Sequence-Specific Ni(II)-Dependent Peptide Bond Hydrolysis for Protein Engineering. Combinatorial Library Determination of Optimal Sequences

2010 ◽  
Vol 132 (10) ◽  
pp. 3355-3366 ◽  
Author(s):  
Artur Krȩżel ◽  
Edyta Kopera ◽  
Anna Maria Protas ◽  
Jarosław Poznański ◽  
Aleksandra Wysłouch-Cieszyńska ◽  
...  
Keyword(s):  
Protein Engineering ◽  
Combinatorial Library ◽  
Peptide Bond

Sequence-Specific Ni(II)-Dependent Peptide Bond Hydrolysis for Protein Engineering: Reaction Conditions and Molecular Mechanism

2010 ◽  
Vol 49 (14) ◽  
pp. 6636-6645 ◽  
Author(s):  
Edyta Kopera ◽  
Artur Krȩżel ◽  
Anna Maria Protas ◽  
Agnieszka Belczyk ◽  
Arkadiusz Bonna ◽  
...  
Keyword(s):  
Protein Engineering ◽  
Molecular Mechanism ◽  
Peptide Bond ◽  
Reaction Conditions

scholarly journals Quantitative determination of N-terminal amino acids of peptides and proteins with cobalt(III) chelates

1976 ◽  
Vol 153 (1) ◽  
pp. 137-138 ◽  
Author(s):  
K W Bentley
Keyword(s):  
Amino Acids ◽  
Quantitative Determination ◽  
Peptide Bond ◽  
Small Peptides ◽  
Acidic Hydrolysis ◽  
Terminal Amino ◽  
A Chain ◽  
Glucagon And Insulin

Quantitative N-terminal peptide-bond hydrolysis with the cis-beta-hydroxyaquo(triethylenetetramine) cobal (III) ion, i.e. β-[Co(trien)(OH)(OH2)]2+, is reported. The method has been demonstrated with 20 small peptides, a hexapeptide, bradykinin, insulin A chain (oxidized), glucagon and insulin. The procedure involves no acidic hydrolysis step and thus no destruction of labile amino acids.

Quantitative Determination of Single-Bead Metal Content from a Peptide Combinatorial Library

2006 ◽  
Vol 8 (6) ◽  
pp. 929-934 ◽  
Author(s):  
Jacqueline L. Stair ◽  
Brianna R. White ◽  
Adam Rowland ◽  
James A. Holcombe
Keyword(s):  
Quantitative Determination ◽  
Metal Content ◽  
Combinatorial Library ◽  
Single Bead

Substrate processing in intramembrane proteolysis by γ-secretase – the role of protein dynamics

2017 ◽  
Vol 398 (4) ◽  
pp. 441-453 ◽  
Author(s):  
Dieter Langosch ◽  
Harald Steiner
Keyword(s):  
Transmembrane Helix ◽  
Peptide Bond ◽  
Common Denominator ◽  
Transmembrane Helices ◽  
Intramembrane Proteases ◽  
Bond Scission ◽  
Catalytic Sites ◽  
Substrate Processing

Abstract Intramembrane proteases comprise a number of different membrane proteins with different types of catalytic sites. Their common denominator is cleavage within the plane of the membrane, which usually results in peptide bond scission within the transmembrane helices of their substrates. Despite recent progress in the determination of high-resolution structures, as illustrated here for the γ-secretase complex and its substrate C99, it is still unknown how these enzymes function and how they distinguish between substrates and non-substrates. In principle, substrate/non-substrate discrimination could occur at the level of substrate binding and/or cleavage. Focusing on the γ-secretase/C99 pair, we will discuss recent observations suggesting that global motions within a substrate transmembrane helix may be much more important for defining a substrate than local unraveling at cleavage sites.

scholarly journals Large facilities and the evolving ribosome, the cellular machine for genetic-code translation

2009 ◽  
Vol 6 (suppl_5) ◽  
Author(s):  
Ada Yonath
Keyword(s):  
Synchrotron Radiation ◽  
Genetic Code ◽  
Structural Information ◽  
Peptide Bond ◽  
Polymerase Activity ◽  
Resistance Mechanisms ◽  
Peptide Bond Formation ◽  
Peptide Bonds ◽  
Polypeptide Chains

Well-focused X-ray beams, generated by advanced synchrotron radiation facilities, yielded high-resolution diffraction data from crystals of ribosomes, the cellular nano-machines that translate the genetic code into proteins. These structures revealed the decoding mechanism, localized the mRNA path and the positions of the tRNA molecules in the ribosome and illuminated the interactions of the ribosome with initiation, release and recycling factors. They also showed that the ribosome is a ribozyme whose active site is situated within a universal symmetrical region that is embedded in the otherwise asymmetric ribosome structure. As this highly conserved region provides the machinery required for peptide bond formation and for ribosome polymerase activity, it may be the remnant of the proto-ribosome, a dimeric pre-biotic machine that formed peptide bonds and non-coded polypeptide chains. Synchrotron radiation also enabled the determination of structures of complexes of ribosomes with antibiotics targeting them, which revealed the principles allowing for their clinical use, revealed resistance mechanisms and showed the bases for discriminating pathogens from hosts, hence providing valuable structural information for antibiotics improvement.

Determination of Caspase Specificities Using a Peptide Combinatorial Library

2000 ◽  
pp. 100-110 ◽  
Author(s):  
Nancy A. Thornberry ◽  
Kevin T. Chapman ◽  
Donald W. Nicholson
Keyword(s):  
Combinatorial Library

scholarly journals Structural evidence for a proline-specific glycopeptide recognition domain in an O-glycopeptidase

Glycobiology ◽  
2020 ◽  
Author(s):  
Ilit Noach ◽  
Alisdair B Boraston
Keyword(s):  
Active Sites ◽  
Substrate Recognition ◽  
Peptide Bond ◽  
Multidomain Protein ◽  
Threonine Residue ◽  
Tyrosine Residues ◽  
Host Pathogen Interaction ◽  
A Site ◽  
Insight Into

Abstract The glycosylation of proteins is typically considered as a stabilizing modification, including resistance to proteolysis. A class of peptidases, referred to as glycopeptidases or O-glycopeptidases, circumvent the protective effect of glycans against proteolysis by accommodating the glycans in their active sites as specific features of substrate recognition. IMPa from Pseudomonas aeruginosa is such an O-glycopeptidase that cleaves the peptide bond immediately preceding a site of O-glycosylation, and through this glycoprotein-degrading function contributes to the host-pathogen interaction. IMPa, however, is a relatively large multidomain protein and how its additional domains may contribute to its function remains unknown. Here, through the determination of a crystal structure of IMPa in complex with an O-glycopeptide, we reveal that the N-terminal domain of IMPa, which is classified in Pfam as IMPa_N_2, is a proline recognition domain that also shows the properties of recognizing an O-linked glycan on the serine/threonine residue following the proline. The proline is bound in the center of a bowl formed by four functionally conserved aromatic amino acid side chains while the glycan wraps around one of the tyrosine residues in the bowl to make classic aromatic ring-carbohydrate CH-π interactions. This structural evidence provides unprecedented insight into how the ancillary domains in glycoprotein-specific peptidases can noncatalytically recognize specific glycosylated motifs that are common in mucin and mucin-like molecules.

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