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Title: Machine Learning on a Robotic Platform for the Design of Polymer–Protein Hybrids

Journal Article · · Advanced Materials

Polymer–protein hybrids are intriguing materials that can bolster protein stability in non-native environments, thereby enhancing their utility in diverse medicinal, commercial, and industrial applications. One stabilization strategy involves designing synthetic random copolymers with compositions attuned to the protein surface, but rational design is complicated by the vast chemical and composition space. Here, a strategy is reported to design protein-stabilizing copolymers based on active machine learning, facilitated by automated material synthesis and characterization platforms. The versatility and robustness of the approach is demonstrated by the successful identification of copolymers that preserve, or even enhance, the activity of three chemically distinct enzymes following exposure to thermal denaturing conditions. Although systematic screening results in mixed success, active learning appropriately identifies unique and effective copolymer chemistries for the stabilization of each enzyme. Overall, this work broadens the capabilities to design fit-for-purpose synthetic copolymers that promote or otherwise manipulate protein activity, with extensions toward the design of robust polymer–protein hybrid materials.

Research Organization:
Brookhaven National Laboratory (BNL), Upton, NY (United States). National Synchrotron Light Source II (NSLS-II)
Sponsoring Organization:
USDOE Office of Science (SC), Basic Energy Sciences (BES); USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institute of General Medical Sciences (NIGMS); National Institutes of Health (NIH); National Science Foundation (NSF)
Grant/Contract Number:
SC0012704
OSTI ID:
1981354
Journal Information:
Advanced Materials, Journal Name: Advanced Materials Journal Issue: 30 Vol. 34; ISSN 0935-9648
Publisher:
WileyCopyright Statement
Country of Publication:
United States
Language:
English

References (49)

Machine‐Assisted Discovery of Chondroitinase ABC Complexes toward Sustained Neural Regeneration journal February 2022
Synergistic Enzyme Mixtures to Realize Near‐Complete Depolymerization in Biodegradable Polymer/Additive Blends journal October 2021
Automation of Controlled/Living Radical Polymerization journal January 2020
An Oxygen‐Tolerant PET‐RAFT Polymerization for Screening Structure–Activity Relationships journal January 2018
Precise Polymer Synthesis by Autonomous Self‐Optimizing Flow Reactors journal March 2019
Biocatalysis: Enzymatic Synthesis for Industrial Applications journal August 2020
Nano-Encapsulation of Lipase by Self-Assembled Nanogels: Induction of High Enzyme Activity and Thermal Stabilization journal January 2010
VMD: Visual molecular dynamics journal February 1996
Automation and data-driven design of polymer therapeutics journal April 2021
Enzyme immobilization on poly(ethylene-co-acrylic acid) films studied by quartz crystal microbalance with dissipation monitoring journal July 2005
Polymer informatics: Current status and critical next steps journal April 2021
Toward Designing Highly Conductive Polymer Electrolytes by Machine Learning Assisted Coarse-Grained Molecular Dynamics journal April 2020
PI1M: A Benchmark Database for Polymer Informatics journal September 2020
Discovery of Self-Assembling π-Conjugated Peptides by Active Learning-Directed Coarse-Grained Molecular Simulation journal March 2020
Pushing the Limits of High Throughput PET-RAFT Polymerization journal September 2018
BigSMILES: A Structurally-Based Line Notation for Describing Macromolecules journal September 2019
Polymer Informatics: Opportunities and Challenges journal September 2017
Efficient Polymer-Mediated Delivery of Gene-Editing Ribonucleoprotein Payloads through Combinatorial Design, Parallelized Experimentation, and Machine Learning journal November 2020
Structural and Conformational Stability of Horseradish Peroxidase:  Effect of Temperature and pH journal December 1999
Therapeutic Protein–Polymer Conjugates: Advancing Beyond PEGylation journal September 2014
Machine-Learning-Guided Discovery of 19F MRI Agents Enabled by Automated Copolymer Synthesis journal October 2021
All Wrapped up: Stabilization of Enzymes within Single Enzyme Nanoparticles journal January 2019
Oxygen Tolerance Study of Photoinduced Electron Transfer–Reversible Addition–Fragmentation Chain Transfer (PET-RAFT) Polymerization Mediated by Ru(bpy) 3 Cl 2 journal June 2014
Design of efficient molecular organic light-emitting diodes by a high-throughput virtual screening and experimental approach journal August 2016
Bias free multiobjective active learning for materials design and discovery journal April 2021
Machine learning in materials informatics: recent applications and prospects journal December 2017
New frontiers for the materials genome initiative journal April 2019
Machine learning enables polymer cloud-point engineering via inverse design journal July 2019
Machine learning for accelerating the discovery of high-performance donor/acceptor pairs in non-fullerene organic solar cells journal August 2020
Machine learning in combinatorial polymer chemistry journal February 2021
Near-complete depolymerization of polyesters with nano-dispersed enzymes journal April 2021
From local explanations to global understanding with explainable AI for trees journal January 2020
Engineering enzyme microenvironments for enhanced biocatalysis journal January 2018
A guide to maximizing the therapeutic potential of protein–polymer conjugates by rational design journal January 2018
Cellulose solvent-based pretreatment for enhanced second-generation biofuel production: a review journal January 2019
Enabling technologies in polymer synthesis: accessing a new design space for advanced polymer materials journal January 2020
Featurization strategies for polymer sequence or composition design by machine learning journal January 2022
Irreversible Thermal Denaturation of Glucose Oxidase from Aspergillus niger Is the Transition to the Denatured State with Residual Structure journal November 2004
A new family of power transformations to improve normality or symmetry journal December 2000
New developments in the ATSAS program package for small-angle scattering data analysis journal March 2012
ATSAS 2.8 : a comprehensive data analysis suite for small-angle scattering from macromolecular solutions journal June 2017
BioXTAS RAW : improvements to a free open-source program for small-angle X-ray scattering data reduction and analysis journal September 2017
Designing exceptional gas-separation polymer membranes using machine learning journal May 2020
Self-driving laboratory for accelerated discovery of thin-film materials journal May 2020
Targeted sequence design within the coarse-grained polymer genome journal October 2020
Random heteropolymers preserve protein function in foreign environments journal March 2018
Active-learning and materials design: the example of high glass transition temperature polymers journal June 2019
Multi-criteria-based strategy to stop active learning for data annotation conference January 2008
A Practical Model of Quartz Crystal Microbalance in Actual Applications journal August 2017