Assessment of the PETase conformational changes induced by poly(ethylene terephthalate) binding

Computational Redesign of a PETase for Plastic Biodegradation under Ambient Condition by the GRAPE Strategy

(2021) Yinglu Cui et al.   ACS Catalysis

Conformational Changes of Glutamine 5′-Phosphoribosylpyrophosphate Amidotransferase for Two Substrates Analogue Binding: Insight from Conventional Molecular Dynamics and Accelerated Molecular Dynamics Simulations

(2021) Congcong Li et al.   Frontiers in Chemistry

An engineered PET depolymerase to break down and recycle plastic bottles

(2020) V. Tournier et al.   NATURE

Constituents of buriti oil (Mauritia flexuosa L.) like inhibitors of the SARS-Coronavirus main peptidase: an investigation by docking and molecular dynamics

(2020) Allan N. Costa et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Using Accelerated Molecular Dynamics Simulation to elucidate the effects of the T198F mutation on the molecular flexibility of the West Nile virus envelope protein

(2020) Renan Patrick da Penha Valente et al.   Scientific Reports

Characterization and engineering of a two-enzyme system for plastics depolymerization

(2020) Brandon C. Knott et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rational Protein Engineering of Thermo-Stable PETase from Ideonella sakaiensis for Highly Efficient PET Degradation

(2019) Hyeoncheol Francis Son et al.   ACS Catalysis

Modeling and Simulations of Polymers: A Roadmap

(2019) Thomas E. Gartner et al.   MACROMOLECULES

Current knowledge on enzymatic PET degradation and its possible application to waste stream management and other fields

(2019) Fusako Kawai et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Measuring the structural impact of mutations on cytochrome P450 21A2, the major steroid 21-hydroxylase related to congenital adrenal hyperplasia

(2019) Jorddy Neves Cruz et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Biodegradation of PET: Current Status and Application Aspects

(2019) Ikuo Taniguchi et al.   ACS Catalysis

A comparative multivariate analysis of nitrilase enzymes: an ensemble based computational approach

(2019) Priya Kumari et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Structure of the plastic-degrading Ideonella sakaiensis MHETase bound to a substrate

(2019) Gottfried J. Palm et al.   Nature Communications

Analysis and Prevention of Microplastics Pollution in Water: Current Perspectives and Future Directions

(2019) Yolanda Picó et al.   ACS Omega

Efficient biodegradation of highly crystallized polyethylene terephthalate through cell surface display of bacterial PETase

(2019) Zhuozhi Chen et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Conformational fitting of a flexible oligomeric substrate does not explain the enzymatic PET degradation

(2019) Ren Wei et al.   Nature Communications

Active Site Flexibility as a Hallmark for Efficient PET Degradation by I. sakaiensis PETase

(2018) Tobias Fecker et al.   BIOPHYSICAL JOURNAL

Protein Crystallography and Site-Direct Mutagenesis Analysis of the Poly(ethylene terephthalate) Hydrolase PETase from Ideonella sakaiensis

(2018) Bing Liu et al.   CHEMBIOCHEM

A random version of principal component analysis in data clustering

(2018) Luigi Leonardo Palese   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Characterization and engineering of a plastic-degrading aromatic polyesterase

(2018) Harry P. Austin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural insight into molecular mechanism of poly(ethylene terephthalate) degradation

(2018) Seongjoon Joo et al.   Nature Communications

Structural studies reveal the molecular mechanism of PETase

(2018) Chun-Chi Chen et al.   FEBS Journal

Ability of fungi isolated from plastic debris floating in the shoreline of a lake to degrade plastics

(2018) Ivano Brunner et al.   PLoS One

Enhanced Poly(ethylene terephthalate) Hydrolase Activity by Protein Engineering

(2018) Yuan Ma et al.   Engineering

Computational Study of Conformational Changes in Human 3-hydroxy-3-methylglutaryl Coenzyme Reductase Induced by Substrate Binding

(2018) Clauber Henrique Souza da Costa et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Structural insight into catalytic mechanism of PET hydrolase

(2017) Xu Han et al.   Nature Communications

Machine Learning and Network Analysis of Molecular Dynamics Trajectories Reveal Two Chains of Red/Ox-specific Residue Interactions in Human Protein Disulfide Isomerase

(2017) Razieh Karamzadeh et al.   Scientific Reports

Biocatalysis as a green route for recycling the recalcitrant plastic polyethylene terephthalate

(2017) Ren Wei et al.   Microbial Biotechnology

Ideonella sakaiensis sp. nov., isolated from a microbial consortium that degrades poly(ethylene terephthalate)

(2016) Somboon Tanasupawat et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

A bacterium that degrades and assimilates poly(ethylene terephthalate)

(2016) Shosuke Yoshida et al.   SCIENCE

On the analysis and comparison of conformer-specific essential dynamics upon ligand binding to a protein

(2015) Marcos Grosso et al.   JOURNAL OF CHEMICAL PHYSICS

Plastic waste inputs from land into the ocean

(2015) J. R. Jambeck et al.   SCIENCE

Investigation of Inhibition Mechanism of Chemokine Receptor CCR5 by Micro-second Molecular Dynamics Simulations

(2015) Ramin Ekhteiari Salmas et al.   Scientific Reports

Structural and functional studies on a thermostable polyethylene terephthalate degrading hydrolase from Thermobifida fusca

(2014) Christian Roth et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Microbial degradation and deterioration of polyethylene – A review

(2014) Juan-Manuel Restrepo-Flórez et al.   INTERNATIONAL BIODETERIORATION & BIODEGRADATION

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

Challenges in Multiscale Modeling of Polymer Dynamics

(2013) Ying Li et al.   Polymers

Edge effects control helical wrapping of carbon nanotubes by polysaccharides

(2012) Yingzhe Liu et al.   Nanoscale

Crystal structure of cutinase Est119 from Thermobifida alba AHK119 that can degrade modified polyethylene terephthalate at 1.76Å resolution

(2012) Kengo Kitadokoro et al.   POLYMER DEGRADATION AND STABILITY

A New Esterase from Thermobifida halotolerans Hydrolyses Polyethylene Terephthalate (PET) and Polylactic Acid (PLA)

(2012) Doris Ribitsch et al.   Polymers

Isolation of a Novel Cutinase Homolog with Polyethylene Terephthalate-Degrading Activity from Leaf-Branch Compost by Using a Metagenomic Approach

(2011) Sintawee Sulaiman et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Enzymatic Surface Hydrolysis of PET: Effect of Structural Diversity on Kinetic Properties of Cutinases from Thermobifida

(2011) Enrique Herrero Acero et al.   MACROMOLECULES

Hydrolysis of cyclic poly(ethylene terephthalate) trimers by a carboxylesterase from Thermobifida fusca KW3

(2010) Susan Billig et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

MolDock Applied to Structure-Based Virtual Screening

(2010) Walter De Azevedo Jr.   CURRENT DRUG TARGETS

Free-energy landscape, principal component analysis, and structural clustering to identify representative conformations from molecular dynamics simulations: The myoglobin case

(2009) Elena Papaleo et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Accumulation and fragmentation of plastic debris in global environments

(2009) D. K. A. Barnes et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES