Studying the binding mechanisms of veratryl alcohol to P. chrysosporium lignin peroxidase: insights from theoretical approaches

Recabarren, Rodrigo; Fuenzalida-Valdivia, Isabel; Alzate‐Morales, Jans

doi:10.1007/s00214-016-1828-6

Cited by 14 publications

(14 citation statements)

References 66 publications

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“…Protonation states were adjusted at pH 3.0 with PROPKA [13]. Glu168 and Asp264 (that were protonated by PROPKA) were manually deprotonated in agreement with Recabarren et al [14]. The heme group was modeled as compound I according to the OPLS-2005 force field parameters.…”

Section: Methodsmentioning

confidence: 99%

“…The heme group was modeled as compound I according to the OPLS-2005 force field parameters. For this, the formal charge of iron was set to +3 (Fe +3 ) and it was connected via zero-order bonds to 6 atoms: the indolic nitrogen of proximal His176, the four nitrogen atoms of the porphyrin ring (two of these nitrogens were set with formal charge of −1) and the distal oxygen atom with zero formal charge coordinating Fe +3 [14].…”

Section: Methodsmentioning

confidence: 99%

“…A minimization protocol for relaxing the structure of each mutant was performed using the MACROMODEL software package [16] applying the steepest descent minimization method with a convergence criterion of energy gradient to <0.05 kJ/Å·mol. The MD simulations were performed as previously described [14], with details of the protocol used given in the supporting information section. For each MD simulation one frame was saved every 50 ps to carry out calculations of the solvent accessible surface area (SASA) [17] around residue Trp171 using a script (Script S1) in tool command language (TCL) included in the visual molecular dynamics (VMD) software version 1.9.2 for Linux [18].…”

Section: Methodsmentioning

confidence: 99%

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Binding and Catalytic Mechanisms of Veratryl Alcohol Oxidation by Lignin Peroxidase: A Theoretical and Experimental Study

Romero

Fernández‐Fueyo

Ávila-Salas

et al. 2019

Computational and Structural Biotechnology Journal

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Lignin peroxidase (LiP) and its natural substrate veratryl alcohol (VA) play a crucial role in lignin degradation by white-rot fungi. Understanding the molecular determinants for the interaction of this enzyme with its substrates is essential in the rational design of engineered peroxidases for biotechnological application. Here, we combine computational and experimental approaches to analyze the interaction of Phanerochaete chrysosporium LiP (isoenzyme H8) with VA and its radical cation (VA •+ , resulting from substrate oxidation by the enzyme). Interaction energy calculations at semiempirical quantum mechanical level (SQM) between LiP and VA/VA •+ enabled to identify those residues at the acidic environment of catalytic Trp171 involved in the main interactions. Then, a battery of variants, with single and multiple mutations at these residues (Glu168, Asp165, Glu250, Asp264, and Phe267), was generated by directed mutagenesis, and their kinetics parameters were estimated on VA and two additional substrates. The experimental results show that Glu168 and Glu250 are crucial for the binding of VA, with Glu250 also contributing to the turnover of the enzyme. The experimental results were further rationalized through new calculations of interaction energies between VA/VA •+ and LiP with each of the single mutations. Finally, the delocalization of spin density was determined with quantum mechanics/molecular mechanics calculations (QM/MM), further supporting the contribution of Glu250 to VA oxidation at Trp171.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Binding and Catalytic Mechanisms of Veratryl Alcohol Oxidation by Lignin Peroxidase: A Theoretical and Experimental Study

Romero

Fernández‐Fueyo

Ávila-Salas

et al. 2019

Computational and Structural Biotechnology Journal

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“…Overall, our sampling results are in agreement with a recent study combining docking and molecular dynamics techniques, where VA was found to adopt multiple orientations and a short bound life span. 39 Five representative structures were then analyzed using the QM/MM e-pathway method, identifying for each pose the top seven residues with larger electron affinity in the transfer region.…”

Section: Computational Analysis Of Intramolecular Lret In Vpmentioning

confidence: 99%

Mapping the Long-Range Electron Transfer Route in Ligninolytic Peroxidases

et al. 2017

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Abstract:Combining a computational analysis with site-directed mutagenesis, we have studied the long-range electron transfer pathway in versatile and lignin peroxidases, two enzymes of biotechnological interest that play a key role for fungal degradation of lignin in plant biomass. The in silico study established two possible electron transfer routes starting at the surface tryptophan residue previously identified as responsible for oxidation of the bulky lignin polymer. Moreover, in both enzymes, a second buried tryptophan residue appears as a top electron transfer carrier, indicating the prevalence of one pathway. Site-directed mutagenesis of versatile peroxidase (from Pleurotus eryngii) allowed us to corroborate the computational analysis and the role played by the buried tryptophan (Trp244) and a neighbor phenylalanine residue (Phe198), together with the surface tryptophan, in the electron transfer. These three aromatic residues are highly conserved in all the sequences analyzed (up to a total of 169). The importance of the surface (Trp171) and buried (Trp251) tryptophan residues in lignin peroxidase has been also confirmed by directed mutagenesis of the Phanerochaete chrysosporium enzyme. Overall, the combined procedure identifies analogous electron transfer pathways in the long-range oxidation mechanism for both ligninolytic peroxidases, constituting a good example of how computational analysis avoids making extensive trial-error mutagenic experiments.3

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“…Besides experimental findings, its existence was confirmed by EPR-based quantum calculations and it was further characterized by QM calculations to study the most favorable binding position of VA at the ring of Tyr181. On the other hand, in a similar research work [68], the binding of VA at Trp171 in P. chrysosporium LiP was studied with different computational methods and QM/MM calculations were used to compute spin densities for different VA-Trp171…”

Section: Lignin Peroxidase (Lip)mentioning

confidence: 99%

Computational Modeling Methods for Understanding the Interaction of Lignin and Its Derivatives with Oxidoreductases as Biocatalysts

Alzate‐Morales¹,

Recabarren²,

Fuenzalida-Valdivia³

et al. 2018

Lignin - Trends and Applications

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This chapter will be presented as follow. First, a brief introduction to structure and characterization of lignin and its derivatives is presented, as well as their importance as chemical scaffolds for obtaining value-added products in chemical, food, pharmaceutical and agriculture industry. Second, an extensive review of different reports using computational modeling methods-like molecular dynamics simulations, quantum mechanics and hybrid calculation methods, among others-in the understanding of enzyme-substrate interaction and biocatalysis will be presented. Third, and as last part of chapter, some hand picked examples from literature will be chosen as successful cases where the interplay between experiment and computation has given as a result protein engineered oxidoreductases with improved catalytic capabilities.

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Studying the binding mechanisms of veratryl alcohol to P. chrysosporium lignin peroxidase: insights from theoretical approaches

Cited by 14 publications

References 66 publications

Binding and Catalytic Mechanisms of Veratryl Alcohol Oxidation by Lignin Peroxidase: A Theoretical and Experimental Study

Binding and Catalytic Mechanisms of Veratryl Alcohol Oxidation by Lignin Peroxidase: A Theoretical and Experimental Study

Mapping the Long-Range Electron Transfer Route in Ligninolytic Peroxidases

Computational Modeling Methods for Understanding the Interaction of Lignin and Its Derivatives with Oxidoreductases as Biocatalysts

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