β-structures of polypeptides with L- and D-residues

Summary It was previously shown that nuclei of-sheets surrounded by unordered segments are formed in polypeptide chains built up with alternating hydrophobic and hydrophilic residues and containing both L- and D-enantiomers. It was also established that segments of residues having the same configuration tend to segregate in these nuclei when the starting composition of stereomonomers departs from the racemic mixture.Soft acidic hydrolysis of these polymers has been studied. Kinetic measurements show two pseudo first order rate constants, in agreement with the existence of two conformational species. The unordered part of the chains is hydrolyzed more rapidly, allowing the isolation of a-fraction enriched in one enantiomer. Thus, a plausible process of enrichment in enantiomer during prebiotic evolution has been described, which however does not explain the preference of one enantiomer over the other one.     

β-structures of polypeptides with L- and D-residues

The possible formation of beta-structures from polypeptide chains with L-and D-Residues randomly distributed was statistically analyzed within the frame of two hypotheses. Firstly, only those segments containing residues of identical chirality can associate to form antiparallel beta-structures, and secondly these segments must have a minimum length. The influence of different factors was examined: initial ratio of the L-and D-monomer, minimum length required for the segments to be incorporated into beta-sheets, average length of the peptide molecules, and stereoselectivity in the course of the polymerization process. The results show that in all cases nuclei of beta-sheets surrounded by random coil segments are formed, the optical activity of which very increases to purity when the initial ratio of monomers deviates from the racemic mixture. This suggests experiments to enrich the system in one enantiomer. Comparison is made with the corresponding behavior and properties of the alpha-helical structure.     

β-structures of polypeptides with L- and D-residues

Summary A series of five alternating poly(leucyl-lysyl) samples with varying amounts of L- and D-residues randomly distributed along the chain, but evenly shared out amongst leucyl and lysyl residues were synthesized by condensation of a mixture of the four diastereoisomeric dipeptidep-nitro-phenylesters. Their behavior in aqueous solution at various ionic strengths was studied by infrared spectroscopy which allowed measurement of the total amount of-structures, and by circular dichroism which gives the excess of L-residues over D-residues in the same structures. Comparison with the properties of the all L-poly(Lys-Leu-Lys-Leu) shows that incorporation of a few D-residues in a L-chain seems to reduce the width of the-sheets obtained in presence of salt. Higher proportions of D-isomers prevent the coil transition from occurring when the ionic strength is increased except for segments containing at least 6 to 7 adjacent residues of the same configuration.     

Intramolecular distortion of the α-helical structure of polypeptides

Broadening of the infrared amide A, amide I and amide II bands of α-helical polypeptides has been observed for thermodynamically unstable α-helices. This spectroscopic fact can be explained now by the geometrical distortions of the backbone of the helical structure. Two models for distorted helices which include regular or irregular distortions of the angles of internal rotation of the main polypeptide chain have been considered. It is pointed out that the instability of α-helix is associated with irregular distortions of the polypeptide backbone.     

pH responsiveness of fibrous assemblies of repeat-sequence amphipathic α-helix polypeptides

We reported previously that our designed polypeptide α3 (21 residues), which has three repeats of a seven-amino-acid sequence (LETLAKA)₃, forms not only an amphipathic α-helix structure but also long fibrous assemblies in aqueous solution. To address the relationship between the electrical states of the polypeptide and its α-helix and fibrous assembly formation, we characterized mutated polypeptides in which charged amino acid residues of α3 were replaced with Ser. We prepared the following polypeptides: 2Sα3 (LSTLAKA)₃, in which all Glu residues were replaced with Ser residues; 6Sα3 (LETLASA)₃, in which all Lys residues were replaced with Ser; and 2S6Sα3 (LSTLASA)₃; in which all Glu and Lys residues were replaced with Ser. In 0.1M KCl, 2Sα3 formed an α-helix under basic conditions and 6Sα3 formed an α-helix under acid conditions. In 1M KCl, they both formed α-helices under a wide pH range. In addition, 2Sα3 and 6Sα3 formed fibrous assemblies under the same buffer conditions in which they formed α-helices. α-Helix and fibrous assembly formation by these polypeptides was reversible in a pH-dependent manner. In contrast, 2S6Sα3 formed an α-helix under basic conditions in 1M KCl. Taken together, these findings reveal that the charge states of the charged amino acid residues and the charge state of the Leu residue located at the terminus play an important role in α-helix formation.     

The internal rotational barriers about NCα and CαC backbone bonds of polypeptides

In many studies on the protein folding problem it is assumed that the internal rotational barriers about NC^α and C^αC backbone bonds in unfolded polypeptides are quite small, around 0.7 kcal/mol, of an order comparable to the energy of kT at normal temperature (where k is Boltzmann’s constant and T is the temperature in K) and hence that rotations about these bonds occur almost freely. Here it is highlighted that such consideration is an unfortunate mistake. Approximate values for the rotational barriers of NC^α and C^αC bonds are suggested from computations of U(f \phi , ψ) potential energy surface (PES) maps of a number of oligopeptides by a semiempirical method for conformational analysis. The proposed values are about 16 kcal/mol for NC^α bonds and 6 kcal/mol for C^αC bonds. The values of the same barriers estimated from some ab initio quantum-mechanical PES maps for several dipeptides available in literature are also highlighted.     

Calpain II induced insolubilization of lens β-crystallin polypeptides may induce cataract

Addition of calpain II (EC 3.4.22.17) to soluble proteins from 10-day-old rat lens caused an increase in turbidity and production of water-insoluble protein. The insolubilization increased with higher concentrations of both lens protein and calpain II, it could be prevented by the cysteine protease inhibitor E-64; it required at least 0.5 mM Ca²⁺, it was limited to 6% of the soluble protein present and resulted from precipitation β-crystallin polypeptides. When compared by two-dimensional electrophoresis, the insoluble β-crystallin polypeptides produced by calpain II were similar to insoluble β-crystallin polypeptides found incataractous lenses. Trypsin also caused insolubilization of β-crystallin polypeptides, but these polypeptides were unlike polypeptides produced during cataract formation. These data suggested that the loss of solubility was due to a specific removal of N/or C-terminal extensions from β-crystallin polypeptides by calpain II, and that a similar process may occur in vivo during cataract formation. It is hypothesized that the insoluble protein produced by calpain II causes cataract by increasing light scatter in the lens.     

The β2 subunit of human placenta hexosaminidase (Hex) A and B is a non-random association of the two polypeptides αa and βb

The subunit structures of placental Hex A and B have previously been assigned as _a and _b, respectively. The ₂ subunit is composed of two non-identical polypeptide chains, _a and _b. Purified Hex A and B were fractionated on a chromatofocusing column, and the fractions were reduced and then alkylated with iodo-I-¹⁴C-acetamide. The polypeptide chains were separated by polyacrylamide-gel isoelectric focusing. From the radioactivity measurements of the polypeptides a constant value for ₂ was obtained in all the chromatofocusing fractions, demonstrating a non-random structure of (₂) in each ₂ subunit.     

Catalytic activity of linear-, cyclic- and polypeptides having a sequence of -Asp-β-Ala-Gly-ser-β-Ala-Gly-His-β-Ala-Gly in the hydrolysis of p-nitrophenyl acetate

Catalytic activities of Boc-Asp-β-Ala-Gly-Ser-β-Ala-Gly-His-β-Ala-Gly-OEt(Boc-9-Oet), Boc-Asp-β-Ala-Gly-Ser-β-Ala-Gly-His-β-Ala-Gly-OH(Boc-9-OH), cyclo(Asp-β-Ala-Gly-Ser-β-Ala-Gly-His-β-Ala-Gly) (Cyclic 9) and poly(Asp-β-Ala-Gly-Ser-β-Ala-Gly-His-β-Ala-Gly) (Poly 9) in the Hydrolysis of p-nitrophenyl acetate were investigated in detail and compared with each other and with poly(His-β-Ala-Gly) (Poly 3) which has no Ser and Asp residues. Generally, Poly 3 was less active than the others, which contain Ser and Asp residues together with the His residue. The reaction rate-substrate concentration for Boc-9-OEt, Boc-9-OH. Cyclic 9 and Poly 3 gave straight lines, while that for Poly 9 showed slightly the tendency of saturation at high substrate concentration. The reaction rates were all proportional to the concentration of the peptides. All peptides gave similar, sigmoid-type pH-k_cat profiles. The pK values obtained from these pH-k_cat profiles agreed fairly well with those of histidine residues obtained from ¹³C n.m.r. chemical shifts, which suggests that the predominant participating functional group in the catalytic reaction is the imidazole group in the histidine residue. The pK values of the His residue in peptides with the -Asp-β-Ala-Gly-Ser-β-Ala-Gly-His-β-Ala-Gly- sequence were shifted to higher pH region compared with Poly 3, suggesting that the effect of the carboxyl group in the Asp residue and the extents of pK-shift for linear peptides were larger than for Cyclic 9 or Poly 9. The catalytic reaction rates by Boc-9-OEt or Cyclic 9 increased steadily with increase in temperature, while the reaction rate-temperature profiles for Poly 9 and Poly 3 gave the optimum temperatures at around 40–50°C.     

14 What RNA world ?? Ancestral polypeptides likely participated in the origins of translation

A widespread consensus holds that protein synthesis according to a genetic code was launched entirely by sophisticated RNA molecules that played both coding and functional roles. This belief persists, unsupported by phylogenetic evidence for ancestral ribozymes that catalyzed either amino acid activation or tRNA aminoacylation. By contrast, we have adduced strong experimental evidence that the most highly conserved portions of contemporary aminoacyl-tRNA synthetases (aaRS) accelerate both reactions well in excess of rates achieved by RNA aptomers derived from combinatorial libraries and of rates required for primordial protein synthesis. Such ancestral enzymes, or “Urzymes”, characterized for Class I (TrpRS (Pham et al., 2010, 2007) and LeuRS (Collier et al., 2013); 130 residues) and Class II (HisRS; 120–140 residues; (Li et al., 2011)) synthetases generally have promiscuous amino acid specificities, whereas ATP and cognate tRNA affinities are within an order of magnitude of those for contemporary enzymes. These characteristics match or exceed expectations for the primordial catalysts necessary to launch protein synthesis. Structural hierarchies in Class I and II aaRS also exhibit plateaus of increasing enzymatic activity, suggesting that catalysis by peptides similar to the Aleph motif identified by Trifonov (Sobolevsky et al.) may have been both necessary and sufficient to launch protein synthesis. Sense/antisense alignments of TrpRS and HisRS Urzyme coding sequences reveal unexpectedly high middle-base complementarity that increases in reconstructed ancestral nodes (Chandrasekaran et al.), consistent with the proposal of Rodin and Ohno (Rodin & Ohno, 1995). Thus, these ancestors were likely coded by opposite strands of the same gene, favoring simultaneous expression of aaRS activating both hydrophobic (core) and hydrophilic (surface) amino acids. Our results support the view that aaRS coevolved with cognate tRNAs from a much earlier stage than that envisioned under the RNA World hypothesis, and that their descendants make up appreciable portions of the proteome.     

Synthesis of linear,cyclic and polypeptides having the sequence -Asp-βAla-Gly-Ser-βAla-Gly-His-βAla-Gly- as catalysts in hydrolytic reactions

Boc-Asp-βAla-Gly-Ser-βAla-Gly-His-βAla-Gly-OEt, Boc-Asp-βAla-Gly-Ser-βAla-Gly-Ser-βAla-Gly-His-βAla-Gly-OH, cyclo(Asp-βAla-Gly-Ser-βAla-Gly-His-βAla-Gly) and poly(Asp-βAla-Gly-Ser-βAla-Gly-His-βAla-Gly) were synthesized as catalysts in hydrolytic reactions. Asp and Ser residues were protected with a benzyl group, but the His residue was not protected during the synthesis. The protected linear-nonapeptides were prepared by synthesis and subsequent fragment condensation of three kinds of tripeptide which have the sequences-Asp(OBzl)-βAla-Gly-,-Ser(Bzl)-βAla-Gly- and -His-βAla-Gly-, respectively. The protected cyclic-nonapeptide was obtained by cyclization of H-Asp(OBzl)-βAla-Gly-Ser(Bzl)-βAla-Gly-His-βAla-Gly-OH with DCC-HOBr and the subsequent purification by silica gel column chromatography. The protected poly-nonapeptide was prepared by polymerization of H-Asp(OBzl)-βAla-Gly-Ser(Bzl)-βAla-Gly-His-βAla-Gly-OH with DPPA. Deprotection was performed with catalytic hydrogenation for the protected linear- and cyclic-nonapeptides, and with methanesulphonic acid for the protected polynonapeptide, respectively, to give final products. Catalytic actions of the linear-, cyclic- and polypeptides for hydrolysis of p-nitrophenyl acetate are also reported briefly.     

Regulation of tubulin polypeptides and microtubule function: Rki1p interacts with the β-tubulin binding protein Rbl2p

Genetic analysis of microtubule functions in the yeast Saccharomyces cerevisiae suggests that cells manage the levels and activities of the tubulin polypeptides. These reactions may be involved in protein folding, formation of the heterodimer, and maintenance of the appropriate balance between α- and β-tubulin. One protein involved in these functions is Rbl2p, which forms a complex with β-tubulin. Here we describe the identification of a novel yeast gene, RKI1, that interacts genetically with RBL2. Deletion of rki1 causes conditional defects in microtubule assembly and cell growth. Rki1p can be isolated in a complex containing Rbl2p. The results support the existence of cellular mechanisms for regulating microtubule function through the tubulin polypeptides. Received: 8 August 1998 / Accepted: 13 September 1998     

Production of the human immunoglobulin γ1 chain constant region polypeptides in Escherichia coli

We have determined the nucleotide sequence of the constant region exons of the rearranged human immunoglobulin γ₁ chain gene cloned from a human plasma cell leukemia line, ARH-77. The amino acid sequence deduced from the nucleotide sequence revealed that the allotype of the ARH-77 γ₁ chain was Glm (−1, −2, 3).Recombinant plasmids were then constructed in order to express the human γ₁ chain constant region genes (the Fc region gene and the C_H2-C_H3 domains gene) in Escherichia coli. The human γ₁ chain constant region genes without introns were derived from the genomic gene using synthetic DNA fragments. E. coli carrying each expression plasmid produced antigenically active constant region polypeptides as soluble proteins. In the case of the E. coli-derived Fc region polypeptides, they were generated as monomeric forms in the cytoplasm.     

Surfactant bound polypeptides: 1. Conformation in solution and solid state of poly (γ-benzyl-l-glutamate) — Triton X-100

N-carboxyanhydride of γ-benzyl-l-glutamate was polymerized using the potassium salt of the non-ionic surfactant Triton X-100, octylphenoxypolyethoxyethanol, as the initiator. N.m.r. spectra revealed the presence of the initiator moiety in the polymer. The surfactant bound polypeptides with a degree of polymerization of 21 and 26 had excellent solubility in several non-aqueous solvents as compared to the homopolypeptide poly-γ-benzyl-l-glutamate (PBLG). The circular dichroic profiles of the polymers in the helicogenic solvents trifluoroethanol and trimethyl phosphate were helical. I.r. spectra of films of the polymers also indicated α-helical conformation for the peptide block. X-ray diffraction data, on the other hand, showed along with a spacing corresponding to the hexagonal packing of helices, a 22 Å spacing, indicative of a new kind of long range order not observed with the homopoly-γ-benzyl-l-glutamate. Again, the polymers formed with facility mesophases in various solvents at concentrations, unlike PBLG, as low as 5–8% (w/v).     

Tryptic peptide comparison of Ia antigen α and β polypeptides from the I-A Mutant B6.C-H-2 bm12 and its congenic parental strain B6

Previous studies of the B6.C-H-2 bm12 (bm12) strain have demonstrated the presence of a mutation localized to the I-A subregion of the mouse H-2 major histocompatibility complex. This mutation has been shown to be responsible for defects in Ir-gene function and in Ia and MLR determinants. A comparison of the molecular size of the bm12 mutant and the parental B6 Ia-antigen component polypeptides failed to demonstrate any differences in the and polypeptides. Thus, no major structural additions or deletions are present in the Ia and chain polypeptide or carbohydrate structure. A significant decrease in the amount of invariant (31K) polypeptide was, however, consistently observed in the bm12 Ia antigen preparations. Tryptic peptide comparisons of ¹⁴C B6 and ³H bm 12 and polypeptides demonstrated a limited number of peptide differences in the bm12 polypeptide but none in the bm12 polypeptide. The significance of these biochemical mutations and altered biological phenomena are discussed in relation to a model of the immunological interaction sites on Ia antigens.