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Biochimica Et Biophysica Acta May 2016
Topics: Animals; Electron Transport; Electron Transport Chain Complex Proteins; Energy Metabolism; Gene Regulatory Networks; Humans; Protein Engineering
PubMed: 26940515
DOI: 10.1016/j.bbabio.2016.02.017 -
Bioinformatics (Oxford, England) Jan 2020Structure-based computational protein design (CPD) plays a critical role in advancing the field of protein engineering. Using an all-atom energy function, CPD tries to...
MOTIVATION
Structure-based computational protein design (CPD) plays a critical role in advancing the field of protein engineering. Using an all-atom energy function, CPD tries to identify amino acid sequences that fold into a target structure and ultimately perform a desired function. The usual approach considers a single rigid backbone as a target, which ignores backbone flexibility. Multistate design (MSD) allows instead to consider several backbone states simultaneously, defining challenging computational problems.
RESULTS
We introduce efficient reductions of positive MSD problems to Cost Function Networks with two different fitness definitions and implement them in the Pompd (Positive Multistate Protein design) software. Pompd is able to identify guaranteed optimal sequences of positive multistate full protein redesign problems and exhaustively enumerate suboptimal sequences close to the MSD optimum. Applied to nuclear magnetic resonance and back-rubbed X-ray structures, we observe that the average energy fitness provides the best sequence recovery. Our method outperforms state-of-the-art guaranteed computational design approaches by orders of magnitudes and can solve MSD problems with sizes previously unreachable with guaranteed algorithms.
AVAILABILITY AND IMPLEMENTATION
https://forgemia.inra.fr/thomas.schiex/pompd as documented Open Source.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
Topics: Algorithms; Amino Acid Sequence; Computational Biology; Protein Conformation; Protein Engineering; Proteins; Software
PubMed: 31199465
DOI: 10.1093/bioinformatics/btz497 -
Current Opinion in Structural Biology Aug 2016Therapeutic proteins are powerful next-generation drugs able to effectively treat diverse and devastating diseases, but the development and use of biotherapeutics... (Review)
Review
Therapeutic proteins are powerful next-generation drugs able to effectively treat diverse and devastating diseases, but the development and use of biotherapeutics entails unique challenges and risks. In particular, protein drugs are subject to immune surveillance in the human body, and ensuing antidrug immune responses can cause a wide range of problems including altered pharmacokinetics, loss of efficacy, and even life-threating complications. Here we review recent progress in technologies for engineering deimmunized biotherapeutics, placing particular emphasis on deletion of immunogenic antibody and T cell epitopes via experimentally or computationally guided mutagenesis.
Topics: Epitopes, T-Lymphocyte; Humans; Immunization; Protein Engineering; Proteins
PubMed: 27322891
DOI: 10.1016/j.sbi.2016.06.003 -
Faraday Discussions 2011Fundamental research into bioinorganic catalysis of the kind presented at this Faraday Discussion has the potential to turn inspiration drawn from impressive natural...
Fundamental research into bioinorganic catalysis of the kind presented at this Faraday Discussion has the potential to turn inspiration drawn from impressive natural energy and chemical transformations into artificial catalyst constructions useful to mankind. Creating bio-inspired artificial constructions requires a level of understanding well beyond simple description of structures and mechanisms of natural enzymes. To be useful, such description must be augmented by a practical sense of structural and energetic engineering tolerances of the mechanism. Significant barriers to achieving an engineering understanding of enzyme mechanisms arise from natural protein complexity. In certain cases we can surmount these barriers to understanding, such as natural electron tunneling, coupling of electron tunneling to light capture and proton exchange as well as simpler bond breaking redox catalysis. Hope for similar solutions of more complex bioinorganic enzymes is indicated in several papers presented in this Discussion. Armed with an engineering understanding of mechanism, the current serious frustrations to successful creation of functional artificial proteins that are rooted in protein complexity can fall away. Here we discuss the genetic and biological roots of protein complexity and show how to dodge and minimize the effects of complexity. In the best-understood cases, artificial enzymes can be designed from scratch using the simplest of protein scaffolds.
Topics: Biocatalysis; Enzymes; Protein Engineering
PubMed: 21322497
DOI: 10.1039/c005523a -
Bioorganic & Medicinal Chemistry Letters Sep 2022Miniproteins exhibit great potential as scaffolds for drug candidates because of their well-defined structure and good synthetic availability. Because of recently... (Review)
Review
Miniproteins exhibit great potential as scaffolds for drug candidates because of their well-defined structure and good synthetic availability. Because of recently described methodologies for their de novo design, the field of miniproteins is emerging and can provide molecules that effectively bind to problematic targets, i.e., those that have been previously considered to be undruggable. This review describes methodologies for the development of miniprotein scaffolds and for the construction of biologically active miniproteins.
Topics: Chemistry, Pharmaceutical; Protein Engineering
PubMed: 35660515
DOI: 10.1016/j.bmcl.2022.128806 -
Current Opinion in Structural Biology Aug 2009
Topics: Protein Engineering
PubMed: 19683427
DOI: 10.1016/j.sbi.2009.07.010 -
ACS Synthetic Biology Mar 2022In addition to its biological function, the stability of a protein is a major determinant for its applicability. Unfortunately, engineering proteins for improved... (Review)
Review
In addition to its biological function, the stability of a protein is a major determinant for its applicability. Unfortunately, engineering proteins for improved functionality usually results in destabilization of the protein. This so-called stability-function trade-off can be explained by the simple fact that the generation of a novel protein function─or the improvement of an existing one─necessitates the insertion of mutations, , deviations from the evolutionarily optimized wild-type sequence. In fact, it was demonstrated that gain-of-function mutations are not more destabilizing than other random mutations. The stability-function trade-off is a universal phenomenon during protein evolution that has been observed with completely different types of proteins, including enzymes, antibodies, and engineered binding scaffolds. In this review, we discuss three types of strategies that have been successfully deployed to overcome this omnipresent obstacle in protein engineering approaches: (i) using highly stable parental proteins, (ii) minimizing the extent of destabilization during functional engineering (by library optimization and/or coselection for stability and function), and (iii) repairing damaged mutants through stability engineering. The implementation of these strategies in protein engineering campaigns will facilitate the efficient generation of protein variants that are not only functional but also stable and therefore better-suited for subsequent applications.
Topics: Gene Library; Mutant Proteins; Mutation; Protein Engineering; Proteins
PubMed: 35258287
DOI: 10.1021/acssynbio.1c00512 -
Biochemical Society Transactions Feb 2016Glycosyltransferases (GTs) are powerful tools for the synthesis of complex and biologically-important carbohydrates. Wild-type GTs may not have all the properties and... (Review)
Review
Glycosyltransferases (GTs) are powerful tools for the synthesis of complex and biologically-important carbohydrates. Wild-type GTs may not have all the properties and functions that are desired for large-scale production of carbohydrates that exist in nature and those with non-natural modifications. With the increasing availability of crystal structures of GTs, especially those in the presence of donor and acceptor analogues, crystal structure-guided rational design has been quite successful in obtaining mutants with desired functionalities. With current limited understanding of the structure-activity relationship of GTs, directed evolution continues to be a useful approach for generating additional mutants with functionality that can be screened for in a high-throughput format. Mutating the amino acid residues constituting or close to the substrate-binding sites of GTs by structure-guided directed evolution (SGDE) further explores the biotechnological potential of GTs that can only be realized through enzyme engineering. This mini-review discusses the progress made towards GT engineering and the lessons learned for future engineering efforts and assay development.
Topics: Carbohydrates; Directed Molecular Evolution; Enzyme Assays; Glycosyltransferases; Protein Engineering; Structure-Activity Relationship
PubMed: 26862198
DOI: 10.1042/BST20150200 -
Molecules (Basel, Switzerland) Sep 2021Enzymes underpin the processes required for most biotransformations. However, natural enzymes are often not optimal for biotechnological uses and must be engineered for... (Review)
Review
Enzymes underpin the processes required for most biotransformations. However, natural enzymes are often not optimal for biotechnological uses and must be engineered for improved activity, specificity and stability. A rich and growing variety of wet-lab methods have been developed by researchers over decades to accomplish this goal. In this review such methods and their specific attributes are examined.
Topics: Animals; Biocatalysis; Catalytic Domain; Directed Molecular Evolution; Humans; Protein Engineering
PubMed: 34577070
DOI: 10.3390/molecules26185599 -
The Yale Journal of Biology and Medicine Dec 2017Nature has invented photoreceptor proteins that are involved in sensing and response to light in living organisms. Genetic code expansion (GCE) technology has provided... (Review)
Review
Nature has invented photoreceptor proteins that are involved in sensing and response to light in living organisms. Genetic code expansion (GCE) technology has provided new tools to transform light insensitive proteins into novel photoreceptor proteins. It is achieved by the site-specific incorporation of unnatural amino acids (Uaas) that carry light sensitive moieties serving as "pigments" that react to light via photo-decaging, cross-linking, or isomerization. Over the last two decades, various proteins including ion channels, GPCRs, transporters, and kinases have been successfully rendered light responsive owing to the functionalities of Uaas. Very recently, Cas9 protein has been engineered to enable light activation of genomic editing by CRISPR. Those novel proteins have not only led to discoveries of dynamic protein conformational changes with implications in diseases, but also facilitated the screening of ligand-protein and protein-protein interactions of pharmacological significance. This review covers the genetic editing principles for genetic code expansion and design concepts that guide the engineering of light-sensitive proteins. The applications have brought up a new concept of "optoproteomics" that, in contrast to "optogenetics," aims to combine optical methods and site-specific proteomics for investigating and intervening in biological functions.
Topics: Amino Acids; Animals; Gene Editing; Genetic Code; Humans; Mutagenesis, Site-Directed; Optogenetics; Photochemistry; Protein Engineering; Proteomics; RNA, Transfer; Recombinant Proteins
PubMed: 29259524
DOI: No ID Found