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Methods (San Diego, Calif.) Feb 2019Non-immunoglobulin scaffolds represent a proven group of small affinity proteins that can be engineered in vitro to similar affinity and potency as monoclonal... (Review)
Review
Non-immunoglobulin scaffolds represent a proven group of small affinity proteins that can be engineered in vitro to similar affinity and potency as monoclonal antibodies. Several novel candidate biotherapeutics that exploit the potential advantages scaffold proteins hold over larger and more complex antibodies have been developed over the past decade. The ease of using small and robust binding proteins as flexible and modular building blocks has led to the development of a wide range of innovative approaches to combine them in various bi- and multispecific formats. This progress is expected to aid the ongoing challenge of identifying niche applications where clear differentiation from antibody-based molecules will be key to success. Given the many engineering options that are available for non-immunoglobulin scaffold proteins, they have potential to not only complement but probably also surpass antibodies in certain applications.
Topics: Animals; Humans; Protein Engineering
PubMed: 30287281
DOI: 10.1016/j.ymeth.2018.09.010 -
Methods in Molecular Biology (Clifton,... 2021Protein engineering can yield new molecular tools for nanotechnology and therapeutic applications through modulating physiochemical and biological properties....
Protein engineering can yield new molecular tools for nanotechnology and therapeutic applications through modulating physiochemical and biological properties. Engineering membrane proteins is especially attractive because they perform key cellular processes including transport, nutrient uptake, removal of toxins, respiration, motility, and signaling. In this chapter, we describe two protocols for membrane protein engineering with the Rosetta software: (1) ΔΔG calculations for single point mutations and (2) sequence optimization in different membrane lipid compositions. These modular protocols are easily adaptable for more complex problems and serve as a foundation for efficient membrane protein engineering calculations.
Topics: Biological Transport; Membrane Lipids; Membrane Proteins; Membranes; Models, Molecular; Protein Engineering; Software
PubMed: 34302669
DOI: 10.1007/978-1-0716-1468-6_3 -
Current Opinion in Biotechnology Jun 2022Machine learning (ML) is revolutionizing our ability to understand and predict the complex relationships between protein sequence, structure, and function. Predictive... (Review)
Review
Machine learning (ML) is revolutionizing our ability to understand and predict the complex relationships between protein sequence, structure, and function. Predictive sequence-function models are enabling protein engineers to efficiently search the sequence space for useful proteins with broad applications in biotechnology. In this review, we highlight the recent advances in applying ML to protein engineering. We discuss supervised learning methods that infer the sequence-function mapping from experimental data and new sequence representation strategies for data-efficient modeling. We then describe the various ways in which ML can be incorporated into protein engineering workflows, including purely in silico searches, ML-assisted directed evolution, and generative models that can learn the underlying distribution of the protein function in a sequence space. ML-driven protein engineering will become increasingly powerful with continued advances in high-throughput data generation, data science, and deep learning.
Topics: Amino Acid Sequence; Biotechnology; Machine Learning; Protein Engineering; Proteins
PubMed: 35413604
DOI: 10.1016/j.copbio.2022.102713 -
Biomolecules Jul 2022This Special Issue of demonstrates the almost unlimited possibilities of modern protein engineering in gene expression, protein production and modification, as well as...
This Special Issue of demonstrates the almost unlimited possibilities of modern protein engineering in gene expression, protein production and modification, as well as the design and creation of new proteins [...].
Topics: Protein Engineering
PubMed: 35883522
DOI: 10.3390/biom12070966 -
Current Opinion in Chemical Biology Dec 2021Protein engineering seeks to identify protein sequences with optimized properties. When guided by machine learning, protein sequence generation methods can draw on prior... (Review)
Review
Protein engineering seeks to identify protein sequences with optimized properties. When guided by machine learning, protein sequence generation methods can draw on prior knowledge and experimental efforts to improve this process. In this review, we highlight recent applications of machine learning to generate protein sequences, focusing on the emerging field of deep generative methods.
Topics: Amino Acid Sequence; Machine Learning; Protein Engineering
PubMed: 34051682
DOI: 10.1016/j.cbpa.2021.04.004 -
Biopolymers Jul 2015Building on the pioneering work of Ho and DeGrado (J Am Chem Soc 1987, 109, 6751-6758) in the late 1980s, protein design approaches have revealed many fundamental... (Review)
Review
Building on the pioneering work of Ho and DeGrado (J Am Chem Soc 1987, 109, 6751-6758) in the late 1980s, protein design approaches have revealed many fundamental features of protein structure and stability. We are now in the era that the early work presaged - the design of new proteins with practical applications and uses. Here we briefly survey some past milestones in protein design, in addition to highlighting recent progress and future aspirations.
Topics: Animals; Humans; Protein Engineering
PubMed: 25784145
DOI: 10.1002/bip.22639 -
Current Opinion in Biotechnology Oct 2017Taking inspiration from Nature, synthetic biology utilizes and modifies biological components to expand the range of biological functions for engineering new practical... (Review)
Review
Taking inspiration from Nature, synthetic biology utilizes and modifies biological components to expand the range of biological functions for engineering new practical devices and therapeutics. While early breakthroughs mainly concerned the design of gene circuits, recent efforts have focused on engineering signaling pathways to reprogram cellular functions. Since signal transduction across cell membranes initiates and controls intracellular signaling, membrane receptors have been targeted by diverse protein engineering approaches despite limited mechanistic understanding of their function. The modular architecture of several receptor families has enabled the empirical construction of chimeric receptors combining domains from distinct native receptors which have found successful immunotherapeutic applications. Meanwhile, progress in membrane protein structure determination, computational modeling and rational design promise to foster the engineering of a broader range of membrane receptor functions. Marrying empirical and rational membrane protein engineering approaches should enable the reprogramming of cells with widely diverse fine-tuned functions.
Topics: Animals; Cellular Reprogramming; Humans; Membrane Proteins; Models, Biological; Protein Engineering; Signal Transduction
PubMed: 28709113
DOI: 10.1016/j.copbio.2017.06.009 -
Drug Discovery Today Jan 2022Biological drugs or biopharmaceuticals off patent open a large market for biosimilars and biobetters, follow-on biologics. Biobetters, in particular, are new drugs... (Review)
Review
Biological drugs or biopharmaceuticals off patent open a large market for biosimilars and biobetters, follow-on biologics. Biobetters, in particular, are new drugs designed from existing ones with improved properties such as higher selectivity, stability, half-life and/or lower toxicity/immunogenicity. Glycosylation is one of the most used strategies to improve biological drugs, nonetheless bioconjugation is an additional alternative and refers to the covalent attachment of polymers to biological drugs. Extensive research on novel polymers is underway, nonetheless PEGylation is still the best alternative with the longest clinical track record. Innovative trends based on genetic engineering techniques such as fusion proteins and PASylation are also promising. In this review, all these alternatives wereexplored as well as current market trends, legislation and future perspectives.
Topics: Biological Products; Biosimilar Pharmaceuticals; Drug Therapy; Humans; Metabolic Engineering; Protein Engineering; Quality Improvement
PubMed: 34461236
DOI: 10.1016/j.drudis.2021.08.009 -
International Journal of Molecular... Oct 2015Over the last three decades, protein engineering has established itself as an important tool for the development of enzymes and (therapeutic) proteins with improved... (Review)
Review
Over the last three decades, protein engineering has established itself as an important tool for the development of enzymes and (therapeutic) proteins with improved characteristics. New mutagenesis techniques and computational design tools have greatly aided in the advancement of protein engineering. Yet, one of the pivotal components to further advance protein engineering strategies is the high-throughput screening of variants. Compartmentalization is one of the key features allowing miniaturization and acceleration of screening. This review focuses on novel screening technologies applied in protein engineering, highlighting flow cytometry- and microfluidics-based platforms.
Topics: Flow Cytometry; High-Throughput Screening Assays; Humans; Microfluidics; Protein Engineering
PubMed: 26492240
DOI: 10.3390/ijms161024918 -
Biotechnology Journal May 2013Protein engineering in the context of metabolic engineering is increasingly important to the field of industrial biotechnology. As the demand for biologically produced... (Review)
Review
Protein engineering in the context of metabolic engineering is increasingly important to the field of industrial biotechnology. As the demand for biologically produced food, fuels, chemicals, food additives, and pharmaceuticals continues to grow, the ability to design and modify proteins to accomplish new functions will be required to meet the high productivity demands for the metabolism of engineered organisms. We review advances in selecting, modeling, and engineering proteins to improve or alter their activity. Some of the methods have only recently been developed for general use and are just beginning to find greater application in the metabolic engineering community. We also discuss methods of generating random and targeted diversity in proteins to generate mutant libraries for analysis. Recent uses of these techniques to alter cofactor use; produce non-natural amino acids, alcohols, and carboxylic acids; and alter organism phenotypes are presented and discussed as examples of the successful engineering of proteins for metabolic engineering purposes.
Topics: Biotechnology; Metabolic Engineering; Protein Engineering; Synthetic Biology
PubMed: 23589443
DOI: 10.1002/biot.201200371