Prediction of hydrogen-bonding networks around tyrosyl radical in P. eryngii versatile peroxidase W164Y variants: a QM/MM MD study

REFERENCES

• DempseyJL, WinklerJR, GrayHB. Proton-coupled electron flow in protein redox machines. Chem Rev. 2010;110:7024–7039.
   PubMed Web of Science ®Google Scholar
• StubbeJ, Der DonkWA. Protein radicals in enzyme catalysis. Chem Rev. 1998;98:705–762.
   PubMed Web of Science ®Google Scholar
• BerniniC, AndruniówT, OlivucciM, PogniR, BasosiR, SinicropiA. Effects of the protein environment on the spectral properties of tryptophan radicals in Pseudomonas aeruginosa Azurin. J Am Chem Soc. 2013;135:4822–4833.
   PubMed Web of Science ®Google Scholar
• BerniniC, PogniR, BasosiR, SinicropiA. The nature of tryptophan radicals involved in the long-range electron transfer of lignin peroxidase and lignin peroxidase-like systems: insights from quantum mechanical/molecular mechanics simulations. Proteins Struct Funct Bioinform. 2012;80:1476–1483.
   PubMed Web of Science ®Google Scholar
• BerniniC, PogniR, Ruiz-DueñasFJ, MartínezAT, BasosiR, SinicropiA. EPR parameters of amino acid radicals in P. eryngii versatile peroxidase and its W164Y variant computed at the QM/MM level. Phys Chem Chem Phys. 2011;13:5078–5098.
   PubMed Web of Science ®Google Scholar
• BerniniC, SinicropiA, BasosiR, PogniR. Tyrosyl radical in the W164Y mutant of P. eryngii versatile peroxidase: an EPR and DFT/PCM study. Appl Magn Res. 2010;37:279–288.
   Web of Science ®Google Scholar
• Ruiz-DueñasFJ, PogniR, MoralesM, GiansantiS, MateMJ, RomeroA, MartínezMJ, BasosiR, MartínezAT. Protein radicals in fungal versatile peroxidase: catalytic tryptophan radical in both compound I and compound II and studies on W164Y, W164H, and W164S variants. J Biol Chem. 2009;284:7986–7994.
   PubMed Web of Science ®Google Scholar
• PogniR, BarattoMC, TeutloffC, GiansantiS, Ruiz-DuenasFJ, ChoinowskiT, PiontekK, MartinezAT, LendzianF, BasosiR. A tryptophan neutral radical in the oxidized state of versatile peroxidase from Pleurotus eryngii. J Biol Chem. 2006;28:9517–9526.
   Google Scholar
• BreindelAJ, StuartRE, BockWJ, StelterDN, KravecSM, ConwellEM. Hole wave functions and transport with deazaadenines replacing adenines in DNA. J Phys Chem B. 2013;117:3086–3090.
   PubMed Web of Science ®Google Scholar
• LeendersEJM, Vande VondeleJ, BolhuisPG, Jan MeijerE. Solvation of p-coumaric acid in water. J Phys Chem B. 2007;111:13591–13599.
   PubMed Web of Science ®Google Scholar
• PincuM, CocineroEJ, MayorkasN, BrauerB, DavisBG, GerberRB, SimonsJP. Isotopic hydration of cellobiose: vibrational spectroscopy and dynamical simulations. J Phys Chem A. 2011;115:9498–9509.
   PubMed Web of Science ®Google Scholar
• HumphreyW, DalkeA, SchultenK. VMD – visual molecular dynamics. J Mol Graphics. 1996;14:33–38.
   PubMed Web of Science ®Google Scholar
• MacKerellADJr, BashfordD, BellottM, DunbrackRLJr, EvanseckJD, FieldMJ, FischerS, GaoJ, GuoH, HaS, Joseph-McCarthyD, KuchnirL, KuczeraK, LauFTK, MattosC, MichnickS, NgoT, NguyenDT, ProdhomB, ReiherWEIII, RoucxB, SchlenkrichM, SmithJC, StoteR, StraubJ, WatanabeM, Wiórkiewicz-KuczeraJ, YinD, KarplusM. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B. 1998;102:3586–3616.
   PubMed Web of Science ®Google Scholar
• PhillipsJC, BraunR, WangW, GumbartJ, TajkhorshidE, VillaE, ChipotC, SkeelRD, KaleL, ShultenK. Scalable molecular dynamics with NAMD. J Comput Chem. 2005;26:1781–1802.
   PubMed Web of Science ®Google Scholar
• DardenT, YorkD, PedersonL. Particle mesh Ewald: an N-log(N) method for Ewald sums in large systems. J Chem Phys. 1993;98:10089–10092.
   Web of Science ®Google Scholar
• LainoT, MohamedF, LaioA, ParrinelloM. An efficient real space multigrid QM/MM electrostatic coupling. J Chem Theor Comput. 2005;1:1176–1184.
   PubMed Web of Science ®Google Scholar
• LainoT, MohamedF, LaioA, ParrinelloM. An efficient linear-scaling electrostatic coupling for treating periodic boundary conditions in QM/MM simulations. J Chem Theor Comput. 2006;2:1370–1378.
   PubMed Web of Science ®Google Scholar
• LippertG, HutterJ, ParrinelloM. The Gaussian and augmented-plane-wave density functional method for ab initio molecular dynamics simulations. Theor Chem Acc. 1999;103:124–140.
   Web of Science ®Google Scholar
• VandeVondeleJ, KrackM, MohamedF, ParrinelloM, ChassaingT, HutterJ. QUICKSTEP: fast and accurate density functional calculations using a mixed Gaussian and plane waves approach. Comput Phys Commun. 2005;167:103–128.
   Web of Science ®Google Scholar
• CP2K. Available from: http://www.cp2k.org.
   Google Scholar
• LeeC, YangW, ParrRG. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys Rev B. 1988;37:785–789.
   PubMed Web of Science ®Google Scholar
• SchäferA, HuberC, AhlrichsR. Fully optimized contracted Gaussian basis sets of triple zeta valence quality for atoms Li to Kr. J Chem Phys. 1994 :5829–5835.
   Web of Science ®Google Scholar
• MassonF, LainoT, RothlisbergerU, HutterJ. A QM/MM investigation of thymine dimer radical anion splitting catalyzed by DNA photolyase. Chem Phys Chem. 2009;10:400–410.
   Google Scholar
• MassonF, LainoT, TavernelliI, RothlisbergerU, HutterJ. Computational study of thymine dimer radical anion splitting in the self-repair process of duplex DNA. J Am Chem Soc. 2008;130:3443–3450.
   PubMed Web of Science ®Google Scholar
• StantonCL, KuoI-FW, MundyCJ, LainoT, HoukKN. QM/MM metadynamics study of the direct decarboxylation mechanism for orotidine-5′-monophosphate decarboxylase using two different QM regions: acceleration too small to explain rate of enzyme catalysis. J Phys Chem B. 2007;111:12573–12581.
   PubMed Web of Science ®Google Scholar
• GoedeckerS, TeterM, HutterJ. Separable dual-space Gaussian pseudopotentials. Phys Rev B. 1996;54:1703–1710.
   PubMed Web of Science ®Google Scholar
• HartwigsenC, GoedeckerS, HutterJ. Relativistic separable dual-space Gaussian pseudopotentials from H to Rn. Phys Rev B. 1998;58:3641–3662.
   Web of Science ®Google Scholar
• HooverWG. Canonical dynamics: equilibrium phase-space distributions. Phys Rev A. 1985;31:1695–1697.
   PubMed Web of Science ®Google Scholar
• NoséSJ. A unified formulation of the constant temperature molecular dynamics methods. J Chem Phys. 1984;81:511–519.
   Web of Science ®Google Scholar