scholarly journals The ligand binding mechanism to purine nucleoside phosphorylase elucidated via molecular dynamics and machine learning

2015 ◽  
Vol 6 (1) ◽  
Author(s):  
Sergio Decherchi ◽  
Anna Berteotti ◽  
Giovanni Bottegoni ◽  
Walter Rocchia ◽  
Andrea Cavalli
Keyword(s):  
Machine Learning ◽  
Molecular Dynamics ◽  
Ligand Binding ◽  
Purine Nucleoside Phosphorylase ◽  
Purine Nucleoside ◽  
Binding Mechanism ◽  
Nucleoside Phosphorylase

scholarly journals Crystal structure and molecular dynamics studies of purine nucleoside phosphorylase from Mycobacterium tuberculosis associated with acyclovir

Biochimie ◽  
2012 ◽  
Vol 94 (1) ◽  
pp. 155-165 ◽  
Author(s):  
Rafael A. Caceres ◽  
Luís F.S.M. Timmers ◽  
Rodrigo G. Ducati ◽  
Diego O.N. da Silva ◽  
Luiz A. Basso ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Mycobacterium Tuberculosis ◽  
Purine Nucleoside Phosphorylase ◽  
Purine Nucleoside ◽  
Nucleoside Phosphorylase

scholarly journals Design of an adenosine phosphorylase by active-site modification of murine purine nucleoside phosphorylase: Enzyme kinetics and molecular dynamics simulation of Asn-243 and Lys-244 substitutions of purine nucleoside phosphorylase

1999 ◽  
Vol 344 (2) ◽  
pp. 585-592 ◽  
Author(s):  
Jason T. MAYNES ◽  
W.-S. YAM ◽  
Jack P. JENUTH ◽  
R. Gang YUAN ◽  
Steven A. LITSTER ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Purine Nucleoside Phosphorylase ◽  
Fold Increase ◽  
Purine Nucleoside ◽  
Dynamics Simulation ◽  
Amino Group ◽  
Wild Type ◽  
Nucleoside Phosphorylase ◽  
Purine Ring

Our objective was to alter the substrate specificity of purine nucleoside phosphorylase such that it would catalyse the phosphorolysis of 6-aminopurine nucleosides. We modified both Asn-243 and Lys-244 in order to promote the acceptance of the C6-amino group of adenosine. The Asn-243-Asp substitution resulted in an 8-fold increase in Km for inosine from 58 to 484 μM and a 1000-fold decrease in kcat/Km. The Asn-243-Asp construct catalysed the phosphorolysis of adenosine with a Km of 45 μM and a kcat/Km 8-fold that with inosine. The Lys-244-Gln construct showed only marginal reduction in kcat/Km, 83% of wild type, but had no activity with adenosine. The Asn-243-Asp;Lys-244-Gln construct had a 14-fold increase in Km with inosine and 7-fold decrease in kcat/Km as compared to wild type. This double substitution catalysed the phosphorolysis of adenosine with a Km of 42 μM and a kcat/Km twice that of the single Asn-243-Asp substitution. Molecular dynamics simulation of the engineered proteins with adenine as substrate revealed favourable hydrogen bond distances between N7 of the purine ring and the Asp-243 carboxylate at 2.93 and 2.88 Å, for Asn-243-Asp and the Asn-243-Asp;Lys-244-Gln constructs respectively. Simulation also supported a favourable hydrogen bond distance between the purine C6-amino group and Asp-243 at 2.83 and 2.88 Å for each construct respectively. The Asn-243-Thr substitution did not yield activity with adenosine and simulation gave unfavourable hydrogen bond distances between Thr-243 and both the C6-amino group and N7 of the purine ring. The substitutions were not in the region of phosphate binding and the apparent S0.5 for phosphate with wild type and the Asn-243-Asp enzymes were 1.35±0.01 and 1.84±0.06 mM, respectively. Both proteins exhibited positive co-operativity with phosphate giving Hill coefficients of 7.9 and 3.8 respectively.

scholarly journals Single tryptophan Y160W mutant of homooligomeric E. coli purine nucleoside phosphorylase implies that dimers forming the hexamer are functionally not equivalent

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Marta Narczyk ◽  
Łukasz Mioduszewski ◽  
Aleksandra Oksiejuk ◽  
Maria Winiewska-Szajewska ◽  
Beata Wielgus-Kutrowska ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Binding Site ◽  
Active Sites ◽  
Purine Nucleoside Phosphorylase ◽  
Purine Nucleoside ◽  
Kinetic Properties ◽  
Nucleoside Phosphorylase ◽  
E Coli ◽  
Site Model ◽  
Open Conformation

AbstractE. coli purine nucleoside phosphorylase is a homohexamer, which structure, in the apo form, can be described as a trimer of dimers. Earlier studies suggested that ligand binding and kinetic properties are well described by two binding constants and two sets of kinetic constants. However, most of the crystal structures of this enzyme complexes with ligands do not hold the three-fold symmetry, but only two-fold symmetry, as one of the three dimers is different (both active sites in the open conformation) from the other two (one active site in the open and one in the closed conformation). Our recent detailed studies conducted over broad ligand concentration range suggest that protein–ligand complex formation in solution actually deviates from the two-binding-site model. To reveal the details of interactions present in the hexameric molecule we have engineered a single tryptophan Y160W mutant, responding with substantial intrinsic fluorescence change upon ligand binding. By observing various physical properties of the protein and its various complexes with substrate and substrate analogues we have shown that indeed three-binding-site model is necessary to properly describe binding of ligands by both the wild type enzyme and the Y160W mutant. Thus we have pointed out that a symmetrical dimer with both active sites in the open conformation is not forced to adopt this conformation by interactions in the crystal, but most probably the dimers forming the hexamer in solution are not equivalent as well. This, in turn, implies that an allosteric cooperation occurs not only within a dimer, but also among all three dimers forming a hexameric molecule.

Molecular dynamics studies of a hexameric purine nucleoside phosphorylase

2009 ◽  
Vol 16 (3) ◽  
pp. 543-550 ◽  
Author(s):  
Fernando Berton Zanchi ◽  
Rafael Andrade Caceres ◽  
Rodrigo Guerino Stabeli ◽  
Walter Filgueira de Azevedo
Keyword(s):  
Molecular Dynamics ◽  
Purine Nucleoside Phosphorylase ◽  
Purine Nucleoside ◽  
Nucleoside Phosphorylase

scholarly journals Crystal structure and molecular dynamics studies of human purine nucleoside phosphorylase complexed with 7-deazaguanine

2010 ◽  
Vol 169 (3) ◽  
pp. 379-388 ◽  
Author(s):  
Rafael Andrade Caceres ◽  
Luis Fernando Saraiva Macedo Timmers ◽  
Ivani Pauli ◽  
Lisandra Marques Gava ◽  
Rodrigo Gay Ducati ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Purine Nucleoside Phosphorylase ◽  
Purine Nucleoside ◽  
Nucleoside Phosphorylase
Sign in / Sign up

Export Citation Format

Share Document