scholarly journals Structural and molecular dynamics studies of a C1‐oxidizing lytic polysaccharide monooxygenase from Heterobasidion irregulare reveal amino acids important for substrate recognition

FEBS Journal ◽  
2018 ◽  
Vol 285 (12) ◽  
pp. 2225-2242 ◽  
Author(s):  
Bing Liu ◽  
Abhishek A. Kognole ◽  
Miao Wu ◽  
Bjørge Westereng ◽  
Michael F. Crowley ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Substrate Recognition ◽  
Lytic Polysaccharide Monooxygenase ◽  
Polysaccharide Monooxygenase ◽  
Heterobasidion Irregulare

scholarly journals On the Use of the Discrete Constant pH Molecular Dynamics to Describe the Conformational Space of Peptides

Polymers ◽  
2020 ◽  
Vol 13 (1) ◽  
pp. 99
Author(s):  
Cristian Privat ◽  
Sergio Madurga ◽  
Francesc Mas ◽  
Jaime Rubio-Martínez
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Md Simulations ◽  
Point Of View ◽  
Conformational Space ◽  
Conformational Sampling ◽  
Protonation State ◽  
Constant Ph ◽  
Biochemical Systems ◽  
Constant Ph Molecular Dynamics

Solvent pH is an important property that defines the protonation state of the amino acids and, therefore, modulates the interactions and the conformational space of the biochemical systems. Generally, this thermodynamic variable is poorly considered in Molecular Dynamics (MD) simulations. Fortunately, this lack has been overcome by means of the Constant pH Molecular Dynamics (CPHMD) methods in the recent decades. Several studies have reported promising results from these approaches that include pH in simulations but focus on the prediction of the effective pKa of the amino acids. In this work, we want to shed some light on the CPHMD method and its implementation in the AMBER suitcase from a conformational point of view. To achieve this goal, we performed CPHMD and conventional MD (CMD) simulations of six protonatable amino acids in a blocked tripeptide structure to compare the conformational sampling and energy distributions of both methods. The results reveal strengths and weaknesses of the CPHMD method in the implementation of AMBER18 version. The change of the protonation state according to the chemical environment is presumably an improvement in the accuracy of the simulations. However, the simulations of the deprotonated forms are not consistent, which is related to an inaccurate assignment of the partial charges of the backbone atoms in the CPHMD residues. Therefore, we recommend the CPHMD methods of AMBER program but pointing out the need to compare structural properties with experimental data to bring reliability to the conformational sampling of the simulations.

Probing the Hirudin−Thrombin Interaction by Incorporation of Noncoded Amino Acids and Molecular Dynamics Simulation†,‡

Biochemistry ◽  
2002 ◽  
Vol 41 (46) ◽  
pp. 13556-13569 ◽  
Author(s):  
Vincenzo De Filippis ◽  
Giorgio Colombo ◽  
Ilaria Russo ◽  
Barbara Spadari ◽  
Angelo Fontana
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation

scholarly journals A Lytic Polysaccharide Monooxygenase with Broad Xyloglucan Specificity from the Brown-Rot Fungus Gloeophyllum trabeum and Its Action on Cellulose-Xyloglucan Complexes

2016 ◽  
Vol 82 (22) ◽  
pp. 6557-6572 ◽  
Author(s):  
Yuka Kojima ◽  
Anikó Várnai ◽  
Takuya Ishida ◽  
Naoki Sunagawa ◽  
Dejan M. Petrovic ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Dynamic Viscosity ◽  
Brown Rot ◽  
Primary Cell Wall ◽  
Gloeophyllum Trabeum ◽  
Lytic Polysaccharide Monooxygenase ◽  
Content Type ◽  
Brown Rot Fungus ◽  
Sensitive Method ◽  
Polysaccharide Monooxygenase

ABSTRACTFungi secrete a set of glycoside hydrolases and lytic polysaccharide monooxygenases (LPMOs) to degrade plant polysaccharides. Brown-rot fungi, such asGloeophyllum trabeum, tend to have few LPMOs, and information on these enzymes is scarce. The genome ofG. trabeumencodes four auxiliary activity 9 (AA9) LPMOs (GtLPMO9s), whose coding sequences were amplified from cDNA. Due to alternative splicing, two variants ofGtLPMO9A seem to be produced, a single-domain variant,GtLPMO9A-1, and a longer variant,GtLPMO9A-2, which contains a C-terminal domain comprising approximately 55 residues without a predicted function. We have overexpressed the phylogenetically distinctGtLPMO9A-2 inPichia pastorisand investigated its properties. Standard analyses using high-performance anion-exchange chromatography–pulsed amperometric detection (HPAEC-PAD) and mass spectrometry (MS) showed thatGtLPMO9A-2 is active on cellulose, carboxymethyl cellulose, and xyloglucan. Importantly, compared to other known xyloglucan-active LPMOs,GtLPMO9A-2 has broad specificity, cleaving at any position along the β-glucan backbone of xyloglucan, regardless of substitutions. Using dynamic viscosity measurements to compare the hemicellulolytic action ofGtLPMO9A-2 to that of a well-characterized hemicellulolytic LPMO,NcLPMO9C fromNeurospora crassarevealed thatGtLPMO9A-2 is more efficient in depolymerizing xyloglucan. These measurements also revealed minor activity on glucomannan that could not be detected by the analysis of soluble products by HPAEC-PAD and MS and that was lower than the activity ofNcLPMO9C. Experiments with copolymeric substrates showed an inhibitory effect of hemicellulose coating on cellulolytic LPMO activity and did not reveal additional activities ofGtLPMO9A-2. These results provide insight into the LPMO potential ofG. trabeumand provide a novel sensitive method, a measurement of dynamic viscosity, for monitoring LPMO activity.IMPORTANCECurrently, there are only a few methods available to analyze end products of lytic polysaccharide monooxygenase (LPMO) activity, the most common ones being liquid chromatography and mass spectrometry. Here, we present an alternative and sensitive method based on measurement of dynamic viscosity for real-time continuous monitoring of LPMO activity in the presence of water-soluble hemicelluloses, such as xyloglucan. We have used both these novel and existing analytical methods to characterize a xyloglucan-active LPMO from a brown-rot fungus. This enzyme,GtLPMO9A-2, differs from previously characterized LPMOs in having broad substrate specificity, enabling almost random cleavage of the xyloglucan backbone.GtLPMO9A-2 acts preferentially on free xyloglucan, suggesting a preference for xyloglucan chains that tether cellulose fibers together. The xyloglucan-degrading potential ofGtLPMO9A-2 suggests a role in decreasing wood strength at the initial stage of brown rot through degradation of the primary cell wall.

Self-assembly of aromatic amino acids: a molecular dynamics study

2018 ◽  
Vol 20 (48) ◽  
pp. 30525-30536 ◽  
Author(s):  
Sahin Uyaver ◽  
Helen W. Hernandez ◽  
M. Gokhan Habiboglu
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Self Assembly ◽  
Aromatic Amino Acids

Common structures identified in the assembly of aromatic amino acids and their mixtures include the four-fold tube (a and b) and the zig-zag structure (c and d).

scholarly journals Anionic amino acids support hydrolysis of poly-β-(1,6)-N-acetylglucosamine exopolysaccharides by the biofilm dispersing glycosidase Dispersin B

2020 ◽  
pp. jbc.RA120.015524
Author(s):  
Alexandra P Breslawec ◽  
Shaochi Wang ◽  
Crystal Li ◽  
Myles B Poulin
Keyword(s):  
Amino Acids ◽  
Bacterial Infections ◽  
Substrate Recognition ◽  
Site Directed Mutagenesis ◽  
Binding Surface ◽  
Activity Measurements ◽  
Rate Of Hydrolysis ◽  
Biofilm Dispersal ◽  
Hydrolysis Of

The exopolysaccharide poly-β-(1→6)-N-acetylglucosamine (PNAG) is a major structural determinant of bacterial biofilms responsible for persistent and nosocomial infections. The enzymatic dispersal of biofilms by PNAG-hydrolyzing glycosidase enzymes, such as Dispersin B (DspB), is a possible approach to treat biofilm dependent bacterial infections. The cationic charge resulting from partial de-N-acetylation of native PNAG is critical for PNAG-dependent biofilm formation. We recently demonstrated that DspB has increased catalytic activity on de-N-acetylated PNAG oligosaccharides, but the molecular basis for this increased activity is not known. Here, we analyze the role of anionic amino acids surrounding the catalytic pocket of DspB in PNAG substrate recognition and hydrolysis using a combination of site directed mutagenesis, activity measurements using synthetic PNAG oligosaccharide analogs, and in vitro biofilm dispersal assays. The results of these studies support a model in which bound PNAG is weakly associated with a shallow anionic groove on the DspB protein surface with recognition driven by interactions with the –1 GlcNAc residue in the catalytic pocket. An increased rate of hydrolysis for cationic PNAG was driven, in part, by interaction with D147 on the anionic surface. Moreover, we identified that a DspB mutant with improved hydrolysis of fully acetylated PNAG oligosaccharides correlates with improved in vitro dispersal of PNAG dependent Staphylococcus epidermidis biofilms. These results provide insight into the mechanism of substrate recognition by DspB and suggest a method to improve DspB biofilm dispersal activity by mutation of the amino acids within the anionic binding surface.

scholarly journals Recent Advances in Screening Methods for the Functional Investigation of Lytic Polysaccharide Monooxygenases

2021 ◽  
Vol 9 ◽  
Author(s):  
Damao Wang ◽  
Yanping Li ◽  
Yuting Zheng ◽  
Yves S. Y. Hsieh
Keyword(s):  
Copper Ions ◽  
Biomass Conversion ◽  
Screening Methods ◽  
Lytic Polysaccharide Monooxygenase ◽  
Indirect Measurements ◽  
Glycosidic Bonds ◽  
Lytic Polysaccharide Monooxygenases ◽  
Polysaccharide Monooxygenases ◽  
Functional Investigation ◽  
Polysaccharide Monooxygenase

Lytic polysaccharide monooxygenase (LPMO) is a newly discovered and widely studied enzyme in recent years. These enzymes play a key role in the depolymerization of sugar-based biopolymers (including cellulose, hemicellulose, chitin and starch), and have a positive significance for biomass conversion. LPMO is a copper-dependent enzyme that can oxidize and cleave glycosidic bonds in cellulose and other polysaccharides. Their mechanism of action depends on the correct coordination of copper ions in the active site. There are still difficulties in the analysis of LPMO activity, which often requires multiple methods to be used in concert. In this review, we discussed various LPMO activity analysis methods reported so far, including mature mass spectrometry, chromatography, labeling, and indirect measurements, and summarized the advantages, disadvantages and applicability of different methods.

scholarly journals NEW ASPECTS OF THE ENZYMATIC BREAKDOWN OF CHITIN: A REVIEW

2021 ◽  
Vol 26 ◽  
pp. 5-10
Author(s):  
Urszula Jankiewicz ◽  
◽  
Arletta Kochańska-Jeziorska ◽  
Agnieszka Gałązka
Keyword(s):  
Crystalline Structure ◽  
Enzymatic Degradation ◽  
Soluble Sugars ◽  
Practical Importance ◽  
Oxidative Cleavage ◽  
Lytic Polysaccharide Monooxygenase ◽  
Great Practical Importance ◽  
Polysaccharide Monooxygenase

This review focuses on the enzymatic breakdown of chitin, taking into account the latest scientific reports on the activity of lytic polysaccharide monooxygenase (LPMO). Chitin is a natural, abundant polysaccharide of great practical importance in the environment. However, the insolubility in water and the tightly packed crystalline structure of chitin pose a serious obstacle to enzymatic degradation. This substrate can be converted into soluble sugars by the action of glycosidic hydrolases (GH), also known as chitinases. LPMO could prove to be helpful in enzymatic processes that increase the rate of chitin depolymerisation by improving the availability of substrates for chitinases. The unique action of LPMO is based on the ability to catalyse the oxidative cleavage of glycosidic chains present in complex, resistant crystal networks of chitin, and this cleavage facilitates the subsequent action of glycolytic hydrolases.

scholarly journals Deformation twinning and the role of amino acids and magnesium in calcite hardness from molecular simulation

2015 ◽  
Vol 17 (31) ◽  
pp. 20178-20184 ◽  
Author(s):  
A. S. Côté ◽  
R. Darkins ◽  
D. M. Duffy
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Molecular Simulation ◽  
Elastic Properties ◽  
Deformation Twinning ◽  
Pure Crystal ◽  
Classical Molecular Dynamics ◽  
Deformation Twins

We employ classical molecular dynamics to calculate elastic properties and to model the nucleation and propagation of deformation twins in calcite, both as a pure crystal and with magnesium and aspartate inclusions.

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