1
|
Olijslager L, Weijers D, Swarts D. Distribution of specific prokaryotic immune systems correlates with host optimal growth temperature. NAR Genom Bioinform 2024; 6:lqae105. [PMID: 39165676 PMCID: PMC11333966 DOI: 10.1093/nargab/lqae105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 07/15/2024] [Accepted: 08/02/2024] [Indexed: 08/22/2024] Open
Abstract
Prokaryotes encode an arsenal of highly diverse immune systems to protect themselves against invading nucleic acids such as viruses, plasmids and transposons. This includes invader-interfering systems that neutralize invaders to protect their host, and abortive-infection systems, which trigger dormancy or cell death in their host to offer population-level immunity. Most prokaryotic immune systems are found across different environments and prokaryotic phyla, but their distribution appears biased and the factors that influence their distribution are largely unknown. Here, we compared and combined the prokaryotic immune system identification tools DefenseFinder and PADLOC to obtain an expanded view of the immune system arsenal. Our results show that the number of immune systems encoded is positively correlated with genome size and that the distribution of specific immune systems is linked to phylogeny. Furthermore, we reveal that certain invader-interfering systems are more frequently encoded by hosts with a relatively high optimum growth temperature, while abortive-infection systems are generally more frequently encoded by hosts with a relatively low optimum growth temperature. Combined, our study reveals several factors that correlate with differences in the distribution of prokaryotic immune systems and extends our understanding of how prokaryotes protect themselves from invaders in different environments.
Collapse
Affiliation(s)
- Lisa H Olijslager
- Laboratory of Biochemistry, Wageningen University, Wageningen, Stippeneng 4, 6708WE, the Netherlands
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Wageningen, Stippeneng 4, 6708WE, the Netherlands
| | - Daan C Swarts
- Laboratory of Biochemistry, Wageningen University, Wageningen, Stippeneng 4, 6708WE, the Netherlands
| |
Collapse
|
2
|
Pasquevich MY, Dreon MS, Diupotex-Chong ME, Heras H. Phylogenetic variations in a novel family of hyperstable apple snail egg proteins: insights into structural stability and functional trends. J Exp Biol 2024; 227:jeb247277. [PMID: 39022896 DOI: 10.1242/jeb.247277] [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: 01/18/2024] [Accepted: 07/08/2024] [Indexed: 07/20/2024]
Abstract
The relationship between protein stability and functional evolution is little explored in proteins purified from natural sources. Here, we investigated a novel family of egg proteins (Perivitellin-1, PV1) from Pomacea snails. Their remarkable stability and clade-related functions in most derived clades (Canaliculata and Bridgesii) make them excellent candidates for exploring this issue. To that aim, we studied PV1 (PpaPV1) from the most basal lineage, Flagellata. PpaPV1 displays unparalleled structural and kinetic stability, surpassing PV1s from derived clades, ranking among the most hyperstable proteins documented in nature. Its spectral features contribute to a pale egg coloration, exhibiting a milder glycan binding lectin activity with a narrower specificity than PV1s from the closely related Bridgesii clade. These findings provide evidence for substantial structural and functional changes throughout the genus' PV1 evolution. We observed that structural and kinetic stability decreased in a clade-related fashion and was associated with large variations in defensive traits. For instance, pale PpaPV1 lectin turns potent in the Bridgesii clade, adversely affecting gut morphology, while giving rise to brightly colored PV1s providing eggs with a conspicuous, probably warning signal in the Canaliculata clade. This work provides a comprehensive comparative analysis of PV1s from various apple snail species within a phylogenetic framework, offering insights into the interplay among their structural features, stability profiles and functional roles. More broadly, our work provides one of the first examples from natural evolution showing the crucial link among protein structure, stability and evolution of new functions.
Collapse
Affiliation(s)
- María Y Pasquevich
- Instituto de Investigaciones Bioquímicas de La Plata 'Prof. Dr. Rodolfo R. Brenner' (INIBIOLP), Universidad Nacional de La Plata (UNLP) - CONICET, C. P. 1900 La Plata, Argentina
- Cátedra de Bioquímica y Biología Molecular, Facultad de Ciencias Médicas, UNLP, C. P. 1900 La Plata, Argentina
| | - Marcos S Dreon
- Instituto de Investigaciones Bioquímicas de La Plata 'Prof. Dr. Rodolfo R. Brenner' (INIBIOLP), Universidad Nacional de La Plata (UNLP) - CONICET, C. P. 1900 La Plata, Argentina
- Cátedra de Bioquímica y Biología Molecular, Facultad de Ciencias Médicas, UNLP, C. P. 1900 La Plata, Argentina
| | - María E Diupotex-Chong
- Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, 04510 Ciudad de México, México
| | - Horacio Heras
- Instituto de Investigaciones Bioquímicas de La Plata 'Prof. Dr. Rodolfo R. Brenner' (INIBIOLP), Universidad Nacional de La Plata (UNLP) - CONICET, C. P. 1900 La Plata, Argentina
- Cátedra de Química Biológica, Facultad de Ciencias Naturales y Museo, UNLP, C. P. 1900 La Plata, Argentina
| |
Collapse
|
3
|
Vila JA. Analysis of proteins in the light of mutations. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2024; 53:255-265. [PMID: 38955858 DOI: 10.1007/s00249-024-01714-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 05/23/2024] [Accepted: 06/18/2024] [Indexed: 07/04/2024]
Abstract
Proteins have evolved through mutations-amino acid substitutions-since life appeared on Earth, some 109 years ago. The study of these phenomena has been of particular significance because of their impact on protein stability, function, and structure. This study offers a new viewpoint on how the most recent findings in these areas can be used to explore the impact of mutations on protein sequence, stability, and evolvability. Preliminary results indicate that: (1) mutations can be viewed as sensitive probes to identify 'typos' in the amino-acid sequence, and also to assess the resistance of naturally occurring proteins to unwanted sequence alterations; (2) the presence of 'typos' in the amino acid sequence, rather than being an evolutionary obstacle, could promote faster evolvability and, in turn, increase the likelihood of higher protein stability; (3) the mutation site is far more important than the substituted amino acid in terms of the marginal stability changes of the protein, and (4) the unpredictability of protein evolution at the molecular level-by mutations-exists even in the absence of epistasis effects. Finally, the Darwinian concept of evolution "descent with modification" and experimental evidence endorse one of the results of this study, which suggests that some regions of any protein sequence are susceptible to mutations while others are not. This work contributes to our general understanding of protein responses to mutations and may spur significant progress in our efforts to develop methods to accurately forecast changes in protein stability, their propensity for metamorphism, and their ability to evolve.
Collapse
Affiliation(s)
- Jorge A Vila
- IMASL-CONICET, Universidad Nacional de San Luis, Ejército de los Andes 950, 5700, San Luis, Argentina.
| |
Collapse
|
4
|
Chamness LM, Kuntz CP, McKee AG, Penn WD, Hemmerich CM, Rusch DB, Woods H, Dyotima, Meiler J, Schlebach JP. Divergent folding-mediated epistasis among unstable membrane protein variants. eLife 2024; 12:RP92406. [PMID: 39078397 PMCID: PMC11288631 DOI: 10.7554/elife.92406] [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: 07/31/2024] Open
Abstract
Many membrane proteins are prone to misfolding, which compromises their functional expression at the plasma membrane. This is particularly true for the mammalian gonadotropin-releasing hormone receptor GPCRs (GnRHR). We recently demonstrated that evolutionary GnRHR modifications appear to have coincided with adaptive changes in cotranslational folding efficiency. Though protein stability is known to shape evolution, it is unclear how cotranslational folding constraints modulate the synergistic, epistatic interactions between mutations. We therefore compared the pairwise interactions formed by mutations that disrupt the membrane topology (V276T) or tertiary structure (W107A) of GnRHR. Using deep mutational scanning, we evaluated how the plasma membrane expression of these variants is modified by hundreds of secondary mutations. An analysis of 251 mutants in three genetic backgrounds reveals that V276T and W107A form distinct epistatic interactions that depend on both the severity and the mechanism of destabilization. V276T forms predominantly negative epistatic interactions with destabilizing mutations in soluble loops. In contrast, W107A forms positive interactions with mutations in both loops and transmembrane domains that reflect the diminishing impacts of the destabilizing mutations in variants that are already unstable. These findings reveal how epistasis is remodeled by conformational defects in membrane proteins and in unstable proteins more generally.
Collapse
Affiliation(s)
- Laura M Chamness
- Department of Chemistry, Indiana UniversityBloomingtonUnited States
| | - Charles P Kuntz
- The James Tarpo Jr. and Margaret Tarpo Department of Chemistry, Purdue UniversityWest LafayetteUnited States
| | - Andrew G McKee
- Department of Chemistry, Indiana UniversityBloomingtonUnited States
| | - Wesley D Penn
- Department of Chemistry, Indiana UniversityBloomingtonUnited States
| | | | - Douglas B Rusch
- Center for Genomics and Bioinformatics, Indiana UniversityBloomingtonUnited States
| | - Hope Woods
- Department of Chemistry, Vanderbilt UniversityNashvilleUnited States
- Chemical and Physical Biology Program, Vanderbilt UniversityNashvilleUnited States
| | - Dyotima
- Department of Chemistry, Indiana UniversityBloomingtonUnited States
| | - Jens Meiler
- Department of Chemistry, Vanderbilt UniversityNashvilleUnited States
- Institute for Drug Discovery, Leipzig UniversityLeipzigGermany
| | - Jonathan P Schlebach
- The James Tarpo Jr. and Margaret Tarpo Department of Chemistry, Purdue UniversityWest LafayetteUnited States
| |
Collapse
|
5
|
Cuturello F, Celoria M, Ansuini A, Cazzaniga A. Enhancing predictions of protein stability changes induced by single mutations using MSA-based Language Models. Bioinformatics 2024; 40:btae447. [PMID: 39012369 PMCID: PMC11269464 DOI: 10.1093/bioinformatics/btae447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/19/2024] [Accepted: 07/10/2024] [Indexed: 07/17/2024] Open
Abstract
MOTIVATION Protein Language Models offer a new perspective for addressing challenges in structural biology, while relying solely on sequence information. Recent studies have investigated their effectiveness in forecasting shifts in thermodynamic stability caused by single amino acid mutations, a task known for its complexity due to the sparse availability of data, constrained by experimental limitations. To tackle this problem, we introduce two key novelties: leveraging a Protein Language Model that incorporates Multiple Sequence Alignments to capture evolutionary information, and using a recently released mega-scale dataset with rigorous data pre-processing to mitigate overfitting. RESULTS We ensure comprehensive comparisons by fine-tuning various pre-trained models, taking advantage of analyses such as ablation studies and baselines evaluation. Our methodology introduces a stringent policy to reduce the widespread issue of data leakage, rigorously removing sequences from the training set when they exhibit significant similarity with the test set. The MSA Transformer emerges as the most accurate among the models under investigation, given its capability to leverage co-evolution signals encoded in aligned homologous sequences. Moreover, the optimized MSA Transformer outperforms existing methods and exhibits enhanced generalization power, leading to a notable improvement in predicting changes in protein stability resulting from point mutations. AVAILABILITY AND IMPLEMENTATION Code and data at https://github.com/RitAreaSciencePark/PLM4Muts. SUPPLEMENTARY INFORMATION Supplementary Information is available at Bioinformatics online.
Collapse
Affiliation(s)
- Francesca Cuturello
- Research and Technology Institute, , AREA Science Park, Trieste 34149, Italy
| | - Marco Celoria
- Research and Technology Institute, , AREA Science Park, Trieste 34149, Italy
- HPC Department, , CINECA National Supercomputing Center, Bologna 40033, Italy
| | - Alessio Ansuini
- Research and Technology Institute, , AREA Science Park, Trieste 34149, Italy
| | - Alberto Cazzaniga
- Research and Technology Institute, , AREA Science Park, Trieste 34149, Italy
| |
Collapse
|
6
|
Meijers M, Ruchnewitz D, Eberhardt J, Karmakar M, Łuksza M, Lässig M. Concepts and methods for predicting viral evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.19.585703. [PMID: 38746108 PMCID: PMC11092427 DOI: 10.1101/2024.03.19.585703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The seasonal human influenza virus undergoes rapid evolution, leading to significant changes in circulating viral strains from year to year. These changes are typically driven by adaptive mutations, particularly in the antigenic epitopes, the regions of the viral surface protein haemagglutinin targeted by human antibodies. Here we describe a consistent set of methods for data-driven predictive analysis of viral evolution. Our pipeline integrates four types of data: (1) sequence data of viral isolates collected on a worldwide scale, (2) epidemiological data on incidences, (3) antigenic characterization of circulating viruses, and (4) intrinsic viral phenotypes. From the combined analysis of these data, we obtain estimates of relative fitness for circulating strains and predictions of clade frequencies for periods of up to one year. Furthermore, we obtain comparative estimates of protection against future viral populations for candidate vaccine strains, providing a basis for pre-emptive vaccine strain selection. Continuously updated predictions obtained from the prediction pipeline for influenza and SARS-CoV-2 are available on the website previr.app .
Collapse
|
7
|
Meijers M, Ruchnewitz D, Eberhardt J, Karmakar M, Łuksza M, Lässig M. Concepts and methods for predicting viral evolution. ARXIV 2024:arXiv:2403.12684v2. [PMID: 38745695 PMCID: PMC11092678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The seasonal human influenza virus undergoes rapid evolution, leading to significant changes in circulating viral strains from year to year. These changes are typically driven by adaptive mutations, particularly in the antigenic epitopes, the regions of the viral surface protein haemagglutinin targeted by human antibodies. Here we describe a consistent set of methods for data-driven predictive analysis of viral evolution. Our pipeline integrates four types of data: (1) sequence data of viral isolates collected on a worldwide scale, (2) epidemiological data on incidences, (3) antigenic characterization of circulating viruses, and (4) intrinsic viral phenotypes. From the combined analysis of these data, we obtain estimates of relative fitness for circulating strains and predictions of clade frequencies for periods of up to one year. Furthermore, we obtain comparative estimates of protection against future viral populations for candidate vaccine strains, providing a basis for pre-emptive vaccine strain selection. Continuously updated predictions obtained from the prediction pipeline for influenza and SARS-CoV-2 are available on the website previr.app.
Collapse
Affiliation(s)
- Matthijs Meijers
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937, Köln, Germany
| | - Denis Ruchnewitz
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937, Köln, Germany
| | - Jan Eberhardt
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937, Köln, Germany
| | - Malancha Karmakar
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937, Köln, Germany
| | - Marta Łuksza
- Tisch Cancer Institute, Departments of Oncological Sciences and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Lässig
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937, Köln, Germany
| |
Collapse
|
8
|
Caviglia B, Di Bari D, Timr S, Guiral M, Giudici-Orticoni MT, Petrillo C, Peters J, Sterpone F, Paciaroni A. Decoding the Role of the Global Proteome Dynamics for Cellular Thermal Stability. J Phys Chem Lett 2024; 15:1435-1441. [PMID: 38291814 DOI: 10.1021/acs.jpclett.3c03351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Molecular mechanisms underlying the thermal response of cells remain elusive. On the basis of the recent result that the short-time diffusive dynamics of the Escherichia coli proteome is an excellent indicator of temperature-dependent bacterial metabolism and death, we used neutron scattering (NS) spectroscopy and molecular dynamics (MD) simulations to investigate the sub-nanosecond proteome mobility in psychro-, meso-, and hyperthermophilic bacteria over a wide temperature range. The magnitude of thermal fluctuations, measured by atomic mean square displacements, is similar among all studied bacteria at their respective thermal cell death. Global roto-translational motions turn out to be the main factor distinguishing the bacterial dynamical properties. We ascribe this behavior to the difference in the average proteome net charge, which becomes less negative for increasing bacterial thermal stability. We propose that the chemical-physical properties of the cytoplasm and the global dynamics of the resulting proteome are fine-tuned by evolution to uphold optimal thermal stability conditions.
Collapse
Affiliation(s)
- Beatrice Caviglia
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
- Laboratoire de Biochimie Théorique (UPR 9080), Centre National de la Recherche Scientifique (CNRS), Université de Paris Cité, 75005 Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Daniele Di Bari
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Stepan Timr
- Laboratoire de Biochimie Théorique (UPR 9080), Centre National de la Recherche Scientifique (CNRS), Université de Paris Cité, 75005 Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005 Paris, France
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, 182 23 Prague, Czech Republic
| | - Marianne Guiral
- Laboratoire de Bioénergétique et Ingénierie des Protéines (BIP), Centre National de la Recherche Scientifique (CNRS), Aix-Marseille Université, 13400 Marseille, France
| | - Marie-Thérèse Giudici-Orticoni
- Laboratoire de Bioénergétique et Ingénierie des Protéines (BIP), Centre National de la Recherche Scientifique (CNRS), Aix-Marseille Université, 13400 Marseille, France
| | - Caterina Petrillo
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Judith Peters
- Laboratoire Interdisciplinaire de Physique, Centre National de la Recherche Scientifique (CNRS), Univ. Grenoble Alpes, 140 Rue de la Physique, 38402 Saint-Martin-d'Hères, France
- Institut Laue-Langevin, 71 Avenue des Martyrs, CS 20156, 38042 Grenoble, France
- Institut Universitaire de France, 75231 Paris, France
| | - Fabio Sterpone
- Laboratoire de Biochimie Théorique (UPR 9080), Centre National de la Recherche Scientifique (CNRS), Université de Paris Cité, 75005 Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Alessandro Paciaroni
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| |
Collapse
|
9
|
Thayyil Menambath D, Adiga U, Rai T, Adiga S, Shetty V. Identification of the SIRT1 gene's most harmful non-synonymous SNPs and their effects on functional and structural features-an in silico analysis. F1000Res 2024; 12:66. [PMID: 38283900 PMCID: PMC10822041 DOI: 10.12688/f1000research.128706.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/16/2024] [Indexed: 01/30/2024] Open
Abstract
Introduction The sirtuin (Silent mating type information regulation 2 homolog)1(SIRT1) protein plays a vital role in many disorders such as diabetes, cancer, obesity, inflammation, and neurodegenerative and cardiovascular diseases. The objective of this in silico analysis of SIRT1's functional single nucleotide polymorphisms (SNPs) was to gain valuable insight into the harmful effects of non-synonymous SNPs (nsSNPs) on the protein. The objective of the study was to use bioinformatics methods to investigate the genetic variations and modifications that may have an impact on the SIRT1 gene's expression and function. Methods nsSNPs of SIRT1 protein were collected from the dbSNP site, from its three (3) different protein accession IDs. These were then fed to various bioinformatic tools such as SIFT, Provean, and I- Mutant to find the most deleterious ones. Functional and structural effects were examined using the HOPE server and I-Tasser. Gene interactions were predicted by STRING software. The SIFT, Provean, and I-Mutant tools detected the most deleterious three nsSNPs (rs769519031, rs778184510, and rs199983221). Results Out of 252 nsSNPs, SIFT analysis showed that 94 were deleterious, Provean listed 67 dangerous, and I-Mutant found 58 nsSNPs resulting in lowered stability of proteins. HOPE modelling of rs199983221 and rs769519031 suggested reduced hydrophobicity due to Ile 4Thr and Ile223Ser resulting in decreased hydrophobic interactions. In contrast, on modelling rs778184510, the mutant protein had a higher hydrophobicity than the wild type. Conclusions Our study reports that three nsSNPs (D357A, I223S, I4T) are the most damaging mutations of the SIRT1 gene. Mutations may result in altered protein structure and functions. Such altered protein may be the basis for various disorders. Our findings may be a crucial guide in establishing the pathogenesis of various disorders.
Collapse
Affiliation(s)
| | - Usha Adiga
- Biochemistry, KS Hegde Medical Academy, NITTE (DU), Mangalore, Karnataka, 575018, India
| | - Tirthal Rai
- Biochemistry, KS Hegde Medical Academy, NITTE (DU), Mangalore, Karnataka, 575018, India
| | - Sachidananda Adiga
- Pharmacology, KS Hegde Medical Academy, NITTE(DU), Mangalore, Karnataka, 575018, India
| | - Vijith Shetty
- Oncology, KS Hegde Medical Academy, NITTE(DU), Mangalore, Karnataka, 575018, India
| |
Collapse
|
10
|
Pasquevich MY, Dreon MS, Diupotex-Chong ME, Heras H. Phylogenetic variations in a novel family of hyperstable apple snail egg proteins: insights into structural stability and functional trends. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.28.538759. [PMID: 37162868 PMCID: PMC10168382 DOI: 10.1101/2023.04.28.538759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The relationship between protein stability and function evolution has not been explored in proteins from natural sources. Here, we investigate the phylogenetic differences of Perivitellin-1 (PV1) a novel family of hyperstable egg carotenoproteins crucial to the reproductive success of Pomacea snails, as they have evolved clade-specific protective functions. We studied P. patula PV1 (PpaPV1) from Flagellata clade eggs, the most basal of Pomacea and compared it with PV1s orthologs from derived clades. PpaPV1 stands as the most stable, with longer unfolding half-life, resistance to detergent unfolding, and therefore higher kinetic stability than PV1s from derived clades. In fact, PpaPV1 is among the most hyperstable proteins described in nature. In addition, its spectral characteristics providing a pale egg coloration, mild lectin activity and glycan specificity are narrower than derived clades. Our results provide evidence indicating large structural and functional changes along the evolution of the genus. Notably, the lectin binding of PpaPV1 is less pronounced, and its glycan specificity is narrower compared to PV1s in the sister Bridgesii clade. Our findings underscore the phylogenetic disparities in terms of structural and kinetic stability, as well as defensive traits like a potent lectin activity affecting the gut morphology of potential predators within the Bridgesii clade or a conspicuous, likely warning coloration, within the Canaliculata clade. This work provides a comprehensive comparison of the structural attributes, stability profiles, and functional roles of apple snail egg PV1s from multiple species within a phylogenetic context. Furthermore, it proposes an evolutionary hypothesis suggesting a trade-off between structural stability and the functional aspects of apple snail's major egg defense protein.
Collapse
Affiliation(s)
- M Y Pasquevich
- Instituto de Investigaciones Bioquímicas de La Plata ¨Prof. Dr. Rodolfo R. Brenner¨ (INIBIOLP), Universidad Nacional de La Plata (UNLP) -CONICET CCT-La Plata, La Plata, Argentina
- Cátedra de Bioquímica y Biología Molecular, Facultad de Ciencias Médicas, UNLP, Argentina
| | - M S Dreon
- Instituto de Investigaciones Bioquímicas de La Plata ¨Prof. Dr. Rodolfo R. Brenner¨ (INIBIOLP), Universidad Nacional de La Plata (UNLP) -CONICET CCT-La Plata, La Plata, Argentina
- Cátedra de Bioquímica y Biología Molecular, Facultad de Ciencias Médicas, UNLP, Argentina
| | - M E Diupotex-Chong
- Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - H Heras
- Instituto de Investigaciones Bioquímicas de La Plata ¨Prof. Dr. Rodolfo R. Brenner¨ (INIBIOLP), Universidad Nacional de La Plata (UNLP) -CONICET CCT-La Plata, La Plata, Argentina
- Cátedra de Química Biológica, Facultad de Ciencias Naturales y Museo, UNLP, Argentina
| |
Collapse
|
11
|
Akl H, Emison B, Zhao X, Mondal A, Perez A, Dixit PD. GENERALIST: A latent space based generative model for protein sequence families. PLoS Comput Biol 2023; 19:e1011655. [PMID: 38011273 PMCID: PMC10703406 DOI: 10.1371/journal.pcbi.1011655] [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: 01/18/2023] [Revised: 12/07/2023] [Accepted: 11/03/2023] [Indexed: 11/29/2023] Open
Abstract
Generative models of protein sequence families are an important tool in the repertoire of protein scientists and engineers alike. However, state-of-the-art generative approaches face inference, accuracy, and overfitting- related obstacles when modeling moderately sized to large proteins and/or protein families with low sequence coverage. Here, we present a simple to learn, tunable, and accurate generative model, GENERALIST: GENERAtive nonLInear tenSor-factorizaTion for protein sequences. GENERALIST accurately captures several high order summary statistics of amino acid covariation. GENERALIST also predicts conservative local optimal sequences which are likely to fold in stable 3D structure. Importantly, unlike current methods, the density of sequences in GENERALIST-modeled sequence ensembles closely resembles the corresponding natural ensembles. Finally, GENERALIST embeds protein sequences in an informative latent space. GENERALIST will be an important tool to study protein sequence variability.
Collapse
Affiliation(s)
- Hoda Akl
- Department of Physics, University of Florida, Gainesville, Florida, United States of America
| | - Brooke Emison
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut, United States of America
| | - Xiaochuan Zhao
- Department of Physics, University of Florida, Gainesville, Florida, United States of America
| | - Arup Mondal
- Department of Chemistry, University of Florida, Gainesville, Florida, United States of America
| | - Alberto Perez
- Department of Chemistry, University of Florida, Gainesville, Florida, United States of America
| | - Purushottam D. Dixit
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut, United States of America
- Systems Biology Institute, Yale University, West Haven, Connecticut, United States of America
| |
Collapse
|
12
|
Abstract
Understanding the factors that shape viral evolution is critical for developing effective antiviral strategies, accurately predicting viral evolution, and preventing pandemics. One fundamental determinant of viral evolution is the interplay between viral protein biophysics and the host machineries that regulate protein folding and quality control. Most adaptive mutations in viruses are biophysically deleterious, resulting in a viral protein product with folding defects. In cells, protein folding is assisted by a dynamic system of chaperones and quality control processes known as the proteostasis network. Host proteostasis networks can determine the fates of viral proteins with biophysical defects, either by assisting with folding or by targeting them for degradation. In this review, we discuss and analyze new discoveries revealing that host proteostasis factors can profoundly shape the sequence space accessible to evolving viral proteins. We also discuss the many opportunities for research progress proffered by the proteostasis perspective on viral evolution and adaptation.
Collapse
Affiliation(s)
- Jimin Yoon
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
| | - Jessica E Patrick
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
| | - C Brandon Ogbunugafor
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
- Santa Fe Institute, Santa Fe, New Mexico, USA
| | - Matthew D Shoulders
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
| |
Collapse
|
13
|
Vila JA. Protein folding rate evolution upon mutations. Biophys Rev 2023; 15:661-669. [PMID: 37681091 PMCID: PMC10480377 DOI: 10.1007/s12551-023-01088-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/24/2023] [Indexed: 09/09/2023] Open
Abstract
Despite the spectacular success of cutting-edge protein fold prediction methods, many critical questions remain unanswered, including why proteins can reach their native state in a biologically reasonable time. A satisfactory answer to this simple question could shed light on the slowest folding rate of proteins as well as how mutations-amino-acid substitutions and/or post-translational modifications-might affect it. Preliminary results indicate that (i) Anfinsen's dogma validity ensures that proteins reach their native state on a reasonable timescale regardless of their sequence or length, and (ii) it is feasible to determine the evolution of protein folding rates without accounting for epistasis effects or the mutational trajectories between the starting and target sequences. These results have direct implications for evolutionary biology because they lay the groundwork for a better understanding of why, and to what extent, mutations-a crucial element of evolution and a factor influencing it-affect protein evolvability. Furthermore, they may spur significant progress in our efforts to solve crucial structural biology problems, such as how a sequence encodes its folding.
Collapse
Affiliation(s)
- Jorge A. Vila
- IMASL-CONICET, Universidad Nacional de San Luis, Ejército de Los Andes 950, 5700 San Luis, Argentina
| |
Collapse
|
14
|
Di Bari D, Timr S, Guiral M, Giudici-Orticoni MT, Seydel T, Beck C, Petrillo C, Derreumaux P, Melchionna S, Sterpone F, Peters J, Paciaroni A. Diffusive Dynamics of Bacterial Proteome as a Proxy of Cell Death. ACS CENTRAL SCIENCE 2023; 9:93-102. [PMID: 36712493 PMCID: PMC9881203 DOI: 10.1021/acscentsci.2c01078] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Indexed: 05/30/2023]
Abstract
Temperature variations have a big impact on bacterial metabolism and death, yet an exhaustive molecular picture of these processes is still missing. For instance, whether thermal death is determined by the deterioration of the whole or a specific part of the proteome is hotly debated. Here, by monitoring the proteome dynamics of E. coli, we clearly show that only a minor fraction of the proteome unfolds at the cell death. First, we prove that the dynamical state of the E. coli proteome is an excellent proxy for temperature-dependent bacterial metabolism and death. The proteome diffusive dynamics peaks at about the bacterial optimal growth temperature, then a dramatic dynamical slowdown is observed that starts just below the cell's death temperature. Next, we show that this slowdown is caused by the unfolding of just a small fraction of proteins that establish an entangling interprotein network, dominated by hydrophobic interactions, across the cytoplasm. Finally, the deduced progress of the proteome unfolding and its diffusive dynamics are both key to correctly reproduce the E. coli growth rate.
Collapse
Affiliation(s)
- Daniele Di Bari
- Università
degli Studi di Perugia, Dipartimento di
Fisica e Geologia, Via
A. Pascoli, 06123Perugia PG, Italy
- Université
Grenoble Alpes, CNRS, Laboratoire Interdisciplinaire de Physique, 38400Saint-Martin-d’Héres, France
- Institut
Laue-Langevin, 38000Grenoble, France
| | - Stepan Timr
- Laboratoire
de Biochimie Théorique (UPR9080), CNRS, Université de Paris Cité, 13 Rue Pierre et Marie Curie, 75005Paris, France
- Institut
de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005Paris, France
- J.
Heyrovský
Institute of Physical Chemistry, Czech Academy
of Sciences, 182 23Prague 8, Czechia
| | - Marianne Guiral
- Laboratoire
de Bioénergétique et Ingénierie des Protéines, BIP, CNRS, Aix-Marseille Université, 13400Marseille, France
| | | | - Tilo Seydel
- Institut
Laue-Langevin, 38000Grenoble, France
| | | | - Caterina Petrillo
- Università
degli Studi di Perugia, Dipartimento di
Fisica e Geologia, Via
A. Pascoli, 06123Perugia PG, Italy
| | - Philippe Derreumaux
- Laboratoire
de Biochimie Théorique (UPR9080), CNRS, Université de Paris Cité, 13 Rue Pierre et Marie Curie, 75005Paris, France
- Institut
de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005Paris, France
- Institut Universitaire de France, 75005Paris, France
| | - Simone Melchionna
- ISC-CNR,
Dipartimento di Fisica, Università
Sapienza, 00185Rome, Italy
- Lexma
Technology1337 Massachusetts
Avenue, Arlington, Massachusetts02476, United States
| | - Fabio Sterpone
- Laboratoire
de Biochimie Théorique (UPR9080), CNRS, Université de Paris Cité, 13 Rue Pierre et Marie Curie, 75005Paris, France
- Institut
de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005Paris, France
| | - Judith Peters
- Université
Grenoble Alpes, CNRS, Laboratoire Interdisciplinaire de Physique, 38400Saint-Martin-d’Héres, France
- Institut
Laue-Langevin, 38000Grenoble, France
- Institut Universitaire de France, 75005Paris, France
| | - Alessandro Paciaroni
- Università
degli Studi di Perugia, Dipartimento di
Fisica e Geologia, Via
A. Pascoli, 06123Perugia PG, Italy
| |
Collapse
|
15
|
Design of an artificial phage-display library based on a new scaffold improved for average stability of the randomized proteins. Sci Rep 2023; 13:1339. [PMID: 36693880 PMCID: PMC9873692 DOI: 10.1038/s41598-023-27710-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 01/06/2023] [Indexed: 01/25/2023] Open
Abstract
Scaffold-based protein libraries are designed to be both diverse and rich in functional/folded proteins. However, introducing an extended diversity while preserving stability of the initial scaffold remains a challenge. Here we developed an original approach to select the ensemble of folded proteins from an initial library. The thermostable CheY protein from Thermotoga maritima was chosen as scaffold. Four loops of CheY were diversified to create a new binding surface. The subset of the library giving rise to folded proteins was first selected using a natural protein partner of the template scaffold. Then, a gene shuffling approach based on a single restriction enzyme was used to recombine DNA sequences encoding these filtrated variants. Taken together, the filtration strategy and the shuffling of the filtrated sequences were shown to enrich the library in folded and stable sequences while maintaining a large diversity in the final library (Lib-Cheytins 2.1). Binders of the Oplophorus luciferase Kaz domain were then selected by phage display from the final library, showing affinities in the μM range. One of the best variants induced a loss of 92% of luminescent activity, suggesting that this Cheytin preferentially binds to the Kaz active site.
Collapse
|
16
|
Ó'Fágáin C. Protein Stability: Enhancement and Measurement. Methods Mol Biol 2023; 2699:369-419. [PMID: 37647007 DOI: 10.1007/978-1-0716-3362-5_18] [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] [Indexed: 09/01/2023]
Abstract
This chapter defines protein stability, emphasizes its importance, and surveys the field of protein stabilization, with summary reference to a selection of 2014-2021 publications. One can enhance stability, particularly by protein engineering strategies but also by chemical modification and by other means. General protocols are set out on how to measure a given protein's (i) kinetic thermal stability and (ii) oxidative stability and (iii) how to undertake chemical modification of a protein in solution.
Collapse
Affiliation(s)
- Ciarán Ó'Fágáin
- School of Biotechnology, Dublin City University, Dublin, Ireland.
| |
Collapse
|
17
|
Ferreiro D, Khalil R, Gallego MJ, Osorio NS, Arenas M. The evolution of the HIV-1 protease folding stability. Virus Evol 2022; 8:veac115. [PMID: 36601299 PMCID: PMC9802575 DOI: 10.1093/ve/veac115] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 10/10/2022] [Accepted: 12/03/2022] [Indexed: 12/11/2022] Open
Abstract
The evolution of structural proteins is generally constrained by the folding stability. However, little is known about the particular capacity of viral proteins to accommodate mutations that can potentially affect the protein stability and, in general, the evolution of the protein stability over time. As an illustrative model case, here, we investigated the evolution of the stability of the human immunodeficiency virus (HIV-1) protease (PR), which is a common HIV-1 drug target, under diverse evolutionary scenarios that include (1) intra-host virus evolution in a cohort of seventy-five patients sampled over time, (2) intra-host virus evolution sampled before and after specific PR-based treatments, and (3) inter-host evolution considering extant and ancestral (reconstructed) PR sequences from diverse HIV-1 subtypes. We also investigated the specific influence of currently known HIV-1 PR resistance mutations on the PR folding stability. We found that the HIV-1 PR stability fluctuated over time within a constant and wide range in any studied evolutionary scenario, accommodating multiple mutations that partially affected the stability while maintaining activity. We did not identify relationships between change of PR stability and diverse clinical parameters such as viral load, CD4+ T-cell counts, and a surrogate of time from infection. Counterintuitively, we predicted that nearly half of the studied HIV-1 PR resistance mutations do not significantly decrease stability, which, together with compensatory mutations, would allow the protein to adapt without requiring dramatic stability changes. We conclude that the HIV-1 PR presents a wide structural plasticity to acquire molecular adaptations without affecting the overall evolution of stability.
Collapse
Affiliation(s)
- David Ferreiro
- CINBIO, Universidade de Vigo, Vigo 36310, Spain,Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, Vigo 36310, Spain
| | - Ruqaiya Khalil
- CINBIO, Universidade de Vigo, Vigo 36310, Spain,Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, Vigo 36310, Spain
| | - María J Gallego
- CINBIO, Universidade de Vigo, Vigo 36310, Spain,Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, Vigo 36310, Spain
| | - Nuno S Osorio
- Life and Health Sciences Research Institute, School of Medicine, University of Minho, Braga 4710-057, Portugal,ICVS/3Bs—PT Government Associate Laboratory, Guimarães 4806-909, Portugal
| | | |
Collapse
|
18
|
Iyengar BR, Wagner A. Bacterial Hsp90 predominantly buffers but does not potentiate the phenotypic effects of deleterious mutations during fluorescent protein evolution. Genetics 2022; 222:iyac154. [PMID: 36227141 PMCID: PMC9713429 DOI: 10.1093/genetics/iyac154] [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: 07/29/2022] [Accepted: 09/26/2022] [Indexed: 12/13/2022] Open
Abstract
Chaperones facilitate the folding of other ("client") proteins and can thus affect the adaptive evolution of these clients. Specifically, chaperones affect the phenotype of proteins via two opposing mechanisms. On the one hand, they can buffer the effects of mutations in proteins and thus help preserve an ancestral, premutation phenotype. On the other hand, they can potentiate the effects of mutations and thus enhance the phenotypic changes caused by a mutation. We study that how the bacterial Hsp90 chaperone (HtpG) affects the evolution of green fluorescent protein. To this end, we performed directed evolution of green fluorescent protein under low and high cellular concentrations of Hsp90. Specifically, we evolved green fluorescent protein under both stabilizing selection for its ancestral (green) phenotype and directional selection toward a new (cyan) phenotype. While Hsp90 did only affect the rate of adaptive evolution transiently, it did affect the phenotypic effects of mutations that occurred during adaptive evolution. Specifically, Hsp90 allowed strongly deleterious mutations to accumulate in evolving populations by buffering their effects. Our observations show that the role of a chaperone for adaptive evolution depends on the organism and the trait being studied.
Collapse
Affiliation(s)
- Bharat Ravi Iyengar
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, 1015 Lausanne, Switzerland
- Institute for Evolution and Biodiversity, Westfalian Wilhelms—University of Münster, 48149 Münster, Germany
| | - Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, 1015 Lausanne, Switzerland
- The Santa Fe Institute, Santa Fe, NM 87501, USA
- Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, 7600 Stellenbosch, South Africa
| |
Collapse
|
19
|
Norrild RK, Johansson KE, O’Shea C, Morth JP, Lindorff-Larsen K, Winther JR. Increasing protein stability by inferring substitution effects from high-throughput experiments. CELL REPORTS METHODS 2022; 2:100333. [PMID: 36452862 PMCID: PMC9701609 DOI: 10.1016/j.crmeth.2022.100333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/22/2022] [Accepted: 10/19/2022] [Indexed: 06/17/2023]
Abstract
We apply a computational model, global multi-mutant analysis (GMMA), to inform on effects of most amino acid substitutions from a randomly mutated gene library. Using a high mutation frequency, the method can determine mutations that increase the stability of even very stable proteins for which conventional selection systems have reached their limit. As a demonstration of this, we screened a mutant library of a highly stable and computationally redesigned model protein using an in vivo genetic sensor for folding and assigned a stability effect to 374 of 912 possible single amino acid substitutions. Combining the top 9 substitutions increased the unfolding energy 47 to 69 kJ/mol in a single engineering step. Crystal structures of stabilized variants showed small perturbations in helices 1 and 2, which rendered them closer in structure to the redesign template. This case study illustrates the capability of the method, which is applicable to any screen for protein function.
Collapse
Affiliation(s)
- Rasmus Krogh Norrild
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Kristoffer Enøe Johansson
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Charlotte O’Shea
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Jens Preben Morth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Kresten Lindorff-Larsen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Jakob Rahr Winther
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
| |
Collapse
|
20
|
Stability and expression of SARS-CoV-2 spike-protein mutations. Mol Cell Biochem 2022; 478:1269-1280. [PMID: 36302994 PMCID: PMC9612610 DOI: 10.1007/s11010-022-04588-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 10/12/2022] [Indexed: 12/02/2022]
Abstract
Protein fold stability likely plays a role in SARS-CoV-2 S-protein evolution, together with ACE2 binding and antibody evasion. While few thermodynamic stability data are available for S-protein mutants, many systematic experimental data exist for their expression. In this paper, we explore whether such expression levels relate to the thermodynamic stability of the mutants. We studied mutation-induced SARS-CoV-2 S-protein fold stability, as computed by three very distinct methods and eight different protein structures to account for method- and structure-dependencies. For all methods and structures used (24 comparisons), computed stability changes correlate significantly (99% confidence level) with experimental yeast expression from the literature, such that higher expression is associated with relatively higher fold stability. Also significant, albeit weaker, correlations were seen between stability and ACE2 binding effects. The effect of thermodynamic fold stability may be direct or a correlate of amino acid or site properties, notably the solvent exposure of the site. Correlation between computed stability and experimental expression and ACE2 binding suggests that functional properties of the SARS-CoV-2 S-protein mutant space are largely determined by a few simple features, due to underlying correlations. Our study lends promise to the development of computational tools that may ideally aid in understanding and predicting SARS-CoV-2 S-protein evolution.
Collapse
|
21
|
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.
Collapse
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
| |
Collapse
|
22
|
Nurhafizuddin M, Azizi A, Ming LC, Shafqat N. In Silico Analysis of PORD Mutations on the 3D Structure of P450 Oxidoreductase. Molecules 2022; 27:molecules27144646. [PMID: 35889519 PMCID: PMC9323898 DOI: 10.3390/molecules27144646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/14/2022] [Accepted: 07/18/2022] [Indexed: 11/24/2022] Open
Abstract
Cytochrome P450 oxidoreductase (POR) is a membrane-bound flavoprotein that helps in transferring electrons from its NADPH domain to all cytochrome P450 (CYP450) enzymes. Mutations in the POR gene could severely affect the metabolism of steroid hormones and the development of skeletal muscles, a condition known as Cytochrome P450 oxidoreductase deficiency (PORD). PORD is associated with clinical presentations of disorders of sex development, Antley and Bixler’s syndrome (ABS), as well as an abnormal steroid hormone profile. We have performed an in silico analysis of POR 3D X-ray protein crystal structure to study the effects of reported mutations on the POR enzyme structure. A total of 32 missense mutations were identified, from 170 PORD patients, and mapped on the 3D crystal structure of the POR enzyme. In addition, five of the missense mutations (R457H, A287P, D210G, Y181D and Y607C) were further selected for an in-depth in silico analysis to correlate the observed changes in POR protein structure with the clinical phenotypes observed in PORD patients. Overall, missense mutations found in the binding sites of POR cofactors could lead to a severe form of PORD, emphasizing the importance of POR cofactor binding domains in transferring electrons to the CYP450 enzyme family.
Collapse
|
23
|
Vila JA. Proteins' Evolution upon Point Mutations. ACS OMEGA 2022; 7:14371-14376. [PMID: 35573218 PMCID: PMC9089682 DOI: 10.1021/acsomega.2c01407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 04/05/2022] [Indexed: 05/03/2023]
Abstract
As the reader must be already aware, state-of-the-art protein folding prediction methods have reached a smashing success in their goal of accurately determining the three-dimensional structures of proteins. Yet, a solution to simple problems such as the effects of protein point mutations on their (i) native conformation; (ii) marginal stability; (iii) ensemble of high-energy nativelike conformations; and (iv) metamorphism propensity and, hence, their evolvability, remains as an unsolved problem. As a plausible solution to the latter, some properties of the amide hydrogen-deuterium exchange, a highly sensitive probe of the structure, stability, and folding of proteins, are assessed from a new perspective. The preliminary results indicate that the protein marginal stability change upon point mutations provides the necessary and sufficient information to estimate, through a Boltzmann factor, the evolution of the amide hydrogen exchange protection factors and, consequently, that of the ensemble of folded conformations coexisting with the native state. This work contributes to our general understanding of the effects of point mutations on proteins and may spur significant progress in our efforts to develop methods to determine the appearance of new folds and functions accurately.
Collapse
|
24
|
Protein folding stabilities are a major determinant of oxidation rates for buried methionine residues. J Biol Chem 2022; 298:101872. [PMID: 35346688 PMCID: PMC9062257 DOI: 10.1016/j.jbc.2022.101872] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/19/2022] [Accepted: 03/21/2022] [Indexed: 12/20/2022] Open
Abstract
The oxidation of protein-bound methionines to form methionine sulfoxides has a broad range of biological ramifications, making it important to delineate factors that influence methionine oxidation rates within a given protein. This is especially important for biopharmaceuticals, where oxidation can lead to deactivation and degradation. Previously, neighboring residue effects and solvent accessibility have been shown to impact the susceptibility of methionine residues to oxidation. In this study, we provide proteome-wide evidence that oxidation rates of buried methionine residues are also strongly influenced by the thermodynamic folding stability of proteins. We surveyed the Escherichia coli proteome using several proteomic methodologies and globally measured oxidation rates of methionine residues in the presence and absence of tertiary structure, as well as the folding stabilities of methionine-containing domains. These data indicated that buried methionines have a wide range of protection factors against oxidation that correlate strongly with folding stabilities. Consistent with this, we show that in comparison to E. coli, the proteome of the thermophile Thermus thermophilus is significantly more stable and thus more resistant to methionine oxidation. To demonstrate the utility of this correlation, we used native methionine oxidation rates to survey the folding stabilities of E. coli and T. thermophilus proteomes at various temperatures and propose a model that relates the temperature dependence of the folding stabilities of these two species to their optimal growth temperatures. Overall, these results indicate that oxidation rates of buried methionines from the native state of proteins can be used as a metric of folding stability.
Collapse
|
25
|
Iyengar BR, Wagner A. GroEL/S overexpression helps to purge deleterious mutations and reduce genetic diversity during adaptive protein evolution. Mol Biol Evol 2022; 39:6540901. [PMID: 35234895 PMCID: PMC9188349 DOI: 10.1093/molbev/msac047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Chaperones are proteins that help other proteins fold. They also affect the adaptive evolution of their client proteins by buffering the effect of deleterious mutations and increasing the genetic diversity of evolving proteins. We study how the bacterial chaperone GroE (GroEL + GroES) affects the evolution of green fluorescent protein (GFP). To this end we subjected GFP to multiple rounds of mutation and selection for its color phenotype in four replicate E. coli populations, and studied its evolutionary dynamics through high-throughput sequencing and mutant engineering. We evolved GFP both under stabilizing selection for its ancestral (green) phenotype, and to directional selection for a new (cyan) phenotype. We did so both under low and high expression of the chaperone GroE. In contrast to previous work, we observe that GroE does not just buffer but also helps purge deleterious (fluorescence reducing) mutations from evolving populations. In doing so, GroE helps reduce the genetic diversity of evolving populations. In addition, it causes phenotypic heterogeneity in mutants with the same genotype, helping to enhance their fluorescence in some cells, and reducing it in others. Our observations show that chaperones can affect adaptive evolution in more than one way.
Collapse
|
26
|
Main protease mutants of SARS-CoV-2 variants remain susceptible to nirmatrelvir. Bioorg Med Chem Lett 2022; 62:128629. [PMID: 35182772 PMCID: PMC8856729 DOI: 10.1016/j.bmcl.2022.128629] [Citation(s) in RCA: 108] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/11/2022] [Accepted: 02/13/2022] [Indexed: 12/25/2022]
Abstract
The COVID-19 pandemic continues to be a public health threat. Multiple mutations in the spike protein of emerging variants of SARS-CoV-2 appear to impact on the effectiveness of available vaccines. Specific antiviral agents are keenly anticipated but their efficacy may also be compromised in emerging variants. One of the most attractive coronaviral drug targets is the main protease (Mpro). A promising Mpro inhibitor of clinical relevance is the peptidomimetic nirmatrelvir (PF-07321332). We expressed Mpro of six SARS-CoV-2 lineages (C.37 Lambda, B.1.1.318, B.1.2, B.1.351 Beta, B.1.1.529 Omicron, P.2 Zeta), each of which carries a strongly prevalent missense mutation (G15S, T21I, L89F, K90R, P132H, L205V). Enzyme kinetics reveal that these Mpro variants are catalytically competent to a similar degree as the wildtype. We show that nirmatrelvir has similar potency against the variants as the wildtype. Our in vitro data suggest that the efficacy of the specific Mpro inhibitor nirmatrelvir is not compromised in current COVID-19 variants.
Collapse
|
27
|
Morales-Arce AY, Johri P, Jensen JD. Inferring the distribution of fitness effects in patient-sampled and experimental virus populations: two case studies. Heredity (Edinb) 2022; 128:79-87. [PMID: 34987185 PMCID: PMC8728706 DOI: 10.1038/s41437-021-00493-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 12/12/2021] [Accepted: 12/13/2021] [Indexed: 11/19/2022] Open
Abstract
We here propose an analysis pipeline for inferring the distribution of fitness effects (DFE) from either patient-sampled or experimentally-evolved viral populations, that explicitly accounts for non-Wright-Fisher and non-equilibrium population dynamics inherent to pathogens. We examine the performance of this approach via extensive power and performance analyses, and highlight two illustrative applications - one from an experimentally-passaged RNA virus, and the other from a clinically-sampled DNA virus. Finally, we discuss how such DFE inference may shed light on major research questions in virus evolution, ranging from a quantification of the population genetic processes governing genome size, to the role of Hill-Robertson interference in dictating adaptive outcomes, to the potential design of novel therapeutic approaches to eradicate within-patient viral populations via induced mutational meltdown.
Collapse
Affiliation(s)
- Ana Y Morales-Arce
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Parul Johri
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Jeffrey D Jensen
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA.
| |
Collapse
|
28
|
Baek KT, Kepp KP. Data set and fitting dependencies when estimating protein mutant stability: Toward simple, balanced, and interpretable models. J Comput Chem 2022; 43:504-518. [PMID: 35040492 DOI: 10.1002/jcc.26810] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/13/2021] [Accepted: 01/03/2022] [Indexed: 12/27/2022]
Abstract
Accurate prediction of protein stability changes upon mutation (ΔΔG) is increasingly important to evolution studies, protein engineering, and screening of disease-causing gene variants but is challenged by biases in training data. We investigated 45 linear regression models trained on data sets that account systematically for destabilization bias and mutation-type bias BM . The models were externally validated on three test data sets probing different pathologies and for internal consistency (symmetry and neutrality). Model structure and performance substantially depended on training data and even fitting method. We developed two final models: SimBa-IB for typical natural mutations and SimBa-SYM for situations where stabilizing and destabilizing mutations occur to a similar extent. SimBa-SYM, despite is simplicity, is essentially non-biased (vs. the Ssym data set) while still performing well for all data sets (R ~ 0.46-0.54, MAE = 1.16-1.24 kcal/mol). The simple models provide advantage in terms of interpretability, use and future improvement, and are freely available on GitHub.
Collapse
Affiliation(s)
| | - Kasper P Kepp
- DTU Chemistry, Technical University of Denmark, Lyngby, Denmark
| |
Collapse
|
29
|
Abstract
The spike protein (S-protein) of SARS-CoV-2, the protein that enables the virus to infect human cells, is the basis for many vaccines and a hotspot of concerning virus evolution. Here, we discuss the outstanding progress in structural characterization of the S-protein and how these structures facilitate analysis of virus function and evolution. We emphasize the differences in reported structures and that analysis of structure-function relationships is sensitive to the structure used. We show that the average residue solvent exposure in nearly complete structures is a good descriptor of open vs closed conformation states. Because of structural heterogeneity of functionally important surface-exposed residues, we recommend using averages of a group of high-quality protein structures rather than a single structure before reaching conclusions on specific structure-function relationships. To illustrate these points, we analyze some significant chemical tendencies of prominent S-protein mutations in the context of the available structures. In the discussion of new variants, we emphasize the selectivity of binding to ACE2 vs prominent antibodies rather than simply the antibody escape or ACE2 affinity separately. We note that larger chemical changes, in particular increased electrostatic charge or side-chain volume of exposed surface residues, are recurring in mutations of concern, plausibly related to adaptation to the negative surface potential of human ACE2. We also find indications that the fixated mutations of the S-protein in the main variants are less destabilizing than would be expected on average, possibly pointing toward a selection pressure on the S-protein. The richness of available structures for all of these situations provides an enormously valuable basis for future research into these structure-function relationships.
Collapse
Affiliation(s)
- Rukmankesh Mehra
- Department of Chemistry, Indian Institute
of Technology Bhilai, Sejbahar, Raipur 492015, Chhattisgarh,
India
| | - Kasper P. Kepp
- DTU Chemistry, Technical University of
Denmark, Building 206, 2800 Kongens Lyngby,
Denmark
| |
Collapse
|
30
|
Sorokina I, Mushegian AR, Koonin EV. Is Protein Folding a Thermodynamically Unfavorable, Active, Energy-Dependent Process? Int J Mol Sci 2022; 23:521. [PMID: 35008947 PMCID: PMC8745595 DOI: 10.3390/ijms23010521] [Citation(s) in RCA: 18] [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] [Received: 12/06/2021] [Revised: 12/30/2021] [Accepted: 12/31/2021] [Indexed: 02/04/2023] Open
Abstract
The prevailing current view of protein folding is the thermodynamic hypothesis, under which the native folded conformation of a protein corresponds to the global minimum of Gibbs free energy G. We question this concept and show that the empirical evidence behind the thermodynamic hypothesis of folding is far from strong. Furthermore, physical theory-based approaches to the prediction of protein folds and their folding pathways so far have invariably failed except for some very small proteins, despite decades of intensive theory development and the enormous increase of computer power. The recent spectacular successes in protein structure prediction owe to evolutionary modeling of amino acid sequence substitutions enhanced by deep learning methods, but even these breakthroughs provide no information on the protein folding mechanisms and pathways. We discuss an alternative view of protein folding, under which the native state of most proteins does not occupy the global free energy minimum, but rather, a local minimum on a fluctuating free energy landscape. We further argue that ΔG of folding is likely to be positive for the majority of proteins, which therefore fold into their native conformations only through interactions with the energy-dependent molecular machinery of living cells, in particular, the translation system and chaperones. Accordingly, protein folding should be modeled as it occurs in vivo, that is, as a non-equilibrium, active, energy-dependent process.
Collapse
Affiliation(s)
| | - Arcady R. Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, Alexandria, VA 22314, USA;
- Clare Hall College, University of Cambridge, Cambridge CB3 9AL, UK
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| |
Collapse
|
31
|
Sternke M, Tripp KW, Barrick D. Surface residues and non-additive interactions stabilize a consensus homeodomain protein. Biophys J 2021; 120:5267-5278. [PMID: 34757081 DOI: 10.1016/j.bpj.2021.10.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 09/01/2021] [Accepted: 10/26/2021] [Indexed: 11/26/2022] Open
Abstract
Despite the widely reported success of consensus design in producing highly stabilized proteins, little is known about the physical mechanisms underlying this stabilization. Here we explore the potential sources of stabilization by performing a systematic analysis of the 29 substitutions that we previously found to collectively stabilize a consensus homeodomain compared to an extant homeodomain. By separately introducing groups of consensus substitutions that alter or preserve charge state, occur at varying degrees of residue burial, and occur at positions of varying degrees of conservation, we determine the extent to which these three features contribute to the consensus stability enhancement. Surprisingly, we find that the largest total contribution to stability comes from consensus substitutions on the protein surface and that the largest per-substitution contributions come from substitutions that maintain charge state. This finding suggests that although consensus proteins are often enriched in charged residues, consensus stabilization does not result primarily from interactions involving charged residues. Although consensus substitutions at strongly conserved positions also contribute disproportionately to stabilization, significant stabilization is also contributed from substitutions at weakly conserved positions. Furthermore, we find that identical consensus substitutions show larger stabilizing effects when introduced into the consensus background than when introduced into an extant homeodomain, indicating that synergistic, stabilizing interactions among the consensus residues contribute to consensus stability enhancement of the homeodomain. By measuring DNA binding affinity for the same set of variants, we find that although consensus design of the homeodomain increases both affinity and folding stability, it does so using a largely non-overlapping set of substitutions.
Collapse
Affiliation(s)
- Matt Sternke
- The T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218 USA
| | - Katherine W Tripp
- The T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218 USA
| | - Doug Barrick
- The T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218 USA.
| |
Collapse
|
32
|
Latrille T, Lartillot N. Quantifying the impact of changes in effective population size and expression level on the rate of coding sequence evolution. Theor Popul Biol 2021; 142:57-66. [PMID: 34563555 DOI: 10.1016/j.tpb.2021.09.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 09/08/2021] [Accepted: 09/11/2021] [Indexed: 02/07/2023]
Abstract
Molecular sequences are shaped by selection, where the strength of selection relative to drift is determined by effective population size (Ne). Populations with high Ne are expected to undergo stronger purifying selection, and consequently to show a lower substitution rate for selected mutations relative to the substitution rate for neutral mutations (ω). However, computational models based on biophysics of protein stability have suggested that ω can also be independent of Ne. Together, the response of ω to changes in Ne depends on the specific mapping from sequence to fitness. Importantly, an increase in protein expression level has been found empirically to result in decrease of ω, an observation predicted by theoretical models assuming selection for protein stability. Here, we derive a theoretical approximation for the response of ω to changes in Ne and expression level, under an explicit genotype-phenotype-fitness map. The method is generally valid for additive traits and log-concave fitness functions. We applied these results to protein undergoing selection for their conformational stability and corroborate out findings with simulations under more complex models. We predict a weak response of ω to changes in either Ne or expression level, which are interchangeable. Based on empirical data, we propose that fitness based on the conformational stability may not be a sufficient mechanism to explain the empirically observed variation in ω across species. Other aspects of protein biophysics might be explored, such as protein-protein interactions, which can lead to a stronger response of ω to changes in Ne.
Collapse
Affiliation(s)
- T Latrille
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR 5558, F-69622 Villeurbanne, France; École Normale Supérieure de Lyon, Université de Lyon, Université Lyon 1, Lyon, France.
| | - N Lartillot
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR 5558, F-69622 Villeurbanne, France
| |
Collapse
|
33
|
Dultz G, Srikakulam SK, Konetschnik M, Shimakami T, Doncheva NT, Dietz J, Sarrazin C, Biondi RM, Zeuzem S, Tampé R, Kalinina OV, Welsch C. Epistatic interactions promote persistence of NS3-Q80K in HCV infection by compensating for protein folding instability. J Biol Chem 2021; 297:101031. [PMID: 34339738 PMCID: PMC8405986 DOI: 10.1016/j.jbc.2021.101031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/27/2021] [Accepted: 07/29/2021] [Indexed: 11/28/2022] Open
Abstract
The Q80K polymorphism in the NS3-4A protease of the hepatitis C virus is associated with treatment failure of direct-acting antiviral agents. This polymorphism is highly prevalent in genotype 1a infections and stably transmitted between hosts. Here, we investigated the underlying molecular mechanisms of evolutionarily conserved coevolving amino acids in NS3-Q80K and revealed potential implications of epistatic interactions in immune escape and variants persistence. Using purified protein, we characterized the impact of epistatic amino acid substitutions on the physicochemical properties and peptide cleavage kinetics of the NS3-Q80K protease. We found that Q80K destabilized the protease protein fold (p < 0.0001). Although NS3-Q80K showed reduced peptide substrate turnover (p < 0.0002), replicative fitness in an H77S.3 cell culture model of infection was not significantly inferior to the WT virus. Epistatic substitutions at residues 91 and 174 in NS3-Q80K stabilized the protein fold (p < 0.0001) and leveraged the WT protease stability. However, changes in protease stability inversely correlated with enzymatic activity. In infectious cell culture, these secondary substitutions were not associated with a gain of replicative fitness in NS3-Q80K variants. Using molecular dynamics, we observed that the total number of residue contacts in NS3-Q80K mutants correlated with protein folding stability. Changes in the number of contacts reflected the compensatory effect on protein folding instability by epistatic substitutions. In summary, epistatic substitutions in NS3-Q80K contribute to viral fitness by mechanisms not directly related to RNA replication. By compensating for protein-folding instability, epistatic interactions likely protect NS3-Q80K variants from immune cell recognition.
Collapse
Affiliation(s)
- Georg Dultz
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Sanjay K Srikakulam
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University Campus, Saarbrücken, Germany; Graduate School of Computer Science, Saarland University, Saarbrücken, Germany; Interdisciplinary Graduate School of Natural Product Research, Saarland University, Saarbrücken, Germany
| | - Michael Konetschnik
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Tetsuro Shimakami
- Department of Gastroenterology, Kanazawa University Hospital, Kanazawa, Japan
| | - Nadezhda T Doncheva
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Julia Dietz
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Christoph Sarrazin
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Ricardo M Biondi
- Molecular Targeting, Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Stefan Zeuzem
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt am Main, Germany; University Center for Infectious Diseases, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Olga V Kalinina
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University Campus, Saarbrücken, Germany; Medical Faculty, Saarland University, Homburg, Germany; Center for Bioinformatics, Saarland Informatics Campus, Saarbrücken, Germany
| | - Christoph Welsch
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt am Main, Germany; University Center for Infectious Diseases, University Hospital Frankfurt, Frankfurt am Main, Germany.
| |
Collapse
|
34
|
Intra-Population Competition during Adaptation to Increased Temperature in an RNA Bacteriophage. Int J Mol Sci 2021; 22:ijms22136815. [PMID: 34202838 PMCID: PMC8268601 DOI: 10.3390/ijms22136815] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/17/2021] [Accepted: 06/22/2021] [Indexed: 01/21/2023] Open
Abstract
Evolution of RNA bacteriophages of the family Leviviridae is governed by the high error rates of their RNA-dependent RNA polymerases. This fact, together with their large population sizes, leads to the generation of highly heterogeneous populations that adapt rapidly to most changes in the environment. Throughout adaptation, the different mutants that make up a viral population compete with each other in a non-trivial process in which their selective values change over time due to the generation of new mutations. In this work we have characterised the intra-population dynamics of a well-studied levivirus, Qβ, when it is propagated at a higher-than-optimal temperature. Our results show that adapting populations experienced rapid changes that involved the ascent of particular genotypes and the loss of some beneficial mutations of early generation. Artificially reconstructed populations, containing a fraction of the diversity present in actual populations, fixed mutations more rapidly, illustrating how population bottlenecks may guide the adaptive pathways. The conclusion is that, when the availability of beneficial mutations under a particular selective condition is elevated, the final outcome of adaptation depends more on the occasional occurrence of population bottlenecks and how mutations combine in genomes than on the selective value of particular mutations.
Collapse
|
35
|
Razban RM, Dasmeh P, Serohijos AWR, Shakhnovich EI. Avoidance of protein unfolding constrains protein stability in long-term evolution. Biophys J 2021; 120:2413-2424. [PMID: 33932438 PMCID: PMC8390877 DOI: 10.1016/j.bpj.2021.03.042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 02/24/2021] [Accepted: 03/17/2021] [Indexed: 11/28/2022] Open
Abstract
Every amino acid residue can influence a protein's overall stability, making stability highly susceptible to change throughout evolution. We consider the distribution of protein stabilities evolutionarily permittable under two previously reported protein fitness functions: flux dynamics and misfolding avoidance. We develop an evolutionary dynamics theory and find that it agrees better with an extensive protein stability data set for dihydrofolate reductase orthologs under the misfolding avoidance fitness function rather than the flux dynamics fitness function. Further investigation with ribonuclease H data demonstrates that not any misfolded state is avoided; rather, it is only the unfolded state. At the end, we discuss how our work pertains to the universal protein abundance-evolutionary rate correlation seen across organisms' proteomes. We derive a closed-form expression relating protein abundance to evolutionary rate that captures Escherichia coli, Saccharomyces cerevisiae, and Homo sapiens experimental trends without fitted parameters.
Collapse
Affiliation(s)
- Rostam M Razban
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts
| | - Pouria Dasmeh
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts; Departement de Biochimie, Université de Montréal, Montreal, Quebec, Canada
| | | | - Eugene I Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts.
| |
Collapse
|
36
|
Manrubia S, Cuesta JA, Aguirre J, Ahnert SE, Altenberg L, Cano AV, Catalán P, Diaz-Uriarte R, Elena SF, García-Martín JA, Hogeweg P, Khatri BS, Krug J, Louis AA, Martin NS, Payne JL, Tarnowski MJ, Weiß M. From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics. Phys Life Rev 2021; 38:55-106. [PMID: 34088608 DOI: 10.1016/j.plrev.2021.03.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/01/2021] [Indexed: 12/21/2022]
Abstract
Understanding how genotypes map onto phenotypes, fitness, and eventually organisms is arguably the next major missing piece in a fully predictive theory of evolution. We refer to this generally as the problem of the genotype-phenotype map. Though we are still far from achieving a complete picture of these relationships, our current understanding of simpler questions, such as the structure induced in the space of genotypes by sequences mapped to molecular structures, has revealed important facts that deeply affect the dynamical description of evolutionary processes. Empirical evidence supporting the fundamental relevance of features such as phenotypic bias is mounting as well, while the synthesis of conceptual and experimental progress leads to questioning current assumptions on the nature of evolutionary dynamics-cancer progression models or synthetic biology approaches being notable examples. This work delves with a critical and constructive attitude into our current knowledge of how genotypes map onto molecular phenotypes and organismal functions, and discusses theoretical and empirical avenues to broaden and improve this comprehension. As a final goal, this community should aim at deriving an updated picture of evolutionary processes soundly relying on the structural properties of genotype spaces, as revealed by modern techniques of molecular and functional analysis.
Collapse
Affiliation(s)
- Susanna Manrubia
- Department of Systems Biology, Centro Nacional de Biotecnología (CSIC), Madrid, Spain; Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain.
| | - José A Cuesta
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain; Departamento de Matemáticas, Universidad Carlos III de Madrid, Leganés, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (BiFi), Universidad de Zaragoza, Spain; UC3M-Santander Big Data Institute (IBiDat), Getafe, Madrid, Spain
| | - Jacobo Aguirre
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain; Centro de Astrobiología, CSIC-INTA, ctra. de Ajalvir km 4, 28850 Torrejón de Ardoz, Madrid, Spain
| | - Sebastian E Ahnert
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, UK; The Alan Turing Institute, British Library, 96 Euston Road, London NW1 2DB, UK
| | | | - Alejandro V Cano
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Pablo Catalán
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain; Departamento de Matemáticas, Universidad Carlos III de Madrid, Leganés, Spain
| | - Ramon Diaz-Uriarte
- Department of Biochemistry, Universidad Autónoma de Madrid, Madrid, Spain; Instituto de Investigaciones Biomédicas "Alberto Sols" (UAM-CSIC), Madrid, Spain
| | - Santiago F Elena
- Instituto de Biología Integrativa de Sistemas, I(2)SysBio (CSIC-UV), València, Spain; The Santa Fe Institute, Santa Fe, NM, USA
| | | | - Paulien Hogeweg
- Theoretical Biology and Bioinformatics Group, Utrecht University, the Netherlands
| | - Bhavin S Khatri
- The Francis Crick Institute, London, UK; Department of Life Sciences, Imperial College London, London, UK
| | - Joachim Krug
- Institute for Biological Physics, University of Cologne, Köln, Germany
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford, UK
| | - Nora S Martin
- Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, Cambridge, UK; Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Joshua L Payne
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Marcel Weiß
- Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, Cambridge, UK; Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| |
Collapse
|
37
|
Endoplasmic reticulum stress regulates the intestinal stem cell state through CtBP2. Sci Rep 2021; 11:9892. [PMID: 33972635 PMCID: PMC8111031 DOI: 10.1038/s41598-021-89326-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 04/09/2021] [Indexed: 02/06/2023] Open
Abstract
Enforcing differentiation of cancer stem cells is considered as a potential strategy to sensitize colorectal cancer cells to irradiation and chemotherapy. Activation of the unfolded protein response, due to endoplasmic reticulum (ER) stress, causes rapid stem cell differentiation in normal intestinal and colon cancer cells. We previously found that stem cell differentiation was mediated by a Protein kinase R-like ER kinase (PERK) dependent arrest of mRNA translation, resulting in rapid protein depletion of WNT-dependent transcription factor c-MYC. We hypothesize that ER stress dependent stem cell differentiation may rely on the depletion of additional transcriptional regulators with a short protein half-life that are rapidly depleted due to a PERK-dependent translational pause. Using a novel screening method, we identify novel transcription factors that regulate the intestinal stem cell fate upon ER stress. ER stress was induced in LS174T cells with thapsigargin or subtilase cytotoxin (SubAB) and immediate alterations in nuclear transcription factor activity were assessed by the CatTFRE assay in which transcription factors present in nuclear lysate are bound to plasmid DNA, co-extracted and quantified using mass-spectrometry. The role of altered activity of transcription factor CtBP2 was further examined by modification of its expression levels using CAG-rtTA3-CtBP2 overexpression in small intestinal organoids, shCtBP2 knockdown in LS174T cells, and familial adenomatous polyposis patient-derived organoids. CtBP2 overexpression organoids were challenged by ER stress and ionizing irradiation. We identified a unique set of transcription factors with altered activation upon ER stress. Gene ontology analysis showed that transcription factors with diminished binding were involved in cellular differentiation processes. ER stress decreased CtBP2 protein expression in mouse small intestine. ER stress induced loss of CtBP2 expression which was rescued by inhibition of PERK signaling. CtBP2 was overexpressed in mouse and human colorectal adenomas. Inducible CtBP2 overexpression in organoids conferred higher clonogenic potential, resilience to irradiation-induced damage and a partial rescue of ER stress-induced loss of stemness. Using an unbiased proteomics approach, we identified a unique set of transcription factors for which DNA-binding activity is lost directly upon ER stress. We continued investigating the function of co-regulator CtBP2, and show that CtBP2 mediates ER stress-induced loss of stemness which supports the intestinal stem cell state in homeostatic stem cells and colorectal cancer cells.
Collapse
|
38
|
A meta-analysis of the activity, stability, and mutational characteristics of temperature-adapted enzymes. Biosci Rep 2021; 41:228416. [PMID: 33871022 PMCID: PMC8150157 DOI: 10.1042/bsr20210336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/29/2021] [Accepted: 04/19/2021] [Indexed: 11/17/2022] Open
Abstract
Understanding the characteristics that define temperature-adapted enzymes has been a major goal of extremophile enzymology in recent decades. In the present study, we explore these characteristics by comparing psychrophilic, mesophilic, and thermophilic enzymes. Through a meta-analysis of existing data, we show that psychrophilic enzymes exhibit a significantly larger gap (Tg) between their optimum and melting temperatures compared with mesophilic and thermophilic enzymes. These results suggest that Tg may be a useful indicator as to whether an enzyme is psychrophilic or not and that models of psychrophilic enzyme catalysis need to account for this gap. Additionally, by using predictive protein stability software, HoTMuSiC and PoPMuSiC, we show that the deleterious nature of amino acid substitutions to protein stability increases from psychrophiles to thermophiles. How this ultimately affects the mutational tolerance and evolutionary rate of temperature adapted organisms is currently unknown.
Collapse
|
39
|
Caldararu O, Blundell TL, Kepp KP. Three Simple Properties Explain Protein Stability Change upon Mutation. J Chem Inf Model 2021; 61:1981-1988. [PMID: 33848149 DOI: 10.1021/acs.jcim.1c00201] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Accurate prediction of protein stability upon mutation enables rational engineering of new proteins and insights into protein evolution and monogenetic diseases caused by single-point amino acid substitutions. Many tools have been developed to this aim, ranging from energy-based models to machine-learning methods that use large amounts of experimental data. However, as the methods become more complex, the interpretation of the chemistry underlying the protein stability effects becomes obscure. It is thus of interest to identify the simplest prediction model that retains complete amino acid specific interpretation; for a given number of input descriptors, we expect such a model to be almost universal. In this study, we identify such a limiting model, SimBa, a simple multilinear regression model trained on a substitution-type-balanced experimental data set. The model accounts only for the solvent accessibility of the site, volume difference, and polarity difference caused by mutation. Our results show that this very simple and directly applicable model performs comparably to other much more complex, widely used protein stability prediction methods. This suggests that a hard limit of ∼1 kcal/mol numerical accuracy and an R ∼ 0.5 trend accuracy exists and that new features, such as account of unfolded states, water colocalization, and amino acid correlations, are required to improve accuracy to, e.g., 1/2 kcal/mol.
Collapse
Affiliation(s)
- Octav Caldararu
- DTU Chemistry, Technical University of Denmark, Building 206, 2800 Kgs. Lyngby, Denmark
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, United Kingdom
| | - Kasper P Kepp
- DTU Chemistry, Technical University of Denmark, Building 206, 2800 Kgs. Lyngby, Denmark
| |
Collapse
|
40
|
Reiskind MOB, Moody ML, Bolnick DI, Hanifin CT, Farrior CE. Nothing in Evolution Makes Sense Except in the Light of Biology. Bioscience 2021; 71:370-382. [PMID: 33867868 PMCID: PMC8038875 DOI: 10.1093/biosci/biaa170] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
A key question in biology is the predictability of the evolutionary process. If we can correctly predict the outcome of evolution, we may be better equipped to anticipate and manage species' adaptation to climate change, habitat loss, invasive species, or emerging infectious diseases, as well as improve our basic understanding of the history of life on Earth. In the present article, we ask the questions when, why, and if the outcome of future evolution is predictable. We first define predictable and then discuss two conflicting views: that evolution is inherently unpredictable and that evolution is predictable given the ability to collect the right data. We identify factors that generate unpredictability, the data that might be required to make predictions at some level of precision or at a specific timescale, and the intellectual and translational value of understanding when prediction is or is not possible.
Collapse
Affiliation(s)
- Martha O Burford Reiskind
- Department of Biological Sciences and the director of the Genetic and Genomic Scholars graduate program, North Carolina State University, Raleigh, North Carolina, United States
| | - Michael L Moody
- Department of Biological Sciences and director of Herbarium UTEP, University of Texas, El Paso, El Paso, Texas, United States
| | - Daniel I Bolnick
- University of Connecticut, Mansfield, Connecticut, United States, and editor-in-chief of The American Naturalist, Chicago, Illinois, United States
| | | | - Caroline E Farrior
- University of Texas at Austin, Austin, Texas, United States, The author order was determined by a random number generator
| |
Collapse
|
41
|
Perez AM, Wolfe JA, Schermerhorn JT, Qian Y, Cela BA, Kalinowski CR, Largoza GE, Fields PA, Brandt GS. Thermal stability and structure of glyceraldehyde-3-phosphate dehydrogenase from the coral Acropora millepora. RSC Adv 2021; 11:10364-10374. [PMID: 35423531 PMCID: PMC8695597 DOI: 10.1039/d0ra10119b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/03/2021] [Indexed: 11/21/2022] Open
Abstract
Corals are vulnerable to increasing ocean temperatures. It is known that elevated temperatures lead to the breakdown of an essential mutualistic relationship with photosynthetic algae. The molecular mechanisms of this temperature-dependent loss of symbiosis are less well understood. Here, the thermal stability of a critical metabolic enzyme, glyceraldehyde-3-phosphate dehydrogenase, from the stony coral Acropora millepora was found to increase significantly in the presence of its cofactor NAD+. Determination of the structure of the cofactor-enzyme complex (PDB ID 6PX2) revealed variable NAD+ occupancy across the four monomers of the tetrameric enzyme. The structure of the fully occupied monomers was compared to those with partial cofactor occupancy, identifying regions of difference that may account for the increased thermal stability.
Collapse
Affiliation(s)
- Astrid M Perez
- Department of Chemistry, Franklin & Marshall College Lancaster PA 17604 USA +1 717 358 4846 +1 717 358 4846
| | - Jacob A Wolfe
- Department of Chemistry, Franklin & Marshall College Lancaster PA 17604 USA +1 717 358 4846 +1 717 358 4846
| | - Janse T Schermerhorn
- Department of Chemistry, Franklin & Marshall College Lancaster PA 17604 USA +1 717 358 4846 +1 717 358 4846
- Department of Biology, Franklin & Marshall College Lancaster PA 17604 USA
| | - Yiwen Qian
- Department of Chemistry, Franklin & Marshall College Lancaster PA 17604 USA +1 717 358 4846 +1 717 358 4846
| | - Bekim A Cela
- Department of Biology, Franklin & Marshall College Lancaster PA 17604 USA
| | - Cody R Kalinowski
- Department of Biology, Franklin & Marshall College Lancaster PA 17604 USA
| | - Garrett E Largoza
- Department of Biology, Franklin & Marshall College Lancaster PA 17604 USA
| | - Peter A Fields
- Department of Biology, Franklin & Marshall College Lancaster PA 17604 USA
| | - Gabriel S Brandt
- Department of Chemistry, Franklin & Marshall College Lancaster PA 17604 USA +1 717 358 4846 +1 717 358 4846
| |
Collapse
|
42
|
Caldararu O, Blundell TL, Kepp KP. A base measure of precision for protein stability predictors: structural sensitivity. BMC Bioinformatics 2021; 22:88. [PMID: 33632133 PMCID: PMC7908712 DOI: 10.1186/s12859-021-04030-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 02/15/2021] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Prediction of the change in fold stability (ΔΔG) of a protein upon mutation is of major importance to protein engineering and screening of disease-causing variants. Many prediction methods can use 3D structural information to predict ΔΔG. While the performance of these methods has been extensively studied, a new problem has arisen due to the abundance of crystal structures: How precise are these methods in terms of structure input used, which structure should be used, and how much does it matter? Thus, there is a need to quantify the structural sensitivity of protein stability prediction methods. RESULTS We computed the structural sensitivity of six widely-used prediction methods by use of saturated computational mutagenesis on a diverse set of 87 structures of 25 proteins. Our results show that structural sensitivity varies massively and surprisingly falls into two very distinct groups, with methods that take detailed account of the local environment showing a sensitivity of ~ 0.6 to 0.8 kcal/mol, whereas machine-learning methods display much lower sensitivity (~ 0.1 kcal/mol). We also observe that the precision correlates with the accuracy for mutation-type-balanced data sets but not generally reported accuracy of the methods, indicating the importance of mutation-type balance in both contexts. CONCLUSIONS The structural sensitivity of stability prediction methods varies greatly and is caused mainly by the models and less by the actual protein structural differences. As a new recommended standard, we therefore suggest that ΔΔG values are evaluated on three protein structures when available and the associated standard deviation reported, to emphasize not just the accuracy but also the precision of the method in a specific study. Our observation that machine-learning methods deemphasize structure may indicate that folded wild-type structures alone, without the folded mutant and unfolded structures, only add modest value for assessing protein stability effects, and that side-chain-sensitive methods overstate the significance of the folded wild-type structure.
Collapse
Affiliation(s)
- Octav Caldararu
- DTU Chemistry, Technical University of Denmark, Building 206, 2800, Kgs. Lyngby, Denmark
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Kasper P Kepp
- DTU Chemistry, Technical University of Denmark, Building 206, 2800, Kgs. Lyngby, Denmark.
| |
Collapse
|
43
|
Crippa M, Andreghetti D, Capelli R, Tiana G. Evolution of frustrated and stabilising contacts in reconstructed ancient proteins. EUROPEAN BIOPHYSICS JOURNAL 2021; 50:699-712. [PMID: 33569610 PMCID: PMC8260555 DOI: 10.1007/s00249-021-01500-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 12/14/2020] [Accepted: 01/13/2021] [Indexed: 11/30/2022]
Abstract
Energetic properties of a protein are a major determinant of its evolutionary fitness. Using a reconstruction algorithm, dating the reconstructed proteins and calculating the interaction network between their amino acids through a coevolutionary approach, we studied how the interactions that stabilise 890 proteins, belonging to five families, evolved for billions of years. In particular, we focused our attention on the network of most strongly attractive contacts and on that of poorly optimised, frustrated contacts. Our results support the idea that the cluster of most attractive interactions extends its size along evolutionary time, but from the data, we cannot conclude that protein stability or that the degree of frustration tends always to decrease.
Collapse
Affiliation(s)
- Martina Crippa
- Department of Physics and Center for Complexity and Biosystems, Università degli Studi di Milano and INFN, via Celoria 16, 20133, Milan, Italy
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129, Turin, Italy
| | - Damiano Andreghetti
- Department of Physics and Center for Complexity and Biosystems, Università degli Studi di Milano and INFN, via Celoria 16, 20133, Milan, Italy
| | - Riccardo Capelli
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129, Turin, Italy
| | - Guido Tiana
- Department of Physics and Center for Complexity and Biosystems, Università degli Studi di Milano and INFN, via Celoria 16, 20133, Milan, Italy.
| |
Collapse
|
44
|
Berger D, Stångberg J, Baur J, Walters RJ. Elevated temperature increases genome-wide selection on de novo mutations. Proc Biol Sci 2021; 288:20203094. [PMID: 33529558 DOI: 10.1098/rspb.2020.3094] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Adaptation in new environments depends on the amount of genetic variation available for evolution, and the efficacy by which natural selection discriminates among this variation. However, whether some ecological factors reveal more genetic variation, or impose stronger selection pressures than others, is typically not known. Here, we apply the enzyme kinetic theory to show that rising global temperatures are predicted to intensify natural selection throughout the genome by increasing the effects of DNA sequence variation on protein stability. We test this prediction by (i) estimating temperature-dependent fitness effects of induced mutations in seed beetles adapted to ancestral or elevated temperature, and (ii) calculate 100 paired selection estimates on mutations in benign versus stressful environments from unicellular and multicellular organisms. Environmental stress per se did not increase mean selection on de novo mutation, suggesting that the cost of adaptation does not generally increase in new ecological settings to which the organism is maladapted. However, elevated temperature increased the mean strength of selection on genome-wide polymorphism, signified by increases in both mutation load and mutational variance in fitness. These results have important implications for genetic diversity gradients and the rate and repeatability of evolution under climate change.
Collapse
Affiliation(s)
- David Berger
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Josefine Stångberg
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Julian Baur
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Richard J Walters
- Centre for Environmental and Climate Research, Lund University, Sölvegatan 37, 223 62 Lund, Sweden
| |
Collapse
|
45
|
Abstract
An accurate estimation of the Protein Space size, in light of the factors that govern it, is a long-standing problem and of paramount importance in evolutionary biology, since it determines the nature of protein evolvability. A simple analysis will enable us to, firstly, reduce an unrealistic Protein Space size of ~ 10130 sequences, for a 100-residues polypeptide chain, to ~ 109 functional proteins and, secondly, estimate a robust average-mutation rate per amino acid (ξ ~ 1.23) and infer from it, in light of the protein marginal stability, that only a fraction of the sequence will be available at any one time for a functional protein to evolve. Although this result does not solve the Protein Space vastness problem frames it in a more rational one and illustrates the impact of the marginal stability on protein evolvability.
Collapse
|
46
|
Kurahashi R, Tanaka SI, Takano K. Highly active enzymes produced by directed evolution with stability-based selection. Enzyme Microb Technol 2020; 140:109626. [DOI: 10.1016/j.enzmictec.2020.109626] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 06/12/2020] [Accepted: 06/12/2020] [Indexed: 12/22/2022]
|
47
|
Tian P, Best RB. Exploring the sequence fitness landscape of a bridge between protein folds. PLoS Comput Biol 2020; 16:e1008285. [PMID: 33048928 PMCID: PMC7553338 DOI: 10.1371/journal.pcbi.1008285] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 08/24/2020] [Indexed: 12/15/2022] Open
Abstract
Most foldable protein sequences adopt only a single native fold. Recent protein design studies have, however, created protein sequences which fold into different structures apon changes of environment, or single point mutation, the best characterized example being the switch between the folds of the GA and GB binding domains of streptococcal protein G. To obtain further insight into the design of sequences which can switch folds, we have used a computational model for the fitness landscape of a single fold, built from the observed sequence variation of protein homologues. We have recently shown that such coevolutionary models can be used to design novel foldable sequences. By appropriately combining two of these models to describe the joint fitness landscape of GA and GB, we are able to describe the propensity of a given sequence for each of the two folds. We have successfully tested the combined model against the known series of designed GA/GB hybrids. Using Monte Carlo simulations on this landscape, we are able to identify pathways of mutations connecting the two folds. In the absence of a requirement for domain stability, the most frequent paths go via sequences in which neither domain is stably folded, reminiscent of the propensity for certain intrinsically disordered proteins to fold into different structures according to context. Even if the folded state is required to be stable, we find that there is nonetheless still a wide range of sequences which are close to the transition region and therefore likely fold switches, consistent with recent estimates that fold switching may be more widespread than had been thought.
Collapse
Affiliation(s)
- Pengfei Tian
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, U.S.A
| | - Robert B. Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, U.S.A
| |
Collapse
|
48
|
Ballal A, Laurendon C, Salmon M, Vardakou M, Cheema J, Defernez M, O'Maille PE, Morozov AV. Sparse Epistatic Patterns in the Evolution of Terpene Synthases. Mol Biol Evol 2020; 37:1907-1924. [PMID: 32119077 DOI: 10.1093/molbev/msaa052] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
We explore sequence determinants of enzyme activity and specificity in a major enzyme family of terpene synthases. Most enzymes in this family catalyze reactions that produce cyclic terpenes-complex hydrocarbons widely used by plants and insects in diverse biological processes such as defense, communication, and symbiosis. To analyze the molecular mechanisms of emergence of terpene cyclization, we have carried out in-depth examination of mutational space around (E)-β-farnesene synthase, an Artemisia annua enzyme which catalyzes production of a linear hydrocarbon chain. Each mutant enzyme in our synthetic libraries was characterized biochemically, and the resulting reaction rate data were used as input to the Michaelis-Menten model of enzyme kinetics, in which free energies were represented as sums of one-amino-acid contributions and two-amino-acid couplings. Our model predicts measured reaction rates with high accuracy and yields free energy landscapes characterized by relatively few coupling terms. As a result, the Michaelis-Menten free energy landscapes have simple, interpretable structure and exhibit little epistasis. We have also developed biophysical fitness models based on the assumption that highly fit enzymes have evolved to maximize the output of correct products, such as cyclic products or a specific product of interest, while minimizing the output of byproducts. This approach results in nonlinear fitness landscapes that are considerably more epistatic. Overall, our experimental and computational framework provides focused characterization of evolutionary emergence of novel enzymatic functions in the context of microevolutionary exploration of sequence space around naturally occurring enzymes.
Collapse
Affiliation(s)
- Aditya Ballal
- Department of Physics & Astronomy and Center for Quantitative Biology, Rutgers University, Piscataway, NJ
| | - Caroline Laurendon
- John Innes Centre, Department of Metabolic Biology, Norwich Research Park, Norwich, United Kingdom.,Food & Health Programme, Institute of Food Research, Norwich Research Park, Norwich, United Kingdom
| | - Melissa Salmon
- John Innes Centre, Department of Metabolic Biology, Norwich Research Park, Norwich, United Kingdom.,Food & Health Programme, Institute of Food Research, Norwich Research Park, Norwich, United Kingdom.,Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Maria Vardakou
- John Innes Centre, Department of Metabolic Biology, Norwich Research Park, Norwich, United Kingdom.,Food & Health Programme, Institute of Food Research, Norwich Research Park, Norwich, United Kingdom.,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Jitender Cheema
- John Innes Centre, Department of Computational and Systems Biology, Norwich Research Park, Norwich, United Kingdom
| | - Marianne Defernez
- Core Science Resources, Quadram Institute, Norwich Research Park, Norwich, United Kingdom
| | - Paul E O'Maille
- John Innes Centre, Department of Metabolic Biology, Norwich Research Park, Norwich, United Kingdom.,Food & Health Programme, Institute of Food Research, Norwich Research Park, Norwich, United Kingdom.,SRI International, Menlo Park, CA
| | - Alexandre V Morozov
- Department of Physics & Astronomy and Center for Quantitative Biology, Rutgers University, Piscataway, NJ
| |
Collapse
|
49
|
Abstract
Cells adapt to changing environments. Perturb a cell and it returns to a point of homeostasis. Perturb a population and it evolves toward a fitness peak. We review quantitative models of the forces of adaptation and their visualizations on landscapes. While some adaptations result from single mutations or few-gene effects, others are more cooperative, more delocalized in the genome, and more universal and physical. For example, homeostasis and evolution depend on protein folding and aggregation, energy and protein production, protein diffusion, molecular motor speeds and efficiencies, and protein expression levels. Models provide a way to learn about the fitness of cells and cell populations by making and testing hypotheses.
Collapse
Affiliation(s)
- Luca Agozzino
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, USA; .,Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York 11794, USA
| | - Gábor Balázsi
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, USA; .,Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York 11794, USA
| | - Jin Wang
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, USA; .,Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York 11794, USA.,Department of Chemistry, Stony Brook University, Stony Brook, New York 11790, USA
| | - Ken A Dill
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, USA; .,Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York 11794, USA.,Department of Chemistry, Stony Brook University, Stony Brook, New York 11790, USA
| |
Collapse
|
50
|
Effects of Single Mutations on Protein Stability Are Gaussian Distributed. Biophys J 2020; 118:2872-2878. [PMID: 32416078 DOI: 10.1016/j.bpj.2020.04.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/14/2020] [Accepted: 04/24/2020] [Indexed: 12/16/2022] Open
Abstract
The distribution of protein stability effects is known to be well approximated by a Gaussian distribution from previous empirical fits. Starting from first-principles statistical mechanics, we more rigorously motivate this empirical observation by deriving per-residue-position protein stability effects to be Gaussian. Our derivation requires the number of amino acids to be large, which is satisfied by the standard set of 20 amino acids found in nature. No assumption is needed on the number of residues in close proximity in space, in contrast to previous applications of the central limit theorem to protein energetics. We support our derivation results with computational and experimental data on mutant protein stabilities across all types of protein residues.
Collapse
|