scholarly journals Hydrolysis, polarity, and conformational impact of C-terminal partially fluorinated ethyl esters in peptide models

2017 ◽  
Vol 13 ◽  
pp. 2442-2457 ◽  
Author(s):  
Vladimir Kubyshkin ◽  
Nediljko Budisa
Keyword(s):  
Chemical Reactivity ◽  
Hydrolytic Stability ◽  
Ethyl Esters ◽  
Peptide Sequence ◽  
Molecular Scaffolds ◽  
Biologically Relevant ◽  
C Terminus ◽  
Ester Moiety ◽  
Peptide Models ◽  
Ph Range

Fluorinated moieties are highly valuable to chemists due to the sensitive NMR detectability of the 19F nucleus. Fluorination of molecular scaffolds can also selectively influence a molecule’s polarity, conformational preferences and chemical reactivity, properties that can be exploited for various chemical applications. A powerful route for incorporating fluorine atoms in biomolecules is last-stage fluorination of peptide scaffolds. One of these methods involves esterification of the C-terminus of peptides using a diazomethane species. Here, we provide an investigation of the physicochemical consequences of peptide esterification with partially fluorinated ethyl groups. Derivatives of N-acetylproline are used to model the effects of fluorination on the lipophilicity, hydrolytic stability and on conformational properties. The conformational impact of the 2,2-difluoromethyl ester on several neutral and charged oligopeptides was also investigated. Our results demonstrate that partially fluorinated esters undergo variable hydrolysis in biologically relevant buffers. The hydrolytic stability can be tailored over a broad pH range by varying the number of fluorine atoms in the ester moiety or by introducing adjacent charges in the peptide sequence.

scholarly journals Phosphorylation of the RB C-terminus regulates condensin II release from chromatin

2020 ◽  
pp. jbc.RA120.016511
Author(s):  
Seung J Kim ◽  
James I MacDonald ◽  
Frederick A. Dick
Keyword(s):  
Cell Cycle ◽  
Genome Stability ◽  
Cell Cycle Control ◽  
Cell Receptor ◽  
Receptor Activation ◽  
Biologically Relevant ◽  
C Terminus ◽  
Independent Functions ◽  
Phosphorylation Event ◽  
Rb Phosphorylation

The retinoblastoma tumour suppressor protein (RB) plays an important role in biological processes such as cell cycle control, DNA damage repair, epigenetic regulation, and genome stability. The canonical model of RB regulation is that cyclin-CDKs phosphorylate, and render RB inactive in late G1/S, promoting entry into S phase. Recently, mono-phosphorylated RB species were described to have distinct cell-cycle independent functions, suggesting that a phosphorylation code dictates diversity of RB function. However, a biologically relevant, functional role of RB phosphorylation at non-CDK sites has remained elusive. Here, we investigated S838/T841 dual phosphorylation, its upstream stimulus, and downstream functional output.  We found that mimicking T-cell receptor activation in Jurkat leukemia cells induced sequential activation of downstream kinases including p38 MAPK, and RB S838/T841 phosphorylation.  This signaling pathway disrupts RB and condensin II interaction with chromatin.  Using cells expressing a WT or S838A/T841A mutant RB fragment, we present evidence that deficiency for this phosphorylation event prevents condensin II release from chromatin.

scholarly journals Donor Atom Preference of Organoruthenium and Organorhodium Cations on the Interaction with Novel Ambidentate (N,N) and (O,O) Chelating Ligands in Aqueous Solution

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3586
Author(s):  
Sándor Nagy ◽  
András Ozsváth ◽  
Attila Cs. Bényei ◽  
Etelka Farkas ◽  
Péter Buglyó
Keyword(s):  
Aqueous Solution ◽  
Metal Ion ◽  
Platinum Group Metal ◽  
Molecular Structures ◽  
Chelating Ligands ◽  
Metal Ion Binding ◽  
Biologically Relevant ◽  
X Ray Crystallography ◽  
Ligand Ratio ◽  
Ph Range

Two novel, pyridinone-based chelating ligands containing separated (O,O) and (Namino,Nhet) chelating sets (Namino = secondary amine; Nhet = pyrrole N for H(L3) (1-(3-(((1H-pyrrole-2-yl)methyl)amino)propyl)-3-hydroxy-2-methylpyridin-4(1H)-one) or pyridine N for H(L5) (3-hydroxy-2-methyl-1-(3-((pyridin-2-ylmethyl)amino)propyl)pyridin-4(1H)-one)) were synthesized via reduction of the appropriate imines. Their proton dissociation processes were explored, and the molecular structures of two synthons were assessed by X-ray crystallography. These ambidentate chelating ligands are intended to develop Co(III)/PGM (PGM = platinum group metal) heterobimetallic multitargeted complexes with anticancer potential. To explore their metal ion binding ability, the interaction with Pd(II), [(η6-p-cym)Ru]2+ and [(η5-Cp*)Rh]2+ (p-cym = 1-methyl-4-isopropylbenzene, Cp* = pentamethyl-cyclopentadienyl anion) cations was studied in aqueous solution with the combined use of pH-potentiometry, NMR and HR ESI-MS. In general, organorhodium was found to form more labile complexes over ruthenium, while complexation of the (N,N) chelating set was slower than the processes of the pyridinone unit with (O,O) coordination. Formation of the organoruthenium complexes starts at lower pH (higher thermodynamic stabilities of the corresponding complexes) than for [(η5-Cp*)Rh]2+ but, due to the higher affinity of [η6-p-cym)Ru]2+ towards hydrolysis, the complexed ligands are capable of competing with hydroxide ion in a lesser extent than for the rhodium systems. As a result, under biologically relevant conditions, the rhodium binding effectivity of the ligands becomes comparable or even slightly higher than their effectivity towards ruthenium. Our results indicate that H(L3) is a less efficient (N,N) chelator for these metal ions than H(L5). Similarly, due to the relative effectivity of the (O,O) and (N,N) chelates at a 1:1 metal-ion-to-ligand ratio, H(L5) coordinates in a (N,N) manner to both cations in the whole pH range studied while, for H(L3), the complexation starts with (O,O) coordination. At a 2:1 metal-ion-to-ligand ratio, H(L3) cannot hinder the intensive hydrolysis of the second metal ion, although a small amount of 2:1 complex with [(η5-Cp*)Rh]2+ can also be detected.

Molecular cloning of a 47 kDa tissue-specific and differentiation-dependent urothelial cell surface glycoprotein

1993 ◽  
Vol 106 (1) ◽  
pp. 31-43 ◽  
Author(s):  
X.R. Wu ◽  
T.T. Sun
Keyword(s):  
Transmembrane Domain ◽  
Core Protein ◽  
Surface Glycoprotein ◽  
Peptide Sequence ◽  
Type I ◽  
Apical Surface ◽  
Bladder Epithelium ◽  
Cell Surface Glycoprotein ◽  
Signal Peptide Sequence ◽  
C Terminus

Despite the fact that bladder epithelium has many interesting biological features and is a frequent site of carcinoma formation, relatively little is known about its biochemical differentiation. We have shown recently that a 47 kDa glycoprotein, uroplakin III (UPIII), in conjunction with uroplakins I (27 kDa) and II (15 kDa), forms the asymmetric unit membrane (AUM)--a highly specialized biomembrane characteristic of the apical surface of bladder epithelium. Deglycosylation and cDNA sequencing revealed that UPIII contains up to 20 kDa of N-linked sugars attached to a core protein of 28.9 kDa. The presence of an N-terminal signal peptide sequence and a single transmembrane domain located near the C terminus, plus the N-terminal location of all the potential N-glycosylation sites, points to a type I (N-exo/C-cyto) configuration. Thus the mass of the extracellular domain (20 kDa plus up to 20 kDa of sugar) of UPIII greatly exceeds that of its intracellular domain (5 kDa). Such an asymmetrical mass distribution, a feature shared by the other two major uroplakins, provides a molecular explanation as to why the luminal leaflet of AUM is almost twice as thick as the cytoplasmic one. The fact that of the three major proteins of AUM only UPIII has a significant cytoplasmic domain suggests that this molecule may play an important role in AUM-cytoskeleton interaction in terminally differentiated urothelial cells.

Electrochemical characterization of Cu(II) complexes of brain-related tau peptides

2021 ◽  
Vol 99 (7) ◽  
pp. 628-636
Author(s):  
Camilla Golec ◽  
Jose O. Esteves-Villanueva ◽  
Sanela Martic
Keyword(s):  
Metal Ions ◽  
Tau Protein ◽  
Metal Ion ◽  
Differential Pulse ◽  
Redox Couple ◽  
Peptide Sequence ◽  
Binding Studies ◽  
Biologically Relevant ◽  
Redox Active ◽  
Competition Binding

Metal ion dyshomeostasis plays an important role in diseases, including neurodegeneration. Tau protein is a known neurodegeneration biomarker, but its interactions with biologically relevant metal ions, such as Cu(II), are not fully understood. Herein, the Cu(II) complexes of four tau R peptides, based on the tau repeat domains, R1, R2, R3, and R4, were characterized by electrochemical methods, including cyclic voltammetry, square-wave voltammetry, and differential pulse voltammetry in solution under aerobic conditions. The current and potential associated with Cu(II)/(I) redox couple was modulated as a function of R peptide sequence and concentration. All R peptides coordinated Cu(II) resulting in a dramatic decrease in the current associated with free Cu(II), and the appearance of a new redox couple due to metallo–peptide complex. The metallo–peptide complexes were characterized by the irreversible redox couple at more positive potentials and slower electron-transfer rates compared with the free Cu(II). The competition binding studies between R peptides with Cu(II) indicated that the strongest binding affinity was observed for the R3 peptide, which contained 2 His and 1 Cys residues. The formation of complexes was also evaluated as a function of peptide concentration and in the presence of competing Zn(II) ions. Data indicate that all metallo–peptides remain redox active pointing to the potential importance of the interactions between tau protein with metal ions in a biological setting.

scholarly journals Ln(iii)-complexes of a DOTA analogue with an ethylenediamine pendant arm as pH-responsive PARACEST contrast agents

2016 ◽  
Vol 45 (8) ◽  
pp. 3486-3496 ◽  
Author(s):  
T. Krchová ◽  
A. Gálisová ◽  
D. Jirák ◽  
P. Hermann ◽  
J. Kotek
Keyword(s):  
Contrast Agents ◽  
Magnetization Transfer ◽  
Magnetization Transfer Ratio ◽  
Ph Responsive ◽  
Resonance Imaging ◽  
Biologically Relevant ◽  
Pendant Arm ◽  
Ratio Approach ◽  
Magnetic Resonance Imaging Mri ◽  
Ph Range

New contrast agents useful for pH determination (in the biologically relevant pH range) by Magnetic Resonance Imaging (MRI) using magnetization transfer ratio approach are presented.

Kinetics and Mechanisms for the Isomerization of Internucleosidic 3'-O-P-CH2-5' and 3'-O-P-CH(OH)-5' Linkages to Their 2',5'-Counterparts

2006 ◽  
Vol 71 (6) ◽  
pp. 859-870 ◽  
Author(s):  
Tuomas Lönnberg ◽  
Šárka Králíková ◽  
Ivan Rosenberg ◽  
Harri Lönnberg
Keyword(s):  
Hydrogen Bond ◽  
Hydroxy Group ◽  
Phosphorus Atom ◽  
Hydrolytic Stability ◽  
Model Compounds ◽  
Hydroxide Ion ◽  
Wide Ph Range ◽  
Acid Catalyzed ◽  
Ph Range

Isomerization of internucleosidic 3'-O-P-CH2-5' and 3'-O-P-CH(OH)-5' phosphonate linkages to their 2',5'-counterparts has been studied over a wide pH-range. The model compounds employed are phosphonate analogs of adenylyl-(3',5')-adenosine and adenylyl-(2',5')-adenosine having either adenosine ((R,S)-1, (R,S)-2) or 5'-deoxyadenosine (3, 4) bonded to the phosphorus atom through the C5'-atom. For comparative purposes, the hydrolytic stability of C5'-hydroxyphosphonate analogs derived from 2'-deoxyadenosine ((R,S)-5) has also been studied. In addition to the expected acid-catalyzed (pH < 3) and pH-independent reactions (pH 3-9), the diastereomeric C5'-hydroxyphosphonate analogs ((R,S)-1, (R,S)-2), but not their deoxy counterparts (3, 4), have been observed to undergo a hydroxide-ion-catalyzed isomerization around pH 11 (90 °C). Evidently a hydrogen bond between the dianionic phosphorane and the C5'-hydroxy group stabilize the phosphorane to such an extent that isomerization via kinetically invisible protonation to monoanion becomes possible. The mechanisms of the isomerization reactions taking place under various conditions are discussed.

Farnesyl cysteine C-terminal methyltransferase activity is dependent upon the STE14 gene product in Saccharomyces cerevisiae

1990 ◽  
Vol 10 (10) ◽  
pp. 5071-5076
Author(s):  
C A Hrycyna ◽  
S Clarke
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Cysteine Residue ◽  
Peptide Sequence ◽  
Direct Result ◽  
Wild Type ◽  
Methyltransferase Activity ◽  
Ras Protein ◽  
Carboxyl Methyltransferase ◽  
C Terminus ◽  
Mutant Cells

Membrane extracts of sterile Saccharomyces cerevisiae strains containing the a-specific ste14 mutation lack a farnesyl cysteine C-terminal carboxyl methyltransferase activity that is present in wild-type a and alpha cells. Other a-specific sterile strains with ste6 and ste16 mutations also have wild-type levels of the farnesyl cysteine carboxyl methyltransferase activity. This enzyme activity, detected by using a synthetic peptide sequence based on the C-terminus of a ras protein, may be responsible not only for the essential methylation of the farnesyl cysteine residue of a mating factor, but also for the methylation of yeast RAS1 and RAS2 proteins and possibly other polypeptides with similar C-terminal structures. We demonstrate that the farnesylation of the cysteine residue in the peptide is required for the methyltransferase activity, suggesting that methyl esterification follows the lipidation reaction in the cell. To show that the loss of methyltransferase activity is a direct result of the ste14 mutation, we transformed ste14 mutant cells with a plasmid complementing the mating defect of this strain and found that active enzyme was produced. Finally, we demonstrated that a similar transformation of cells possessing the wild-type STE14 gene resulted in sixfold overproduction of the enzyme. Although more complicated possibilities cannot be ruled out, these results suggest that STE14 is a candidate for the structural gene for a methyltransferase involved in the formation of isoprenylated cysteine alpha-methyl ester C-terminal structures.

scholarly journals Molecular cloning of MADM: a catalytically active mammalian disintegrin-metalloprotease expressed in various cell types

1996 ◽  
Vol 317 (1) ◽  
pp. 45-50 ◽  
Author(s):  
Linda HOWARD ◽  
Xiaohong LU ◽  
Sally MITCHELL ◽  
Susan GRIFFITHS ◽  
Paul GLYNN
Keyword(s):  
Snake Venom ◽  
Transmembrane Helix ◽  
Cell Types ◽  
Bovine Brain ◽  
Peptide Sequence ◽  
Cdna Libraries ◽  
Northern Analysis ◽  
Cdna Clones ◽  
Mammalian Cell Lines ◽  
C Terminus

A peptide sequence of a metalloprotease purified from bovine brain [Chantry, Gregson and Glynn (1989) J. Biol. Chem. 264, 21603–21607] was used to design an oligonucleotide probe for screening a bovine brain cDNA library. A contig of the two overlapping cDNA clones that were isolated encoded a 748-amino-acid polypeptide with similarity to the disintegrin–metalloprotease precursor proteins of haemorrhagic snake venom. The bovine protein has been named MADM, for mammalian disintegrin–metalloprotease. The predicted mature protein has 534 amino acids arrayed as extracellular metalloprotease and disintegrin (potential integrin-binding) domains, a transmembrane helix and a basic/proline-rich cytoplasmic C-terminus. Highly conserved homologues of bovine MADM were found in cDNA libraries of rat brain and a human U937 histiocytic lymphoma cell line. A wide variety of mammalian cell lines expressed low levels of MADM mRNA (4.5 and 3.2 kb transcripts) and mature polypeptide (Mr 62000), as assessed by Northern analysis and Western blotting with an antiserum raised to a peptide within the disintegrin domain. MADM appears to be a rather distantly related member of the reprolysin protein family, which includes both the snake venom disintegrin–metalloproteases and a number of predicted cell-surface disintegrin-containing mammalian proteins.

scholarly journals Peptides as antigens. Importance of orientation.

1986 ◽  
Vol 164 (4) ◽  
pp. 1344-1349 ◽  
Author(s):  
T Dyrberg ◽  
M B Oldstone
Keyword(s):  
Peptide Sequence ◽  
Carrier Protein ◽  
Binding Pattern ◽  
Terminal Amino Acid ◽  
C Terminus ◽  
Terminal Amino ◽  
Peptide Characterization ◽  
A Site ◽  
Peptide Antibodies

Factors known to be important in producing protein-reactive peptide antibodies include the accessibility of the region from which the peptide sequence is derived, the hydrophilic-phobic character of the sequence, and the length of the peptide. The data presented here indicate that the orientation of the peptide coupled to a carrier protein also influences the binding pattern of peptide antibodies. An octapeptide, representing a sequence from the alpha chain of the human acetylcholine receptor, was coupled either through an N- or C-terminal cysteine-glycine-glycine linker to a carrier protein and used to immunize rabbits. The resulting antisera reacted at comparable titers to the uncoupled immunizing peptides, but did not crossreact with the identical but opposite-linked peptide. Characterization of the binding to other homologous peptides showed that immunization with the N-terminal-linked peptide induced antibodies reactive specifically with the C-terminal amino acid(s). Immunization with the C-linked peptide resulted in antibodies reactive with a site of the peptide near the C-terminus.

Peptide Selectivity of the Proton-Coupled Oligopeptide Transporter from Neisseria meningitidis

2016 ◽  
Vol 26 (5) ◽  
pp. 312-319 ◽  
Author(s):  
Neha Sharma ◽  
Nanda G. Aduri ◽  
Anna Iqbal ◽  
Bala K. Prabhala ◽  
Osman Mirza
Keyword(s):  
Neisseria Meningitidis ◽  
Peptide Sequence ◽  
Peptide Transport ◽  
Ligand Specificity ◽  
Oligopeptide Transporter ◽  
Gene Encoding ◽  
Peptide Residue ◽  
C Terminus ◽  
Substrate Peptide ◽  
Living Organisms

Peptide transport in living organisms is facilitated by either primary transport, hydrolysis of ATP, or secondary transport, cotransport of protons. In this study, we focused on investigating the ligand specificity of the <i>Neisseria meningitidis</i> proton-coupled oligopeptide transporter (NmPOT). It has been shown that the gene encoding this transporter is upregulated during infection. NmPOT conformed to the typical chain length preference as observed in prototypical transporters of this family. In contrast to prototypical transporters, it was unable to accommodate a positively charged peptide residue at the C-terminus position of the substrate peptide. Sequence analysis of the active site of NmPOT displayed a distinctive aromatic patch, which has not been observed in any other transporters from this family. This aromatic patch may be involved in providing NmPOT with its atypical preferences. This study provides important novel information towards understanding how these transporters recognize their substrates.

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