Online citations, reference lists, and bibliographies.
← Back to Search

Structural Explanation For The Tunable Substrate Specificity Of An E. Coli Nucleoside Hydrolase: Insights From Molecular Dynamics Simulations

Stefan A. P. Lenz, S. Wetmore
Published 2018 · Chemistry, Medicine, Computer Science

Save to my Library
Download PDF
Analyze on Scholarcy
Share
Parasitic protozoa rely on nucleoside hydrolases that play key roles in the purine salvage pathway by catalyzing the hydrolytic cleavage of the N-glycosidic bond that connects nucleobases to ribose sugars. Cytidine–uridine nucleoside hydrolase (CU–NH) is generally specific toward pyrimidine nucleosides; however, previous work has shown that replacing two active site residues with Tyr, specifically the Thr223Tyr and Gln227Tyr mutations, allows CU–NH to process inosine. The current study uses molecular dynamics (MD) simulations to gain atomic-level insight into the activity of wild-type and mutant E. coli CU–NH toward inosine. By examining systems that differ in the identity and protonation states of active site catalytic residues, key enzyme-substrate interactions that dictate the substrate specificity of CU–NH are identified. Regardless of the wild-type or mutant CU–NH considered, our calculations suggest that inosine binding is facilitated by interactions of the ribose moiety with active site residues and Ca2+, and π-interactions between two His residues (His82 and His239) and the nucleobase. However, the lack of observed activity toward inosine for wild-type CU–NH is explained by no residue being correctly aligned to stabilize the departing nucleobase. In contrast, a hydrogen-bonding network between hypoxanthine and a newly identified general acid (Asp15) is present when the two Tyr mutations are engineered into the active site. Investigation of the single CU–NH mutants reveals that this hydrogen-bonding network is only maintained when both Tyr mutations are present due to a π-interaction between the residues. These results rationalize previous experiments that show the single Tyr mutants are unable to efficiently hydrolyze inosine and explain how the Tyr residues work synergistically in the double mutant to stabilize the nucleobase leaving group during hydrolysis. Overall, our simulations provide a structural explanation for the substrate specificity of nucleoside hydrolases, which may be used to rationally develop new treatments for kinetoplastid diseases.Graphical Abstract
This paper references
10.1016/S0163-7258(03)00071-8
Potential chemotherapeutic targets in the purine metabolism of parasites.
M. H. Kouni (2003)
10.1080/07391102.2012.674293
Molecular modeling studies on nucleoside hydrolase from the biological warfare agent Brucella suis
D. T. Mancini (2012)
10.1016/J.TMAID.2006.09.004
Cutaneous leishmaniasis treatment.
P. Minodier (2007)
10.1016/J.BMCL.2007.02.017
1,2,3-Triazolylalkylribitol derivatives as nucleoside hydrolase inhibitors.
A. Goeminne (2007)
10.1016/j.cpc.2012.09.022
SPFP: Speed without compromise - A mixed precision model for GPU accelerated molecular dynamics simulations
S. Grand (2013)
10.1021/ja207181c
Modeling the chemical step utilized by human alkyladenine DNA glycosylase: a concerted mechanism AIDS in selectively excising damaged purines.
Lesley R. Rutledge (2011)
10.1093/nar/gks375
H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations
Ramu Anandakrishnan (2012)
10.1371/journal.pntd.0005074
One Health Interactions of Chagas Disease Vectors, Canid Hosts, and Human Residents along the Texas-Mexico Border
M. Garcia (2016)
10.1021/bi702448s
Structural basis for substrate specificity in group I nucleoside hydrolases.
E. Iovane (2008)
10.1093/nar/gku269
DNA–protein π-interactions in nature: abundance, structure, composition and strength of contacts between aromatic amino acids and DNA nucleobases or deoxyribose sugar
K. A. Wilson (2014)
10.1021/BI973012E
Trypanosomal nucleoside hydrolase. A novel mechanism from the structure with a transition-state inhibitor.
M. Degano (1998)
10.1016/S1474-4422(12)70296-X
Clinical features, diagnosis, and treatment of human African trypanosomiasis (sleeping sickness)
P. Kennedy (2013)
10.1016/j.bmc.2008.05.056
N-Arylmethyl substituted iminoribitol derivatives as inhibitors of a purine specific nucleoside hydrolase.
A. Goeminne (2008)
10.1016/J.SBI.2003.10.002
Catalysis by nucleoside hydrolases.
W. Versées (2003)
10.1371/journal.pntd.0003981
Historical Perspectives on the Epidemiology of Human Chagas Disease in Texas and Recommendations for Enhanced Understanding of Clinical Chagas Disease in the Southern United States
M. Garcia (2015)
to 1 . 7 angstrom of the Escherichia coli pyrimidine nucleoside hydrolase YeiK , a novel candidate for cancer gene therapy
DN Gopaul (1996)
10.1021/BI047394H
Computational study of IAG-nucleoside hydrolase: determination of the preferred ground state conformation and the role of active site residues.
Devleena Mazumder-Shivakumar (2005)
10.1021/bi100697d
Structure and mechanism of the 6-oxopurine nucleosidase from Trypanosoma brucei brucei.
An Vandemeulebroucke (2010)
10.2174/092986710791556023
Inhibitors of the Purine Salvage Pathway: A Valuable Approach for Antiprotozoal Chemotherapy?
M. Berg (2010)
10.1021/acs.biochem.5b01179
Evaluating the Substrate Selectivity of Alkyladenine DNA Glycosylase: The Synergistic Interplay of Active Site Flexibility and Water Reorganization.
Stefan A. P. Lenz (2016)
10.1021/acs.jpcb.6b09620
Hydrolytic Glycosidic Bond Cleavage in RNA Nucleosides: Effects of the 2'-Hydroxy Group and Acid-Base Catalysis.
Stefan A. P. Lenz (2016)
10.1016/j.bbapap.2014.01.010
Characterization of inosine-uridine nucleoside hydrolase (RihC) from Escherichia coli.
Brock A Arivett (2014)
10.1007/978-0-387-77570-8_12
Purine and pyrimidine metabolism in Leishmania.
N. Carter (2008)
10.1016/J.DRUP.2007.02.004
Drugs and drug resistance in African trypanosomiasis.
V. Delespaux (2007)
10.1016/j.bbapap.2009.02.011
Crystal structures of T. vivax nucleoside hydrolase in complex with new potent and specific inhibitors.
W. Versées (2009)
10.1021/JA021088E
Exploring nucleoside hydrolase catalysis in silico: molecular dynamics study of enzyme-bound substrate and transition state.
Devleena Mazumder (2002)
Purine and pyrimidine metabolism in Leishmania.
J. Marr (1985)
10.1016/S0040-4020(00)00194-0
Synthesis of transition state analogue inhibitors for purine nucleoside phosphorylase and N-riboside hydrolases
G. Evans (2000)
10.1021/acs.jpcb.7b10524
QM/MM and MM MD Simulations on the Pyrimidine-Specific Nucleoside Hydrolase: A Comprehensive Understanding of Enzymatic Hydrolysis of Uridine.
F. Fan (2018)
10.1093/bmb/lds031
Management of trypanosomiasis and leishmaniasis
M. Barrett (2012)
Crystal
B Giabbai (2004)
10.1021/BI00042A030
Binding modes for substrate and a proposed transition-state analogue of protozoan nucleoside hydrolase.
D. W. Parkin (1995)
10.1074/jbc.274.30.21114
Nucleoside Hydrolase from Leishmania major
W. Shi (1999)
10.1107/S0907444913010792
Structures of purine nucleosidase from Trypanosoma brucei bound to isozyme-specific trypanocidals and a novel metalorganic inhibitor.
F. Giannese (2013)
10.1503/cmaj.120694
Cutaneous leishmaniasis in a returning traveller
Eric Demers (2013)
10.1021/BI00496A010
pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model.
D. Bashford (1990)
10.1074/jbc.M112.346502
Genetic Dissection of Pyrimidine Biosynthesis and Salvage in Leishmania donovani*
Zachary N Wilson (2012)
10.1016/J.EJMECH.2007.03.027
Synthesis and biochemical evaluation of guanidino-alkyl-ribitol derivatives as nucleoside hydrolase inhibitors.
A. Goeminne (2008)
10.1021/ct400341p
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data.
D. Roe (2013)
10.1002/(SICI)1097-461X(1996)60:7<1271::AID-QUA8>3.0.CO;2-W
Calculation of intramolecular force fields from second‐derivative tensors
J. M. Seminario (1996)
10.2174/09298673113206660285
Transition-state-guided drug design for treatment of parasitic neglected tropical diseases.
A. S. Murkin (2014)
10.1016/j.pt.2012.05.005
Purine salvage in Leishmania: complex or simple by design?
Jan M. Boitz (2012)
10.1021/BI952998U
Inosine-uridine nucleoside hydrolase from Crithidia fasciculata. Genetic characterization, crystallization, and identification of histidine 241 as a catalytic site residue.
D. N. Gopaul (1996)
10.1074/jbc.M803705200
A Flexible Loop as a Functional Element in the Catalytic Mechanism of Nucleoside Hydrolase from Trypanosoma vivax*
An Vandemeulebroucke (2008)
10.1016/B978-012473345-9/50007-6
Purine and Pyrimidine Metabolism
R. Berens (1995)
10.1128/AAC.01787-09
Evaluation of Nucleoside Hydrolase Inhibitors for Treatment of African Trypanosomiasis
M. Berg (2010)
10.1016/j.ejmech.2012.07.052
Kinetics and docking studies of two potential new inhibitors of the nucleoside hydrolase from Leishmania donovani.
M. N. Rennó (2012)
10.1590/S0103-50532008000100011
Design of inhibitors for nucleoside hydrolase from Leishmania donovani using molecular dynamics studies
Tanos C. C. França (2008)
10.1021/jp211403j
QM/MM molecular dynamics study of purine-specific nucleoside hydrolase.
Ruibo Wu (2012)
10.1016/J.JMB.2004.02.049
Leaving group activation by aromatic stacking: an alternative to general acid catalysis.
W. Versées (2004)
10.1080/07391102.2015.1013157
Landscape of π–π and sugar–π contacts in DNA–protein interactions
K. A. Wilson (2016)
10.1016/S0040-4039(00)79290-2
A new class of C-nucleoside analogues. 1-(S)-aryl-1,4-dideoxy-1,4-imino-D-ribitols, transition state analogue inhibitors of nucleoside hydrolase
B. Horenstein (1993)
10.1006/JMBI.2001.4548
Structure and function of a novel purine specific nucleoside hydrolase from Trypanosoma vivax.
W. Versées (2001)
10.1021/JA00778A043
Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation.
C. Altona (1972)
10.1007/s00894-011-0968-9
Analysis of Bacillus anthracis nucleoside hydrolase via in silico docking with inhibitors and molecular dynamics simulation
A. P. Guimarães (2011)
10.1021/ct400314y
Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald.
Romelia Salomón-Ferrer (2013)
10.1074/JBC.M111735200
Enzyme-Substrate Interactions in the Purine-specific Nucleoside Hydrolase from Trypanosoma vivax*
W. Versées (2002)
10.1021/acs.jcim.5b00674
MCPB.py: A Python Based Metal Center Parameter Builder
P. Li (2016)
10.1016/0166-6851(84)90117-8
Purine and pyrimidine metabolism in the Trypanosomatidae.
D. Hammond (1984)
10.1021/ja107640u
Energy landscapes associated with macromolecular conformational changes from endpoint structures.
A. Fornili (2010)
10.1021/BI952999M
Three-dimensional structure of the inosine-uridine nucleoside N-ribohydrolase from Crithidia fasciculata.
M. Degano (1996)
10.1016/J.STR.2004.03.018
Crystal structure to 1.7 a of the Escherichia coli pyrimidine nucleoside hydrolase YeiK, a novel candidate for cancer gene therapy.
B. Giabbai (2004)
10.1002/jcc.20035
Development and testing of a general amber force field
J. Wang (2004)
10.1021/BI00108A026
Transition-state analysis of nucleoside hydrolase from Crithidia fasciculata.
B. Horenstein (1991)
10.1093/emboj/17.17.5214
Base excision repair initiation revealed by crystal structures and binding kinetics of human uracil‐DNA glycosylase with DNA
Sudip S. Parikh (1998)



Semantic Scholar Logo Some data provided by SemanticScholar