Detection and Location of N-Methyl-amino-acid Residues in N-Acyloligopeptide Methyl Esters by Mass Spectrometry

Nature ◽  
1968 ◽  
Vol 217 (5128) ◽  
pp. 547-548 ◽  
Author(s):  
B. C. DAS ◽  
S. D. GÉRO ◽  
E. LEDERER
Keyword(s):  
Mass Spectrometry ◽  
Amino Acid ◽  
Methyl Esters ◽  
Amino Acid Residues

scholarly journals Phosphonamidate analogues of dipeptides with carboxypeptidase A and β-lactamase-inhibitory activity: elucidation of the mechanism of β-lactamase inhibition by electrospray mass spectrometry

1996 ◽  
Vol 314 (2) ◽  
pp. 457-461 ◽  
Author(s):  
David J. PAYNE ◽  
John H. BATESON ◽  
David TOLSON ◽  
Brian GASSON ◽  
Teresa KHUSHI ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Amino Acid ◽  
Electrospray Mass Spectrometry ◽  
Methyl Esters ◽  
Amino Acid Residues ◽  
Carboxypeptidase A ◽  
Mechanism Of Inhibition ◽  
Primary Amino ◽  
Active Nature ◽  
Proline Derivatives

A series of phosphonamidate compounds with different P1´ amino acid residues have been shown to be irreversible inactivators of the serine β-lactamase from Enterobacter cloacae P99. The efficiency of inhibition (based on k2/K values) of P99 by these derivatives, ordered in decreasing potency, is: β-phenyl-β-Ala> L-Phe> β-Ala> Gly>D-Phe>D-Pro> D-thiazolidine. The D- and L-Phe compounds also inhibit carboxypeptidase A. The proline and thiazolidine derivatives were phosphonamidate methyl esters, whereas the others were salts of diacids. Electrospray mass spectrometry showed that equimolar mixtures of the P99 enzyme with each of the following derivatives, Gly, D-Phe, L-Phe, β-Ala and β-phenyl-β-Ala, effected efficient adduct formation (70–95% of enzyme modified), illustrating the particularly active nature of some of these compounds. All the primary amino acid derivatives gave a similar mass increment, which suggests the displacement of the variable P1´ part of the molecule. This observation provides evidence that the compounds phosphonylate the active-site serine, with the phosphonamidate bond as the scissile bond and the amino acid as the leaving group. The thiazolidine derivative (phosphonamidate methyl ester) also appeared to work by the same mechanism. The comparable proline derivatives caused lower than expected mass shifts of 227–229, and therefore it is proposed that with these compounds both the amino acid and the phosphonamidate ester methoxy group were displaced at the phosphorus atom during the inhibition process. Therefore, electrospray mass spectrometry has provided both a measure of potency and a rationale for the mechanism of inhibition of P99 by these compounds.

Statistical Force-Field for Structural Modeling Using Chemical Cross-Linking/mass Spectrometry Distance Constraints

2018 ◽  
Author(s):  
Allan J. R. Ferrari ◽  
Fabio C. Gozzo ◽  
Leandro Martinez
Keyword(s):  
Mass Spectrometry ◽  
Amino Acid ◽  
Force Field ◽  
Protein Structures ◽  
Protein Structure Determination ◽  
Structural Modeling ◽  
Cross Linking ◽  
Amino Acid Residues ◽  
Distance Constraints ◽  
Chemical Cross Linking

<div><p>Chemical cross-linking/Mass Spectrometry (XLMS) is an experimental method to obtain distance constraints between amino acid residues, which can be applied to structural modeling of tertiary and quaternary biomolecular structures. These constraints provide, in principle, only upper limits to the distance between amino acid residues along the surface of the biomolecule. In practice, attempts to use of XLMS constraints for tertiary protein structure determination have not been widely successful. This indicates the need of specifically designed strategies for the representation of these constraints within modeling algorithms. Here, a force-field designed to represent XLMS-derived constraints is proposed. The potential energy functions are obtained by computing, in the database of known protein structures, the probability of satisfaction of a topological cross-linking distance as a function of the Euclidean distance between amino acid residues. The force-field can be easily incorporated into current modeling methods and software. In this work, the force-field was implemented within the Rosetta ab initio relax protocol. We show a significant improvement in the quality of the models obtained relative to current strategies for constraint representation. This force-field contributes to the long-desired goal of obtaining the tertiary structures of proteins using XLMS data. Force-field parameters and usage instructions are freely available at http://m3g.iqm.unicamp.br/topolink/xlff <br></p></div><p></p><p></p>

Development of a derivatisation method for the analysis of aldehyde modified amino acid residues in proteins by Fourier transform mass spectrometry

2009 ◽  
Vol 633 (2) ◽  
pp. 216-222 ◽  
Author(s):  
Mostafa Pournamdari ◽  
Ahmed Saadi ◽  
Elizabeth Ellis ◽  
Ruth Andrew ◽  
Brian Walker ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Fourier Transform ◽  
Amino Acid ◽  
Fourier Transform Mass Spectrometry ◽  
Amino Acid Residues

New Antibiotic Uperin Peptides From the Dorsal Glands of the Australian Toadlet Uperoleia mjobergii

1996 ◽  
Vol 49 (12) ◽  
pp. 1325 ◽  
Author(s):  
AM Bradford ◽  
JH Bowie ◽  
MJ Tyler ◽  
JC Wallace
Keyword(s):  
Mass Spectrometry ◽  
Amino Acid ◽  
Related Species ◽  
Antibiotic Activity ◽  
Amino Acid Sequences ◽  
The Other ◽  
Cationic Peptides ◽  
Amino Acid Residues ◽  
Skin Glands ◽  
Edman Sequencing

The dorsal glandular extract of the toadlet Uperoleia mjobergii contains more than 20 peptides. We report the amino acid sequences of the seven major peptides: these were determined by a combination of mass spectrometry and automated Edman sequencing. Three of these peptides have 19 amino acid residues and belong to the uperin 2 group of peptides [e.g. uperin 2.6, Gly Ile Leu Asp Ile Ala Lys Lys Leu Val Gly Gly Ile Arg Asn Val Leu Gly Ile (OH)], while the other four have 17 residues and are classified as uperins 3 [e.g. Uperin 3.4, Gly Val Gly Asp Leu Ile Arg Lys Ala Val Ala Ala Ile Lys Asn Ile Val (NH2)]. Several of these cationic peptides have been synthesized in order for bioassays to be carried out: they show significant antibiotic activity against a range of Gram-positive microorganisms. A major skin peptide from the related species Uperoleia inundata is a powerful neuropeptide named uperin 1.1 ([Ala2] uperolein ): no corresponding neuropeptide is detected in the skin glands of Uperoleia mjobergii.

scholarly journals E. coli GyrA Tower Domain Interacts with QnrB1 Loop B and Plays an Important Role in QnrB1 Protection from Quinolone Inhibition

2021 ◽  
Author(s):  
Chunhui Chen ◽  
Yin Wang ◽  
Hidemasa Nakaminami ◽  
Eu Suk Kim ◽  
George A. Jacoby ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Amino Acids ◽  
Amino Acid ◽  
Dna Gyrase ◽  
Amino Acid Residues ◽  
Site Specific ◽  
E Coli ◽  
Small Deletion ◽  
Interaction Sites ◽  
Repeat Proteins

The Qnr pentapeptide repeat proteins interact with DNA gyrase and protect it from quinolone inhibition. The two external loops, particularly the larger loop B, of Qnr proteins are essential for quinolone protection of DNA gyrase. The specific QnrB1 interaction sites on DNA gyrase are not known. In this study, we investigated the interaction between GyrA and QnrB1 using site-specific photo crosslinking of QnrB1 loop B combined with mass spectrometry. We found that amino acid residues 286-298 on the Tower domain of GyrA interact with QnrB1 and play a key role in QnrB1 protection of gyrase from quinolone inhibition. Alanine replacement of arginine at residue 293 and a small deletion of amino acids 286-289 of GyrA resulted in a decrease in the QnrB1-mediated increase in quinolone MICs and also abolished the QnrB1 protection of purified DNA gyrase from ciprofloxacin inhibition.

Statistical Force-Field for Structural Modeling Using Chemical Cross-Linking/mass Spectrometry Distance Constraints

2018 ◽  
Author(s):  
Allan J. R. Ferrari ◽  
Fabio C. Gozzo ◽  
Leandro Martinez
Keyword(s):  
Mass Spectrometry ◽  
Amino Acid ◽  
Force Field ◽  
Protein Structures ◽  
Protein Structure Determination ◽  
Structural Modeling ◽  
Cross Linking ◽  
Amino Acid Residues ◽  
Distance Constraints ◽  
Chemical Cross Linking

<div><p>Chemical cross-linking/Mass Spectrometry (XLMS) is an experimental method to obtain distance constraints between amino acid residues, which can be applied to structural modeling of tertiary and quaternary biomolecular structures. These constraints provide, in principle, only upper limits to the distance between amino acid residues along the surface of the biomolecule. In practice, attempts to use of XLMS constraints for tertiary protein structure determination have not been widely successful. This indicates the need of specifically designed strategies for the representation of these constraints within modeling algorithms. Here, a force-field designed to represent XLMS-derived constraints is proposed. The potential energy functions are obtained by computing, in the database of known protein structures, the probability of satisfaction of a topological cross-linking distance as a function of the Euclidean distance between amino acid residues. The force-field can be easily incorporated into current modeling methods and software. In this work, the force-field was implemented within the Rosetta ab initio relax protocol. We show a significant improvement in the quality of the models obtained relative to current strategies for constraint representation. This force-field contributes to the long-desired goal of obtaining the tertiary structures of proteins using XLMS data. Force-field parameters and usage instructions are freely available at http://m3g.iqm.unicamp.br/topolink/xlff <br></p></div><p></p><p></p>

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