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Incorporation of amino acids into soluble and membrane protein fractions of dystrophic hamsters.

ABSTRACT: The incorporation of labelled leucine was measured in protein fractions of muscle in intact control and dystrophic female hamsters and also in cell-free preparations obtained from these animals. The labelling of the soluble sarcoplasmic protein fraction, the microsomal protein fraction and the sarcolemma protein fraction was increased in the dystrophic hindleg muscle. The specific radioactivities of the sarcolemma protein fraction and other fractions were increased markedly relative to that of free leucine in the dystrophic muscle. In cell-free preparations where ribonuclease effects were avoided, the dystrophic muscle exhibited an increased synthesis of peptide bonds.

SUBMITTER: Nicholls DM

PROVIDER: S-EPMC1162099 | biostudies-other | 1980 Aug

REPOSITORIES: biostudies-other

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Synthesis and Protein Incorporation of Azido-Modified Unnatural Amino Acids.

Project description:Two new azidophenylalanine residues (3 and 4) have been synthesized and, in combination with 4-azido-L-phenylalanine (1) and 4-azidomethyl-L-phenylalanine (2), form a series of unnatural amino acids (UAAs) containing the azide vibrational reporter at varying distances from the aromatic ring of phenylalanine. These UAAs were designed to probe protein hydration with high spatial resolution by utilizing the large extinction coefficient and environmental sensitivity of the azide asymmetric stretch vibration. The sensitivity of the azide reporters was investigated in solvents that mimic distinct local protein environments. Three of the four azido-modified phenylalanine residues were successfully genetically incorporated into a surface site in superfolder green fluorescent protein (sfGFP) utilizing an engineered, orthogonal aminoacyl-tRNA synthetase in response to an amber codon with high efficiency and fidelity. SDS-PAGE and ESI-Q-TOF mass analysis verified the site-specific incorporation of these UAAs. The observed azide asymmetric stretch in the linear IR spectra of these UAAs incorporated into sfGFP indicated that the azide groups were hydrated in the protein.

| S-EPMC4603873 | biostudies-literature

Protein Synthesis with Ribosomes Selected for the Incorporation of ?-Amino Acids.

Project description:In an earlier study, ?³-puromycin was used for the selection of modified ribosomes, which were utilized for the incorporation of five different ?-amino acids into Escherichia coli dihydrofolate reductase (DHFR). The selected ribosomes were able to incorporate structurally disparate ?-amino acids into DHFR, in spite of the use of a single puromycin for the selection of the individual clones. In this study, we examine the extent to which the structure of the ?³-puromycin employed for ribosome selection influences the regio- and stereochemical preferences of the modified ribosomes during protein synthesis; the mechanistic probe was a single suppressor tRNA(CUA) activated with each of four methyl-?-alanine isomers (1-4). The modified ribosomes were found to incorporate each of the four isomeric methyl-?-alanines into DHFR but exhibited a preference for incorporation of 3(S)-methyl-?-alanine (?-mAla; 4), i.e., the isomer having the same regio- and stereochemistry as the O-methylated ?-tyrosine moiety of ?³-puromycin. Also conducted were a selection of clones that are responsive to ?²-puromycin and a demonstration of reversal of the regio- and stereochemical preferences of these clones during protein synthesis. These results were incorporated into a structural model of the modified regions of 23S rRNA, which included in silico prediction of a H-bonding network. Finally, it was demonstrated that incorporation of 3(S)-methyl-?-alanine (?-mAla; 4) into a short ?-helical region of the nucleic acid binding domain of hnRNP LL significantly stabilized the helix without affecting its DNA binding properties.

| S-EPMC4472090 | biostudies-literature

Protein synthesis in muscles from normal and dystrophic hamsters.

Project description:Homogenates of hindleg muscle were obtained from control and dystrophic male hamsters, 30 and 190 days of age, and were used to prepare the postmicrosomal pH5-supernatant fraction. The activity of this fraction in the incorporation of [14C]phenylalanyl-tRNA into peptides was increased in the dystrophic-muscle preparations. No such increase was found in brain or liver preparations from dystrophic hamsters. The increased capacity for aminoacyl-tRNA binding that was observed in preparations from dystrophic animals is discussed.

| S-EPMC1161018 | biostudies-other

Gait disturbances in dystrophic hamsters.

Project description:The delta-sarcoglycan-deficient hamster is an excellent model to study muscular dystrophy. Gait disturbances, important clinically, have not been described in this animal model. We applied ventral plane videography (DigiGait) to analyze gait in BIO TO-2 dystrophic and BIO F1B control hamsters walking on a transparent treadmill belt. Stride length was ?13% shorter (P < .05) in TO-2 hamsters at 9 months of age compared to F1B hamsters. Hindlimb propulsion duration, an indicator of muscle strength, was shorter in 9-month-old TO-2 (247 ± 8?ms) compared to F1B hamsters (272 ± 11?ms; P < .05). Braking duration, reflecting generation of ground reaction forces, was delayed in 9-month-old TO-2 (147 ± 6?ms) compared to F1B hamsters (126 ± 8?ms; P < .05). Hindpaw eversion, evidence of muscle weakness, was greater in 9-month-old TO-2 than in F1B hamsters (17.7 ± 1.2° versus 8.7 ± 1.6°; P < .05). Incline and decline walking aggravated gait disturbances in TO-2 hamsters at 3 months of age. Several gait deficits were apparent in TO-2 hamsters at 1 month of age. Quantitative gait analysis demonstrates that dystrophic TO-2 hamsters recapitulate functional aspects of human muscular dystrophy. Early detection of gait abnormalities in a convenient animal model may accelerate the development of therapies for muscular dystrophy.

| S-EPMC3035808 | biostudies-other

Incorporation of photo-amino acids in HeLa cells

Project description:In order to assess the efficiency of photo-labeling, total HeLa cell lysates treated with photo-amino acids were subjected to proteome analysis.

2017-04-10 | PXD005346 | Pride

Engineering Translation Components Improve Incorporation of Exotic Amino Acids.

Project description:Methods of genetic code manipulation, such as nonsense codon suppression and genetic code reprogramming, have enabled the incorporation of various nonproteinogenic amino acids into the peptide nascent chain. However, the incorporation efficiency of such amino acids largely varies depending on their structural characteristics. For instance, l-?-amino acids with artificial, bulky side chains are poorer substrates for ribosomal incorporation into the nascent peptide chain, mainly owing to the lower affinity of their aminoacyl-tRNA toward elongation factor-thermo unstable (EF-Tu). Phosphorylated Ser and Tyr are also poorer substrates for the same reason; engineering EF-Tu has turned out to be effective in improving their incorporation efficiencies. On the other hand, exotic amino acids such as d-amino acids and ?-amino acids are even poorer substrates owing to their low affinity to EF-Tu and poor compatibility to the ribosome active site. Moreover, their consecutive incorporation is extremely difficult. To solve these problems, the engineering of ribosomes and tRNAs has been executed, leading to successful but limited improvement of their incorporation efficiency. In this review, we comprehensively summarize recent attempts to engineer the translation systems, resulting in a significant improvement of the incorporation of exotic amino acids.

| S-EPMC6386890 | biostudies-literature

Cell-free protein synthesis from genomically recoded bacteria enables multisite incorporation of noncanonical amino acids.

Project description:Cell-free protein synthesis has emerged as a powerful approach for expanding the range of genetically encoded chemistry into proteins. Unfortunately, efforts to site-specifically incorporate multiple non-canonical amino acids into proteins using crude extract-based cell-free systems have been limited by release factor 1 competition. Here we address this limitation by establishing a bacterial cell-free protein synthesis platform based on genomically recoded Escherichia coli lacking release factor 1. This platform was developed by exploiting multiplex genome engineering to enhance extract performance by functionally inactivating negative effectors. Our most productive cell extracts enabled synthesis of 1,780?±?30?mg/L superfolder green fluorescent protein. Using an optimized platform, we demonstrated the ability to introduce 40 identical p-acetyl-L-phenylalanine residues site specifically into an elastin-like polypeptide with high accuracy of incorporation (???98%) and yield (96?±?3?mg/L). We expect this cell-free platform to facilitate fundamental understanding and enable manufacturing paradigms for proteins with new and diverse chemistries.

| S-EPMC5865108 | biostudies-literature

Incorporation of noncanonical amino acids into Rosetta and use in computational protein-peptide interface design.

Project description:Noncanonical amino acids (NCAAs) can be used in a variety of protein design contexts. For example, they can be used in place of the canonical amino acids (CAAs) to improve the biophysical properties of peptides that target protein interfaces. We describe the incorporation of 114 NCAAs into the protein-modeling suite Rosetta. We describe our methods for building backbone dependent rotamer libraries and the parameterization and construction of a scoring function that can be used to score NCAA containing peptides and proteins. We validate these additions to Rosetta and our NCAA-rotamer libraries by showing that we can improve the binding of a calpastatin derived peptides to calpain-1 by substituting NCAAs for native amino acids using Rosetta. Rosetta (executables and source), auxiliary scripts and code, and documentation can be found at (http://www.rosettacommons.org/).

| S-EPMC3303795 | biostudies-literature

Transpeptidase-mediated incorporation of D-amino acids into bacterial peptidoglycan.

Project description:The ?-lactams are the most important class of antibiotics in clinical use. Their lethal targets are the transpeptidase domains of penicillin binding proteins (PBPs), which catalyze the cross-linking of bacterial peptidoglycan (PG) during cell wall synthesis. The transpeptidation reaction occurs in two steps, the first being formation of a covalent enzyme intermediate and the second involving attack of an amine on this intermediate. Here we use defined PG substrates to dissect the individual steps catalyzed by a purified E. coli transpeptidase. We demonstrate that this transpeptidase accepts a set of structurally diverse D-amino acid substrates and incorporates them into PG fragments. These results provide new information on donor and acceptor requirements as well as a mechanistic basis for previous observations that noncanonical D-amino acids can be introduced into the bacterial cell wall.

| S-EPMC3172152 | biostudies-literature

The genetic incorporation of thirteen novel non-canonical amino acids.

Project description:Thirteen novel non-canonical amino acids were synthesized and tested for suppression of an amber codon using a mutant pyrrolysyl-tRNA synthetase-tRNA(Pyl)(CUA) pair. Suppression was observed with varied efficiencies. One non-canonical amino acid in particular contains an azide that can be applied for site-selective protein labeling.

| S-EPMC4011397 | biostudies-literature

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