Binding properties of cucurbit[7]uril to neutral and protonated amino acids: A theoretical study

2020 ◽  
Author(s):  
Fenfen Ma ◽  
Xiaoyan Zheng ◽  
Jing Xie ◽  
Zesheng Li
Keyword(s):  
Amino Acids ◽  
Theoretical Study ◽  
Binding Properties

scholarly journals Human Rev1 relies on insert-2 to promote selective binding and accurate replication of stabilized G-quadruplex motifs

2021 ◽  
Author(s):  
Amit Ketkar ◽  
Lane Smith ◽  
Callie Johnson ◽  
Alyssa Richey ◽  
Makayla Berry ◽  
...  
Keyword(s):  
Amino Acids ◽  
Mutation Frequency ◽  
Control Sequence ◽  
Wild Type ◽  
Binding Properties ◽  
High Affinity ◽  
G4 Dna ◽  
G Quadruplex ◽  
Forward Mutagenesis

Abstract We previously reported that human Rev1 (hRev1) bound to a parallel-stranded G-quadruplex (G4) from the c-MYC promoter with high affinity. We have extended those results to include other G4 motifs, finding that hRev1 exhibited stronger affinity for parallel-stranded G4 than either anti-parallel or hybrid folds. Amino acids in the αE helix of insert-2 were identified as being important for G4 binding. Mutating E466 and Y470 to alanine selectively perturbed G4 binding affinity. The E466K mutant restored wild-type G4 binding properties. Using a forward mutagenesis assay, we discovered that loss of hRev1 increased G4 mutation frequency >200-fold compared to the control sequence. Base substitutions and deletions occurred around and within the G4 motif. Pyridostatin (PDS) exacerbated this effect, as the mutation frequency increased >700-fold over control and deletions upstream of the G4 site more than doubled. Mutagenic replication of G4 DNA (±PDS) was partially rescued by wild-type and E466K hRev1. The E466A or Y470A mutants failed to suppress the PDS-induced increase in G4 mutation frequency. These findings have implications for the role of insert-2, a motif conserved in vertebrates but not yeast or plants, in Rev1-mediated suppression of mutagenesis during G4 replication.

Metal-Binding Properties of Glycated Proteins and Amino Acids

2005 ◽  
pp. 429 ◽  
Author(s):  
Valeri V Mossine ◽  
Milton S Feather
Keyword(s):  
Amino Acids ◽  
Metal Binding ◽  
Binding Properties ◽  
Glycated Proteins

Synthesis, Conformational Studies and Binding Properties of Acyclic Receptors for N-Protected Amino Acids and Dipeptides

2001 ◽  
Vol 2001 (24) ◽  
pp. 4625 ◽  
Author(s):  
Enrique Botana ◽  
Sandrine Ongeri ◽  
Rosa Arienzo ◽  
Mariangela Demarcus ◽  
Jeremy G. Frey ◽  
...  
Keyword(s):  
Amino Acids ◽  
Binding Properties ◽  
Conformational Studies

scholarly journals Effect of N- and C-Terminal Amino Acids on the Interfacial Binding Properties of Phospholipase D from Vibrio parahaemolyticus

2018 ◽  
Vol 19 (8) ◽  
pp. 2447
Author(s):  
Fanghua Wang ◽  
Ruixia Wei ◽  
Abdelkarim Abousalham ◽  
Wuchong Chen ◽  
Bo Yang ◽  
...  
Keyword(s):  
Amino Acids ◽  
Secondary Structure ◽  
Phospholipase D ◽  
Vibrio Parahaemolyticus ◽  
Terminal Segment ◽  
Amino Acid Sequences ◽  
Loop Structure ◽  
Binding Properties ◽  
Phospholipid Monolayers ◽  
Terminal Amino

The effects of N-terminal (1–34 amino acids) and C-terminal (434–487 amino acids) amino acid sequences on the interfacial binding properties of Phospholipase D from Vibrio parahaemolyticus (VpPLD) were characterized by using monomolecular film technology. Online tools allowed the prediction of the secondary structure of the target N- and C-terminal VpPLD sequences. Various truncated forms of VpPLD with different N- or C-terminal deletions were designed, based on their secondary structure, and their membrane binding properties were examined. The analysis of the maximum insertion pressure (MIP) and synergy factor “a” indicated that the loop structure (1–25 amino acids) in the N-terminal segment of VpPLD had a positive effect on the binding of VpPLD to phospholipid monolayers, especially to 1,2-dimyristoyl-sn-glycero-3-phosphoserine and 1,2-dimyristoyl-sn-glycero-3-phosphocholine. The deletion affecting the N-terminus loop structure caused a significant decrease of the MIP and synergy factor a of the protein for these phospholipid monolayers. Conversely, the deletion of the helix structure (26–34 amino acids) basically had no influence on the binding of VpPLD to phospholipid monolayers. The deletion of the C-terminal amino acids 434–487 did not significantly change the binding selectivity of VpPLD for the various phospholipid monolayer tested here. However, a significant increase of the MIP value for all the phospholipid monolayers strongly indicated that the three-strand segment (434–469 amino acids) had a great negative effect on the interfacial binding to these phospholipid monolayers. The deletion of this peptide caused a significantly greater insertion of the protein into the phospholipid monolayers examined. The present study provides detailed information on the effect of the N- and C-terminal segments of VpPLD on the interfacial binding properties of the enzyme and improves our understanding of the interactions between this enzyme and cell membranes.

scholarly journals The mechanism of action of dd-peptidases: the role of Threonine-299 and -301 in the Streptomyces R61 dd-peptidase

1994 ◽  
Vol 301 (2) ◽  
pp. 477-483 ◽  
Author(s):  
J M Wilkin ◽  
A Dubus ◽  
B Joris ◽  
J M Frère
Keyword(s):  
Amino Acids ◽  
Active Site ◽  
Site Directed Mutagenesis ◽  
Directed Mutagenesis ◽  
Peptide Substrate ◽  
Binding Properties ◽  
Beta Lactamases ◽  
Penicillin Binding Proteins ◽  
Active Site Cavity

The side chains of residues Thr299 and Thr301 in the Streptomyces R61 DD-peptidase have been modified by site-directed mutagenesis. These amino acids are part of a beta-strand which forms a wall of the active-site cavity. Thr299 corresponds to the second residue of the Lys-Thr(Ser)-Gly triad, highly conserved in active-site beta-lactamases and penicillin-binding proteins (PBPs). Modification of Thr301 resulted only in minor alterations of the catalytic and penicillin-binding properties of the enzyme. No selective decrease of the rate of acylation was observed for any particular class of compounds. By contrast, the loss of the hydroxy group of the residue in position 299 yielded a seriously impaired enzyme. The rates of inactivation by penicillins were decreased 30-50-fold, whereas the reactions with cephalosporins were even more affected. The efficiency of hydrolysis against the peptide substrate was also seriously decreased. More surprisingly, the mutant was completely unable to catalyse transpeptidation reactions. The conservation of an hydroxylated residue in this position in PBPs is thus easily explained by these results.

Synthesis and Peptide Binding Properties of Methoxypyrrole Amino Acids (MOPAS)

2004 ◽  
Vol 6 (9) ◽  
pp. 1349-1352 ◽  
Author(s):  
Christoph Bonauer ◽  
Manfred Zabel ◽  
Burkhard König
Keyword(s):  
Amino Acids ◽  
Peptide Binding ◽  
Binding Properties

Theoretical study of host–guest interactions in complexes of cucurbit[7]uril with protonated amino acids

2016 ◽  
Vol 28 (9-10) ◽  
pp. 857-863 ◽  
Author(s):  
Irina V. Mirzaeva ◽  
Ekaterina A. Kovalenko ◽  
Vladimir P. Fedin
Keyword(s):  
Amino Acids ◽  
Theoretical Study

AMELIORATING THE FORMATION OF FULLERENE COMPLEXES WITH AMINO ACIDS: A THEORETICAL STUDY

2011 ◽  
Vol 25 (32) ◽  
pp. 4667-4678 ◽  
Author(s):  
ABRAHAM F. JALBOUT
Keyword(s):  
Amino Acids ◽  
Theoretical Study ◽  
Biological Systems ◽  
Band Gaps ◽  
Dissociation Energies ◽  
Fullerene Complexes ◽  
Homo Lumo

The present study is geared towards investigating methods to increase the tendency of fullerene structures to aggregate with biological systems. To accomplish this task, the encapsulation of metals inside a fullerene structure was performed. The calculations performed demonstrate that the Ca @ C 60 structure leads to stronger interactions with amino acids at the DFT-BLYP/DND level of theory. Correlations of the dissociation energies, HOMO/LUMO band gaps and hardness are discussed.

Radical-Cationic Gaseous Amino Acids:  A Theoretical Study

2007 ◽  
Vol 111 (32) ◽  
pp. 7906-7914 ◽  
Author(s):  
Kailee N. Sutherland ◽  
Philippe C. Mineau ◽  
Galina Orlova
Keyword(s):  
Amino Acids ◽  
Theoretical Study
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