity purification of a difficult‐sequence protein

A biotinylated derivative of a designed, difficult-sequence protein (the Minibody, Bianchi, E., Tramontano, A., Sollazzo, M. & Pessi, A. (1993) Int. J. Peptide Protein Res. 41, 385-393) which represented only 3.7% of the crude, cleaved material was quantitatively recovered with about 70% purity, in a single step, by affinity chromatography on immobilised avidin. Purification to homogeneity was then easily achieved by preparative HPLC. This highly effective purification scheme must be contrasted with the previously shown multidimensional, low-yield chromatographic protocol. Since no facilitation of the purification had been obtained by capping alone, this result suggests that capping is useful only in conjunction with affinity chromatography.

Acidolytic cleavage of tris(alkoxy)benzylamide (PAL) “internal reference” amino acyl (IRAA) anchoring linkages: validation of accepted procedures in solid‐phase peptide synthesis (SPPS)

Under the normal conditions of acidolytic cleavage/deprotection of tris(alkoxy)benzylamide (PAL) anchoring linkages in Fmoc solid-phase peptide synthesis (SPPS), product release occurs by a straightforward single-step pathway. A recently reported cleavage of the NH--alpha CH bond of an amino acyl residue adjacent to PAL [see Int. J. Peptide Protein Res. 38, 146-153 (1991)] could not be confirmed in novel experiments incorporating a double "internal reference" amino acid (IRAA) design. The results of the present work revalidate the widely accepted application of IRAAs to monitor yields in SPPS, and confirm the reliability of PAL methodology for the preparation of C-terminal peptide amides.

Divalent metal ion mediated interaction of proteins with negatively charged membranes A model study employing molecular mechanics

Previous molecular mechanics calculations on the effect of Ca(II) and Mg(II) ions on the conformation of the 18-23 loop of bovine prothrombin [Maynard et al. 1988, Int. J. Peptide Protein Res. 31, 137-149] are extended to include the effect of a model phospholipid head group methyl[L-seryl] phosphate. Whereas the conformation of the Gla-21 Pro-22 amide bond remains decidedly trans in the absence of the model head group, in its presence, the cis Ca(II) ion induced (but not Mg(II] form is significantly lowered in relative energy. The low energy Ca(II) structures establish a coordination sphere with more ligands than do the low energy Mg(II) ion structures.

Environment‐dependent conformation of Boc‐Pro‐Ser‐NHCH3

AbstractThe conformation of Boc‐Pro‐Ser‐NHCH3 (1) was studied in the solid state and in solution. In the crystal, the steric structure of 1 is characterized by an E(cis) urethane tertiary amide bond and the lack of intramolecular H bonds. Four‐hundred megahertz 1H‐ and 101‐MHz 13C‐nmr studies in CDCl3 clearly show the presence of two conformers differing in the rotameric state of the tertiary‐amide bond. Selective 1H‐13C nuclear Overhauser enhancement experiments at −20°C as well as 1H‐nmr and ir data indicate that the major trans conformer (84% in CDC13) may adopt a type I β‐turn conformation with a possible Oγ  H‐N interaction, similarly to Piv‐Pro‐Ser HCH3 (2) [A. Aubry, N. Ghermani, and M. Mar‐raud (1984) Int. J. Peptide Protein Res. 23, 113‐122]. Molecular mechanics calculations on the cis rotamer show that the β‐pleated‐like backbone conformation of serine in the crystal of 1 is not a low‐energy state for the isolated molecule; it is caused by packing forces, particularly by the helical network of intermolecular H bonds.

Chicken Protamine Genes Are Intronless: The complete genomic sequence and organization of the two loci

A positive cosmid clone obtained from a pwe15-rooster DNA library using a chicken protamine cDNA probe reveals the complete sequence of the two loci for the rooster protamine genes. The organization of these two loci within the cosmid clone matches that of genomic DNA. The copy number per haploid genome is two. The sequence for the rooster protamine predicted from the coding region shows differences from that previously determined at the protein level (Nakano, M., Tobita, T., and Ando, T. (1976) Int. J. Peptide Protein Res. 8, 565-578). A recent re-determination of the rooster protamine amino acid sequence (28 residues from the N terminus) matches that predicted from the genome rather than the sequence of Nakano et al. (1976). Both loci are intronless and the gene is extremely GC-rich (88% in the coding region). The 5' region of the gene contains a typical TATAAA box, several CG boxes, as well as other characteristic motifs. The 3' region of the gene contains the polyadenylation signal and several GT repeats of known Z-DNA forming potential. A correlation between the functional map of the gene and the tendency of the DNA to bend or to adopt the Z-conformation is presented and possible roles for these conformations in the transcription of this gene are discussed.

Dynorphin A (1–13) peptide NH groups are solvent exposed: FT-IR and 500 MHz 1H NMR spectroscopic evidence

FT-IR spectroscopic studies of dynorphin A(1-13) in H2O and D2O are utilized to derive the aqueous phase secondary structure of the opioid peptide. Resolution enhancement of the amide I region of dynorphin A(1-13) in H2O revealed a doublet at 1652 cm-1 and 1669 cm-1 which are interpreted as indicative of "unordered" and extended structures. From FT-IR and 1H NMR deuterium exchange studies, the peptide NH groups appeared to be solvent accessible which is suggestive of an essentially extended structure with aperiodically interwoven "unordered" structure. The results are consistent with Raman Spectroscopic (Rapaka et al., (1987) Int. J. Peptide Protein Res. 30:284-287) and 2D NMR studies (Huang et al. submitted), from our laboratory.

Effect of calcium (II) and magnesium (II) ions on the 18-23 gamma-carboxyglutamic acid containing cyclic peptide loop of bovine prothrombin. An AMBER molecular mechanics study.

The effect of calcium (II) and magnesium (II) ions on the conformation of the 18-23 cyclic peptide loop of bovine prothrombin are investigated by the molecular mechanics program AMBER (Assisted Model Building with Energy Refinement). The work is an extension of an earlier paper (Eastman et al., Int. J. Peptide Protein Res. 27, 1986, 530-553) that employed the program ECEPP (Empirical Conformational Energy Program for Peptides). In the absence of either metal ion, or in the presence of either one Ca(II) or one Mg(II) ion, the lowest-energy forms found by AMBER have the Gla21-Pro22 peptide bond in a trans conformation. In the presence of two Ca(II) or Mg(II) ions, the loop form of lowest energy is decidedly cis. The coordination about the Ca(II) and Mg(II) ions is different in both the single and double metal cases. In addition, the peptide chains that emerge from the loop are oriented parallel to each other in the lowest-energy complex with two Ca(II) ions, but are not parallel in the lowest-energy complex with two Mg(II) ions.

Effect of alkylation with different sized substituents on the conformation of ovomucoid, lysozyme and ovotransferrin.

Conformational changes induced in ovomucoid, lysozyme and ovotransferrin on reductive addition of different sized substituents have been studied employing differential scanning calorimetry (DSC) and circular dichroic spectroscopy (CD). The thermograms obtained by DSC revealed that extensive introduction of methyl, isopropyl, cyclopentyl, cyclohexyl, benzyl or n-butyl groups has a detrimental effect on thermal stability (enthalpy of denaturation); the effect generally increases with the size of the substituent. Circular dichroic spectra were affected only to a very limited extent by the modifications, near-u.v. spectra remaining much the same while far-u.v. spectra displayed minor changes. The general conclusion drawn is that the modifications had only limited effects on the conformation of the proteins while, nonetheless, perturbing (or breaking) long-range intramolecular interactions so as to destabilize the structure. Derivatization of lysozyme and ovotransferrin with some of the larger groups has been reported to result in spontaneous precipitation of the proteins [Fretheim, K., Iwai, S. & Feeney, R.E. (1979) Int. J. Peptide Protein Res. 14, 451-456]. The present investigation indicates that precipitation was caused by (partial) denaturation (and ensuing aggregation) as a consequence of modification.

Dynamics of amino acid residues in globular proteins.

The dynamic differential equation model developed and tested for bovine pancreatic trypsin inhibitor and tuna ferrocytochrome c in Ponnuswamy, P.K. & Bhaskaran, R. (Int. J. Peptide Protein Res. 24, 168-179, 1984) is extended for 17 more protein crystals in this work. Average displacements are computed for 20 amino acid residues observed in 19 proteins. Detailed information on the dynamic behaviour of the individual proteins and individual residues is presented. The effect of atomic packing on the fluctuations of the amino acid residues in alpha-chymotrypsin is illustrated. A number of general points on the dynamic characteristics of globular protein molecules are presented.