1
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Lipsh-Sokolik R, Fleishman SJ. Addressing epistasis in the design of protein function. Proc Natl Acad Sci U S A 2024; 121:e2314999121. [PMID: 39133844 PMCID: PMC11348311 DOI: 10.1073/pnas.2314999121] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024] Open
Abstract
Mutations in protein active sites can dramatically improve function. The active site, however, is densely packed and extremely sensitive to mutations. Therefore, some mutations may only be tolerated in combination with others in a phenomenon known as epistasis. Epistasis reduces the likelihood of obtaining improved functional variants and dramatically slows natural and lab evolutionary processes. Research has shed light on the molecular origins of epistasis and its role in shaping evolutionary trajectories and outcomes. In addition, sequence- and AI-based strategies that infer epistatic relationships from mutational patterns in natural or experimental evolution data have been used to design functional protein variants. In recent years, combinations of such approaches and atomistic design calculations have successfully predicted highly functional combinatorial mutations in active sites. These were used to design thousands of functional active-site variants, demonstrating that, while our understanding of epistasis remains incomplete, some of the determinants that are critical for accurate design are now sufficiently understood. We conclude that the space of active-site variants that has been explored by evolution may be expanded dramatically to enhance natural activities or discover new ones. Furthermore, design opens the way to systematically exploring sequence and structure space and mutational impacts on function, deepening our understanding and control over protein activity.
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Affiliation(s)
- Rosalie Lipsh-Sokolik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sarel J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
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2
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Tanoz I, Timsit Y. Protein Fold Usages in Ribosomes: Another Glance to the Past. Int J Mol Sci 2024; 25:8806. [PMID: 39201491 PMCID: PMC11354259 DOI: 10.3390/ijms25168806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Revised: 08/07/2024] [Accepted: 08/08/2024] [Indexed: 09/02/2024] Open
Abstract
The analysis of protein fold usage, similar to codon usage, offers profound insights into the evolution of biological systems and the origins of modern proteomes. While previous studies have examined fold distribution in modern genomes, our study focuses on the comparative distribution and usage of protein folds in ribosomes across bacteria, archaea, and eukaryotes. We identify the prevalence of certain 'super-ribosome folds,' such as the OB fold in bacteria and the SH3 domain in archaea and eukaryotes. The observed protein fold distribution in the ribosomes announces the future power-law distribution where only a few folds are highly prevalent, and most are rare. Additionally, we highlight the presence of three copies of proto-Rossmann folds in ribosomes across all kingdoms, showing its ancient and fundamental role in ribosomal structure and function. Our study also explores early mechanisms of molecular convergence, where different protein folds bind equivalent ribosomal RNA structures in ribosomes across different kingdoms. This comparative analysis enhances our understanding of ribosomal evolution, particularly the distinct evolutionary paths of the large and small subunits, and underscores the complex interplay between RNA and protein components in the transition from the RNA world to modern cellular life. Transcending the concept of folds also makes it possible to group a large number of ribosomal proteins into five categories of urfolds or metafolds, which could attest to their ancestral character and common origins. This work also demonstrates that the gradual acquisition of extensions by simple but ordered folds constitutes an inexorable evolutionary mechanism. This observation supports the idea that simple but structured ribosomal proteins preceded the development of their disordered extensions.
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Affiliation(s)
- Inzhu Tanoz
- Aix-Marseille Université, Université de Toulon, IRD, CNRS, Mediterranean Institute of Oceanography (MIO), UM 110, 13288 Marseille, France;
| | - Youri Timsit
- Aix-Marseille Université, Université de Toulon, IRD, CNRS, Mediterranean Institute of Oceanography (MIO), UM 110, 13288 Marseille, France;
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 3 Rue Michel-Ange, 75016 Paris, France
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3
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Middendorf L, Ravi Iyengar B, Eicholt LA. Sequence, Structure, and Functional Space of Drosophila De Novo Proteins. Genome Biol Evol 2024; 16:evae176. [PMID: 39212966 PMCID: PMC11363682 DOI: 10.1093/gbe/evae176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/29/2024] [Indexed: 09/04/2024] Open
Abstract
During de novo emergence, new protein coding genes emerge from previously nongenic sequences. The de novo proteins they encode are dissimilar in composition and predicted biochemical properties to conserved proteins. However, functional de novo proteins indeed exist. Both identification of functional de novo proteins and their structural characterization are experimentally laborious. To identify functional and structured de novo proteins in silico, we applied recently developed machine learning based tools and found that most de novo proteins are indeed different from conserved proteins both in their structure and sequence. However, some de novo proteins are predicted to adopt known protein folds, participate in cellular reactions, and to form biomolecular condensates. Apart from broadening our understanding of de novo protein evolution, our study also provides a large set of testable hypotheses for focused experimental studies on structure and function of de novo proteins in Drosophila.
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Affiliation(s)
- Lasse Middendorf
- Institute for Evolution and Biodiversity, University of Muenster, Huefferstrasse 1, 48149 Muenster, Germany
| | - Bharat Ravi Iyengar
- Institute for Evolution and Biodiversity, University of Muenster, Huefferstrasse 1, 48149 Muenster, Germany
| | - Lars A Eicholt
- Institute for Evolution and Biodiversity, University of Muenster, Huefferstrasse 1, 48149 Muenster, Germany
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4
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Listov D, Goverde CA, Correia BE, Fleishman SJ. Opportunities and challenges in design and optimization of protein function. Nat Rev Mol Cell Biol 2024; 25:639-653. [PMID: 38565617 PMCID: PMC7616297 DOI: 10.1038/s41580-024-00718-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2024] [Indexed: 04/04/2024]
Abstract
The field of protein design has made remarkable progress over the past decade. Historically, the low reliability of purely structure-based design methods limited their application, but recent strategies that combine structure-based and sequence-based calculations, as well as machine learning tools, have dramatically improved protein engineering and design. In this Review, we discuss how these methods have enabled the design of increasingly complex structures and therapeutically relevant activities. Additionally, protein optimization methods have improved the stability and activity of complex eukaryotic proteins. Thanks to their increased reliability, computational design methods have been applied to improve therapeutics and enzymes for green chemistry and have generated vaccine antigens, antivirals and drug-delivery nano-vehicles. Moreover, the high success of design methods reflects an increased understanding of basic rules that govern the relationships among protein sequence, structure and function. However, de novo design is still limited mostly to α-helix bundles, restricting its potential to generate sophisticated enzymes and diverse protein and small-molecule binders. Designing complex protein structures is a challenging but necessary next step if we are to realize our objective of generating new-to-nature activities.
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Affiliation(s)
- Dina Listov
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Casper A Goverde
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Bruno E Correia
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| | - Sarel Jacob Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
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5
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Alpay BA, Desai MM. Effects of selection stringency on the outcomes of directed evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.09.598029. [PMID: 38895455 PMCID: PMC11185767 DOI: 10.1101/2024.06.09.598029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Directed evolution makes mutant lineages compete in climbing complicated sequence-function landscapes. Given this underlying complexity it is unclear how selection stringency, a ubiquitous parameter of directed evolution, impacts the outcome. Here we approach this question in terms of the fitnesses of the candidate variants at each round and the heterogeneity of their distributions of fitness effects. We show that even if the fittest mutant is most likely to yield the fittest mutants in the next round of selection, diversification can improve outcomes by sampling a larger variety of fitness effects. We find that heterogeneity in fitness effects between variants, larger population sizes, and evolution over a greater number of rounds all encourage diversification.
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Affiliation(s)
- Berk A. Alpay
- Systems, Synthetic, and Quantitative Biology Program, Harvard University, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Michael M. Desai
- Systems, Synthetic, and Quantitative Biology Program, Harvard University, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Physics, Harvard University, Cambridge, MA, USA
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6
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Toledo-Patiño S, Goetz SK, Shanmugaratnam S, Höcker B, Farías-Rico JA. Molecular handcraft of a well-folded protein chimera. FEBS Lett 2024; 598:1375-1386. [PMID: 38508768 DOI: 10.1002/1873-3468.14856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 02/11/2024] [Accepted: 02/12/2024] [Indexed: 03/22/2024]
Abstract
Modular assembly is a compelling pathway to create new proteins, a concept supported by protein engineering and millennia of evolution. Natural evolution provided a repository of building blocks, known as domains, which trace back to even shorter segments that underwent numerous 'copy-paste' processes culminating in the scaffolds we see today. Utilizing the subdomain-database Fuzzle, we constructed a fold-chimera by integrating a flavodoxin-like fragment into a periplasmic binding protein. This chimera is well-folded and a crystal structure reveals stable interfaces between the fragments. These findings demonstrate the adaptability of α/β-proteins and offer a stepping stone for optimization. By emphasizing the practicality of fragment databases, our work pioneers new pathways in protein engineering. Ultimately, the results substantiate the conjecture that periplasmic binding proteins originated from a flavodoxin-like ancestor.
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Affiliation(s)
- Saacnicteh Toledo-Patiño
- Max Planck Institute for Developmental Biology, Tübingen, Germany
- Okinawa Institute of Science and Technology Graduate University, Japan
| | | | - Sooruban Shanmugaratnam
- Max Planck Institute for Developmental Biology, Tübingen, Germany
- Department of Biochemistry, University of Bayreuth, Germany
| | - Birte Höcker
- Max Planck Institute for Developmental Biology, Tübingen, Germany
- Department of Biochemistry, University of Bayreuth, Germany
| | - José Arcadio Farías-Rico
- Max Planck Institute for Developmental Biology, Tübingen, Germany
- Synthetic Biology Program, Center for Genome Sciences, National Autonomous University of Mexico, Cuernavaca, Mexico
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7
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Blanchard PL, Knick BJ, Whelan SA, Hackel BJ. Hyperstable Synthetic Mini-Proteins as Effective Ligand Scaffolds. ACS Synth Biol 2023; 12:3608-3622. [PMID: 38010428 PMCID: PMC10822706 DOI: 10.1021/acssynbio.3c00409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Small, single-domain protein scaffolds are compelling sources of molecular binding ligands with the potential for efficient physiological transport, modularity, and manufacturing. Yet, mini-proteins require a balance between biophysical robustness and diversity to enable new functions. We tested the developability and evolvability of millions of variants of 43 designed libraries of synthetic 40-amino acid βαββ proteins with diversified sheet, loop, or helix paratopes. We discovered a scaffold library that yielded hundreds of binders to seven targets while exhibiting high stability and soluble expression. Binder discovery yielded 6-122 nM affinities without affinity maturation and Tms averaging ≥78 °C. Broader βαββ libraries exhibited varied developability and evolvability. Sheet paratopes were the most consistently developable, and framework 1 was the most evolvable. Paratope evolvability was dependent on target, though several libraries were evolvable across many targets while exhibiting high stability and soluble expression. Select βαββ proteins are strong starting points for engineering performant binders.
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Affiliation(s)
- Paul L. Blanchard
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Avenue SE, Minneapolis, MN 55455
| | - Brandon J. Knick
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Avenue SE, Minneapolis, MN 55455
| | - Sarah A. Whelan
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Avenue SE, Minneapolis, MN 55455
| | - Benjamin J. Hackel
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Avenue SE, Minneapolis, MN 55455
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8
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McConnell A, Batten SL, Hackel BJ. Determinants of Developability and Evolvability of Synthetic Miniproteins as Ligand Scaffolds. J Mol Biol 2023; 435:168339. [PMID: 37923119 PMCID: PMC10872777 DOI: 10.1016/j.jmb.2023.168339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/23/2023] [Accepted: 10/28/2023] [Indexed: 11/07/2023]
Abstract
Binding ligands empower molecular therapeutics and diagnostics. Despite an array of protein scaffolds engineered for binding, the biophysical elements that drive developability and evolvability are not fully understood. In particular, engineering novel function while maintaining biophysical integrity within the context of small, single-domain proteins is challenged by integration of the structural framework and the evolved binding site. Miniproteins present a challenge to our limits of protein engineering capability and provide advantages in physiological targeting, modularity for multi-functional constructs, and unique binding modes. Herein, we evaluate the ability of hyperstable synthetic miniproteins, originally designed for foldedness, to function as binding scaffolds. We synthesized 45 combinatorial libraries, with 109 variants, systematically varied across two topologies, each with five starting frameworks and four or five diverse, structurally distinct paratopes, to elucidate their impact on evolvability and developability. We evaluated evolvability with yeast display binding selections against four targets. High-throughput assays -stability via yeast display and soluble expression via split-GFP in E. coli - measured developability. The comprehensive, robust dataset demonstrates how protein topology, parental framework, and paratope structure and location all impact scaffold performance. A hyperstable framework and localized diversity are not sufficient for an effective scaffold, but several designs of these elements within synthetic miniproteins designed solely for stability result in scaffold libraries with effective evolvability and developability. Engineered variants were well-folded, thermally stable, and bound target with single-digit nanomolar affinity. Thus, hyperstable synthetic miniproteins can serve as precursors to developable, evolvable mini-scaffolds with unique potential for physiological transport, modularity, and binding modes.
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Affiliation(s)
- Adam McConnell
- Department of Biomedical Engineering, University of Minnesota - Twin Cities, Minneapolis, MN 55455, United States
| | - Sun Li Batten
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, Minneapolis, MN 55455, United States
| | - Benjamin J Hackel
- Department of Biomedical Engineering, University of Minnesota - Twin Cities, Minneapolis, MN 55455, United States; Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, Minneapolis, MN 55455, United States.
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9
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Buda K, Miton CM, Fan XC, Tokuriki N. Molecular determinants of protein evolvability. Trends Biochem Sci 2023; 48:751-760. [PMID: 37330341 DOI: 10.1016/j.tibs.2023.05.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/18/2023] [Accepted: 05/23/2023] [Indexed: 06/19/2023]
Abstract
The plethora of biological functions that sustain life is rooted in the remarkable evolvability of proteins. An emerging view highlights the importance of a protein's initial state in dictating evolutionary success. A deeper comprehension of the mechanisms that govern the evolvability of these initial states can provide invaluable insights into protein evolution. In this review, we describe several molecular determinants of protein evolvability, unveiled by experimental evolution and ancestral sequence reconstruction studies. We further discuss how genetic variation and epistasis can promote or constrain functional innovation and suggest putative underlying mechanisms. By establishing a clear framework for these determinants, we provide potential indicators enabling the forecast of suitable evolutionary starting points and delineate molecular mechanisms in need of deeper exploration.
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Affiliation(s)
- Karol Buda
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Charlotte M Miton
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Xingyu Cara Fan
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada.
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10
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Dhamayanti E, Priyowidodo D, Nurcahyo W, Firdausy LW. Morphological and molecular characteristics of Plasmodium juxtanucleare in layer chicken from three districts of Yogyakarta, Indonesia. Vet World 2023; 16:1576-1583. [PMID: 37766720 PMCID: PMC10521189 DOI: 10.14202/vetworld.2023.1576-1583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 06/22/2023] [Indexed: 09/29/2023] Open
Abstract
Background and Aim Blood parasite infections in poultry, such as Plasmodium, are a serious threat to the poultry industry due to their potential to cause economic losses. To date, there has been inadequate research on the morphological and molecular detection of the different Plasmodium species that infect poultry in Indonesia. Therefore, this study aimed to analyze the morphological and molecular characteristics of Plasmodium spp. and the several predisposing factors for Plasmodium infection in layer chickens from three districts of Yogyakarta, Indonesia. Materials and Methods One hundred and five blood samples from layer chickens were collected from 13 farms located in three districts of Yogyakarta (Sleman, Bantul, and Kulon Progo) between September and November 2022. Blood samples were subjected to microscopic and polymerase chain reaction (PCR) analyses. Sequencing was performed using basic local alignment search tools to identify the nucleotide structure of cytochrome b. Phylogenetic analysis of Plasmodium was performed using the MEGA-X software. Results Microscopic examination revealed that 17/105 positives (16.19%) were positive for blood parasite infection. Trophozoites, erythrocytic meronts, and microgametocytes of Plasmodium were found in blood samples. Based on the morphological examination, the species found in the samples was close to Plasmodium juxtanucleare. Polymerase chain reaction examination revealed that 21/60 samples were positive for Plasmodium (35%). The Plasmodium species identified from the sequenced samples were proven to be P. juxtanucleare. The P. juxtanucleare from Thailand was closely related to samples (99.64%-100%) with a genetic distance of 0%-1%. In addition, age, population, and cage type were not significantly associated with Plasmodium infection. Conclusion Based on microscopic and PCR examinations, the Plasmodium species found in the three districts of Yogyakarta was P. juxtanucleare. The genetic distance between samples from the three districts of Yogyakarta was closely related (0%-1%) to P. juxtanucleare from Thailand and Japan. There was no correlation between Plasmodium infection and age, cage type, or population.
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Affiliation(s)
- Esti Dhamayanti
- Department of Poultry Health and Disease Management, Veterinary Science Program, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Dwi Priyowidodo
- Department of Parasitology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Wisnu Nurcahyo
- Department of Parasitology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Lintang Winantya Firdausy
- Department of Parasitology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
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11
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Wozniak K, Brzezinski K. Biological Catalysis and Information Storage Have Relied on N-Glycosyl Derivatives of β-D-Ribofuranose since the Origins of Life. Biomolecules 2023; 13:biom13050782. [PMID: 37238652 DOI: 10.3390/biom13050782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/24/2023] [Accepted: 04/29/2023] [Indexed: 05/28/2023] Open
Abstract
Most naturally occurring nucleotides and nucleosides are N-glycosyl derivatives of β-d-ribose. These N-ribosides are involved in most metabolic processes that occur in cells. They are essential components of nucleic acids, forming the basis for genetic information storage and flow. Moreover, these compounds are involved in numerous catalytic processes, including chemical energy production and storage, in which they serve as cofactors or coribozymes. From a chemical point of view, the overall structure of nucleotides and nucleosides is very similar and simple. However, their unique chemical and structural features render these compounds versatile building blocks that are crucial for life processes in all known organisms. Notably, the universal function of these compounds in encoding genetic information and cellular catalysis strongly suggests their essential role in the origins of life. In this review, we summarize major issues related to the role of N-ribosides in biological systems, especially in the context of the origin of life and its further evolution, through the RNA-based World(s), toward the life we observe today. We also discuss possible reasons why life has arisen from derivatives of β-d-ribofuranose instead of compounds based on other sugar moieties.
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Affiliation(s)
- Katarzyna Wozniak
- Department of Structural Biology of Prokaryotic Organisms, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-074 Poznan, Poland
| | - Krzysztof Brzezinski
- Department of Structural Biology of Prokaryotic Organisms, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-074 Poznan, Poland
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12
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Aubel M, Eicholt L, Bornberg-Bauer E. Assessing structure and disorder prediction tools for de novo emerged proteins in the age of machine learning. F1000Res 2023; 12:347. [PMID: 37113259 PMCID: PMC10126731 DOI: 10.12688/f1000research.130443.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/17/2023] [Indexed: 03/31/2023] Open
Abstract
Background: De novo protein coding genes emerge from scratch in the non-coding regions of the genome and have, per definition, no homology to other genes. Therefore, their encoded de novo proteins belong to the so-called "dark protein space". So far, only four de novo protein structures have been experimentally approximated. Low homology, presumed high disorder and limited structures result in low confidence structural predictions for de novo proteins in most cases. Here, we look at the most widely used structure and disorder predictors and assess their applicability for de novo emerged proteins. Since AlphaFold2 is based on the generation of multiple sequence alignments and was trained on solved structures of largely conserved and globular proteins, its performance on de novo proteins remains unknown. More recently, natural language models of proteins have been used for alignment-free structure predictions, potentially making them more suitable for de novo proteins than AlphaFold2. Methods: We applied different disorder predictors (IUPred3 short/long, flDPnn) and structure predictors, AlphaFold2 on the one hand and language-based models (Omegafold, ESMfold, RGN2) on the other hand, to four de novo proteins with experimental evidence on structure. We compared the resulting predictions between the different predictors as well as to the existing experimental evidence. Results: Results from IUPred, the most widely used disorder predictor, depend heavily on the choice of parameters and differ significantly from flDPnn which has been found to outperform most other predictors in a comparative assessment study recently. Similarly, different structure predictors yielded varying results and confidence scores for de novo proteins. Conclusions: We suggest that, while in some cases protein language model based approaches might be more accurate than AlphaFold2, the structure prediction of de novo emerged proteins remains a difficult task for any predictor, be it disorder or structure.
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Affiliation(s)
- Margaux Aubel
- Institute for Evolution and Bidiversity, University of Muenster, Muenster, 48149, Germany
| | - Lars Eicholt
- Institute for Evolution and Bidiversity, University of Muenster, Muenster, 48149, Germany
| | - Erich Bornberg-Bauer
- Institute for Evolution and Bidiversity, University of Muenster, Muenster, 48149, Germany
- Department Protein Evolution, Max Planck-Institute for Biology, Tuebingen, 72076, Germany
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13
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Triveri A, Casali E, Frasnetti E, Doria F, Frigerio F, Cinquini F, Pavoni S, Moroni E, Marchetti F, Serapian SA, Colombo G. Conformational Behavior of SARS-Cov-2 Spike Protein Variants: Evolutionary Jumps in Sequence Reverberate in Structural Dynamic Differences. J Chem Theory Comput 2023; 19:2120-2134. [PMID: 36926878 PMCID: PMC10029694 DOI: 10.1021/acs.jctc.3c00077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
SARS-CoV-2 has evolved rapidly in the first 3 years of pandemic diffusion. The initial evolution of the virus appeared to proceed through big jumps in sequence changes rather than through the stepwise accumulation of point mutations on already established variants. Here, we examine whether this nonlinear mutational process reverberates in variations of the conformational dynamics of the SARS-CoV-2 Spike protein (S-protein), the first point of contact between the virus and the human host. We run extensive microsecond-scale molecular dynamics simulations of seven distinct variants of the protein in their fully glycosylated state and set out to elucidate possible links between the mutational spectrum of the S-protein and the structural dynamics of the respective variant, at global and local levels. The results reveal that mutation-dependent structural and dynamic modulations mostly consist of increased coordinated motions in variants that acquire stability and in an increased internal flexibility in variants that are less stable. Importantly, a limited number of functionally important substructures (the receptor binding domain, in particular) share the same time of movements in all variants, indicating efficient preorganization for functional regions dedicated to host interactions. Our results support a model in which the internal dynamics of the S-proteins from different strains varies in a way that reflects the observed random and non-stepwise jumps in sequence evolution, while conserving the functionally oriented traits of conformational dynamics necessary to support productive interactions with host receptors.
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Affiliation(s)
- Alice Triveri
- Dipartimento di Chimica,
Università di Pavia, via Taramelli 12, 27100 Pavia,
Italy
| | - Emanuele Casali
- Dipartimento di Chimica,
Università di Pavia, via Taramelli 12, 27100 Pavia,
Italy
| | - Elena Frasnetti
- Dipartimento di Chimica,
Università di Pavia, via Taramelli 12, 27100 Pavia,
Italy
| | - Filippo Doria
- Dipartimento di Chimica,
Università di Pavia, via Taramelli 12, 27100 Pavia,
Italy
| | - Francesco Frigerio
- Department of Physical Chemistry, R&D
Eni SpA, via Maritano 27, 20097 San Donato Milanese (Mi),
Italy
| | - Fabrizio Cinquini
- Upstream & Technical
Services—TECS/STES—Eni Spa, via Emilia 1, 20097 San Donato
Milanese (Mi), Italy
| | - Silvia Pavoni
- Department of Physical Chemistry, R&D
Eni SpA, via Maritano 27, 20097 San Donato Milanese (Mi),
Italy
| | | | - Filippo Marchetti
- Dipartimento di Chimica,
Università di Pavia, via Taramelli 12, 27100 Pavia,
Italy
| | - Stefano A. Serapian
- Dipartimento di Chimica,
Università di Pavia, via Taramelli 12, 27100 Pavia,
Italy
| | - Giorgio Colombo
- Dipartimento di Chimica,
Università di Pavia, via Taramelli 12, 27100 Pavia,
Italy
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14
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Lipsh-Sokolik R, Khersonsky O, Schröder SP, de Boer C, Hoch SY, Davies GJ, Overkleeft HS, Fleishman SJ. Combinatorial assembly and design of enzymes. Science 2023; 379:195-201. [PMID: 36634164 DOI: 10.1126/science.ade9434] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The design of structurally diverse enzymes is constrained by long-range interactions that are necessary for accurate folding. We introduce an atomistic and machine learning strategy for the combinatorial assembly and design of enzymes (CADENZ) to design fragments that combine with one another to generate diverse, low-energy structures with stable catalytic constellations. We applied CADENZ to endoxylanases and used activity-based protein profiling to recover thousands of structurally diverse enzymes. Functional designs exhibit high active-site preorganization and more stable and compact packing outside the active site. Implementing these lessons into CADENZ led to a 10-fold improved hit rate and more than 10,000 recovered enzymes. This design-test-learn loop can be applied, in principle, to any modular protein family, yielding huge diversity and general lessons on protein design principles.
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Affiliation(s)
- R Lipsh-Sokolik
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - O Khersonsky
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - S P Schröder
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, Netherlands
| | - C de Boer
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, Netherlands
| | - S-Y Hoch
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - G J Davies
- York Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York YO10 5DD, UK
| | - H S Overkleeft
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, Netherlands
| | - S J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
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15
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Kipnis Y, Chaib AO, Vorobieva AA, Cai G, Reggiano G, Basanta B, Kumar E, Mittl PR, Hilvert D, Baker D. Design and optimization of enzymatic activity in a de novo β-barrel scaffold. Protein Sci 2022; 31:e4405. [PMID: 36305767 PMCID: PMC9601869 DOI: 10.1002/pro.4405] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/11/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022]
Abstract
While native scaffolds offer a large diversity of shapes and topologies for enzyme engineering, their often unpredictable behavior in response to sequence modification makes de novo generated scaffolds an exciting alternative. Here we explore the customization of the backbone and sequence of a de novo designed eight stranded β-barrel protein to create catalysts for a retro-aldolase model reaction. We show that active and specific catalysts can be designed in this fold and use directed evolution to further optimize activity and stereoselectivity. Our results support previous suggestions that different folds have different inherent amenability to evolution and this property could account, in part, for the distribution of natural enzymes among different folds.
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Affiliation(s)
- Yakov Kipnis
- Department of BiochemistryUniversity of WashingtonSeattleUSA
- Institute for Protein DesignUniversity of WashingtonSeattleUSA
- Howard Hughes Medical InstituteUniversity of WashingtonSeattleUSA
| | | | - Anastassia A. Vorobieva
- Department of BiochemistryUniversity of WashingtonSeattleUSA
- Institute for Protein DesignUniversity of WashingtonSeattleUSA
- Howard Hughes Medical InstituteUniversity of WashingtonSeattleUSA
- VIB‐VUB Center for Structural BiologyVlaams Instituut voor BiotechnologieBrusselsBelgium
- Structural Biology BrusselsVrije Universiteit BrusselBrusselsBelgium
| | - Guangyang Cai
- Department of BiochemistryUniversity of WashingtonSeattleUSA
- Institute for Protein DesignUniversity of WashingtonSeattleUSA
| | - Gabriella Reggiano
- Department of BiochemistryUniversity of WashingtonSeattleUSA
- Institute for Protein DesignUniversity of WashingtonSeattleUSA
| | - Benjamin Basanta
- Department of BiochemistryUniversity of WashingtonSeattleUSA
- Institute for Protein DesignUniversity of WashingtonSeattleUSA
| | - Eshan Kumar
- Department of BiochemistryUniversity of WashingtonSeattleUSA
- Institute for Protein DesignUniversity of WashingtonSeattleUSA
| | - Peer R.E. Mittl
- Department of BiochemistryUniversity of ZurichZurichSwitzerland
| | - Donald Hilvert
- Laboratory of Organic ChemistryETH ZurichZurichSwitzerland
| | - David Baker
- Department of BiochemistryUniversity of WashingtonSeattleUSA
- Institute for Protein DesignUniversity of WashingtonSeattleUSA
- Howard Hughes Medical InstituteUniversity of WashingtonSeattleUSA
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16
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Harman JL, Reardon PN, Costello SM, Warren GD, Phillips SR, Connor PJ, Marqusee S, Harms MJ. Evolution avoids a pathological stabilizing interaction in the immune protein S100A9. Proc Natl Acad Sci U S A 2022; 119:e2208029119. [PMID: 36194634 PMCID: PMC9565474 DOI: 10.1073/pnas.2208029119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 09/07/2022] [Indexed: 01/03/2023] Open
Abstract
Stability constrains evolution. While much is known about constraints on destabilizing mutations, less is known about the constraints on stabilizing mutations. We recently identified a mutation in the innate immune protein S100A9 that provides insight into such constraints. When introduced into human S100A9, M63F simultaneously increases the stability of the protein and disrupts its natural ability to activate Toll-like receptor 4. Using chemical denaturation, we found that M63F stabilizes a calcium-bound conformation of hS100A9. We then used NMR to solve the structure of the mutant protein, revealing that the mutation distorts the hydrophobic binding surface of hS100A9, explaining its deleterious effect on function. Hydrogen-deuterium exchange (HDX) experiments revealed stabilization of the region around M63F in the structure, notably Phe37. In the structure of the M63F mutant, the Phe37 and Phe63 sidechains are in contact, plausibly forming an edge-face π-stack. Mutating Phe37 to Leu abolished the stabilizing effect of M63F as probed by both chemical denaturation and HDX. It also restored the biological activity of S100A9 disrupted by M63F. These findings reveal that Phe63 creates a molecular staple with Phe37 that stabilizes a nonfunctional conformation of the protein, thus disrupting function. Using a bioinformatic analysis, we found that S100A9 proteins from different organisms rarely have Phe at both positions 37 and 63, suggesting that avoiding a pathological stabilizing interaction indeed constrains S100A9 evolution. This work highlights an important evolutionary constraint on stabilizing mutations, namely, that they must avoid inappropriately stabilizing nonfunctional protein conformations.
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Affiliation(s)
- Joseph L. Harman
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403
| | - Patrick N. Reardon
- College of Science, NMR Facility, Oregon State University, Corvallis, OR 97331
| | - Shawn M. Costello
- Biophysics Graduate Program, University of California, Berkeley, Berkeley, CA 94720
| | - Gus D. Warren
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403
| | - Sophia R. Phillips
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403
| | - Patrick J. Connor
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403
| | - Susan Marqusee
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720
| | - Michael J. Harms
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403
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17
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Romero Romero ML, Landerer C, Poehls J, Toth‐Petroczy A. Phenotypic mutations contribute to protein diversity and shape protein evolution. Protein Sci 2022; 31:e4397. [PMID: 36040266 PMCID: PMC9375231 DOI: 10.1002/pro.4397] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/14/2022] [Accepted: 07/04/2022] [Indexed: 11/16/2022]
Abstract
Errors in DNA replication generate genetic mutations, while errors in transcription and translation lead to phenotypic mutations. Phenotypic mutations are orders of magnitude more frequent than genetic ones, yet they are less understood. Here, we review the types of phenotypic mutations, their quantifications, and their role in protein evolution and disease. The diversity generated by phenotypic mutation can facilitate adaptive evolution. Indeed, phenotypic mutations, such as ribosomal frameshift and stop codon readthrough, sometimes serve to regulate protein expression and function. Phenotypic mutations have often been linked to fitness decrease and diseases. Thus, understanding the protein heterogeneity and phenotypic diversity caused by phenotypic mutations will advance our understanding of protein evolution and have implications on human health and diseases.
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Affiliation(s)
- Maria Luisa Romero Romero
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Center for Systems Biology DresdenDresdenGermany
| | - Cedric Landerer
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Center for Systems Biology DresdenDresdenGermany
| | - Jonas Poehls
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Center for Systems Biology DresdenDresdenGermany
| | - Agnes Toth‐Petroczy
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Center for Systems Biology DresdenDresdenGermany
- Cluster of Excellence Physics of LifeTU DresdenDresdenGermany
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18
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Matsumura I, Patrick WM. Dan Tawfik's Lessons for Protein Engineers about Enzymes Adapting to New Substrates. Biochemistry 2022; 62:158-162. [PMID: 35820168 PMCID: PMC9851151 DOI: 10.1021/acs.biochem.2c00230] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Natural evolution has been creating new complex systems for billions of years. The process is spontaneous and requires neither intelligence nor moral purpose but is nevertheless difficult to understand. The late Dan Tawfik spent years studying enzymes as they adapted to recognize new substrates. Much of his work focused on gaining fundamental insights, so the practical utility of his experiments may not be obvious even to accomplished protein engineers. Here we focus on two questions fundamental to any directed evolution experiment. Which proteins are the best starting points for such experiments? Which trait(s) of the chosen parental protein should be evolved to achieve the desired outcome? We summarize Tawfik's contributions to our understanding of these problems, to honor his memory and encourage those unfamiliar with his ideas to read his publications.
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Affiliation(s)
- Ichiro Matsumura
- O.
Wayne Rollins Research Center, 1510 Clifton Road NE, Room 4001, Atlanta, Georgia 30322, United States,E-mail:
| | - Wayne M. Patrick
- Centre
for Biodiscovery, School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand,E-mail:
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19
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Harris KL, Thomson RES, Gumulya Y, Foley G, Carrera-Pacheco SE, Syed P, Janosik T, Sandinge AS, Andersson S, Jurva U, Bodén M, Gillam EMJ. Ancestral sequence reconstruction of a cytochrome P450 family involved in chemical defence reveals the functional evolution of a promiscuous, xenobiotic-metabolizing enzyme in vertebrates. Mol Biol Evol 2022; 39:6593376. [PMID: 35639613 PMCID: PMC9185370 DOI: 10.1093/molbev/msac116] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The cytochrome P450 family 1 enzymes (CYP1s) are a diverse family of hemoprotein monooxygenases, which metabolize many xenobiotics including numerous environmental carcinogens. However, their historical function and evolution remain largely unstudied. Here we investigate CYP1 evolution via the reconstruction and characterization of the vertebrate CYP1 ancestors. Younger ancestors and extant forms generally demonstrated higher activity toward typical CYP1 xenobiotic and steroid substrates than older ancestors, suggesting significant diversification away from the original CYP1 function. Caffeine metabolism appears to be a recently evolved trait of the CYP1A subfamily, observed in the mammalian CYP1A lineage, and may parallel the recent evolution of caffeine synthesis in multiple separate plant species. Likewise, the aryl hydrocarbon receptor agonist, 6-formylindolo[3,2-b]carbazole (FICZ) was metabolized to a greater extent by certain younger ancestors and extant forms, suggesting that activity toward FICZ increased in specific CYP1 evolutionary branches, a process that may have occurred in parallel to the exploitation of land where UV-exposure was higher than in aquatic environments. As observed with previous reconstructions of P450 enzymes, thermostability correlated with evolutionary age; the oldest ancestor was up to 35 °C more thermostable than the extant forms, with a 10T50 (temperature at which 50% of the hemoprotein remains intact after 10 min) of 71 °C. This robustness may have facilitated evolutionary diversification of the CYP1s by buffering the destabilizing effects of mutations that conferred novel functions, a phenomenon which may also be useful in exploiting the catalytic versatility of these ancestral enzymes for commercial application as biocatalysts.
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Affiliation(s)
- Kurt L Harris
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, 4072 Australia
| | - Raine E S Thomson
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, 4072 Australia
| | - Yosephine Gumulya
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, 4072 Australia
| | - Gabriel Foley
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, 4072 Australia
| | - Saskya E Carrera-Pacheco
- Centro de Investigación Biomédica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito 170147, Ecuador
| | - Parnayan Syed
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, 4072 Australia
| | - Tomasz Janosik
- RISE Research Institutes of Sweden, Division Bioeconomy and Health, Chemical Process and Pharmaceutical Development, Södertälje, Sweden
| | - Ann-Sofie Sandinge
- DMPK, Early Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, Astrazeneca, Gothenburg, Sweden
| | - Shalini Andersson
- Discovery Sciences, BioPharmaceuticals R&D, Astrazeneca, Gothenburg, Sweden
| | - Ulrik Jurva
- DMPK, Early Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, Astrazeneca, Gothenburg, Sweden
| | - Mikael Bodén
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, 4072 Australia
| | - Elizabeth M J Gillam
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, 4072 Australia
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20
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Planas-Iglesias J, Opaleny F, Ulbrich P, Stourac J, Sanusi Z, Pinto GP, Schenkmayerova A, Byska J, Damborsky J, Kozlikova B, Bednar D. LoopGrafter: a web tool for transplanting dynamical loops for protein engineering. Nucleic Acids Res 2022; 50:W465-W473. [PMID: 35438789 PMCID: PMC9252738 DOI: 10.1093/nar/gkac249] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/15/2022] [Accepted: 04/01/2022] [Indexed: 01/01/2023] Open
Abstract
The transplantation of loops between structurally related proteins is a compelling method to improve the activity, specificity and stability of enzymes. However, despite the interest of loop regions in protein engineering, the available methods of loop-based rational protein design are scarce. One particular difficulty related to loop engineering is the unique dynamism that enables them to exert allosteric control over the catalytic function of enzymes. Thus, when engaging in a transplantation effort, such dynamics in the context of protein structure need consideration. A second practical challenge is identifying successful excision points for the transplantation or grafting. Here, we present LoopGrafter (https://loschmidt.chemi.muni.cz/loopgrafter/), a web server that specifically guides in the loop grafting process between structurally related proteins. The server provides a step-by-step interactive procedure in which the user can successively identify loops in the two input proteins, calculate their geometries, assess their similarities and dynamics, and select a number of loops to be transplanted. All possible different chimeric proteins derived from any existing recombination point are calculated, and 3D models for each of them are constructed and energetically evaluated. The obtained results can be interactively visualized in a user-friendly graphical interface and downloaded for detailed structural analyses.
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Affiliation(s)
- Joan Planas-Iglesias
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic.,International Clinical Research Center, St Anne's University Hospital Brno, 656 916 Brno, Czech Republic
| | - Filip Opaleny
- Department of Visual Computing, Faculty of Informatics, Masaryk University, 602 00 Brno, Czech Republic
| | - Pavol Ulbrich
- Department of Visual Computing, Faculty of Informatics, Masaryk University, 602 00 Brno, Czech Republic
| | - Jan Stourac
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic.,International Clinical Research Center, St Anne's University Hospital Brno, 656 916 Brno, Czech Republic
| | - Zainab Sanusi
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Gaspar P Pinto
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic.,International Clinical Research Center, St Anne's University Hospital Brno, 656 916 Brno, Czech Republic
| | - Andrea Schenkmayerova
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic.,International Clinical Research Center, St Anne's University Hospital Brno, 656 916 Brno, Czech Republic
| | - Jan Byska
- Department of Visual Computing, Faculty of Informatics, Masaryk University, 602 00 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic.,International Clinical Research Center, St Anne's University Hospital Brno, 656 916 Brno, Czech Republic
| | - Barbora Kozlikova
- Department of Visual Computing, Faculty of Informatics, Masaryk University, 602 00 Brno, Czech Republic
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic.,International Clinical Research Center, St Anne's University Hospital Brno, 656 916 Brno, Czech Republic
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21
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Tee WV, Wah Tan Z, Guarnera E, Berezovsky IN. Conservation and diversity in allosteric fingerprints of proteins for evolutionary-inspired engineering and design. J Mol Biol 2022; 434:167577. [PMID: 35395233 DOI: 10.1016/j.jmb.2022.167577] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 03/30/2022] [Accepted: 03/30/2022] [Indexed: 11/26/2022]
Abstract
Hand-in-hand work of physics and evolution delivered protein universe with diversity of forms, sizes, and functions. Pervasiveness and advantageous traits of allostery made it an important component of the protein function regulation, calling for thorough investigation of its structural determinants and evolution. Learning directly from nature, we explored here allosteric communication in several major folds and repeat proteins, including α/β and β-barrels, β-propellers, Ig-like fold, ankyrin and α/β leucine-rich repeat proteins, which provide structural platforms for many different enzymatic and signalling functions. We obtained a picture of conserved allosteric communication characteristic in different fold types, modifications of the structure-driven signalling patterns via sequence-determined divergence to specific functions, as well as emergence and potential diversification of allosteric regulation in multi-domain proteins and oligomeric assemblies. Our observations will be instrumental in facilitating the engineering and de novo design of proteins with allosterically regulated functions, including development of therapeutic biologics. In particular, results described here may guide the identification of the optimal structural platforms (e.g. fold type, size, and oligomerization states) and the types of diversifications/perturbations, such as mutations, effector binding, and order-disorder transition. The tunable allosteric linkage across distant regions can be used as a pivotal component in the design/engineering of modular biological systems beyond the traditional scaffolding function.
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Affiliation(s)
- Wei-Ven Tee
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671
| | - Zhen Wah Tan
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671
| | - Enrico Guarnera
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671
| | - Igor N Berezovsky
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671; Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, Singapore 117597.
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22
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Linking protein structural and functional change to mutation using amino acid networks. PLoS One 2022; 17:e0261829. [PMID: 35061689 PMCID: PMC8782487 DOI: 10.1371/journal.pone.0261829] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 12/11/2021] [Indexed: 11/30/2022] Open
Abstract
The function of a protein is strongly dependent on its structure. During evolution, proteins acquire new functions through mutations in the amino-acid sequence. Given the advance in deep mutational scanning, recent findings have found functional change to be position dependent, notwithstanding the chemical properties of mutant and mutated amino acids. This could indicate that structural properties of a given position are potentially responsible for the functional relevance of a mutation. Here, we looked at the relation between structure and function of positions using five proteins with experimental data of functional change available. In order to measure structural change, we modeled mutated proteins via amino-acid networks and quantified the perturbation of each mutation. We found that structural change is position dependent, and strongly related to functional change. Strong changes in protein structure correlate with functional loss, and positions with functional gain due to mutations tend to be structurally robust. Finally, we constructed a computational method to predict functionally sensitive positions to mutations using structural change that performs well on all five proteins with a mean precision of 74.7% and recall of 69.3% of all functional positions.
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23
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Mascotti ML. Resurrecting Enzymes by Ancestral Sequence Reconstruction. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2397:111-136. [PMID: 34813062 DOI: 10.1007/978-1-0716-1826-4_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Ancestral Sequence Reconstruction (ASR) allows one to infer the sequences of extinct proteins using the phylogeny of extant proteins. It consists of disclosing the evolutionary history-i.e., the phylogeny-of a protein family of interest and then inferring the sequences of its ancestors-i.e., the nodes in the phylogeny. Assisted by gene synthesis, the selected ancestors can be resurrected in the lab and experimentally characterized. The crucial step to succeed with ASR is starting from a reliable phylogeny. At the same time, it is of the utmost importance to have a clear idea on the evolutionary history of the family under study and the events that influenced it. This allows us to implement ASR with well-defined hypotheses and to apply the appropriate experimental methods. In the last years, ASR has become popular to test hypotheses about the origin of functionalities, changes in activities, understanding physicochemical properties of proteins, among others. In this context, the aim of this chapter is to present the ASR approach applied to the reconstruction of enzymes-i.e., proteins with catalytic roles. The spirit of this contribution is to provide a basic, hands-to-work guide for biochemists and biologists who are unfamiliar with molecular phylogenetics.
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Affiliation(s)
- Maria Laura Mascotti
- Molecular Enzymology group, University of Groningen, Groningen, The Netherlands. .,IMIBIO-SL CONICET, Facultad de Química Bioquímica y Farmacia, Universidad Nacional de San Luis, San Luis, Argentina.
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24
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d’Oelsnitz S, Nguyen V, Alper HS, Ellington AD. Evolving a Generalist Biosensor for Bicyclic Monoterpenes. ACS Synth Biol 2022; 11:265-272. [PMID: 34985281 DOI: 10.1021/acssynbio.1c00402] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Prokaryotic transcription factors can be repurposed as analytical and synthetic tools for precise chemical measurement and regulation. Monoterpenes encompass a broad chemical family that are commercially valuable as flavors, cosmetics, and fragrances, but have proven difficult to measure, especially in cells. Herein, we develop genetically encoded, generalist monoterpene biosensors by using directed evolution to expand the effector specificity of the camphor-responsive TetR-family regulator CamR from Pseudomonas putida. Using a novel negative selection coupled with a high-throughput positive screen (Seamless Enrichment of Ligand-Inducible Sensors, SELIS), we evolve CamR biosensors that can recognize four distinct monoterpenes: borneol, fenchol, eucalyptol, and camphene. Different evolutionary trajectories surprisingly yielded common mutations, emphasizing the utility of CamR as a platform for creating generalist biosensors. Systematic promoter optimization driving the reporter increased the system's signal-to-noise ratio to 150-fold. These sensors can serve as a starting point for the high-throughput screening and dynamic regulation of bicyclic monoterpene production strains.
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Affiliation(s)
- Simon d’Oelsnitz
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Vylan Nguyen
- Freshman Research Initiative, University of Texas at Austin, Austin, Texas 78712, United States
| | - Hal S. Alper
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Andrew D. Ellington
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
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25
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Jackson C, Toth-Petroczy A, Kolodny R, Hollfelder F, Fuxreiter M, Caroline Lynn Kamerlin S, Tokuriki N. Adventures on the routes of protein evolution — in memoriam Dan Salah Tawfik (1955 - 2021). J Mol Biol 2022; 434:167462. [DOI: 10.1016/j.jmb.2022.167462] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 01/17/2022] [Indexed: 12/21/2022]
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26
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Structural and biochemical basis of a marine bacterial glycoside hydrolase family 2 β-glycosidase with broad substrate specificity. Appl Environ Microbiol 2021; 88:e0222621. [PMID: 34818100 DOI: 10.1128/aem.02226-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Uronic acids are commonly found in marine polysaccharides and increase structural complexity sanand intrinsic recalcitrance to enzymatic attack. The glycoside hydrolase family 2 (GH2) include proteins that target sugar conjugates with hexuronates and are involved in the catabolism and cycling of marine polysaccharides. Here, we reported a novel GH2, AqGalA from a marine algae-associated Bacteroidetes with broad-substrate specificity. Biochemical analyses revealed that AqGalA exhibits hydrolyzing activities against β-galacturonide, β-glucuronide, and β-galactopyranoside via retaining mechanisms. We solved the AqGalA crystal structure in complex with galacturonic acid (GalA) and showed (via mutagenesis) that charge characteristics at uronate-binding subsites controlled substrate selectivity for uronide hydrolysis. Additionally, conformational flexibility of the AqGalA active site pocket was proposed as a key component for broad substrate enzyme selectivity. Our AqGalA structural and functional data augments the current understanding of substrate recognition of GH2 enzymes and provided key insights into the bacterial use of uronic acid containing polysaccharides. IMPORTANCE The decomposition of algal glycans driven by marine bacterial communities represents one of the largest heterotrophic transformation of organic matter fueling marine food webs and global carbon cycling. However, our knowledge of the carbohydrate cycling is limited due to structural complexity of marine polysaccharides and the complicated enzymatic machinery of marine microbes. To degrade algal glycan, marine bacteria such as members of Bacteroidetes produce a complex repertoire of carbohydrate-active enzymes (CAZymes) matching the structural specificity of the different carbohydrates. In this study, we investigated an extracellular GH2 β-glycosidase, AqGalA from a marine Bacteroidetes to identify the key components responsible for glycuronides recognition and hydrolysis. The broad substrate specificity of AqGalA against glycosides with diverse stereochemical substitutions indicates its potential in processing complex marine polysaccharides. Our findings promote a better understanding of microbially-driven mechanisms of marine carbohydrate cycling.
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27
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Caetano-Anollés G, Aziz MF, Mughal F, Caetano-Anollés D. Tracing protein and proteome history with chronologies and networks: folding recapitulates evolution. Expert Rev Proteomics 2021; 18:863-880. [PMID: 34628994 DOI: 10.1080/14789450.2021.1992277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
INTRODUCTION While the origin and evolution of proteins remain mysterious, advances in evolutionary genomics and systems biology are facilitating the historical exploration of the structure, function and organization of proteins and proteomes. Molecular chronologies are series of time events describing the history of biological systems and subsystems and the rise of biological innovations. Together with time-varying networks, these chronologies provide a window into the past. AREAS COVERED Here, we review molecular chronologies and networks built with modern methods of phylogeny reconstruction. We discuss how chronologies of structural domain families uncover the explosive emergence of metabolism, the late rise of translation, the co-evolution of ribosomal proteins and rRNA, and the late development of the ribosomal exit tunnel; events that coincided with a tendency to shorten folding time. Evolving networks described the early emergence of domains and a late 'big bang' of domain combinations. EXPERT OPINION Two processes, folding and recruitment appear central to the evolutionary progression. The former increases protein persistence. The later fosters diversity. Chronologically, protein evolution mirrors folding by combining supersecondary structures into domains, developing translation machinery to facilitate folding speed and stability, and enhancing structural complexity by establishing long-distance interactions in novel structural and architectural designs.
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Affiliation(s)
- Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA.,C. R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, USA
| | - M Fayez Aziz
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA
| | - Fizza Mughal
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA
| | - Derek Caetano-Anollés
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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28
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Zhao VY, Rodrigues JV, Lozovsky ER, Hartl DL, Shakhnovich EI. Switching an active site helix in dihydrofolate reductase reveals limits to subdomain modularity. Biophys J 2021; 120:4738-4750. [PMID: 34571014 PMCID: PMC8595743 DOI: 10.1016/j.bpj.2021.09.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/14/2021] [Accepted: 09/22/2021] [Indexed: 11/23/2022] Open
Abstract
To what degree are individual structural elements within proteins modular such that similar structures from unrelated proteins can be interchanged? We study subdomain modularity by creating 20 chimeras of an enzyme, Escherichia coli dihydrofolate reductase (DHFR), in which a catalytically important, 10-residue α-helical sequence is replaced by α-helical sequences from a diverse set of proteins. The chimeras stably fold but have a range of diminished thermal stabilities and catalytic activities. Evolutionary coupling analysis indicates that the residues of this α-helix are under selection pressure to maintain catalytic activity in DHFR. Reversion to phenylalanine at key position 31 was found to partially restore catalytic activity, which could be explained by evolutionary coupling values. We performed molecular dynamics simulations using replica exchange with solute tempering. Chimeras with low catalytic activity exhibit nonhelical conformations that block the binding site and disrupt the positioning of the catalytically essential residue D27. Simulation observables and in vitro measurements of thermal stability and substrate-binding affinity are strongly correlated. Several E. coli strains with chromosomally integrated chimeric DHFRs can grow, with growth rates that follow predictions from a kinetic flux model that depends on the intracellular abundance and catalytic activity of DHFR. Our findings show that although α-helices are not universally substitutable, the molecular and fitness effects of modular segments can be predicted by the biophysical compatibility of the replacement segment.
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Affiliation(s)
- Victor Y Zhao
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts
| | - João V Rodrigues
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts
| | - Elena R Lozovsky
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts
| | - Daniel L Hartl
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts
| | - Eugene I Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts.
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29
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Triveri A, Serapian SA, Marchetti F, Doria F, Pavoni S, Cinquini F, Moroni E, Rasola A, Frigerio F, Colombo G. SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: A Computational Model of Epitope Loss in Variants of Concern. J Chem Inf Model 2021; 61:4687-4700. [PMID: 34468141 PMCID: PMC8479857 DOI: 10.1021/acs.jcim.1c00857] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Indexed: 12/30/2022]
Abstract
The SARS-CoV-2 spike (S) protein is exposed on the viral surface and is the first point of contact between the virus and the host. For these reasons it represents the prime target for Covid-19 vaccines. In recent months, variants of this protein have started to emerge. Their ability to reduce or evade recognition by S-targeting antibodies poses a threat to immunological treatments and raises concerns for their consequences on vaccine efficacy. To develop a model able to predict the potential impact of S-protein mutations on antibody binding sites, we performed unbiased multi-microsecond molecular dynamics of several glycosylated S-protein variants and applied a straightforward structure-dynamics-energy based strategy to predict potential changes in immunogenic regions on each variant. We recover known epitopes on the reference D614G sequence. By comparing our results, obtained on isolated S-proteins in solution, to recently published data on antibody binding and reactivity in new S variants, we directly show that modifications in the S-protein consistently translate into the loss of potentially immunoreactive regions. Our findings can thus be qualitatively reconnected to the experimentally characterized decreased ability of some of the Abs elicited against the dominant S-sequence to recognize variants. While based on the study of SARS-CoV-2 spike variants, our computational epitope-prediction strategy is portable and could be applied to study immunoreactivity in mutants of proteins of interest whose structures have been characterized, helping the development/selection of vaccines and antibodies able to control emerging variants.
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Affiliation(s)
- Alice Triveri
- Department
of Chemistry, University of Pavia, Via Taramelli 12, Pavia 27100, Italy
| | - Stefano A. Serapian
- Department
of Chemistry, University of Pavia, Via Taramelli 12, Pavia 27100, Italy
| | - Filippo Marchetti
- Department
of Chemistry, University of Pavia, Via Taramelli 12, Pavia 27100, Italy
| | - Filippo Doria
- Department
of Chemistry, University of Pavia, Via Taramelli 12, Pavia 27100, Italy
| | - Silvia Pavoni
- Department
of Physical Chemistry, R&D Eni SpA, Via Maritano 27, San Donato Milanese, Milan 20097, Italy
| | - Fabrizio Cinquini
- Upstream
& Technical Services—TECS/STES—Eni Spa, Via Emilia 1, San
Donato Milanese, Milan 20097, Italy
| | - Elisabetta Moroni
- Istituto
di Scienze e Tecnologie Chimiche “Giulio Natta”—SCITEC, CNR Via Mario Bianco 9, Milano 20131, Italy
| | - Andrea Rasola
- Department
of Biomedical Sciences, University of Padua, Viale G. Colombo 3, Padova 35131, Italy
| | - Francesco Frigerio
- Department
of Physical Chemistry, R&D Eni SpA, Via Maritano 27, San Donato Milanese, Milan 20097, Italy
| | - Giorgio Colombo
- Department
of Chemistry, University of Pavia, Via Taramelli 12, Pavia 27100, Italy
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30
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Kamiński K, Ludwiczak J, Jasiński M, Bukala A, Madaj R, Szczepaniak K, Dunin-Horkawicz S. Rossmann-toolbox: a deep learning-based protocol for the prediction and design of cofactor specificity in Rossmann fold proteins. Brief Bioinform 2021; 23:6375059. [PMID: 34571541 PMCID: PMC8769691 DOI: 10.1093/bib/bbab371] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/04/2021] [Accepted: 08/22/2021] [Indexed: 11/15/2022] Open
Abstract
The Rossmann fold enzymes are involved in essential biochemical pathways such as nucleotide and amino acid metabolism. Their functioning relies on interaction with cofactors, small nucleoside-based compounds specifically recognized by a conserved βαβ motif shared by all Rossmann fold proteins. While Rossmann methyltransferases recognize only a single cofactor type, the S-adenosylmethionine, the oxidoreductases, depending on the family, bind nicotinamide (nicotinamide adenine dinucleotide, nicotinamide adenine dinucleotide phosphate) or flavin-based (flavin adenine dinucleotide) cofactors. In this study, we showed that despite its short length, the βαβ motif unambiguously defines the specificity towards the cofactor. Following this observation, we trained two complementary deep learning models for the prediction of the cofactor specificity based on the sequence and structural features of the βαβ motif. A benchmark on two independent test sets, one containing βαβ motifs bearing no resemblance to those of the training set, and the other comprising 38 experimentally confirmed cases of rational design of the cofactor specificity, revealed the nearly perfect performance of the two methods. The Rossmann-toolbox protocols can be accessed via the webserver at https://lbs.cent.uw.edu.pl/rossmann-toolbox and are available as a Python package at https://github.com/labstructbioinf/rossmann-toolbox.
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Affiliation(s)
- Kamil Kamiński
- Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Jan Ludwiczak
- Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland.,Laboratory of Bioinformatics, Nencki Institute of Experimental Biology, Pasteura 3, 02-093 Warsaw, Poland
| | - Maciej Jasiński
- Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Adriana Bukala
- Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Rafal Madaj
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Lodz, Poland
| | - Krzysztof Szczepaniak
- Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Stanisław Dunin-Horkawicz
- Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
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31
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Stodola TJ, Chi YI, De Assuncao TM, Leverence EN, Tripathi S, Dsouza NR, Mathison AJ, Volkman BF, Smith BC, Lomberk G, Zimmermann MT, Urrutia R. Computational modeling reveals key molecular properties and dynamic behavior of disruptor of telomeric silencing 1-like (DOT1L) and partnering complexes involved in leukemogenesis. Proteins 2021; 90:282-298. [PMID: 34414607 PMCID: PMC8671179 DOI: 10.1002/prot.26219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 08/16/2021] [Indexed: 11/18/2022]
Abstract
Disruptor of telomeric silencing 1‐like (DOT1L) is the only non‐SET domain histone lysine methyltransferase (KMT) and writer of H3K79 methylation on nucleosomes marked by H2B ubiquitination. DOT1L has elicited significant attention because of its interaction or fusion with members of the AF protein family in blood cell biology and leukemogenic transformation. Here, our goal was to extend previous structural information by performing a robust molecular dynamic study of DOT1L and its leukemogenic partners combined with mutational analysis. We show that statically and dynamically, D161, G163, E186, and F223 make frequent time‐dependent interactions with SAM, while additional residues T139, K187, and N241 interact with SAM only under dynamics. Dynamics models reveal DOT1L, SAM, and H4 moving as one and show that more than twice the number of DOT1L residues interacts with these partners, relative to the static structure. Mutational analyses indicate that six of these residues are intolerant to substitution. We describe the dynamic behavior of DOT1L interacting with AF10 and AF9. Studies on the dynamics of a heterotrimeric complex of DOT1L1‐AF10 illuminated describe coordinated motions that impact the relative position of the DOT1L HMT domain to the nucleosome. The molecular motions of the DOT1L–AF9 complex are less extensive and highly dynamic, resembling a swivel‐like mechanics. Through molecular dynamics and mutational analysis, we extend the knowledge previous provided by static measurements. These results are important to consider when describing the biochemical properties of DOT1L, under normal and in disease conditions, as well as for the development of novel therapeutic agents.
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Affiliation(s)
- Timothy J Stodola
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Young-In Chi
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Thiago M De Assuncao
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Elise N Leverence
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Swarnendu Tripathi
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Nikita R Dsouza
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Angela J Mathison
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Brian F Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Brian C Smith
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Gwen Lomberk
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Michael T Zimmermann
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Raul Urrutia
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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32
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Gruic-Sovulj I, Longo LM, Jabłońska J, Tawfik DS. The evolutionary history of the HUP domain. Crit Rev Biochem Mol Biol 2021; 57:1-15. [PMID: 34384295 DOI: 10.1080/10409238.2021.1957764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Among the enzyme lineages that undoubtedly emerged prior to the last universal common ancestor is the so-called HUP, which includes Class I aminoacyl tRNA synthetases (AARSs) as well as enzymes mediating NAD, FAD, and CoA biosynthesis. Here, we provide a detailed analysis of HUP evolution, from emergence to structural and functional diversification. The HUP is a nucleotide binding domain that uniquely catalyzes adenylation via the release of pyrophosphate. In contrast to other ancient nucleotide binding domains with the αβα sandwich architecture, such as P-loop NTPases, the HUP's most conserved feature is not phosphate binding, but rather ribose binding by backbone interactions to the tips of β1 and/or β4. Indeed, the HUP exhibits unusual evolutionary plasticity and, while ribose binding is conserved, the location and mode of binding to the base and phosphate moieties of the nucleotide, and to the substrate(s) reacting with it, have diverged with time, foremost along the emergence of the AARSs. The HUP also beautifully demonstrates how a well-packed scaffold combined with evolvable surface elements promotes evolutionary innovation. Finally, we offer a scenario for the emergence of the HUP from a seed βαβ fragment, and suggest that despite an identical architecture, the HUP and the Rossmann represent independent emergences.
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Affiliation(s)
- Ita Gruic-Sovulj
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Liam M Longo
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.,Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
| | - Jagoda Jabłońska
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Dan S Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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33
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Álvarez-Lugo A, Becerra A. The Role of Gene Duplication in the Divergence of Enzyme Function: A Comparative Approach. Front Genet 2021; 12:641817. [PMID: 34335678 PMCID: PMC8318041 DOI: 10.3389/fgene.2021.641817] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 06/21/2021] [Indexed: 11/13/2022] Open
Abstract
Gene duplication is a crucial process involved in the appearance of new genes and functions. It is thought to have played a major role in the growth of enzyme families and the expansion of metabolism at the biosphere's dawn and in recent times. Here, we analyzed paralogous enzyme content within each of the seven enzymatic classes for a representative sample of prokaryotes by a comparative approach. We found a high ratio of paralogs for three enzymatic classes: oxidoreductases, isomerases, and translocases, and within each of them, most of the paralogs belong to only a few subclasses. Our results suggest an intricate scenario for the evolution of prokaryotic enzymes, involving different fates for duplicated enzymes fixed in the genome, where around 20-40% of prokaryotic enzymes have paralogs. Intracellular organisms have a lesser ratio of duplicated enzymes, whereas free-living enzymes show the highest ratios. We also found that phylogenetically close phyla and some unrelated but with the same lifestyle share similar genomic and biochemical traits, which ultimately support the idea that gene duplication is associated with environmental adaptation.
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Affiliation(s)
- Alejandro Álvarez-Lugo
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Arturo Becerra
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
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34
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Kolodny R, Nepomnyachiy S, Tawfik DS, Ben-Tal N. Bridging Themes: Short Protein Segments Found in Different Architectures. Mol Biol Evol 2021; 38:2191-2208. [PMID: 33502503 PMCID: PMC8136508 DOI: 10.1093/molbev/msab017] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The vast majority of theoretically possible polypeptide chains do not fold, let alone confer function. Hence, protein evolution from preexisting building blocks has clear potential advantages over ab initio emergence from random sequences. In support of this view, sequence similarities between different proteins is generally indicative of common ancestry, and we collectively refer to such homologous sequences as "themes." At the domain level, sequence homology is routinely detected. However, short themes which are segments, or fragments of intact domains, are particularly interesting because they may provide hints about the emergence of domains, as opposed to divergence of preexisting domains, or their mixing-and-matching to form multi-domain proteins. Here we identified 525 representative short themes, comprising 20-80 residues that are unexpectedly shared between domains considered to have emerged independently. Among these "bridging themes" are ones shared between the most ancient domains, for example, Rossmann, P-loop NTPase, TIM-barrel, flavodoxin, and ferredoxin-like. We elaborate on several particularly interesting cases, where the bridging themes mediate ligand binding. Ligand binding may have contributed to the stability and the plasticity of these building blocks, and to their ability to invade preexisting domains or serve as starting points for completely new domains.
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Affiliation(s)
- Rachel Kolodny
- Department of Computer Science, University of Haifa, Haifa, Israel
| | | | - Dan S Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Nir Ben-Tal
- George S. Wise Faculty of Life Sciences, Department of Biochemistry and Molecular Biology, Tel Aviv University, Tel Aviv, Israel
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35
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Heizinger L, Merkl R. Evidence for the preferential reuse of sub-domain motifs in primordial protein folds. Proteins 2021; 89:1167-1179. [PMID: 33957009 DOI: 10.1002/prot.26089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 04/15/2021] [Accepted: 04/28/2021] [Indexed: 11/06/2022]
Abstract
A comparison of protein backbones makes clear that not more than approximately 1400 different folds exist, each specifying the three-dimensional topology of a protein domain. Large proteins are composed of specific domain combinations and many domains can accommodate different functions. These findings confirm that the reuse of domains is key for the evolution of multi-domain proteins. If reuse was also the driving force for domain evolution, ancestral fragments of sub-domain size exist that are shared between domains possessing significantly different topologies. For the fully automated detection of putatively ancestral motifs, we developed the algorithm Fragstatt that compares proteins pairwise to identify fragments, that is, instantiations of the same motif. To reach maximal sensitivity, Fragstatt compares sequences by means of cascaded alignments of profile Hidden Markov Models. If the fragment sequences are sufficiently similar, the program determines and scores the structural concordance of the fragments. By analyzing a comprehensive set of proteins from the CATH database, Fragstatt identified 12 532 partially overlapping and structurally similar motifs that clustered to 134 unique motifs. The dissemination of these motifs is limited: We found only two domain topologies that contain two different motifs and generally, these motifs occur in not more than 18% of the CATH topologies. Interestingly, motifs are enriched in topologies that are considered ancestral. Thus, our findings suggest that the reuse of sub-domain sized fragments was relevant in early phases of protein evolution and became less important later on.
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Affiliation(s)
- Leonhard Heizinger
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
| | - Rainer Merkl
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
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36
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Tizei PAG, Harris E, Withanage S, Renders M, Pinheiro VB. A novel framework for engineering protein loops exploring length and compositional variation. Sci Rep 2021; 11:9134. [PMID: 33911147 PMCID: PMC8080606 DOI: 10.1038/s41598-021-88708-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 04/12/2021] [Indexed: 02/02/2023] Open
Abstract
Insertions and deletions (indels) are known to affect function, biophysical properties and substrate specificity of enzymes, and they play a central role in evolution. Despite such clear significance, this class of mutation remains an underexploited tool in protein engineering with few available platforms capable of systematically generating and analysing libraries of varying sequence composition and length. We present a novel DNA assembly platform (InDel assembly), based on cycles of endonuclease restriction digestion and ligation of standardised dsDNA building blocks, that can generate libraries exploring both composition and sequence length variation. In addition, we developed a framework to analyse the output of selection from InDel-generated libraries, combining next generation sequencing and alignment-free strategies for sequence analysis. We demonstrate the approach by engineering the well-characterized TEM-1 β-lactamase Ω-loop, involved in substrate specificity, identifying multiple novel extended spectrum β-lactamases with loops of modified length and composition-areas of the sequence space not previously explored. Together, the InDel assembly and analysis platforms provide an efficient route to engineer protein loops or linkers where sequence length and composition are both essential functional parameters.
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Affiliation(s)
- Pedro A. G. Tizei
- grid.83440.3b0000000121901201Department of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT UK
| | - Emma Harris
- grid.4464.20000 0001 2161 2573Department of Biological Sciences, University of London, Malet Street, Birkbeck, WC1E 7HX UK
| | - Shamal Withanage
- grid.415751.3KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49, Box 1041, 3000 Leuven, Belgium
| | - Marleen Renders
- grid.415751.3KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49, Box 1041, 3000 Leuven, Belgium
| | - Vitor B. Pinheiro
- grid.83440.3b0000000121901201Department of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT UK ,grid.4464.20000 0001 2161 2573Department of Biological Sciences, University of London, Malet Street, Birkbeck, WC1E 7HX UK ,grid.415751.3KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49, Box 1041, 3000 Leuven, Belgium
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37
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Yang Z, Sun J, Li Z, Qi Y, Wang P, Xu X. Robustness of protein: Using pH shifting and low speed shearing to partially recover conformation and dispersibility of myosin from pale, soft, exudative (PSE)-like chicken breast. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2020.110786] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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38
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Wang CK, Craik DJ. Linking molecular evolution to molecular grafting. J Biol Chem 2021; 296:100425. [PMID: 33600801 PMCID: PMC8005815 DOI: 10.1016/j.jbc.2021.100425] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 02/09/2021] [Accepted: 02/13/2021] [Indexed: 12/01/2022] Open
Abstract
Molecular grafting is a strategy for the engineering of molecular scaffolds into new functional agents, such as next-generation therapeutics. Despite its wide use, studies so far have focused almost exclusively on demonstrating its utility rather than understanding the factors that lead to either poor or successful grafting outcomes. Here, we examine protein evolution and identify parallels between the natural process of protein functional diversification and the artificial process of molecular grafting. We discuss features of natural proteins that are correlated to innovability-the capacity to acquire new functions-and describe their implications to molecular grafting scaffolds. Disulfide-rich peptides are used as exemplars because they are particularly promising scaffolds onto which new functions can be grafted. This article provides a perspective on why some scaffolds are more suitable for grafting than others, identifying opportunities on how molecular grafting might be improved.
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Affiliation(s)
- Conan K Wang
- Institute for Molecular Bioscience and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia.
| | - David J Craik
- Institute for Molecular Bioscience and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
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39
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Escudero JA, Nivina A, Kemble HE, Loot C, Tenaillon O, Mazel D. Primary and promiscuous functions coexist during evolutionary innovation through whole protein domain acquisitions. eLife 2020; 9:58061. [PMID: 33319743 PMCID: PMC7790495 DOI: 10.7554/elife.58061] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 12/14/2020] [Indexed: 11/13/2022] Open
Abstract
Molecular examples of evolutionary innovation are scarce and generally involve point mutations. Innovation can occur through larger rearrangements, but here experimental data is extremely limited. Integron integrases innovated from double-strand- toward single-strand-DNA recombination through the acquisition of the I2 α-helix. To investigate how this transition was possible, we have evolved integrase IntI1 to what should correspond to an early innovation state by selecting for its ancestral activity. Using synonymous alleles to enlarge sequence space exploration, we have retrieved 13 mutations affecting both I2 and the multimerization domains of IntI1. We circumvented epistasis constraints among them using a combinatorial library that revealed their individual and collective fitness effects. We obtained up to 104-fold increases in ancestral activity with various asymmetrical trade-offs in single-strand-DNA recombination. We show that high levels of primary and promiscuous functions could have initially coexisted following I2 acquisition, paving the way for a gradual evolution toward innovation.
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Affiliation(s)
- José Antonio Escudero
- Institut Pasteur, Unité de Plasticité du Génome Bactérien, Département Génomes et Génétique, Paris, France.,CNRS, UMR3525, Paris, France.,Molecular Basis of Adaptation, Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain.,VISAVET Health Surveillance Centre. Universidad Complutense Madrid. Avenida Puerta de Hierro, Madrid, Spain
| | - Aleksandra Nivina
- Institut Pasteur, Unité de Plasticité du Génome Bactérien, Département Génomes et Génétique, Paris, France.,CNRS, UMR3525, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Harry E Kemble
- Infection, Antimicrobials, Modelling, Evolution, INSERM, UMR 1137, Université Paris Diderot, Université Paris Nord, Paris, France
| | - Céline Loot
- Institut Pasteur, Unité de Plasticité du Génome Bactérien, Département Génomes et Génétique, Paris, France.,CNRS, UMR3525, Paris, France
| | - Olivier Tenaillon
- Infection, Antimicrobials, Modelling, Evolution, INSERM, UMR 1137, Université Paris Diderot, Université Paris Nord, Paris, France
| | - Didier Mazel
- Institut Pasteur, Unité de Plasticité du Génome Bactérien, Département Génomes et Génétique, Paris, France.,CNRS, UMR3525, Paris, France
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40
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Caldwell SJ, Haydon IC, Piperidou N, Huang PS, Bick MJ, Sjöström HS, Hilvert D, Baker D, Zeymer C. Tight and specific lanthanide binding in a de novo TIM barrel with a large internal cavity designed by symmetric domain fusion. Proc Natl Acad Sci U S A 2020; 117:30362-30369. [PMID: 33203677 PMCID: PMC7720202 DOI: 10.1073/pnas.2008535117] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
De novo protein design has succeeded in generating a large variety of globular proteins, but the construction of protein scaffolds with cavities that could accommodate large signaling molecules, cofactors, and substrates remains an outstanding challenge. The long, often flexible loops that form such cavities in many natural proteins are difficult to precisely program and thus challenging for computational protein design. Here we describe an alternative approach to this problem. We fused two stable proteins with C2 symmetry-a de novo designed dimeric ferredoxin fold and a de novo designed TIM barrel-such that their symmetry axes are aligned to create scaffolds with large cavities that can serve as binding pockets or enzymatic reaction chambers. The crystal structures of two such designs confirm the presence of a 420 cubic Ångström chamber defined by the top of the designed TIM barrel and the bottom of the ferredoxin dimer. We functionalized the scaffold by installing a metal-binding site consisting of four glutamate residues close to the symmetry axis. The protein binds lanthanide ions with very high affinity as demonstrated by tryptophan-enhanced terbium luminescence. This approach can be extended to other metals and cofactors, making this scaffold a modular platform for the design of binding proteins and biocatalysts.
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Affiliation(s)
- Shane J Caldwell
- Department of Biochemistry, University of Washington, Seattle, WA 98195
- Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Ian C Haydon
- Department of Biochemistry, University of Washington, Seattle, WA 98195
- Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Nikoletta Piperidou
- Laboratory of Organic Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zürich, Switzerland
| | - Po-Ssu Huang
- Department of Biochemistry, University of Washington, Seattle, WA 98195
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- Department of Bioengineering, Stanford University, Shriram Center for Bioengineering and Chemical Engineering, Stanford, CA 94305
| | - Matthew J Bick
- Department of Biochemistry, University of Washington, Seattle, WA 98195
- Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - H Sebastian Sjöström
- Laboratory of Organic Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zürich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zürich, Switzerland
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195;
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195
| | - Cathleen Zeymer
- Laboratory of Organic Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zürich, Switzerland;
- Department of Chemistry, Technische Universität München, 85747 Garching, Germany
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41
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Lipsh-Sokolik R, Listov D, Fleishman SJ. The AbDesign computational pipeline for modular backbone assembly and design of binders and enzymes. Protein Sci 2020; 30:151-159. [PMID: 33040418 PMCID: PMC7737780 DOI: 10.1002/pro.3970] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/07/2020] [Accepted: 10/09/2020] [Indexed: 12/12/2022]
Abstract
The functional sites of many protein families are dominated by diverse backbone regions that lack secondary structure (loops) but fold stably into their functionally competent state. Nevertheless, the design of structured loop regions from scratch, especially in functional sites, has met with great difficulty. We therefore developed an approach, called AbDesign, to exploit the natural modularity of many protein families and computationally assemble a large number of new backbones by combining naturally occurring modular fragments. This strategy yielded large, atomically accurate, and highly efficient proteins, including antibodies and enzymes exhibiting dozens of mutations from any natural protein. The combinatorial backbone‐conformation space that can be accessed by AbDesign even for a modestly sized family of homologs may exceed the diversity in the entire PDB, providing the sub‐Ångstrom level of control over the positioning of active‐site groups that is necessary for obtaining highly active proteins. This manuscript describes how to implement the pipeline using code that is freely available at https://github.com/Fleishman‐Lab/AbDesign_for_enzymes.
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Affiliation(s)
| | - Dina Listov
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Sarel J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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42
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Chalopin Y. The physical origin of rate promoting vibrations in enzymes revealed by structural rigidity. Sci Rep 2020; 10:17465. [PMID: 33060716 PMCID: PMC7566648 DOI: 10.1038/s41598-020-74439-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 09/30/2020] [Indexed: 02/07/2023] Open
Abstract
Enzymes are the most efficient catalysts known to date. However, decades of research have failed to fully explain the catalytic power of enzymes, and most of the current attempts to uncloak the details of atomic motions at active sites remain incomplete. Here, a straightforward manner for understanding the interplay between the complex or irregular enzyme topology and dynamical effects at catalytic sites is introduced, by revealing how fast localized vibrations form spontaneously in the stiffest parts of the scaffold. While shedding light on a physical mechanism that allowed the selection of the picosecond (ps) timescale to increase the catalytic proficiency, this approach exposes the functional importance of localized motions as a by-product of the stability-function tradeoff in enzyme evolution. From this framework of analysis—directly accessible from available diffraction data—experimental strategies for engineering the catalytic rate in enzymatic proteins are proposed.
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Affiliation(s)
- Yann Chalopin
- Laboratoire EM2C, CNRS & CentraleSupelec, University of Paris-Saclay, 91190, Gif-sur-Yvette, France.
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43
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Yang G, Miton CM, Tokuriki N. A mechanistic view of enzyme evolution. Protein Sci 2020; 29:1724-1747. [PMID: 32557882 PMCID: PMC7380680 DOI: 10.1002/pro.3901] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/14/2020] [Accepted: 06/16/2020] [Indexed: 12/15/2022]
Abstract
New enzyme functions often evolve through the recruitment and optimization of latent promiscuous activities. How do mutations alter the molecular architecture of enzymes to enhance their activities? Can we infer general mechanisms that are common to most enzymes, or does each enzyme require a unique optimization process? The ability to predict the location and type of mutations necessary to enhance an enzyme's activity is critical to protein engineering and rational design. In this review, via the detailed examination of recent studies that have shed new light on the molecular changes underlying the optimization of enzyme function, we provide a mechanistic perspective of enzyme evolution. We first present a global survey of the prevalence of activity-enhancing mutations and their distribution within protein structures. We then delve into the molecular solutions that mediate functional optimization, specifically highlighting several common mechanisms that have been observed across multiple examples. As distinct protein sequences encounter different evolutionary bottlenecks, different mechanisms are likely to emerge along evolutionary trajectories toward improved function. Identifying the specific mechanism(s) that need to be improved upon, and tailoring our engineering efforts to each sequence, may considerably improve our chances to succeed in generating highly efficient catalysts in the future.
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Affiliation(s)
- Gloria Yang
- Michael Smith LaboratoriesUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Charlotte M. Miton
- Michael Smith LaboratoriesUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Nobuhiko Tokuriki
- Michael Smith LaboratoriesUniversity of British ColumbiaVancouverBritish ColumbiaCanada
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44
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Yang J, Xiao YZ, Li R, Liu Y, Long LJ. Repurposing a bacterial prolidase for organophosphorus hydrolysis: Reshaped catalytic cavity switches substrate selectivity. Biotechnol Bioeng 2020; 117:2694-2702. [PMID: 32515491 DOI: 10.1002/bit.27455] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 02/13/2020] [Accepted: 06/08/2020] [Indexed: 01/30/2023]
Abstract
Enzyme promiscuity is critical to the acquisition of evolutionary plasticity in cells and can be recruited for high-value chemical synthesis or xenobiotic degradation. The molecular determinants of substrate ambiguity are essential to this activity; however, these details remain unknown. Here, we performed the directed evolution of a prolidase to enhance its initially weak paraoxonase activity. The in vitro evolution led to an unexpected 1,000,000-fold switch in substrate selectivity, with a 30-fold increase in paraoxon hydrolysis and 40,000-fold decrease in peptide hydrolysis. Structural and in silico analyses revealed enlarged catalytic cavities and substrate repositioning as responsible for rapid catalytic transitions between distinct chemical reactions.
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Affiliation(s)
- Jian Yang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Yun-Zhu Xiao
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanology, Shenzhen University, Shenzhen, China
| | - Ru Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Yu Liu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Li-Juan Long
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China.,University of the Chinese Academy of Sciences, Beijing, China
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45
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Narunsky A, Kessel A, Solan R, Alva V, Kolodny R, Ben-Tal N. On the evolution of protein-adenine binding. Proc Natl Acad Sci U S A 2020; 117:4701-4709. [PMID: 32079721 PMCID: PMC7060716 DOI: 10.1073/pnas.1911349117] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Proteins' interactions with ancient ligands may reveal how molecular recognition emerged and evolved. We explore how proteins recognize adenine: a planar rigid fragment found in the most common and ancient ligands. We have developed a computational pipeline that extracts protein-adenine complexes from the Protein Data Bank, structurally superimposes their adenine fragments, and detects the hydrogen bonds mediating the interaction. Our analysis extends the known motifs of protein-adenine interactions in the Watson-Crick edge of adenine and shows that all of adenine's edges may contribute to molecular recognition. We further show that, on the proteins' side, binding is often mediated by specific amino acid segments ("themes") that recur across different proteins, such that different proteins use the same themes when binding the same adenine-containing ligands. We identify numerous proteins that feature these themes and are thus likely to bind adenine-containing ligands. Our analysis suggests that adenine binding has emerged multiple times in evolution.
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Affiliation(s)
- Aya Narunsky
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978 Ramat Aviv, Israel
| | - Amit Kessel
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978 Ramat Aviv, Israel
| | - Ron Solan
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978 Ramat Aviv, Israel
| | - Vikram Alva
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Rachel Kolodny
- Department of Computer Science, University of Haifa, Mount Carmel, 3498838 Haifa, Israel
| | - Nir Ben-Tal
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978 Ramat Aviv, Israel;
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46
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Mayorov A, Dal Peraro M, Abriata LA. Active Site-Induced Evolutionary Constraints Follow Fold Polarity Principles in Soluble Globular Enzymes. Mol Biol Evol 2020; 36:1728-1733. [PMID: 31004173 DOI: 10.1093/molbev/msz096] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
A recent analysis of evolutionary rates in >500 globular soluble enzymes revealed pervasive conservation gradients toward catalytic residues. By looking at amino acid preference profiles rather than evolutionary rates in the same data set, we quantified the effects of active sites on site-specific constraints for physicochemical traits. We found that conservation gradients respond to constraints for polarity, hydrophobicity, flexibility, rigidity and structure in ways consistent with fold polarity principles; while sites far from active sites seem to experience no physicochemical constraint, rather being highly variable and favoring amino acids of low metabolic cost. Globally, our results highlight that amino acid variation contains finer information about protein structure than usually regarded in evolutionary models, and that this information is retrievable automatically with simple fits. We propose that analyses of the kind presented here incorporated into models of protein evolution should allow for better description of the physical chemistry that underlies molecular evolution.
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Affiliation(s)
- Alexander Mayorov
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Matteo Dal Peraro
- Laboratory for Biomolecular Modeling, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Luciano A Abriata
- Laboratory for Biomolecular Modeling, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Protein Production and Structure Core Facility, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
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47
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Chevrette MG, Gutiérrez-García K, Selem-Mojica N, Aguilar-Martínez C, Yañez-Olvera A, Ramos-Aboites HE, Hoskisson PA, Barona-Gómez F. Evolutionary dynamics of natural product biosynthesis in bacteria. Nat Prod Rep 2019; 37:566-599. [PMID: 31822877 DOI: 10.1039/c9np00048h] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Covering: 2008 up to 2019The forces of biochemical adaptive evolution operate at the level of genes, manifesting in complex phenotypes and the global biodiversity of proteins and metabolites. While evolutionary histories have been deciphered for some other complex traits, the origins of natural product biosynthesis largely remain a mystery. This fundamental knowledge gap is surprising given the many decades of research probing the genetic, chemical, and biophysical mechanisms of bacterial natural product biosynthesis. Recently, evolutionary thinking has begun to permeate this otherwise mechanistically dominated field. Natural products are now sometimes referred to as 'specialized' rather than 'secondary' metabolites, reinforcing the importance of their biological and ecological functions. Here, we review known evolutionary mechanisms underlying the overwhelming chemical diversity of bacterial secondary metabolism, focusing on enzyme promiscuity and the evolution of enzymatic domains that enable metabolic traits. We discuss the mechanisms that drive the assembly of natural product biosynthetic gene clusters and propose formal definitions for 'specialized' and 'secondary' metabolism. We further explore how biosynthetic gene clusters evolve to synthesize related molecular species, and in turn how the biological and ecological roles that emerge from metabolic diversity are acted on by selection. Finally, we reconcile chemical, functional, and genetic data into an evolutionary model, the dynamic chemical matrix evolutionary hypothesis, in which the relationships between chemical distance, biomolecular activity, and relative fitness shape adaptive landscapes.
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Affiliation(s)
- Marc G Chevrette
- Wisconsin Institute for Discovery, Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA.
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48
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Medvedev KE, Kinch LN, Schaeffer RD, Grishin NV. Functional analysis of Rossmann-like domains reveals convergent evolution of topology and reaction pathways. PLoS Comput Biol 2019; 15:e1007569. [PMID: 31869345 PMCID: PMC6957218 DOI: 10.1371/journal.pcbi.1007569] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 01/13/2020] [Accepted: 11/26/2019] [Indexed: 12/18/2022] Open
Abstract
Rossmann folds are ancient, frequently diverged domains found in many biological reaction pathways where they have adapted for different functions. Consequently, discernment and classification of their homologous relations and function can be complicated. We define a minimal Rossmann-like structure motif (RLM) that corresponds for the common core of known Rossmann domains and use this motif to identify all RLM domains in the Protein Data Bank (PDB), thus finding they constitute about 20% of all known 3D structures. The Evolutionary Classification of protein structure Domains (ECOD) classifies RLM domains in a number of groups that lack evidence for homology (X-groups), which suggests that they could have evolved independently multiple times. Closely related, homologous RLM enzyme families can diverge to bind different ligands using similar binding sites and to catalyze different reactions. Conversely, non-homologous RLM domains can converge to catalyze the same reactions or to bind the same ligand with alternate binding modes. We discuss a special case of such convergent evolution that is relevant to the polypharmacology paradigm, wherein the same drug (methotrexate) binds to multiple non-homologous RLM drug targets with different topologies. Finally, assigning proteins with RLM domain to the Enzyme Commission classification suggest that RLM enzymes function mainly in metabolism (and comprise 38% of reference metabolic pathways) and are overrepresented in extant pathways that represent ancient biosynthetic routes such as nucleotide metabolism, energy metabolism, and metabolism of amino acids. In fact, RLM enzymes take part in five out of eight enzymatic reactions of the Wood-Ljungdahl metabolic pathway thought to be used by the last universal common ancestor (LUCA). The prevalence of RLM domains in this ancient metabolism might explain their wide distribution among enzymes.
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Affiliation(s)
- Kirill E. Medvedev
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Lisa N. Kinch
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - R. Dustin Schaeffer
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Nick V. Grishin
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
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49
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Bourgeat L, Serghei A, Lesieur C. Experimental Protein Molecular Dynamics: Broadband Dielectric Spectroscopy coupled with nanoconfinement. Sci Rep 2019; 9:17988. [PMID: 31784681 PMCID: PMC6884508 DOI: 10.1038/s41598-019-54562-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 11/05/2019] [Indexed: 11/09/2022] Open
Abstract
Protein dynamics covers multiple spatiotemporal scale processes, among which slow motions, not much understood even though they are underlying protein folding and protein functions. Protein slow motions are associated with structural heterogeneity, short-lived and poorly populated conformations, hard to detect individually. In addition, they involve collective motions of many atoms, not easily tracked by simulation and experimental devices. Here we propose a biophysical approach, coupling geometrical nanoconfinement and broadband dielectric spectroscopy (BDS), which distinguishes protein conformations by their respective molecular dynamics. In particular, protein-unfolding intermediates, usually poorly populated in macroscopic solutions are detected. The protein dynamics is observed under unusual conditions (sample nanoconfinement and dehydration) highlighting the robustness of protein structure and protein dynamics to a variety of conditions consistent with protein sustainability. The protein dielectric signals evolve with the temperature of thermal treatments indicating sensitivity to atomic and molecular interaction changes triggered by the protein thermal unfolding. As dipole fluctuations depend on both collective large-scale motions and local motions, the approach offers a prospect to track in-depth unfolding events.
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Affiliation(s)
- Laëtitia Bourgeat
- AMPERE, CNRS, Univ. Lyon, 69622, Lyon, France
- IMP, CNRS, Univ. Lyon, 69622, Lyon, France
| | | | - Claire Lesieur
- AMPERE, CNRS, Univ. Lyon, 69622, Lyon, France.
- Institut Rhônalpin des systèmes complexes, IXXI-ENS-Lyon, 69007, Lyon, France.
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50
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Zhang C, Wang X, Liu X, Fan Y, Zhang Y, Zhou X, Li W. A Novel ' Candidatus Liberibacter asiaticus'-Encoded Sec-Dependent Secretory Protein Suppresses Programmed Cell Death in Nicotiana benthamiana. Int J Mol Sci 2019; 20:E5802. [PMID: 31752214 PMCID: PMC6888338 DOI: 10.3390/ijms20225802] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/12/2019] [Accepted: 11/15/2019] [Indexed: 12/28/2022] Open
Abstract
'Candidatus Liberibacter asiaticus' (CLas) is one of the causal agents of citrus Huanglongbing (HLB), a bacterial disease of citrus trees that greatly reduces fruit yield and quality. CLas strains produce an array of currently uncharacterized Sec-dependent secretory proteins. In this study, the conserved chromosomally encoded protein CLIBASIA_03875 was identified as a novel Sec-dependent secreted protein. We show that CLIBASIA_03875 contains a putative Sec- secretion signal peptide (SP), a 29 amino acid residue located at the N-terminus, with a mature protein (m3875) of 22 amino acids found to localize in multiple subcellular components of the leaf epidermal cells of Nicotiana benthamiana. When overexpressed via a Potato virus X (PVX)-based expression vector in N. benthamiana, m3875 suppressed programmed cell death (PCD) and the H2O2 accumulation triggered by the pro-apoptotic mouse protein BAX and the Phytophthora infestans elicitin INF1. Overexpression also resulted in a phenotype of dwarfing, leaf deformation and mosaics, suggesting that m3875 has roles in plant immune response, growth, and development. Substitution mutagenesis of the charged amino acid (D7, R9, R11, and K22) with alanine within m3875 did not recover the phenotypes for PCD and normal growth. In addition, the transiently overexpressed m3875 regulated the transcriptional levels of N. benthamiana orthologs of CNGCs (cyclic nucleotide-gated channels), BI-1 (Bax-inhibitor 1), and WRKY33 that are involved in plant defense mechanisms. To our knowledge, m3875 is the first PCD suppressor identified from CLas. Studying the function of this protein provides insight as to how CLas attenuates the host immune responses to proliferate and cause Huanglongbing disease in citrus plants.
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Affiliation(s)
- Chao Zhang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100094, China;
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.L.); (Y.F.); (Y.Z.)
| | - Xuefeng Wang
- Citrus Research Institute, Southwest University, Chongqing 400712, China;
| | - Xuelu Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.L.); (Y.F.); (Y.Z.)
- Citrus Research Institute, Southwest University, Chongqing 400712, China;
| | - Yanyan Fan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.L.); (Y.F.); (Y.Z.)
- College of Life Science, Shandong Normal University, Jinan 250014, China
| | - Yongqiang Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.L.); (Y.F.); (Y.Z.)
| | - Xueping Zhou
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100094, China;
| | - Weimin Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.L.); (Y.F.); (Y.Z.)
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